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Bacteria were first observed by Antonie van Leeuwenhoek
Bacteria in the seventeenth century, using a single-lens microscope
of his own design (Porter 1976). He called them animal-
FRANCISCO RODRIGUEZ-VALERA cules and published his observations in a series of letters
Microbiologia, Universidad Miguel Hernandez, San Juan, to the Royal Society (van Leeuwenhoek 1684). The name
Alicante, Spain bacterium was introduced much later, by Christian
Gottfried Ehrenberg in 1838.
Louis Pasteur demonstrated in the mid-eighteenth
Synonyms century that fermentation is caused by the growth of
Bacterium microorganisms, and that this growth is not due to
spontaneous generation. Along with his contemporary,
Keywords Robert Koch, Pasteur was an early advocate of the germ
Cell, domain, phylogeny, prokaryote, tree of life theory of disease. In his research into tuberculosis, Koch
finally proved the germ theory, for which he was awarded
Definition a Nobel Prize in 1905. In Kochs postulates, he set out
Bacteria are a large group of single-celled phylogenetically criteria to test if an organism is the cause of a disease, and
related prokaryotes distinct from Archaea. Bacteria have these postulates are still used today. A major step in the
a wide range of shapes, ranging from spheres to rods and study of bacteria was the development, in the middle of
spirals. They are ubiquitous, growing in soil, water, the last century, of molecular biology techniques with
extreme environments, and deep in the Earths crust which much was learned about their biochemistry and
(Vreeland et al. 2000; Wanger et al. 2008). There are genetics. In 1977, Carl Woese (Woese and Fox 1977)
typically 40 million bacterial cells in a gram of soil and made an important breakthrough in our knowledge of
a million bacterial cells in a milliliter of fresh water. There evolution, when, in comparing the sequences of 16 S ribo-
are approximately 5 1030 bacteria on Earth, forming somal RNA genes, he observed that a group of prokaryotic
much of the worlds biomass (Whitman et al. 1998). organisms, Archaea, have a separate line of evolutionary
Bacteria are vital in recycling nutrients and important descent from that of Bacteria (Woese et al. 1990).
archaeal) world is still a matter of controversy but some Porter JR (1976) Antony van Leeuwenhoek: tercentenary of his discovery
of bacteria. Bacterio Rev 40:260269
authors consider that a biologically consistent tree of life
Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority.
based on evolutionary relationships could simply be Annu Rev Microbiol 57:369394. doi:10.1146/annurev.micro. B
a human fabrication. 57.030502.090759
Schulz H, Jorgensen B (2001) Big bacteria. Annu Rev Microbiol
See also 55:105137. doi:10.1146/annurev.micro.55.1.105
Archea Shih YL, Rothfield L (2006) The bacterial cytoskeleton. Microbiol Mol
Biol Rev 70(3):729754. doi:10.1128/MMBR.00017-06
Aerobic Respiration
van Leeuwenhoek A (1684) An abstract of a letter from Mr. Anthony
Anaerobic Respiration Leevvenhoek at Delft, dated 17 Sep 1683, containing some micro-
Anoxygenic Photosynthesis scopical observations, about animals in the scurf of the teeth, the
Bioenergetics substance calld worms in the nose, the Cuticula consisting of scales.
Biofilm Philos Trans (16831775) 14:568574
Vreeland R, Rosenzweig W, Powers D (2000) Isolation of a 250 million-
Carbon Cycle (Biological)
year-old halotolerant bacterium from a primary salt crystal. Nature
Chemolithotroph 407:897900. doi:10.1038/35038060
Chemoorganotroph Wanger G, Onstott TC, Southam G (2008) Stars of the terrestrial deep
Common Ancestor subsurface: a novel star-shaped bacterial morphotype from a South
Fermentation African platinum mine. Geobiology 6:325330. doi:10.1111/j.1472-
4669.2008.00163
Genotype
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen
Gram-Positive Bacteria majority. Proc Natl Acad Sci USA 95:65786583. doi:10.1073/
Gram Negative Bacteria pnas.95.12.6578
Lateral Gene Transfer Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system
Metabolic Diversity of organisms: proposal for the domains archaea, bacteria, and
eucarya. Proc Natl Acad Sci USA 87:45764579. doi:10.1073/
Microorganism
pnas.87.12.4576
Motility Woese C, Fox G (1977) Phylogenetic structure of the prokaryotic domain:
Organelle the primary kingdoms. Proc Natl Acad Sci USA 74(11):50885090.
Peroxisome doi:10.1073/pnas.74.11.5088
Phenotype Xu J (2006) Microbial ecology in the age of genomics and metagenomics:
concepts, tools, and recent advances. Mol Ecol 15:17131731.
Photosynthesis
doi:10.1111/j.1365-294X.2006.02882
Phylogenetic Tree Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (2008)
Phylogeny Protein-based organelles in bacteria: carboxysomes and related
Phylum microcompartments. Nat Rev Microbiol 6:681691. doi:10.1038/
Prokaryote nrmicro1913
Young K (2006) The selective value of bacterial shape. Microbiol Mol Biol
Proteobacteria
Rev 70(3):660703. doi:10.1128/MMBR.00001-06
Quorum Sensing Zoetendal E, Vaughan E, de Vos W (2006) A microbial world within us.
Respiration Mol Microbiol 59:16391650. doi:10.1111/j.1365-2958.2006.05056
Ribosome
Secondary Metabolism
Sequence Analysis
Transcription
Translation Bacterial Spore
References and Further Reading Endospore
DeLong E, Pace N (2001) Environmental diversity of bacteria and archaea. Spore
Syst Biol 50:470478. doi:10.1080/106351501750435040
Dyall S, Brown M, Johnson P (2004) Ancient invasions: from endosym-
bionts to organelles. Science 304(5668):253257. doi:10.1126/
science.1094884
Fuerst J (2005) Intracellular compartmentation in planctomycetes.
Annu Rev Microbiol 59:299328. doi:10.1146/annurev.micro.
59.030804.121258
Bacteriochlorophyll
Kojima S, Blair D (2004) The bacterial flagellar motor: structure and
function of a complex molecular machine. Int Rev Cytol 233:93 Synonyms
134. doi:10.1016/S0074-7696(04)33003-2 Chlorophylls
140 B Bacterium
See also
Band Scans
Anoxygenic Photosynthesis
Molecular Line Surveys
Oxygenic Photosynthesis
Photosynthesis
Synonyms
Balys Experiment BIF; Itabirite; Taconite
Definition Keywords
Regarding origin of life, Balys experiment (1922) is one of Precambrian, iron oxides, silica, oxygenation, Great
the most emblematic organic chemistry experiments of Oxygenation Event, Hydrothermalism
the beginning of the twentieth century (Baly 18711948).
It has demonstrated that ultraviolet light could act on Definition
a solution of water, carbon dioxide, and ammonia and Banded iron formation (BIF) is a lithological term applied
produce a lot of organic compounds, such as sugars and to a thinly bedded or laminated chemical sedimentary
amino acids. rock consisting of successive layers of fine-grained quartz,
J.B.S. Haldane quoted these experiments in his famous iron oxides, carbonates, and/or silicates, typically
text in 1929; for him this was a chemical proof of the containing 2040% of iron and 4050% of silica (Trendall
possibility of a link between mineral and organic chemistry 2002; Klein 2005).
in the prebiotic soup.
Overview
See also Banded iron formations (BIF) comprise the largest iron
Haldanes Conception of Origins of Life resource on Earth. They formed throughout much of the
Precambrian (3,800545 Ma), reaching their maximum
abundance between 2,700 and 2,400 Ma years ago.
Numerous examples can be found on almost every conti-
Band Pass nent and their deposition has been linked to significant
compositional changes in the Earths atmosphere and
Definition hydrosphere, and possibly the diversification of the
The bandpass is a well-defined range of frequencies (or biosphere.
wavelengths) determined by a filter that cuts out all other BIF has been classified on the basis of mineralogy, tec-
frequencies (or wavelengths) above and below this band. tonic setting, and depositional environment (Trendall 2002).
In visual and infrared photometry, different sets of stan- The main iron mineral phases were used to define four
dard filters with well-defined bandpasses have been iron formation facies: oxide, silicate, carbonate, and sul-
defined and are used to perform color photometry. fide. The dominant minerals, in their least metamorphosed
A given set defines a photometric system, the measures state, are hematite [Fe23+O3] and magnetite [Fe2+Fe23+O4]
in the different filters being generally given in magnitudes. in the oxide facies; greenalite [(Fe2+Mg)6Si4O10(OH)8]
Banded Iron Formation B 141
and minnesotaite [(Fe2+Mg)3Si4O10(OH)2] in the silicate to contain iron granules, oolites, and other fragments
facies; siderite [Fe2+(CO3)2] and ankerite [CaFe2+(CO3)2] embedded in a silica matrix (e.g., in the Lake Superior
in the carbonate facies; and pyrite [Fe2+S2] in the sulfide Region and the Labrador Trough, Canada; Nabberu Basin, B
facies (Klein 2005). Today, sulfide-facies iron formations Australia) (Klein 2005). This granular variety, called gran-
(i.e., pyritic carbonaceous shale or slate) are no longer ular iron formation, possesses clear detrital textures and it
classified as BIF as they represent rock types that were is thought to be the eroded and redeposited fragments of
deposited in different environments and developed preexisting BIF (Trendall 2002) (Fig. 1).
in sedimentary successions of different ages without A third type of BIF, the younger (750560 Ma) Rapitan
systematic association with BIF. type, is a special case in that they are linked to global
In terms of their size and lithological associations, BIF glaciations (Snowball Earth events). Isolation of the
are subdivided into Algoma and Superior types (Trendall oceans by glacial ice led to ocean stagnation and a buildup
2002). The Algoma type BIF are comparatively small, with of dissolved, hydrothermally sourced Fe(II), and then as
lateral extents rarely exceeding 10 km, thickness ranging the ice melted and ocean circulation became reestablished,
from 10 to 100 m, and primary iron contents typically less the iron became oxidized and formed a suite of iron for-
than 1010 t (e.g., Condie 1981; James and Trendall 1982). mations in the oxic zone of upwelling areas (Klein 2005).
They are associated with volcanogenic complexes and are Most Eo-and Mesoarchean BIF are of the Algoma
inferred to have formed close to volcanic centers such as type and are associated with granite-greenstone belts
hydrothermal vents, back-arc basins, and intracontinental (volcano-sedimentary sequences). They are found in the
rift zones (Gross 1980). By comparison, Superior type BIF North Atlantic Craton (Northern Labrador, southwestern
are hundreds of meters thick, have areal extents to the Greenland); Guyana Shield (Venezuela, Guyana);
order of 105 km2, and have total primary iron contents Kaapvaal Craton (South Africa); Liberian Shield (Sierra
that exceed 1013 t (Isley 1995). They are typically associ- Leone, Guinea, Liberia, and Ivory Coast); and Yilgarn
ated with sedimentary lithologies (dolomite, quartzites, Craton (Western Australia). Neoarchean to Proterozoic
and shales) and are inferred to have been deposited on the BIF are mostly of the Superior type, and are found in the
continental shelves of passive margins (Beukes 1983; Pilbara Craton (Hamersley Group, Western Australia);
Simonson 1985). Though the water depth of deposition Kalahari Craton (Transvaal Supergroup, South Africa),
is still poorly constrained, the absence of wave- and Sao Francisco Craton (Quadrilatero Ferrfero), and the
current-generated features sets a minimum depth of Superior Province (Labrador Trough and Lake Superior
200 m (Trendall 2002). Regions, Canada/USA) (Trendall 2002; Klein 2005). Major
Banding in BIF is observed on a wide range of scales, deposits of the Rapitan type include the Rapitan Group in
from coarse macrobands (meters in thickness) to northern Canada and those in the Urucum district of
mesobands (centimeter-thick units) to millimeter and Brazil (Klein 2005).
submillimeter layers. Among the latter is the wide variety
of varve-like repetitive laminae, known as microbands that Key Research Findings
may represent annual deposits (Trendall and Blockley Three fundamental questions regarding the origin of BIF
1970). Some Proterozoic iron formations are also found are: (1) what is the source of the silica and iron, (2) what
Banded Iron Formation. Figure 1 (a) Outcrop in the Nuuvuagittuq Supracrustal Belt; (b) in hand sample (freshly cut surface)
from the Nuuvuagittuq Supracrustal Belt (Images provided by A.M Mloszewska)
142 B Banded Iron Formation
are the mechanisms through which the primary minerals observed in both freshwater and marine environ-
were precipitated, and (3) what caused the layering? ments, and laboratory experiments demonstrate that
this form of metabolism could generate enough Fe(III)
1. The majority of evidence suggests that chemical com-
to account for all the oxidized iron in BIF (Kappler
ponents of BIF were sourced from hydrothermal
et al. 2005).
systems that contained abundant Fe and SiO2 (Morris
3. Two fundamentally different models have been used to
1993). The most accepted evidence of this is the typical
explain the banding in iron formations. One view
BIF rare earth element (REE) profile, which is depleted
suggests the episodic pulsing of Fe(II) and nutrients
in light-REE, enriched in heavy-REE, and has positive
into the depositional basin. During periods of upwell-
Eu anomalies. Furthermore, the REE profiles of BIF
ing, increased bacterial activity in the photic zone
from the Isua Supracrustal Belt (southwestern
would induce Fe(III) precipitation, irrespective of
Greenland) were successfully reproduced in the
whether biogenically or abiogenically mediated,
laboratory by mixing solutions of seawater and
while periods of no upwelling corresponded to low
high-temperature hydrothermal solutions at a 100:1
iron mineralization but high silicification from back-
ratio (Klein 2005).
ground waters (Morris 1993). Most recently, Posth
2. Traditional models of BIF deposition propose that Fe
et al. (2008) experimentally demonstrated that
(II) was oxidized in the presence of free oxygen derived
banding could also be due to natural fluctuations in
from oxygenic microbial photosynthesis, and the age
temperature controlling the efficiency of iron-
of the most voluminous BIF (e.g., Hamersley Group,
oxidizing bacteria; in summer the warm waters pro-
Western Australia; Transvaal Supergroup, South
mote increased bacterial Fe(II) oxidation while
Africa) overlap with the rise of atmospheric oxygen
maintaining silica in solution, while during winter,
at the ArcheanProterozoic boundary, at 2.5 Ga.
the decline in water temperature diminishes bacterial
While this suggests that the Fe(III) component in
activity but induced silicification. The second view is
these BIF formed via an oxic mechanism, the low
that the banding is the result of postdepositional pro-
atmospheric oxygen concentrations in the Archean
cesses in which either silica was remobilized into more
suggests that the pre-2.5 Ga BIF formed via an anoxic
compacted bands (Trendall and Blockley 1970) or
oxidizing mechanism. Both abiotic and biogenic BIF
Fe(III) was reduced and lost from the sediment
formation mechanisms have been suggested. In the
(Nealson and Myers 1990). Significantly, coupling
former case, it is postulated that the absorption of
the reduction of Fe(III) minerals to the oxidation of
ultraviolet radiation by either Fe(II) or Fe(OH)+ in
organic matter not only explains the reduced iron
the water column could have triggered the
mineralogy in BIF and the low organic-matter con-
hydrolization of these species according to the follow-
tent, but also explains the abundance of light carbon
ing equation (Cairns-Smith 1978):
isotopic signatures associated with the interlayered
2Fe2 aq 2H hv , 2Fe3 aq H2 " carbonate minerals (Konhauser et al. 2005).
so-called Great Oxidation Event. Future work on BIF will Konhauser KO, Hamade T, Raiswell R, Morris R, Ferris F, Southam G,
Canfield D (2002) Could bacteria have formed the Precambrian
no doubt investigate the temporal variations in other trace
banded iron formations? Geology 30:10791082
elements with the view of assessing changing environmen- Konhauser K, Newman DK, Kappler A (2005) The potential significance B
tal conditions during the Precambrian. Such geochemical of microbial Fe(III) reduction during deposition of Precambrian
studies will be enhanced by new analytical developments banded iron formations. Geobiology 3:167177
in stable isotopes, whereby relatively new metal isotopes Konhauser KO, Amskold L, Lalonde SV, Posth NR, Kappler A, Anbar A
(2007) Decoupling photochemical Fe(II) oxidation from shallow-
(e.g., Fe, Cr; Dauphas et al. 2007; Frei et al. 2009) or multi-
water deposition. Earth Planet Sci Lett 258:87100
isotope surveys (i.e., combining Fe and Si; Steinhofel et al. Konhauser KO, Pecoits E, Lalonde SV, Papineau D, Nisbet EG, Barley ME,
2010) will improve our understanding of paleoredox con- Arndt NT, Zahnle K, Kamber BS (2009) Ocean nickel depletion and
ditions under which BIF formed. a methanogen famine before the great oxidation event. Nature
458:750754
Morris R (1993) Genetic modelling for banded iron formation of the
See also Hamersley Group, Pilbara craton, western Australia. Precambrian
Archean Environmental Conditions Res 60:243286
Archean Traces of Life Nealson KH, Myers CR (1990) Iron reduction by bacteria: a potential role
Bacteria in the genesis of banded iron formations. Am J Sci 290:3545
Earths Atmosphere, Origin and Evolution of Posth NR, Hegler F, Konhauser KO, Kappler A (2008) Alternating Si and
Fe deposition caused by temperature fluctuations in Precambrian
Iron Cycle
Oceans. Nature 1:703707
Iron Isotopes Simonson BM (1985) Sedimentological constraints on the origins of
Iron Oxyhydroxides Precambiran iron-formations. Geol Soc Am Bull 96:244252
Jaspilite Steinhofel G, Blanckenburg F, Horn I, Konhauser KO, Beukes NJ,
Magnetite Gutzmer J (2010) Deciphering formation processes of banded iron
formations from the Transvaal and the Hamersley successions by
Ocean, Chemical Evolution of
combined Si and Fe isotope analysis using UV femtosecond laser
Oxygenation of the Earths Atmosphere ablation. Geochim Cosmochim Acta 74:26772696
Trendall AF (2002) The significance of iron-formation in the Precambrian
References and Further Reading stratigraphic record. Int Assoc Sedimentol Spec Publ 33:3366
Beukes NJ (1983) Paleoenvironmental setting of iron-formations in the Trendall AF, Blockley JG (1970) The iron formations of the Precambrian
depositional basin of the Transvaal Supergroup, South Africa. In: Hamersley Group, Western Australia: With special reference to asso-
Trendall AF, Morris RC (eds) Iron-formation: facts and problems. ciated crocidolite. Western Aus Geol Surv Bull 119:336
Elsevier, New York, pp 131209
Cairns-Smith AG (1978) Precambrian solution photochemistry, inverse
segregation, and banded iron-formations. Nature 276:807808
Condie KC (1981) Archean greenstone belts. Elsevier, Amsterdam, p 442
Dauphas N, Cates NL, Mojszis SJ, Busigny V (2007) Identification of
chemical sedimentary protoliths using iron isotopes in the >3750 Ma Barberton Greenstone Belt
Nuuvuagittuq supracrustal belt, Canada. Earth Planet Sci Lett 34:
358376
NICHOLAS ARNDT
Frei R, Gaucher C, Simon PW, Canfield DE (2009) Fluctuations in
Precambrian atmospheric oxygenation recorded by chromium iso-
Maison des Geosciences LGCA, Universite Joseph Fourier,
topes. Nature 461:250253 Grenoble, St-Martin dHeres, France
Garrels RM, Perry EA, MacKenzie FT (1973) Genesis of Precambrian
iron-formations and the development of atmospheric oxygen. Econ
Geol 68:11731179
Keywords
Gross GA (1980) A classification of iron formations based on depositional
environments. Can Mineralog 18:215222
Chert, greenstone belt, komatiite, sediment, South Africa,
Isley AE (1995) Hydrothermal plumes and the delivery of iron to banded traces of life
iron-formation. J Geol 103:169185
James HL, Trendall AF (1982) Banded iron formation: distribution in
time and paleoenvironmental significance. In: Holland HD,
Definition
Schidlowski M (eds) Mineral deposits and the evolution of the The Barberton greenstone belt in South Africa is one of the
biosphere. Springer, New York, pp 199218 best-preserved successions of mid-Archean (3.53.2 Ga)
Kappler A, Pasquero C, Konhauser KO, Newman DK (2005) Deposition supracrustal rocks in the world, together with the
of banded iron formations by anoxygenic phototrophic Fe(II)-
Pilbara craton, in Western Australia. As such, it is
oxidizing bacteria. Geology 33:865868
Klein C (2005) Some Precambrian banded iron formations (BIFs) from
a remarkable natural laboratory where conditions and
around the world: their age, geological setting, mineralogy, meta- processes at the surface of the Archean Earth can be
morphism, geochemistry, and origin. Am Mineralog 90:14731499 studied in detail. The volcanic sequences include
144 B Barberton Greenstone Belt
The sedimentary sequences themselves provide infor- sections through lower parts of the succession will provide
mation about conditions at the Earths surface: the nature information about tectonic processes that operated during
of erosion, the transport, deposition and diagenesis of deposition of volcanic, sedimentary, and granitic rocks and B
sedimentary material, structural control, the thermal his- during accretion of these materials to the continent.
tory and evolution of sedimentary basins, and thus the
overall geodynamic setting on the early Earth. See also
The ultramafic lavas of the Barberton belt have Archean Traces of Life
unusual compositions that define the Al-depleted or Barberton Supergroup
Barberton-type komatiite (Nesbitt and Sun 1976; Arndt Chert
et al. 2008). These rocks are formed through melting Impact Melt Rock
under unusual conditions in the mantle. Controversy sur- Komatiite
rounds the exact setting: most geologists support a model Pilbara Craton
in which the melts form in an unusually hot mantle plume Stromatolites
(e.g., Arndt et al. 2008) but others advocate melting in
cooler conditions in an Archean subduction zone (e.g., References and Further Reading
Grove and Parman 2004). Resolution of the issue has Altermann W (2001) The oldest fossils of Africa a brief reappraisal of
reports from the Archean. J Afr Earth Sci 33:427436
important implications for our understanding of Archean
Anhaeusser CR (1980) A geological investigation of the Archean granite-
geodynamics. Despite more than 30 years of research, very greenstone terrane south of the boesmanskop syenite pluton barber-
few complete chemical analyses of Barberton komatiites ton mountain land. Trans Geol Soc South Afr 9:73106
are available, yet this information is crucial if the potential Armstrong RA, Compston W, De Wit MJ, Williams IS (1990) The stra-
of these rocks as tracers of Archean geodynamic processes tigraphy of the 3.5-3.2 Ga Barberton greenstone belt revisited: a single
zircon ion microprobe study. Earth Planet Sci Lett 101:90106
is to be realized. Black and white smokers on the Archean
Arndt NT, Barnes SJ, Lesher CM (2008) Komatiite. Cambridge University
ocean floor, the exits of hydrothermal fluids that circu- Press, Cambridge
lated through basaltic crust, represent one possible setting Dann JC (2000) The komati formation, Barberton greenstone belt, South
for the emergence and evolution of life (Russell et al. Africa, part I: new map and magmatic architecture. S Afr J Earth Sci
2005). Examples of these may well exist in the Barberton 6:681730
de Ronde CEJ, Ebbesen TW (1996) 3.2 b.y. of organic compound forma-
greenstone belt but, as for most of the crucial geological
tion near seafloor hot springs. Geology 24:791794
and biological aspects of the Archean mentioned above, de Wit MJ, Hart RA, Hart RJ (1987) The Jamestown ophiolite complex,
also these are the subject of considerable debate (e.g., de Barberton mountain belt: a section through 3.5 Ga oceanic crust.
Ronde and Ebbesen 1996; Lowe and Byerly 2007). J Afr Earth Sci 6:681730
de Wit MJ, Roering C, Hart RJ, Armstrong RA, de Ronde CEJ, Green
RWE, Tredoux M, Peberdy E, Hart RA (1992) Formation of an
Future Directions Archean continent. Nature 357:553562
Much of future work in the belt will focus around scientific Duchac K, Hanor JS (1987) Origin and timing of the metasomatic
drilling projects that are aimed at recovering continuous silicification of an early Archean komatiite sequence, Barberton
sections of well-preserved volcanic and sedimentary rocks. mountain land, South Africa. Precambrian Res 37:125146
Work on the sedimentary sequences will provide informa- Eriksson KA, Simpson EL (2000) Quantifying the oldest tidal record: the
3.2 Ga moodies group, Barberton greenstone belt, South Africa.
tion about erosion and sedimentation on the early Earth,
Geology 28:831834
the composition and temperature of Archean seawater, and Furnes H, Banerjee NR, Muehlenbachs K, Staudigel H, de Wit MJ (2004)
one possible site where life may have emerged and evolved. Early life recorded in Archean pillow lavas. Science 304:578581
Study of tidal sequences will provide information about the Grove TL, Parman S (2004) Thermal evolution of the Earth as recorded by
dynamics of the Earth-Moon system, and the investigation komatiites. Earth Planet Sci Lett 219:173187
Heinrichs TK, Reimer TO (1977) A sedimentary barite deposit from
of spherule layers (including impact debris) provide infor-
the Archean fig tree group of the Barberton mountain land
mation about the nature and magnitude of meteorite (South Africa). Econ Geol 72:14261441
impacts on the early Earth. Work on the ultramafic to felsic Hofmann A, Reimold UW, Koeberl C (2006) Archean spherule layers in
volcanic rocks will provide new insights into volcanic the Barberton Greenstone Belt, South Africa: a discussion of prob-
processes, dynamics of the crust and mantle, interaction lematics related to the impact interpretation. In: Reimold WU,
Gibson R (eds) Processes on the early Earth. Geological Society of
between oceanic volcanic crust and the hydrosphere and
America Special Paper 405, pp 3356
biosphere. The sources of hydrothermal fluids on the ocean Knauth LP, Lowe DR (2003) High Archean climatic temperatures inferred
floor, driven by circulation of seawater through the volcanic from oxygen isotope geochemistry of cherts in the 3.5 Ga Swaziland
pile, constitute a second habitat of early life. Work on deeper supergroup, South Africa. Geol Soc Am Bull 115:566580
146 B Barberton Greenstone Belt, Sedimentology
Lopez Martinez M, York D, Hall CM, Hanes JA (1984) Oldest reliable shallow-marine siliciclastic sedimentary rocks make up
40Ar/39Ar ages for terrestrial rocks: Barberton mountainland
the dominant part of the Fig Tree Group. The Moodies
komatiites. Nature 307:352354
Lowe DR, Byerly GR (eds) (1999a) Geologic evolution of the barberton
Group is characterized by relatively coarse-grained,
greenstone belt, South Africa. Geological Society of America Special siliciclastic, shallow-marine, and fluvial deposits. Detailed
Paper 329, p 312 sedimentological and geochemical studies of the sedimen-
Lowe DR, Byerly GR (2007) Ironstone bodies of the Barberton greenstone tary rocks of the Barberton Supergroup have provided
belt, South Africa: products of a cenozoic hydrological system, not
major advances in the understanding of surface processes
Archean hydrothermal vents! Geol Soc Am Bull 119:6587
Lowe DR, Knauth LP (1977) Sedimentology of the onverwacht group
in the Paleoarchean.
(3.4 billion years), transvaal, South Africa, and its bearing on the
characteristics and evolution of the early Earth. J Geol 85:699723 Overview
Lowe DR, Byerly GR, Kyte F, Shukolyukov A, Asaro F, Krull A (2003) Bedded chert horizons of the Onverwacht Group are typ-
Spherule beds 3.473.24 billion years old in the Barberton greenstone
ically 120 m thick and represent interflow sedimentary
belt, South Africa: a record of large meteorite impacts and their
influence on early crustal and biological evolution. Astrobiology 3:748
units that were deposited on the seafloor in between
Nesbitt RW, Sun S-S (1976) Geochemistry of Archean spinifex-textured phases of extrusive submarine volcanic activity. The cherts
peridotites and magnesian and low-magnesian tholeiites. Earth consist of a variety of silicified sediments (Lowe 1999; Tice
Planet Sci Lett 31:433453 and Lowe 2006; Hofmann and Bolhar 2007). Silicification
Russell MJ, Hall AJ, Boyce AJ, Fallick AE (2005) On hydrothermal con-
took place as a result of low-temperature hydrothermal
vection systems and the emergence of life. Econ Geol 100:419438
Tice MM, Lowe DR (2006) The origin of carbonaceous matter in pre-
activity on the seafloor, resulting in excellent preservation
3.0 Ga greenstone terrains: A review and new evidence from the of these rocks. Silicified volcaniclastic sediments are com-
3.42 Ga buck reef chert. Earth Sci Rev 76:259300 mon and include silicified beds of ultramafic to mafic ash
Viljoen MJ, Viljoen RP (1969) Evidence for the existence of a mobile and accretionary lapilli. Laminated cherts of various
extrusive peridotitic magma from the Komati Formation of the
shades of gray to black represent mixtures of volcaniclastic
Onverwacht Group. Geological Society of South Africa, Special Pub-
lication 21, 87112
material and carbonaceous matter (Fig. 1). Deposition
Walsh MM (1992) Microfossils and possible microfossils from the early took place in a low-energy, predominantly sub-wave base
Archean onverwacht Group, Barberton mountain land, South Africa. setting with episodic, high-energy current events during
Precambrian Res 54:271293 which coarse volcaniclastic material and, in rare cases,
Westall F, de Wit MJ, Dann JC, van der Gaast S, de Ronde CEJ, Gerneke
meteorite impact ejecta were deposited. Cherts have
D (2001) Early Archean fossil bacteria and biofilms in hydrother-
mally influenced sediments from the Barberton greenstone belt,
been used extensively to study surface processes, seawater
South Africa. Precambrian Res 106:93116 composition, and life in the Archean.
The Fig Tree Group consists of a several kilometers
thick siliciclastic-volcaniclastic sedimentary sequence that
is capped by felsic volcanic rocks (Heinrichs 1980; Lowe
and Nocita 1999; Hofmann 2005). In the southern part of
Barberton Greenstone Belt, the belt, a variety of siliciclastic lithofacies with abundant
Sedimentology felsic volcanic detritus are present that formed in deep- to
shallow-water, fan delta, and alluvial environments
AXEL HOFMANN (southern facies). The local presence of beds of jaspilitic-
Department of Geology, University of Johannesburg, banded iron formation, chert, and barite indicate syn-
Auckland Park, Johannesburg, South Africa depositional hydrothermal activity. In the northern part,
the Fig Tree Group is mainly characterized by turbiditic
sandstones and shales that formed in a relatively deep-water
Keywords environment (northern facies). Several spherule horizons of
Archean, chert, sedimentary rock, surface processes quenched liquid silicate droplets are present and represent
fallout and tsunami wave-reworked meteorite impact
Definition deposits (Lowe et al. 2003).
Sedimentary rocks can be found throughout the The Moodies Group refers to quartz-rich, predomi-
Barberton Supergroup. In the volcano-sedimentary nantly arenaceous rocks in contrast to the quartz-poor Fig
Onverwacht Group, sedimentary rocks make up less Tree sandstones and graywackes. It consists of alluvial
than 10% of the succession. They consist of bedded conglomerate, braided fluvial, tidal and shallow-marine
cherts, a variety of silicified clastic, chemical, and bio- sandstones, and minor shale and banded iron-formation
genic sediments. Predominantly fine-grained, deep- to (Anhaeusser 1976; Heubeck and Lowe 1994). Intertidal
Barberton Greenstone Belt, Traces of Early Life B 147
Barberton Greenstone Belt, Sedimentology. Figure 1 Carbonaceous chert with discontinuous layers of silicified ultramafic ash
(gray chert) showing ripple lamination (characteristic of subaqueous deposition). Onverwacht Group, Kromberg Formation,
Josefsdal Farm
sedimentary rocks are locally well preserved. Tidal bundles hydrothermal and surface processes during mid-Archaean times.
Precambrian Res 143:2349
and microbial mat-related sedimentary structures have
Hofmann A, Bolhar R (2007) The origin of carbonaceous cherts in the
been reported (Eriksson and Simpson 2000). Deposition Barberton greenstone belt and their significance for the study of early
of the Moodies Group was syn-tectonic with extensional life in mid-Archaean rocks. Astrobiology 7:355388
and later compressional deformation in a foreland basin. Lowe DR (1999) Petrology and sedimentology of cherts and related silici-
fied sedimentary rocks in the Swaziland supergroup. In: Lowe DR,
Byerly GR (eds) Geologic evolution of the Barberton greenstone belt,
See also vol 329. Geol Soc Am Spec Pap, South Africa, pp 83114
Archean Environmental Conditions Lowe DR, Nocita BW (1999) Foreland basin sedimentation in the Mapepe
Barberton Greenstone Belt formation, southern-facies Fig tree group. In: Lowe DR, Byerly GR
Barberton Greenstone Belt, Traces of Early Life (eds) Geologic evolution of the Barberton greenstone belt, vol 329.
Chert Geol Soc Am Spec Pap, South Africa, pp 233258
Lowe DR, Byerly GR, Kyte F, Shukolyukov A, Asaro F, Krull A (2003)
Earth, Formation and Early Evolution
Spherule beds 3.473.24 billion years old in the Barberton Green-
Ejecta stone Belt, South Africa: a record of large meteorite impacts and their
Greenstone Belts influence on early crustal and biological evolution. Astrobiology
Sedimentary Rock 3:748
Swaziland Supergroup Tice MM, Lowe DR (2006) The origin of carbonaceous matter in pre-3.0
Ga greenstone terrains: A review and new evidence from the 3.42 Ga
Buck Reef Chert. Earth Sci Rev 76:259300
References and Further Reading
Anhaeusser CR (1976) The geology of the Sheba hills area of the
Barberton mountain land, South Africa, with particular reference
to the Eureka syncline. Trans Geol Soc S Afr 79:253280
Eriksson KA, Simpson EL (2000) Quantifying the oldest tidal record: the
3.2 Ga Moodies Group, Barberton greenstone belt, South Africa.
Barberton Greenstone Belt, Traces
Geology 28:831834 of Early Life
Heinrichs T (1980) Lithostratigraphische Untersuchungen in der Fig Tree
Gruppe des Barberton Greenstone Belt zwischen Umsoli und Lomati FRANCES WESTALL
(Sudafrika). Gottinger Arbeiten zur Geologie und Palaontologie
Centre de Biophysique Moleculaire, CNRS, Orleans
22:118
Heubeck C, Lowe DR (1994) Depositional and tectonic setting of the cedex 2, France
Archean Moodies Group, Barberton greenstone belt, South Africa.
Precambrian Res 68:257290
Hofmann A (2005) The geochemistry of sedimentary rocks from the Fig Synonyms
tree group, Barberton greenstone belt: implications for tectonic, Early life
148 B Barberton Greenstone Belt, Traces of Early Life
Keywords Definition
Anaerobic photosynthesis, basalt, biosignatures, carbon The Barberton Greenstone Belt contains, together with
isotopes, chemolithotrophy, Early Archean, early life, the Pilbara Greenstone Belt in Australia, the oldest
microfossils, prokaryotes, volcanic sediments (3.53.3 Ga) well-preserved terrestrial rocks, including
a b
c d
Barberton Greenstone Belt, Traces of Early Life. Figure 1 (a) Purported microbial tunnels in the vitreous rind of an 3.5-Ga-old
pillow lava from the Barberton Greenstone Belt (Furnes et al. 2004). (b) Silicified colony of chemolithotrophic microorganisms on
the surface of a volcanic particle in silicified volcaniclastic sediments from the Pilbara, Australia (Westall et al. 2006a). (c) Thin
section micrograph of possible photosynthetic microbial mat with filaments from 3.4-Ga-old cherts from Barberton (Walsh
2004). (d) Well-preserved silicified filaments in a 3.3-Ga-old microbial mat from Barberton (Westall et al. 2006b). (e) Hollow
spherical carbonaceous structures interpreted as acritarchs from 3.2-Ga-old siliciclastic sediments from Barberton (Javaux et al.
2010)
Barberton Greenstone Belt, Traces of Early Life B 149
both sedimentary and volcanic lithologies, that host fossil extremely well-preserved silicified mat documented the
signatures of life. Chemolithotrophic microorganisms presence of filaments 0.25 mm in diameter and tens of
that corroded the lava in search of essential nutrients for microns in length that are embedded in thick polymer B
growth may have produced geochemical signatures asso- on the mat surface (Westall et al. 2006b) (Fig. 1d). The
ciated with microscopic tunnels in the vitreous surfaces carbon isotope signatures of the sediment containing the
of pillow lavas extruded under water. Sediments deposited mat (d13C = 22.6 to 27.8%) are consistent with micro-
at shallow depths under water contain the remains bial fractionation. The silicified sediments also contain
of microbial mats formed probably by anaerobic detrital particles of carbon that may be derived from
photosynthesizing bacteria. eroded microbial colonies. Thus, carbon (d13C) and sulfur
(d34S) isotope signatures have been interpreted to indicate
Overview the presence of a variety of organisms including
The Early to Mid Archean (3.53.2 Ga) Barberton Green- photosynthesizers (pelagic as well as sessile), heterotrophs,
stone Belt consists mostly of igneous rocks and associated and chemotrophs, such as methanogens (see review in
sediments. Largely basic to ultrabasic lavas were extruded Westall and Southam 2006).
onto relatively shallow water platform areas. Interspersed Recently, the compressed remains of extremely large
with the volcanics are thin horizons of volcaniclastic and (300 mm diameter) hollow spherical carbonaceous
hydrothermal sediments deposited in water depths rang- structures of unknown affinity have been found in
ing from the littoral to sub-wave base. Early diagenetic 3.2-Ga-old siliciclastic sediments from Barberton and
silicification of both sediments and underlying volcanics interpreted as acritarchs or organic-walled microfossils
was related to circulating hydrothermal fluids (Hofmann (Javaux et al. 2010).
and Bohlar 2007). The resulting cherts host a variety of
traces of early life. See also
Microbial corrosion features occur in the vitreous Anoxygenic Photosynthesis
rinds of pillow lavas (Furnes et al. 2004, 2007) (Fig. 1a), Archean Traces of Life
similar to those observed in modern lavas. The corrosion Barberton Greenstone Belt
features consist of tubes containing carbon and nitrogen Biomarkers
that are lined with Ti oxides. The C isotopic signature Chemolithotroph
(d13C) of the altered pillow lava rinds is significantly Microbial Mats
different to that of the bulk of the volcanic rock and may Microfossils
have been influenced by microbial activity. Pilbara Craton
Chemolithotrophic bacteria that obtain essential nutrients
and their energy from chemical redox reactions at the References and Further Reading
surfaces of minerals and rocks formed these textures and Furnes H, Banerjee NR, Muehlenbachs K, Staudigel H, de Wit M (2004)
geochemical signatures. Colonies of such organisms on Early life recorded in archean pillow lavas. Science 304:578581
the surfaces of volcanic particles and associated tunnels Furnes H, Banerjee NR, Staudigel H, Muehlenbachs K, McLoughlin N,
have been described in sediments of similar age (3.446 Ga) de Wit M, van Kranendonk M (2007) Comparing petrographic
signatures of bioalteration in recent to Mesoarchean pillow lavas:
from the Pilbara, Australia (Westall et al. 2006a) (Fig. 1b).
tracing subsurface life in oceanic igneous rocks. Precambrian Res
The surfaces of volcaniclastic sediments deposited in 158:156176
sunlight-bathed shallow environments were host to Hofmann A, Bohlar R (2007) Carbonaceous cherts in the Barberton
microbial mats probably formed by anaerobic photosyn- Greenstone Belt and their significance for the study of early life in
thetic organisms. When observed in rock thin sections by the Archaean record. Astrobiology 7:355388
Javaux EJ, Marshall CP, Bekker A (2010) Organic-walled microfossils in
optical microscopy, microbial mats are characterized by
3.2-billion-year-old shallow-marine siliciclastic deposits. Nature
packets of fine, carbon-rich layers that form more or less 463:934938
continuous wispy, wavy horizons on sediment surfaces Tice MM (2009) Environmental controls on photosynthetic microbial
(Walsh 1992, 2004; Walsh and Lowe 1999; Tice and Lowe mat distribution and morphogenesis on a 3.42 Ga clastic-starved
2004; Tice 2009). Rarely, carbonaceous filament-like platform. Astrobiology 9:9891000
Tice M, Lowe DR (2004) Photosynthetic microbial mats in the 3,416-
structures have been observed in silicified interstitial
Myr-old ocean. Nature 431:549552
spaces between mat layers (Walsh 1992) (Fig. 1c). Walsh MM (1992) Microfossils and possible microfossils from the Early
Although the organisms forming the mats are seldom Archean Onverwacht Group, Barberton Mountain Land, South
preserved, a scanning electron microscope study of an Africa. Precambrian Res 54:271293
150 B Barberton Supergroup
Walsh MM (2004) Evaluation of early Archean volcanoclastic and Barberton Greenstone Belt, Traces of Early Life
volcanic flow rocks as possible sites for carbonaceous fossil microbes.
Earth, Formation and Early Evolution
Astrobiology 4:429437
Walsh MM, Lowe DR (1999) Modes of accumulation of carbonaceous
Greenstone Belts
matter in the early Archaean: a petrographic and geochemical study Igneous Rock
of carbonaceous cherts from the Swaziland Supergroup, Special Mafic and Felsic
Paper 329. In: Lowe DR, Byerly GR (eds) Geologic evolution of the Metasediments
Barberton greenstone belt, South Africa. Geological Society of
Sedimentary Rock
America, Boulder, pp 115132
Westall F, Southam G (2006) Early life on Earth. In: Benn K, Marecha JC,
Volcaniclastic Sediment
Condie KC (eds) Archean geodynamics and environments geophys-
ical, Monograph 164. American Geophysical Union, Washington,
pp 283304
Westall F, de Vries ST, Nijman W, Rouchon V, Orberger B, Pearson V,
Watson J, Verchovsky A, Wright I, Rouzaud J-N, Marchesini D, Barophile
Anne S (2006a) The 3.466 Ga Kittys Gap Chert, an early archaean
microbial ecosystem. In: Reimold WU, Gibson R (eds) Processes on Piezophile
the early earth, Special paper 405. Geological Society of America,
Boulder, pp 105131
Westall F, de Ronde CEJ, Southam G, Grassineau N, Colas M, Cockell C,
Lammer H (2006b) Implications of a 3.472-3.333 Ga-old subaerial
microbial mat from the Barberton greenstone belt, South Africa for Barophilic
the UV environmental conditions on the early Earth. Philos Trans R
Soc Lond B 361:18571875
Piezophile
Definition Definition
The volcano-sedimentary sequence that constitutes the In astronomy, the barycenter is the center of mass of
Barberton greenstone belt has been grouped stratigra- a system of two or more bodies. For the purposes of
phically into the Barberton Supergroup, also known as most calculations, the system can be considered to be
the Swaziland Supergroup in the older literature. The concentrated at the position of the barycenter, with
Barberton Supergroup formed ca. 3.55 to 3.22 Ga ago, a total mass equal to the sum of the masses of the indi-
and is subdivided in ascending order into three strati- vidual objects. The barycentric radial velocity of an object,
graphic units. The Onverwacht Group consists of subma- such as stars, and measured by a terrestrial observer is
rine ultramafic-mafic volcanic rocks and minor felsic calculated relative to the center of mass of the Solar Sys-
volcanic and silicified sedimentary rocks. The Fig Tree tem; it is slightly different from the heliocentric velocity of
Group comprises of shale, graywacke, and felsic such a star, which is centered on the Sun and varies slightly
volcaniclastic rocks with minor conglomerate and with time according to the position of the planets.
banded iron formation. The Moodies Group consists
of shallow-marine to fluvial sandstone and conglomerate See also
with minor shale and banded iron formation. Astrometric Planets
See also
Archean Environmental Conditions
Banded Iron Formation Barycenter Velocity
Barberton Greenstone Belt
Barberton Greenstone Belt, Sedimentology Center of Mass Velocity
Bathybius Haeckelii B 151
Definition
The Beagle 2 mission, named after the famed ship in
which Charles Darwin traveled the world, was part of the Belcher Group, Microfossils
European Space Agencys Mars Express mission. It
was launched in June 2003 and was supposed to land in Definition
December 2003. Unfortunately, all contact with the The Belcher Group comprises sedimentary rocks from
33.2 kg lander was lost a few days before touchdown and the Belcher Islands, Canada, dated at 1.9 Ga. These rocks
its fate remains a mystery. The lander was a compact include chert lenses and nodules in silicified stromat-
assemblage of instruments designed to address science olites growing in tidal and shallow subtidal waters
questions ranging from the search for traces of past and on a carbonate platform. The cherts contain tri-
extant life, measurement of the composition of the atmo- dimensionally preserved filamentous and coccoidal (sphe-
sphere and other environmental parameters, the oxidation roidal) microfossils, including fossilized colonies of
state at the surface, and analysis of the geomorphology of microscopic pigmented cells. The distribution and pattern
the landing site in a sedimentary Basin of Isidis Planitia. of division of these later microfossils (called Eoentophysallis
belcherensis) suggest a relationship to the extant genera of
Overview cyanobacteria Entophysallis. These microfossils repre-
The lander was constructed by a British consortium, coor- sent some of the oldest remains of identified cyanobacteria,
dinated by Prof. Colin Pillinger of the Open University. It together with cyst-like cyanobacteria microfossils
was equipped with a 75 cm long robotic arm holding at its (akinetes) from Gabon dated at 2.1 Ga (Fig. 1).
end an array of instruments called the PAW (Payload
Adjustable Workbench) that included stereo cameras, See also
a Mossbauer spectrometer to measure the oxidation states Chert
of iron-containing compounds, an X-ray spectrometer for Cyanobacteria
determining mineral composition, and a (dentists) drill Fossilization, Process of
for collecting samples. Also on board the lander was a Gas
Analysis Package (GAP) that included a gas chromato-
graph-mass spectrometer to analyze carbon isotopes as
a signature for life. Finally, a mole or subsurface sampler
(PLUTO Planetary Undersurface Tool) was designed to
penetrate beneath the loose regolith surface to obtain
samples for analysis.
The 1 m diameter lander was equipped with a UHF
radio antenna, telecommunications, a battery, electronic
processors, heaters, solar panels, and other payload instru-
ments, such as radiation and oxidation sensors to address
the environmental objectives of the mission. Upon arrival,
the lander was supposed to have broadcast a piece of
music specially composed by the British rock band Blur.
Various hypotheses involving malfunctioning of vari-
ous pieces of equipment have been put forward to explain Belcher Group, Microfossils. Figure 1 The mat-building
the failure of the mission. The lander could have bounced colony of the cyanobacteria Eoentophysallis belcherensis,
off the atmosphere of Mars and burnt up, or the parachute preserved in stromatolites of the 1.5 Ga Bilyakh Group, Siberia
failed to deploy and/or the airbags did not function and (photograph courtesy of A. Knoll)
Bernals Conception of Origins of Life B 153
Microbial Mats
Microfossils Bernals Conception of Origins
Sedimentary Rock of Life B
Stromatolites
STEPHANE TIRARD
Faculte des Sciences et des Techniques de Nantes, Centre
Francois Viete dHistoire des Sciences et des Techniques
Benthic Mats EA 1161, Nantes, France
Microbial Mats
Keywords
Clays, catalysis
Abstract
Benzene John Desmond Bernal (10911971) was a British physicist
who claimed in his text entitled The Physical Basis of
Synonyms Life that the origin of life process was located on clay
C6H6; Cyclohexa-1,3,5-triene deposits.
Definition
Benzene is an aromatic hydrocarbon in which the six History
carbon atoms are arranged in a ring, with all carbon bonds John Desmond Bernal was a pioneer of diffraction X-ray
equal and intermediate in length between single and dou- method. His interest for biology increased during the
ble bonds. Under standard laboratory conditions benzene 1930s and the 1940s, probably in relation with the study
is a colorless and highly flammable liquid with a sweet of biological molecules (peptides, nucleic acids, etc.) with
smell. Benzene is a known carcinogen and has various this new physical method.
toxic effects on humans. An astronomical detection in His work on origin of life was marked by his first
the protoplanetary nebula CRL 618 has been reported by publication on this topic in 1951: a little book entitled
Cernicharo et al. (2001) from mid-infrared observations, The Physical Basis of Life, which came from a previous
and the measured abundance is matched by chemical lecture (1947), and from a paper published in 1949 in the
models (Woods et al. 2003). Proceedings of the Physical Society.
In this text, Bernal gave a synthesis of previous theo-
History ries, that is, Oparines (1924, 1937), Haldanes (1929), or
Benzene was first isolated by the English chemist/physicist Dauvilliers (1947) ones. Such as he claimed that primitive
Michael Faraday in 1825, although the natural aromatic atmosphere of earth contained CO2 and he described the
resin that contains benzene comes from Southeast Asia possibility of a progressive production of organic mole-
and was known to Arab traders during the Middle Ages. cules and finally of life.
The cyclic structure of benzene was announced in 1865 by His main and original assumption regarded problems
the German chemist Friedrich A. Kekule, with the data on of dispersion and catalysis. Indeed, Bernal claimed that
carbon bond lengths coming from X-ray diffraction fundamental reactions could exist on clay deposits, marine
measurements. and freshwater, which could insure confinement and
catalysis.
See also During the 1950s and 1960s, he actively participated to
Aromatic Hydrocarbon the scientific debates on origin of life and was very active
Planetary Nebula in the diffusion of ideas on origin of life.
Peebles PJE (2009) Finding the big bang. Cambridge University Press, Overview
Cambridge. ISBN 13:978-0521519823
Astronomers have long known that most stars have binary
Weinberg S (1972) Gravitation and cosmology: principles and applica-
tions of the general theory of relativity. Wiley, New York. ISBN 13:
partners, that is, companions locked gravitationally into B
978-0471925675 orbit. About 60% of solar-type, main-sequence stars have
at least one such companion. The vast majority of these
multiple systems are binaries, but triples and even qua-
druples also exist. Binarity is also common for stars of
other spectral types.
Bimolecular Reactions Some binary companions are so close together that
one can detect the induced wobble in the stars motion,
Synonyms through a periodic Doppler shift in the wavelength of
Two-body reactions spectral lines. Such spectroscopic binaries are relatively
rare. Most systems are discovered because the two stars
Definition share a common spatial motion. This implies that their
Bimolecular reactions are chemical processes involving pairing is physical, and not a chance superposition. Over-
two reactants. Reactants may be electrons, or atoms and all, the observed range of periods is vast, from less than
molecules existing in various combinations of charge a day to millions of years, corresponding to separations
states (neutral, anionic, or cationic). The most impor- from 0.01 to 10,000 astronomical units.
tant reactant combinations for interstellar chemistry are The fact that most mature stars have companions
ion-neutral, neutral-neutral, anion-neutral, electron- naturally leads us to wonder if this situation held further
neutral, and electron-ion. back in time. Are pre-main-sequence stars, those too
young to fuse hydrogen into helium, also preferentially
See also found in binaries? What about even younger objects, those
Anions still gathering mass from their parent molecular clouds?
Interstellar Chemical Processes Since the 1980s, many researchers have investigated the
matter, and the answer is now clear. Pre-main-sequence
stars are also very likely to have a binary companion.
Indeed, the binary fraction in some young clusters is
even greater than for main-sequence stars in the field.
Binary Stars, Young The systems being found show a wide range in orbital
separations. Some are tight enough to be detected as
STEVEN STAHLER spectroscopic binaries. Most young binaries, however,
Department of Astronomy, University of California, are noticed because they exhibit a common spatial velocity
Berkeley, CA, USA within their parent stellar group. On the whole, pre-main-
sequence binaries span a wide range of separations and
periods, just as do main-sequence systems.
Keywords Many individual pre-main-sequence stars have planet-
Star formation forming disks, as evidenced by their excess infrared and
millimeter emission. The same is true for stars within
Definition binaries, but with a significant caveat. If the binary
Most stars are not isolated objects, but have an orbiting separation is less than about 100 astronomical units,
companion. This basic fact holds not only for mature corresponding to a period of about 1,000 years, then the
stars, but also for objects at an earlier stage of evolution. excess emission is absent. Apparently, the relatively nearby
Indeed, several young star clusters have a higher fraction companion star prevents formation of any circumstellar
of binaries than do main-sequence stars generally. disk. For periods as low as a few days, the primary and its
Young binaries exhibit a very broad range in separations, companion are locked into perfectly circular orbits.
and therefore orbital periods. In the widest pairs, the
orbits are highly eccentric. Conversely, the tightest pairs See also
are locked into circular orbits. Planet-forming disks are Main Sequence
absent in these latter systems, apparently because of the Pre-Main-Sequence Star
disturbing influence of the companion. Protobinary
158 B Binding Constant
See also
Biobarrier Bioburden
Clean Room B
Definition Planetary Protection
In planetary protection, a biobarrier is a mechanical
barrier to protect a spacecraft or associated component
(s) against microbial recontamination following the appli-
cation of bioburden reduction procedures. Bioburden Reduction
See also
Bioburden
Definition
Bioburden reduction involves any activities designed to
Bioburden Reduction
remove or destroy microorganisms that are performed
Planetary Protection
in order to reduce bioburden levels on or in an item of
interest. These activities could involve cleaning and wiping
with appropriate alcohol or chemical solutions, dry heat
Biobloc microbial reduction ( DHMR), ultraviolet or g ray irra-
diation, treatment with a sterilizing gas.
Biostack
See also
DHMR
Pasteurization
Bioburden Planetary Protection
Sterilization
Definition
In planetary protection, the bioburden is the total
amount of viable microorganisms sitting on the surface
and inside a spacecraft. The bioburden is evaluated using
assays in or on items of interest. To evaluate or measure Biochirality
the bioburden, the assays can be standardized by specific
procedures. Homochirality
See also
Assay
Microorganism
Planetary Protection Biodetection System
Biosensor
Bioburden Controlled
Environment
Definition Biodiversity
In planetary protection, a bioburden-controlled
environment is a place where the number of viable SIMON TILLIER, GUILLAUME LECOINTRE
microorganisms, and therefore the potential for con- Departement Systematique et Evolution, UMR 7138
taminating spaceflight hardware, is controlled and mini- CNRS-MNHN-UPMC-IRD, Museum National dHistoire
mized. Clean rooms, laminar flow hoods or cabinets, Naturelle, Paris Cedex 05, France
and other environments in which the quantity of micro-
organisms and/or particulates are monitored and
maintained at a specified level are considered bioburden Synonyms
controlled. Biological diversity; Diversity of life
160 B Biodiversity
Keywords knowledge; and provide the scientific basis for the conser-
Ecology, ecosystem services, environment, evolution, vation and sustainable use of biodiversity. Ten years after
systematics, taxonomy Rio, the second Earth Summit held in Johannesburg in
2002 set the so-called 2010 target: to achieve by 2010
Definition a significant reduction of the current rate of biodiversity
Biodiversity designates the condition of life on Earth in loss at the global, regional and national level as
terms of its variation at all levels of biological organiza- a contribution to poverty alleviation and to the benefit
tion, from genes to ecosystems. By extension, it is of all life on Earth. Clearly the target has not been met, in
used to designate life on Earth itself, most generally at the absence of instruments of measure as well as of effec-
species level but often also at all organization levels tive policies.
altogether. The political impact of the term led to However, the conjunction of scientific interest and
a definition adopted by the International Convention on social pressures has modified how ecologists, taxonomists,
Biological Diversity (Art.2): Biological diversity means population geneticists, paleontologists, and social scien-
the variability among living organisms from all sources tists of environment situate their own disciplines, toward
including, inter alia, terrestrial, marine and other aquatic an integrated vision where most see themselves as contrib-
ecosystems and the ecological complexes of which they are utors to biodiversity research.
part; this includes diversity within species, between species
and of ecosystems (Convention on Biological Diversity Overview
1992). Biodiversity Science is above all integrative. The central
problem of biodiversity research is to understand how diver-
History sity of life, that is, the variation in quality and quantities of
Although first introduced in the end of the 1960s, the living things at any scale, relates to the functioning and
word biodiversity, as a contraction of biological diversity, evolution of ecosystems including the human populations
has been coined by Walter G. Rosen while preparing and societies. In consequence, all population level research
a National US scientific Forum held in Washington in may be relevant at any scale, from any local group of living
1986. The objective of this Forum was to discuss the organisms to all past, present, and future life. Taxonomists
importance of the quality and variety of living organisms (or systematists, including paleontologists) explore and
in relation with the threats constituted by environment describe the patterns of biodiversity, present and past,
degradation, species extinction, and potential losses of proposing scenarios illustrating how in terms of
socioeconomic benefits (Wilson 1988). In parallel, the a suite of inferred historical events biodiversity reached
convergence of interest from the scientific community, its present state at the largest scales. Evolutionary biolo-
from the nature conservation organizations, and from gists aim at understanding how in terms of biological
the southern countries, who want to control the economic processes biodiversity reached its present state at genetic
benefit from their living resources, led the United Nations and population levels. Ecologists explore the patterns of
Environment Programme (UNEP) to explore the need for species interactions in ecosystems and the mechanisms of
an international convention on biological diversity. This ecosystem functioning; and social scientists explore the
approach led to an international legal instrument for the relationships between human populations and societies,
conservation and sustainable use of biological diversity: and nonhuman biodiversity. Focus on socioeconomic
the Convention on Biological Diversity was opened for benefits, which were already encompassed by the initial
signature on June 5, 1992, at the United Nations Confer- thoughts in the 1980s, has brought emphasis of the con-
ence on Environment and Development, better known as cept of ecosystem services, that is, the part of the ecosys-
the Rio Earth Summit, and was adopted by 168 coun- tem functions and products that is used by our species.
tries within the next year. In terms of scientific organiza- We understood as late as in the 1980s that the number
tion and programming, an international research program of living species is probably tenfold the previous estimates,
on Biodiversity, named Diversitas, was established in 1991 in the 1040 million living species range, rather than
jointly by UNESCO, SCOPE (Scientific Committee on the 12 millions (Erwin 1982 and subsequent papers). In par-
Problems of the Environment or the International Council allel, it has become progressively evident that unprece-
of Scientific Unions), and the IUBS (International Union dented losses and changes in biological diversity are
of Biological Sciences) to promote an integrative biodi- taking place at the genetic, species, and ecosystem levels,
versity science, linking biological, ecological and social particularly in nonmarine groups of organisms so far.
disciplines in an effort to produce socially relevant new Comparison with major extinction crises in the geological
Biodiversity B 161
history of the Earth reveals that the current rate of extinc- state. The present distribution of organisms is explained
tion is at least in the same order of magnitude, and several by a suite or series of events, not necessarily linked to each
hundred times greater than the average between crises other by causal relations. Phylogeny provides part of the B
(Dirzo and Raven 2003). The present extinction crisis information needed for the ordering of events through
does not strike us because it is not catastrophic at the time. Other data, paleontological, stratigraphical, geolog-
scale of the human lifespan, but rather in a time span of ical, etc., also participate in our knowledge of the history
several millennia, which we do not perceive directly but is of biodiversity. The answer to the historical how has
still a very short instant in the more than 3.5 billion years made decisive progress in the last two decades through the
long history of life on Earth. This crisis, sometimes referred association of the phylogenetic method introduced by Will
to as The Sixth Extinction, is likely the direct result of Hennig (Hennig 1966) with informatics and use of DNA
human activities. sequences: phyloinformatics now allows processing large
Understanding the patterns and processes of biodiversity data sets, whether molecular or morpho-anatomical.
loss and change is crucial for our species, not only because of Thanks to phylogenetic methods applied to molecular
the aesthetic, ethical, or cultural values attached to biodiver- characters, our vision of the tree of life has been radically
sity, but also because it could have numerous far-reaching modified within the last 25 years, and is still evolving.
consequences for our own life-support system. Even the Within 25 years, our vision of the tree of life has shifted
chemical composition of the air we breathe and of sea from five kingdoms to three main branches or clades, of
water depends upon biological activity well beyond the which two are bacteria domains diverging from each other
increase of carbon dioxide in the atmosphere and of acidity just as much as from ours, the eukaryotes (the organisms
in the sea water, which results directly from human activities. constituted by one to many cells with a nucleus). Con-
One of the likely consequences of man-induced vincing evidence has been brought to explain the origin of
changes in the environment is the reduction in the capacity eukaryotes by multiple bacterial endosymbioses: our own
of natural and managed ecosystems to deliver ecological cells, their mitochondria, and plasmids originate indeed
services, such as production of food and fiber, carbon from as many bacterial lineages. It is now admitted that
storage, nutrient cycling and resistance to climate, and lateral gene transfer (i.e., gene transmission between
other environmental changes. Assessing the causes and two otherwise independent lineages) is a relatively fre-
consequences of biodiversity changes, and establishing quent phenomenon at least in bacteria, and may well
the bases for the conservation and sustainable use of bio- influence significantly their evolution.
diversity, are major scientific challenges of our time. The At ecosystem level, how is also a question from both
major questions that research is facing are summarized in points of view: from an ecological processes point of view,
the Diversitas research program (Diversitas 2002, 2010). not only chance, that is, the initial conditions, but also
species interactions doubtless shape the local communi-
How Did Biodiversity Evolve in Space and ties in time, even though we are hardly able to understand
Time to Reach the Current State? and even less to predict the change when more than very
There are two kinds of sciences answering the how few species interact. The historical how may be easier to
questions. The first one is focusing on the biological pro- grasp, thanks to both paleontological observations and,
cesses by which living matter diversifies its forms (see the possibly, by combining the phylogeny of the species com-
entry Evolution (biological)). The way these scientists posing a community with the composition of the latter
demonstrate their statements is close to that of chemistry through time. An objective is to relate ecosystem change
or physics. By manipulating populations of organisms with causal factors such as climate change, entry of a clade
with very short generation times, it is possible to develop into a new region or the origin of innovations in a clade.
a hypothetico-deductive experimental approach to these
how questions: population genetics is of first impor- How Much Biodiversity Exists and How Does
tance in the field. But there are also other experimental Its Change or Loss Affect the System as
sciences like causal embryology or physiology that partic- a Whole?
ipate to the understanding of this how, though without A prerequisite to the how is the what, that is,
any population approach. documenting biodiversity. Understanding how little we
The second approach is the historical how. A set of know about the existing species implies that traditional
sciences like descriptive and comparative embryology and methods and techniques are inappropriate, and new strate-
anatomy, paleontology and systematics participate in gies are developed to increase the efficiency of field sampling,
a historical interpretation of how life arrived to its present the quality and accessibility of collections for field work, the
162 B Biodiversity
collection and curation of voucher specimens, the technolo- nineteenth century have allowed us to show that
gies for imaging and DNA sequencing, the digitization of overfishing started at least more than one century ago,
legacy data, and the development, maintenance, and con- leading to constant diminution of tonnage and size of the
nectivity of relevant databases. The need for rapid-capture fish at the world level and unpredictable consequences
technologies for identifying known species and discovering over the food web and equilibrium of the global ocean.
new ones has led to the development of the Barcode of Life However, assessing is not enough in both scientific and
initiative, which aims at providing IT tools for identifying societal terms: we want to be able to predict the change, for
species through short DNA sequences obtained from speci- scientific reasons as well as for decision making in envi-
mens identified by an expert, and kept in legacy collections ronmental policy. The solution lies in modelling, opera-
(Consortium Barcode of Life 2010; Golding et al. 2009). tionally based so far upon statistics on species distribution
The need for access to the information on species occur- in terms of environmental parameters. This approach,
rences and on the collections, which may well soon include called niche modelling, allows one to calculate an ecolog-
the only remaining specimens of many species in view of ical envelope that can be projected on a map to delimit
the current rate of extinctions, has led to the constitution species potential distribution in space. It is then easy to
of the so-called GBIF (Global Biodiversity Information modify some environmental parameters, including cli-
Facility 2010; Edwards et al. 2000), which is an interna- matic ones, to predict the consequences of changes on
tional informatics infrastructure that allows the interop- species occurrences and, to some extent, on composition
erability of the innumerable data bases on collection of communities. This approach has proved very powerful
specimens and species occurrences worldwide. to define policies and strategies regarding invasive pest
A serious problem for assessing species diversity is the species in Mexico, or design of protected areas; but it is
uneven distribution of expertise among taxa and countries: somewhat rudimentary by not taking into account eco-
groups of very high diversity and ecological importance, logical structures and processes, nor metapopulation
such as nematode worms, acarians, most insects or microbes, dynamics, habitat fragmentation, etc. The ultimate goal
in general, are notoriously understudied and very poorly is not just to understand, but to predict biodiversity
known, whereas groups that are closer to us in terms of change, developing biodiversity scenarios that predict bio-
body organization, size, and appeal to imagination may diversity change at the landscape, regional, and global
even have more specialists than species, as is the case of scales in response to various scenarios of how anthropo-
birds or elephants. In parallel, expertise is located mainly in genic drivers will change in the future.
Western developed countries, principally in Europe and
North America, whereas most megadiverse tropical coun- How Does Biodiversity Correspond to the
tries have very few specialists and insufficient research infra- Delivery of Ecosystem Functions and
structures: biodiversity is in the South but expertise and Services, and What Is the True Value of These
infrastructures are in the North. Commodities?
For their own biodiversity assessments and in response Over two decades of research in ecology have shown that the
to the environmental concerns, which are at the origin of combination of abiotic (physical and chemical) factors
environmental regulations, rich countries have developed together with biological interactions determines the limit
observation networks that are feeding large observational of biodiversity in a community, and that the composition
databases, managing billions of observational data. These of this community influences, in turn, the way it functions.
databases provide the basic tool for the application of A large number of experiments since the beginning of the
environmental regulations regarding species and habitats, 1990s has confirmed that generally the increase in biodiver-
but also constitute a tool for research when standardized sity has a positive effect on ecosystem functioning.
and made interoperable, inter alia thanks to the GBIF. Three mechanisms have been proposed to explain this
Their weakness is that they necessarily concentrate on positive effect. The first is a simple sampling effect: spe-
taxa for which there are a number of observers, that is, cies-rich ecosystems would produce more biomass, simply
principally higher plants and vertebrates. However, when because the probability for including a highly productive
enough data have been collected in the medium and long species is higher as the number of species is increased. The
term, it has been possible to show such phenomena as the second is the functional complementarity of species
decline of populations of common birds in Europe, or the resulting from a favorable pattern of traits in the commu-
shift in distribution toward the north of bird and plant nity: by increasing diversity one increases the number of
species as a consequence of global warming. In the domain effective ecological functions as more ecological niches are
of fisheries, fishing data collected since the end of the exploited. For example, two plant species having different
Biodiversity B 163
root lengths extending down in the ground will better marine, lacustrine, or terrestrial) stabilize the role played
exploit resources in the soil, and then produce more bio- by these environmental communities in the biosphere.
mass together, than a single of them. Finally, interaction of Generally speaking, the question of positive feedback of B
two species, then called facilitation, may have a positive diversity is fundamental in view of present changes in
effect on production: for example, brambles in a meadow ecosystems and still requires further research at various
may create favorable conditions for smaller species that levels of ecosystem organization. If it is true, human activ-
need moisture and shade, such as arum lilies, and doing so ities endanger self-regulation of ecosystems, of which
favors the increase in productivity of the system. many are at risk of collapsing with unavoidably serious
These mechanisms may be effective at any time and risk for our own species.
space scale, from bacteria and fungi in a piece of cheese, to
entire tropical forests and oceans. However, for practical How Can Scientific Investigation Support
reasons most experiments have been based on plant com- Policy and Decision Making to Encourage
munities, including the two best known: the European More Sustainable Use of Biodiversity?
Biodepth and the American Cedar Creek experiments, In view of the societal needs for a better understanding of
which have both shown a positive effect of diversity the functions of biodiversity for human beings (and well-
upon biomass accumulation in the communities. being where possible), communicating scientific results to
The relationship between diversity and stability of relevant political levels is crucial. Researchers are trained
ecological communities has also been studied, showing in research and communication with other researchers,
at least theoretically that some species may have a key but not in communication toward decision makers, which
role for the persistence of the community when facing results in numerous misunderstandings. This renders the
environmental disruption: roughly, having more species formation of an ad hoc mechanism a necessity. Based on
increases the chance for having at least one or a few able to the example of the IPCC (Intergovernmental Panel on
develop under modified conditions and so doing allow Climate Change), the United Nations and the G8 have
persistence of the community. Few experiments have endorsed in 2010 the creation of such a mechanism, called
tested this conclusion, but these few confirm so far the the Intergovernmental Science-Policy Platform for Biodi-
theoretical prediction of a relation between diversity and versity and Ecosystem Services (IPBES 2010; Larigauderie
stability of ecosystem functioning. and Mooney 2010) as initially proposed by France in 2005.
However, most experiments neglect the trophic rela- The IPBES progresses at intergovernmental pace, which is
tionships between species, which we know are very com- slower than species extinctions and ecosystem change, but
plex in species-rich ecosystems, from predation and will hopefully allow progress in the implementation of the
parasitism to mutual dependence such as in pollination necessary policies.
processes. A starting point may be the top-down effect,
through which a predator controls the density of prey,
which themselves control production at lower trophic
Key Research Findings
Since the beginning of the 1980s, a few points have been
levels. Diminution in density at the top levels may allow
understood:
an indirect increase in production at lowest levels; but it
may also have just the opposite effect when top levels First is a revolution in our vision of the tree of life and
participate significantly in nutrient recycling, which itself of the origin and diversification of eukaryotes. All
increases productivity: This may well be what happens as eukaryotes are no more nor less than each of the two
mankind clearly exploits and overexploits large predators. main prokaryotic clades (Bacteria and Archaea),
Overall, we know now that diversity favors ecosystem fungi and animals now appear as originating from
resilience and biomass production. It is also suspected that a common ancestor not shared with other groups,
diversity favors diversity. An illustration of this is, for and humans are nothing more than the tip of a tiny
example, the recent discovery of very high levels of twig among all mammals, which occupy nothing more
horizontal or lateral transfers of DNA in microbial than a small branch of the small clade constituted by
communities, in a way that genomes exhibit functional- all animals in the Tree of Life.
environmental patterns as well as historical patterns. Then is the change of paradigm in both taxonomy and
Horizontal heritage is far more important than previously ecology: we now know that we know nothing about
thought, compared to classical vertical heritage. These most living species, and that the way we interact with
networks of permanent DNA exchanges among a diversity biodiversity is not sustainable for present ecosystems
of microbial species in a given environment (either at any level, whether marine or land based.
164 B Biodiversity
The whole biosphere is changing at all levels, possibly Evolutionary biology is also important because we
faster than ever, and surely through a process without cannot pretend to understand and properly protect bio-
precedent, which is provoked by our species: destruc- diversity without having a deep knowledge of the pro-
tion of whole ecosystems and modification of others cesses that generate biological diversity at all levels. This
through anthropic activities including transport of is going to be important because it is not sufficient to save
species are realities that we have to face. the present state of Nature as if it would not be going to
In scientific terms, we understand better how biodi- change again. Life is continuously changing. It is impor-
versity acts in the functioning of whole ecosystems: tant to protect the potential ability to get adapted to new
biodiversity favors both production and stability of conditions, so maintaining genetic variability and our
ecosystems, and likely has a positive feedback on diver- knowledge about processes that generate it (and select it
sity itself. afterwards) is of key importance.
The second relevant direction for our knowledge and
action is to consider human societies and their products as
Future Directions
parts of biodiversity. There is a philosophical tradition that
On the purely scientific point of view, the main future
keeps human kind separated from an undefined nonhuman
direction to maintain our understanding of biodiversity is
Nature or an undefined category of animal and that
to keep all contributing sciences visible at the political
keeps culture separated from nature. In contrast, we are
level. The study of biodiversity is not merely a matter of
not only trying to change the world to save the diversity of
counting the species that are found in a given area or
this wonderful life, but also to save the cultural-material
proposing models predicting responses of ecosystems to
heritage for the few next human generations.
anthropic perturbations. The future in studies and under-
Although the economics of biodiversity is a rapidly
standing of biodiversity must keep systematics and evolu-
expanding field, and understanding the relationship
tionary biology as central disciplines along with
between biodiversity and ecosystem functioning is still
inventories and ecological modelling.
seen as a research priority, for practical reasons focus is
Systematics is important to understanding the reasons
presently made on observations and monitoring. Not only
why we classify living and fossil organisms as we do. System-
scientists, but also all kinds of decision and policy makers
atics provides the reason why the platypus is classified well
need reliable information on what is happening and pro-
apart among mammals. Phylogenetic systematics explains
jections of what may happen, both locally and globally.
why the collection of traits exhibited by the platypus is so
Decreases of coral reefs and more generally ecological
unique. If a decision has to be made concerning the preser-
consequences of acidification of the oceans, changes in
vation of the platypus, the ecological role of the platypus is
composition of the atmosphere, invasion of exotic species,
going to have a negligible weight compared to the argument
changes in the species distribution resulting from climate
from systematics. The platypus (or the coelacanth, choose
warming and transportation by humans, and destruction
the one you prefer) is negligible in terms of biomass and its
of habitats under anthropogenic pressures are all happen-
role in his environment could be replaced by another
ing and hardly evaluated due to the lack of appropriate
imported species. In terms of what organisms do in their
instruments. This observation calls for at least two lines
environment, the platypus (or the coelacanth) can perfectly
for action from the scientific community:
well be sacrificed. By contrast, phylogenetic systematics will
provide the arguments to regard this species as a very impor- The first one is improving our capacity for analysis and
tant one. Phylogeny will show that the platypus is the prod- prediction of the change in biodiversity. Operational
uct of a very ancient mammal lineage represented today by models based upon niche modelling that are already in
three species only. The characters exhibited by the platypus use to assist decisions should be developed further. The
show this: it lays eggs and it has a bizarre anatomy of the predictive value of models could doubtless still be
temporal area. In parallel, the lineage gained characters on its improved by incorporation of ecosystem functional
own branch, such as a duck-like beak or venomous fangs on parameters, as ambitioned by many ecologists; however,
the posterior limbs. The combination of the whole set of this development is impeded so far by the weakness of
properties makes the platypus a kind of unique evolutionary the concepts relating to ecosystem functions, which still
heritage a rare combination of characters. Protecting spe- requires a qualitative jump forward.
cies should therefore be considered in terms of what they Complementary and necessary for development of
have (systematics), not only through what they do (ecology). modelling is documenting what occurs and what
Biodiversity (Planetary Protection) B 165
happens, because without reliable data we may hardly References and Further Reading
hope to understand what is happening globally. Even Consortium Barcode of Life (2010) http://www.barcodinglife.org/
local predictions require global data sets because, like in Convention on Biological Diversity (1992). N 30619. United Nations,
Treaty Series, 1760, 1993:142308 B
meteorology, operational modelling is based upon sta-
Dirzo R, Raven PH (2003) Global state of biodiversity and loss. Annu Rev
tistical approaches of which precision and reliability are Environ Resour 28:137167
in proportion to the amount of observations available. Diversitas (2010) An International Programme of Biodiversity Science.
This need for data and monitoring is taken into account http://www.diversitas-international.org
by the projected construction of the Global Earth Biodi- Diversitas (2002) Diversitas Science Plan. Diversitas, Paris, France
Edwards JL, Lane MA, Nielsen ES (2000) Interoperability of biodiversity
versity Observation Network (GEO-BON), which is
databases: biodiversity information on every desktop. Science
a program for coordination of observations on biodiver- 289(5488):23122314
sity promoted by Diversitas. GEO-BON is a component Erwin TL (1982) Tropical forests: their richness in Coleoptera and other
of the Global Earth Observations System of Systems arthropod species, 3Coleopterists Bulletin 36:7475
(GEOSS), an initiative led by the World Meteorological GBIF (2010) Global Biodiversity Information Facility. http://www.gbif.
org.
Organization (Scholes et al. 2008).
Golding GB, Hanner R, Hebert P (eds) (2009) Special issue on barcoding.
Clearly, biodiversity research is shifting from tradi- Molecular Ecology Resources, 9(supplement) 1:1267
Hennig W (1966) Phylogenetic systematics. Univ. of Illinois Press, Urbana
tional fundamental questions on what is there, why it is
IPBES (2010) Intergovernmental Science-Policy Platform for Biodiversity
there, and how it works, to questions relating directly to and Ecosystem Services. http://IPBES.net
societal concerns guided by the central question of where Larigauderie A, Mooney HA (2010) The Intergovernmental science-
is mankind going in a context of radical ecological change policy Platform on Biodiversity and Ecosystem Services: moving
at the global scale. So far, this shift is beneficial rather than a step closer to an IPCC-like mechanism for biodiversity. Curr
Opin Environ Sustain 2:12
detrimental to fundamental research; and indeed the
Millenium Ecosystem Assessment (2005) http://www.maweb.org
questions raised by society regarding its own future as Naeem S, Bunker D, Hector A, Loreau M, Perrings C (2009) Biodiversity,
a constituent of biodiversity will not find their answers if ecosystem functioning and ecosystem services. Oxford University
progress is not going on in fundamental ecology, system- Press, Oxford
atics, and evolutionary biology. Scholes RJ et al (2008) Toward a global biodiversity observation system.
Science 321:10441045
To conclude on a positive note, we are right to be
Wilson EO (ed) (1988) Biodiversity. National Academy Press,
concerned by the ongoing Sixth Extinction. However, life Washington, DC
has to be considered in the very long term. The Sixth Extinc-
tion is a problem of our responsibility for the next 2 to some
200 human generations, but it is not a problem for Life itself.
Several drastic extinctions have taken place in the past
million years; there will be others. Our theoretical framework
allows us to predict that Biodiversity will be recovered, as rich
Biodiversity (Planetary
as ever or more, and Life and Earth will continue to change Protection)
together as time will continue going by.
Definition
For planetary protection, the biological diversity (bio-
See also diversity) in an environment is the inventory of types of
Adaptation microorganisms identified as being present. For micro-
Domain (Taxonomy) organisms, the identification depends also of the assay
Ecosystem which is used. For instance, to prepare future missions to
Environment Mars, the space agencies are conducting studies in the
Evolution (Biological) clean rooms due to be used for instrument and spacecraft
Gene assembly.
Genome
Lateral Gene Transfer See also
Phylogenetic Tree Bioburden
Phylogeny Bioburden Reduction
Species Planetary Protection
166 B Bioenergetics
generation of proton motive force. Examples of second- fuel energy requiring cellular reactions, is transformed in
ary active transport are the transport of nutrients to the proton motive force, a useful cellular energy source. In the
cell, the maintenance of homeostatic ionic concentrations absence of coupling between both transports, only diffu-
inside and outside of the cell, the bacterial flagellar move- sion applies and the potential energy is lost. It has been
ment produced or the synthesis of ATP, all of them calculated that up to one third of the cellular energy used
coupled to the dissipation of the proton motive force. by fermentation organisms can be generated by this pecu-
In respiration (see respiration), an electron donor liar active transport system.
gives electrons to an appropriated electron acceptor All these are examples of primary active transport
through the use of an electron transport chain located in systems because they can transform different energy
the cell membrane in bacteria, and in the mitochondrial sources in proton motive force. Once there is enough
membrane in eukaryotes. The passage of electrons energy stored as proton motive force it can be used to
through the chain promotes the translocation of protons, promote reactions that require work. The best-known
generating a gradient of protons between both sides of the example is the translocation of cellular substrates (i.e.,
membrane. The difference in potential energy (chemical glucose) to the interior of the cell against a concentration
energy) between the electron donor and the acceptor is gradient. Normally organisms, especially bacteria, live in
transformed in proton motive force, a universal storage habitats with extremely low concentration of useful sub-
system of cellular energy. strates to obtain energy. The required concentrations of
In photosynthesis, the photosynthetic reaction cen- these substrates inside the cell for metabolic reactions to
ter is excited (oxidized) by radiation, and the excited proceed are several orders of magnitude higher than their
electron is trapped by a constituent of an associated elec- concentration in the environment. Thus, very active
tron transport chain, and as in the respiration, the passage transport system is required to concentrate these sub-
of the excited electron through the different components strates inside the cell. To do this osmotic work, energy in
of the chain can promote (i) the translocation of protons the form of proton motive force is used. In this case,
producing a gradient of protons (proton motive force) or the translocation of a specific substrate is coupled to the
(ii) the generation of cellular reducing power, depending dissipation (transport) of proton motive force.
of the type of photosynthesis. In the first case, the same Similarly, proton motive force can be used to maintain
excited electron goes back to the oxidized reaction center a high concentration of K+ or a low concentration of Na+
to reduce it to the ground state (cyclic anoxygenic inside the cell. Due to simple diffusion, the high concen-
photosynthesis). In the second case, an electron donor tration of potassium stored inside the cell and required for
must donate an electron to the reaction center to bring it an optimal performance of the different functional enzy-
to the ground state (oxygenic photosynthesis, noncyclic matic activities licks out because the concentration of this
anoxygenic photosynthesis), getting in both cases ready cation is rather low outside of the cells. To maintain a high
for another excitation reaction using radiative energy. In concentration of potassium in the cytoplasm an active
the photosynthesis, the source of energy is radiation and is transport is required, because it has to be performed
transformed through a more or less complex system against a concentration gradient. The coupling between
(depending on the type of photosynthesis) in cellular the translocation of potassium to the interior of the cell
energy (proton motive force and/or reducing power). with the dissipation of the proton motive force allows
Fermentation is the only bioenergetic system that does maintaining the optimal cellular potassium concentra-
not make use of an electron transport chain to conserve tion. A similar situation can be found with the sodium
energy (see fermentation), instead cytoplasmic soluble concentration. In this case, the optimal cellular condition
enzymatic reactions are able to generate cellular useful is a lower concentration of this cation in the cytoplasm
energy (ATP) from chemical energy (reduced carbon sub- than in the environment. In this case, simple diffusion
strates). Interestingly enough, because fermentation is the licks sodium to the cytoplasm, so the active transport
main source of energy for these organisms an important required to pump sodium out of the cell can be performed
amount of substrate must be fermented for growth, and as using the energy stored as proton motive force through the
a consequence a high concentration of fermentation prod- coupling of both transport systems.
ucts are produced (i.e., ethanol, organic acids). If the But energy stored in the form of proton motive force
organism is able to couple the translocation of the fer- can be used for other cellular functions different than
mentation products to the generation of a proton gradi- transport, like the bacterial movement of flagella. In this
ent, then the potential energy stored as a concentration case the dissipation of the proton motive force is used to
gradient of fermentation products, which is not useful to perform a mechanical work: the rotation of the flagella; or
Bioenergetics B 169
the reverse transport of electrons in the electron transport Proton Motive Force
chain to generate reducing power for microorganisms that Reduction
need it and cannot produce it by other means (many Respiration B
chemolithoautotrophs).
A special case of active transport that requires atten-
tion is related with a membrane enzymatic complex References and Further Reading
involved in the synthesis and hydrolysis of ATP (see Allen JF, Martin W (2007) Evolutionary biology: out of thin air. Nature
445:610612
ATPase and ATP synthase). The membrane-bound
Bryant DA, Frigaard NU (2006) Prokaryotic photosynthesis and
synthesis of ATP from ADP and phosphate is an ender- phototrophy illuminated. Trends Microbiol 14:488496
gonic reaction that requires energy. This reaction, named Buch-Pedersen MJ, Pedersen BP, Veierskov B, Nissen P, Palmgren MG
ATP synthase, can be fuelled by the use of the energy (2009) Protons and how they are transported by proton pumps. Eur
stored as proton motive force. In this case, it will perform J Physiol 457:573579
Gruber G, Marshansky V (2008) New insights into structure-function
as a secondary active transport system. But the same
relationships between archeal ATP synthase (A1A0) and vacuolar type
enzymatic complex can perform in the opposite direction: ATPase (V1V0). BioEssays 30:10961109
hydrolyzing ATP and using the released energy to promote Heathcote P, Fyfe PK, Jones MR (2002) Reaction centers: the structure
the translocation of protons outside the membrane, gen- and evolution of solar power. Trends Biochem Sci 27:7987
erating proton motive force. In this case it is performing as Itoh H, Takahashi A, Adachi K, Noji H, Yasuda R, Yoshida M, Kinosita
K Jr (2004) Mechanically driven ATP synthesis by F1-ATPase. Nature
a primary active transport system. The reversibility of this
427:465468
reaction is the core of the bioenergetic regulation of pro- Kiang NY, Siefert J, Govindjee, Blankenship RE (2007a) Spectral signa-
karyotic cells. Experimentally it can be shown that there is tures of photosynthesis. I. Review of Earth organisms. Astrobiology
a linear relationship between the intracellular concentra- 7:222251
tion of ATP and the proton motive force. If the proton Kiang NY, Segura A, Tinetti G, Govindjee, Blankenship RE, Cohen M,
Siefert J, Crisp D, Meadows VS (2007b) Spectral signatures of pho-
motive force measured as membrane potential corre-
tosynthesis. II. Coevolution with other stars and the atmosphere on
sponds to the concentration of ATP measured inside the extrasolar worlds. Astrobiology 7:252274
cell, no activity can be detected. If the proton motive force Krah A, Pogoryelov D, Meier T, Faraldo-Gomez JD (2010) On the struc-
is lower than the value that will correspond to a given ture of the proton-binding site in the Fo rotor of chloroplast ATP
concentration of ATP, then ATP is hydrolyzed to generate Synthases. J Mol Biol 395:2027
Kuhlbrandt W (2004) Biology, structure and mechanism of P-type
proton motive force until both systems are equilibrated. If
ATPases. Nat Rev Mol Cell Biol 5:282295
the proton motive force is higher than the value that Madigan MT, Martinko JM, Dunlap PV, Clark DP (2008) Brock biology
should correspond to the ATP concentration, then the of microorganisms, 12th edn. Benjamin Cumming, San Francisco
proton motive force is dissipated to increase the ATP Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV
concentration until both systems reach equilibrium. (2007) Inventing the dynamo machine: the evolution of the F-type
and V-type ATPases. Nat Rev Microbiol 5:892899
With only one metabolic activity, prokaryotes can regulate
Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV
in an efficient manner and with little genomic investment (2008) Evolutionary primacy of sodium bioenergetics. Biol Direct 3:13
the bioenergetics of the cell. Nelson DL, Cox MM (2009) Lehninger principles of biochemistry,
5th edn. WH Freeman, New York
See also Nicholls DG, Ferguson SJ (2001) Photosynthetic generators of
protonmotive force. In: Bioenergetics3. Academic, London
Anoxygenic Photosynthesis
Nicholls DG, Ferguson SJ (2002) Bioenergetics 3. Academic, London
ATP Noji H, Yasuda R, Yoshida M, Kinosita K Jr (1997) Direct observation of
ATP Synthase the rotation of F1-ATPase. Nature 386:299302
ATPase Pennazio S (2008) Photosynthesis: the years of light. Riv Biol 101:443462
Cell Membrane Renger G, Kuhn P (2007) Reaction pattern and mechanism of light
induced oxidative water splitting in photosynthesis. Biochim
Electrochemical Potential
Biophys Acta 1767:458471
Energy Stephan E, Giovanni F, Francis-Andre W (2008) The dynamics of photo-
Energy Conservation synthesis. Annu Rev Genet 42:463515
Energy Sources Voet D, Voet JG (2004) Biochemistry, 3rd edn. Wiley, New York
Metabolism (Biological) White D (1999) The physiology and biochemistry of prokaryotes,
2nd edn. Oxford University Press, New York
Mitochondrion
Xion J, Bauer CE (2002) Complex evolution of photosynthesis. Annu Rev
Oxidation Plant Biol 53:503521
Photosynthesis Xiong J (2006) Photosynthesis: what color was its origin? Genome Biol
Proton Pump 206:14656914
170 B Biofilm
Biofilm
JANA KVIDEROVA
Institute of Botany, Academy of Sciences of the Czech
Republic, Trebon, Czech Republic
Synonyms
Microbial mats; Periphyton
Keywords
Adaptation, biofilm, biomarkers, community, extreme
environment, microorganisms, species composition,
structure
Definition
Biofilm is a layer of microorganism(s) or microbial com-
munities growing on a solid surface, usually of thicknesses
ranging between several mm to several mm. The thicker
biofilms are also referred as microbial mats.
have been proposed by Buick (1990) and Brasier et al. References and Further Reading
(2004), and in summary these focus on the size distribu- Buick R (1990) Microfossil recognition in Archaean rocks: an appraisal of
tion of the population; morphological features such as spheroids and filaments from 3500 M.Y old chert-barite at North
Pole, Western Australia. Palaios 5:441459
branching, septation, evidence for cell walls, nuclei, or
Buick R, Dunlop JSR, Groves DI (1981) Stromatolite recognition in
extra-cellular polymeric substances; their orientation, ancient rocks: an appraisal of irregularly laminated structures in an
especially evidence of colonial behavior, tiering or photo- Early Archean chert-barite unit from North Pole, Western Australia.
taxis; and lastly evidence of primary environmentally con- Alcheringa 5:161181
trolled distribution and/or subsequent decay. The Brasier MD, Green OR, McLoughlin N (2004) Characterization and
critical testing of potential microfossils from the early Earth: the
importance of such criteria has been highlighted by abiotic
Apex microfossil debate and its lessons for Mars sample return.
experiments that produce microfossil-like filamentous Int J Astrobiol 3:139150
biomorphs in the laboratory (Garcia-Ruiz et al. 2003). Garcia-Ruiz JM, Carnerup AM, Christy AG, Welham NJ (2003) Morphol-
These microfossil biogenicity criteria have also been ogy and ambiguous indicator for biogenicity. Astrobiology
adapted for meteorite samples, especially for those pur- 2:353369
Hofmann HJ (1971) Precambrian fossils, pseudofossils, and problematica
ported to contain fossilized magnetobacteria (Thomas-
in Canada. Bull Geol Surv Can 189:146
Kerpta et al. 2001). Hofmann HJ (2000) Archean Stromatolites as microbial Archives. In:
For laminated sedimentary structures known as Riding RE, Awramik SM (eds) Microbial sediments. Springer-Verlag,
stromatolites that are formed by the interaction of Berlin
microbial mats and sediments, biogenicity criteria McLoughlin N, Wilson LA, Brasier MD (2008) Growth of synthetic
stromatolites and wrinkle structures in the absence of microbes -
have been advanced by Buick et al. (1981) and contrasted
implications for the early fossil record. Geobiology 6:95105
with abiotic artifacts by McLoughlin et al. (2008). McLoughlin N, Brasier MD, Wacey D, Green OR, Perry RS (2007) On
A primary sedimentary origin along with complex lami- biogenicity criteria for endolithic microborings on early Earth and
nated macro-morphologies such as domes, columns, and beyond. Astrobiology 7:1026
branches are supportive of a biological origin, but it is the Noffke N (2009) The criteria for the biogenicity of microbially induced
sedimentary structures (MISS) in Archean and younger, sandy
micro-fabrics of stromatolites, which, preservation per-
deposits. Earth Sci Rev 96:173180
mitting, can be one of the best indicators of a biological Thomas-Kerpta KL, Clemett SJ, Bazylinski DA, Kirschvink JL, McKay DS,
origin (Hofmann, 2000). For the related phenomenon of Wentworth SJ, Vali H, Gibson JEK, McKay MF, Romanek CS
wrinkle mat textures, also termed microbially induced (2001) Truncated hexa-octahedral magnetite crystals in ALH84001:
sedimentary structures, biogenicity criteria have been presumptive biosignatures. Proc Natl Acad Sci USA 98:21642169
formulated by Noffke (2009). Lastly, for micro-cavities
produced by rock-dwelling organisms that tunnel into
rock substrates including carbonates and volcanic glass,
biogenicity criteria have been developed by McLoughlin Biogeochemical Cycles
et al. (2007).
DAVID C. FERNANDEZ-REMOLAR
See also Centro de Astrobiologa (INTA-CSIC), Torrejon de
Archean Traces of Life Ardoz, Spain
Biomarkers
Biomarkers, Isotopic
Biomarkers, Morphological Synonyms
Dubiofossil Nutrient cycles
Endogenicity
Endolithic Keywords
Fossil Biogeochemistry, biosphere, earth systems, ecosphere,
Life geobiology, habitability, homeostasis, hydrosphere,
Magnetotactic Bacteria matter, energy fluxes
Microbial Mats
Microfossils Definition
Pseudofossil The biogeochemical cycles are a theoretical concept that
Stromatolites describes the transfer of matter and energy between the
Syngenicity biosphere and the other active reservoirs of Earth like
Biogeochemical Cycles B 173
the atmosphere, hydrosphere, and lithosphere over long-term periods, which in some cases show homeo-
(Schlessinger 1997). The main processes can be under- static properties, without long-lasting nutrient recycling
stood as the storage or release of energy by the biosphere over geological time. As a consequence, the biogeochem- B
through the uptake or liberation of those molecular spe- ical cycles make up the global network that interconnects
cies bearing essential components, the so-called nutrients, the biotic and abiotic systems to other essential elements
for life. The main biogeochemical cycles involve different of Earth biogeochemistry. Such components with their
molecular species whose composition provides the essen- different functions, structures, and distribution on Earth
tial elements for both building polymeric structures and are indeed cornerstones for the cyclical emergence and
the biochemical transduction of energy in cells, like C, N, maintenance by inflow and outflow of matter and energy
S, P, and O. The biogeochemical cycles are activated when in the form of nutrient exchange. The essential unit in
the biosphere couples to the nutrient fluxes that are sup- biogeochemistry is the reservoir that corresponds to the
plied from specific sites or active centers on Earth (e.g., storing component for molecular nutrient-bearing spe-
volcanic centers, hydrothermal systems) that are essen- cies. In this sense, the four main reservoirs on Earth
tially energy sources which maintain the supply of matter (atmosphere, hydrosphere, biosphere, and lithosphere)
and energy to the Earth surface. The biosphere, as the top- are capable of harvesting nutrients from elements with
level ecosystem, has its own energy transducers, a role different redox and chemical state.
played by the primary producers that occupy the different The framework of reservoirs is strongly constrained by
habitats of the planet. They promote the transport of the inflow and outflow of the nutrient through critical
energy in the form of molecular compounds from the locations where the energy is collected, transformed, or
lithosphere to the different reservoirs of the Earth derived to another reservoir. Some of these critical sites, or
(Lovelock 2000). Most of these active systems are powered active centers, have been considered to serve as planetary
by the release of the inner heat of Earth, which, in the form organs (Lovelock 2000), whose disintegration would col-
of aerial or subaqueous systems, introduce at the regional lapse the energy flows that supply the biosphere. In this
or global scale different volatiles and other chemical spe- sense, the biosphere has provided itself with some of them
cies usable by living forms (Schlessinger 1997). Matter and in the form of specific trophic groups led by autotrophic
energy cycling is accomplished when the Earth fluxes drive organisms that occupy specific habitats. In the biosphere,
the nutrients and other components to specific sinks where the energy collectors supply nutrients to the rest of their
they are generally recycled by biochemical or geochemical- biological components, which are stored in the biosphere
mediated reactions to compounds having a different in the form of biomolecules. However, the nutrient and
chemical state. One typical example of this process is the energy supply is not only located in the biogeochemical
biogeochemical cycling of sulfur in its highest oxidized active centers of the biosphere, but also in some biologi-
state, SO42 to more reduced compounds, which are cally independent systems that are essentially associated to
sourced in volcanic centers or precipitated throughout heat dissipation centers. A good example of these are the
the hydrothermal systems as metallic sulfides (e.g., Fe2S), volcanic centers that are responsible for introducing huge
hydrogen sulfide (H2S), or dioxide of sulfur (SO2). All quantities of key nutrients for the biosphere in the form of
these molecular species can be potentially used by organ- volatiles (e.g., H2S, SO2, CO2, CH4, H2, NH3, NO2, etc.)
isms as electron donors to obtain energy, as well as raw into the atmosphere or, after their transportation, into the
material to produce sulfur-bearing machinery under hydrosphere (Fig. 1). They are eventually integrated by the
microbial assimilation (Fenchel et al. 1998). biosphere through direct uptake of gases or, after their
dissolution into a fluid phase to be used as raw material for
Overview building biomolecules or as an energy source.
The biogeochemical cycles can be considered a complex The activity of the biosphere can precipitate,
network of interrelated mechanisms by which the bio- biomineralize, or release a wide range of inorganic com-
sphere globally interacts with the different reservoirs pounds bearing nutrients such as sulfur, carbon, or phos-
through very complex, positive and negative, feedback- phorous (Sundquist and Visser 2003; Ruttenberg 2005)
controlled reactions (Margaleff 1968). As the biosphere that can potentially provide chemical energy to the bio-
requires numerous nutrients, it benefits from the many sphere itself (e.g., sulfide, ammonia, or hydrocarbon bio-
fluxes of matter and energy sourced in some Earth sys- oxidation), or raw material to the other reservoirs (Fig. 1).
tems, which transport energy and matter to the biosphere. They can be exchanged as simple volatile exchange,
Such planetary processes would not have been adopted anionic flow or biosedimentation toward the other three
174 B Biogeochemical Cycles
Carbonates
Main carbon sources in geothermal systems through CO2 supply to the atmopshere
Organic carbon reservoir (biosphere and organic by-products)
Inorganic carbon reservoir (carbonates)
Inorganic and organic carbon sinks
Recycle of carbon back to the atmosphere from crust and ocean
Precursor formation for sulfuric acid (H2S oxidation through UV-mediated reactions)
Cloud nucleation by sulfuric acid generation
Biogeochemical Cycles. Figure 1 Biogeochemical cycle of carbon coupled to the sulfur cycle. Diagram shows the main
pathways and reservoirs integrating the whole carbon cycle, and how it interplays with the sulfur cycle. Volcanic centers and
other geothermal-driven systems (e.g., hydrothermal systems) release carbon to the atmosphere (1) mainly in form of CO2, but
also CH4 and CO. The carbon is fixed as organic or inorganic carbon through the biosphere growth and the production of organics
(2), and the precipitation of carbonates (3), which can be produced by biomineralization, simple precipitation by biological
mediation, oversaturation by abiotic mechanisms and/or simple weathering. The carbon is removed from the crust by sediment
burial of carbonates and organics (4); carbonate precipitation in the subsurface by biological uptake and weathering mechanisms
are also effective processes to remove carbon from the Earth surface. The organic oxidation, thermal decomposition or simple
carbonate dissolution through diagenesis can cycle back into the atmosphere (5) the carbon as carbon dioxide to compensate
the carbon loss through the microbial uptake, carbonate precipitation and/or simple weathering. Sulfur can be oxidized to
sulfuric acid through very complex photochemical reactions starting on hydrogen sulfide oxidation and ending on the sulfite
hydration. Thus, sulfuric anion as a powerful nucleation agent of clouds (6) favor the supply of meteoric water to the surface that
transport C-bearing gases and other volatiles to the crust, making the carbon available for its fixation as organic or inorganic
compounds. Sulfur is released back to the atmosphere (7) in combination with sulfur as dimethyl sulfide by algal activity
reservoirs that, after their chemical transformations, can nutrient loss from the biosphere into the lithosphere is
then be recycled by the biosphere. Such processes result in limestone production by unicellular planktonic algae and
the elimination of nutrients from the biosphere through foraminifera, which biomineralize carbonate forming
specific sites or sinks where matter and energy is driven to shells ((Zondervan et al. 2001); Fig. 1). After the micro-
the other Earth reservoirs. One paradigmatic example of organisms death, the carbonatic shells continuously rain
Biogeochemical Cycles B 175
down on the ocean floor and eventually lead to the global most of the transporting agents are powered by the
formation of sedimentary carbonates (Fig. 1). Moreover, latitudinal difference in temperature resulted from the
these oceanic deposits can be transported from the varying incidence angle of solar radiation on the Earths B
sedimentary areas to the subduction zones where the surface. The hydrological cycle on Earth provides
carbonate is transformed back into CO2 by thermal several agents (rainfall, streams, and fluvial systems, etc.)
decomposition in deep areas of the lithosphere (Sundquist that are involved in the transportation of nutrients to the
and Visser 2003), which can then be returned to the different Earth reservoirs involved in sustaining element
atmosphere through exhalation of volatile compounds in cycling.
the volcanic centers. Some other nutrients are directly
released to the atmosphere in form of volatilized organics, Basic Methodology
which can be released back to both hydrosphere and the Biogeochemistry, the discipline that studies the interac-
biosphere once they are oxidized by reactions driven by tions among the biosphere and the different Earth reser-
photochemistry. This is the case of some organic com- voirs, emerges from the interaction of experimental
pounds like dimethyl sulfide (Fig. 1), one of the main sciences like physics, chemistry, biology, and geology,
sources of sulfur in the biosphere, which is released into which use a wide diversity of methodologies and tech-
the atmosphere by phytoplankton, but is returned to the niques. The biogeochemical cycles are powered by matter
hydrosphere in the form of sulfate after being oxidized by and energy exchanges that are experimentally measurable
UV in the atmosphere (Brimblecombe 2005). Interest- by reservoir imbalance over timescales. In this sense, reac-
ingly, the introduction of sulfur-bearing compounds into tion kinetics plus thermodynamics, related to energy flow
the atmosphere and their subsequent oxidation into sul- and storage, are the essential background concepts in the
fate has been found to be a key mechanism in nucleating description of how biogeochemical cycles are maintained
clouds, which has a planetary impact as it increases the (Schlessinger 1997). Furthermore, system modeling, an
albedo and, therefore, decreases the solar radiation affect- essential tool deeply rooted in linear and nonlinear math-
ing the Earths surface (Charlson et al. 1987). As ematics, has not only increased our understanding the
a consequence, sulfur cycling by phytoplankton is an dynamics of cycling on Earth connecting research on
essential feedback mechanism to control to some extent local and regional biogeochemical cycling of single nutri-
climatic conditions in the planet. There are other nutrients ents to other compounds, but also provides a context on
that are essential for life in very low concentrations and are a higher planetary scales (Sellers et al. 1997). Obviously,
released back to the atmosphere following the pathways building up system models requires the collection of
similar to that of dimethyl sulfide. This is the case of quantitative data to sustain consistent modeling. The
iodine that is released into the atmosphere by marine most direct, but not the easiest, way to quantify fluxes
phytoplankton in the form of different volatile com- and storage of matter and energy through and in Earth
pounds such as methyl iodide (Butler et al. 1981; Manley reservoirs is based on experimental measurements that
and de la Cuesta 1997), which is decomposed by photol- determine the gain or loss of measurable quantities of
ysis to more oxidized forms of iodine under reaction with units per year. This can be done on local or regional scales
oxidants in the troposphere. The iodine is returned back after collecting samples of air, water, sediments, soils, or
to the lithosphere or hydrosphere by rainfall or simple rocks through fieldwork. In most of cases, specific sampler
influx from the atmosphere after being included in the devices are used to recover gas, liquid, organic, or biolog-
aerosols which are active cloud nucleating agents on Earth ical materials that are gathered over time in order to infer
(Baker 2005). Interestingly, the nutrient exchange between the rates of biogeochemical fluxes. In the case of volatiles,
the different reservoirs activates some feedback mecha- the analysis of different reservoirs interacting in a given
nisms involved in maintaining homeostasis conditions area requires different in situ techniques made possible by
on a planetary scale (Charlson et al. 1987; Lovelock 2000). recent state of the art analytical instruments such as spec-
A last party in the distribution of components are the trophotometers, visible, and infrared spectroscopy, gas
transport agents in the atmosphere, the hydrosphere or chromatography, or mass spectrometry among others
the lithosphere, which act as natural carriers to spread (Viollier et al. 2003). However, accurate analysis for gases
these compounds to the different reservoirs including in geological and water samples is frequently based on
the biosphere. Most of them are activated by simple phys- careful sampling processes, which require pressurized
ical gradients depending on local or regional changes in sampling cells to collect the volatile phases under con-
temperature, density, pressure, or gravity. Although trolled conditions. The quantification and determination
potential energy plays an essential role in fluvial transport, of volatile fluxes in water masses, soils, or sediments are
176 B Biogeochemical Cycles
their affinity to target proteins through protein-drug Bourne PE, Weissig H (eds) (2003) Structural bioinformatics. Wiley-Liss,
Hoboken
docking or other techniques. (4) Analysis, classification,
Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence
and prediction of protein function. (5) Molecular evolu- analysis. Cambridge University Press, Cambridge
tion: Reconstruction of evolutionary patterns and phylo- Lesk AM (2002) Introduction to bioinformatics. Oxford University Press,
genetic trees; Simulations of evolutionary processes. USA
(6) Gene expression analysis: Statistical analysis of Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford
University Press, Oxford
mRNA levels measured through microarrays and other
Ouzounis CA, Valencia A (2003) Early bioinformatics: the birth of
techniques to detect co-regulated genes and compare dif- a disciplinea personal view. Bioinformatics 19:21762190
ferent cell types and tissues in health and disease. (7) Pro-
teomic analysis to detect gene expression by measuring
protein content. (8) Analysis and prediction of gene net-
works: DNA regulation through transcription factors;
Posttranslational modifications of proteins, in particular Biological Diversity
phosphorylation; Proteinprotein interaction networks;
Biochemical pathways. (9) Algorithm improvement. Biodiversity
(10) Database management and integration. (11) Last
but not least, literature mining to retrieve information
about biological systems of interest.
Points 68 also belong to Systems biology, an interdis- Biological Efficacy
ciplinary field that focuses its study on the interactions
between the components of biological systems, while Definition
mathematical modeling of evolutionary processes has The biological efficacy of a process is used to describe the
been demonstrated to have a rigorous formal analogy effectiveness of a specified process at affecting biological
with statistical physics. Bioinformatics and its sister disci- organisms. Efficacy refers to an expected result. For
plines are more and more central in a dialogue with instance, the biological efficacy of the DHMR is
experimental biology, both as tools for predictions and described by the measured reduction of the bioburden.
information retrieval, and as a conceptual framework to
look for general organizational and evolutionary princi- See also
ples that help us to better understand living matter. Bioburden
DHMR
See also Planetary Protection
Evolution, Molecular
Genome
Genomics
Nucleic Acids
Phylogenetic Tree Biological Evolution
Phylogeny
Primary Structure (Protein) Evolution (Biological)
Protein
Proteome, Proteomics
Quaternary Structure (Protein)
Secondary Structure (Protein) Biological Indicator
Tertiary Structure (Protein)
Definition
References and Further Reading In planetary protection, biological indicators are used
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local to establish the efficacy of a bioburden reduction pro-
alignment search tool. J Mol Biol 215:403410
cess. A well-characterized preparation of microorgan-
Anfinsen CB (1973) Principles that govern the folding of protein chains.
Science 181:223230
isms (usually spores) is subjected to the bioburden
Bastolla U, Porto M, Roman HE, Vendruscolo M (eds) (2007) Structural reduction protocol. A number of biological indicators are
approaches to sequence evolution. Springer-Verlag, Berlin/Heidelberg commercially available in the form of a population of
Biological Networks B 179
spores generated from a species of microorganism with between nodes representing interactions, the essential
known levels of resistance to a particular bioburden reduc- properties of the system can be captured in an abstracted
tion process. form with definite topological structure which can be B
linked to functional properties of the system. This abstrac-
See also tion enables the applications of tools developed in fields
Bioburden such as complex network theory, statistical physics, and
Bioburden Reduction sociology to be applied to biological networks, greatly
Microorganism facilitating their analysis (Wuchty et al. 2003; Barabasi
Planetary Protection and Oltvai 2004; Barabasi and Albert 1999). It further
Spore enables the comparison of biological systems to
engineered systems which are traditionally described in
network form (e.g., as a flowchart), and thereby enables
the identification of shared principles such as robustness,
fragility, tolerance, and modularity (Alon 2003).
Biological Networks Many biological systems have been studied from the
perspective of network theory (Zhu et al. 2007), for
EMMA HART
example:
School of Computing, Edinburgh Napier University,
Edinburgh, UK Transcription factors: Data obtained from chroma-
tin-immunoprecipitation (ChIP) followed by probing
of genomic microarrays and from DNA sequencing
Synonyms has been used to assemble networks describing tran-
Metabolic networks; Proteinprotein interaction net- scription factor-binding sites in yeast and mammalian
works; Transcription networks cells.
Proteinprotein interactions: Such interactions repre-
Keywords sent the most readily available biological networks to
Biological network, graph, hub, motif, power law, scale- date. Data is generated from techniques such as two-
free network hybrid assays and other high-throughput techniques
such as purification and mass spectrometry. In such
Definition networks, nodes represent proteins with edges
A biological network is an abstract representation of denoting physical interactions between proteins
a biological system as a graph in which nodes in the (Jeong et al. 2001). Examples of particular protein
graph represent components in the system (genes, cells, interaction networks studied include Saccharomyces
molecules) and links between the nodes represent interac- cerevisiae (yeast), Helicobacter pylori ( bacteria) as
tions between components. Links may be weighted to well as those in Drosophila and humans.
represent strength of interactions. The resulting graph Metabolic networks: Biochemical data has enabled the
has a particular topology which can be used to understand construction of metabolic networks (e.g., glycolysis)
function. which describe the metabolic and physical processes
that determine the physiological and biochemical
Overview properties of cells, usually focusing on the basic chem-
Recent advances in technology have resulted in an explo- ical pathways that generate the essential components
sion in the amount of data that can be collected from used in biochemical reactions. Nodes in such networks
biological systems. Techniques such as mass spectrometry, generally represent enzymes, with edges denoting
yeast two-hybrid assays, and other high-throughput interactions between them (Jeong et al. 2000).
methods have enabled significant advances in the identi- Immune networks: The mammalian immune system
fication of components, expression patterns, and interac- can be considered as a number of interacting networks
tions within biological systems. Analyzing such vast data operating at different levels separated in both time and
sets is challenging. Furthermore, the data sets are often space. Within cells, gene networks link genes and
incomplete and perhaps inaccurate. However, by consid- transcription factors controlling gene expression;
ering the biological system as a network or graph in which intracellular signaling networks link surface receptors
entities in the network are represented by nodes, with links on cells to gene-regulatory events; other cells of the
180 B Biological Networks
immune system such as B-cells and T-cells communi- a mutual parent are also connected (Watts and
cate via mediators such as cytokines and hence form Strogatz 1998); using social network terminology this
cellular networks (Callard and Stark 2007). can be interpreted as the friend of your friend is likely
Neuronal networks: The brain consists of intricately to be your friend. The clustering coefficient reveals
organized networks of cortical connections; these con- important information regarding network structure.
nections can be modeled by networks in which nodes C(k) measures the average clustering coefficient of
are brain regions or areas and edges represent fiber nodes with k links; if C(k) is independent of k, the
connections between them (Kepes 2007). network is either homogeneous or it is dominated by
numerous small tightly linked clusters. On the other
The examples above provide a brief insight into the
hand, if C(k) follows C(k) k1, the network has
diversity of biological systems that can be modelled using
a hierarchical architecture meaning that sparsely
a network approach. Despite the obvious differences
connected nodes are part of highly clustered regions
between the systems listed, the network approach provides
with communication between the different regions
a common framework in which these systems can be
maintained by a few hubs (Wuchty et al. 2001).
analyzed and therefore compared. Such comparisons
have revealed many similarities between networks; not These properties can be used to classify the topology of
only those derived from biological systems but also social a network into a number of models. Biological networks
systems (e.g., friendship networks) and engineered sys- tend to be scale free in that they are characterized
tems (e.g., the World Wide Web) (Barabasi and Albert by a degree distribution which follows a power law P(k)
1999). This tends to indicate generic principles of organi- kg, i.e., most nodes in the network participate in very
zation which can be exploited to gain further understand- few interactions, but a small number participate in
ing and will ultimately enable systems biology to combine many and therefore function as hubs. Many biological
the numerous details about molecular interactions into systems are intrinsically modular, i.e., functionality is
a single framework, thereby offering a means to address achieved via a set of physically or functionally linked
the structure of the cell as a whole. modules which work together. Modularity is accounted
for in hierarchical network models which assume that
Basic Methodology clusters can combine together in an iterative manner to
Network topology plays a key role in understanding the generate a hierarchical or layered structure (Barabasi and
architecture and function of biological networks. Oltvai 2004).
A number of measures are commonly used to describe
the structure of a biological network: Key Research Findings
The application of network analysis techniques to biolog-
Degree: The degree of a node defines the numbers of
ical systems, made possible by the abstraction of biological
links the node has to other nodes and is the most basic
systems as networks, indicates:
measure used. The average degree < k > can be calcu-
lated; however, a more useful measure is the degree Power-law degree distributions emerge as a universal
distribution P(k) which describes the number of nodes law characterizing cellular networks (Barabasi and
in the network having k links. A Poisson-shaped Albert 1999).
degree distribution indicates that there are no highly Many biological networks have the same topological
connected nodes; in contrast, a power-law degree dis- scaling properties as complex nonbiological systems
tribution indicates the presence of a few highly such as social networks or the World Wide Web,
connected nodes known as hubs. despite obvious differences in their components and
Mean shortest path: The shortest path is a measure of structure, and furthermore show striking similarities
the navigability of a network and describes the mean to the inherent organization of nonbiological systems
shortest distance between any two nodes in the net- (Barabasi and Albert 1999).
work. Biological networks (e.g., protein interaction Integrity and robustness of biological networks is facil-
networks and transcriptional networks) exhibit itated by structures which contain a few highly
a small-world property in which the mean shortest connected hubs, e.g., genes which can integrate mul-
path is very small. tiple signals or trigger widespread attacks (Wuchty
Clustering coefficient: This measures the average prob- et al. 2003; Jeong et al. 2001); this ensures robustness
ability in a network that two nodes which have against random failures but at the same time makes
Biological Networks B 181
Biological Polymer
Synonyms
Biopolymer Bioindice; Biosignature; Chemical fossil; Molecular Bio-
markers; Molecular Biosignatures; Morphological fossil;
Trace of life
Definition Overview
The Biological Safety Level (BSL) is used in the USA to Biomarkers or markers of life or traces of life include
describe a set of specifications for the precautions required chemical, morphological, sedimentary, or isotopic pro-
to isolate potentially-hazardous biological agents in cesses or structures that are biogenic and could be detected
a containment facility at a specified stringency, ranging to infer the past or present presence of life.
from BSL-1, which indicates the least strict containment, However, in practice, astrophysicists use biomarkers
to BSL-4, which is the containment required for the most for gases of possible biological origin that could be
hazardous human pathogens. A similar scale is used in the detected in a planetary atmosphere. Geochemists use
EU using the abbreviation P1-P4, where P indicates either biomarkers for molecular fossils (fossil molecules
Pathogen or Protection. For instance, a BSL-4 laboratory such as steranes and hopanes). Paleontologists use
(P4 in Europe) is under reduced pressure relative to biomarkers for morphological and biosedimentary
atmospheric pressure, the exhausted air is filtered, and fossils. Some scientists would use biomarkers for all
all wastes including water and any hardware leaving the possible traces of life. The term biosignatures is very
high-containment area are sterilized chemically or by common in the literature as a general term for all possible
heating. Trained personnel work inside the area in traces of life. However, astrobiologists now realize that
protective suits, over-pressurized by air pumped in from discriminating possible traces of life from unambiguous
outside through a dedicated system. The exterior of the traces of life is extremely difficult in the early Earth rock
suit is chemically disinfected when workers leave the area. record, and possibly or probably impossible in an extra-
terrestrial context. Detecting life requires a set of multidis-
ciplinary approaches and criteria and a large (and always
improving but never completed) understanding of natural
processes. Therefore, rather than using the term signa-
Biological Sensors tures or biosignatures, the expression traces of life or
even better indices of life or bioindices should be
Biosensor favored.
Biomarkers, Isotopic B 183
information not only on the biological origin of organic Key Research Findings
remains but also on the pertinent metabolic pathways of Without any experimental or natural data, Russian chem-
formation and degradation of organic matter and related ist and mineralogist Vladimir Ivanovitch Vernadski was
biominerals as well as environmental conditions at the the first to propose that isotopic fractionation of light
time of deposition. They are also powerful tools to recon- elements should occur in living matter (see Sharp 2007).
struct the biogeochemical cycle for a given element The carbon isotope ratio (12C/13C) was first measured on
through geologic time. The validity of using stable iso- various terrestrial and extraterrestrial materials (meteor-
topes as biomarkers hinges on the fact that life fractionates ites, sediments, plants, oils) by Nier and Gulbransen
isotopes in a diagnostic way that is different to other (1939) and Murphy and Nier (1941). These studies were
abiotic chemical and physical processes. This arises from the first to recognize the potential of carbon isotopes as
the activity of enzymes, which help organisms to drive a signature of biological activity using the comparison of
desirable but thermodynamically unfavorable reactions by the isotopic compositions of modern plants and fossil
coupling them to a favorable one. In most cases, for the organic matter (i.e., coal). 13C depletion of similar mag-
same reaction (same reagents and products), biotic and nitude (20) in both materials when compared to inor-
abiotic pathways differ strongly in the mechanism and ganic carbonate led them to conclude the biogenic origin
number of steps involved, and therefore in speed, yield, of this fossil organic matter. As such, this represented the
and in the magnitude of stable isotope fractionation. Here, first use of an isotopic biomarker (Wickman 1941). Sub-
we review the basic methodology and present possible sequently, Wickman (1952) and Craig (1953) showed that
interpretations of stable isotope data in our search for plants are systematically depleted in 13C due to the pref-
past biosignatures. Limits and cautions when dealing erential assimilation of the light 12C isotope but also that
with the isotopic record will also be discussed. To illustrate the magnitude of fractionation depends on plant ecology.
this concept, examples for most commonly used isotopic The link to plant metabolism was made by Bender (1968)
biomarkers (C, N, Fe, and S) are provided. The extensive who recognized differences in carbon isotope fraction-
fields of application and future research directions will ation between C3 and C4 type photosynthesis. Following
also be examined. these discoveries, isotopic biomarkers were extended to
elements related to life, either preserved in the organic
Basic Methodology matters (such as nitrogen) or representing a biomineral
The current state-of-the-art method to study isotopic such as pyritic sulfur or iron hydroxide (for a recent
compositions of any potential bio-derived materials is review, see Thomazo et al. 2009). The latest major inven-
isotope ratio mass spectrometry (IRMS). The principle tion in the field of isotopic biomarkers is the distinction of
of IRMS is based on the separation of the different iso- different types of sulfur metabolisms using multiple sul-
topes of one chemical species (e.g., for nitrogen, measured fur isotopes (Johnston et al. 2005).
as N2 gas: 14N14N, 15N14N, and 15N15N) according to their
differences in mass/electric charge ratio (m/z). Measure- Applications
ments are performed on purified gas molecules intro-
duced directly into the IRMS (e.g., SO2 or SF6 for sulfur) Isotopic Biomarkers and the Search for Early
or on a solution vaporized in a plasma chamber (e.g., Life
FeHNO3 for iron) using an inductively coupled plasma In astrobiology, isotopic biomarkers are powerful tracers
mass spectrometer (ICP-MS). Micro- to nanoscale in situ of microbial processes and the origin of biomolecules.
measurements can be done by coupling a laser (laser They can be used as (i) a direct biological signature by
ablation technique; Franchi et al. 1989) to the IRMS or analyzing fossil organic matter; (ii) a proxy for biological
using a secondary ion mass spectrometry (SIMS). Basics activity, by measuring the isotopic composition of bio-
on IRMS are provided by Hoefs (2009). Because of its derived remains such as biominerals. In both cases, iso-
design, an IRMS measures isotope ratios (e.g., 13C/12C, tope measurements unequivocally identify the presence of
34 32
S/ S, 15 N/14 N, and 56Fe/54Fe for carbon, sulfur, nitro- living organisms but frequently also a distinct metabolic
gen, and iron, respectively), with results always calibrated pathway (i.e., anabolism and/or catabolism). During the
against an international standard (e.g., V-PDB for carbon, last decades, isotopic biomarkers were extensively used in
V-CDT for sulfur, AIR for nitrogen, and IRMM-14 for order to further constrain the emergence of life on Earth.
iron; Coplen 1996; Hoefs 2009) and expressed as d in parts Figure 1 provides time series for sedimentary carbon,
per thousand (see delta notation). sulfur, nitrogen, and iron isotopes from the early
Biomarkers, Isotopic B 185
Archean (3.8 Ga) to the early Paleoproterozoic eon terrestrial atmospherehydrosphere system (Thomazo
(2.0 Ga). The records of carbon isotopes in organic matter et al. 2009). In more detail those isotopic excursions of
and in carbonates between 3.5 and 2.0 Ga and the system- carbon, nitrogen, sulfur, and iron can be related to the B
atic carbonate-organic matter isotopic difference (i.e., onset of methanotrophy, dissimilatory iron reduction,
30 provide evidence for the uninterrupted presence nitrificationdenitrification, and dissimilatory sulfate
of a substantial biosphere over geological time). Moreover, reduction while the termination of mass-independent
the combined carbon, sulfur, nitrogen, and iron isotope fractionation of sulfur (D33S) records the oxygenation of
records archive major changes in isotopic compositions Earths atmosphere (Farquhar et al. 2000). This example of
between 2.8 and 2.4 Ga (Fig. 1). These changes can be secular variations in the isotopic composition of elements
interpreted in terms of environmental and associated met- of life illustrates the substantial potential of isotopic bio-
abolic changes in response to the oxygenation of the markers as a powerful tracer of past life and their
Calcite Sulfides
15 Dolomite 10 Sulfates and barite
Others carbonate
13Ccarb ()
5 6
33S ()
5 2
15 2
0
Sulfides
10 30 Sulfates and barite
20 20
13Corg ()
10
34S ()
30
0
40
10
50
20
60 30
Kerogen
45 3
Kerogen
Micas 2
35 Chert and BIF
Shale 1
56Fe ()
25
15N ()
0
15 1
Fe sulfides
5 2 Fe oxides
Shales
3 BIF
5 Carbonates
2,000 2,400 2,800 3,200 3,600 4,000 2,000 2,400 2,800 3,200 3,600 4,000
Age (Ma) Age (Ma)
Biomarkers, Isotopic. Figure 1 Secular variations of C (kerogens and carbonates), N (kerogens, micas and bulk shales, cherts and
BIF), S (sulfides, sulfate and barite), and Fe (sulfides, Fe oxides from BIF, carbonates, bulk shales and BIF) isotopic compositions
through the Archean and late Proterozoc eon (3.82.0 Ga). Mass-independent fractionation of sulfur is expressed using the
conventional D33S, and the blue field refers to mass-dependent range of D33S (Courtesy of Elsevier Masson SAS)
186 B Biomarkers, Isotopic
associated metabolisms and could also give clues on the Future Directions
interplay between life and the environment evolution of Following technical improvements of IRMS techniques
planetary surfaces. and the conceptual development of novel isotopic
biosignatures, future progress will be achieved through
multi-isotope studies (e.g., carbon and nitrogen from
Cautions and Limits When Dealing with
organic matter or sulfur and iron from sedimentary sul-
Geological Samples
fides) combined with chemical, mineralogical, and mor-
Caution needs to be applied when studying the rock
phological observations. Moreover, novel nontraditional
record because primary signatures might be altered due
isotopes such as chlorine (e.g., Ader et al. 2008) or molyb-
to physical and chemical reworking during diagenesis and
denum (Anbar 2004) are also promising elements in the
metamorphism. Considering metamorphic processes, any
search for signatures of past or even extraterrestrial life.
organic matter will experience thermal devolatilization of
carbon (CH4 and CO2) and nitrogen (N2). This shifts the
isotopic composition of the residual organic matter
See also
Biomarkers, Morphological
toward higher values due to preferential loss of the lighter
Biomarkers, Spectral
isotope (12C, 14 N). For carbon isotopes the magnitude of
Carbon Isotopes as a Geochemical Tracer
the isotopic shift is usually estimated from a relation
FischerTropsch Effects on Isotopic Fractionation
between the d13C of organic matter (i.e., d13Corg) and its
Fractionation, Mass Independent and Dependent
elemental ratio of hydrogen to carbon (H/C ratio: Strauss
Iron Isotopes
et al. 1992) and can be corrected in most cases (Schwab
Isotopic Exchange Reactions
et al. 2005). In addition, carbon isotope ratios can be
Isotopic Fractionation (Interstellar Medium)
strongly affected by isotope exchange between carbon-
Isotopic Ratio
bearing species at elevated temperatures (i.e., organic
Molecular Biomarkers
and inorganic carbon in carbonates), which tends to
Nitrogen Isotopes
decrease the apparent isotope fractionation. A famous
Sulfur Isotopes
example of this complexity regarding carbon isotopic bio-
markers in old rocks is given by ambiguous d13Corg values
References and Further Reading
recorded for the 3.8 Ga metasedimentary rocks of Isua
Ader M, Chaudhuri S, Coates JD, Coleman M (2008) Microbial perchlo-
(Southwest Greenland) (affected by amphibolite grade rate reduction: a precise laboratory determination of the chlorine
metamorphism at 500 C and 4 kbar pressure). In these isotope fractionation and its possible biochemical basis. Earth Planet
metacarbonates, the graphite-associated carbonate isoto- Sci Lett 269:605613
pic composition was interpreted to mostly reflect isotopic Anbar AD (2004) Molybdenum stable isotopes: observations, interpreta-
tions and directions. Rev Mineral Geochem 55:429454
exchange during metamorphism (van Zuilen et al. 2002),
Bender MM (1968) Mass spectrometric studies of carbon 13 variations in
while graphite globules armored in garnet crystals show corn and other grasses. Radiocarbon 10:468472
d13Corg values arguably recording Earths oldest isotopic Coplen TB (1996) New guidelines for the reporting of stable hydrogen,
biomarker (Rosing 1999). These differing interpretations carbon, and oxygen isotope ratio data. Geochim Cosmochim Acta
of carbon isotopic biomarkers from the same rock offer 60:359
Craig H (1953) The geochemistry of the stable carbon isotopes. Geochim
a good example of the crucial combination of isotopic
Cosmochim Acta 3:5392
analyses and geological context. Finally, another impor- Farquhar J, Bao H, Thiemens M (2000) Atmospheric influence of Earths
tant concern that could invalidate the use of isotopes as earliest sulfur cycle. Science 289:756758
a biosignature would be abiotic processes mimicking Franchi IA, Boyd SR, Wright IP, Pillinger CT (1989) Application of lasers
metabolic reactions and associated isotope fractionations. in small-sample stable isotopic analysis. In: New frontiers in stable
isotope research: laser probes and small sample analysis. U.S. Geo-
Little is known in that respect from experimental and
logical Survey Bulletin 1890:5159
natural isotope data. For example, nitrogen isotopic Hoefs J (2009) Stable isotope geochemistry, 6th edn. Springer-Verlag,
fractionation during MillerUrey reactions of CH4 Berlin, pp 133
NH3 H2 mixtures (which are good analogues of Titans Johnston DT, Farquhar J, Wing BA, Kaufman AJ, Canfield DE, Habicht KS
atmospheric chemistry) have produced N-containing (2005) Multiple sulfur isotope fractionations in biological systems:
a case study with sulfate reducers and sulfur disproportionators.
nonvolatile soluble organics (amino acids, organic
Am J Sci 305:645660
acids) and polymers with d15N values of comparable Kung CC, Hayatsu R, Studier MH, Clayton RN (1979) Nitrogen isotope
magnitude to biological ammonium assimilation (Kung fractionations in the Fischer-Tropsch synthesis and in the Miller-
et al. 1979). Urey reaction. Earth Planet Sci Lett 46:141146
Biomarkers, Morphological B 187
Murphy BF, Nier AO (1941) Variations in the relative abundance of the Overview
carbon isotopes. Phys Rev 59:771772
Body fossils include microfossils and macrofossils of var-
Nier AO, Gulbransen EA (1939) Variations in the relative abundance of
the carbon isotopes. J Am Chem Soc 61:697698
ious compositions and modes of fossilization. B
Rosing M (1999) 13C-depleted carbon microparticles in >3700-Ma sea- Microbially influenced sedimentary structures include
floor sedimentary rocks from West Greenland. Science 283:674676 stromatolites (laminated carbonate rocks precipitated or
Schwab V, Spangenberg JE, Grimalt JO (2005) Chemical and carbon trapped by microorganisms), thrombolites (unlaminated
isotopic evolution of hydrocarbons during prograde metamorphism
carbonate rocks precipitated or trapped by microorgan-
from 100 C to 550 C: Case study in the Liassic black shale formation
of Central Swiss Alps. Geochim Cosmochim Acta 69:18251840
isms), oncolithes (small carbonate spheres with concentric
Sharp Z (2007) Historical background. In: Principles of stable isotope laminations precipitated by microorganisms), and
geochemistry, 1st edn. Prentice Hall, Upper Saddle River, pp 214 MISS (a range of sedimentary structures produced by
Strauss H, Des Marais DJ, Summons RE, Hayes JM (1992) The carbon the presence and activity of microbial mats in
isotopic record. In: Schopf JW, Klein C (eds) The proterozoic bio-
siliciclastic sediments). Biominerals can be passively pro-
sphere: a multidisciplinary study. Cambridge University Press,
Cambridge, pp 117127
duced or actively produced by the organisms, and the
Thomazo C, Pinti DL, Busigny V, Ader M, Hashizume K, Philippot P frontier between a biological or abiological origin is ten-
(2009) Biological activity and the Earths surface evolution: Insights uous. Ichnofossils or fossil traces of activities such as
from carbon, sulfur, nitrogen and iron stable isotopes in the rock burrows, trails, and tracks are sometimes considered as
record. CR Palevol 8:665678
morphological biomarkers. Abiotic processes can produce
van Zuilen MA, Lepland A, Arrhenius G (2002) Reassessing the evidence
for the earliest traces of life. Nature 418:627630
structures resembling microfossils ( pseudofossils).
Watanabe Y, Naraoka H, Wronkiewicz DJ, Condie KC, Ohmoto H (1997) Chemical precipitates can look like stromatolites. Min-
Carbon, nitrogen, and sulfur geochemistry of Archean and Protero- erals can self-assemble into complex structures that resem-
zoic shales from the Kaapvaal Craton, South Africa. Geochim ble body fossils or biominerals. Deciphering the
Cosmochim Acta 61:34413459
biogenicity of an object or a structure is thus very difficult
Wickman FE (1941) On a new possibility of calculating the total amount
of coal and bitumen. Geol Foren Stockholm Forhandl 63:419
even using cutting-edge in situ techniques. Several criteria
Wickman FE (1952) Variations in the relative abundance of carbon iso- have been proposed in the literature in order to test their
topes in plants. Geochim Cosmochim Acta 2:243254 biogenicity. Most of them underline the importance of
proving the endogenicity, the syngeneity, and the
biogenicity of the structures in question in a well-
characterized geological context. An additional falsifica-
tion approach is required to exclude all possible abiotic
Biomarkers, Morphological hypotheses before a biological origin can be accepted.
EMMANUELLE J. JAVAUX
Department of Geology, Paleobotany-Paleopalynology- Basic Methodology
Micropaleontology Research Unit, University of Liege, Geobiological investigations in recent and past environ-
Liege, Belgium ments have determined the criteria for biogenicity of
macroscopic and microscopic morphological signatures
of life.
Synonyms Laboratory studies including artificial cell degrada-
Biosignature; Trace of life tion, bioalteration of minerals, and mineralization exper-
iments might reveal biotic patterns and preservable
Keywords properties, although these studies may not reflect the full
Biominerals, biosignatures, fossils, microfossils, MISS, complexity of natural environmental conditions. Docu-
stromatolites, traces of life mentation of abiotic patterns and morphologies is also
essential, but is difficult outside the lab on our biological
Definition planet.
Morphological biosignatures comprise objects or struc- When trying to understand the origin of a possible
tures of biological origin. They include body fossils, morphological biomarker, three main aspects need to be
biominerals, as well as microbially influenced sedimen- considered: (1) The preservational environments: what
tary structures preserved in carbonates (such as stromat- conditions preserve cells with varying biochemical prop-
olites), in siliciclastics (such as MISS), or other rock erties? (2) The taphonomy: how do processes of degrada-
types. tion and preservation retain, alter, or erase original
188 B Biomarkers, Morphological
biological properties? (3) The criteria for biogenicity: how sedimentation of planktonic cells, pattern of cellular divi-
can we tell biological from non-biological? sion, and very importantly, their taphonomy (producing
features such as collapsed folded flexible hollow vesicles,
Key Research Findings and Applications sinuous segmented filamentous shape, pigmented surfaces
of colonies).
Body Fossils
A body fossil is any morphological remain of an organism Biominerals
after its death. It can have various sizes (microscopic to Biominerals are minerals formed by organisms.
macroscopic) and composition (organic or mineral), and Biominerals can be passively produced or actively pro-
may represent a whole organism, part of an organism, or duced by the organisms, and the frontier between
colonial organisms. Body fossils can have a variety of a biological or abiological origin is ambiguous. Biologi-
morphologies and chemical composition, depending on cally induced mineralization (BIM) includes biominerals
their original properties and the conditions in which they formed through the metabolic activity of microorganisms.
are preserved. The organic composition may be Biologically controlled mineralization (BCM) includes
transformed to various extents or erased by the complex biominerals whose formation is genetically controlled by
processes of fossilization. The mineral composition may microorganisms. Associations of biological tissues with
be primary (produced or precipitated by the organism) or minerals like bones or macroscopic and microscopic shells
secondary (the original carbonaceous or mineral walls or or plates are easy to consider as body fossils and are
envelopes being in that case partially or completely examples of BCM. Microscopic mineral precipitates onto
replaced by other minerals). Body fossils may also be cells or sheaths or coated streamers or filament bundles are
preserved as molds. In that case, the fossils are first more difficult to interpret in absence of the cell or fila-
dissolved then the hole in shape of the fossil is filled with ment, and can be BIM or BCM. These precipitates may or
a secondary mineral. not form in absence of the microorganisms. The contro-
It is difficult to prove the biogenicity of microscopic versy regarding the magnetite minerals found in the
body fossils in absence of carbonaceous material. Micro- Martian meteorite ALH84001 is a good illustration of
scopic cellular casts and molds formed by various minerals the problem. Observations in natural settings and exper-
can preserve or obscure the presence of a sheath and/or iments in the laboratory can help determine criteria for
significantly alter the size of the microbes. For example, biogenicity.
bacterial cells preserved by silicification (replaced by silica)
are difficult to discriminate from chemical precipitates. Microbially Induced Sedimentary Structures
The organic composition of a structure does not prove its (MISS) and Stromatolites
biogenicity. The term organic just indicates the presence These structures are produced by the interaction between
of molecules with carbon and hydrogen. Organic matter is a microbial mat and the surrounding sedimentary envi-
common in the universe and occurs in interstellar ronment. They can be preserved in carbonates or in
medium, in meteorites, or is produced abiotically by siliciclastics. They include a variety of laminated or
chemical reactions in hydrothermal conditions on Earth. unlaminated precipitates and/or trapped and bound min-
Therefore, more criteria are required to assert the eral grains. Stromatolites are found in the rock record
biogenicity of carbonaceous material. since the early Archean. They reach large sizes around
Microscopic and micro-chemical analyses of fossils 2.7 Ga when their biogenicity is not questioned. Criteria
isolated from shales or embedded in various rocks are such as rock fabrics, presence and distribution of carbo-
needed to demonstrate a range of preservable biological naceous material or cells or filaments, unevenness of lam-
properties, as well as to determine the taphonomic pro- inae, angle of repose of laminae, etc., are investigated to
cesses specific to the preservational environment and to prove or disprove the biogenicty of these carbonate
the original biology. The microfossils can be characterized structures.
by their preserved walls (structure and ultrastructure) or The process controlling the genesis of stromatolites is
sheaths, pigment and biopolymer composition, morphol- not yet well understood, although the association of mac-
ogy (regular cellular shape, complex shape, ornamenta- roscopic morphology with water energy is clear. Other
tion, structured organic matter), abundance (population) structures indicating the presence of microbial mat
and distribution in the rock, orientation recording behav- interacting with the sediment include particular fabric in
ior and motility of benthic organisms (ex: mats with sandstone, pinnacles, and other irregular mat surface
vertical filaments erected towards light), or passive morphologies. Again, observations in natural settings
Biomarkers, Spectral B 189
and experiments in the laboratory can help determine References and Further Reading
criteria of biogenicity. The presence of body fossils Botta O, Javaux EJ, Summons R, Rosing M, Bada J, Gomez Elvira J,
strengthens the biogenicity of the microbially induced Selsis F (eds) (2008) Strategies for life detection ISSI space science
serie. Springer-Verlag, p 380 B
sedimentary structures.
Brasier MD, McLoughin N, Green O, Wacay D (2006) A fresh look at the
fossil evidence for early Archaean cellular life. Philos Trans R Soc
Future Directions B 361:887902
Defining morphological (and other) biosignatures is not Buick R (2001) Life in the Archean. In: Briggs DEG, Crowther PR (eds)
a simple task. The taphonomic processes differ depending Paleobiology II. Blackwell Science, London, UK, pp 1321
Cady SL, Farmer JD, Grotzinger JP, Schopf JW, Steele A (2003) Morpho-
on the preservational environments and the original biol-
logical biosignatures and the search for life on Mars. Astrobiology
ogy, leading to bias in fossil diversity and morphology, 3(2):351369
often preventing identification or even recognition. Fortin F (2004) What biogenic minerals tell us. Science 303:16181619
A better understanding of these environments and their Gargaud M, Mustin C, Reisse J, Vandenabeele-Trambouze O (eds)
particular fossilization processes will help to make pre- (2009) Traces de vie presente ou passee : quels indices, signatures
ou marqueurs? Comptes rendus Academie des Sciences Paris,
dictions of the types of biosignatures to search for in
PalEvol 8, 691 p
possible past or present extraterrestrial habitats (where Grotzinger JP, Rothman DH (1996) An abiotic model for stromatolite
and what to look for), important when deciding landing morphogenesis. Nature 383:423425
sites and instrumentation for exobiological missions in Hofmann HJ (2004) Archean microfossils and abiomorphs. Astrobiology
situ and for returned samples. Characterizing the tapho- 4(2):135136
Knoll AH (2003) Life on a young planet. Princeton Univ. Press, Princeton,
nomic processes and the criteria for recognition of
NJ, 277 p
biogenicity will help interpret future observations in Konhauser KO (2007) Introduction to geomicrobiology. Blackwell Publ,
early Earth and extraterrestrial records. Oxford, p 425
However, the early Archean record of stromatolites Krumbein WE, Paterson DM, Zvarzin GA (eds) (2003) Fossil and recent
and of microscopic biosignatures is still actively debated, biofilms. A natural history of life on Earth. Springer, New York, p 504
Walter MR (ed) (1976) Developments in sedimentology, vol 20, Stromat-
illustrating the difficulty (or impossibility) of defining
olites. Elsevier, New York
unambiguous traces of life in very old rocks, much less Westall F (1999) The nature of fossil bacteria: a guide to the search for
on another planet where knowledge of the geological extraterrestrial life. J Geophys Res 104:1643716451
background is limited. Therefore, when searching for
traces of life in ancient and extraterrestrial materials,
a multitude of complementary studies and biomarkers
or bio-indices (not only morphological biomarkers)
should be used. All possible abiotic explanations should Biomarkers, Spectral
be considered and discarded before reaching an acceptable
level of reliability in any interpretation of biogenicity. LISA KALTENEGGER
Nevertheless, the conclusions will always be limited by Harvard University, Cambridge, MA, USA
our current understanding of the natural processes MPIA, Heidelberg, Germany
involved.
characterizing a habitable planet using spectroscopy and Our search for signs of life is based on the assumption
see what features point toward a biological origin (see also that extraterrestrial life shares fundamental characteristics
Biomarkers, atmospheric; Habitable planet, charac- with life on Earth, in that it requires liquid water as
terization; Habitability, effects of eccentricity; Habit- a solvent and has a carbon-based chemistry (see, e.g., Brack
ability, effects of stellar irradiation; Habitability of the 1993; DesMarais et al. 2002). Life on the basis of a different
solar system). chemistry is not considered here, because the vast range of
conceivably possible life-forms might produce signatures
History in their atmosphere that are so far unknown. Therefore,
Sagan et al. (1993) analyzed a spectrum of the Earth taken we assume that extraterrestrial life is similar to life on
by the Galileo probe, searching for signatures of life, and Earth in its use of the same input and output gases, and
concluded that the large amount of O2 and the simulta- that it exists out of thermodynamic equilibrium (Lovelock
neous presence of traces of CH4 are strongly suggestive of 1975). Biomarkers are used here to mean detectable
biology. After a decade rich in giant exoplanet detections, species, or a set of species, whose presence at significant
observational techniques have now reached the ability to abundance strongly suggests a biological origin (e.g., cou-
find planets of less than 10 MEarth (so-called Super- ple CH4 + O2, or CH4 + O3 (Lovelock 1975)). Bio-
Earths) that may potentially be habitable. indicators are indicative of biological processes but can
also be produced abiotically. It is their abundance and
Overview detection along with other atmospheric species and in
We discuss how we can read a planets spectrum to assess a certain context (for instance the properties of the star
its habitability and search for the spectral signatures of and the planet) that points toward a biological origin.
a biosphere. To characterize a planets atmosphere and its Chemoautotrophic life, whose metabolism does not
potential habitability, we look for absorption features in depend on the stellar light, can still exist outside the HZ,
the reflection and transmission spectrum of the planet. thriving in the interior of the planet where liquid water is
On Earth, some atmospheric species exhibiting noticeable available. Such metabolisms (see Extremophile) rely on
spectral features in the planets spectrum result directly or very limited sources of energy (compared to stellar light)
indirectly from biological activity: The main ones are O2, and electron donors (compared to H2O on Earth). They
O3, CH4, and N2O. CO2 and H2O are in addition impor- mainly catalyze reactions that would occur at a slower rate
tant as greenhouse gases in a planets atmosphere and in purely abiotic conditions, and they are thus not
potential sources for high O2 concentration from photo- expected to modify a whole planetary environment in
synthesis. Future remote-sensing characterization of plan- a way detectable remotely.
etary environments can be used to test our understanding
of the factors that contribute to planetary habitability. To Basic Methodology
detect such features remotely with first-generation spec-
troscopy mission that will not resolve the planet, the Atmospheric Features of a Habitable Planet
atmosphere has to show such chemical features globally. A planet observed remotely is a very faint, small object
close to a very bright and large object, its parent star.
Introduction The Earth is about a million times fainter than the Sun
Dedicated future space missions will have the explicit in the mid-infrared and about a billion times fainter
purpose of detecting other Earth-like worlds, analyzing than the Sun in the visible. Suppressing the starlight to
their characteristics, determining the composition of that degree allows collecting the planets light and
their atmospheres, investigating their capability to sustain characterizing its atmosphere.
life as we know it, and searching for signs of life. This can
set our own planet, the only known habitat, in context Key Research Findings
with other rocky worlds and expand our statistics of 3 for
rocky planets that could potentially support life. Searches Spectra of Earth in Reflection, Emission,
will concentrate on planet in the so-called habitable and Transmission
zone (HZ) where water could remain liquid if present Figure 1 shows observations and model fits to spectra of
and gases produced by biota could easily exchange with the Earth in three wavelength ranges, the visible and near-
and influence the atmosphere. The HZ is defined for infrared represent the reflected starlight, while the infrared
surface conditions only. (IR) spectrum is generated by the emitted heat flux of the
Biomarkers, Spectral B 191
1.2
Data
1 B
Model
0.8
Relative reflectance
0.6
0.4
1
0.8 O3 O2 O2 O2 H 2O
0.6
0.4
0.2
0
0.6 0.8
a Wavelength (mm)
0.8 10
Data
Model
0.6
Data
0.4 Model 5
0.2
0
0 1
0.8 CH4 CH4
H2O O2 CO2
0.6 H2 O O3 CO2 H2O
0.4
0.2
0 0
1 1.2 1.4 1.6 1.8 5 10 15 20
b Wavelength (mm) c Wavelength (mm)
Biomarkers, Spectral. Figure 1 Observed reflectivity spectrum in the visible (Woolf et al. 2002) (a) and near-infrared (Turnbull
et al. 2006) (b), and emission spectrum in the infrared (IR) (Christensen and Pearl 1997) (c) of the integrated Earth, as determined
from Earthshine and space respectively. The data are shown in black and the Smithsonian Astrophysical Observatory model in red.
The reflectivity scale is arbitrary
planet (Kaltenegger et al. 2007). For the data shown in spectra in a clear atmosphere are shown below, illustrating
Fig. 1 (a) is the visible Earthshine spectrum (Woolf et al. how each molecule contributes to the overall spectrum.
2002), (b) is the near-infrared Earthshine spectrum Figure 2 (a) shows observations (Irione 2002) and
(Turnbull et al. 2006), and (c) is the thermal infrared model fits to transmission spectra of the Earth
spectrum of Earth as measured by a spectrometer en (Kaltenegger and Traub 2009) that represent the transit
route to Mars (Christensen and Pearl 1997). The data are of Earth. The data are shown in blue, the model in red.
shown in black and the Smithsonian Astrophysical Obser- A transmission spectrum gives the apparent radius of
vatory model in red. In each case, the constituent gas a planet versus wavelength. Different molecules in the
192 B Biomarkers, Spectral
1
90 km
10
75 km
10
50 km
10
40 km
(Relative transmission) 10
30 km
10
25 km
10
20 km
10
12 km
10
10 km
10
6 km
10
4 km
10
1 km
0
8 10 12 14 16
a Wavelength (mm)
60
CO2
Effective height
CO2
40 H2O O3
O3
O2 H2O CH4
20 HNO3 H2O
0
5 10 15 20
1
0.8
O2 HNO3 H2O
0.6 H2O CH4
O3 H2O O3
0.4
CO2 CO2
Rel. transmission
0.2
0
5 10 15 20
1
0.8
HNO3 H2O
0.6 O2 CH4
O3
0.4
CO2
0.2
0
5 10 15 20
b Wavelength (mm)
Biomarkers, Spectral. Figure 2 Synthetic transmission spectra of the Earth from UV to IR (Kaltenegger and Traub 2009) for a
cloud-less atmosphere based on shuttle data (Irione 2002) and calculated for a line of sight at the tangent height indicated on the
right (a). A transmission spectrum gives the apparent radius of a planet versus wavelength. Different molecules in the planets
atmosphere absorb the stellar light and make the planet appear bigger than its solid radius at characteristic wavelengths, depending
on the molecule. This is shown here as effective height in the atmosphere (b). The atmospheric features are indicated below
Biomarkers, Spectral B 193
planets atmosphere absorb part of the stellar light and Temperature and Radius of a Planet
make the planet appear bigger than its solid radius at Knowing the temperature and planetary radius is crucial
characteristic wavelengths, depending on the molecule. for a general understanding of the physical and chemical B
This is shown here as effective height in the atmosphere. processes occurring on the planet (e.g., Tectonism,
The atmospheric features are indicated. For details on the Atmospherere, escape). In theory, spectroscopy can
Earths transmission spectrum during a lunar eclipse, see provide some detailed information on the thermal profile
Palle et al. 2009 and Vidal-Madjar et al. (2010). of a planetary atmosphere (see Atmospheric structure).
Both spectral regions contain the signature of atmo- This, however, requires a spectral resolution and
spheric gases that may indicate habitable conditions and, a sensitivity that are well beyond the performance of
possibly, the presence of a biosphere: CO2, H2O, O3, CH4, a first-generation spacecraft. Generally, the surface tem-
and N2O in the thermal infrared, and H2O, O3, O2, CH4, perature of a planet at a specific distance from its star
and CO2 in the visible to near-infrared in reflection depends on its albedo and on the greenhouse warming
(Fig. 1) and transmission spectra (Fig. 2). The presence by atmospheric compounds. However, even with a low-
or absence of these spectral features (detected individually resolution spectrum of the thermal emission, the mean
or collectively) will indicate similarities or differences effective temperature can be obtained from the peak of the
among the atmospheres of terrestrial planets and their Black Body curve in the infrared (IR). The measured IR
astrobiological potential. flux can directly be converted into a brightness tempera-
ture that will provide information on the temperature of
the atmospheric layers responsible for the emission. The
Characterizing Planetary Environments overall flux of the planet in the IR is determined by the
It is relatively straightforward to remotely ascertain that surface area of the planet and its effective temperature,
Earth is a habitable planet, replete with oceans, therefore the radius of the emitting surface (e.g., ground
a greenhouse atmosphere, global geochemical cycles, or cloud layers; see Clouds) of the planet can be
and life if one has data with arbitrarily high signal-to- obtained.
noise ratio and spatial and spectral resolutions. The inter- The ability to associate the spectrum with a surface
pretation of observations of other planets with limited temperature relies on the existence and identification of
signal-to-noise ratio and spectral resolution, as well as spectral windows probing the surface or specific atmo-
absolutely no spatial resolution, as envisioned for the spheric levels. Such identification is not trivial. For an
first-generation instruments, will be far more challenging. Earth-like planet, there are some atmospheric windows
This implies that we need to gather information on the that can be used in most of the cases, especially between
planets environment to understand what we will see. We 8 and 11 mm, as seen in Fig. 1 (a). This window would,
can then test if we have an abiotic explanation of all however, become opaque at high H2O partial pressure
compounds seen in the atmosphere of such a planet. If (e.g., in the inner part of the Habitable Zone (HZ) where
we do not, we can work with the exciting biotic a lot of water is vaporized) and at high CO2 pressure (e.g.,
hypothesis. a very young Earth or the outer part of the HZ). The
O2 and O3 in combination with a reducing gas like accuracy of the radius and temperature determination
CH4 are good biomarker candidates. Reduced gases and will depend on the quality of the fit (and thus on the
oxygen have to be produced concurrently to be detectable sensitivity and resolution of the spectrum), the precision
in the atmosphere, as they react rapidly with each other. of the Sunstar distance, the cloud coverage, and also the
Thus, the chemical imbalance traced by the simultaneous distribution of brightness temperatures over the planetary
signature of O2 and/or O3 and of a reduced gas like CH4 surface. Assuming the effective temperature of our planet
can be considered as a signature of biological activity were radiated from the uppermost cloud deck at about
(Lovelock 1975). These species can be detected by a low- 12 km would introduce about 2% error on the Earths
resolution spectrograph (O2 in the visible with radius derived from emergent and/or transmission spec-
a resolution <100, O3 and CH4 in the infrared with tra. For transiting planets, the accuracy of the radius of the
a resolution <50). Note that if the presence of biogenic planet depends on how well the host star is characterized.
gases such as O2/O3 + CH4 may imply the presence of
a massive and active biosphere, their absence does not Potential Biomarkers
imply the absence of life. Life existed on Earth before the Owen (1980) suggested searching for O2 as a tracer of life.
interplay between oxygenic photosynthesis and carbon Oxygen in high abundance is a promising bio-indicator.
cycling produced an oxygen-rich atmosphere. Oxygenic photosynthesis, the by-product of which is
194 B Biomarkers, Spectral
molecular oxygen extracted from water, allows terrestrial Earths N2O is produced by the activities of anaerobic
plants and photosynthetic bacteria (cyanobacteria) to use denitrifying bacteria. N2O would be hard to detect in
abundant H2O, instead of having to rely on scarce supplies Earths atmosphere with low resolution, as its abundance
of electron donors like H2 and H2S to reduce CO2. With is low at the surface (0.3 ppmv) and falls off rapidly in the
oxygenic photosynthesis, the production of the biomass stratosphere. Spectral features of N2O would become
becomes limited only by nutrients and no longer by energy more apparent in atmospheres with more N2O and/or
(light in this case) nor by the abundance of electron less H2O vapor. Segura et al. (2003) have calculated the
donors. Oxygenic photosynthesis at a planetary scale level of N2O for different O2 levels and found that its
results in the storage of large amounts of radiative energy abundance decreases together with O2. This is due to the
in chemical energy, in the form of organic matter. For this fact a decrease in O2 produces an increase of H2O photol-
reason, oxygenic photosynthesis had a tremendous impact ysis resulting in the production of more hydroxyl radicals
on biogeochemical cycles on Earth and eventually resulted (OH) responsible for the destruction of N2O.
in the global transformation of Earths environment. Less The methane found in the present atmosphere of the
than 1ppm of atmospheric O2 comes from abiotic Earth has a biological origin, except for a small fraction
processes (Walker 1977). Cyanobacteria and plants are produced abiotically in hydrothermal systems where hydro-
responsible for the biotic production by using solar pho- gen is released by the oxidation of Fe by H2O and reacts with
tons to extract hydrogen from water and using it to pro- CO2. Depending on the degree of oxidation of a planets
duce organic molecules from CO2. This metabolism is crust and upper mantle, such nonbiological mechanisms
called oxygenic photosynthesis. The reverse reaction, can produce large amounts of CH4 under certain circum-
using O2 to oxidize the organics produced by photosyn- stances. Therefore, the detection of methane alone cannot
thesis, can occur abiotically when organics are exposed to be considered a sign of life, while its detection in an
free oxygen, or biotically by both eukaryotes and certain oxygen-rich atmosphere would be difficult to explain in
prokaryotes using O2 and consuming organics. the absence of a biosphere. Note that methane on Mars
Because of this balance, the net release of O2 in the has been suggested (Mumma et al. 2009), while the
atmosphere is due to the burial of organics in sediments. atmosphere of Mars contains 0.1% of O2 and some
Each reduced carbon buried results in a free O2 molecule ozone. In this case, the amounts involved are extremely
in the atmosphere. This net release rate is also counter- low and the origin of the Martian O2 and O3 is known to
balanced by weathering of fossilized carbon when exposed be photochemical reactions initiated by the photolysis of
to the surface. The oxidation of reduced volcanic gases CO2 and water vapor. If confirmed, the presence of meth-
such as H2 and H2S also accounts for a significant fraction ane could be explained by subsurface geochemical process,
of the oxygen losses. The atmospheric oxygen is recycled assuming that reducing conditions exist on Mars below
through respiration and photosynthesis in less than 10,000 the highly oxidized surface. The case of NH3 is similar
years. In the case of a total extinction of Earths biosphere, to the one of CH4. They are both released into Earths
the atmospheric O2 would disappear in a few million atmosphere by the biosphere with similar rates, but the
years. atmospheric abundance of NH3 is orders of magnitude
The spectrum of the Earth has exhibited a strong lower due to its very short lifetime under UV irradiation.
infrared signature of ozone for more than 2 billion years, The detection of NH3 in the atmosphere of a habitable
and a strong visible signature of O2 for an undetermined planet would thus be extremely interesting, especially if
period of time between 2 and 0.8 billion years (depending found with oxidized species. The detection of H2O and
on the required depth of the band for detection and also CO2 are important in the search for signs of life not as
the actual evolution of the O2 level; Kaltenegger et al. biosignatures themselves, but because they are raw
2007). This difference is due to the fact that a saturated materials for life and thus necessary for planetary
ozone band appears already at very low levels of O2 (104 habitability.
ppm), while the oxygen line remains unsaturated at values There are other molecules that could, under some
below the present atmospheric level (Segura et al. 2003). circumstances, act as excellent biomarkers; for example,
The depth of the saturated O3 band is determined by the the manufactured chlorofluorocarbons (CCl2F2 and
temperature difference between the surface-clouds CCl3F) are observed in our current atmosphere in the
producing spectral continuum and the ozone layer. thermal infrared waveband, but their abundances are cur-
N2O is produced in abundance by life but only in rently too low to be spectroscopically observed at low
negligible amounts by abiotic processes. Nearly all of resolution.
Biomarkers, Spectral B 195
biomarkers is crucial, but only very few studies have been See also
dedicated to it (Rosenqvist and Chassefiere 1995; Leger Albedo
et al. 1993; Lagrange et al. 2009; Selsis et al. 2002). Atmosphere, Structure
Biomarkers, Atmospheric (Evolution Over Geological
Cryptic Worlds Time)
On the Earth, photosynthetic organisms are responsible Clouds
for the production of nearly all of the oxygen in the Greenhouse Effect
atmosphere. However, in many regions of the Earth, and Habitability (Effect of Eccentricity)
particularly where surface conditions are extreme, for Habitability (Effects of Stellar Irradiation)
example in hot and cold deserts, photosynthetic organ- Habitability of the Solar System
isms can be driven into and under substrates where light is Habitable Planet (Characterization)
still sufficient for photosynthesis. These communities Habitable Zone
exhibit no detectable surface spectral signature. The Habitable Zone, Effect of Tidal Locking
same is true of the assemblages of photosynthetic organ- Mars
isms at more than a few meters depth in water bodies. Super-Earths
These communities are widespread and dominate local Venus
photosynthetic productivity on Earth. Such worlds could
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due to chlorophyll, in the disk-averaged spectrum search for life on extrasolar planets. Looking for the terrestrial veg-
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392:231237
Brack A (1993) Liquid water and the origin of life. Orig Life Evol Biosph
Summary
23(1):310
Dedicated future space missions will have the explicit pur- Christensen PR, Pearl JC (1997) Initial data from the Mars Global Sur-
pose of detecting other Earth-like worlds, analyzing their veyor thermal emission spectrometer experiment: observations of
characteristics, determining the composition of their atmo- the Earth. J Geophys Res 102:1087510880
spheres, investigating their capability to sustain life as we Cockell CS, Kaltenegger L, Raven JA (2009) Cryptic photosynthesis
extrasolar planetary oxygen without a surface biological signature.
know it, and searching for signs of life. These searches for
Astrobiology (in press)
signs of life will be based on the assumption that extrater- Des Marais DJ, Harwit MO, Jucks KW, Kasting JF, Lin DNC, Lunine JI,
restrial life shares fundamental characteristics with life on Schneider J, Seager S, Traub WA, Woolf NJ (2002) Remote sensing of
Earth, in that it requires liquid water as a solvent and has planetary properties and biosignatures on extrasolar terrestrial
a carbon-based chemistry. Life on the basis of a different planets. Astrobiology 2:153181
Forget P, Pierehumbert H (1997) Warming early Mars with carbon diox-
chemistry is not considered here, because the vast possible
ide clouds that scatter infrared radiation. Science 278:12731274
range of conceivable life-forms might produce signatures in Kaltenegger L, Traub WA, Jucks KW (2007) Spectral evolution of an
their atmosphere that so far are unknown. We have identified Earth-like planet. Astrophys J 658:598616
some remotely detectable biomarkers whose presence at Kaltenegger L, Traub W (2009) Transits of Earth-like planets. Astrophys J
significant abundance would strongly suggest a biological 698:519527
Kasting JF, Whitmire DP, Reynolds H (1993) Habitable zones around
origin (e.g., the couples CH4 + O2, or CH4 + O3 (Lovelock
main sequence stars. Icarus 101:108119
1975) or N2O). In addition to searching for signs of life, we Leger A, Pirre M, Marceau FJ (1993) Search for primitive life on a distant
need to understand how the observed atmosphere physi- planet: relevance of 02 and 03 detections. Astronaut Aeronaut
cally and chemically works. 277:309316
Lovelock JE (1975) Thermodynamics and the recognition of alien bio-
spheres. Proc R Soc Lond B Biol Sci 189(1095):167180
Future Directions
Mayor M, Udry S, Lovis C, Pepe F, Queloz D, Benz W, Bertaux J-L, Bouchy
Models of habitable worlds with different parameters (e.g., F, Mordasini C, Segransan D (2009) The HARPS search for southern
age, mass, size, composition, temperature, and biota) expand extra-solar planets. XIII. A planetary system with 3 super-Earths (4.2,
our knowledge of how a habitable planets spectrum could 6.9, and 9.2 ML). Astronaut Aeronaut 493:639644
appear and how robust our definition of biomarkers is. We Montanes-Rodriguez P, Palle E, Goode PR (2007) Measurements of the
surface brightness of the Earthshine with applications to calibrate
are just learning how to characterize habitable planets
lunar flashes. Astrophys J 134:11451149
remotely. The results of a first-generation mission will most Montanes-Rodriguez P, Palle E, Goode PR, Hickey J, Koonin SE
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set our own planet in an overall context. tral albedo. Astrophys J 629:11751182
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262271 Biologically controlled biomineralization, biologically
Schopf JW (1993) Microfossils of the early Archean Apex Chert: new induced biomineralization, biosignature
evidence of the antiquity of life. Science 260:640642
Segura A, Krelove K, Kasting JF, Sommerlatt D, Meadows V, Crisp D,
Cohen M, Mlawer E (2003) Ozone concentrations and ultraviolet Definition
fluxes on Earth-like planets around other stars. Astrobiology Biomineralization is the process by which organisms form
3:689708 minerals, which are called biominerals. It is a widespread
Segura A, Kasting JF, Meadows V, Cohen M, Scalo J, Crisp D, Butler RAH,
phenomenon induced or controlled by a huge diversity of
Tinetti G (2005) Biosignatures from Earth-like planets around
M dwarfs. Astrobiology 5:706725 eukaryotes, bacteria, or archaea. There is a very large
Segura A, Meadows VS, Kasting JF, Crisp D, Cohen M (2007) Abiotic diversity of chemical compositions and structures for
formation of O2 and O3 in high-CO2 terrestrial atmospheres. Astro- biominerals, including carbonates (e.g., aragonite,
naut Aeronaut 472:665672 calcite), silicates (e.g., opal), Fe- and/or Mn-oxides.
Selsis F (2000) Review: Physics of Planets I: Darwin and the atmospheres
Biominerals can be used in the search for traces of ancient
of terrestrial planets. In Darwin and astronomy the infrared space
interferometer, Stockholm, Sweden, 1719 November 1999. ESA SP terrestrial or extraterrestrial life. They can be used as
451, Noordwijk, The Netherlands, pp 133142 recorders of paleoenvironmental conditions, especially in
Selsis F (2002) Search for signatures of life on exoplanets. In: Foing B, paleoclimatology (e.g., corals, foraminifers). Finally, their
Battrick B (eds) Earth-like planets and moons. Proceedings of the unique properties can inspire mimetic strategies intending
36th ESLAB Symposium, ESA SP-514, ESTEC, Noordwijk, The
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very small and unstable mineral seeds. They can
indeed stabilize these nuclei by providing larges sur-
faces (e.g., cell walls, extracellular polymers) with
lower surface tension.
3. Finally, organisms can impact mineral growth. Tradi-
tionally, growth takes place layer by layer. Organisms
BioMEMS Devices can inhibit crystal growth along certain directions by
production of poisoning molecules, forming minerals
Biosensor with particular shapes. Alternatively, nuclei may
198 B Biopan
aggregate, forming mesocrystals, sometimes with the Benzerara K, Menguy N (2009) Looking for traces of life in minerals.
CR Palevol 8:617628
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carbonate minerals, including photosynthesis, sul-
fate-reduction, urea degradation, ammonification,
or denitrification (Castanier et al. 2000).
(c) Biologically influenced biomineralization is defined as
passive mineralization of organic matter, whose prop-
Biopan
erties influence crystal morphology and composition.
RENE DEMETS
Polysaccharides and proteins have been shown to
ESTEC (HSF-USL), Noordwijk, The Netherlands
impact biomineralization in many cases (e.g., Obst
et al. 2009). The term organomineralization is some-
times used, encompassing biologically influenced and
biologically induced biomineralization.
Keywords
Exposure experiments, radiation biology
The morphology, the structure, and the chemistry of
prokaryote biominerals have frequently been proposed as Definition
potential biosignatures (e.g., Konhauser 1998) and used to Biopan is a pan-shaped exposure facility for experiments
infer the presence of traces of life in ancient terrestrial or in the domains of astrobiology, radiation biology and
extraterrestrial rocks such as the Martian meteorite radiation dosimetry (Demets et al. 2005). Externally
ALH84001 (McKay et al. 1996). For further reading, mounted on unmanned recoverable satellites of the
reviews on various biomineralizing systems can be found Foton type, Biopan flies 2-week missions in low Earth
(e.g., Bauerlein 2000; Mann 2001; Weiner and Dove 2003; orbit at 63.0 inclination, allowing exposure of biological
Benzerara and Menguy 2009). samples to the harsh space conditions. Six flights have
been completed between 1992 and 2007 with up to ten
See also different experiments per flight. Biopan carries its exper-
Biomarkers, morphological iment packages (total mass 4 kg max.) on two mounting
Mineral plates (total surface area 1,080 cm2).
of the cell walls of arthropods and most fungi, and is also Verlinden RAJ, Hill DJ, Kenward MA, Williams CD, Radecka I (2007)
Bacterial synthesis of biodegradable polyhydroxyalkanoates. J Appl
synthesized by some diatoms, but is not known in Bacteria
Microbiol 102:14371449
or Archaea. Cellulose is a typical plant cell wall compo-
nent but is also synthesized by some bacteria. Peptidogly-
can (murein) is a biopolymer of N-acetyl-glucosamine
and N-acetyl-muramic acid, which serves as the main
cell wall component in bacteria and some archaea (the Bioprecipitate
latter possess a slightly different polymer known as
pseudopeptidoglycan). Silicate is a mostly inorganic poly- Biomineralization
mer of silicium although it is normally associated with Bioprecipitation
organic matter. Silicate is the main component of the
frustules of diatoms. Probably the most diverse and com-
plex biopolymers are exopolymers. These are complex
polymeric carbohydrates with associated glycolipids, pro-
teins, and nucleic acids, as well as a variety of uronic acids,
Bioprecipitation
pyruvate, sulfate, and carboxylic groups. They may serve
Synonyms
as the sheath of microorganisms or be extruded as muci-
Biomineralization; Bioprecipitate
lage in the outer environment and have a variety of func-
tions. Polynucleotides and polypeptides are the key to life.
Definition
Polynucleotides (deoxyribonucleic acid, DNA; and
Bioprecipitation refers to the process of formation of
ribonucleic acid, RNA) are the carrier of information in
mineral phases (bioprecipitates or biominerals) by organ-
cells and are responsible for the translation of this infor-
isms. Cells or associated extracellular polymers can serve
mation into polypeptides. Polypeptides are proteins and
as nucleation surfaces and/or alter the chemical composi-
enzymes that are composed of amino acids that are poly-
tion of fluids and raise the supersaturation of the solution
merized through peptide bonds. Enzymes catalyze most
with a mineral phase. Alternatively, bioprecipitation has
metabolic reactions in the cell.
been used in meteorology to refer to the nucleation of ice
by bacteria in clouds resulting in snow or rainfall.
See also
Cell Wall
Exopolymers
Nucleic Acids Biosensor
Peptidoglycan
Polymer LAURA M. LECHUGA
Polynucleotide Nanobiosensors and Bioanalytical Applications Group,
Polypeptide Research Center on Nanoscience and Nanotechnology
Polysaccharide (CIN2) CSIC, Barcelona, Spain
Protein
Refractory Organic Polymer
Synonyms
Biodetection system; Biological sensors; BioMEMS
References and Further Reading devices
Decho AW (1990) Microbial exopolymer secretions in ocean environ-
mentstheir role(s) in food webs and marine processes. Oceanogr
Mar Biol 28:73153
Keywords
Joshi CP, Mansfield SD (2007) The cellulose paradoxsimple molecule, Bioreceptor layer, electrochemical biosensor, label-free
complex biosynthesis. Curr Opin Plant Biol 10:220226 detection, lab-on-a-chip, optical biosensor, physical trans-
Latge JP (2007) The cell wall: a carbohydrate armour for the fungal cell. ducer, surface plasmon resonance
Mol Microbiol 66:279290
Passow U (2002) Transparent exopolymer particles (TEP) in aquatic
environments. Prog Oceanogr 55:287333
Definition
Rinaudo M (2006) Chitin and chitosan: properties and applications. Prog A biosensor is a compact device incorporating a biological
Polym Sci 31:603632 receptor in direct contact with a physicochemical
Biosensor B 201
transducer or sensor (the term biosensor derives from change is induced, as for example, a redox, mass, resonant
this combination). The biological element specifically rec- frequency, absorption, or refractive index change. The aim
ognizes a substance (chemical or biological) in a sample. of a biosensor is to produce discrete or continuous signals B
This in turn induces a change in the transducer that that are proportional to the concentration of a single
delivers a signal proportional to the concentration of the analyte or a related group of analytes. The biological
substance (see Fig. 1). The main advantages of biosensors element is capable of sensing the presence, activity, or
are the selectivity and sensitivity of the analysis. In addi- concentration of the substance in solution. Substances
tion, biosensors can supply real-time and online informa- capable of being analyzed with biosensors range from
tion. Biological elements can be enzymes, antibodies, protein biomarkers, toxins, antigens, drugs of abuse,
DNA, whole cells, or tissues, for example. Depending on pesticides, peptides, proteins (IgG, albumin, insulin
the physical change being observed, transducers are elec- among others), hormones, vitamins, antibiotics, organic
trochemical, optical, piezoelectric, calorimetric, acoustic, molecules (glucose, lactose, cholesterol, urea), DNA and
magnetic, or mechanical. RNA sequences or mismatches, cancer cells, pathogenic
microorganisms, and many others.
Overview The first demonstration of a biosensor dates from
Biosensor is a general term for a wide range of analytical 1962, when enzyme electrodes for glucose sensing were
devices that measure the presence or concentration of developed by L.C. Clark (US). Since then, intensive effort
biological or chemical molecules in complex samples by has been focused on biosensor research and development,
translating a biomolecular interaction at the transducer a significant output of which was the commercial launch
surface into a quantifiable physical signal. When the of the glucose biosensor in 1975. The glucose biosensor
biospecific interaction takes place, a physicochemical has become a landmark in the diagnostics field, thereby
allowing millions of diabetics to test, in any place and at
any time, their glucose level in blood. Substantial work on
achieving reliable biosensors began in the 1980s and since
then many developments have been demonstrated.
Sample Biosensing technology has been a very active research
field both in academic and in industrial laboratories dur-
ing the last decades. But, until now, only a limited number
of biosensors have met the stringent requirements for
commercialization. This is mainly due to the poor stability
of the biological receptor once it is in contact with the
transducer, as it must be stable under variable conditions
of pH, temperature, humidity, and ionic strength.
Target
The use of biosensor devices has clear advantages in
analytical chemistry. The main characteristics of biosen-
sors are high sensitivity and selectivity. In addition, bio-
Biological receptor sensors can provide rapid, direct, and cost-effective
analyses, ease of operation, high accuracy, and wide detec-
tion range using a minimum volume of sample and
Transducer reagents. This technology avoids the expensive, complex,
and time-consuming procedures typically employed in
standard analytical evaluation.
Data processing
In order to have reliable devices, there are two crucial
steps: (1) the design and fabrication of a highly sensitive
physical transducer, that is, a device capable of efficiently
transforming the biomolecular reaction into a measurable
signal, and (2) the stable and reliable biofunctionalization
of the physical transducer with the appropriate, selective,
Signal monitoring
biological receptor (protein, DNA, cell, aptamer, among
others). The biosensor research and development area is
Biosensor. Figure 1 Scheme of a biosensor device highly multidisciplinary because several aspects need to be
202 B Biosensor
considered in order to achieve successful implementation, magnetic biosensors, and nanomechanical biosensors.
such as the transduction modality used, fluidic design Electrochemical biosensors are based on changes in elec-
(most of the biosensing analyses are performed in liquid), trical currents or potential across electrodes when the
surface biofunctionalization, detection format (direct, biosensing reaction involves redox changes. They are the
indirect, sandwich-type, competitive binding), and data simplest and most developed biosensors. They can be
processing and analysis. amperometric (based on the measurement of the current
resulting from the electrochemical oxidation or reduction
Basic Methodology of electroactive species), potentiometric (based on the
The possible combinations of different bioreceptors and determination of the potential difference between either
transducers result in a vast range of biosensor types. an indicator or a reference electrode (such as ISFET
Depending on the bioreceptor, the transducer or the type devices)) or conductimetric (based on a change in con-
of detection, biosensors can be classified into many types ductance (such as measured by interdigitated electrodes)).
and subtypes. It is important to point out that the selec- Piezoelectric biosensors are based on the piezoelectric
tion of the most suitable combination of bioreceptor/ effect: the frequency of a resonating crystal changes when
transducer/type of detection is dictated by the application molecules are adsorbed on top of the crystal. Surface
itself, which depends on the type of substance and sample acoustic wave systems and quartz crystal microbalances
to be evaluated. are the main examples of piezoelectric devices.
In optical biosensors, the biorecognition event results
Types of Detection in a change in optical properties such as a variation in the
Two main types of detection can be employed: label and emission properties (luminescence), in the absorption
label free. In the label-free scheme the original and coefficient or in the refractive index. This variation
unmodified analyte is detected in a direct manner. In the induces a change in some of the characteristics of light
label approach, the analyte is tagged with a label that (wavelength, intensity, polarization, phase velocity),
acts as an indirect indicator of the presence of the mole- which can be detected using techniques such as emission,
cule. In general, the label approach results in a higher absorption, fluorescence, evanescent wave detection, or
sensitivity of analysis while the label-free approach is polarimetry. Many optical biosensors have been developed
direct, rapid, and avoids the manipulation or degradation because they frequently exhibit higher sensitivity than
of the analyte. Each detection method has advantages and other transducer types. One of the most successful label-
disadvantages and the method employed should be free and commercially accepted optical biosensor is the
selected according to the foreseen application. surface plasmon resonance (SPR) sensor that is based
on an evanescent wave interaction. Other optical biosen-
Classification by Bioreceptor Layer Type sors make use of optical waveguides as the basic element
Depending on the bioreceptor, biosensors can be divided for light transmission, such as the interferometric devices
into two main types: catalytic biosensors and affinity bio- (e.g., Mach-Zehnder or Young interferometer) or optical
sensors. In catalytic biosensors, the receptors are able to fibers. Other optical biosensors include those that employ
recognize (bio)chemical species and transform them into resonant structures, grating couplers, metallic
a product. This type of biosensor is mostly represented by nanoparticles, and nanostructures.
enzymatic biosensors, but whole cells or tissue receptors In nanomechanical sensors, the specific
also fall under this category. Affinity biosensors use the biorecognition on the cantilever surface results in a
specific capabilities of an analyte to bind to a nanomechanical response, which produces a cantilever
biorecognition element. Immunosensors (based on spe- bending of few nanometers and a shift in the resonant
cific interactions between an antibody and an antigen) or frequency. In this way, microcantilevers translate the
DNA biosensors (based on the affinity between comple- molecular reaction into a nanomechanical motion,
mentary oligonucleotides) are the main examples of affin- which is commonly detected using optical or
ity biosensors. Other examples include the use of piezoresistive readout. Nanomechanical sensors achieve
aptamers, cellular receptors, or microorganisms. a high level of sensitivity and are amenable for array
multiplexing and integration in compact platforms.
Classification by Transducer Type
Depending on the transducer employed, biosensors can be Biofunctionalization
divided into the following main types: electrochemical Biofunctionalization is the process of immobilizing the
biosensors, optical biosensors, piezoelectric biosensors, biomolecules onto the transducer surface to provide the
Biosensor B 203
required biospecificity of the biosensor. The bio- elevated number of substances in parallel, and to develop
immobilization process must do all of the following: max- wearable biosensors and biosensors suitable for implanta-
imize the sensitivity, supply a reproducible layer, ensure tion in the human body. Other important aspects to be B
optimal coverage density of the receptor, orient the recep- considered in the future are issues associated with the
tor properly for efficient kinetics, minimize background commercialization of biosensors for relevant applications,
and nonspecific adsorption, and insure long-term stabil- which still face significant technological hurdles. Develop-
ity. Among the various bio-immobilization approaches, ment cycles tend to be long and commercial success
the most commonly used are physical adsorption, cova- remains limited. The main issues in biosensor technology,
lent binding, affinity based (via avidin/biotin), and such as the stability and reliability of the biorecognition
entrapment (physical or covalent) within host matrices layer, still need to be addressed.
(e.g., polymers, polymeric hydrogels, and sol-gels).
Usually, covalent binding to the substrate is the preferred See also
route for most bioreceptors through the use of self- Antibody
assembled monolayers but the most suitable technique Aptamer
depends on the bioreceptor type and the sample to be DNA
evaluated. Fluorescence
Hybridization
Applications Molecular Recognition
The fields of application for biosensors are almost endless. Surface Plasmon Resonance
Applications for these devices include clinical diagnostics
(including personal health monitoring), basic research in
life sciences, drug research in the pharmaceutical industry, References and Further Reading
Alvarez M, LM Lechuga (2010) Microcantilever-based platforms as
online screening of water quality for both household and
biosensing tools. Analyst 135:827836
industrial use, control of industrial processes, veterinary Borisov SM, Wolfbeis OS (2008) Optical biosensors. Chem Rev 108:423461
diagnostics, quality control in the food and beverage Comeaux R, Novotny P (2009) Biosensors: properties, materials and
industry, detection of harmful substances, military and applications (Biotechnology in agriculture, industry and medicine
homeland security or environmental monitoring, and series). Nova Science, New York
Cooper MA (ed) (2009) Label-free biosensors: techniques and applica-
many others. The most significant applications are related
tions. Cambridge University Press, Cambridge
to the clinical diagnostics field, mainly due to the great Erickson D, Yang MS, AHJ CB (2008) Nanobiosensors: optofluidic, elec-
success of glucose biosensors since their invention. Indeed, trical and mechanical approaches to biomolecular detection at the
glucose biosensors account for about 85% of the entire nanoscale. Microfluid Nanofluid 4:3352
biosensor market. In the Astrobiology area, biosensors are Fan X, White IM, Shopova SI, Zhu H, Suter JD, Sun Y (2008) Sensitive
optical biosensors for unlabeled targets: a review. Anal Chim Acta
useful tools for detecting biomarkers or biosignatures
620:826
of extant or extinct life, which could be produced in Goeders KM, Colton JS, Bottomley LA (2008) Microcantilevers: sensing
biotic or abiotic processes (such as bacteria strains, cells, chemical interactions via mechanical motion. Chem Rev 108:522542
extracellular materials, isolated macromolecules, or Homola J (ed) (2006) Surface plasmon resonance based sensors (Springer
biomarkers). series on chemical sensors and biosensors). Springer, Berlin
Homola J (2008) Surface plasmon resonance sensors for detection of
chemical and biological species. Chem Rev 108:462493
Future Directions Lange K, Rapp BE, Rapp M (2008) Surface acoustic wave biosensors:
The ultimate aim in biosensor technology is the achieve- a review. Anal Bioanal Chem 391:15091519
ment of a fully integrated, low-cost, portable and reliable Ligler F (ed) (2008) Optical biosensors: today and tomorrow. Elsevier,
platform, able to simultaneously detect and identify hun- Amsterdam
Ligler FS (2009) Perspective on optical biosensors and integrated sensor
dreds of substances in real time with high sensitivity, even
systems. Anal Chem 81:519526
at the single molecule level and connected through Marks RS, Lowe CR, Cullen DC, Weetall HH, Karube I (eds) (2007) Hand-
a wireless scheme to a central operational station or hos- book of biosensors and biochips, Wiley, New York
pital database. Therefore, the major future objectives in Privett BJ, Shin JH, Schoenfisch MH (2008) Electrochemical sensors. Anal
biosensor technology will be to achieve higher sensitivity, Chem 80:44994517
Rasooly A, Herold KE (ed) (2009) Biosensors and biodetection: 1
to reduce sample volume and reagents through miniatur-
(Methods in molecular biology): methods and protocols, vol 1: opti-
ization at the micro-/nanoscale, to increase the number of cal-based detectors and Vol 2: electrochemical and mechanical detec-
substances detected within the same sample, to develop tors, lateral flow and ligands for biosensors, Humana, Springer
devices of high multiplexing capabilities for analyzing an Protocols, NJ
204 B Biosignature
arises from the integration of all biocoenosis (Leveque combination with global geological events (Knoll 2003)
2003), ranging from those sustained by primary triggered diversity and environmental change in the
photosynthetizers to that uniquely maintained by form of positive feedback on Early Earth that affected
chemolithotrophic producers as in deep crustal regions. not only the ocean habitats, but also led to the
In this sense, the ecosphere would include the biosphere as emergence of habitability on the continental areas of the
the biotic component of the planetary ecosystem, in the Earth.
same manner that biocoenosis accounts for ecosystem
(Huggett 1999). As it is difficult to separate biology from See also
the environment with which it interacts, the biosphere is Algae
currently identified by its interactions with the different Archea
planetary envelops such as the atmosphere, the hydro- Autotroph
sphere, or the crust. As a consequence of the continuous Biogeochemical Cycles
exchange of matter and energy between living forms and Biotope
the planet, such interactions are materialized in form of Carbon Cycle (Biological)
complex mechanisms that induce the control of the phys- Earths Atmosphere, Origin and Evolution of
ical and chemical variables of the environment on regional Ecosystem
and global scales. One paradigmatic example of this is the Gaia Hypothesis
temperature and pH control in the oceans (Orr et al. 2005; Greenhouse Effect
Knoll et al. 1996) through the uptake and sequestration of Habitat
CO2, which is transformed into biomass and carbonates, Heterotroph
which are later buried. The same kind of global feedbacks Homeostasis
have been observed in other compounds bearing nitrogen Hydrosphere
and sulfur, which can induce physical and chemical Nitrogen Cycle (Biological)
changes in the Earths atmosphere after being included in Ocean, Chemical Evolution of
the photochemical pathways of the troposphere (Seinfeld Oxygenation of the Earths Atmosphere
& Pandys 2006). Such processes provoke thermal changes Sulfur Cycle
on the Earths surface by increasing the planetary albedo as Symbiosis
SO2 currently does, or reinforcing the greenhouse effect
as occurs with some N-bearing gases. Moreover, the man- References and Further Reading
ner in which the structure, composition, and substrate of Huggett RJ (1999) Ecosphere, biosphere or Gaia? What to call the global
extensive woodlands control the water and thermal bal- ecosystem. Global Ecol Biogeogr 8(6):425431
ance, which is essential for hydrological cycles at regional Knoll AH, Bambach RK, Canfield DE, Grotzinger JP (1996) Comparative
earth history and late Permian mass extinction. Science 273:452457
and global scales, has been repeatedly described
Knoll AH (2003) Life on a young planet: The first three billion years of
(Rodrguez-Iturbe & Porporato 2004). Interestingly, the evolution on Earth. Princeton University Press, Princeton,
great oxygenation event driven by microbial activity dur- New Jersey
ing the Late Archean-Early Proterozoic can be considered, Leveque C (2003) From ecosystem to biosphere. Science Publishers, inc,
on a greater scale, as a similar process of environmental Enfield, New Hampshire, New England
Lovelock J (2000) Gaia, a new look at life on Earth, 4th edn. Oxford
control leading to the emergence of homeostasis as
University Press, Oxford, United Kingdom
observed in the ecological succession of areas, which are Orr JC, Fabry VJ, Aumont O, Bopp L, Doney SC, Feely RA, Gnanadesikan A,
initially devoid of living forms. This process starts with Gruber N, Ishida A, Joos F, Key RM, Lindsay K, Maier-Reimer E,
few low specialized colonists and ends in a highly diverse Matear R, Monfray P, Mouchet A, Najjar RG, Plattner G-K, Rodgers
ecosystem sustained by very specialized organisms KB, Sabine CL, Sarmiento JL, Schlitzer R, Slater RD, Totterdell IJ,
Weirig M-F, Yamanaka Y, Yool A (2005) Anthropogenic ocean acidifi-
adapted to a wide variety of niches. To the same extent,
cation over the twenty-first century and its impact on calcifying organ-
but at greater scale, and coupled to the evolution of the isms. Nature 437:681686
biosphere, oceanic and atmospheric oxidation was pro- Rodrguez-Iturbe I, Porporato A (2004) Ecohydrology of water-
moted by bacterial communities (cyanobacteria) releasing controlled ecosystems. Cambridge University Press, Cambridge, UK
oxygen into the ocean and the atmosphere, where it was Seinfeld JH, Pandys SN (2006) Atmospheric chemistry and physics,
2nd edn. John Wiley and Sons, Inc, New Jersey, Hoboken
used by more complex microorganisms that were able to
Smil V (2003) The Earths biosphere: evolution, dynamics and change.
use oxygen for respiration, which in turn unleashed The MIT Press, Cambridge, MA
the emergence of the multicellular organisms. As Vernadsky VI (1998) The biosphere (annotated and revised by Mark A. S.
a consequence, microbial-mediated oxygenation in McMenamin). Copernicus, Springer-Verlag, New York
Biostack B 207
Definition
Biostabilization The Biostack concept allows studying the biological effects
of single heavy ions of cosmic rays. Each Biostack device is B
Synonyms composed of a stack of visual track detectors (e.g., nuclear
Microbial sediment fixation emulsions, cellulose nitrate, and polycarbonate) with
layers of biological objects in resting state sandwiched
Definition between them. After exposure to outer space, the track
Biostabilization is fixation of sedimentary grains by detectors are developed, the trajectory of each heavy ion is
biofilms and microbial mats. Three types of biostabil- localized relative to the site of the biological object, and the
izations are distinguished. Type 1 biostabilization is the physical data of each particle are correlated with the
response by benthic microbiota to erosion. Bacterial fila- observed biological effects along its path.
ments are oriented horizontally, and EPS (extracellular
polymeric substances, if present) change their chemical History
structure to a more erosion-resistant phase. Biostabil- The Biostack program has been developed in the late
ization by epibenthic and endobenthic microbial mats is 1960s under the auspices of the Council of Europe within
expressed by the Working Group on Space Biophysics and has been
Y ru 2 =rs rf gDn performed in international cooperation by scientists
from Europe, Russia and USA. Biostack experiments
where u is the shear velocity, rf is the density of fluid, rs
were flown on the NASA missions Apollo 16 and 17
is the density of sediment, g is the gravity constant, D
(1972), Apollo Soyuz Test Project (1975), and the
is the actual grain diameter under the influence of
Long Duration Exposure Facility (19841990), on
biostabilization, and n is the exponent to which D is raised
ESA/NASA missions Spacelab 1 (1983), and Spacelab
for the data to comply to the Shields relationship. Type 2
IML-2 (1994), on the German/NASA mission Spacelab
biostabilization is the flexible deformation of otherwise
D2 (1993), on the ESA mission EURECA (1992
brittle sediment composed of loose sand grains. Type 3
1993), and on ESA/Russian missions of the Biocosmos
biostabilization is sealing of the sedimentary surface so
and Foton series (19921994). The Biostack program
that exchange of gases between sediment and atmosphere
was managed by Horst Bucker and Gunther Reitz, both
or water is prohibited.
from the German Aerospace Center (DLR), Germany.
HZE particle
Trajectory
Detector
Detector
Track
Detector
Biological
foil
Biological
foil
Detector
Detector
Detector
Biostack. Figure 1 The Biostack concept to localize biological effects produced by single HZE particles of cosmic radiation;
Biostack experiments were flown onboard of Apollo 16, 17, ASTP, Spacelab 1, D2, IML-1, IML-2, LDEF, Cosmos 1887 and 2004, and
EURECA (Photo credit DLR)
development was significantly disturbed, as demon- Quantifying various genetic and developmental
strated by up to 90% loss of germination (early lethal- disturbances caused by individual HZE particles of cosmic
ity) or embryo lethality. Seedling abnormalities, such radiation, the Biostack data are of relevance for assessing
as hypertrophy or deformation of cotyledones, hypo- the radiation risks for astronauts, especially during explor-
cotyl or root, or chlorophyll deficiency occurred with atory missions, as well as for estimating the likelihood of
high frequency as a consequence of a passage of a single Lithopanspermia, i.e., the interplanetary transfer of
HZE particle close to the shoot or root meristem. In microorganisms within rocks.
Lactuca sativa seeds, hit by an HZE particle, multiple
chromosomal aberrations developed at high frequen- See also
cies. Zea mays seeds, flown on ASTP, developed large Apollo Mission
yellow strips in all leaves as somatic mutation. Cosmic Rays in the Heliosphere
In 90% of the mosaic eggs of the brine shrimp Artemia EURECA
salina hit by an HZE particle hatching, characterized Foton Capsule (Spacecraft)
by release of a free swimming nauplius, was inhibited. HZE Particle
Anomalies of the body or extremities appeared Ionizing Radiation (Biological Effects)
approximately ten times more frequently than in the Linear Energy Transfer
ground controls. Likewise, hatching of the Indian Lithopanspermia
stick insect Carausius morosus from eggs, hit by Long Duration Exposure Facility
a cosmic HZE particle, was significantly reduced. Panspermia
Malformations were increased in individuals having Radiation Biology
developed from eggs hit. They were characterized by Space Environment
a curved abdomen, fused segments, or shortened legs. Spore
Spores of the bacterium Bacillus subtilis were
inactivated well beyond 1 mm from the HZE particle
References and Further Reading
trajectory, which distance would roughly correspond
Bucker H (1975) BIOSTACK a study of biological effects of HZE galactic
to the dimensions of a spore, thereby pointing to cosmic radiation. In: Biomedical resuls of Apollo, NASA SP-368.
a long-ranging effect of HZE particles. NASA, Washington, DC, pp 343354
Bipolar Flow B 209
Bucker H, Horneck G, Facius R, Reitz G, Schafer M, Schott JU, Beaujean R, habitat, but while the subject of a habitat is a species or
Enge W, Schopper E, Heinrich W, Beer J, Wiegel B, Pfohl R, Francois H,
a population, the subject of a biotope is a biological
Portal G, Bonting SL, Graul EH, Ruther W, Kranz AR, Bork U, Koller-
Lambert K, Kirchheim B, Starke ME, Planel H, Delpoux M (1984)
community. B
Radiobological advanced Biostack experiment. Science 22:222224
Bucker H, Facius R, Horneck G, Reitz G, Graul EH, Berger H, Hoffken H,
See also
Ruther W, Heinrich W, Beaujean R, Enge W (1986) Embryogenesis Colonization (Biological)
and organogenesis of Carausius morosus under spaceflight
conditions. Adv Space Res 12(6):115124
Facius R, Reitz G, Schafer M (1994) Inactivation of individual Bacillus
subtilis spores in dependence on their distance to single cosmic heavy
ions. Adv Space Res 14(10):10271038 Bipolar Flow
Horneck G (1992) Radiobiological experiments in space: a review. Nucl
Tracks Radiat Meas 20:185205 STEVEN STAHLER
Horneck G (1994) HZE particle effects in space. Acta Astronaut
32:749755
Department of Astronomy, University of California,
Horneck G, Baumstark-Khan C, Facius R (2006) Radiation biology. In: Berkeley, CA, USA
Clement G, Slenzka K (eds) Fundamentals of space biology. Kluwer
Academic Publishers/Springer Dordrecht, Heidelberg, Berlin,
pp 292335 Synonyms
Swenberg CE, Horneck G, Stassinopoulos EG (eds) (1993) Biological
Molecular Flow
effects and physics of solar and galactic cosmic radiation, Part A,
vol 243A and B, NATO ASI series A: life sciences. Plenum, New York
Keywords
Star formation
Biosynthesis Definition
Bipolar flows are a phenomenon associated with young
stars still embedded in their parent molecular clouds.
Anabolism
There are two kinds of flows jets and molecular outflows.
The first represent high-speed stellar wind gas, ejected into
two narrow streams. The second are broader cones of
more slowly moving cloud gas. Each molecular outflow
Biotic Crisis is driven by a jet running down its central axis. What is
seen most prominently in the jets are shock waves created
Mass Extinctions when the wind runs into either ambient cloud gas or
slower gas ejected earlier. Neither the launching of the
wind nor its collimation into jets is well understood.
Overview
Biotic Isotope Fractionation It has long been known that massive stars emit strong
winds that drive back nearby gas. Since these objects are
Biomarkers, Isotopic
all relatively young, there is often such a gaseous environ-
ment, the remnant of the cloud that formed the star itself.
In the 1980s, astronomers were surprised to discover that
even young stars of solar mass and below drive vigorous
Biotope outflows. Each outflow appears as two opposite streams
(hence bipolar) emanating from the central object. In
Synonyms the youngest examples, the star is so embedded in ambient
Environment; Habitat dusty gas that it is optically invisible. Even in such cases,
however, bipolar outflows are present. The flows probably
Definition play a key role in clearing away remaining material in star-
A biotope is an area of homogeneous environmental con- forming molecular clouds. Despite extensive study, the
ditions providing living space for a specific assemblage of physical mechanisms underlying both their launching
organisms. Biotope is almost synonymous with the term and collimation remain mysterious.
210 B Bipolar Flow
Flows generated by young stars have two components The high-speed material in stellar jets must represent
jets and molecular outflows. Both have bipolar morphol- the actual wind being emitted by the star or the inner
ogies. Otherwise, their properties are very different, portion of its circumstellar disk. The rough match of the
undoubtedly reflecting their distinct origins. Stellar jets wind speed and the stellar escape velocity occurs in other
consist of gas emitted at high speed into a narrow opening examples of winds from stars over a broad range of masses
angle. A typical jet speed is 300 km/s, which is also the and ages. How the wind is launched in this particular case
magnitude of the escape velocity from the stellar surface. is not clear. The wind from our Sun is pushed outward by
The gas has a temperature of 10,000 K. What we observe the hot gas at the base of the Solar corona. The mass
most prominently are shock waves created when this high- transport rate in a young stellar jet is higher by six orders
speed gas rams into other material. These shock waves, of magnitude, and thermal pressure is inadequate. It is
which radiate in a variety of spectral emission lines, are generally agreed that the wind is tapping rotational energy.
called Herbig-Haro objects. Discovered in the 1950s, the The star, which is indeed rapidly rotating, also contains
shocks appeared as isolated, glowing patches. Thirty years a strong magnetic field. The wind could be flung out along
later, astronomers detected narrow, faint strands linking the magnetic field lines, a process which also occurs in our
the bright knots and leading back to a young, embedded Sun. If this is the basic process, then the jet is also carrying
star. Each arm of a stellar jet has a length of about 0.1 off angular momentum, causing the star to slow its rota-
parsec. Individual Herbig-Haro objects can be detected tion. The outflow could also facilitate accretion of inner
much farther out, up to several parsecs from the driving disk material onto the star.
source. The bright knots (Herbig-Haro objects) observed
Molecular outflows are broader swathes of much along jets mark locations where high-speed gas encounters
slower and cooler gas. They exhibit the same bipolar material moving at lower velocity. But what exactly is this
morphology and axis orientation as jets. Indeed, it is target material? In a few cases, it is clear that wind gas is
now believed that every molecular outflow has a jet run- impacting the ambient molecular cloud. There are some
ning down its center. Gas in the broader outflows moves at well-documented examples, however, of the knots being
speeds of typically 10 km/s, and most of its mass has spaced symmetrically around the central star. No external
a temperature of about 10 K. Since this temperature cloud could possess such a high degree of symmetry.
also characterizes molecular clouds, the broader outflows Hence, most shocks must arise in a different way.
are thought to represent cloud material being pushed An important clue comes from observing the space
outward by the jet. This relatively cold gas is observed motion of Herbig-Haro objects, images taken a few
through the radio emission of molecules in the cloud. decades apart show a marked shift, indicating speeds of
The dominant species, molecular hydrogen, is a weak several hundred kilometers per second. This speed is sim-
emitter at these low temperatures, so astronomers gener- ilar to that detected in the main body of the jet, which we
ally utilize CO, which has a strong spectral line at have said represents stellar wind material. On the other
a wavelength of 2.6 mm. Smaller amounts of much hand, the spectral emission lines from the knots indicate
warmer gas have been detected using other tracer mole- that the shocked material is largely neutral so that gas
cules, such as ammonia. enters the shock front at speeds of only about 30 km/s.
Since stellar jets glow mainly at optical wavelengths, The explanation is that incoming material is hitting
they are easily obscured by dust in the molecular clouds not a static environment, but one already in motion. That
that lie near the driving stars. To see a jet, the star must be is, the shocks arise when relatively fast wind gas encoun-
near the surface of the cloud. Sometimes, the cloud has ters slower gas that was emitted earlier. Thus, the pattern
been partially ablated by ultraviolet radiation from of knots effectively constitutes a record of temporal wind
a nearby massive star, revealing the young, low-mass variations, and the symmetrical patterns observed are
star and its jet. The millimeter radio emission used to neatly explained. The inferred fluctuations in wind speed
detect molecular outflows, however, easily penetrates are of order 10%, with associated periods ranging from
interstellar dust. Thus, these broader flows are relatively decades to millennia.
easy to find, and hundreds of examples exist. In contrast, The most mysterious aspect of stellar jets is their
there are still only a few dozen clear detections of stellar remarkable degree of collimation. Most jets have an aspect
jets. The red-shifted arm of the jet, which is penetrating ratio (length to width) of about 100 to 1. One popular idea
back into the molecular cloud away from the observer, is is that the rotating wind material twists up in its internal
often considerably fainter, but has been detected in magnetic field. A twisted field exerts an inward force along
most cases. the central axis. Perhaps this force keeps the jet from
Birthline B 211
diverging. On the other hand, twisted magnetic fields a few million years old, and there is still a substantial
created in the laboratory are unstable to reconnection. amount of ambient molecular gas. Again, these so-called
So are the twisted flux loops that protrude from the T associations are commonly observed. On the other hand, B
Solar surface; their reconnection gives rise to X-ray flares. we never see such groups with ages as high as 10 million
Researchers are using numerical simulations to see if the years. The reason must be that the stars themselves have
more vigorous outflows along interstellar magnetized jets driven off the molecular cloud, and then dispersed into the
are more stable. field population. The obvious driving mechanism is stel-
An alternative notion is that the expanding jet creates lar winds. In this view, molecular outflows represent the
shocks in the surrounding molecular gas. These so-called dispersal of cloud gas, the key step in terminating star
reflecting shocks effectively bend the flow back toward the formation on both large and small scales.
axis. The converging flow then creates another pair of
shocks and diverges outward once more. Alternating See also
pairs of reflecting shocks are commonly seen in supersonic Convection, Stellar
flows on Earth, such as the exhaust of a rocket. Molecular Cloud
It is clear, in any case, that the jets interact strongly Pre-Main-Sequence Star
with molecular gas. The outflows are observed to be Protostars
clumpier than normal cloud gas. Their speed also Stellar Winds
increases closer to the jet axis. Terrestrial jets create not
only a sequence of shocks, but also a collar of turbulent gas References and Further Reading
that widens until the central jet terminates. An analogous Arce HG, Shepherd D, Gueth F, Lee C-F, Bachiller R, Rosen A,
process could be occurring near young stars. Here, turbu- Beuther H (2007) In: Reipurth B, Jewitt D, Keil K (eds) Protostars
and planets V. University of Arizona Press, Tucson, p 245
lence might be induced by jet material spewing out trans-
Bachiller R (1996) ANNU REV ASTRON ASTR 34:121
versely from each shock. Indeed, careful observation of Reipurth B, Bally J (2001) ANNU REV ASTRON ASTR 39:403
Herbig-Haro shocks does show material ejected in this Stahler SW, Palla F (2004) The formation of stars. Wiley-VCH, Weinheim,
manner, with the hot spray of ionized gas creating chapter 13
a cocoon surrounding the shock. This spray could also
be responsible for stirring up the surrounding cloud gas
and dragging it forward as a molecular outflow.
However, interstellar jets can extend far beyond the Birthline
turbulent, clumpy outflow. Astronomers have detected
a number of stellar jets extending over a parsec from the STEVEN STAHLER
central star, with little or no molecular gas. These long Department of Astronomy, University of California,
chains of Herbig-Haro objects are gently curved, reflecting Berkeley, CA, USA
the rotation or perhaps precession of the underlying jet
source. The period of rotation is of order 10,000 years.
Despite the fact that they are traveling through nearly Keywords
empty space, the shocks are slowing down. It is possible Stellar evolution
that momentum is being continually deposited in the
lateral spray of gas. Indeed, small clumps of gas are some- Definition
times observed off to the side of the main jet flow. After they have acquired most of their mass, but before
While much of the underlying physics is still murky, the they begin to fuse hydrogen, stars slowly contract. In the
phenomenon of bipolar flows has clear importance in HR diagram, these pre-main-sequence stars descend
the process of star formation. First, solar-type stars form along paths whose location depends on the stellar mass.
inside relatively small molecular clouds called dense cores. All paths start at the birthline, a curve lying above and
Since only about a third of the core mass winds up in the roughly parallel to the main sequence. When the stars
star, the rest must somehow be dispersed. Winds are the within young clusters are placed in the HR diagram, they
obvious candidate. On a larger scale, stars are born not as lie between the birthline and the main sequence. The two
isolated objects but in groups. Initially, these clusters are curves intersect at a mass of about ten solar masses. Stars
embedded within large molecular clouds. Many such prim- of greater mass ignite hydrogen while they are
itive groups have been detected by infrared telescopes. still protostars. If a young cluster contains such objects,
When the group first appears in optical light, the stars are they lie on the main sequence.
212 B Bitumen
Overview Protostars
Astronomers view the evolution of stars using the Stellar Cluster
HertzprungRussell (HR) diagram. Within this plot of T Association
stellar luminosity versus surface temperature, the point
representing a star moves about as the object evolves.
References and Further Reading
Mature stars that are fusing hydrogen lie along the
Hillenbrand L (1997) On the stellar population and star-forming history
so-called main sequence. Pre-main-sequence stars are of the Orion nebula cluster. Astron J 113:17331768
situated higher in the diagram, and gradually descend to Stahler SW (1983) The birthline for low-mass stars. Astrophys J 274:
the main sequence. The actual path of descent, known as 822829
the pre-main-sequence track, depends on the stellar mass. Stahler SW, Palla F (2004) The formation of stars. Weinheim, Wiley-VCH,
Chapter 16
All pre-main-sequence tracks begin on another curve
known as the birthline.
This description of the birthline is essentially theoreti-
cal. Observationally, young stellar clusters are studied by
placing their members in the HR diagram (also called the
color-magnitude diagram in this context). The birthline is Bitumen
the upper envelope of the stellar distribution. That is, the
member stars lie in the region below the birthline and Definition
above the main sequence. In the very youngest clusters, Bitumen is the fraction of fossil organic matter in sedi-
most stars are crowded close to the birthline. In older mentary rocks that is soluble in organic solvents (such as
groups, stars of lower mass lie further below the envelope, dichloromethane, hexanes, and methanol). It is a dark
while more massive objects are already on the main brown to black, highly viscous material that includes
sequence. diverse organic macromolecules and chemical bio-
To see why there is a birthline, one needs to consider markers. Bitumen is a component in petroleum.
stellar evolution prior to the pre-main-sequence phase.
The very youngest stars, known as protostars, are optically See also
invisible and still acquiring their masses from the sur- Hydrocarbons
rounding clouds. As a protostars mass increases, so does Kerogen
its radius. Indeed, the radius of the protostar can be
predicted with fair accuracy from knowledge of its mass
alone. Once cloud infall ceases, the star appears as a visible
object on the appropriate pre-main-sequence track. The Black Hole
protostar massradius relationship dictates the initial
positions of stars on their tracks. The locus of initial Definition
positions for various stellar masses defines a curve in the A black hole is a region of space-time inside a fictitious
HR diagram that is the birthline. surface (the event horizon), from which nothing - not even
An interesting feature of the birthline is that it inter- light may escape. Astrophysical black holes are either
sects the main sequence. Specifically, the two curves join at stellar or galactic. The former are the end products of the
about 10 solar masses. More massive objects have no pre- evolution of massive stars, and they are produced through
main-sequence phase, but ignite hydrogen while they are gravitational collapse (after the exhaustion of all nuclear
still protostars. Thus, the early evolution of massive stars is fuels and the subsequent supernova explosion) if the
quite different from that of the more common objects akin mass of the residue is above the Oppenheimer-Volkoff
to the Sun. The intersection of the birthline and main limit (23 MJ). Galactic (supermassive) black holes
sequence can be seen clearly in the HR diagram of the are found in the centers of most galaxies (including the
Orion Nebula Cluster, the nearest region currently Milky Way), they have masses in the 106109 MJ range,
forming massive stars. but their origin is poorly understood at present.
Bolometric Magnitude
BNSC
Definition
Synonyms The bolometric magnitude is a way to quantify the total
British National Space Council power emitted by a celestial object in the form of electro-
magnetic radiation. The bolometric magnitude is the
Definition magnitude of a celestial object based on its flux integrated
The British National Space Council (BNSC) was established over the whole electromagnetic spectrum. By convention,
in 1985 replacing the Space Research Management Unit that the bolometric magnitude of the star Vega is zero. The
was running the UK space activities since 1963. The BNSC bolometric correction, BC, is the difference between the
aimed to help Britain to get an optimal return of national visual and the bolometric magnitudes.
and international activities in space, both economically and
scientifically. BNSC was a voluntary partnership between See also
ten government departments and research councils. Their Magnitude
combined expenditure on civil space amounts to around Magnitude, Absolute
180 million per year.
The UK Space Agency took over in March 2010 to
become a full agency replacing the BNSC by April 1, 2011.
While B isotopic variations inherited from nucleosyn- incorporated into the structure of the minerals (Spivack
thesis might be present in the accretion disk (Chaussidon et al. 1987). This property allows the boron isotopic frac-
and Robert 1995, 1998), they are most probably averaged tionation to be calculated between a mineral and the pH of B
at planetary scale. However, B isotopic variations around the solution, and has been widely used and investigated to
this ratio of 4.04 are widespread in terrestrial rocks. They try to reconstruct paleovariations of seawater pH and
are due to low-temperature stable isotopic fractionations atmospheric PCO2 (e.g., Pearson and Palmer 2000, refs.
and are generally reported as deviations in permil from the therein). These reconstructions are complicated by the fact
11 10
B/ B ratio of the international standard (NBS boric acid that the d11B of seawater might have changed over geo-
SRM 951 with 11B/10B = 4.04367, Catanzaro et al. 1970) logical times (Lemarchand et al. 2000) and that a signifi-
using the classical delta notation (d11Bsample= cant fraction of B3 can also be adsorbed. However, boron
((11B/10B)sample/(11B/10B)SRM951 1) 1,000). Boron in isotopes are one of the best tools used to infer the pH of a
the silicate Earth is grossly distributed as follows: 10% in solution from which a mineral grew. This has been useful
seawater, 35% in the crust (continental and oceanic), to unravel the origin of the so-called vital effect on the
and 55% in the mantle (upper plus lower mantle). Very oxygen isotopic fractionation between biogenic carbon-
few is known for boron isotope variations in organic ates and seawater. Micrometer scale variations of d11B
matter (Williams et al. 2001) because of analytical diffi- values in coral skeletons have shown that strong pH var-
culties, even though boron is a key element for life and has iations occurred during the formation of calcite and that
a complex biogeochemical cycle (Park and Schlesinger these changes of pH modify the kinetic of oxygen isotopic
2002). Boron in the primitive mantle has a d11B exchanges between dissolved carbonate species (H2CO3,
10 as indicated by oceanic basalt glasses (Chaussidon HCO3 and CO32) and water via the two reactions of
and Marty 1995) and this is most probably the bulk d11B hydration and hydroxylation (Rollion-Bard et al. 2003).
of the Earth. There is no significant isotopic fractionation Boron isotopes in sedimentary rocks are thus key for the
associated to the extraction of boron from the mantle to reconstruction of past paleo-environmental changes on
the crust, because boron isotopic fractionations at mantle Earth.
temperatures are minimum. This is confirmed by analyses
of tourmalines from granitic rocks of various ages which See also
allow to define an average d11B for the continental crust CAIs
(at a mean age of 2 Ga) between 8 and 13 Chondrite
(Chaussidon and Albarede 1992). However, in more Stellar Nucleosynthesis
details, mass balance implies that the d11B of the crust
has evolved over geologic times in response to crustal
References and Further Reading
growth and to the change of the relative fractions of
Burbidge EM, Burbidge GR, Fowler WA, Hoyle F (1957) Synthesis of the
B hosted in the main surface reservoirs. In fact, a major elements in stars. Rev Mod Phys 29:547650
isotopic fractionation occurs for boron during adsorption Catanzaro EJ et al (1970) Standard reference materials: boric acid; isoto-
processes on clay minerals (Schwartz et al. 1969; Palmer pic, and assay standard reference materials. National Bureau of
et al. 1987) and various other phases such as, for instance, Standards Special Publication 260-17. US Govt. Print. Off.,
Washington, DC, 70 pp
humic acids (Lemarchand et al. 2005). This isotopic frac-
Chaussidon M, Albarede F (1992) Secular boron isotope variations in the
tionation is due to the facts that (1) boron in solution continental crust: an ion microprobe study. Earth Planet Sci Lett
occurs both as boric acid (B(OH)3, named B3 in the 108:229241
following) and borate anion (B(OH)4, named B4 in the Chaussidon M, Gounelle M (2006) Irradiation processes in the early solar
following), the relative proportions of the two species system. In: Lauretta DS, McSween HY Jr (eds) Meteorites and the
early solar system II. University of Arizona Press, Tucson, pp 323339
depending on the acidity constant (pK) of boric acid,
Chaussidon M, Marty B (1995) Primitive boron isotope composition of
which itself depends on temperature and salinity and the mantle. Science 269:383386
(2) there is a strong equilibrium isotopic fractionation Chaussidon M, Robert F (1995) Nucleosynthesis of 11B-rich boron in the
between boric acid and borate anion (aB3B4 = 0.97352 pre-solar cloud recorded in meteoritic chondrules. Nature 374:
at 25 C, Pagani et al. 2005; Klochko et al. 2006; Rollion- 337339
Chaussidon M, Robert F (1998) 7Li/6Li and 11B/10B variations in chon-
Bard and Erez 2010). Boron adsorbed at the surface of
drules from the Semarkona unequilibrated chondrite. Earth Planet
growing minerals (clays, carbonates) is dominantly B4, Sci Lett 164:577589
which is thus strongly isotopically fractionated from the Chaussidon M, Robert F, McKeegan KD (2006) Li and B isotopic varia-
solution. During crystal growth, this adsorbed boron is tions in an Allende CAI: evidence for the in situ decay of short-lived
218 B Branching Fraction
10
Be and for the possible presence of the short-lived nuclide 7Be in
the early solar system. Geochim Cosmochim Acta 70:224245 Branching Ratio
Klochko K, Kaufman AJ, Yao W, Byrne RH, Tossell J (2006) Experimental
measurements of boron isotopic fractionation in seawater. Earth
Planet Sci Lett 248:276285 Synonyms
Krombel KE, Wiedenbeck ME (1988) Isotopic composition of cosmic-ray Branching fraction
boron and nitrogen. Astrophys J 328:940953
Lambert DL, Sheffer Y, Federman SR, Cardelli JA, Sofia UJ, Knauth
DC (1998) The 11B/10B ratio of local interstellar diffuse clouds.
Definition
Astrophys J 494:614622 In chemistry and physics, the branching ratio is the ratio
Lemarchand D, Gaillardet J, Lewin E, Allegre CJ (2000) The influence of of the rate constant for a particular product of a reaction
rivers on marine boron isotopes and implications for reconstructing to the rate constant for the total set of possible products.
past ocean pH. Nature 408:951954 For example, in nuclear physics, the branching ratio for
Lemarchand E, Schott J, Gaillardet J (2005) Boron isotopic fractionation
a decay process is the ratio of the number of particles
related to boron sorption on humic acid and the structure of surface
complexes formed. Geochim Cosmochim Acta 69:35193533 which decay via a specific decay mode with respect to the
Lodders K (2003) Solar system abundances and condensation tempera- total number of particles which decay via all decay modes.
tures of the elements. Astrophy J 591:12201247 It is also equal to the ratio of the partial decay constant to
McKeegan KD, Chaussidon M, Robert F (2000) Incorporation of short- the overall decay constant.
lived 10Be in a calcium-aluminium-rich inclusion from the Allende
meteorite. Science 289:13341337
Pagani M, Lemarchand D, Spivack A, Gaillardet J (2005) A critical eval-
uation of the boron isotope-pH proxy: the accuracy of ancient pH
estimates. Geochim Cosmochim Acta 69:953961
Palmer MR, Spivack AJ, Edmond JM (1987) Temperature and pH con- Brazilian Space Agency
trols over isotopic fractionation during adsorption of boron on
marine clay. Geochim Cosmochim Acta 51:23192323
AEB
Palmer MR, Swihart GH (1996) Boron isotope geochemistry: an over-
view. In: Grew ES, Anovitz LM (eds) Boron, mineralogy, petrology
and geochemistry. Rev Mineral, vol 33. Mineralogical Society of
America, pp 709744
Park H, Schlesinger WH (2002) Global biogeochemical cycle of boron.
Glob Biogeochem Cycles 16:1072
Pearson PN, Palmer MR (2000) Atmospheric carbon dioxide concentra-
Breccia
tions over the past 60 million years. Nature 406:695699
Reeves H (1994) On the origin of the light elements (Z < 6). Rev Mod Synonyms
Phys 66:193216 Rubblerock
Reeves H, Fowler W, Hoyle F (1970) Galactic cosmic rays origin of Li, Be
and B in stars. Nature 226:727729
Rollion-Bard C, Chaussidon M, France-Lanord C (2003) pH control on
Definition
oxygen isotopic composition of symbiotic corals. Earth Planet Sci Breccia is a rock composed of angular fragments. It is
Lett 215:275288 produced by sedimentary, magmatic, or tectonic pro-
Rollion-Bard C, Erez J (2010) Intra-shell boron isotope ratios in the cesses. A sedimentary breccia is a coarse-grained (particle
symbiont-bearing benthic foraminiferan Amphistegina lobifera: size > 2 mm) rock composed of angular rock fragments
Implications for d11B vital effects and paleo-pH reconstructions.
Geochim Cosmochim Acta 74:15301536
held together by cement or dispersed in a fine-grained
Schwartz HP, Agyei EK, McMullen CC (1969) Boron isotopic fraction- solidified matrix. It originates as a result of sedimentary
ation during clay adsorption from seawater. Earth Planet Sci Lett 6:15 processes such as talus accumulation (sedimentary brec-
Spivack AJ, Palmer MR, Edmond JM (1987) The sedimentary cycle of cia), disturbance during sedimentation (intraclastic brec-
boron isotopes. Geochim Cosmochim Acta 51:19391949
cia), or collapse of rocky surfaces such as the roof of a cave
Williams LB, Hervig RL, Wieser ME, Hutcheon I (2001) The influence of
organic matter on the boron isotope geochemistry of the gulf coast
(collapse breccia). Magmatic breccia results from explosive
sedimentary basin. USA Chem Geol 174:445461 eruptions (pyroclastic breccia), hydrovolcanic fragmenta-
tion in diatremes (funnel-shaped pipes), or mechanical
fragmentation in intrusive settings. Tectonic processes
such as frictional slip along a fault produce fault breccia.
Breccia containing angular clasts and fine-grained matrix
Branching Fraction produced by meteoritic impact is a common rock on
planetary surfaces. The anorthosite breccia of the lunar
Branching Ratio highlands is a well-known example.
Brown Dwarfs B 219
are then known as white dwarfs (which are much dwarf will be uncertain unless it is located within a cluster
more massive and so can be as small as the Earth, and (or binary) of known age, or is in a known orbit. Eclipsing
initially much hotter hence white). binary brown dwarf systems (where both size and mass
can be independently found) are extremely valuable in
Basic Methodology testing models for brown dwarfs (the first systems have
Brown dwarfs were first hypothesized in 1963 by Shiv recently been discovered).
Kumar, who called them black dwarfs. Jill Tarter pro- Objects below about 2,200 K have mineral grains in
posed the name brown dwarf in 1975. They are not their atmospheres, and hence are dusty (Allard et al.
actually brown, but would appear to the eye from deep 2001; Lodders and Fegley 2006). The dust is made of the
red to magenta depending on their temperature. No most refractory compounds, Ca-, Al-, and Ti- oxides like
brown dwarfs were definitively known before 1994. In corundum (Al2O3) and perovskite (CaTiO3). The pres-
order to distinguish (brighter, warmer) brown dwarfs ence of dust makes the spectra of most brown dwarfs look
from stars of the same temperature, one can search for quite different than red dwarfs; the latter show many
lithium in their spectrum (the primoridal complement of bands from molecules like TiO and VO at visible wave-
lithium created by the Big Bang is destroyed when hydro- lengths, whereas brown dwarfs have fairly smooth spectra
gen fusion begins). Objects as cool as red or brown dwarfs (dust has replaced the molecules) and enormous features
are fully convective, so all parts of the object are mixed to due to atomic transitions of alkali elements, especially
the core on fairly short timescales, and the core properties sodium and potassium (and lithium), which form above
are simply related to mass and age. Brown dwarfs below 60 the dust. In the infrared, brown dwarfs show molecular
Jupiter masses will never destroy lithium, while all low- features due to water, carbon monoxide, and in the cooler
mass stars will, within a few tens of millions of years. ones, methane. These spectral differences led to the delin-
Alternatively, one can look for (much fainter) objects eation of the first new astronomical spectral class (L) to
below the minimum stellar temperature (which was tried be defined since the early twentieth century. The coolest
first with stellar companions). In 1995, both methods actual stars also extend into this L class. The next new
produced verified discoveries (Basri 2000). The lithium spectral class, T, is defined by the appearance of methane
test was successfully employed at UC Berkeley on an object in the infrared spectra of brown dwarfs (Kirkpatrick 2005)
in the Pleiades (PPl 15, which later also proved to be the with surface temperatures below about 1,300 K.
first brown dwarf binary). In the same time frame, astron- The dust can form clouds, which gives rise to a sort of
omers at Palomar Observatory and Johns Hopkins weather that can sometimes be detected as rotational
University found a companion to a red dwarf star (Gliese modulation of brightness variations (clouds will be darker
229; red dwarfs are very low-mass stars). The detection and cooler). For objects at the boundary between spectral
of methane in the companions spectrum showed that it classes L and T, the refractory clouds sink down below the
has a surface temperature less than 1,300 K. Its extremely atmosphere. The colors and spectra of very cool objects are
low luminosity, coupled with the age of its stellar complicated by the formation of clouds, and the most
companion, implies that it has about 50 Jupiter masses. successful models have to incorporate various amounts
Christened Gliese 229 B, this was the first object widely of mixing of cloudy and clear atmospheres (Saumon and
accepted as a brown dwarf. Marley 2008). The spectral sequence has a looser relation
to the temperature sequence in this regime. The actual
Key Research Findings formation of condensates, their sizes and settling proper-
The surface temperatures of brown dwarfs depend on both ties, are not well understood (even the formation of clouds
their mass and age; they start off as large and hot as they on the Earth is tricky).
will ever be. A younger, less massive object can have the It appears that brown dwarfs form in much the same
same temperature as an older, more massive object. This way as stars, constituting the very low-mass end of the
makes them fundamentally different from main sequence star formation process (Luhman et al. 2007). They pos-
stars, which are hotter when more massive. The most sess circumstellar disks when forming, and thus might also
massive and youngest brown dwarfs have temperatures sometimes have planets (a couple of giant planet compan-
as high as 2,800 K (overlapping with red dwarfs). All ions have been found already). They exhibit all the phe-
brown dwarfs eventually cool below the minimum main nomenology of newly forming stars, but with lower
sequence stellar temperature of about 1,800 K. The oldest accretion rates. Brown dwarfs, like Gl 229B, the first one
and least massive can be as cool as about 500 K. Since age discovered, can be found as companions to stars, or even
and size are often hard to determine, the mass of a brown to each other. Their binary fraction is comparable to that
BuchererBergs Synthesis B 221
for red dwarfs (about one quarter) and in line with the References and Further Reading
decrease observed with stellar mass along the main Allard F, Hauschildt HP, Alexander RD, Tamanai A, Schweitzer A (2001)
sequence. An alternative formation scenario, that brown The limiting effects of dust in brown dwarf model atmospheres.
Astrophys J 556:357372 B
dwarfs are stars whose birth is interrupted by being ejected
Basri G (2000) Annu Rev Astron Astrophys 38:485519
from a multiple system before they can gather enough Burrows A, Hubbard WB, Lunine JI, Liebert J (2001) Rev Mod Phys
mass, is not supported by most observations. The disk 73:719765
lifetimes are not very different, and the wide binary fre- Chabrier G, Baraffe I (2000) Annu Rev Astron Astrophys 38:337377
quency is not easily compatible with that hypothesis. Kirkpatrick J (2005) Davy. Annu Rev Astron Astrophy 43:195245
Lodders K, Fegley B Jr (2006) Chemistry of low mass substellar objects. In:
There also seems to be a population of isolated objects
Mason JW (ed) Astrophysics update 2. Springer, Heidelberg,
forming like stars all the way down into the high planetary Germany, p 1
mass domain. Luhman KL, Joergens V, Lada C, Muzerolle J, Pascucci I, White R (2007)
One respect in which brown dwarfs are more like giant The formation of brown dwarfs: observations. In: Reipurth B, Jewitt
planets than stars is that they tend to rotate in a few hours D, Keil K (eds) Protostars and planets V. University of Arizona Press,
Tucson, pp 443457
rather than days or weeks like most stars. This has to do
Reiners A, Basri G (2008) Astrophys J 684:13901403
with the fact that although young brown dwarfs are mag- Saumon D, Marley MS (2008) Astrophys J 689:13271344
netically active (as are young stars), they are not able to
sustain magnetically driven mass loss (which also causes
angular momentum losses that slow the rotation down in
stars). The reason behind this is that as their surfaces cool,
the magnetic field gets decoupled from the increasingly Brownlee Particles
neutral plasma, making it difficult to sustain the coronal
heating that drives winds (Reiners and Basri 2008). Interplanetary Dust Particles
Infrared sky surveys and other techniques have now
uncovered hundreds of brown dwarfs. By studying very
young clusters, we are able to assess how many brown
dwarfs form relative to stars. The result is that there
seem to be as many as a few percent of brown dwarfs
BSL
compared to stars, which implies there are billions of
Biological Safety Level
them in our Galaxy. Before their discovery, it was thought
that brown dwarfs might be a significant component of
dark matter (they are too faint to be seen except when
very close by), but they do not add up to nearly enough
mass to be interesting in that respect. From a physical BuchererBergs Synthesis
point of view, each brown dwarf begins with stellar surface
temperatures and ends with surface temperatures like Synonyms
those of young giant planets by the time the current age Hydantoin formation
of the universe has passed. We have much to learn from
studying them. Definition
The BuchererBergs synthesis (Ware 1950) of hydantoins
See also (Hyd) is carried out by reacting cyanohydrins (the addi-
Binary Stars, Young tion products of cyanide anion to aldehydes or ketones)
Dwarf Stars with ammonium carbonate (or CO2 and NH3). Its
Main Sequence mechanism, closely related to the Strecker synthesis,
Planet involves a-aminonitriles as intermediates that are
Protostars processed via a carbon dioxide-promoted reaction
Spectral Type (Fig. 1) (Pascal et al. 2005).
Spectroscopy These hydantoins (Hyd) can be ring-opened hydrolyt-
Star Formation ically to form N-carbamoylamino acids. It is considered
Stars (Low Mass) relevant to amino acid formation on early Earth because it
Stellar Rotation is likely to have prevailed over Strecker synthesis under
White Dwarf a CO2-rich atmosphere. Peptides are potentially produced
222 B Buckminsterfullerene
O HCN CN
R R Buffer
H OH
Definition
NH3, HCN
Buffer is a solution of a conjugated pair of acid and base
O that at a pH around its pKa can tolerate moderate addi-
CN CO2 CN
NH tions of acid or base without a remarkable pH change.
R R O R
NH2 HN N O
AN O Hyd H
History
Buffon was one of the most important French naturalists
through conversion of N-carbamoylamino acids into
of the eighteenth century. In 1739, he became Intendant du
amino acid N-carboxyanhydrides (Pascal et al. 2005)
Jardin et du Cabinet dHistoire Naturelle du Roi. For four
(Fig. 1).
decades (17491789), he published his Histoire Naturelle
(22 volumes, with the supplements).
See also
From the beginning of this voluminous work, he
Amino Acid N-Carboxy Anhydride
presented several important concepts and used them in
N-Carbamoyl-Amino Acid
his description of living beings. According to him, every
Strecker Synthesis
animal and vegetable organism was made of organic
molecules, which were the smallest living entities. In
References and Further Reading
each body, the organic molecules took the mark of the
Pascal R, Boiteau L, Commeyras A (2005) From the prebiotic synthesis of
a-amino acids towards a primitive translation apparatus for the internal mold specific for each species. During repro-
synthesis of peptides. Top Curr Chem 259:69122 duction, the male and the female would give some organic
Ware E (1950) The chemistry of hydantions. Chem Rev 46:403470 molecules with the mark of the parental internal molds
and the young organism would then depend on it.
It is very important to note that Buffon was not
a transformist. Indeed, he conceived some modifications
in the limit of each species, which could be reversible;
Buckminsterfullerene however, he never accepted any link between species by
means of modifications.
Fullerenes
As far as the history of Earth is concerned, Buffons
conception evolved during his career. In the first volume
of his Histoire Naturelle, he developed a cyclic conception
of the history of Earth. Thirty years later, he claimed
Buckyballs a sagittal theory and gave a description of the Epochs of
the Nature in a supplementary volume (V) of his Histoire
Fullerenes Naturelle. He described seven epochs. At the beginning,
Burgess Shale Biota B 223
the Earth was an incandescent sphere of matter. The tem- Smithsonian Institution. He quickly recognized the
perature progressively decreased and the Earth became importance of the fossils, and coined the term Burgess
solid. Therefore, his history of Earth was irreversible and Shale. Later, expeditions from Harvard University, the B
depended on the decrease in temperature. Geological Survey of Canada, and the Royal Ontario
Buffon asserted that species were formed by spon- Museum discovered new localities and amassed substan-
taneous generation and had been constituted by the tial new collections of fossils.
organic molecules that were very abundant in the soil
during the first epochs of nature. For him, spontaneous Overview
generations were still active in nature, but only for the The Burgess Shale biota figures strongly in discussions of
little species. early animal evolution and the Cambrian explosion of
life. Unlike most fossil localities, the Burgess Shale yields
See also exquisitely preserved remains of comparatively soft-
Spontaneous Generation (History of) bodied animals, alongside more familiar and routinely
preserved biomineralizing (shelly) groups, thus reveal-
ing a far more complete picture of contemporaneous
References and Further Reading
diversity, disparity, and ecologic range.
Roger J (1993) Les sciences de la vie dans la pensee francaise au XVIIIe
siecle (nouvelle edition). Albin Michel, Paris Interpreting the Burgess Shale animals has not been
straightforward, not least because they are separated from
living relatives by approximately half a billion years of
evolution. Following the early work of Walcott, the fossils
were generally assigned to members of familiar, living
Building Blocks of Primitive Life animal groups. Later research questioned this approach,
which has been described by Gould as shoehorning,
Endogenous Synthesis because the unusual morphologies of many of the fossils
Origin of Life apparently excluded them from known groups. This led to
the view that the Cambrian Period was a time of unprec-
edented evolutionary experimentation, with the invention
of many phylum-level body plans, only some of which
Burgess Shale Biota survived to the present day. Increasingly, however, this
conclusion is viewed as an artifact of classification. The
THOMAS H. P. HARVEY application of cladistic methods of phylogenetic analysis
Department of Earth Sciences, University of Cambridge, suggests that the Burgess Shale taxa, like all other fossils,
Cambridge, UK can be accommodated in stem groups, which possess
some but not all of the characters shared by extant mem-
bers of a lineage (the crown). In this light, the Burgess
Keywords Shale biota helps to resolve the evolutionary steps involved
Cambrian, evolution, metazoans, paleobiology in the emergence of the various animal body plans.
The exceptional fossils of the Burgess Shale are pre-
served as macroscopic carbonaceous compressions in fine-
Definition grained rocks. Cambrian fossil assemblages of comparable
The Burgess Shale biota is an assemblage of exceptionally Burgess-Shale-type preservation have subsequently
preserved fossil organisms from rock units within the been identified from some tens of sites around the
Burgess Shale Formation of the Rocky Mountains world, among the most spectacular being the Sirius Passet
of British Columbia, Canada. It is dated at ca. 505510 biota of northern Greenland and the Chengjiang biota
Ma, within the middle part of the Cambrian Period of of Yunnan Province, China, both several million years
geologic time, and is renowned for providing a detailed older than the Burgess Shale itself. The preservational
snapshot of early animal evolution. window that provides this particular view onto early and
middle Cambrian life appears to be restricted in time, and
History to particular marine settings. The origins and evolution-
The principal fossil locality near Mount Burgess was dis- ary fate of Burgess-shale-type biotas are thus unclear, and
covered in 1909 by Charles D. Walcott, Secretary of the form a focus of current research.
224 B Butadiyne
History
The astronomical identification of C4H in the envelope of
the carbon star IRC + 10216 (Guelin et al. 1978) prior to Butyrine
laboratory measurements of the rotational spectrum pro-
vides another example of the ability of high frequency Amino Butyric Acid