Role of extremophiles in biotechnology

CHARACTERISTICS :- • "Thermopiles" are heat loving microorganisms which can grow in the temperature
55-65 °C • minimum growth temperature:- 45°C • optimal growth temprature:-55- 65°C • Maximum
growth temperature:- 110 °C • They contain heat-stable enzymes. • Used in biotechnology & medicine.
• Example:-Thermos aquatics and Thermococcus littorals are used as sources of the enzyme DNA
polymerase, for the PCR technique in DNA fingerprinting. the heat-stable enzymes of
thermophiles proved to be very important to the field of biotechnology.

1. EXTREMOPHILES  Organisms found living in extreme harsh environments.  Word

originated from Greek- Extremus + Philia which means extreme loving.  Most members of
this group comes under the domain Archae.  3. DEFINITION Organisms lives in
physically/geochemically extreme conditions that are mostly detrimental for other forms of
life. In other words, an extremophile is a microorganism, mostly an Achaeon that lives in
conditions of extreme acidity, alkalinity, temperature, salinity, pressure, nutrient scarcities
etc.
2. These include thermophiles, hyperthermophiles, thermoacidophiles, alkaliphiles,
psychrophiles, halophiles, barophiles, radiation resistant bacteria and endoliths.
3. Psychrophiles  Temperatue range is -15 to 150 C  Also known as cryophiles.  Have an
optimum temperature of 150 C or lower  Isolated from Arctic and Antarctic habitats (90% of
the ocean is 50 C or colder)  Also found in ice bergs, glaciers, snowfields etc  Metabolism is
quite normal at colder temperatures.  Cell membranes-high levels of fatty acids which
remain fluid at colder temperatures.  Proteinaceous antifreeze mechanism to protect the cell
and DNA  Some of them cause spoilage in refrigerated food materials.  Eg: Arthrobacter
spp, Psychrobacter spp, Halomonas spp, Pseudomonas, sphingomonas
4. 8. FIRMICUTES  Gram positive, spore forming bacterial family that can survive desiccation
and can survive extreme conditions.  This group also is an example for extremophilic true
bacteria (eubacteria).  Plays an important role in the spoilage of beer, wine and cider.  Eg:
Helicobacterium spp, Mycoplasma, Clostridium spp.
5. 9.  Many members of the Family Firmicutes are also thermophiles.  Eg: Bacillus
stearothermophilus  Recently, a DNA polymerase derived from these bacteria, Bst
polymerase has become important in biotechnology.  Bst polymerase- helicase like activity
(making it able to unwind DNA strands.  Optimum functional temperature is 60-650 C and
get inactivated at temperatures above 800C
6. 10. THERMOPHILES  Greek- thermotita (heat) and philia (love)  Temperature loving
organisms.  Most members are Archae  Grows in a temperature range of 55-1130C  Mostly
found in geothermally heated regions on earth viz., hot springs, hydrothermal vents etc.  As
they need extreme temperature, its very hard to study them under laboratory conditions. 
Also that some members can produce heat by themselves (compost and garbage landfills). 
Eg : Cyanidium caldarium, Chaetomium thermophile
7. 11.  Deinococcus-thermus is a small group of eubacteria which can thrive environmental
hazards.  Stains Gram positive (thick cell wall) but possesses an outer membrane, similar to
the Gram negative cell wall.  Several thermophilic bacteria comes under this group.  It is the
source of heat resistant enzyme- taq polymerase, which is well used in PCR.  The enzyme
is isolated from Thermus aquaticus.
8. 12. Grand Prismatic Spring and Midway Geyser Basin- Yellowstone National Park, USA
Source: Internet
9. 13. CLASSIFICATION OF THERMOPHILES 1. Obligate thermophiles  Also known as
extreme thermophiles.  Temperature range is 80-1220 C.  Membranes and proteins are
unusually stable at these extreme temperatures.  For this reason, most biological processes
utilize thermophilic enzymes because of their ability to withstand intense heat.  Many of this
group can resist radiation too.  Eg: Methanopyrus kandleri, can survive and reproduce at
1220 C, Sulfolobus spp , Pyrococcus spp, Pyrodictium spp (optimum of 1130 C)
10. 14.  Most of the members require elemental sulfur for growth.  Anaerobic members use
sulfur as electron acceptor instead of oxygen in cellular respiration.  Some are lithotrophs
that oxidizes sulfur to sulfururic acid as an energy source.  Such organisms require a very
low pH and hence known as thermoacidophiles.  Inhabits regions associated with volcanic
eruption viz; hot, sulfur rich, acidic regions such as hot springs, natural geysers, fumaroles
etc .
11. 15. HABITATS OF EXTREMOPHILES

12. Hot spring situated in Atlanta, USA Courtsey: Obligate Thermophile

13. 16. Castle Geyser, Yellowstone National Park, USA Courtesy: With over 10,000
geothermal features all being driven by volcanism and an underlying hotspot,
Yellowstone National Park is home to a wide variety of thermotolerant and
thermophilic organisms. The microorganism Sulfolobus acidocaldarius lives in
extreme environments, such as Emerald Hot Spring in Yellowstone National Park.
14.
15. Black smoker at a mid-ocean ridge hydrothermal vent
Situated along the mid-ocean ridge of the Atlantic Ocean, Iceland is a geologic "hot
zone". Thermophiles can be found colonizing a variety of geothermal features
including hot springs, mudpots, fumaroles, and geysers.

16.  Thermoacidophiles  Requires both high temperature and highly acidic environment for
optimum growth.  Preferred temperature range is 70-800 C and have an optimum pH range
of 2-3.  All the organisms discovered belongs to the Domain Archae, so far.  They can thrive
in acidous and sulfur rich environments.  Instead of cell wall, possesses a unique membrane
composed of tetraether lipoglycan, which gives the unusual stability for the bacteria.  Eg:
Thermoplasma acidophilum and T.volcanium
17. 19. Facultative Thermophiles  Rare group of organisms that can live both in higher
temperature and normal temperature are referred to as facultative thermophiles.  These
organisms can live at 200 C, and have an optimum of 500 C. Maximum temperature that
they can survive is 600 C.  Eg: Bacillus flavothermus
18. 20. ACIDOPHILES  Microorganisms that lives in highly acidic environments are called as
acidophiles.  The pH range is 1-5.  Some members that mainly found in the drainage of coal
mines are able to oxidize sulfur into sulfuric acid.  Mechanism of action is that they have a
proton pump machinery to eliminate protons from the cytoplasm of the cell to maintain low
pH.  Eg: Pyrodictium, Picrophilus, Ferroplasma, Sulfolobus
19. 21. ALKALIPHILES  These are extremophilic microorganisms which thrives in roughly
alkaline environments (8-11), and have an optimum of pH around 10.  Organisms which
needs high pH to survive are called as obligate alkaliphiles.  There are facultative
alkaliphiles and haloalkaliphiles (needs salty environment as well).  Most of the alkaliphiles
possess a bacillus morphology.  Eg: Bacillus halodurans C125, Bacillus firmus OF4
20. 22.  Two methods for surviving 1. The cell will be having a unique cellular machinery that
works best in alkaline range of pH. 2. The cell will have to acidify the cytosol to nullify the
effect of the high pH outside the cell.
21. 23.  Experimental studies revealed that the cytosolic enzymes of alkaliphiles functions best
in a neutral pH range (7.5-8.5).  This shows that for surviving in highly alkaline pH, the cell
must have some pH regulatory mechanism to protect the plasma membrane.  The
mechanism is that the cell wall contains acidic polymers composed of residues such as
galacturonic acid, gluconic acid, glutamic acid, aspartic acid, and phosphoric acid.  This
protects the PM by preventing the entry of hydroxide ions and allowing the entry of sodium
(Na+ ) and hydronium ions(H+)
22. 24. XEROPHILES  A xerophile (from Greek xēros , meaning "dry", and philos, meaning
"loving"), is an extremophilic organism that can grow and reproduce in conditions with a low
availability of water.  Water activity (aw) is a measure of the amount of water within a
substrate an organism can use to support sexual growth.  Xerophiles are often said to be
"xerotolerant", meaning tolerant of dry conditions. They can survive in environments with
water activity below 0.8.  Endoliths and halophiles are often xerotolerant.  Eg: many molds
and yeast, Trichosporonoides nigrescens
23. 25. HALOPHILES  This group comprises microorganisms that can thrive in high salty
environments such as The Great Salt Lake and Dead Sea.  Most of the halophiles belong to
the Domain Archae.  Eg: Salinibacter ruber  There are eukaryotic halophiles such as
Dunaliella salina (algae) and Wallemia icthyophaga (fungus).  Extreme halophiles/obligate
halophiles-adapted to survive high salt concentrations  Organisms from Dead Sea often
requires nearly 33% salt (sea water has only 3%), and the inoculating loop must be dipped in
a saturated salt solution to isolate them.  Microorganisms live in such high salinity are
termed as extreme halophiles
24. 26. Mechanism Mainly employ two mechanism to prevent desiccation through osmosis. Both
strategies work by increasing the osmotic concentration of the cell. 1.In first method (followed
my most halophiles including bacteria, archae etc) organic compounds are accumulated in
the cytoplasm. They are known as osmoprotectants or compatible solutes. It include
sugars, aminoacids, polyols, betaines etc. These compounds can be synthesised or
accumulated from the environment. Eg: Ectothiorhodospira halochloris
25. 27. 2. The second is the selective influx of potassium ions (K+ ) into the cytoplasm.  This
adaptation is restricted to moderately halophilic organisms.  The entire intracellular
machinery (enzymes, structural proteins etc) is highly adapted to withstand the high saline
environment.  Eg: Bacteria comes under the Family Halobacteriaceae  The 16S rRNA
studies opens a broad range of information on the field of evolution.
26. 28. ENDOLITHS  Endolith is an organism (archae, bacterium, fungus, lichen or algae) that
lives in nutritionally poor environments such as inside a rock or something.  Particularly
interesting in the area of astrobiology (exobiology).  These organisms opens a clue for life
beyond earth. There are chances of having life on endolithic environments such as mars and
other planets.
27. 29. Characteristics  Endoliths have been found in rocks down to the depth of 3 km.  It is not
known that whether this is the limit since digging to the deep is highly expensive.  The major
threats to live in such depth is the high temperature.  Recently discovered strains can
reproduce at 1210 C.  All the discovered organisms are autotrophs.  Some utilize gas or
dissolved nutrients from water moving through fractured rocks  Others may incorporate
inorganic compounds found in their rock substrate (possibly by excreting acids to dissolve
the rock).
28. 30. Endoliths can be classified into  Chasmoendoliths Colonizes fissures and cracks in the
rock (chasmo- cleft)  Cryptoendolith Colonizes structural cavities within porous rocks,
including spaces produced and vacated by euendoliths (crypto = hidden)  Euendolith
 Penetrates actively into the interior of rocks forming tunnels that conform with the shape of
its body(eu = good, true).
29. 31. Endolithic life form found inside an Antarctic rock
http://en.wikipedia.org/wiki/File:Cryptoendolith.jpghttp://
en.wikipedia.org/wiki/File:Cryptoendolith.jpg
30. 32. Obligate Anaerobes  Microorganisms which grow strictly in the absence of molecular
oxygen are called as obligate anaerobes.  For these, oxygen is a toxin  For energy
generation, they must employ fermentation or anaerobic respiration pathways.  The toxic
forms of oxygen are Singlet Oxygen(O2 ), Superoxide radicals (O2 - ), peroxide anion (O2
2-), and hydroxyl radical (OH).  Some obligate anaerobes are Clostridium spp,
Methanococcus and Methanopyrus  Microorganisms which can live both in the presence
and absence of oxygen are known as Facultative Anaerobes.  They can utilize oxygen if
available or, continue their growth by fermentation and anaerobic respiration.  Eg: Bacillus
anthracis, Escherichia coli
31. 33. An anaerobic work chamber and incubator Fig: 6.15 page no:129, Prescott, Harley and
Klein’s microbiology
32. 34.  To routinely grow and maintain in pure cultures, reducing media which stored in
ordinary, tightly packed tubes is been used.( media containing thioglycollate or cystein)  For
culturing in petriplates, sealed boxes and jars in which oxygen removed completely is been
used.  Sometimes, certain chemicals which can produce hydrogen and carbon di oxide will
be added and the so formed hydrogen will be incorporated with the oxygen present in the
container to yield water  This water can be utilized by the microorganisms.  The most
advanced system is that the media used for culture will be containing an enzyme- oxyrase
which will bind with oxygen and eliminate as water. No addition of extra chemicals or
hydrogen is needed.
33. 35. Radiation  Although most living things are sensitive to radiation, there are some
microorganisms which can resist high levels of radiation.  Deinococcus radiodurans is the
radioresistant organism discovered so far which is a eubacteria.  Their ability to withstand
radiation is more than that of endospores.  They can survive exposure to radiation doses as
high as 15,000 Grays. This much radiation is 1500 times the dosage that would kill a human.
 The mechanism for this extraordinary resistance lies in a unique arrangement of its DNA
that facilitates a rapid repair of radiation damage.  It is similarly resistant to many mutagenic
chemicals.
34. 36. Barophiles  Microorganisms that can survive under immense hydrostatic pressure. 
Generally found in ocean floors where pressure exceeds 300 atm (38 MPa).  Some have
been found at the bottom of the Pacific Ocean (Mariana Trench-10500 m) where pressure
often exceeds 117 MPa.  These organisms cannot grow in pressure below 400-500 atm 
True obligate barophiles also comprises bacteria which present in the gut of holothurians
and amphipods (crustaceans).  Eg: Photobacterium, Shewanella, Colwellia  Some
thermophilc archae such as Pyrococcus spp., Methanococcus jannaschii are barophiles too.
35. 37. SOME INTERESTING FACTS  Halomonas titanicae- the bacterium which is responsible
for rusting of RMS Titanic.  Pseudomonas putida (super bug) is a genetically engineered
bacteria which literally “eats” petroleum products. These are very much useful in oil spills. 
GFAJ-1 is a strain of rod shaped bacteria in the family Halomonadaceae which is an
extremophile, highly resistant to the dangerous poison-Arsenic.  There are chances of life
forms beyond earth and the field of study is known as astrobiology.
36. 38. ASTROBIOLOGY/EXOBIOLOGY
37. 39.  The study of origin, evolution, distribution, and future of life in the universe and life
forms that are extraterrestrial.  Astrobiology arises a question whether life exists beyond
Earth and if so, how it can be detected by humans.  Nucleic acids might not be the only
biomolecules which codes for life.  Astrobiology makes use of physics, chemistry,
 astronomy, biology, molecula r biology, ecology, planetary science, geography, and geology
to investigate the possibility of life on other worlds and help recognize biosphere that might
be different from the biosphere on Earth.
38. An estuary is a partially enclosed coastal body of brackish water with
one or more rivers or streams flowing into it, and with a free
connection to the open sea. Estuaries form a transition zone
between river environments and maritime environments.

39.

40. Ecosystem: all the plants and animals that live in a particular area together
with the complex relationship that exists between them and their
environment.
41. Estuaries:  bodies of water in coastal areas that are formed when fresh water
from rivers flows into and mixes with salt water from the ocean. In estuaries,
the fresh river water is blocked from streaming into the open ocean by either
surrounding mainland, peninsulas, barrier islands, or fringing salt marshes.
The estuary gathers and holds an abundance of life-giving nutrients from the
land and from the ocean, forming an ecosystem that contains more life per
square inch than the richest Midwest farmland.  
42. Estuaries are a critical source for much of our ocean life. They provide
essential habitat for over 75 percent of our nation's commercial fish catch.
Commercial and recreational fishing, boating and tourism also provide more
than 28 million jobs.  Estuaries, in short, are national treasures -- vital
ecological and community resources whose health affects our health and the
vibrancy of our communities and economy. 

43. The productivity and variety of estuarine habitats support a wonderful

abundance and diversity of species. Thousands of species of fish,
shore birds, marine mammals, clams, shellfish and other wildlife
survive in and around estuarine habitats. Many fish and shellfish
species, including most commercially and recreationally important
 species, depend on the sheltered waters of estuaries as home to
spawn and for their offspring to grow and live. Due to the high
productivity of living organisms, migratory birds also take estuaries as
ideal places for resting and reproducing. In addition to serving as
important habitats for wildlife, estuaries also provide valuable
environmental services. The water flowing to the ocean carries
sediments, organic and inorganic nutrients, and pollutants
44. In Estuaries, salt water mixes with water derived from land drainage.
Mixing is the process whereby water is diluted or redistributed with
other water body. Mixing events can be divided by long or short time
scale. The estuarine circulation movements are the primary
mechanism of mixing. Mixing changes the distribution in time and
space of dissolved material in fresh and ocean water. The estuarine
salinity alone beach is the most important indicator of mixing, that is,
salinity can be used to track water source and 
Q 8 an d9 not found…….

Q 15 Soil organisms

Several reviews on the impact of GM crops on biodiversity, particularly on soil

organisms, have been published. One comprehensive review covering 70 scientific
articles on the effects of Bt crops on soil ecosystem found that there were few or no
toxic effects of Cry proteins on non-target soil organisms including woodlice,
collembolans, mites, earthworms, nematodes, protozoa, as well as the activity of
different enzymes in soil. The minor effects reported were mostly results of differences
in geography, temperature, plant variety, and soil type, and were not linked to Cry
protein presence.9

Another extensive review published in GM Crops also showed the impacts of GM crops
on soil organisms and reached similar conclusion. Some of the studies included in the
review are summarized in Table 1.10

Table 1. Studies on Impact of Bt crops on soil organisms

Organism Crop Event Comparison Effect
corn: Bt11 no significant differences for Cry3Bb1;
(Cry1Ab), significantly higher survival and significantly
enchytraeids Bt and non-Bt
MON88017 lower reproduction for Cry1Ab, likely to be
(Cry3Bb1) caused by differences in plant components
soil microbes corn: MON863 Bt and non-Bt no adverse effects on saprophytic microbial
 communities of soil and decaying roots or on
(Cry3Bb1)
decomposition
the presence of Bt maize did not cause
corn: Event 176
changes in the microbial populations of the
soil microbes (Cry1Ab), MON810 Bt and non-Bt
soil or in the activity of the microbial
(Cry1Ab)
community
corn: Bt11
no significant differences in biomass of
earthworms (Cry1Ab), MON810 Bt and non-Bt
juveniles and adults
(Cry1Ab), MON863
No significant acute toxicity; average weight,
cotton: GK19
earthworms Bt and non-Bt numbers of cocoons and new offspring not
(Cry1Ac)
significantly different
purified protein No negative effect during the observed
Snails Cry1Ab
alone in soil stages

Q 24 Intertidal Zone
The intertidal zone is defined as the area between the high tide and low tide mark.

Organisms that live in this zone have to deal with difficult environmental conditions,
being both submerged in sea water and exposed to the air. They have to bear the great
physical impact of waves, desiccation, and sunlight. Occasionally there are rains which
saturate them in fresh water. There are lots of moving rocks and sediment in the water
which can damage small critters. Plus, there is a risk of predation, not only from ocean-
based animals but terrestrial animals as well.

Adaptations by organisms in the Intertidal zone

The type of organisms occupying the tidal habitat varies greatly depending on where we
are on the planet. For example, temperate rocky intertidal areas will have totally
different species than a tropical mangrove habitat. Coral reefs are also often affected by
tidal differences, which may even totally expose the corals out of the water during low
tides.
The moving water exerts great demands on organisms in the area. If an organism lives
on the substrate, it usually needs to have a way of either attaching itself to the substrate
to prevent being washed away or being able to seek shelter. Barnacles settle and build
a solid and permanently fixed structure on the rock. When under water, they reach out
with a feathery appendage to strain the water for plankton and oxygen. When the tide
goes back down, they close up the opening of the calcium structure with two plates to
prevent desiccation and predation. Limpets are mollusks that stick hard to the rocky
substrate by contracting the muscles in its foot and firmly grip the substrate. When times
are not so rough, they use the foot to crawl on the substrate and graze tiny algae off the
rock. Chitons are also mollusks with eight overlapping plates on their backs. The plates
are flexible and allows the chitons to wrap around a stick to the hard surface with its
muscular foot.

27: Carbon cycling

Bacteria show a variety of metabolic pathways related to carbon flow and
cycling. Photosynthesis is mainly carried out by algae and phytoplankton in
estuarine. Carbon fixing rate of phytoplankton shows marked seasonal
fluctuations in hydrographic and nutrient parameters. As many of the
sediment and water-logged soils of estuaries are anoxic, anaerobic
decomposition is important. Complex organic matter is used by the
fermenters and dissimilatory nitrogenous oxide reducers. The sulfate
reducers and methane producers were once thought to have more
restricted distributions [2]. Studies have shown seasonal and interannual
dynamics of free-living bacterioplankton and labile organic carbon available
to microbes along the salinity gradient of estuaries. Bacterioplankton
abundance may be an important indicator of ecosystem health in
eutrophied estuaries, because of the positive relationships between
bacterioplankton abundance, microbially labile organic carbon (MLOC), and
dissolved oxygen [4].
28 : Nitrogen cycling
Nitrogen is a major limiting nutrient for primary production in estuaries. The
N-cycling processes that are dominated by microbial activity include
nitrification, dissimilatory nitrous oxide reduction, and nitrogen fixation.
Nitrogen cycling in estuaries is related to the water mixing and microbial
community dynamics. Nitrogen cycling across steep gradients in salinity,
oxygen and dissolved inorganic nitrogen in sandy land and sea margin,
coastal permeable sediments', it controls both the amount and form of
 nitrogen discharged to the coastal ocean. In one study, the abundance of
betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) was
dramatically lower in the freshwater compared with saline stations, while
ammonia-oxidizing archaea (AOA) abundance almost remained constant
across estuarine sites. This differing response to salinity altered the ratio of
beta-AOB to AOA. Analysis of ammonia-oxidizing enrichment cultures at a
range of salinities revealed that AOA persisted solely in the freshwater
enrichments [5

Q22: METABOLIC REACTIONS IN THE DARK OCEAN

To understand the microbiology and ecology of microbial habitats in the dark ocean, it is
important to consider how microorganisms utilize substrates and gain energy in these
environments. At the surface of the Earth, diverse autotrophic organisms produce energy-
rich organic matter by fixing carbon dioxide through photosynthesis, and this organic matter
then serves as food for other organisms that convert it back to CO 2 via respiration. These
reactions are often closely coupled spatially and functionally, and our ecosystem-level
understanding of the biological carbon cycle is based in large part on the balance between
these processes. A fundamental distinguishing factor in the dark ocean is that metabolic
strategies are based on chemical redox reactions rather than the photosynthetic processes
occurring in the sunlit world. Furthermore, respiration pathways and the reactions used for
energy generation in the dark ocean are more variably coupled—spatially, temporally, and
functionally. In addition to sinking organic matter created via photosynthesis, additional
pathways of primary productivity exist in the dark ocean that are often unaccounted for in
biogeochemical budgets. Understanding ecological diversity and microbial metabolic
reactions in the dark ocean is a centerpiece of dark ocean research. Furthermore,
understanding the principles affecting microbiology in the most extreme or energy-limited
environments on Earth—for example, hydrothermal vents or the deep marine subsurface,
respectively—provides valuable parameters for constraining the search for life elsewhere in
our solar system and for understanding the evolution of life on Earth.
Microbiologists studying life in the dark ocean and the potential for life on other planets are
developing key unifying reference frames concerning “habitability” of different environments
(491). Energetic constraints that examine the potential of chemical reactions to provide
energy for life in the dark provide one such useful construct (27, 223). Approaches that
define energetic constraints have been applied in a number of dark ocean habitats (for
example, see references 26, 359, and 360) and allow geological and geochemical
information to be used for the purpose of predicting which metabolic and physiological
processes might characterize dark microbial ecosystems. Such information guides
strategies for cultivation and ecological studies as well as for understanding the
biogeochemical consequences of dark microbial ecosystems for the global environment.
All life on Earth requires access to sources of energy and carbon. In the absence of light,
metabolic energy is harnessed from the coupling of reducing and oxidizing (“redox”)
reactions (for examples, see Table 2). Energy is obtained when the coupled redox reactions
are thermodynamically favorable and yield enough energy for ATP generation.
Microorganisms exploit the available chemical energy by developing strategies to overcome
the activation energy of reaction and kinetic constraints or by coupling energetically
unfavorable reactions with other energy-yielding pathways. Carbon acquisition and energy
generation are linked in some cases (i.e., when organic matter is oxidized while another
substrate is reduced), but often catabolic and anabolic reactions are separated

Common redox reactions and associated standard free energies of reaction that occur in
the dark ocean and can be exploited for metabolic energy

The metabolic activities of microorganisms in the dark ocean depend on the availability and
speciation of electron donors (oxidizable compounds) and acceptors (reducable
compounds) (174). Distinct zonations of microbial activity based on available electron
donors and acceptors are well described and characteristic for marine sediments, which
have been studied intensively compared to some other dark ocean habitats. Figure
2 provides a representation of this metabolic zonation in marine sediments, illustrating the
typical cascade of usage of preferred electron acceptors and the impact of delivery rates of
electron donors (i.e., organic matter) on the gradient of metabolic rates. Although this
sequence of usage of electron donors and acceptors is well studied for some environments,
recent research indicates that low-level, cryptic biogeochemical cycling may still occur in
zones where it is not expected (228).
The availability of metabolic substrates and substrate concentration gradients is determined
by diffusive and advective transport processes (for further review, see reference 59).
Diffusion, the random movement of molecules, leads to a spread of substances from areas
of higher concentrations to areas of lower concentrations, depending on concentration
gradients and the speed of diffusion of the molecules, which is typically on the order of
10−9 m2 s−1. In deep ocean water, chemical exchange occurs via the movement of water in
currents and along isopycnal gradients, upwelling and downwelling near coastlines and the
equator, and mixing with hydrothermal, groundwater, and riverine fluid inputs. Chemical
exchange in marine sediments is dictated mostly by molecular diffusion, with advective
processes limited to the bioturbation and bioirrigation activities of animals living in surface
sediment; to the migration of fluids, fluidized mud, and gasses from deep gas sources or
salt deposits; and to the movement of fluids along faults and fractures in the sediment. In
oceanic crust, advective processes include fluid flow through permeable, fractured, and
porous hard rock, driven by pressure and temperature gradients. Hydrothermal vents
provide conspicuous evidence of crustal fluid flow; however, a large fraction of fluid flow in
oceanic crust occurs at lower temperatures (∼20°C) and over broad spatial scales (239).
Electron SourcesThe dominant electron sources in the dark ocean include organic matter,
hydrogen, methane, reduced sulfur compounds, reduced iron and manganese, and
ammonium. These electron donors have different abundances and energy potentials and
therefore differ in significance as substrates for microbial metabolism. Below, we discuss
each of the various electron donors in order, starting from that with the most negative
relative reduction potential.