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Hydrocarbon and Lipid Microbiology Protocols: Microbial Quantitation, Community Profiling and Array Approaches 1st Edition Terry J. Mcgenity
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Terry J. McGenity
Kenneth N. Timmis
Balbina Nogales Editors
Hydrocarbon and
Lipid Microbiology
Protocols
Microbial Quantitation, Community
Profiling and Array Approaches
Springer Protocols Handbooks
Balbina Nogales
Department of Biology
University of the Balearic Islands
and Mediterranean Institute for Advanced
Studies (IMEDEA, UIB-CSIC)
Palma de Mallorca, Spain
All active cellular systems require water as the principal medium and solvent for their metabolic and
ecophysiological activities. Hydrophobic compounds and structures, which tend to exclude water,
although providing inter alia excellent sources of energy and a means of biological compartmental-
ization, present problems of cellular handling, poor bioavailability and, in some cases, toxicity.
Microbes both synthesize and exploit a vast range of hydrophobic organics, which includes biogenic
lipids, oils and volatile compounds, geochemically transformed organics of biological origin
(i.e. petroleum and other fossil hydrocarbons) and manufactured industrial organics. The underlying
interactions between microbes and hydrophobic compounds have major consequences not only for
the lifestyles of the microbes involved but also for biogeochemistry, climate change, environmental
pollution, human health and a range of biotechnological applications. The significance of this
“greasy microbiology” is reflected in both the scale and breadth of research on the various aspects
of the topic. Despite this, there was, as far as we know, no treatise available that covers the subject.
In an attempt to capture the essence of greasy microbiology, the Handbook of Hydrocarbon and
Lipid Microbiology (http://www.springer.com/life+sciences/microbiology/book/978-3-540-77584-
3) was published by Springer in 2010 (Timmis 2010). This five-volume handbook is, we believe,
unique and of considerable service to the community and its research endeavours, as evidenced by
the large number of chapter downloads. Volume 5 of the handbook, unlike volumes 1–4 which
summarize current knowledge on hydrocarbon microbiology, consists of a collection of experimen-
tal protocols and appendices pertinent to research on the topic.
A second edition of the handbook is now in preparation and a decision was taken to split off
the methods section and publish it separately as part of the Springer Protocols program (http://
www.springerprotocols.com/). The multi-volume work Hydrocarbon and Lipid Microbiology
Protocols, while rooted in Volume 5 of the Handbook, has evolved significantly, in terms of
range of topics, conceptual structure and protocol format. Research methods, as well as
instrumentation and strategic approaches to problems and analyses, are evolving at an unprec-
edented pace, which can be bewildering for newcomers to the field and to experienced
researchers desiring to take new approaches to problems. In attempting to be comprehensive
– a one-stop source of protocols for research in greasy microbiology – the protocol volumes
inevitably contain both subject-specific and more generic protocols, including sampling in the
field, chemical analyses, detection of specific functional groups of microorganisms and com-
munity composition, isolation and cultivation of such organisms, biochemical analyses and
activity measurements, ultrastructure and imaging methods, genetic and genomic analyses,
1
Adapted in part from the Preface to Handbook of Hydrocarbon and Lipid Microbiology.
v
vi Preface to Hydrocarbon and Lipid Microbiology Protocols
systems and synthetic biology tool usage, diverse applications, and the exploitation of bioin-
formatic, statistical and modelling tools. Thus, while the work is aimed at researchers working
on the microbiology of hydrocarbons, lipids and other hydrophobic organics, much of it will be
equally applicable to research in environmental microbiology and, indeed, microbiology in
general. This, we believe, is a significant strength of these volumes.
We are extremely grateful to the members of our Scientific Advisory Board, who have
made invaluable suggestions of topics and authors, as well as contributing protocols them-
selves, and to generous ad hoc advisors like Wei Huang, Manfred Auer and Lars Blank. We also
express our appreciation of Jutta Lindenborn of Springer who steered this work with profes-
sionalism, patience and good humour.
Reference
Timmis KN (ed) (2010) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, Heidelberg
Contents
vii
viii Contents
ix
x About the Editors
became paradigms of microbes that degrade organic compounds (Pseudomonas putida and Alcani-
vorax borkumensis). He has had the privilege and pleasure of working with and learning from some
of the most talented young scientists in environmental microbiology, a considerable number of
which are contributing authors to this series, and in particular Balbina and Terry. He is Fellow of the
Royal Society, Member of the EMBO, Recipient of the Erwin Schrödinger Prize, and Fellow of the
American Academy of Microbiology and the European Academy of Microbiology. He founded the
journals Environmental Microbiology, Environmental Microbiology Reports and Microbial Bio-
technology. Kenneth Timmis is currently Emeritus Professor in the Institute of Microbiology at the
Technical University of Braunschweig.
Abstract
Since the discovery of Van Leeuwenhoek’s “wee animalcules,” microbiologists have explored microbial
communities to identify who is where, when, why, and how. Although microbial community analyses were
conducted with cultivation-based methods for most of microbiology’s history, molecular methods have
transformed this discipline over the past few decades. Specifically, the ability to extract and analyze
biomarkers from environmental samples, including lipids, RNA, and DNA, enable characterization of
microbial communities more completely, circumventing many cultivation-based limitations. Microbiolo-
gists now find themselves in an era of rapid experimentation and discovery because the diversity of microbial
communities no longer precludes effective experimental design and analysis. Microbial community analysis
is in a boom era and the protocols in this volume reflect the wide range of methods available for use by
microbiologists to better understand microbial communities in environmental samples.
Keywords: Antibody arrays, Clone library, Denaturing gradient gel electrophoresis (DGGE), DNA,
Lipids, Microscopy, Most probably number (MPN), Nucleic acid, Protists, Quantitative PCR (qPCR),
RNA, Single-strand conformational polymorphism (SSCP), Terminal restriction fragment length
polymorphism (T-RFLP)
1 Main Text
T.J. McGenity et al. (eds.), Hydrocarbon and Lipid Microbiology Protocols, Springer Protocols Handbooks, (2017) 1–5,
DOI 10.1007/8623_2016_195, © Springer-Verlag Berlin Heidelberg 2016, Published online: 03 May 2016
1
2 Josh D. Neufeld
References
1. Nichols D (2007) Cultivation gives context to chloroform fumigation-extraction, phospho-
the microbial ecologist. FEMS Microbiol Ecol lipid fatty acid, and DNA methods to deter-
60:351–357 mine microbial biomass in forest humus. Soil
2. Lappé M, Kallmeyer J (2014) A cell extraction Biol Biochem 36:529–532
method for oily sediments. In: McGenity TJ, 7. Peacock A, White D (2016) Microbial biomass
Timmis KN, Nogales Fernández B (eds) and community composition analysis using
Hydrocarbon and lipid microbiology proto- phospholipid fatty acids. In: McGenity TJ,
cols. Springer Protocols Handbooks Timmis KN, Nogales Fernández B (eds)
3. Edgcomb VP, Kysela DT, Teske A, de Vera Hydrocarbon and lipid microbiology proto-
Gomez A, Sogin ML (2002) Benthic eukary- cols. Springer Protocols Handbooks
otic diversity in the Guaymas Basin hydrother- 8. Wörmer L, Lipp J, Hinrichs K-U (2016) Com-
mal vent environment. Proc Natl Acad Sci USA prehensive analysis of microbial lipids in envi-
99:7658–7662 ronmental samples through HPLC-MS
4. Johnsen A (2014) Introduction to microplate protocols. In: McGenity TJ, Timmis KN,
MPN-enumeration of hydrocarbon degraders. Nogales Fernández B (eds) Hydrocarbon and
In: McGenity TJ, Timmis KN, Nogales Fer- lipid microbiology protocols. Springer Proto-
nández B (eds) Hydrocarbon and lipid micro- cols Handbooks
biology protocols. Springer Protocols 9. McKew B, Smith C (2015) Real-time PCR
Handbooks approaches for analysis of hydrocarbon-
5. Shen Y, Voordouw G (2015). Primers for dsr degrading bacterial communities. In: McGe-
genes and most probable number method for nity TJ, Timmis KN, Nogales Fernández B
detection of sulfate-reducing bacteria in oil (eds) Hydrocarbon and lipid microbiology
reservoirs. In: McGenity TJ, Timmis KN, protocols. Springer Protocols Handbooks
Nogales Fernández B (eds) Hydrocarbon and 10. Dumbrell A (2016) Microbial community
lipid microbiology protocols. Springer Proto- analysis by single-amplicon high-throughput
cols Handbooks sequencing (metagenetics) – preparation, data
6. Leckie SE, Prescott CE, Grayston SJ, Neufeld handling and ecological analysis. In: McGenity
JD, Mohn WW (2004) Comparison of TJ, Timmis KN, Nogales Fernández B (eds)
Introduction to Microbial Quantitation, Community Profiling, and Array Approaches 5
Hydrocarbon and lipid microbiology proto- B (eds) Hydrocarbon and lipid microbiology
cols. Springer Protocols Handbooks protocols. Springer Protocols Handbooks
11. Sutton NB, Maphosa F, Morillo JA, Al-Soud 15. Lynch MD, Bartram AK, Neufeld JD (2012)
WA, Langenhoff AA, Grotenhuis T et al (2013) Targeted recovery of novel phylogenetic diver-
Impact of long-term diesel contamination on sity from next-generation sequence data. ISME
soil microbial community structure. Appl Envi- J 6:2067–2077
ron Microbiol 79:619–630 16. Lynch MD, Neufeld JD (2015) Ecology and
12. Green S, Leigh M, Neufeld JD (2016) Dena- exploration of the rare biosphere. Nat Rev
turing gradient gel electrophoresis (DGGE) for Microbiol 13:217–229
microbial community analysis. In: McGenity 17. Johnke J, Chatzinotas A (2015). Studying pro-
TJ, Timmis KN, Nogales Fernández B (eds) tistan communities in hydrocarbon-
Hydrocarbon and lipid microbiology proto- contaminated environments. In: McGenity
cols. Springer Protocols Handbooks TJ, Timmis KN, Nogales Fernández B (eds)
13. Tebbe C, Dohrmann A, Hemkemeyer M, Hydrocarbon and lipid microbiology proto-
N€ather A (2016) Microbial community cols. Springer Protocols Handbooks
profiling: SSCP and T-RFLP techniques. In: 18. Blanco Y, Moreno-Paz M, Aguirre J, Parro V
McGenity TJ, Timmis KN, Nogales Fernández (2016) Multiplex fluorescent antibody micro-
B (eds) Hydrocarbon and lipid microbiology arrays and antibody graphs for microbial and
protocols. Springer Protocols Handbooks biomarker detection in the environment. In:
14. Leigh M, Taylor L, Neufeld JD (2015) Clone McGenity TJ, Timmis KN, Nogales Fernández
libraries of ribosomal RNA gene sequences for B (eds) Hydrocarbon and lipid microbiology
characterization of microbial communities. In: protocols. Springer Protocols Handbooks
McGenity TJ, Timmis KN, Nogales Fernández
A Cell Extraction Method for Oily Sediments
Michael Lappé and Jens Kallmeyer
Abstract
To get a first impression of the size of the microbial community present in a sediment sample, the
determination of cell abundances in sediments is of great importance for biogeochemical studies. One of
the most simple and reliable methods is direct counting, where the cells are stained with a DNA-binding
stain and counted under an epifluorescence microscope. However, in oily sediments, DNA-specific stains
and molecular probes bind to the hydrocarbons, causing massive background fluorescence, thereby ham-
pering cell enumeration. To overcome this problem, we developed an extraction method in which the
hydrocarbons are removed with organic solvents prior to cell extraction. Due to the reduced background
fluorescence, the microscopic image becomes clearer, making cell identification and enumeration much
easier.
A volumetric ratio of 1:2 to 1:5 between a formalin-fixed sediment slurry and solvent delivers highest cell
counts. n-Hexane delivers best results for samples containing less biodegraded oil, whereas methanol
turned out to be the most appropriate solvent for samples containing strongly biodegraded oil. The optimal
solvent to sample ratio has to be determined prior to analysis for each type of sample.
However, it has to be kept in mind that solvents also tend to lyse cells and that the given protocol has to
be adapted to the individual conditions in order to minimize cell lysis and maximize hydrocarbon removal.
1 Introduction
Oily sediments have received increased attention over the last few
years, especially because of their microbial richness and diversity
[1]. In order to obtain an accurate picture of the microbial
community in oily sediments, it is important first to quantify the
number of cells. Direct counting is fast, cheap and delivers reliable
results. Therefore, it is one of the most frequently used methods for
determination of microbial cell abundance in sediments. For direct
counting, the cells are stained with a DNA-binding stain and
counted under an epifluorescence microscope.
We tried to count cells directly from completely untreated oily
sediment samples similar to the protocol of Cragg et al. [2].
T.J. McGenity et al. (eds.), Hydrocarbon and Lipid Microbiology Protocols, Springer Protocols Handbooks, (2017) 7–16,
DOI 10.1007/8623_2014_19, © Springer-Verlag Berlin Heidelberg 2014, Published online: 20 November 2014
7
8 Michael Lappé and Jens Kallmeyer
Fig. 1 Image of an oil sand sample under the fluorescence microscope. (a)
Sample processed according to the extraction procedure of Kallmeyer et al. [3]
without hydrocarbon extraction. Cells are difficult to identify due to strong
background fluorescence. (b) Sample after hydrocarbon extraction prior to cell
extraction. Background fluorescence is drastically reduced and cells are much
easier to detect. Figure was originally published in Lappé and Kallmeyer [4]
2 Materials
All materials used for the cell extraction have to be absolute cell-
free. To achieve this, all glassware used during the cell extraction
procedure is combusted before use. In order to increase turnover
time, the glass filter towers for the preparation of the filters are not
combusted but first washed in a sodium hypochlorite solution and
then rinsed first with distilled water and then ethanol, followed by a
final flaming with a blowtorch directly before use. Reagents are
autoclaved if possible and always filter sterilized (0.2 μm pore
size) immediately before use to remove all cells. The following
reagents are used:
l To avoid osmotic stress on the cells, the salinity of the slurry has
to be adjusted to in situ conditions. For the preparation of
primary slurries from marine samples, sodium chloride (NaCl)
solution is used, i.e. 25 g L1 NaCl for normal marine samples.
l For preparation of primary slurries from terrestrial samples,
phosphate buffered saline (PBS) is used: 8 g L1 NaCl,
0.2 g L1 KCl, 1.44 g L1 Na2HPO4, and 0.24 g L1
KH2PO4. For samples with extremely high or low salinity, the
concentration has to be adjusted accordingly. For samples from
salt lakes, we used up to 10 PBS.
When preparing primary slurries, a 20 mL L1 of formalin is
added to the abovementioned solutions. As formalin is not just
toxic but also forms volatiles, its use should be limited to the
preparation of primary slurries, where it is necessary to polymerize
and thereby stabilize the cell walls. For all further steps where the
10 Michael Lappé and Jens Kallmeyer
3 Methods
Fig. 2 The flow chart shows the complete hydrocarbon and cell extraction procedure for oily sediments. The
method is based on the cell extraction procedure of Kallmeyer et al. [3]. The hydrocarbon extraction step is
shaded. Details about incubation times and amounts of reagents are provided in the text. Figure was originally
published in Lappé and Kallmeyer [4]
12 Michael Lappé and Jens Kallmeyer
3.1 Sample Fixation 1. The primary sediment slurry is prepared by suspending a sedi-
and Slurry Preparation ment sample in a fixative solution containing 2 vol.% formalin
at the same samples’ salinity. For marine and most terrestrial
samples, 2.5% (w/v) sodium chloride solution and 1 PBS
solution are used, respectively. Ratios between sediment and
fixative solution vary widely between different users. We rec-
ommend using slurries with a 1:5 (v:v) sediment to fixative
ratio. All reagent concentrations are given for 100 μL of a slurry
with a 1:5 ratio.
2. The sample is thoroughly shaken to form a homogenous slurry.
3.3 Carbonate Calcium interferes with the dissolution of the extracellular poly-
Dissolution mers that bind the cells to the mineral grains. Carbonate minerals
are the main source of calcium and therefore have to be dissolved
prior to cell detachment.
1. Slurry and CDM are mixed in a 1:5 ratio, so for 100 μL of
slurry, 500 μL of CDM is added.
2. The mixture is slowly shaken for 20 min. During shaking the
vials should be left open to allow the CO2 produced by the
carbonate dissolution to escape.
3. The sample is centrifuged at 3,000g, and the supernatant
carefully taken off and kept for further analysis.
Cell Extraction from Oily Sediments 13
3.4 First Cell After extraction of hydrocarbons and dissolution of carbonates, the
Extraction cells can be extracted from the sediment.
1. The remaining pellet is suspended with 350 μL of either TE
buffer for terrestrial samples or with NaCl/NaN3 solution for
marine samples.
2. 50 μL each of DM and methanol (MeOH) are added.
3. The mixture of slurry, NaCl/NaN3 or TE buffer, DM and
MeOH is vortexed at maximum speed for 30 min.
4. A cushion of 500 μL 50% (wt/vol) Nycodenz is injected into
the bottom of the vial according to Kallmeyer et al. [3].
5. The mixture is centrifuged at 2,000g for 15 min in a swing-
out rotor. The cells are separated from the sediment particles by
density centrifugation.
6. The supernatant containing the detached cells and most of the
Nycodenz is carefully siphoned off using a syringe with a small
needle and stored in a separate vial.
3.6 Filter Preparation For cell counting, the supernatants are filtered onto 0.2 μm poly-
and Cell Counting carbonate filters (Whatman Cyclopore track-etched membrane)
[8, 9].
1. To ensure an even distribution of the cells on the filter, 5 mL of
0.2 μm filtered TE buffer or NaCl/NaN3 should be placed into
the filter tower prior to the addition of supernatant.
14 Michael Lappé and Jens Kallmeyer
2. After the supernatants have passed through the filters, they are
rinsed inside the filter towers with a few mL of TE buffer to
remove any remaining HF.
3. Staining and embedding of the cells is carried out according to
Morono et al. [10]. About 20 μL of the SYBR-I staining
solution is placed on a microscope glass slide, and then the
filter is placed on top of the droplet. A second 20 μL droplet of
SYBR-I staining solution is placed on the side of a cover slip,
which is carefully placed on top of the filter. Any air bubbles
trapped under the cover slip can then carefully be squeezed.
After about 10 min of incubation at room temperature in the
dark, the filter is ready for microscopic analysis. For longer
storage, the filter should be stored frozen in the dark until
use. Counting can be performed using a fluorescence micro-
scope. Our setup consists of a Leica DM2500 microscope, light
source Leica EL 6000, filter set L5 (excitation filter BP 480/
40, dichromatic mirror 505, suppression filter 527/30), 100x
objective.
4 Notes
4.1 Blank Samples Blank samples should be processed with each batch of samples to
check for possible contamination during processing. Instead of an
actual sediment sample, precombusted (5 h at 450 C) sediment
that is resuspended in 0.2 μm filtered saline solution is used and
processed like a normal sample.
4.2 Sample Fixation 1. It is of great importance to choose the salinity similar to the
and Slurry Preparation environment of the sample. Otherwise, cells might shrink or
inflate, due to osmotic stress. In the worst case, cells lyse and
cannot be counted.
4.5 Filter Preparation The supernatants from both density separation steps and the car-
and Cell Counting bonate dissolution step are pooled and can be used for cell counting
or other applications. In some cases the pooling of the supernatants
caused precipitation of minerals. In such cases the supernatants
from the carbonate dissolution step and the actual cell detachment
have to be kept separate and filtered consecutively onto the
membrane.
3. All handling of SYBR Green I should be carried out under
dimmed light, as the stain is highly sensitive to sunlight. Direct
sunlight has to be strictly avoided. Filters should be stored
frozen until immediately prior to analysis.
References
1. Edgcomb VP, Kysela DT, Teske A, Gomez AD, to deep subsurface sediments. Limnol Ocea-
Sogin ML (2002) Benthic eukaryotic diversity nogr Method 6:236–245
in the Guaymas Basin hydrothermal vent envi- 4. Lappé M, Kallmeyer J (2011) A cell extraction
ronment. Proc Natl Acad Sci U S A 99 method for oily sediments. Frontiers in Micro-
(11):7658–7662. doi:10.1073/Pnas. biology 2:233. doi:10.3389/fmicb.2011.
062186399 00233
2. Cragg BA, Parkes RJ, Fry JC, Herbert RA, 5. Fry JC (1988) Determination of biomass. In:
Wimpenny JWT, Getliff JM (1990) Bacterial Austin B (ed) Methods in aquatic bacteriology.
biomass and activity profiles within deep sedi- Wiley, Chichester, pp 27–72
ment layers. Proc Ocean Drill Prog Sci Res 6. Kallmeyer J (2011) Detection and quantifica-
112:607–619 tion of microbial cells in subsurface sediments.
3. Kallmeyer J, Smith DC, Spivack AJ, D’Hondt S Adv Appl Microbiol 76:79–103. doi:10.1016/
(2008) New cell extraction procedure applied B978-0-12-387048-3.00003-9
16 Michael Lappé and Jens Kallmeyer
Abstract
The number of hydrocarbon-degrading microorganisms in environmental samples or liquid cultures can be
determined by the most probable number (MPN) methods. These procedures are based on serial dilution
of the sample and subsequent determination of the presence or absence of degrader cells for several
subsamples of each dilution. The 96-well format of the microplate is very suitable for such replicate
detection of growth of hydrocarbon degraders. Growth-positive wells can be distinguished from growth-
negative wells by several means, for instance, by increased optical density, by emulsification of a crude oil
film, by the metabolic conversion of colorless tetrazolium compounds into the corresponding colored
formazans, or by mineralization of 14C-labeled substrates. Detailed instructions are given for (1) the
preparation of dilution series; (2) MPN enumeration of total oil degraders, alkane degraders, monoaro-
matic hydrocarbon degraders, and diaromatic hydrocarbon degraders; (3) MPN enumeration of polycyclic
aromatic hydrocarbon (PAH) degraders; (4) a radiotracer MPN method based on the conversion of 14C-
labeled substrate into 14CO2 which is quantified by autoradiography and digital image analysis; and (5) how
to interpret results and calculate MPNs.
1 Introduction
The most probable number (MPN) methods are used for deter-
mining the number of specific types of microorganisms in environ-
mental samples or liquid cultures. Most MPN methods are based
on growth in liquid medium under selective conditions that only
allow growth of the specific target organisms; this is conveniently
done in 96-well microplates. Hydrocarbon degraders are generally
MPN enumerated in minimal medium containing one or more
hydrocarbons. Cells that can use the hydrocarbons as the sole
source of carbon and energy will proliferate, whereas non-
degraders will starve and become metabolically inactive. It is there-
fore important to use very clean glassware so the medium is not
contaminated with non-hydrocarbon substrate.
T.J. McGenity et al. (eds.), Hydrocarbon and Lipid Microbiology Protocols, Springer Protocols Handbooks, (2017) 17–33,
DOI 10.1007/8623_2014_28, © Springer-Verlag Berlin Heidelberg 2014, Published online: 30 December 2014
17
18 Anders R. Johnsen
The material used for dilution series can be soil, sediment, or water
samples, liquid enrichments, or liquid pure cultures. The samples
are serially diluted in half-strength Bushnell-Haas Broth [12] which
has the following composition (per liter): MgSO4, 0.10 g; CaCl2,
0.01 g; KH2PO4, 0.5 g; (NH4) 2HPO4, 0.5 g; KNO3, 0.5 g; and
FeCl3, 0.025 g. Premixed Bushnell-Haas Broth can be obtained
from Difco. When enumerating marine hydrocarbon degraders, the
Bushnell-Haas Broth is often supplemented with 20 g L1 of NaCl.
The pH of the medium is in the following protocol lowered from
the usual 7.2 to 6.8 because 14CO2-release from the medium is very
pH sensitive.
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