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14 - Lipid Biomarkers in Geomicrobiology: Analytical Techniques and Applications

from Part V - Microbiological Techniques

Published online by Cambridge University Press:  06 July 2019

By
Jiasong Fang ,
Shamik Dasgupta ,
Li Zhang  and
Weiqiang Zhao
Edited by
Janice P. L. Kenney ,
Harish Veeramani  and
Daniel S. Alessi
Janice P. L. Kenney
Affiliation:
MacEwan University, Edmonton
Harish Veeramani
Affiliation:
Carleton University, Ottawa
Daniel S. Alessi
Affiliation:
University of Alberta
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Summary

Lipid biomarker analysis is a useful tool for characterizing microbial communities in geomicrobiology. Phospholipid fatty acids (PLFA) are major components of microbial membranes, and analysis of these markers provides insight into microbial biomass, community structure, and metabolic processes. This article reviews the methods for extraction, fractionation, derivatization, and quantification of PLFA, as well as the interpretation of PLFA patterns for microbial community analysis in natural environmental systems. The discussion centers on the development, the subsequent modifications, and the advantages and limitations of the methods. Two case studies are given to illustrate the applications of intact phospholipid profiling (IPP) and PLFA in geomicrobiology. The recent developments and future directions of microbial signature lipid analysis are also discussed.

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Type
Chapter
Information
Analytical Geomicrobiology
A Handbook of Instrumental Techniques
 , pp. 341 - 359
Publisher: Cambridge University Press
Print publication year: 2019

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References

14.6 References

Allwood, J.W., AlRabiah, H., Correa, E., et al., 2015. A workflow for bacterial metabolic fingerprinting and lipid profiling: application to Ciprofloxacin challenged. Escherichia coli. Metabolomics 11(2), 438–453.CrossRefGoogle Scholar
Bligh, E.G. and Dyer, W.J., 1959. A rapid method of total lipid extraction and purification. Canadian Journal of Biochemistry and Physiology 37(8), 911–917.CrossRefGoogle ScholarPubMed
Brake, J.M., Daschner, M.K. and Abbott, N.L., 2005. Formation and characterization of phospholipid monolayers spontaneously assembled at interfaces between aqueous phases and thermotropic liquid crystals. Langmuir 21(6), 2218–2228.Google Scholar
Brake, S.S. and Hasiotis, S.T., 2008. Eukaryote-dominated biofilms in extreme environments: overlooked sources of information in the geologic record. Palaios 23(3), 121–123.Google Scholar
Brake, S.S. and Hasiotis, S.T., 2010. Eukaryote-dominated biofilms and their significance in acidic environments. Geomicrobiology Journal 27(6–7), 534–558.CrossRefGoogle Scholar
Brake, S.S., Hasiotis, S.T., Dannelly, H.K. and Connors, K.A., 2002. Eukaryotic stromatolite builders in acid mine drainage: implications for Precambrian iron formations and oxygenation of the atmosphere? Geology 30, 599–602.Google Scholar
Brondz, I., 2002. Development of fatty acid analysis by high-performance liquid chromatography, gas chromatography, and related techniques. Analytica Chimica Acta 465(1), 1–37.CrossRefGoogle Scholar
Canfield, D.E., 2005. The early history of atmospheric oxygen: homage to Robert M. Garrels. Annual Review of Earth and Planetary Science 33, 1–36.Google Scholar
Carvalho, A.P. and Malcata, F.X., 2005. Preparation of fatty acid methyl esters for gas-chromatographic analysis of marine lipids: insight studies. Journal of Agricultural and Food Chemistry 53(13), 5049–5059.Google Scholar
Cavigelli, M.A., Robertson, G.P. and Klug, M.J., 1995. Fatty acid methyl ester (FAME) profiles as measures of soil microbial community structure. Plant and Soil 170, 99–113.CrossRefGoogle Scholar
Ciobanu, D.A., Zawierucha, K., Moglan, I. and Kaczmarek, Ł., 2014. Milnesium berladnicorum sp. (Eutardigrada, Apochela, Milnesiidae), a new species of water bear from Romania. ZooKeys (429), 1.CrossRefGoogle Scholar
Dasgupta, S., Fang, J., Brake, S.S., Hasiotis, S.T. and Zhang, L., 2012. Biosynthesis of sterols and wax esters by Euglena of acid mine drainage biofilms: implications for eukaryotic evolution and the early Earth. Chemical Geology 306, 139–145.Google Scholar
Dasgupta, S., Fang, J., Brake, S.S., Hasiotis, S.T. and Zhang, L., 2013. Stable carbon isotopic composition of lipids in Euglena-dominated biofilms from an acid mine drainage site: implications of carbon limitation, microbial physiology, and biosynthetic pathways. Chemical Geology 354, 15–21.Google Scholar
Disch, A., Schwender, J., Muller, C., Lichtenthaler, H.K. and Rohmer, M., 1998. Distribution of the mevalonate and glyceraldehyde phosphate/pyruvate pathways for isoprenoid biosynthesis in unicellular algae and the cyanobacterium Synechocystis PCC 6714. Biochemical Journal 333(2), 381–388.Google Scholar
Dowling, N.J.E., Widdel, F. and White, D.C., 1986. Phospholipid ester-linked fatty acid biomarkers of acetate-oxidizing sulfate-reducers and other sulfide-forming bacteria. Journal of General Microbiology 132, 1815–1825.Google Scholar
Dunkleblum, E.S., Tan, E. and Silo, P.J., 1985. Double-bond location in monounsaturated fatty acids by dimethyl disulfide derivatization and mass spectrometry: application to analysis of fatty acids in pheromone glands of four lepidoptera. Journal of Chemical Ecology 11, 265–277.Google Scholar
Edlund, A., Nichols, P.D., Roffey, R. and White, D.C., 1985. Extractable and lipopolysaccharide fatty acid and hydroxy fatty acid profiles from Desulfovibrio species. Journal of Lipid Research 26(8), 982–988.Google Scholar
Fang, J. and Barcelona, M.J., 1998. Structural determination and quantitative analysis of bacterial phospholipids using liquid chromatography/electrospray ionization/mass spectrometry. Journal of Microbiological Methods 33(1), 23–35.Google Scholar
Fang, J., Barcelona, M.J., Nogi, Y. and Kato, C., 2000a. Biochemical function and geochemical significance of novel phospholipids of the extremely barophilic bacteria from the Mariana Trench at 11,000 meters. Deep-Sea Research Part I Oceanographic Research Papers 147, 1173–1182.Google Scholar
Fang, J., Barcelona, M.J. and Semrau, J.D., 2000b. Characterization of methanotrophic bacteria on the basis of intact phospholipid profiles. FEMS Microbiology Letters 189(1), 67–72.Google Scholar
Fang, J., Chan, O., Kato, C., et al., 2003. Phospholipid fatty acid profiles of piezophilic bacteria from the deep sea. Lipids 38, 885–887.Google Scholar
Fang, J. and Findlay, R.H., 1996. The use of a classic lipid extraction method for simultaneous recovery of organic pollutants and microbial lipids from sediments. Journal of Microbiological Methods 27(1), 63–71.Google Scholar
Fang, J., Hasiotis, S.T., Das Gupta, S., Brake, S.S. and Bazylinski, D.A., 2007. Microbial biomass and community structure of a stromatolite from an acid mine drainage system as determined by lipid analysis. Chemical Geology 243, 191–204.Google Scholar
Fang, J., Uhle, M., Billmark, K., Bartlett, D.H. and Kato, C., 2006. Fractionation of carbon isotopes in biosynthesis of fatty acids by a piezophilic bacterium Moritella japonica strain DSK1. Geochimica et Cosmochimica Acta 70(7), 1753–1760.Google Scholar
Fang, J., Zhang, L. and Bazylinski, D.A., 2010. Deep-sea piezosphere and piezophiles: geomicrobiology and biogeochemistry. Trends in Microbiology 18(9), 413–422.CrossRefGoogle ScholarPubMed
Findlay, R.H., King, G.M. and Watling, L., 1989. Efficacy of phospholipid analysis in determining microbial biomass in sediments. Applied and Environmental Microbiology 55(11), 2888–2893.Google Scholar
Findlay, R.H. and Watling, L., 1998. Seasonal variation in the structure of a marine benthic microbial community. Microbial Ecology 36(1), 23–30.Google Scholar
Folch, J., Lees, M. and Sloane-Stanley, G.H., 1957. A simple method for the isolation and purification of total lipids from animal tissues. Journal of Biological Chemistry 226(1), 497–509.Google Scholar
Frostegård, Å., Tunlid, A. and Bååth, E., 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Applied and Environmental Microbiology 59(11), 3605–3617.Google Scholar
Ginger, M.L., McFadden, G.I. and Michels, P.A., 2010. Rewiring and regulation of cross-compartmentalized metabolism in protists. Philosophical Transactions of the Royal Society of London B: Biological Sciences 365(1541), 831–845.Google Scholar
Haack, S.K., Garchow, H., Odelson, D.A., Forney, L.J. and Klug, M.J., 1994. Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities. Applied and Environmental Microbiology 60(7), 2483–2493.Google Scholar
Han, X. and Gross, R.W., 2003. Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics. Journal of Lipid Research 44(6), 1071–1079.CrossRefGoogle ScholarPubMed
Heipieper, H.J., Meinhardt, F. and Segura, A., 2003. The cis–trans isomerase of unsaturated fatty acids in Pseudomonas and Vibrio: biochemistry, molecular biology and physiological function of a unique stress adaptive mechanism. FEMS Microbiology Letters 229(1), 1–7.Google Scholar
Heller, D.N., Cotter, R.J., Fenselau, C. and Uy, O.M., 1987. Profiling of bacteria by fast atom bombardment mass spectrometry. Analytical Chemistry 59(23), 2806–2809.Google Scholar
Kelly, J.J., Häggblom, M. and Tate, R.L., 1999. Changes in soil microbial communities over time resulting from one time application of zinc: a laboratory microcosm study. Soil Biology and Biochemistry 31(10), 1455–1465.CrossRefGoogle Scholar
Kieft, T.L., Ringelberg, D.B. and White, D.C., 1994. Changes in ester-linked phospholipid fatty acid profiles of sub-surface bacteria during starvation and desiccation in a porous-medium. Applied Environmental Microbiology 60, 3292–3299.Google Scholar
Lanni, E.J., Masyuko, R.N., Driscoll, C.M., et al., 2014. MALDI-guided SIMS: multiscale imaging of metabolites in bacterial biofilms. Analytical Chemistry 86, 9139–9145.Google Scholar
Li, M., Yang, L., Bai, Y. and Liu, H., 2013. Analytical methods in lipidomics and their applications. Analytical Chemistry 86(1), 161–175.Google Scholar
Liu, K.S., 1994. Preparation of fatty acid methyl esters for gas-chromatographic analysis of lipids in biological materials. Journal of the American Oil Chemists’ Society 71(11), 1179–1187.Google Scholar
Matyash, V., Liebisch, G., Kurzchalia, T.V., Shevchenko, A., and Schwudke, D., 2008. Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. Journal of Lipid Research 49, 1137–1146.Google Scholar
Murphy, R.C. and Harrison, K.A., 1994. Fast atom bombardment mass spectrometry of phospholipids. Mass Spectrometry Reviews 13, 57–75.CrossRefGoogle Scholar
Nguyen, J. and Russell, S.C., 2010. Targeted proteomics approach to species-level identification of Bacillus thuringiensis spores by AP-MALDI-MS. Journal of American Society of Mass Spectrometry 21, 993–1001.CrossRefGoogle ScholarPubMed
Nichols, P.D., Mancuso, C.A. and White, D.C., 1987. Measurement of methanotroph and methanogen signature phospholipids for use in assessment of biomass and community structure in model systems. Organic Geochemistry 11(6), 451–461.Google Scholar
O’Leary, W.M. 1962. The fatty acids of bacteria. Bacteriological Reviews 26, 421–447.Google Scholar
Peters, K.E., Walters, C.C. and Moldowan, J.M., 2005. The Biomarker Guide (Vol. 1). Cambridge University Press, Cambridge, 249–250.Google Scholar
Ramos, J.L., Duque, E., Gallegos, M.T., et al., 2002. Mechanisms of solvent tolerance in gram‐negative bacteria. Annual Review of Microbiology 56, 743–768.CrossRefGoogle ScholarPubMed
Rath, C.M., Yang, J.Y., Alexandrov, T., and Dorrestein, P.C., 2013. Data-independent microbial metabolomics with ambient ionization mass spectrometry. Journal of American Society of Mass Spectrometry 24, 1167–1176.Google Scholar
Sandrin, T.R. and Demirev, P.A., 2017. Characterization of microbial mixtures by mass spectrometry. Mass Spectrometry Reviews 9999, 1–29.Google Scholar
Schloss, P.D. and Handelsman, J., 2004. Status of the microbial census. Microbiology and Molecular Biology Reviews 68(4), 686–691.Google Scholar
Smith, G.A., Nichols, P.D. and White, D.C., 1986. Fatty acid composition and microbial activity of benthic marine sediment from McMurdo Sound, Antarctica. FEMS Microbiology Ecology 2(4), 219–231.Google Scholar
Spener, F., Lagarde, M., Géloên, A. and Record, M., 2003. Editorial: What is lipidomics? European Journal of Lipid Science and Technology 105, 481–482.Google Scholar
Summons, R.E., Bradley, A.S., Jahnke, L.L. and Waldbauer, J.R., 2006. Steroids, triterpenoids and molecular oxygen. Philosophical Transactions of the Royal Society B: Biological Sciences 361(1470), 951–968.Google Scholar
Tunlid, A. and White, C., 1992. Biochemical analysis of biomass, community structure, nutritional status, and metabolic activity of microbial communities in soil. In Bollag, J.M. and Stotzky, G. (Eds) Soil Biochemistry, Marcel Dekker, 229–262.Google Scholar
Vestal, J.R. and White, D.C., 1989. Lipid analysis in microbial ecology. Bioscience 39(8), 535–541.Google Scholar
White, D.C., 1986. Environmental effects testing with quantitative microbial analysis: Chemical signatures correlated with in situ biofilm analysis by FT/IR. Environmental Toxicology 1(3), 315–338.Google Scholar
White, D.C., 1988. Validation of quantitative analysis for microbial biomass, community structure, and metabolic activity. Advances in Limnology 31(1), 1–18.Google Scholar
White, D.C., Davis, W.M., Nickels, J.S., King, J.D. and Bobbie, R.J., 1979. Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia 40(1), 51–62.Google Scholar
White, D.C. and Frerman, F.E., 1967. Extraction, characterization, and cellular localization of the lipids of Staphylococcus aureus. Journal of Bacteriology 94(6), 1854–1867.Google Scholar
White, D.C., Meadows, P., Eglinton, G., et al., 1993. In situ measurement of microbial biomass. Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences 344, 59–67.Google Scholar
White, D.C., Pinkart, H.C. and Ringelberg, A.B., 1997. Biomass measurements: biochemical approaches. In Hurst, C.J., Knudson, G.R., McInerney, M.J., Stetzenbach, L.D., Walter, M.V. (Eds) Manual of Environmental Microbiology. DC: ASM Press, 91–101.Google Scholar
White, D.C. and Ringelberg, D.B., 1997. Utility of the signature lipid biomarker analysis in determining the in situ viable biomass, community structure, and nutritional/physiologic status of deep subsurface microbiota. In Amy, PS and Haldeman, DL (Eds) The Microbiology of the Terrestrial Deep Subsurface. New York: Elsevier Science Ltd; CRC, 119–136.Google Scholar
Zelles, L. (1997) Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 35, 275–294.Google Scholar
Zhang, J.I., Costa, A.B., Tao, W.A. and Cooks, R.G., 2011b. Direct detection of fatty acid ethyl esters using low temperature plasma (LTP) ambient ionization mass spectrometry for rapid bacterial differentiation. Analyst 139, 3091–3097.CrossRefGoogle Scholar
Zhang, J.I., Talaty, N., Costa, A.B., et al., 2011a. Rapid direct lipid profiling of bacteria using desorption electroscopy ionization mass spectrometry. International Journal of Mass Spectrometry 301, 37–44.CrossRefGoogle Scholar

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