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Environmental Proteomics: Studying Structure and Function of Microbial Communities

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Geomicrobiology: Molecular and Environmental Perspective

Abstract

Microbes such as bacteria, fungi and viruses are omnipresent. They play an essential role in biogeochemical cycles and can decompose virtually all natural compounds, thereby exerting a lasting effect on biosphere and climate. About 20 years ago microbial ecologists started to realize that activity and physiology of a certain environment is strongly dependent on the diversity of microbial communities and interactive processes such as nutrient competition, predation and cellular signalling (Brock 1987). However, the fact that more than 90% of the microorganisms in a given environment are un-cultivable (Amann et al. 1995) hampered investigations aiming towards a deeper insight into the structure and function of biological systems for a long time and individual contributions of different species to a certain environment remained largely unknown.

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References

  • Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207

    Article  PubMed  CAS  Google Scholar 

  • Ahmadian A, Ehn M, Hober S (2006) Pyrosequencing: history, biochemistry and future. Clin Chim Acta 363:83–94

    Article  PubMed  CAS  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. FEMS Microbiol Rev 59:143–169

    CAS  Google Scholar 

  • Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 389:1017–1031

    Article  PubMed  CAS  Google Scholar 

  • Benndorf D, Balcke GU, Harms H, von Bergen M (2007) Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 1:224–234

    Article  PubMed  CAS  Google Scholar 

  • Benndorf D, Vogt C, Jehmlich N, Schmidt Y, Thomas H, Woffendin G, Shevchenko A, Richnow HH, Von Bergen M (2009) Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegration 2009 Apr 21, Epub ahead of print

    Google Scholar 

  • Bochner BR (2009) Global phenotypic characterization of bacteria. FEMS Microbiol Rev 33:191–205

    Article  PubMed  CAS  Google Scholar 

  • Brock TD (1987) The study of microorganisms in situ: progress and problems. Symp Soc Gen Microbiol 41:1–17

    Google Scholar 

  • Choi H, Fermin D, Nesvizhskii AI (2008) Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics 7:2373–2385

    Article  PubMed  CAS  Google Scholar 

  • Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20:1466–1467

    Article  PubMed  CAS  Google Scholar 

  • Denef VJ, Verberkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF (2009) Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol 11:313–325

    Article  PubMed  CAS  Google Scholar 

  • Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312:212–217

    Article  PubMed  CAS  Google Scholar 

  • Eng JK, McCormack AL, Yates JR III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989

    Article  CAS  Google Scholar 

  • García Martín H, Ivanova N, Kunin V et al (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24:1263–1269

    Article  PubMed  Google Scholar 

  • Gilchrist A, Au CE, Hiding J et al (2006) Quantitative proteomics analysis of the secretory pathway. Cell 127:1265–1281

    Article  PubMed  CAS  Google Scholar 

  • Görg A, Postel W, Gunther S (1988) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9:531–546

    Article  PubMed  Google Scholar 

  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999

    Article  PubMed  CAS  Google Scholar 

  • Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham Cooks R (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40:430–443

    Article  PubMed  CAS  Google Scholar 

  • Hunt DF, Yates JR 3rd, Shabanowitz J, Winston S, Hauer CR (1986) Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci USA 83:6233–6237

    Article  PubMed  CAS  Google Scholar 

  • Kan J, Hanson TE, Ginter JM, Wang K, Chen F (2005) Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Syst 1:7–20

    Article  PubMed  Google Scholar 

  • Keller M, Hettich R (2009) Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73:62–70

    Article  PubMed  CAS  Google Scholar 

  • Klaassens ES, de Vos WM, Vaughan EE (2007) Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol 73:1388–1392

    Article  PubMed  CAS  Google Scholar 

  • Lacerda CM, Choe LH, Reardon KF (2007) Metaproteomic analysis of a bacterial community response to cadmium exposure. J Proteome Res 6:1145–52

    Article  PubMed  CAS  Google Scholar 

  • Lane CS (2005) Mass spectrometry-based proteomics in the life sciences. Cell Mol Life Sci 62:848–869

    Article  PubMed  CAS  Google Scholar 

  • Lo I, Denef VJ, Verberkmoes NC et al (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446:537–541

    Article  PubMed  CAS  Google Scholar 

  • Markert S, Arndt C, Felbeck H et al (2007) Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 315:247–250

    Article  PubMed  CAS  Google Scholar 

  • Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486–493

    Article  PubMed  CAS  Google Scholar 

  • Marshall AG, Hendrickson CL, Jackson GS (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev 17:1–35

    Article  PubMed  CAS  Google Scholar 

  • Motoyama A, John R, Yates JR III (2008) Multidimensional LC separations in shotgun proteomics. Anal Chem 80:7187–7193

    Article  PubMed  CAS  Google Scholar 

  • Nesvizhskii AI, Vitek O, Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4:787–797

    Article  PubMed  CAS  Google Scholar 

  • O-Farrel PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021

    Google Scholar 

  • Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, Yamada T (2006) Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics 5:1338–1347

    Article  PubMed  CAS  Google Scholar 

  • Panchaud A, Hansson J, Affolter M, Bel Rhlid R, Piu S, Moreillon P, Kussmann M (2008) ANIBAL, stable isotope-based quantitative proteomics by aniline and benzoic acid labeling of amino and carboxylic groups. Mol Cell Proteomics 7:800–812

    PubMed  CAS  Google Scholar 

  • Park C, Helm RF, Novak JT (2008) Investigating the fate of activated sludge extracellular proteins in sludge digestion using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Water Environ Res 80:2219–2227

    Article  PubMed  CAS  Google Scholar 

  • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–67

    Article  PubMed  CAS  Google Scholar 

  • Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915–1920

    Article  PubMed  CAS  Google Scholar 

  • Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H (2008) Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol 10:727–737

    Article  PubMed  CAS  Google Scholar 

  • Ross PL, Huang YN, Marchese JN et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154–1169

    Article  PubMed  CAS  Google Scholar 

  • Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2:e92

    Article  PubMed  Google Scholar 

  • Schneider T, Riedel K (2009) Environmental proteomics: Analysis of structure and function of microbial communities. Proteomics 10:785–798

    Article  Google Scholar 

  • Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2005) A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142:335–343

    Article  PubMed  Google Scholar 

  • Singleton I, Merrington G, Colvan S, Delahunty JS (2003) The potential of soil protein-based methods to indicate metal contamination. Appl Soil Ecol 23:25–32

    Article  Google Scholar 

  • Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, Carlson CA, Smith RD, Giovanonni SJ (2009) Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 3:93–105

    Article  PubMed  CAS  Google Scholar 

  • Toyoda A, Iio W, Mitsumori M, Minato H (2009) Isolation and identification of cellulose-binding proteins from sheep rumen contents. Appl Environ Microbiol 75:1667–1673

    Article  PubMed  CAS  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A et al (2005) Comparative metagenomics of microbial communities. Science 308:554–557

    Article  PubMed  CAS  Google Scholar 

  • Unlü M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18:2071–2077

    Article  PubMed  Google Scholar 

  • Verberkmoes NC, Denef VJ, Hettich RL, Banfield JF (2009a) Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 7:196–205

    Article  PubMed  CAS  Google Scholar 

  • Verberkmoes NC, Russell AL, Shah M et al (2009b) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3:179–189

    Article  PubMed  CAS  Google Scholar 

  • Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M (2009) Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 33:236–255

    Article  PubMed  CAS  Google Scholar 

  • Warnecke F, Luginbühl P, Ivanova N et al (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565

    Article  PubMed  CAS  Google Scholar 

  • Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL (1995) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50

    Google Scholar 

  • Wilmes P, Bond PL (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol 6:911–920

    Article  PubMed  CAS  Google Scholar 

  • Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 4:92–97

    Article  Google Scholar 

  • Wilmes P, Bond PL (2009) Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth’s biogeochemical cycles. Curr Opin Microbiol May 2, 2009. Epub ahead of print

    Google Scholar 

  • Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC, Banfield JF (2008a) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J 2:853–864

    Article  PubMed  CAS  Google Scholar 

  • Wilmes P, Wexler M, Bond PL (2008b) Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE 3:e1778

    Article  PubMed  Google Scholar 

  • Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207

    Article  PubMed  CAS  Google Scholar 

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Acknowledgement

The authors would like to thank Alexander Grunau for critically reading the manuscript.

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Authors and Affiliations

  1. Department of Microbiology, Institute of Plant Biology, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland

    Thomas Schneider & Kathrin Riedel

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  1. Thomas Schneider
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  2. Kathrin Riedel
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Correspondence to Kathrin Riedel .

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Editors and Affiliations

  1. Dept. Biology, University of New Mexico, Castetter Hall 167, Albuquerque, 87131-0001, USA

    Larry L. Barton

  2. , Faculty of Science, Dept. of Biochmistry, Masaryk University, Kortlarska 2, Brno, 611 37, Czech Republic

    Martin Mandl

  3. , Department of Microbial Ecology, Fac. of, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria

    Alexander Loy

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Schneider, T., Riedel, K. (2010). Environmental Proteomics: Studying Structure and Function of Microbial Communities. In: Barton, L., Mandl, M., Loy, A. (eds) Geomicrobiology: Molecular and Environmental Perspective. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9204-5_4

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