Microbial Ecology

, Volume 53, Issue 3, pp 486–493 | Cite as

Metaproteomics: A New Approach for Studying Functional Microbial Ecology

  • Pierre-Alain Maron
  • Lionel Ranjard
  • Christophe Mougel
  • Philippe LemanceauEmail author


In the postgenomic era, there is a clear recognition of the limitations of nucleic acid-based methods for getting information on functions expressed by microbial communities in situ. In this context, the large-scale study of proteins expressed by indigenous microbial communities (metaproteome) should provide information to gain insights into the functioning of the microbial component in ecosystems. Characterization of the metaproteome is expected to provide data linking genetic and functional diversity of microbial communities. Studies on the metaproteome together with those on the metagenome and the metatranscriptome will contribute to progress in our knowledge of microbial communities and their contribution in ecosystem functioning. Effectiveness of the metaproteomic approach will be improved as increasing metagenomic information is made available thanks to the environmental sequencing projects currently running. More specifically, analysis of metaproteome in contrasted environmental situations should allow (1) tracking new functional genes and metabolic pathways and (2) identifying proteins preferentially associated with specific stresses. These proteins considered as functional bioindicators should contribute, in the future, to help policy makers in defining strategies for sustainable management of our environment.


Microbial Community Activate Sludge Environmental Matrix Protein Pool Indigenous Microbial Community 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors are grateful to K. Klein for helpful comments and correcting the English text.


  1. 1.
    Amann, RI, Ludwig, W, Schleifer, KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. FEMS Microbiol Rev 59: 143–169Google Scholar
  2. 2.
    Anderson, LB, Maderia, M, Ouellette, AJA, Putman-Evans, C, Higgins, L, Krick, T, MacCoss, MJ, Lim, H, Yates, JR III, Barry, BA (2002) Post translational modifications in the CP43 subunit of photosystem II. Proc Natl Acad Sci USA 23: 14676–14681CrossRefGoogle Scholar
  3. 3.
    Bakken, LR (1985) Separation and purification of bacteria from soil. Appl Environ Microbiol 49: 1482–1487PubMedGoogle Scholar
  4. 4.
    Borneman, J (1999) Culture-independent identification of microorganisms that respond to specified stimuli. Appl Environ Microbiol 65: 3398–3400PubMedGoogle Scholar
  5. 5.
    Brock, TD (1987) The study of microorganisms in situ: progress and problems. Symp Soc Gen Microbiol 41: 1–17Google Scholar
  6. 6.
    Cash, P, Argo, E, Ford, L, Lawrie, L, McKenzie, H (1999) A proteomic analysis of erythromycin resistance in Streptococcus pneumoniae. Electrophoresis 20: 2259–2268PubMedCrossRefGoogle Scholar
  7. 7.
    Courtois, S, Frostegård, Å, Göransson, P, Depret, G, Jeannin, P, Simonet, P (2001) Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ Microbiol 3: 431–439PubMedCrossRefGoogle Scholar
  8. 8.
    DeLong, EF (2004) Microbial population genomics and ecology: the road ahead. Environ Microbiol 6: 875–878PubMedCrossRefGoogle Scholar
  9. 9.
    Ehler, MM, Cloete, TE (1999) Comparing the protein profiles of 21 different activated sludge systems after SDS-PAGE. Wat Res 33: 1181–1186CrossRefGoogle Scholar
  10. 10.
    Espina, V, Woodhouse, EC, Wulkuhle, J, Asmussen, HD, Petricoin, EF III, Liotta, LA (2004) Protein microarray detection strategies: focus on direct detection technologies. J Immunol Methods 290: 121–133PubMedCrossRefGoogle Scholar
  11. 11.
    Figeys, D (2000) The Achilles’ heel of proteomics. Trends Biotechnol 18: 483PubMedCrossRefGoogle Scholar
  12. 12.
    Goodacre, R, Vaidyanathan, S, Dunn, WB, Harrigan, GG, Kell, DB (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22: 245–252PubMedCrossRefGoogle Scholar
  13. 13.
    Goodlett, DR, Yi, EC (2003) Stable isotopic labeling and mass spectrometry as a means to determine differences in protein expression. Trends Anal Chem 22: 282–290CrossRefGoogle Scholar
  14. 14.
    Guerreiro, N, Djordjevic, MA, Rolfe, BG (1999) Proteome analysis of the model microsymbiont Sinorhizobium meliloti: isolation and characterisation of novel proteins. Electrophoresis 20: 818–825PubMedCrossRefGoogle Scholar
  15. 15.
    Gygi, SP, Corthals, GL, Zhang, Y, Rochon, Y, Aebersol, R (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 97: 9390–9395PubMedCrossRefGoogle Scholar
  16. 16.
    Heim, S, Ferrer, M, Heuer, H, Regenhardt, D, Nimtz, M, Timmis, KN (2003) Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase. Environ Microbiol 5: 1257–1269PubMedCrossRefGoogle Scholar
  17. 17.
    Hurt, RA, Qiu, X, Wu, L, Roh, Y, Palumbo, AV, Tiedje, JM, Zhou, J (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67: 4495–4503PubMedCrossRefGoogle Scholar
  18. 18.
    Kan, J, Hanson, TE, Ginter, JM, Wang, K, Chen, F (2005) Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Systems 1: 7PubMedCrossRefGoogle Scholar
  19. 19.
    Lee, KH (2001) Proteomics: a technology-driven and technology-limited discovery science. Trends Biotechnol 19: 217–222PubMedCrossRefGoogle Scholar
  20. 20.
    Liesack, W, Stackebrandt, E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174: 5072–5078PubMedGoogle Scholar
  21. 21.
    Manchenko, GP (1994) Handbook of Detection of Enzymes on Electroporetic Gels. CRC Press; Boca Raton, FL, pp 300Google Scholar
  22. 22.
    Mann, M, Pandey, A (2001) Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem Sci 26: 54–61PubMedCrossRefGoogle Scholar
  23. 23.
    Maron, PA, Coeur, C, Pink, C, Clays-Josserand, A, Lensi, R, Richaume, A, Potier, P (2003) Use of polyclonal antibodies to detect and quantify the NOR protein of nitrite oxidizers in complex environments. J Microbiol Methods 53: 87–95PubMedCrossRefGoogle Scholar
  24. 24.
    Maron, PA, Richaume, A, Potier, P, Lata, JC, Lensi, R (2004) Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil. J Microbiol Methods 58: 13–21PubMedCrossRefGoogle Scholar
  25. 25.
    Maron, PA, Schimann, H, Brothier, E, Ranjard, L, Domenach, AM, Lensi, R, Nazaret, S (2006) Evaluation of quantitative and qualitative recovery of bacterial communities from different soil types by density gradient centrifugation. Eur J Soil Biol 42: 65–73CrossRefGoogle Scholar
  26. 26.
    Maron, PA, Mougel, C, Siblot, S, Abbas, H, Lemanceau, P, Ranjard, L Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Micob Ecol (In press)Google Scholar
  27. 27.
    Mounier, E, Hallet, S, Chèneby, D, Benizri, E, Gruet, Y, Nguyen, C, Piutti, S, Robin, C, Slezack-Deschaumes, S, Martin-Laurent, F, Germon, JC, Philippot, L (2004) Influence of maize mucilage on the diversity and activity of the denitrifying community. Environ Microbiol 6: 301–312PubMedCrossRefGoogle Scholar
  28. 28.
    Niimi, M, Cannon, R, Monk, B (1999) Candida albicans pathogenicity: a proteomic perspective. Electrophoresis 20: 2299–2308PubMedCrossRefGoogle Scholar
  29. 29.
    O’Farrell, PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: 4007–4021PubMedGoogle Scholar
  30. 30.
    Ogunseitan, OA (1993) Direct extraction of proteins from environmental samples. J Microbiol Methods 17: 273–281CrossRefGoogle Scholar
  31. 31.
    Ogunseitan, OA (1996) Protein profile in cultivated and native freshwater microorganisms exposed to chemical environmental pollutants. Microb Ecol 31: 291–304PubMedCrossRefGoogle Scholar
  32. 32.
    Ogunseitan, OA (1997) Direct extraction of catalytic proteins from natural microbial communities. J Microbiol Methods 28: 55–63CrossRefGoogle Scholar
  33. 33.
    Ogunseitan, OA (1998) Protein method for investigating mercuric reductase gene expression in aquatic environments. Appl Environ Microbiol 64: 695–702PubMedGoogle Scholar
  34. 34.
    Pace, NR, Stahl, DA, Olsen, GJ, Lane, DJ (1985) Analyzing natural microbial populations by rRNA sequences. Am Soc Microbiol News 51: 4–12Google Scholar
  35. 35.
    Pandey, A, Lewitter, F (1999) Nucleotide sequence databases: a gold mine for biologists. Trends Biochem Sci 24: 276–280PubMedCrossRefGoogle Scholar
  36. 36.
    Pandey, A, Mann, M (2000) Proteomics to study genes and genomes. Nature 405: 837–846PubMedCrossRefGoogle Scholar
  37. 37.
    Panicker, RC, Huang, X, Yao, SQ (2004) Recent advances in peptide-based microarray technologies. Comb Chem High Throughput Screen 7: 547–556PubMedGoogle Scholar
  38. 38.
    Pedersen, S, Bloch, PL, Reeh, S, Neidhardt, FC (1978) Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates. Cell 14: 179–190PubMedCrossRefGoogle Scholar
  39. 39.
    Philippot, L (2002) Denitrifying genes in bacterial and Archeal genomes. Biochim Biophys Acta 1577: 355–376PubMedGoogle Scholar
  40. 40.
    Pimm, SL (1984) The complexity and the stability of ecosystems. Nature 307: 321–326CrossRefGoogle Scholar
  41. 41.
    Radajewski, S, Ineson, P, Parekh, NR, Murrell, JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649PubMedCrossRefGoogle Scholar
  42. 42.
    Ram, RJ, VerBerkmoes, NC, Thelen, MP, Tyson, GW, Baker, BJ, Blake, RC II, Shah, M, Hettich, RL, Banfield, JF (2005) Community proteomics of a natural microbial biofilm. Science 308: 1915–1920PubMedCrossRefGoogle Scholar
  43. 43.
    Ramachandran, N, Hainsworth, E, Bhullar, B, Eisenstein, S, Rosen, B, Lau, AY, Walter, JC, LaBaer, J (2004) Self-assembling protein microarrays. Science 305: 86–90PubMedCrossRefGoogle Scholar
  44. 44.
    Ranjard, L, Poly, F, Nazaret, S (2000) Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res Microbiol 151: 167–177PubMedCrossRefGoogle Scholar
  45. 45.
    Rodriguez-Valera, F (2004) Environmental genomics, the big picture. FEMS Microbiol Lett 231: 153–158PubMedCrossRefGoogle Scholar
  46. 46.
    Rondon, MR, August, PR, Bettermann, AD, Brady, SF, Grossman, TH, Liles, MR, Loiacono, KA, Lynch, BA, MacNeil, IA, Minor, C, Tiong, CL, Gilman, M, Osburne, MS, Clardy, J, Handelsman, J, Goodman, RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66: 2541–2547PubMedCrossRefGoogle Scholar
  47. 47.
    Schulze, WX, Gleixner, G, Kaiser, K, Guggenberger, G, Mann, M, Schulze, ED (2004) A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142: 335–343PubMedCrossRefGoogle Scholar
  48. 48.
    Singleton, I, Merringto, G, Colvan, S, Delahunty, JS (2003) The potential of soil protein-based methods to indicate metal contamination. Appl Soil Ecol 654: 1–8Google Scholar
  49. 49.
    Stein, JL, Marsh, TL, Wu, KY, Shizuya, H, DeLong, EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591–599PubMedGoogle Scholar
  50. 50.
    Torsvik, VL, Ovreas, L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5: 240–245PubMedCrossRefGoogle Scholar
  51. 51.
    Vasseur, C, Labadie, J, Hébraud, M (1999) Differential protein expression by Pseudomonas fragi submitted to various stresses. Electrophoresis 20: 2204–2213PubMedCrossRefGoogle Scholar
  52. 52.
    Wackett, LP, Dodge, AG, Ellis, BM (2004) Microbial genomics and the periodic table. Appl Environ Microbiol 70: 647–655PubMedCrossRefGoogle Scholar
  53. 53.
    Walker, BH (1992) Biodiversity and ecological redundancy. Conserv Biol 6: 18–23CrossRefGoogle Scholar
  54. 54.
    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: 19–50Google Scholar
  55. 55.
    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: 911–920PubMedCrossRefGoogle Scholar
  56. 56.
    Yates, JR 3rd, Speicher, S, Griffin, PR, Hunkapiller, T (1993) Peptide mass maps: a highly informative approach to protein identification. Anal Biochem 214: 397–408PubMedCrossRefGoogle Scholar
  57. 57.
    Yates, JR 3rd (2004) Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 33: 297–316PubMedCrossRefGoogle Scholar
  58. 58.
    Zhou, J, Thompson, DK (2002) Challenges in applying the microarrays to environmental studies. Curr Opin Biotechnol 13: 204–207PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Pierre-Alain Maron
    • 1
  • Lionel Ranjard
    • 1
  • Christophe Mougel
    • 1
  • Philippe Lemanceau
    • 1
    Email author
  1. 1.UMR Microbiologie et Géochimie des SolsINRA/Université de Bourgogne, CMSEDijon CedexFrance

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