Metaproteomics: A New Approach for Studying Functional Microbial Ecology
- 2.2k Downloads
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.
KeywordsMicrobial Community Activate Sludge Environmental Matrix Protein Pool Indigenous Microbial Community
The authors are grateful to K. Klein for helpful comments and correcting the English text.
- 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
- 5.Brock, TD (1987) The study of microorganisms in situ: progress and problems. Symp Soc Gen Microbiol 41: 1–17Google Scholar
- 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
- 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
- 21.Manchenko, GP (1994) Handbook of Detection of Enzymes on Electroporetic Gels. CRC Press; Boca Raton, FL, pp 300Google Scholar
- 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.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
- 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
- 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
- 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
- 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