Browse > Article

Metaproteomics in Microbial Ecology  

Kim, Jong-Shik (Gyeongbuk Institute for Marine Bio-Industry (GIMB))
Woo, Jung-Hee (Gyeongbuk Institute for Marine Bio-Industry (GIMB))
Kim, Jun-Tae (Gyeongbuk Institute for Marine Bio-Industry (GIMB))
Park, Nyun-Ho (Gyeongbuk Institute for Marine Bio-Industry (GIMB))
Kim, Choong-Gon (Gyeongbuk Institute for Marine Bio-Industry (GIMB))
Publication Information
Korean Journal of Microbiology / v.46, no.1, 2010 , pp. 1-8 More about this Journal
Abstract
New technologies are providing unprecedented knowledge into microbial community structure and functions. Even though nucleic acid based approaches provide a lot of information, metaproteomics could provide a high-resolution representation of genotypic and phenotypic traits of distinct microbial communities. Analyzing the metagenome from different microbial ecosystems, metaproteomics has been applied to seawater, human guts, activated sludge, acid mine drainage biofilm, and soil. Although these studies employed different approaches, they elucidated that metaproteomics could provide a link among microbial community structure, function, physiology, interaction, ecology, and evolution. These approaches are reviewed here to help gain insights into the function of microbial community in ecosystems.
Keywords
mass spectrometry; metaproteomics; microbial community; shot-gun analysis;
Citations & Related Records

Times Cited By SCOPUS : 0
연도 인용수 순위
  • Reference
1 Wilmes, P. and P.L. Bond. 2006. Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge. Water Sci. Technol. 54, 217-226.   DOI   ScienceOn
2 Benndorf, D., C. Vogt, N. Jehmlich, Y. Schmidt, H. Thomas, G. Woffendin, A. Shevchenko, H.H. Richnow, and M. von Bergen. 2009. Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 20, 737-750.   DOI   ScienceOn
3 Ram, R.J., N.C. VerBerkmoes, M.P. Thelen, G.W. Tyson, B.J. Baker, R.C. Blake II, M. Shah, and et al. 2005. Community proteomics of a natural microbial biofilm. Science 308, 1915-1920.   DOI
4 Verberkmoes, N.C., A.L. Russell, M. Shah, A. Godzik, M. Rosenquist, J. Halfvarson, M.G. Lefsrud, and et al. 2009. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179-189.   DOI   ScienceOn
5 Zhao, B. and C.L. Poh. 2008. Insights into environmental bioremediation by microorganisms through functional genomics and proteomics.Proteomics 8, 874-881.   DOI   ScienceOn
6 Abram, F., E. Gunnigle, and V. O'Flaherty. 2009. Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms. Electrophoresis 30, 4149-4151.   DOI   ScienceOn
7 Apajalahti, J.H.A., A. Kettunen, M.R. Bedford, and W.E. Holben. 2001. Percent G+C profiling accurately reveals dietrelated differences in the gastrointestinal microbial community of broiler chickens. Appl. Environ. Microbiol. 67, 5656-5667.   DOI   ScienceOn
8 Benndorf, D., G.U. Balcke, H. Harms, and M. von Bergen. 2007. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 1, 224-234.   DOI   ScienceOn
9 Wilmes, P. and P.L. Bond. 2009. Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles. Curr. Opin. Microbiol. 12, 310-317.   DOI   ScienceOn
10 Wilmes, P., M. Wexler, and P.L. Bond. 2008. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE 3, e1778.   DOI
11 Wilmes, P.and P.L. Bond. 2004. The application of twodimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 6, 911-920.   DOI   ScienceOn
12 Venter, J.C., K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu, and et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74.   DOI   ScienceOn
13 Wilhelm, L.J., H.J. Tripp, S.A. Givan, D.P. Smith, and S.J. Giovannoni. 2007. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol. Direct 2, 27.   DOI   ScienceOn
14 Wilmes, P., A.F. Andersson, M.G. Lefsrud, M. Wexler, M. Shah, B. Zhang, R.L. Hettich, and et al. 2008. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J. 2, 853-864.   DOI   ScienceOn
15 Sowell, S.M., L.J. Wilhelm, A. D. Norbeck, M.S. Lipton, C.D. Nicora, D.F. Barofsky, C.A. Carlson, R.D. Smith, and S.J. Giovanonni. 2009. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 3, 93-105.   DOI   ScienceOn
16 Wilmes, P. and P.L. Bond. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14, 92-97.   DOI   ScienceOn
17 Solaiman, Z., M.A. Kashem, and I. Matsumoto. 2007. Environmetal proteomics: extraction and identification of protein in soil, pp. 155-166. In A. Varma and R. Oelmuller (eds.), Advanced techniques in soil microbiology. Soil Biology vol 8, Springer- Verlag Berlin Heidelberg. Germany.
18 Sowell, S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, D.F. Barofsky, and S.J. Giovannoni. 2008. Proteomic analysis of stationary phase in the marine bacterium "Candidatus Pelagibacter ubique". Appl. Environ. Microbiol. 74, 4091-4100.   DOI   ScienceOn
19 Tyson, G.W., J. Chapman, P. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, and et al.2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43.   DOI   ScienceOn
20 Taylor, E.B. and M.A. Williams. 2010. Microbial protein in soil: influence of extraction method and C amendment on extraction and recovery. Microb. Ecol. 59, 390-399.   DOI   ScienceOn
21 Valenzuela, L., A. Chi, S. Beard, A. Orell, N. Guiliani, J. Shabanowitz, D.F. Hunt, and C.A. Jerez. 2006. Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol. Adv. 24, 197-211.   DOI   ScienceOn
22 Pierre-Alain, M., R. Lionel, M. Christophe, and L. Philippe. 2007. Metaproteomics: a new approach for studying functional microbial ecology. Microb. Ecol. 53, 486-493.   DOI   ScienceOn
23 Powell, M.J., J.N. Sutton, C.E. Del Castillo, and A.T. Timperman. 2005. Marine proteomics: generation of sequence tags for dissolved proteins in seawater using tandem mass spectrometry. Marine Chemistry 95, 183-198.   DOI   ScienceOn
24 Lacerda, C.M.R. and K.F. Reardon. 2009. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. Brief. Funct. Genomics Proteomics 8, 75-87.
25 Rappe, M.S., S.A. Connon, K.L. Vergin, and S.J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630-633.   DOI   ScienceOn
26 Schulze, W.X., G. Gleixner, K. Kaiser, G. Guggenberger, M. Mann, and E.D. Schulze. 2005. A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142, 335-343.   DOI   ScienceOn
27 Schweder, T., S. Markert, and M. Hecker. 2008. Proteomics of marine bacteria. Electrophoresis 29, 2603-2616.   DOI   ScienceOn
28 Lo, I., V.J. Denef, N.C. Verberkmoes, M.B. Shah, D. Goltsman, G. DiBartolo, G.W. Tyson, and et al.2007. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537-541.   DOI   ScienceOn
29 Ogunseitan, O.A. 1993. Direct extraction of proteins from environmental samples. J. Microbiol. Methods 17, 273-281.   DOI   ScienceOn
30 Ogunseitan, O.A. 1997. Direct extraction of catalytic proteins from natural microbial communities. J. Microbiol. Methods 28, 55-63.   DOI   ScienceOn
31 Park, C.and R.F. Helm. 2008. Application of metaproteomic analysis for studying extracellular polymeric substances (EPS) in activated sludge flocs and their fate in sludge digestion. Water Sci. Technol. 57, 2009-2015.   DOI   ScienceOn
32 Pierre-Alain, M., M. Christophe, S. Severine, A. Houria, L. Philippe, and R. Lionel. 2007. Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Microb. Ecol. 53, 426-434.   DOI   ScienceOn
33 Giovannoni, S.J., L. Bibbs, J.C. Cho, M.D. Stapels, R. Desiderio, K.L. Vergin, M.S. Rappe, and et al. 2005. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438, 82-85.   DOI   ScienceOn
34 Graham, R.L.J., C. Graham, and G. McMullan. 2007. Microbial proteomics: a mass spectrometry primer for biologists. Microb. Cell Fact. 6, 26.   DOI
35 Kan, J., T.E. Hanson, J.M. Ginter, K. Wang, and F. Chen. 2005. Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Syst. 1, 7.   DOI
36 Graves, P.R. and T.A.J. Haystead. 2002. Molecular biologist's guide to proteomics. Microbiol. Mol. Biol. Rev. 66, 39-63.   DOI   ScienceOn
37 Jehmlich, N., F. Schmidt, M. von Bergen, H.H. Richnow, and C. Vogt. 2008. Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2, 1122-1133.   DOI   ScienceOn
38 Jerez, C.A. 2007. Proteomics and metaproteomics applied to biomining microorganisms, pp. 241-251. In E. Donati and W. Sand (ed.), Microbial Processing of Metal Sulfides, Springer, Germany.
39 Klaassens, E.S., W.M. de Vos, and E.E. Vaughan. 2007. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 73, 1388-1392.   DOI   ScienceOn
40 Lacerda, C.M., L.H. Choe, and K.F. Reardon. 2007. Metaproteomic analysis of a bacterial community response to cadmium exposure. J. Proteome Res. 6, 1145-1152.   DOI   ScienceOn
41 Cardenas, E. and J.M. Tiedje. 2008. New tools for discovering and characterizing microbial diversity. Curr. Opin. Biotechnol. 19, 544-549.   DOI   ScienceOn
42 Farinati, S., G. DalCorso, E. Bona, M. Corbella, S. Lampis, D. Cecconi, R. Polati, and et al. 2009. Proteomic analysis of Arabidopsis halleri shoots in response to the heavy metals cadmium and zinc and rhizosphere microorganisms. Proteomics 9, 4837-4850.   DOI   ScienceOn
43 Chen, S., M.C. Rillig, and W. Wang. 2009. Improving soil protein extraction for metaproteome analysis and glomalin-related soil protein detection. Proteomics 9, 4970-4973.   DOI   ScienceOn
44 Desai, C., H. Pathak, and D. Madamwar. 2010. Advances in molecular and "-omics" technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Bioresour. Technol. 101, 1558-1569.   DOI   ScienceOn