Ecological distribution and population physiology defined by proteomics in a natural microbial community

Molecular Systems Biology

Volumn 6, Issue , 2010, Pages

  Mueller, Ryan S ^a   Denef, Vincent J ^a   Kalnejais, Linda H ^a,d   Suttle, K Blake ^a,e   Thomas, Brian C ^a   Wilmes, Paul ^a   Smith, Richard L ^b   Nordstrom, D Kirk ^b   McCleskey, R Blaine ^b   Shah, Manesh B ^c   VerBerkmoes, Nathan C ^c   Hettich, Robert L ^c   Banfield, Jillian F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b U S GEOLOGICAL SURVEY   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF NEW HAMPSHIRE   (United States)

^e IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Community structure; Metaproteomics; Microbial ecology; Model community; Succession

Indexed keywords

PROTEOME; BACTERIAL PROTEIN;

ABIOTIC STRESS; ACID MINE DRAINAGE; ARTICLE; BACTERIAL COLONIZATION; BIOFILM; DEVELOPMENTAL STAGE; ECOLOGICAL NICHE; ENVIRONMENTAL FACTOR; FLUORESCENCE IN SITU HYBRIDIZATION; GEOCHEMICAL ANALYSIS; METABOLISM; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; ORGANISMAL INTERACTION; POPULATION ABUNDANCE; POPULATION DISTRIBUTION; PRIORITY JOURNAL; PROTEOMICS; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; CLASSIFICATION; CLUSTER ANALYSIS; ECOSYSTEM; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; SPECIES DIFFERENCE;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BACTERIAL PROTEINS; BIOFILMS; CLUSTER ANALYSIS; ECOSYSTEM; PROTEOME; PROTEOMICS; SPECIES SPECIFICITY;

EID: 77953272819     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2010.30     Document Type: Article

References (51)

1. Allen EE, Bartlett DH (2002) Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology 148: 1903-1913
2. Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental-studies in microbiology. J Bacteriol 172: 762-770
3. Baeseman J, Smith R, Silverstein J (2006) Denitrification potential in stream sediments impacted by acid mine drainage: effects of pH, various electron donors, and iron. Microb Ecol 51: 232-241
4. Belnap C (2009) Quantitative Proteomic Comparison of Biofilm versus Planktonic Communities and Biofilm Response to pH Perturbation. Berkeley: University of California
5. Bond PL, Smriga SP, Banfield JF (2000) Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl Environ Microbiol 66: 3842-3849
6. Brown JH (1984) On the relationship between abundance and distribution of species. Am Nat 124: 255-279
7. Clarke KR, Ainsworth M (1993) A method of linking multivariate community structure to environmental variables. Mar Ecol Prog Ser 92: 205-219
8. Connell JH, Slatyer RO (1977) Mechanisms of succession in natural communities and their role in community stability and organization. Am Nat 111: 1119-1144
9. de Hoon MJL, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20: 1453-1454
10. Dean WRJ, Milton SJ, Jeltsch F (1999) Large trees, fertile islands, and birds in arid savanna. J Arid Environ 41: 61-78
11. Del Moral R, Bliss LC (1993) Mechanisms of primary succession- insights resulting fromthe eruption ofMount St.Helens. In Advances in Ecological Research, Begon M (ed), Vol.24, pp 1-66. London: Academic Press Ltd
12. Delmotte Nl, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci 106: 16428-16433
13. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean0s interior. Science 311: 496-503
14. Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, Hettich RL, VerBerkmoes NC, Banfield JF (2010a) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci USA 107: 2383-2390
15. Denef VJ, Mueller RS, Banfield JF (2010b) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4: 599-610
16. 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
17. Druschel GK, Baker BJ, Gihring TM, Banfield JF (2004) Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem Trans 5: 13-32
18. Edwards KJ, Gihring TM, Banfield JF (1999) Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment. Appl Environ Microbiol 65: 3627-3632
19. Eng JK, McCormack AL, Yates JR (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
20. Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, Workman JL, Washburn MP (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40: 303-311
21. Glenn-Lewin DC, Peet RK, Veblen TT (1992) Plant Succession: Theory and Prediction, Vol.11. London, UK: Chapman and Hall
22. Goltsman DSA, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF (2009) Community genomic and proteomic analysis of chemoautotrophic, iron-oxidizing 'Leptospirillum rubarum' (Group II) and Leptospirillum ferrodiazotrophum (Group III) in acid mine drainage biofilms. Appl Environ Microbiol 75: 4599-4615
23. Hanski I, Kouki J, Halkka A (1993) Three explanations of the positive relationship between distribution and abundance of species. In Species Diversity in Ecological Communities: Historical and Geographical Perspectives, Ricklefs RE, Schluter D (eds), pp 108- 116. Chicago, IL: University of Chicago Press
24. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934
25. Jeans C, Singer SW, Chan CS, VerBerkmoes NC, Shah M, Hettich RL, Banfield JF, Thelen MP (2008) Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J 2: 542-550
26. Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4: 198
27. Lacerda CMR, Choe LH, Reardon KF (2007) Metaproteomic analysis of a bacterial community response to cadmium exposure. J Proteome Res 6: 1145-1152
28. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, AndersonI,KyrpidesN,MunkAC, Detter C, HanCS, BrownMV, Robb FT, Kjelleberg S et al (2009) The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA 106: 15527-15533
29. Little AEF, Robinson CJ, Peterson SB, Raffa KF, Handelsman J (2008) Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol 62: 375-401
30. Lo I, Denef VJ, VerBerkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446: 537-541
31. MacArthur RH, Wilson EO (1967) The Theory of Island Biogeography. Princeton, New Jersey: Princeton University Press
32. McCleskey RB, Nordstrom DK, Naus CA (2004) Questa baseline and pre-mining ground-water-quality investigation. 16. Quality assurance and quality control for water analyses. In U.S. Geological Survey Open File Report 2004, p 119
33. Nordstrom DK, Alpers CN, Ptacek CJ, Blowes DW(2000) Negative pH and extremely acidic mine waters from Iron Mountain, California. Environ Sci Technol 34: 254-258
34. Oksanen J, Kindt R, Legendre P, O'Hara B, Stevens MHH (2007) Vegan: Community Ecology Package. R package version 1.8-8
35. Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW (2007) The role of ecological theory in microbial ecology. Nat RevMicrobiol 5: 384-392
36. Raes J, Bork P (2008) Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6: 693-699
37. Ram RJ, VerBerkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake II RC, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308: 1915-1920
38. Roxas B, Li Q (2008) Significance analysis of microarray for relative quantitation of LC/MS data in proteomics. BMC Bioinformatics 9: 187
39. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K et al (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5: e77
40. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248
41. Simmons SL, DiBartolo G, Denef VJ, Goltsman DSA, Thelen MP, Banfield JF (2008) Population genomic analysis of strain variation in Leptospirillum Group II bacteria involved in acid mine drainage formation. PLoS Biol 6: e177
42. Tabb DL, McDonald WH, Yates JR (2002) DTA Select and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1: 21-26
43. Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Mekhedov S, Nikolskaya A, Rao BS, Smirnov S, Sverdlov A, Vasudevan S,Wolf Y, Yin J, Natale D (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41
44. To TB, Nordstrom DK, Cunningham KM, Ball JW, McCleskey RB (1999) Newmethod for the direct determination of dissolved Fe(III) concentration in acid mine waters. Environ Sci Technol 33: 807-813
45. Torgerson W (1952) Multidimensional scaling: I. Theory and method. Psychometrika 17: 401-419
46. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308: 554-557
47. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121
48. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43
49. VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF (2009) Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 7: 196-205
50. Warnecke F, Hugenholtz P (2007) Building on basic metagenomics with complementary technologies. Genome Biol 8: 231
51. Wilmes P, Remis JP, Hwang M, Auer M, Thelen MP, Banfield JF (2009) Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME J 3: 266-270