Competitive and cooperative metabolic interactions in bacterial communities

Nature Communications

Volumn 2, Issue 1, 2011, Pages

  Freilich, Shiri ^a   Zarecki, Raphy ^a   Eilam, Omer ^b   Segal, Ella Shtifman ^a   Henry, Christopher S ^b   Kupiec, Martin ^a   Gophna, Uri ^a   Sharan, Roded ^a   Ruppin, Eytan ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BIOMASS; BIOREMEDIATION; COMMENSALISM; COMPETITION; COMPUTER MODEL; COOPERATION; ECOLOGY; IN VIVO STUDY; METABOLIC INTERACTION; MICROBIAL COMMUNITY; NONHUMAN; PARASITISM; SIMULATION; SYMBIOSIS; ANTIBIOSIS; BACTERIUM; BIOLOGICAL MODEL; COMPUTER SIMULATION; ECOSYSTEM; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIAL CONSORTIUM; PHYSIOLOGY;

ANTIBIOSIS; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; COMPUTER SIMULATION; ECOLOGY; ECOSYSTEM; MICROBIAL CONSORTIA; MODELS, BIOLOGICAL; SYMBIOSIS;

EID: 84455174807     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms1597     Document Type: Article

References (38)

1. Gause, G. F. Experimental studies on the struggle for existence. J. Exp. Biol. 9, 389-402 (1932).
2. Darwin, C. On the Origin of Species by Means of Natural Selection, or, The Preservation of Favoured Races in the Struggle for Life Dover giant thrift edn (Dover Publications, 2006).
3. Boer, P. J. D. The present status of the competitive exclusion principle. Trends Ecol. Evol. 1, 25-28 (1986).
4. Marx, C. J. Microbiology. Getting in touch with your friends. S cience 324, 1150-1151 (2009).
5. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193-199 (2009).
6. Lotem, A., Fishman, M. A. & Stone, L. Evolution of cooperation between individuals. Nature 400, 226-227 (1999).
7. Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15-25 (2010).
8. Gross, K. Positive interactions among competitors can produce species-rich communities. Ecol. Lett. 11, 929-936 (2008).
9. Diamond, J. M. & Gilpin, M. E. Examination of the'null'model of connor and simberlofffor species co-occurrences on islands. Oecologia 52, 64-74 (1982).
10. Connor, E. F. & Simberloff, D. The assembly of species communities: chance or competition? Ecology 60, 1132-1140 (1979).
11. Stolyar, S. et al. Metabolic modeling of a mutualistic microbial community. Mol. Syst. Biol. 3, 92 (2007).
12. Wintermute, E. H. & Silver, P. A. Emergent cooperation in microbial metabolism. M ol. Syst. Biol. 6, 407 (2010).
13. Klitgord, N. & Segre, D. Environments that induce synthetic microbial ecosystems. P LoS Comput. Biol. 6, e1001002 (2010).
14. Henry, C. S. et al. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 28, 977-982 (2010).
15. Ebenhoh, O. & Handorf, T. Functional classification of genome-scale metabolic networks. E URASIP J. Bioinform. Syst. Biol. 2009, 570456 (2009).
16. Freilich, S. et al. Decoupling environment-dependent and independent genetic robustness across bacterial species. PLoS Comput. Biol. 6, e1000690 (2010).
17. Freilich, S. et al. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol. 10, R61 (2009).
18. Mani, R., St Onge, R. P., Hartman, J.L.t., Giaever, G. & Roth, F. P. Defining genetic interaction. Proc. Natl Acad. Sci. USA 105, 3461-3466 (2008). (Pubitemid 351723575)
19. Klitgord, N. & Segre, D. Ecosystems biology of microbial metabolism. Curr. Opin. Biotechnol. 22, 541-546 (2011).
20. MacArthur, R. Species packing and competitive equilibrium for many species. Theor. Popul. Biol. 1, 1-11 (1970).
21. Tilman, D. Resource competition between planktonic algae: experimental and theoretical approach. E cology 58, 338-348 (1977).
22. Cherif, M. & Loreau, M. Stoichiometric constraints on resource use, competitive interactions, and elemental cycling in microbial decomposers. Am. Nat. 169, 709-724 (2007). (Pubitemid 46847327)
23. Orr, H. A. Fitness and its role in evolutionary genetics. Nat. Rev. Genet. 10, 531-539 (2009).
24. Elevi Bardavid, R. & Oren, A. Dihydroxyacetone metabolism in Salinibacter ruber and in Haloquadratum walsbyi. E xtremophiles 12, 125-131 (2008).
25. Mowery, D. C., Oxley, J. E. & Silverman, B. S. Technological overlap and interfirm cooperation: implications for the resource-based view of the firm. Science 27, 507-523 (1998). (Pubitemid 128430812)
26. Schink, B. Synergistic interactions in the microbial world. Antonie van Leeuwenhoek 81, 257-261 (2002). (Pubitemid 35314614)
27. Wintermute, E. H. & Silver, P. A. Dynamics in the mixed microbial concourse. Genes Dev. 24, 2603-2614 (2010).
28. Labrenz, M. & Banfield, J. F. Sulfate-reducing bacteria-dominated biofilms that precipitate ZnS in a subsurface circumneutral-pH mine drainage system. Microb. Ecol. 47, 205-217 (2004). (Pubitemid 38871384)
29. Kato, S., Haruta, S., Cui, Z. J., Ishii, M. & Igarashi, Y. Stable coexistence of five bacterial strains as a cellulose-degrading community. Appl. Environ. Microbiol. 71, 7099-7106 (2005). (Pubitemid 43194200)
30. Chaffron, S., Rehrauer, H., Pernthaler, J. & von Mering, C. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20, 947-959 (2010).
31. Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L. & L illey, A. K. The contribution of species richness and composition to bacterial services. Nature 436, 1157-1160 (2005). (Pubitemid 41232293)
32. Gomes, N. C., Kosheleva, I. A., Abraham, W. R. & Smalla, K. Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community. FEMS Microbiol. Ecol. 54, 21-33 (2005). (Pubitemid 41138018)
33. Hansen, S. K., Rainey, P. B., Haagensen, J. A. & Molin, S. Evolution of species interactions in a biofilm community. Nature 445, 533-536 (2007). (Pubitemid 46197632)
34. Wandersman, C. & Delepelaire, P. Bacterial iron sources: from siderophores to hemophores. A nnu. Rev. Microbiol. 58, 611-647 (2004). (Pubitemid 39551999)
35. Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022-1023 (2006). (Pubitemid 46018512)
36. Hirschman, L. et al. Habitat-Lite: a GSC case study based on free text terms for environmental metadata. O MICS 12, 129-136 (2008). (Pubitemid 351873435)
37. Ogata, H. et al. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27, 29-34 (1999). (Pubitemid 29209394)
38. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997). (Pubitemid 27359211)