Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem

Nature Chemical Biology

Volumn 5, Issue 12, 2009, Pages 929-935

  Song, Hao ^a   Payne, Stephen ^a   Gray, Meagan ^a   You, Lingchong ^a  

^a Duke University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL AGENT;

ARTICLE; BIODIVERSITY; CELL MOTILITY; DYNAMICS; ECOSYSTEM; ESCHERICHIA COLI; HABITAT; MODULATION; PREDATION; PRIORITY JOURNAL; BACTERIAL GENE; BIOLOGICAL MODEL; GENETIC ENGINEERING; GENETICS; MOVEMENT (PHYSIOLOGY); PHYSIOLOGY; PLASMID; QUORUM SENSING;

ESCHERICHIA COLI;

BIODIVERSITY; ECOSYSTEM; ESCHERICHIA COLI; GENES, BACTERIAL; GENETIC ENGINEERING; MODELS, BIOLOGICAL; MOVEMENT; PLASMIDS; QUORUM SENSING;

EID: 73549083223     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.244     Document Type: Article

References (50)

1. Falkowski, P.G., Fenchel, T. & Delong, E.F. The microbial engines that drive Earth's biogeochemical cycles. Science 320, 1034-1039 (2008).
2. Strom, S.L. Microbial ecology of ocean biogeochemistry: a community perspective. Science 320, 1043-1045 (2008).
3. Muyzer, G. & Stams, A.J. The ecology and biotechnology of sulphate-reducing bacteria. Nat. Rev. Microbiol. 6, 441-454 (2008).
4. Jia, W., Li, H., Zhao, L. & Nicholson, J.K. Gut microbiota: a potential new territory for drug targeting. Nat. Rev. Drug Discov. 7, 123-129 (2008).
5. Dethlefsen, L., McFall-Ngai, M. & Relman, D.A. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449, 811-818 (2007).
6. Brenner, K., You, L. & Arnold, F.H. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol. 26, 483-489 (2008).
7. Peet, R. The measurement of species diversity. Annu. Rev. Ecol. Syst. 5, 285-307 (1974).
8. Jessup, C.M. et al. Big questions, small worlds: microbial model systems in ecology. Trends Ecol. Evol. 19, 189-197 (2004).
9. Loreau, M. et al. Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294, 804-808 (2001).
10. Ley, R.E., Peterson, D.A. & Gordon, J.I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837-848 (2006).
11. Dykhuizen, D.E. Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73, 25-33 (1998).
12. Staley, J.T. & Reysenbach, A.-L. (eds.) Biodiversity of Microbial Life: Foundation of Earth's Biosphere (Wiley-Liss, New York, 2001).
13. Ward, D.M., Ferris, M.J., Nold, S.C. & Bateson, M.M. A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62, 1353-1370 (1998).
14. Horner-Devine, M.C., Carney, K.M. & Bohannan, B.J. An ecological perspective on bacterial biodiversity. Proc. Biol. Sci. 271, 113-122 (2004).
15. Tilman, D. The ecological consequences of changes in biodiversity: a search for general principles. Ecology 80, 1455-1474 (1999).
16. Chesson, P. & Kuang, J.J. The interaction between predation and competition. Nature 456, 235-238 (2008).
17. Martin, M.O. Predatory prokaryotes: an emerging research opportunity. J. Mol. Microbiol. Biotechnol. 4, 467-477 (2002).
18. Jurkevitch, E. Predatory behaviors in bacteria - diversity and transitions. Microbe 2, 67-73 (2007).
19. Guerrero, R. et al. Predatory prokaryotes: predation and primary consumption evolved in bacteria. Proc. Natl. Acad. Sci. USA 83, 2138-2142 (1986).
20. Esteve, I., Gaju, N., Mir, J. & Guerrero, R. Comparison of techniques to determine the abundance of predatory bacteria attacking chromatiaceae. FEMS Microbiol. Lett. 86, 205-211 (1992).
21. Lambert, C., Morehouse, K.A., Chang, C.Y. & Sockett, R.E. Bdellovibrio: growth and development during the predatory cycle. Curr. Opin. Microbiol. 9, 639-644 (2006).
22. Shou, W., Ram, S. & Vilar, J.M. Synthetic cooperation in engineered yeast populations. Proc. Natl. Acad. Sci. USA 104, 1877-1882 (2007).
23. Hart, B.A. & Zahler, S.A. Lytic enzyme produced by Myxococcus xanthus. J. Bacteriol. 92, 1632-1637 (1966).
24. Berleman, J.E., Chumley, T., Cheung, P. & Kirby, J.R. Rippling is a predatory behavior in Myxococcus xanthus. J. Bacteriol. 188, 5888-5895 (2006).
25. Pham, V.D., Shebelut, C.W., Diodati, M.E., Bull, C.T. & Singer, M. Mutations affecting predation ability of the soil bacterium Myxococcus xanthus. Microbiology 151, 1865-1874 (2005).
26. Keller, L. & Surette, M.G. Communication in bacteria: an ecological and evolutionary perspective. Nat. Rev. Microbiol. 4, 249-258 (2006).
27. Battin, T.J. et al. Microbial landscapes: new paths to biofilm research. Nat. Rev. Microbiol. 5, 76-81 (2007).
28. Pohnert, G., Steinke, M. & Tollrian, R. Chemical cues, defence metabolites and the shaping of pelagic interspecific interactions. Trends Ecol. Evol. 22, 198-204 (2007).
29. Dicke, M. & Sabelis, M.W. Infochemical terminology: based on cost-benefit analysis rather than origin of compounds? Funct. Ecol. 2, 131-139 (1988).
30. Ianora, A. et al. New trends in marine chemical ecology. Estuaries Coasts 29, 531-551 (2006).
31. Waters, C.M. & Bassler, B.L. Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319-346 (2005).
32. Whittaker, R.H. & Feeny, P.P. Allelochemicals: chemical interactions between species. Science 171, 757-770 (1971).
33. Weissburg, M.J., Ferner, M.C., Pisut, D.P. & Smee, D.L. Ecological consequences of chemically mediated prey perception. J. Chem. Ecol. 28, 1953-1970 (2002).
34. Shiner, E.K., Rumbaugh, K.P. & Williams, S.C. Inter-kingdom signaling: deciphering the language of acyl homoserine lactones. FEMS Microbiol. Rev. 29, 935-947 (2005).
35. Kerr, B., Riley, M.A., Feldman, M.W. & Bohannan, B.J. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418, 171-174 (2002).
36. Reichenbach, T., Mobilia, M. & Frey, E. Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games. Nature 448, 1046-1049 (2007).
37. Balagadde, F.K. et al. A synthetic Escherichia coli predator-prey ecosystem. Mol. Syst. Biol. 4, 187 (2008).
38. Weber, W., Daoud-El Baba, M. & Fussenegger, M. Synthetic ecosystems based on airborne inter- and intrakingdom communication. Proc. Natl. Acad. Sci. USA 104, 10435-10440 (2007).
39. Kosinski, M.J., Rinas, U. & Bailey, J.E. Isopropyl-β-D- thiogalactopyranoside influences the metabolism of Escherichia coli. Appl. Microbiol. Biotechnol. 36, 782-784 (1992).
40. Lauffenburger, D.A. Quantitative studies of bacterial chemotaxis and microbial population dynamics. Microb. Ecol. 22, 175-185 (1991).
41. Kelly, F.X., Dapsis, K.J. & Lauffenburger, D.A. Effect of bacterial chemotaxis on dynamics of microbial competition. Microb. Ecol. 16, 115-131 (1988).
42. Woodward, D.E. et al. Spatio-temporal patterns generated by Salmonella typhimurium. Biophys. J. 68, 2181-2189 (1995).
43. Keller, E.F. & Segel, L.A. Traveling bands of chemotactic bacteria: a theoretical analysis. J. Theor. Biol. 30, 235-248 (1971).
44. Hastings, A. Transients: the key to long-term ecological understanding? Trends Ecol. Evol. 19, 39-45 (2004).
45. Tilman, D. & Kareiva, P. Spatial Ecology (Princeton University Press, Princeton, New Jersey, 1997).
46. Rosenzweig, M.L. Species Diversity in Space and Time (Cambridge University Press, Cambridge, UK, 1995).
47. Stolp, H. Microbial Ecology: Organisms, Habitats, Activities (Cambridge University Press, Cambridge, UK, 1988).
48. Hastings, A. Spatial heterogeneity and the stability of predator-prey systems. Theor. Popul. Biol. 12, 37-48 (1977).
49. Kim, H.J., Boedicker, J.Q., Choi, J.W. & Ismagilov, R.F. Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proc. Natl. Acad. Sci. USA 105, 18188-18193 (2008).
50. Brenner, K., Karig, D.K., Weiss, R. & Arnold, F.H. Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium. Proc. Natl. Acad. Sci. USA 104, 17300-17304 (2007).