Explaining microbial population genomics through phage predation (original) (raw)
Gupta, S. & Maiden, M. C. Exploring the evolution of diversity in pathogen populations. Trends Microbiol.9, 181–185 (2001). ArticleCAS Google Scholar
Whitaker, R. J. & Banfield, J. F. Population genomics in natural microbial communities. Trends Ecol. Evol.21, 508–516 (2006). Article Google Scholar
Medini, D. et al. Microbiology in the post-genomic era. Nature Rev. Microbiol.6, 419–430 (2008). ArticleCAS Google Scholar
Medini, D., Donati, C., Tettelin, H., Masignani, V. & Rappuoli, R. The microbial pan-genome. Curr. Opin. Genet. Dev.15, 589–594 (2005). ArticleCAS Google Scholar
Liti, G. et al. Population genomics of domestic and wild yeasts. Nature458, 337–341 (2009). ArticleCAS Google Scholar
Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl Acad. Sci. USA102, 13950–13955 (2005). ArticleCAS Google Scholar
Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl Acad. Sci. USA102, 2567–2572 (2005). ArticleCAS Google Scholar
Maharjan, R., Seeto, S., Notley-McRobb, L. & Ferenci, T. Clonal adaptive radiation in a constant environment. Science313, 514–517 (2006). ArticleCAS Google Scholar
Atwood, K. C., Schneider, L. K. & Ryan, F. J. Periodic selection in Escherichia coli. Proc. Natl Acad. Sci. USA37, 146–155 (1951). ArticleCAS Google Scholar
Atwood, K. C., Schneider, L. K. & Ryan, F. J. Selective mechanisms in bacteria. Cold Spring Harb. Symp. Quant. Biol.16, 345–355 (1951). ArticleCAS Google Scholar
Feil, E. J. Small change: keeping pace with microevolution. Nature Rev. Microbiol.2, 483–495 (2004). ArticleCAS Google Scholar
Hershberg, R. et al. high functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol.6, e311 (2008). Article Google Scholar
Cohan, F. M. & Koeppel, A. F. The origins of ecological diversity in prokaryotes. Curr. Biol.18, R1024–R1034 (2008). ArticleCAS Google Scholar
Acinas, S. G. et al. Fine-scale phylogenetic architecture of a complex bacterial community. Nature430, 551–554 (2004). ArticleCAS Google Scholar
Gevers, D. et al. Opinion: Re-evaluating prokaryotic species. Nature Rev. Microbiol.3, 733–739 (2005). ArticleCAS Google Scholar
Koeppel, A. et al. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc. Natl Acad. Sci. USA105, 2504–2509 (2008). ArticleCAS Google Scholar
Kassen, R. & Rainey, P. B. The ecology and genetics of microbial diversity. Annu. Rev. Microbiol.58, 207–231 (2004). ArticleCAS Google Scholar
Wildschutte, H. & Lawrence, J. G. Differential Salmonella survival against communities of intestinal amoebae. Microbiology153, 1781–1789 (2007). ArticleCAS Google Scholar
Zubkov, M. V. & Tarran, G. A. High bacterivory by the smallest phytoplankton in the North Atlantic Ocean. Nature455, 224–226 (2008). ArticleCAS Google Scholar
Suttle, C. A. Marine viruses — major players in the global ecosystem. Nature Rev. Microbiol.5, 801–812 (2007). ArticleCAS Google Scholar
Thingstad, T. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic ecosystems. Limnol. Oceanogr.45, 1320–1328 (2000). Article Google Scholar
Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microb. Ecol.13, 19–27 (1997). Article Google Scholar
Coleman, M. L. et al. Genomic islands and the ecology and evolution of Prochlorococcus. Science311, 1768–1770 (2006). CAS Google Scholar
Legault, B. A. et al. Environmental genomics of “_Haloquadratum walsbyi_” in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics7, 171 (2006). Article Google Scholar
Coleman, M. L. & Chisholm, S. W. Code and context: Prochlorococcus as a model for cross-scale biology. Trends Microbiol.15, 398–407 (2007). ArticleCAS Google Scholar
Wilhelm, L. J., Tripp, H. J., Givan, S. A., Smith, D. P. & Giovannoni, S. J. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol. Direct2, 27 (2007). Article Google Scholar
Cuadros-Orellana, S. et al. Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J.1, 235–245 (2007). ArticleCAS Google Scholar
Kettler, G. C. et al. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet.3, e231 (2007). Article Google Scholar
Frias-Lopez, J. et al. Microbial community gene expression in ocean surface waters. Proc. Natl Acad. Sci. USA105, 3805–3810 (2008). ArticleCAS Google Scholar
Garcia Martin, H. et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnol.24, 1263–1269 (2006). Article Google Scholar
Sharma, R. S., Mishra, V., Mohmmed, A. & Babu, C. R. Phage specificity and lipopolysaccarides of stem- and root-nodulating bacteria (Azorhizobium caulinodans, Sinorhizobium spp., and Rhizobium spp.) of Sesbania spp. Arch. Microbiol.189, 411–418 (2008). ArticleCAS Google Scholar
Fitzgerald, C., Sherwood, R., Gheesling, L. L., Brenner, F. W. & Fields, P. I. Molecular analysis of the rfb O antigen gene cluster of Salmonella enterica serogroup O:6,14 and development of a serogroup-specific PCR assay. Appl. Environ. Microbiol.69, 6099–6105 (2003). ArticleCAS Google Scholar
Ivars-Martinez, E. et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J.2, 1194–1212 (2008). ArticleCAS Google Scholar
Reva, O. & Tummler, B. Think big — giant genes in bacteria. Environ. Microbiol.10, 768–777 (2008). ArticleCAS Google Scholar
Leiman, P. G. et al. The structures of bacteriophages K1E and K1–5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J. Mol. Biol.371, 836–849 (2007). ArticleCAS Google Scholar
Mizoguchi, K. et al. Coevolution of bacteriophage PP01 and Escherichia coli O157:H7 in continuous culture. Appl. Environ. Microbiol.69, 170–176 (2003). ArticleCAS Google Scholar
Wilmes, P., Simmons, S. L., Denef, V. J. & Banfield, J. F. The dynamic genetic repertoire of microbial communities. FEMS Microbiol. Rev.33, 109–132 (2009). ArticleCAS Google Scholar
Sorek, R., Kunin, V. & Hugenholtz, P. CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Rev. Microbiol.6, 181–186 (2008). ArticleCAS Google Scholar
Kunin, V. et al. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res.18, 293–297 (2008). ArticleCAS Google Scholar
Cardinale, B. J. et al. Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature443, 989–992 (2006). ArticleCAS Google Scholar
Tylianakis, J. M., Didham, R. K., Bascompte, J. & Wardle, D. A. Global change and species interactions in terrestrial ecosystems. Ecol. Lett.11, 1351–1363 (2008). Article Google Scholar
Thompson, J. R. et al. Genotypic diversity within a natural coastal bacterioplankton population. Science307, 1311–1313 (2005). ArticleCAS Google Scholar
Brown, M. V., Schwalbach, M. S., Hewson, I. & Fuhrman, J. A. Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ. Microbiol.7, 1466–1479 (2005). ArticleCAS Google Scholar
Allen, E. E. et al. Genome dynamics in a natural archaeal population. Proc. Natl Acad. Sci. USA104, 1883–1888 (2007). ArticleCAS Google Scholar
Hunt, D. E. et al. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science320, 1081–1085 (2008). ArticleCAS Google Scholar
Hennes, K. P., Suttle, C. A. & Chan, A. M. Fluorescently labeled virus probes show that natural virus populations can control the structure of marine microbial communities. Appl. Environ. Microbiol.61, 3623–3627 (1995). CASPubMedPubMed Central Google Scholar
Wommack, K. E., Ravel, J., Hill, R. T. & Colwell, R. R. Hybridization analysis of Chesapeake Bay virioplankton. Appl. Environ. Microbiol.65, 241–250 (1999). CASPubMedPubMed Central Google Scholar
Parada, V., Baudoux, A. C., Sintes, E., Weinbauer, M. G. & Herndl, G. J. Dynamics and diversity of newly produced virioplankton in the North Sea. ISME J.2, 924–936 (2008). ArticleCAS Google Scholar
Golomidova, A., Kulikov, E., Isaeva, A., Manykin, A. & Letarov, A. The diversity of coliphages and coliforms in horse feces reveals a complex pattern of ecological interactions. Appl. Environ. Microbiol.73, 5975–5981 (2007). ArticleCAS Google Scholar
Holmfeldt, K., Middelboe, M., Nybroe, O. & Riemann, L. Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl. Environ. Microbiol.73, 6730–6739 (2007). ArticleCAS Google Scholar
Shoresh, N., Hegreness, M. & Kishony, R. Evolution exacerbates the paradox of the plankton. Proc. Natl Acad. Sci. USA105, 12365–12369 (2008). ArticleCAS Google Scholar
Wittebolle, L. et al. Initial community evenness favours functionality under selective stress. Nature458, 623–626 (2009). ArticleCAS Google Scholar
Benton, T. G., Solan, M., Travis, J. M. & Sait, S. M. Microcosm experiments can inform global ecological problems. Trends Ecol. Evol.22, 516–521 (2007). Article Google Scholar
Brockhurst, M. A., Fenton, A., Roulston, B. & Rainey, P. B. The impact of phages on interspecific competition in experimental populations of bacteria. BMC Ecol.6, 19 (2006). Article Google Scholar
Maynard-Smith, J. Evolution and the Theory of Games. (Cambridge Univ. Press, Cambridge, 1982). Book Google Scholar
Simmons, S. L. et al. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol.6, e177 (2008). Article Google Scholar
Strom, S. L. Microbial ecology of ocean biogeochemistry: a community perspective. Science320, 1043–1045 (2008). ArticleCAS Google Scholar
Fraser, C., Hanage, W. P. & Spratt, B. G. Recombination and the nature of bacterial speciation. Science315, 476–480 (2007). ArticleCAS Google Scholar
Schoenfeld, T. et al. Assembly of viral metagenomes from Yellowstone hot springs. Appl. Environ. Microbiol.74, 4164–4174 (2008). ArticleCAS Google Scholar
Konstantinidis, K. T. & Tiedje, J. M. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol.187, 6258–6264 (2005). ArticleCAS Google Scholar
Ochman, H., Lerat, E. & Daubin, V. Examining bacterial species under the specter of gene transfer and exchange. Proc. Natl Acad. Sci. USA102 (Suppl. 1), 6595–6599 (2005). ArticleCAS Google Scholar
Read, T. D. & Ussery, D. W. Opening the pan-genomics box. Curr. Opin. Microbiol.9, 496–498 (2006). Article Google Scholar
Stent, G. S. Molecular Biology of Bacterial Viruses. (W. H. Freeman & Co, San Francisco,1963). Google Scholar
Rusch, D. B. et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol.5, e77 (2007). Article Google Scholar
Dinsdale, E. A. et al. Functional metagenomic profiling of nine biomes. Nature452, 629–632 (2008). ArticleCAS Google Scholar
Qimron, U., Marintcheva, B., Tabor, S. & Richardson, C. C. Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage. Proc. Natl Acad. Sci. USA103, 19039–19044 (2006). ArticleCAS Google Scholar
Forde, S. E., Thompson, J. N., Holt, R. D. & Bohannan, B. J. Coevolution drives temporal changes in fitness and diversity across environments in a bacteria–bacteriophage interaction. Evolution62, 1830–1839 (2008). PubMed Google Scholar