How do bacteria evolve and speciate in natural environments? How does bacterial evolution relate to bacterial systematics? Exploring these answers is essential because bacteria profoundly impact life in general and, in particular, that of humans. Much insight into bacterial microevolution has come from theoretical and computational studies and from multigenerational laboratory systems ("Experimental Evolution"). These studies, however, do not take into account the diversity of modes of how bacteria can evolve under the complexity of the real world, i.e., nature. We argue, therefore, that for a comprehensive understanding of bacterial microevolution, it is essential to study natural populations. We underline our argument by introducing the Bacillus simplex model from "Evolution Canyon", Israel. This metapopulation splits into different evolutionary lineages that have adapted to the microclimatically different slopes of "Evolution Canyon". It was shown that temperature stress is a major environmental factor driving the B. simplex adaptation and speciation progress. Therefore, this model population has proven highly suitable to study bacterial microevolution in natural habitats. Finally, we discuss the B. simplex intrapopulation divergence of lineages in light of current controversies on bacterial species concepts and taxon identification.
Purchase
Buy instant access (PDF download and unlimited online access):
Institutional Login
Log in with Open Athens, Shibboleth, or your institutional credentials
Personal login
Log in with your brill.com account
Adami, C. 2006a. Digital genetics: unravelling the genetic basis of evolution. Nat. Rev. Genet. 7: 109-118.
Adami, C. 2006b. Reducible complexity. Science 312: 61-63.
Amann, R. 2000. Who is out there? Microbial aspects of biodiversity. Syst. Appl. Microbiol. 23: 1-8.
Aris, R.M., Routh, J.C., Lipuma, J.J., Heath, D.G., Gilligan, P.H. 2001. Lung transplantation for cystic fibrosis patients with Burkholderia cepacia complex. Survival linked to Genomovar type. Am. J. Respir. Crit. Care Med. 164: 2102-2106.
Bergstrom, C.T., Lipsitch, M., Levin, B.R. 2000. Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155: 1505-1519.
Bock, W.J. 2004. Species: the concept, category and taxon. J. Zool. Syst. Evol. Res. 42: 178-190.
Coenye, T., Gevers, D., Van de Peer, Y., Vandamme, P., Swings, J. 2005. Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29: 147-167.
Cohan, F.M. 1994. The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Nat. 143: 965-986.
Cohan, F.M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56: 457-487.
Cohan, F.M. 2006. Toward a conceptual and operational union of bacterial systematics, ecology, and evolution. Proc. R. Soc. Lond. [Biol] 361: 1985-1996.
Darwin, C. 1859. On the origin of species by means of natural selection. John Murray, London.
de Queiroz, K. 2005a. Different species problems and their resolution. BioEssays 27: 1263-1269.
de Queiroz, K. 2005b. Ernst Mayr and the modern concept of species. Proc. Natl. Acad. Sci. USA 102: 6600-6607.
De Soyza, A., McDowell, A., Archer, L., Dark, J.H., Elborn, S.J., Mahenthiralingam, E., Gould, K., Corris, P.A. 2001. Burkholderia cepacia complex genomovars and pulmonary transplantation outcomes in patients with cystic fibrosis. Lancet 358: 1780-1781.
Dekel, E., Alon, U. 2005. Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
Derzhavets, E.M., Korol, A.B., Nevo, E. 1996. Increased male recombination rate in D. melanogaster correlated with population adaptation to stressful conditions. Drosoph. Inform. Serv. 77: 92-94.
Derzhavets, E., Korol, A.B., Pavl�ček, T., Nevo, E. 1997. Adaptation to stressful environment and mutation rate: a case study in Drosophila melanogaster. Drosoph. Inform. Serv. 80: 53-56.
Dvornyk, V., Vinogradova, O., Nevo, E. 2002. Long-term microclimatic stress causes rapid adaptive radiation of kaiABC clock gene family in a cyanobacterium, Nostoc linckia, from "Evolution Canyons" I and II, Israel. Proc. Natl. Acad. Sci. USA 99: 2082-2087.
Elena, S.F., Lenski, R.E. 2003. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4: 457-469.
Finkel, M., Chikatunov, V., Nevo, E. 2002. Coleoptera of "Evolution Canyon" II: Lower Nahal Keziv, Western Upper Galilee, Israel. Pensoft Publishers, Sofia, Bulgaria.
Friedberg, E.C., Walker, G.C., Siede, W. 1995. DNA repair and mutagenesis. ASM Press, Washington, D.C.
Gans, J., Wolinsky, M., Dunbar, J. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
Gevers, D., Cohan, F.M., Lawrence, J.G., Spratt, B.G., Coenye, T., Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. 2005. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3: 733-739.
Grishkan, I., Nevo, E., Wasser, S.P., Pavl�ček, T. 2000. Spatiotemporal distribution of soil microfungi in "Evolution Canyon", Lower Nahal Oren, Mount Carmel, Israel. Isr. J. Plant. Sci. 48: 297-308.
Heyrman, J., Logan, N.A., Rodr�guez-D�az, M., Scheldeman, P., Lebbe, L., Swings, J., Heyndrickx, M., De Vos, P. 2005. Study of mural painting isolates, leading to the transfer of ‘Bacillus maroccanus’ and ‘Bacillus carotarum’ to Bacillus simplex, emended description of Bacillus simplex, re-examination of the strains previously attributed to ‘Bacillus macroides’ and description of Bacillus muralis sp. nov. Int. J. Syst. Evol. Microbiol. 55: 119-131.
Ishii, K., Matsuda, H., Iwasa, Y., Sasaki, A. 1989. Evolutionary stable mutation rate in a periodically changing environment. Genetics 121: 163-174.
Jessup, C.M., Kassen, R., Forde, S.E., Kerr, B., Buckling, A., Rainey, P.B., Bohannan, J. 2004. Big questions, small worlds: microbial model systems in ecology. Trends Ecol. Evol. 19: 189-197.
Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E., Schulman, A.H. 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. USA 97: 6603-6607.
Kassen, R., Llewellyn, M., Rainey, P.B. 2004. Ecological constraints on diversification in a model adaptive radiation. Nature 431: 984-988.
Korol, A., Rashkovetsky, E., Iliadi, K., Michalak, P., Ronin, Y., Nevo, E. 2000. Nonrandom mating in Drosophila melanogaster laboratory populations derived from closely adjacent ecologically contrasting slopes at "Evolution Canyon". Proc. Natl. Acad. Sci. USA 97: 12637-12642.
Lamb, B.C., Saleem, M., Scott, W., Thapa, N., Nevo, E. 1998. Inherited and environmentally induced differences in mutation frequencies between wild strains of Sordaria fimicola from "Evolution Canyon". Genetics 149: 87-99.
Lenski, R.E., Ofria, C., Collier, T.C., Adami, C. 1999. Genome complexity, robustness and genetic interactions in digital organisms. Nature 400: 661-664.
Lenski, R.E., Ofria, C., Pennock, R.T., Adami, C. 2003. The evolutionary origin of complex features. Nature 423: 139-144.
MacLean, R.C., Bell, G., Rainey, P.B. 2004. The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 101: 8072-8077.
Maharjan, R., Seeto, S., Notley-McRobb, L., Ferenci, T. 2006. Clonal adaptive radiation in a constant environment. Science 313: 514-517.
Maiden, M.C., Bygraves, J.A., Feil, E., Morelli, G., Russell, J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D.A., Feavers, I.M., Achtman, M., Spratt, B.G. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 3140-3145.
Majewski, J., Cohan, F.M. 1999. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152: 1459-1474.
Mayr, E. 1969. The biological meaning of species. Biol. J. Linn. Soc. 1: 311-320.
Mayr, E. 1982. The growth of biological thought: diversity, evolution, and inheritance. Harvard Univ. Press, Cambridge, MA.
Michalak, R, Minkov, I., Helin, A., Lerman, D.N., Bettencourt, B.R., Feder, M.E., Korol, A.B., Nevo, E. 2001. Genetic evidence for adaptation-driven incipient speciation of Drosophila melanogaster along a microclimatic contrast in "Evolution Canyon," Israel. Proc. Natl. Acad. Sci. USA 98: 13195-13200.
Nevo, E. 1995. Asian, African and European biota meet at "Evolution Canyon" Israel: Local tests of global biodiversity and genetic diversity patterns. Proc. R. Soc. Lond. [Biol] 262: 149-155.
Nevo, E. 1997. Evolution in action across phylogeny caused by microclimatic stresses at "Evolution Canyon". Theor. Popul. Biol. 52: 231-243.
Nevo, E. 2001. Evolution of genome-phenome diversity under environmental stress. Proc. Natl. Acad. Sci. USA 98: 6233-6240.
Nevo, E., Beharav, A., Meyer, R.C., Hackett, C.A., Forster, B.P., Russell, J.R., Powell, W. 2005. Genomic microsatellite adaptive divergence of wild barley by microclimatic stress in ‘Evolution Canyon’, Israel. Biol. J. Linn. Soc. 84: 205-224.
Nicholson, W.L., Munakata, N., Horneck, G., Melosh, H.J., Setlow, P. 2000. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol. Mol. Biol. Rev. 64: 548-572.
Orr, H.A. 2005a. The genetic theory of adaptation: a brief history. Nat. Rev. Genet. 6: 119-127.
Orr, H.A. 2005b. Theories of adaptation: what they do and don't say. Genetica 123: 3-13.
Osmon, S., Ward, S., Fraser, V.J., Kollef, M.H. 2004. Hospital mortality for patients with bacteremia due to Staphylococcus aureus or Pseudomonas aeruginosa. Chest 125: 607-616.
Palys, T., Nakamura, L.K., Cohan, F.M. 1997. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47: 1145-1156.
Papke, R.T., Ramsing, N.B., Bateson, M.M., Ward, D.M. 2003. Geographical isolation in hot spring cyanobacteria. Environ. Microbiol. 5: 650-659.
Pavl�ček, T., Sharon, D., Kravchenko, V., Saaroni, H., Nevo, E. 2003. Microclimatic interslope differences underlying biodiversity contrasts in "Evolution Canyon", Mt. Carmel, Israel. Isr. J. Earth Sci. 52: 1-9.
Pernthaler, J., Amann, R. 2005. Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol. Mol. Biol. Rev. 69: 440-461.
Rainey, P.B., Travisano, M. 1998. Adaptive radiation in a heterogeneous environment. Nature 394: 69-72.
Rashkovetsky, E., Iliadi, K., Michalak, P., Lupu, A., Nevo, E., Feder, M.E., Korol, A. 2006. Adaptive differentiation of thermotolerance in Drosophila along a microclimatic gradient. Heredity 96: 353-359.
Rossell�-Mora, R., Amann, R. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25: 39-67.
Saleem, M., Lamb, B.C., Nevo, E. 2001. Inherited differences in crossing over and gene conversion frequencies between wild strains of Sordaria fimicola from "Evolution Canyon". Genetics 159: 1573-1593.
Sikorski, J., Nevo, E. 2005. Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at "Evolution Canyons" I and II, Israel. Proc. Natl. Acad. Sci. USA 102: 15924-15929.
Sikorski, J., Nevo, E. 2007. Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of "Evolution Canyon" I and II, Israel. Environ. Microbiol. 9: 716-726.
Simpson, G.G. 1961. Principles of animal taxonomy. Columbia University Press, New York.
Sniegowski, P.D., Gerrish, P.J., Johnson, T., Shaver, A. 2000. The evolution of mutation rates: separating causes from consequences. Bioessays 22: 1057-1066.
Stackebrandt, E., Goebel, B. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846-849.
Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A., K�mpfer, P., Maiden, M.C., Nesme, X., Rossello-Mora, R., Swings, J., Tr�per, H.G., Vauterin, L., Ward, A.C., Whitman, W.B. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043-1047.
Tanaka, M.M., Bergstrom, C.T., Levin, B.R. 2003. The evolution of mutator genes in bacterial populations: the roles of environmental change and timing. Genetics 164: 843-854.
Templeton, A.R. 1989. The meaning of species and speciation: a genetic perspective. In: Otte, D., Endler, J.A., eds. Speciation and its consequences. Sinauer, Sunderland, MA.
Torsvik, V., �vre�s, L., Thingstad, T.F. 2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296: 1064-1066.
van Valen, L. 1976. Ecological species, multispecies, and oaks. Taxon 25: 233-239.
Whitman, W.B., Coleman, D.C., Wiebe, W.J. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95: 6578-6583.
Wilke, C.O., Wang, J.L., Ofria, C., Lenski, R.E., Adami, C. 2001. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412: 331-333.
Zavascki, A., Barth, A., Fernandes, J., Moro, A., Goncalves, A., Goldani, L. 2006. Reappraisal of Pseudomonas aeruginosa hospital-acquired pneumonia mortality in the era of metallo-beta-lactamase-mediated multidrug resistance: a prospective observational study. Crit. Care 10: R114.
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 340 | 154 | 26 |
| Full Text Views | 32 | 2 | 0 |
| PDF Views & Downloads | 58 | 3 | 0 |
How do bacteria evolve and speciate in natural environments? How does bacterial evolution relate to bacterial systematics? Exploring these answers is essential because bacteria profoundly impact life in general and, in particular, that of humans. Much insight into bacterial microevolution has come from theoretical and computational studies and from multigenerational laboratory systems ("Experimental Evolution"). These studies, however, do not take into account the diversity of modes of how bacteria can evolve under the complexity of the real world, i.e., nature. We argue, therefore, that for a comprehensive understanding of bacterial microevolution, it is essential to study natural populations. We underline our argument by introducing the Bacillus simplex model from "Evolution Canyon", Israel. This metapopulation splits into different evolutionary lineages that have adapted to the microclimatically different slopes of "Evolution Canyon". It was shown that temperature stress is a major environmental factor driving the B. simplex adaptation and speciation progress. Therefore, this model population has proven highly suitable to study bacterial microevolution in natural habitats. Finally, we discuss the B. simplex intrapopulation divergence of lineages in light of current controversies on bacterial species concepts and taxon identification.
| All Time | Past 365 days | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 340 | 154 | 26 |
| Full Text Views | 32 | 2 | 0 |
| PDF Views & Downloads | 58 | 3 | 0 |