Article

The bacterial species challenge: Making sense of genetic and ecological diversity

Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.
Science (Impact Factor: 31.48). 03/2009; 323(5915):741-6. DOI: 10.1126/science.1159388
Source: PubMed

ABSTRACT The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology-including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination-mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.

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    • "The urgency of this issue has been highlighted over the last decade, as advances in sequencing technology prompted a boom in the study of microbial diversity in natural environments [5] [6] [7] [8] [9] [10] [11]. In the microbial world, the partitioning problem is intensified by the prevalence of asexual reproduction and horizontal gene transfer [12] [13]. Nevertheless, the currently dominant view in the field is that the partitioned community assumption, while conceptually problematic, is operationally necessary [14] [15] [16] [17]. "
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    ABSTRACT: Most of classical theoretical ecology is based on the assumption that organisms in a community can be naturally partitioned into groups of individuals that can be treated as identical. At the same time, mounting experimental evidence from studies of microbial communities raises the intriguing question whether this intuition is an accurate description of the microbial world. This work builds on Mac Arthur's model of competitive coexistence on multiple resources to construct a framework that does not rely on postulated existence of species as fundamental ecological variables. In one parameter regime, effective "species" with a core and accessory genome naturally appear in this model as emergent concepts. However, the same model allows a smooth transition to a highly diverse regime where the species formalism becomes inadequate. An alternative description is proposed based on the dynamical modes of population fluctuations. This approach provides a naturally hierarchical description of community dynamics which is well-defined even when the species description breaks down. The relevance of this framework for understanding the complexity of naturally observed microbial communities is discussed.
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    • "Also, the genomes would be altered greatly while microbiota survive at various niches in rhizosphere. The environmental gradients in rhizosphere could maintain complex niches, where the accessory genomes of microbial strains have been altered greatly (Fraser et al. 2009). "
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    • "Even more, it is noteworthy that at least one population of each genus presented evidence of expansion that was statistically supported. In clonal and free-living populations of bacteria, evolutionary models predict that populations experience strong fluctuations, either by selective sweeps or by metapopulation dynamics (Fraser et al., 2009; Kopac & Cohan, 2011; Shapiro & Polz, 2014). The results obtained in this study can be explained by these models since the analyzed lineages come from a natural setting and present no evidence of recombination (Table S2; Roberts & Cohan, 1995; Spiers, Buckling & Rainey, 2000; Rebollar et al., 2012). "
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    PeerJ 12/2014; 2(2):e696. DOI:10.7717/peerj.696 · 2.10 Impact Factor
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