What are Bacterial Species?

Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170, USA.
Annual Review of Microbiology (Impact Factor: 12.18). 02/2002; 56(1):457-87. DOI: 10.1146/annurev.micro.56.012302.160634
Source: PubMed


Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.

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Available from: Frederick M Cohan, Apr 19, 2014
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    • "conflicting species concepts, such as those based on reproduction or morphology, become compatible through accommodation of the evolutionary process (Wei, 1987; de Queiroz, 1998; Cohan, 2002; Cutter, 2013; Ezard, Thomas & Purvis, 2013; Podani, 2013; White, 2013). Importantly the lineage perspective helps us reconsider the process of evolution over long time periods. "
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    ABSTRACT: Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage-splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage-splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage-splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’.
    Biological Journal of the Linnean Society 09/2015; DOI:10.1111/bij.12665 · 2.26 Impact Factor
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    • "One of the most widely accepted models for microbial species is the clonal ecotype model, in which an " ecotype " is defined as " a group of bacteria that are ecologically similar to one another, so similar that genetic diversity within the ecotype is limited by a cohesive force, either periodic selection or genetic drift, or both " (Cohan and Perry 2007). This model posits that, because microorganisms are clonally reproducing, recombination rarely occurs among individuals within a population (Cohan 2002). In such a situation, periodic selective sweeps of adaptive, niche-specific mutations purge genomic diversity within the ecotypes. "
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    Systematic Biology 08/2015; DOI:10.1093/sysbio/syv050 · 14.39 Impact Factor
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    • "Interestingly, around one-third of the OTUs had identity values lower than 95%, half of the OTUs lower than 97% and 2/3 of the OTUs had values lower than 99%. Although the 97% identity is widely used in microbial ecology studies as a broad proxy for 'species' cutoff (Stackebrandt and Goebel, 1994; Cohan, 2002; Hagström et al., 2002), it is well known that this value may integrate different species and overlook putative ecotypes within species with different ecological roles (Fox et al., 1992; Acinas et al., 2004; Stackebrandt, 2006). Therefore, it is safe to assume that we detected at least between 1687 (at 97%) and 2385 (at 99%) putative new prokaryotic OTUs as well as 986 OTUs belonging to putative new genera (at 95%) not present in the standard prokaryotic rRNA gene databases (corresponding to 45.7%, 64.6% and a 26.7% of the total OTUs, respectively). "
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