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’.
    Full-text · Article · Feb 2016 · Biological Journal of the Linnean Society
    • "The importance of these and other drivers is supported by physiological studies that have demonstrated differences among its clades in optimal light intensity (Moore and Chisholm, 1999), temperature (Moore et al., 1995;Johnson et al., 2006), light harvesting (Hess et al., 2001), virus specificities (Sullivan et al., 2003) and nutrient assimilation (Moore et al., 2002Moore et al., , 2005) among other properties. Hence, the major phylogenetic clades of Prochlorococcus are often referred to as 'ecotypes' (sensuCohan, 2002) because they partition the ocean based on their niche envelope. Genomic (Rocap et al., 2003;Malmstrom et al., 2013) and metagenomic (Rusch et al., 2007;Martiny et al., 2009a;Dupont et al., 2014) evidence provides additional mechanistic support for ecological diversification among the phylogenetic clades and further shows distinct patterns of gene gain and loss (Kettler et al., 2007) associated with the environment. "
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    ABSTRACT: The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some 'sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.The ISME Journal advance online publication, 22 January 2016; doi:10.1038/ismej.2015.244.
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    • "We hypothesize that the clonal population structure of VV, which comprised STs with some recombination potential, may be influenced by ecological factors that restrict the breakdown of linkage disequilibrium. Consistent with this hypothesis, V. cholerae and Haemophilus influenza have been shown to maintain clonal population structures, even though these organisms are naturally transformable[88,118,120]. Alternatively, VV could be comprised of distinct eco- types[121], between which recombination is limited. According to the ecotype model of bacterial species, in which distinct ecotypes evolve primarily by periodic selection or selective sweep, alleles are likely to be in significant linkage disequilibrium[122]. "
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    ABSTRACT: The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23–35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer’s tests) detected significant evidence of recombination. Tajima’s D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus.
    Full-text · Article · Nov 2015 · PLoS ONE
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