What are Bacterial Species?

Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170, USA.
Annual Review of Microbiology (Impact Factor: 13.02). 02/2002; 56(1):457-87. DOI: 10.1146/annurev.micro.56.012302.160634
Source: PubMed

ABSTRACT 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.

Download full-text


Available from: Frederick M Cohan, Apr 19, 2014
  • Source
    • "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). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.The ISME Journal advance online publication, 7 August 2015; doi:10.1038/ismej.2015.137.
    The ISME Journal 08/2015; DOI:10.1038/ismej.2015.137 · 9.27 Impact Factor
  • Source
    • "Because of the central position of sex in theories of speciation in eukaryotes, it has been argued that sex is a necessary requirement for species to arise as independently evolving entities (Maynard Smith and Szathmary 1995). According to population genetic theory, however, an asexual population faced with geographical isolation or divergent selection is also expected to diverge into discrete genetic and phenotypic clusters (Templeton 1989; Cohan 2002; Barraclough et al. 2003). These clusters represent independently evolving entities as defined in evolutionary and general lineage concepts of species (Simpson 1951; De Queiroz 2007). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The possibility for independently evolving entities to form and persist in the absence of sexual recombination in eukaryotes has been questioned; nevertheless, there are organisms that are known to be asexual and that have apparently diversified into multiple species as recognized by taxonomists. These organisms have therefore been identified as an evolutionary paradox. We explore three alternative hypotheses attempting to solve the apparent paradox, focusing on bdelloid rotifers, the most studied group of organisms in which all species are considered asexual: (1) they may have some hidden form of sex; (2) species do not represent biological entities but simply convenient names; and (3) sex may not be a necessary requirement for speciation. We provide ample evidence against the first two hypotheses, reporting several studies supporting (1) bdelloids asexuality from different approaches, and (2) the existence of species from genetics, jaw morphology, ecology, and physiology. Thus, we (3) explore the role of sex in speciation comparing bdelloid and monogonont rotifers, and conclude with some caveats that could still change our understanding of bdelloid species. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email:
    Integrative and Comparative Biology 04/2015; 55(2). DOI:10.1093/icb/icv024 · 2.97 Impact Factor
  • Source
    • "Thus, all RD9 deleted strains lack spacers 9 and 39, and its descendants additionally lack spacer 16 and again its descendants also lack spacers 3 and 40–43; moreover , they incorporated information on the host preference, suggesting the concept of ecotypes for the MTBC. According to Cohan (2002), selective sweeps (selection events) might be the cause for limited divergence within groups of bacteria and these groups should be named ecotypes. Through adaptation of a strain to a new niche it becomes immune to periodic selection events in the other clades and therefore has the characteristics of an ecotype. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Members of the Mycobacterium tuberculosis complex (MTBC) cause a serious disease with similar pathology, tuberculosis; in this review, bovine tuberculosis will be considered as disease caused by any member of the MTBC in bovids. Bovine tuberculosis is responsible for significant economic loss due to costly eradication programs and trade limitations and poses a threat to both endangered and protected species as well as to public health. We here give an overview on all members of the MTBC, focusing on their isolation from different animal hosts. We also review the recent advances made in elucidating the evolutionary and phylogenetic relationships of members of the MTBC. Because the nomenclature of the MTBC is controversial, its members have been considered species, subspecies or ecotypes, this review discusses the possible implications for diagnostics and the legal consequences of naming of new species.
    Research in Veterinary Science 10/2014; 97. DOI:10.1016/j.rvsc.2014.02.009 · 1.51 Impact Factor
Show more