Bacterial Species Concepts

Abstract

To classify bacteria at the species level, systematists may choose between concepts based in theory versus the theory-free definitions used in the practice and tradition of systematics. Theory-based approaches aim to demarcate species as groups that hold certain species-like, dynamic properties. Following Ernst Mayr, many zoologists have attempted to demarcate their species as cohesive lineages—that is, species are classified so that populations of the same species are hindered from diverging owing to recombination between them. Some bacterial systematists have argued for extending recombination-based demarcation to bacterial species. However, both theoretical and experimental evidence argue that recombination is unlikely to hinder either the splitting of bacterial species or their further divergence, owing to the low frequency of recombination in bacteria, although this conclusion is not universally accepted. Among alternative, dynamic properties ascribed to bacterial species is that each species is ecologically distinct and irreversibly separate from other species; moreover, each species is cohesive in that some force constrains diversification within a species. In the rarely recombining bacteria, this force of cohesion may be natural selection favoring novel adaptive mutations within an ecologically homogeneous group (an ecotype). The cohesive, species-like ecotypes may be recognized as sequence clusters, and many such ecotypes may fit within the more broadly defined species recognized by the traditions of bacterial systematics. Alternatively, a “speciation spectrum” model argues that, depending on the bacterial group, either selection or genetic exchange may be more important in the cohesion of species—here, lineages may be classified by their ability to coexist as a result of some combination of ecological divergence and sexual isolation. Most bacterial systematists defer to theory-free traditions on the quantity of diversity that should be included within a species. As the criteria for discovering and characterizing bacterial taxa have shifted from phenotypes to various sequence and whole-genome characters, systematists have aimed to recalibrate the threshold of divergence within species with one aim—that species should appear as clusters with clear phenotypic and molecular gaps between them. Recent developments suggest that theory-based and tradition-based systematics may be able to reach a rapprochement, in that the traditional species recognized by most systematists as well as the theory-based ecotypes may both be subject to a kind of cohesion. Molecular characterizations of bacterial diversity have shown that systematists will never come close to describing all bacterial species unless radical changes are made in how species can be classified. To characterize and classify all bacterial diversity at all taxonomic levels, from infraspecific ecotypes to species to phyla, systematists will need to streamline classification using genome-based methods.

Keywords

Identifiers

DOI

10.1093/obo/9780199941728-0156

Journal

Evolutionary Biology

Year

2024