Re-evaluating prokaryotic species

@article{Gevers2005ReevaluatingPS,
  title={Re-evaluating prokaryotic species},
  author={Dirk Gevers and Frederick Cohan and Jeffrey G. Lawrence and Brian G. Spratt and Tom Coenye and Edward J. Feil and Erko Stackebrandt and Yves Van de Peer and Peter A. Vandamme and Fabiano Lopes Thompson and Jean Swings},
  journal={Nature Reviews Microbiology},
  year={2005},
  volume={3},
  pages={733-739}
}
There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we… 
Searching for species in haloarchaea
TLDR
It is suggested that no nonarbitrary way to circumscribe “species” is likely to emerge for the haloarchaeal genus Halorubrum, or by extension, to apply generally across prokaryotes, because barriers to exchange between them are leaky.
Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification
TLDR
There appears to be a tendency to classify new species on the basis of comparative sequence analyses of 16S rRNA gene sequences and other gene sequence data (multilocus sequence analyses, MLSA), contrary to the indications of other data.
On a Non-Discrete Concept of Prokaryotic Species
TLDR
A continuous species concept for microorganisms is proposed, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea, and could be extended to eukaryotic microorganisms.
A critique of prokaryotic species concepts.
Developments in DNA sequencing and population genetics analyses have revealed unanticipated complexity in prokaryotic variation. The observation that genetic traits are horizontally inherited at
Taxonomic Characterization of Prokaryotic Microorganisms
TLDR
This chapter presents microbiologists in biotechnology and molecular biology with the basic conceptual framework and the currently accepted procedures for characterization and consistent naming of newly isolated prokaryotic strains.
Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features
TLDR
A new taxonomic framework for Parasynechococcus is proposed based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data.
The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity
TLDR
The need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion is emphasized, and the resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 56 REFERENCES
Polyphasic taxonomy, a consensus approach to bacterial systematics.
TLDR
In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae.
A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model.
TLDR
The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree.
What are bacterial species?
  • F. Cohan
  • Biology, Environmental Science
    Annual review of microbiology
  • 2002
TLDR
These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species, which is more like a genus than a species.
Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data.
TLDR
Sequence similarity clustering in protein-coding genes is recommended as a primary criterion for demarcating taxa and can be expected to disclose many previously unknown ecological populations of bacteria.
Phylogeny and Molecular Identification of Vibrios on the Basis of Multilocus Sequence Analysis
TLDR
Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences, and it can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins.
TLDR
To standardize the set of protein-coding loci assayed in bacterial genomes, over 100 widely distributed genes were examined to identify sets of universal primers for use in the PCR amplification of protein coding regions that are common to virtually all bacteria.
How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity.
TLDR
Although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.
Diversity and significance of Burkholderia species occupying diverse ecological niches.
TLDR
An overview of the taxonomic and ecological diversity of the Burkholderia genus with particular emphasis on strains belonging to the Burk holderia cepacia complex is given and the important question whether 'good' and 'bad' strains are actually the same is addressed.
Gradual evolution in bacteria: evidence from Bacillus systematics.
The bacterial genome projects have suggested a central role for horizontal transfer in bacterial adaptation, but it is difficult to rule out an adaptive role for ordinary genetic change in existing
Ecology and evolution of bacterial microdiversity.
TLDR
Information available from some of the first complete genome sequences of bacteria was used to highlight possible mechanisms of molecular evolution through which mutations are created; these include mutator enzymes.
...
1
2
3
4
5
...