A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales.

@article{Papke2011AMS,
  title={A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales.},
  author={R Thane Papke and Emma White and Prajwal Reddy and Griffin Weigel and Masahiro Kamekura and Hiroaki Minegishi and Ron Usami and Antonio Ventosa},
  journal={International journal of systematic and evolutionary microbiology},
  year={2011},
  volume={61 Pt 12},
  pages={
          2984-95
        }
}
  • R. Papke, E. White, +5 authors A. Ventosa
  • Published 1 December 2011
  • Biology
  • International journal of systematic and evolutionary microbiology
Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA… 
View on PubMed
ijs.microbiologyresearch.org
41 Citations
Highly Influential Citations
1
Background Citations
17
Methods Citations
13

Figures and Tables from this paper

41 Citations

Citation Type

Citation Type

Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus Salinivibrio
TLDR
A MultiLocus Sequence Analysis of the new isolates and the type strains of the species of Salinivibrio based on the individual as well as concatenated sequences of four housekeeping genes found four clearly differentiated species-like clusters called phylogroups to validate the MLSA study.
A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae
TLDR
A comprehensive comparative analysis of 129 sequenced genomes from members of the class Halobacteria is completed in order to identify shared molecular characteristics, in the forms of conserved signature insertions/deletions (CSIs) and Conserved signature proteins (CSPs), which can provide reliable evidence, independent of phylogenetic trees, that the species from the groups in which they are found are specifically related to each other due to common ancestry.
Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations
TLDR
This study examines the genetic and genomic variation of cultured, naturally co-occurring environmental populations of Halobacteria and indicates that accumulation of genomic variation is rapid: faster than the rate of third codon substitutions.
Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure
TLDR
The data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.
Taxonomy of halophilic Archaea: current status and future challenges
  • A. Oren
  • Biology, Environmental Science
    Extremophiles
  • 2014
TLDR
Metagenomic studies in an Antarctic lake showed that large identical regions of up to 35 kb in length can be shared by members of different genera living together in the same environment, which has important implications not only for the taxonomy of the Halobacteriaceae, but also for species concepts and questions on taxonomy and classification for prokaryotic microorganisms in general.
Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena
TLDR
The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes clearly indicate that the species Halenerrigena hispanica, Haloterrigena limicola, Halkerrigena longa, Halotolerans, and Haloter Rigena mahii should be transferred to the genus Natrinema, while other species should remain but some of the species should be reassigned.
Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake.
TLDR
DNA-DNA hybridization studies and average nucleotide identity confirmed that strain C49T constitutes a distinct genospecies, for which the name Halorubrum persicum sp.
Gene Transfer Mechanisms, Population Genetics/Genomics and the Evolution of Haloarchaea
TLDR
Evidence indicating the evolutionary history of haloarchaea is riddled with gene transfer events and homologous recombination is presented, and the impact of LGT on the evolution of this halophilic group is discussed.
Quantifying Homologous Replacement of Loci between Haloarchaeal Species
TLDR
These findings are unexpected, because the transfer and homologous recombination of relaxed core genes between members of the class Halobacteria disrupts the coevolution of genes; however, the generation of new combinations of divergent but functionally related genes may lead to adaptive phenotypes not available through cumulative mutations and recombination within a single population.
Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake.
TLDR
Data obtained in this study show that the two strains represent a novel species, for which the name Halorubrum halodurans sp.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 50 REFERENCES
Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene.
TLDR
The full sequence of the rpoB' gene may provide a supplementary tool for determining the phylogenetic position of new isolates, and Phylogenetic trees reconstructed from nucleotide sequences and deduced amino acid sequences by the maximum-likelihood method demonstrated that multiple species/strains in most genera individually formed cohesive clusters.
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies
TLDR
The single-copy gene rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution.
A multilocus sequence analysis of the genus Xanthomonas.
Intragenomic Heterogeneity and Intergenomic Recombination among Haloarchaeal rRNA Genes
TLDR
It is suggested that intragenomic heterogeneity of rRNA operons is an ancient and stable trait in several lineages of the Halobacteriales.
Intragenomic 16S rDNA Divergence in Haloarcula marismortui Is an Adaptation to Different Temperatures
TLDR
This study supports the idea that divergent rRNA genes can be adaptive, with different variants being functional under different environmental conditions (e.g., temperature), and the use of 16S rDNA as a phylogenetic marker and indicator of biodiversity should be used with caution.
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.
Genomic plasticity in prokaryotes: the case of the square haloarchaeon
TLDR
This work analyzed genomic islands (GI) in the genome of Haloquadratum walsbyi strain DSM 16790 and compared them with the complete sequence of some fosmids from the environmental library, finding two of the islands overlapped with two large guanine and cytosine (GC)-rich regions that showed evidence of high variability through mobile elements.
Use of rpoB Gene Analysis for Detection and Identification of Bartonella Species
TLDR
This study investigated the possible identification of various Bartonella species by comparison of RNA polymerase beta-subunit gene (rpoB) sequences and found three restriction enzymes useful for discerning the different strains by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis.
Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies
TLDR
It is found that halophilic archaea dominate the archaeal populations in these three hypersaline environments and show that culturability of the organisms predicted by molecular surveys might strongly depend on the habitat chosen.
Microbial life at high salt concentrations: phylogenetic and metabolic diversity
TLDR
Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range.
...
1
2
3
4
5
...