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

  title={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 },
  author={Radhey S. Gupta and Sohail Naushad and Reena Fabros and Mobolaji Adeolu},
  journal={Antonie van Leeuwenhoek},
The evolutionary interrelationships between the archaeal organisms which comprise the class Halobacteria have proven difficult to elucidate using traditional phylogenetic tools. The class currently contains three orders. However, little is known about the family level relationships within these orders. In this work, we have completed a comprehensive comparative analysis of 129 sequenced genomes from members of the class Halobacteria in order to identify shared molecular characteristics, in the… 

Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.

The work presented here represents the first comprehensive, genome-scale taxonomic analysis of the entirety of the order 'Enterobacteriales', and a proposal is made here for the order Enterobacterales ord. nov. which consists of seven families.

Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena

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.

A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera

The taxonomic reclassifications proposed here accurately reflect the species relationships within this group of Tenericutes and they should lead to a better understanding of their biological and pathogenic characteristics.

Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera

The taxonomic reclassifications proposed here, which more accurately portray the genetic diversity among the Tenericutes/Mycoplasma species, provide a new framework for understanding the biological and clinical aspects of these important microbes.

Halocin C8: an antimicrobial peptide distributed among four halophilic archaeal genera: Natrinema, Haloterrigena, Haloferax, and Halobacterium

The full-length halC8 gene is restricted and consistently found in the genomes of strains belonging to the phylogenetically related genera Natrinema and Haloterrigena, along with transport and regulation genes, and was shown to contain five disulphide bridges, presumably conferring a compact structure resistant to harsh environmental conditions.

Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments

This review focuses on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges.

Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006.

Multilocus sequence analysis using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB', and phylogenetic analysis based on the 757 core protein sequences obtained from their genomes showed that Hrr.

Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades

Detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales have identified numerous molecular markers that are specific for this group of bacteria and are predicted to play important roles in modifying cellular functions of the affected proteins.

Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

Comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species and three novel genera are proposed, establishing a coherent taxonomy and evolutionary history for this family.



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

This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within the Halobacteriales.

Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) a

The results of phylogenetic/compatibility studies along with the species distribution patterns of 22 identified CSIs provide compelling evidence that the current genus Thermotoga is comprised of two evolutionary distinct groups and that it should be divided into two genera.

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.

In comparing the physiologies of the two halophilic archaea, in addition to the expected extensive similarity, it is discovered several differences in their metabolic strategies and physiological responses such as distinct pathways for arginine breakdown in each halophile.

Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacte

We report here detailed phylogenetic and comparative analyses on 11 sequenced genomes from the phylum Aquificae to identify molecular markers that are specific for the species from this phylum or its

Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea.

Phylogenetic analysis revealed that the strain formed a distinct lineage within the family Halobacteriaceae, and it is proposed that strain DS12T represents the type strain of a novel species in a new genus, Halalkalicoccus tibetensis gen. nov.

Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene.

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.

Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences.

  • A. Wright
  • Biology
    International journal of systematic and evolutionary microbiology
  • 2006
Trees produced using distance-matrix and neighbour-joining methods affirm with strong bootstrap support that the members of the order Halobacteriales are a monophyletic group and additional representation from the currently monospecific genera and/or the use of other macromolecules may be required to resolve the relationships within the orders.

Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui.

Comparison of H. marismortui sequences to the 16S gene sequences from related halophilic genera suggests that (i) in diverging genera, mutational differences in 16S Gene sequences are not clustered but rather are more generally distributed throughout the length of the16S sequence, and (ii) the rrnB sequence, particularly within the 508-823 domain, is more different from the out group sequences than is the rnA sequence.

Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species

Based upon the results of phylogenetic analyses, the identified CSIs and the pathogenicity profile of Burkholderia species, the emended genus Burk holderia will correspond to the Clade I and it will contain only the clinically relevant and phytopathogenic BurkHolderia species.

Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales

The study of leucyl-tRNA synthetase in haloarchaea illustrates the importance of gene transfer originating in lineages that went extinct since the transfer occurred, and reveals that LeuRS evolved independently of its cognate tRNA.