Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater

Park, Sanghwa; Song, Jaeho; Yoshizawa, Susumu; Choi, Jae‐Suk; Cho, Jang-Cheon; Kogure, Kazuhiro

doi:10.1099/ijs.0.046318-0

Cited by 21 publications

(18 citation statements)

References 25 publications

(20 reference statements)

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“… All data are from the original descriptions (Alfredsson et al, 1988; Antón et al, 2002; Choi et al, 2009; Vaisman and Oren, 2009; Marteinsson et al, 2010; Park et al, 2011, 2013; Urios et al, 2006, 2008; Makhdoumi-Kakhki et al, 2012; Wang et al, 2012, 2013a,b; Cho et al, 2013) except for the polar lipids of Salinibacter ruber (Corcelli et al, 2004) and Salisaeta longa (Baronio et al, 2010). Question marks indicate missing information.…”

Section: Resultsmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

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Section: Resultsmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…The observed transition from a halophilic and desiccation-tolerant surface community to one dominated by marine taxa would then result from both niche and stochastic processes. The abundance of such halophiles as Halarchaeum, Rhodothermaceae, and Truepera [86][87][88] did not differ by depth or hydration and are likely able to exploit niches unaffected by differences in soil moisture. They would only become less abundant relative to marine taxa due to random flood immigration events.…”

Section: Discussionmentioning

confidence: 93%

The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

2020

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Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles.

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“…The family Rhodothermaceae is placed under the order Cytophagales of the class Cytophagia within the phylum Bacteroidetes . At the time of writing, Rhodothermaceae consisted of six genera: Rhodothermus (Alfredsson et al, 1988 ; Marteinsson et al, 2010 ), Salinibacter (Antón et al, 2002 ; Makhdoumi-Kakhki et al, 2012 ), Salisaeta (Vaisman and Oren, 2009 ), Rubricoccus (Park et al, 2011 ), Rubrivirga (Park et al, 2013 ), and the recently described genus Longimonas (Xia et al, 2015 ). Rhodothermaceae is a family of gram-negative, non-sporulating, chemoorganotrophic aerobes shaped as rods or cocci, and most strains are pigmented (Park et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Genome Analysis of a New Rhodothermaceae Strain Isolated from a Hot Spring

et al. 2016

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A bacterial strain, designated RA, was isolated from water sample of a hot spring on Langkawi Island of Malaysia using marine agar. Strain RA is an aerophilic and thermophilic microorganism that grows optimally at 50–60°C and is capable of growing in marine broth containing 1–10% (w/v) NaCl. 16S rRNA gene sequence analysis demonstrated that this strain is most closely related (<90% sequence identity) to Rhodothermaceae, which currently comprises of six genera: Rhodothermus (two species), Salinibacter (three species), Salisaeta (one species), Rubricoccus (one species), Rubrivirga (one species), and Longimonas (one species). Notably, analysis of average nucleotide identity (ANI) values indicated that strain RA may represent the first member of a novel genus of Rhodothermaceae. The draft genome of strain RA is 4,616,094 bp with 3630 protein-coding gene sequences. Its GC content is 68.3%, which is higher than that of most other genomes of Rhodothermaceae. Strain RA has genes for sulfate permease and arylsulfatase to withstand the high sulfur and sulfate contents of the hot spring. Putative genes encoding proteins involved in adaptation to osmotic stress were identified which encode proteins namely Na+/H+ antiporters, a sodium/solute symporter, a sodium/glutamate symporter, trehalose synthase, malto-oligosyltrehalose synthase, choline-sulfatase, potassium uptake proteins (TrkA and TrkH), osmotically inducible protein C, and the K+ channel histidine kinase KdpD. Furthermore, genome description of strain RA and comparative genome studies in relation to other related genera provide an overview of the uniqueness of this bacterium.

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Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater

Cited by 21 publications

References 25 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration

Genome Analysis of a New Rhodothermaceae Strain Isolated from a Hot Spring

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