Polaribacter sejongensis sp. nov., isolated from Antarctic soil, and emended descriptions of the genus 
               
                  Polaribacter
               
            , 
               
                  Polaribacter butkevichii
               
             and 
               
                  Polaribacter irgensii

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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“…The description is as given by Kim et al (2013) with the following modification. The genomic G+C content of the type strain is 34.5%.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…It also has a comparatively low GCcontent (33%). However, the Polaribacter MAG cluster (BACL22), which has the largest genome and lowest gene density of the Bacteroidetes genome MAG clusters, has equally low GCcontent (32%), as previously observed in planktonic and algaeattached Polaribacter isolates (66)(67)(68)(69)(70)(71)(72)(73) . Since, in general, GCcontent correlates very weakly with either genome size or gene density (Fig.…”

Section: Genome Streamlining and Inferred Cell Sizesmentioning

confidence: 52%

Metagenome-assembled genomes uncover a global brackish microbiome

Hugerth

Larsson

Alneberg

et al. 2015

Preprint

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Background: Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. Results: We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts.

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“…Association of Polaribacter spp. with phytoplankton was also observed in the open North Atlantic (Gó mez-Pereira et al, 2012) and the coastal North Sea (Bennke et al, 2013) and has been inferred in a recent study on an Antarctic polynya (Kim et al, 2013). Because of their presence in cold and temperate waters, in oligotrophic and copiotrophic nutrient regimes within open ocean and coastal zones, members of the genus Polaribacter have recently been recognized as 'widely distributed in marine habitats' (Nedashkovskaya et al, 2013).…”

Section: Introductionmentioning

confidence: 80%

“…Pure culture studies on Polaribacter strains have demonstrated growth on biopolymers, such as aesculin, casein, starch and gelatin (Gosink et al, 1998;Nedashkovskaya et al, 2005;Yoon et al, 2006;Lee et al, 2011;Fukui et al, 2013;Kim et al, 2013;Nedashkovskaya et al, 2013). Growth on algal polysaccharides has not yet been investigated in detail, but Polaribacter co-occurrences with phytoplankton and metagenome data support this capability (Gó mez-Pereira et al, 2012;Teeling et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom

Xing¹,

et al. 2014

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Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfataserich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.

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Polaribacter sejongensis sp. nov., isolated from Antarctic soil, and emended descriptions of the genus Polaribacter , Polaribacter butkevichii and Polaribacter irgensii

Cited by 36 publications

References 26 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

Metagenome-assembled genomes uncover a global brackish microbiome

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom

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