Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

Breider, Sven; Scheuner, Carmen; Schümann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans‐Peter; Brinkhoff, Thorsten; Göker, Markus

doi:10.3389/fmicb.2014.00416

Cited by 74 publications

(50 citation statements)

References 77 publications

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“…For instance, horizontal gene transfer is known as a cause of topological conflict between analyses of single genes and has even been be used to argue against hierarchical classification (Bapteste and Boucher, 2009; Klenk and Göker, 2010). However, adding more genes, up to virtually all genes available in a genome, increases support in phylogenomic analyses (Breider et al, 2014), indicating that there is a strong hierarchical signal. In contrast, selection of few genes (or any number of characters not on the same order of magnitude as the overall number of genomic characters) can hardly be called genome-scale and also depends on assumptions about the relative suitability of genes for the analysis (Lienau and DeSalle, 2009; Klenk and Göker, 2010).…”

Section: Discussionmentioning

confidence: 99%

“…The anaerobic Bacteroidia used to be considered separate from the aerobic groups such as Flavobacteriia and Cytophagia , but 16S rRNA gene sequencing clarified their interconnections (Paster et al, 1985; Weisburg et al, 1985; Woese, 1987). Despite its usefulness in resolving such taxonomic questions, the 16S rRNA gene contains only a limited number of characters and thus usually yields only partially resolved phylogenies, i.e., trees with many statistically unsupported branches (Klenk and Göker, 2010; Breider et al, 2014). Recently, Munoz et al (2016) revised the phylogeny of Bacteroidetes and removed the incertae sedis taxa from the Balneola group and Rhodothermaceae ( Bacteroidetes Order II.…”

Section: Introductionmentioning

confidence: 99%

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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: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…Strains within this group share >89% identity of the 16S rRNA gene (Brinkhoff et al , 2008; Luo and Moran, 2014) but a reliable delineation of this group from other Rhodobacteraceae cannot be carried out with this gene (Breider et al , 2014), as branch support and other rationales for suggested 16S rRNA gene-derived Rhodobacteracea e lineages (Pujalte et al , 2014) are lacking.…”

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confidence: 99%

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

et al. 2017

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Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As ‘Roseobacter clade', these ‘roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term ‘Roseobacter group' for the marine Rhodobacteraceae strains.

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“…16S rRNA gene analysis places strain Y4I within the Phaeobacter genus; however, the researchers who published a recent genome-scale study (39) suggested that a formal reclassification of this genus may be forthcoming. We have previously demonstrated that indigoidine production is an exclusively surface-attached phenotype in Y4I and that its production allows this strain to outcompete Vibrio fischeri for surface niches in coculture (28).…”

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Phaeobacter sp. Strain Y4I Utilizes Two Separate Cell-to-Cell Communication Systems To Regulate Production of the Antimicrobial Indigoidine

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et al. 2015

Appl Environ Microbiol

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The marine roseobacter Phaeobacter sp. strain Y4I synthesizes the blue antimicrobial secondary metabolite indigoidine when grown in a biofilm or on agar plates. Prior studies suggested that indigoidine production may be, in part, regulated by cell-to-cell communication systems. Phaeobacter sp. strain Y4I possesses two luxR and luxI homologous N-acyl-L-homoserine lactone (AHL)-mediated cell-to-cell communication systems, designated pgaRI and phaRI. We show here that Y4I produces two dominant AHLs, the novel monounsaturated N-(3-hydroxydodecenoyl)-L-homoserine lactone (3OHC 12:1 -HSL) and the relatively common N-octanoyl-L-homoserine lactone (C 8 -HSL), and provide evidence that they are synthesized by PhaI and PgaI, respectively. A Tn5 insertional mutation in either genetic locus results in the abolishment (pgaR::Tn5) or reduction (phaR::Tn5) of pigment production. Motility defects and denser biofilms were also observed in these mutant backgrounds, suggesting an overlap in the functional roles of these systems. Production of the AHLs occurs at distinct points during growth on an agar surface and was determined by isotope dilution high-performance liquid chromatography-tandem mass spectrometry (ID-HPLC-MS/MS) analysis. Within 2 h of surface inoculation, only 3OHC 12:1 -HSL was detected in agar extracts. As surface-attached cells became established (at ϳ10 h), the concentration of 3OHC 12:1 -HSL decreased, and the concentration of C 8 -HSL increased rapidly over 14 h. After longer (>24-h) establishment periods, the concentrations of the two AHLs increased to and stabilized at ϳ15 nM and ϳ600 nM for 3OHC 12:1 -HSL and C 8 -HSL, respectively. In contrast, the total amount of indigoidine increased steadily from undetectable to 642 M by 48 h. Gene expression profiles of the AHL and indigoidine synthases (pgaI, phaI, and igiD) were consistent with their metabolite profiles. These data provide evidence that pgaRI and phaRI play overlapping roles in the regulation of indigoidine biosynthesis, and it is postulated that this allows Phaeobacter sp. strain Y4I to coordinate production of indigoidine with different growth-phase-dependent physiologies. Bacteria are in constant competition for niches in the environment, and the ability to coordinate gene expression may provide a competitive advantage (1). Some bacteria are able to synchronize gene expression in a cell-density-dependent manner by sensing and responding to small diffusible molecules synthesized by individuals; in proteobacteria, members of the broadly distributed and chemically diverse class of N-acyl-L-homoserine lactones (AHLs) are among the best-characterized signaling molecules (2). Proteobacterial AHL synthases are fairly well conserved and form the LuxI protein family. Members of the LuxR protein family are cytoplasmic transcriptional regulators that can modulate gene expression, most typically when bound to the corresponding cognate AHL (3-7). It has been shown that luxI-luxR (luxIR) pairs are frequently colocalized within chromosomes and constitutively exp...

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Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

Cited by 74 publications

References 77 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

Phaeobacter sp. Strain Y4I Utilizes Two Separate Cell-to-Cell Communication Systems To Regulate Production of the Antimicrobial Indigoidine

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