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

Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk HP, Brinkhoff T, Göker M - Front Microbiol (2014)

Bottom Line: Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic.We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov.The genera Phaeobacter and Leisingera are accordingly emended.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg Oldenburg, Germany.

ABSTRACT
Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

No MeSH data available.


Related in: MedlinePlus

Phylogeny inferred from the ortholog-content matrix under the maximum likelihood (ML) criterion and rooted with Roseobacter. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values (if larger than 60%) from (i) ML ortholog-content matrix; (ii) maximum-parsimony (MP) ortholog-content matrix; (iii) ML gene-content matrix; (iv) MP gene-content matrix analysis. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings. On the right side two potential new taxonomic arrangements into genera are shown that are in agreement with the tree.
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Figure 2: Phylogeny inferred from the ortholog-content matrix under the maximum likelihood (ML) criterion and rooted with Roseobacter. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values (if larger than 60%) from (i) ML ortholog-content matrix; (ii) maximum-parsimony (MP) ortholog-content matrix; (iii) ML gene-content matrix; (iv) MP gene-content matrix analysis. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings. On the right side two potential new taxonomic arrangements into genera are shown that are in agreement with the tree.

Mentions: The ortholog-content matrix contained 13,676 characters, and the resulting best trees had a log likelihood of -77923.13 and a length of 19,909 steps, respectively. The gene-content matrix comprised 9844 characters and yielded best trees with a log likelihood of -54954.97 and a parsimony score of 13,580, respectively. Both ML trees were topologically identical and are shown in Figure 2 with bootstrap support values for ML and MP if larger than 60%. The MP gene-content tree showed the monophyly of Ruegeria, whereas P. arcticus DSM 23566T was grouped as in the supermatrix tree (see Figure 1). Like the supermatrix trees, a maximally supported clade comprising P. daeponensis, P. caeruleus, L. methylohalidivorans as well as L. aquimarina and another one containing P. gallaeciensis and P. inhibens were revealed. In addition to Ruegeria spp., in the gene- and ortholog-content trees Oceanibulbus and Sediminimonas were indicated as more closely related than L. nanhaiensis to the remaining Leisingera and Phaeobacter species. None of the branches in conflict with the supermatrix trees were particularly well supported.


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

Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk HP, Brinkhoff T, Göker M - Front Microbiol (2014)

Phylogeny inferred from the ortholog-content matrix under the maximum likelihood (ML) criterion and rooted with Roseobacter. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values (if larger than 60%) from (i) ML ortholog-content matrix; (ii) maximum-parsimony (MP) ortholog-content matrix; (iii) ML gene-content matrix; (iv) MP gene-content matrix analysis. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings. On the right side two potential new taxonomic arrangements into genera are shown that are in agreement with the tree.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4127530&req=5

Figure 2: Phylogeny inferred from the ortholog-content matrix under the maximum likelihood (ML) criterion and rooted with Roseobacter. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values (if larger than 60%) from (i) ML ortholog-content matrix; (ii) maximum-parsimony (MP) ortholog-content matrix; (iii) ML gene-content matrix; (iv) MP gene-content matrix analysis. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings. On the right side two potential new taxonomic arrangements into genera are shown that are in agreement with the tree.
Mentions: The ortholog-content matrix contained 13,676 characters, and the resulting best trees had a log likelihood of -77923.13 and a length of 19,909 steps, respectively. The gene-content matrix comprised 9844 characters and yielded best trees with a log likelihood of -54954.97 and a parsimony score of 13,580, respectively. Both ML trees were topologically identical and are shown in Figure 2 with bootstrap support values for ML and MP if larger than 60%. The MP gene-content tree showed the monophyly of Ruegeria, whereas P. arcticus DSM 23566T was grouped as in the supermatrix tree (see Figure 1). Like the supermatrix trees, a maximally supported clade comprising P. daeponensis, P. caeruleus, L. methylohalidivorans as well as L. aquimarina and another one containing P. gallaeciensis and P. inhibens were revealed. In addition to Ruegeria spp., in the gene- and ortholog-content trees Oceanibulbus and Sediminimonas were indicated as more closely related than L. nanhaiensis to the remaining Leisingera and Phaeobacter species. None of the branches in conflict with the supermatrix trees were particularly well supported.

Bottom Line: Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic.We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov.The genera Phaeobacter and Leisingera are accordingly emended.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg Oldenburg, Germany.

ABSTRACT
Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

No MeSH data available.


Related in: MedlinePlus