Phaeobacter
               
            
            leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments

Gaboyer, F.; Tindall, Brian J.; Ciobanu, Maria; Duthoit, F; Romancer, Marc Le; Alain, Karine

doi:10.1099/ijs.0.046128-0

Cited by 22 publications

(23 citation statements)

References 17 publications

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“…Recently, Phaeobacter strains retrieved a lot of interest because of their production of various secondary metabolites (e.g., Berger et al, 2011). Analyses of the 16S rRNA gene and in some publications also preliminary genomic analyses were in conflict with the current classification (Jin et al, 2011; Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Gaboyer et al, 2013; Riedel et al, 2013; Breider et al, 2014; Liu et al, 2014; Park et al, 2014). These analyses mostly showed that P. aquaemixtae, P. caeruleus, P. daeponensis, Leisingera methylohalodivorans , and L. aquimarina form a clade, P. arcticus and P. leonis comprise a distinct monophyletic group, and P. gallaeciensis and P. inhibens form a third clade.…”

Section: Introductionmentioning

confidence: 97%

“…The genus Phaeobacter was introduced by Martens et al (2006) and currently comprises the species Phaeobacter aquaemixtae (Park et al, 2014), Phaeobacter arcticus (Zhang et al, 2008), Phaeobacter caeruleus (Vandecandelaere et al, 2009), Phaeobacter daeponensis (Yoon et al, 2007), Phaeobacter inhibens (Martens et al, 2006), Phaeobacter leonis (Gaboyer et al, 2013), and Phaeobacter gallaeciensis (Ruiz-Ponte et al, 1998; Martens et al, 2006), which is the type species, its type strain being BS107 T = CIP 105210 T = DSM 26640 T but not DSM 17395 (Buddruhs et al, 2013b). The Phaeobacter species were isolated from a mixing zone of the ocean and a freshwater spring, marine arctic sediment, a marine electro-active biofilm, tidal flat sediment, a tidal mud flat, marine surface sediment and rearings and collectors of the scallop Pecten maximus , respectively.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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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.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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“…The genus Phaeobacter, currently comprising the species Phaeobacter gallaeciensis, P. inhibens, P. daeponensis, P. caeruleus, P. arcticus and P. leonis (Gaboyer et al, 2013), belongs to the marine Roseobacter clade. It was established by Martens et al (2006) after reclassification of Roseobacter gallaeciensis (Ruiz-Ponte et al, 1998) as P. gallaeciensis, which is the type species of the genus, and description of P. inhibens as a new species.…”

Section: Introductionmentioning

confidence: 99%

Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395

Buddruhs

Pradella

Göker

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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The marine genus Phaeobacter currently comprises six species, some of which were intensively studied mainly due to their ability to produce secondary metabolites. The type strain of the type species, Phaeobacter gallaeciensis BS107 T , has been deposited at several public culture collections worldwide. Based on differences in plasmid profiles, we detected that the alleged P. gallaeciensis type strains deposited at the Collection Institute Pasteur (CIP; Paris, France) as CIP 105210 and at the German Collection of Microorganisms and Cell Cultures (DSMZ; Braunschweig, Germany) as DSM 17395 are not identical. To determine the identity of these strains, we conducted DNA-DNA hybridization, matrix-assisted laser desorption/ionization timeof-flight mass spectrometry (MALDI-TOF), 16S rRNA gene and internal transcribed spacer (ITS) sequence analyses, as well as physiological experiments. Based on the detailed 16S rRNA gene reanalysis we showed that strain CIP 105210 most likely corresponds to the original P. gallaeciensis type strain BS107 T . In contrast, the Phaeobacter strain DSM 17395 exhibits a much closer affiliation to Phaeobacter inhibens DSM 16374 T (5T5 T ) and should thus be allocated to this species. The detection of the dissimilarity of strains CIP 105210 T and DSM 17395 will influence future comparative studies within the genus Phaeobacter.

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“…Among them is that of Phaeobacter inhibens DSM 17395 (12), which was recently reclassified from Phaeobacter gallaeciensis DSM 17395 (13). Phaeobacter species are globally distributed in the marine system, e.g., in sediments of the Arctic Ocean (14), the Yellow Sea (15), and the Mediterranean Sea (16), and in surface water of the German Wadden Sea (17). Furthermore, they are constituents of marine biofilms (18) and are associated with scallops (19) and algae (12).…”

mentioning

confidence: 99%

Carbohydrate Catabolism in Phaeobacter inhibens DSM 17395, a Member of the Marine Roseobacter Clade

Wiegmann

Hensler

Wöhlbrand

et al. 2014

Appl Environ Microbiol

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Since genome analysis did not allow unambiguous reconstruction of transport, catabolism, and substrate-specific regulation for several important carbohydrates in Phaeobacter inhibens DSM 17395, proteomic and metabolomic analyses of N-acetylglucosamine-, mannitol-, sucrose-, glucose-, and xylose-grown cells were carried out to close this knowledge gap. These carbohydrates can pass through the outer membrane via porins identified in the outer membrane fraction. For transport across the cytoplasmic membrane, carbohydrate-specific ABC transport systems were identified. Their coding genes mostly colocalize with the respective "catabolic" and "regulatory" genes. The degradation of N-acetylglucosamine proceeds via N-acetylglucosamine-6-phosphate and glucosamine-6-phosphate directly to fructose-6-phosphate; two of the three enzymes involved were newly predicted and identified. Mannitol is catabolized via fructose, sucrose via fructose and glucose, glucose via glucose-6-phosphate, and xylose via xylulose-5-phosphate. Of the 30 proteins predicted to be involved in uptake, regulation, and degradation, 28 were identified by proteomics and 19 were assigned to their respective functions for the first time. The peripheral degradation pathways feed into the Entner-Doudoroff (ED) pathway, which is connected to the lower branch of the Embden-Meyerhof-Parnas (EMP) pathway. The enzyme constituents of these pathways displayed higher abundances in P. inhibens DSM 17395 cells grown with any of the five carbohydrates tested than in succinate-grown cells. Conversely, gluconeogenesis is turned on during succinate utilization. While tricarboxylic acid (TCA) cycle proteins remained mainly unchanged, the abundance profiles of their metabolites reflected the differing growth rates achieved with the different substrates tested. Homologs of the 74 genes involved in the reconstructed catabolic pathways and central metabolism are present in various Roseobacter clade members.

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Phaeobacter leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments

Cited by 22 publications

References 17 publications

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

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

Molecular and phenotypic analyses reveal the non-identity of the Phaeobacter gallaeciensis type strain deposits CIP 105210T and DSM 17395

Carbohydrate Catabolism in Phaeobacter inhibens DSM 17395, a Member of the Marine Roseobacter Clade

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