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Ch V Ramana - One of the best experts on this subject based on the ideXlab platform.
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Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.
Frontiers in microbiology, 2019Co-Authors: G. Suresh, Ch Sasikala, Tushar Lodha, B Indu, Ch V RamanaAbstract:The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.
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Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov.
International journal of systematic and evolutionary microbiology, 2017Co-Authors: G. Suresh, Ch Sasikala, B. Sailaja, A. Ashif, Bharti P. Dave, Ch V RamanaAbstract:Three strains (JA826T, JA912T and JA913), which were yellowish brown colour, rod to oval shaped, Gram-stain-negative, motile, phototrophic bacteria with a vesicular architecture of intracytoplasmic membranes, were isolated from different pond samples. The DNA G+C content of the three strains was between 64.6 and 65.5 mol%. The highest 16S rRNA gene sequence similarity of all three strains was with the type strains of the genus Rhodobacter sensu stricto in the family Rhodobacteraceae . Strain JA826T had highest sequence similarity with Rhodobacter maris JA276T (98.5 %), Rhodobacter viridis JA737T (97.5 %) and other members of the genus Rhodobacter (
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Rhodobacter viridis sp nov a phototrophic bacterium isolated from mud of a stream
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Shalem P Raj, Ch Sasikala, E V V Ramaprasad, S Vaseef, Ch V RamanaAbstract:A green phototrophic bacterium (strain JA737(T)), which was oval- to rod-shaped, Gram-negative and motile, was isolated from mud of a stream in the Western Ghats of India. Strain JA737(T) contained bacteriochlorophyll a, and the major carotenoid was neurosporene. The major quinone was Q-10 and the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. Phylogenetic analysis showed that the strain clustered with members of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strain JA737(T) had highest sequence similarity with Rhodobacter capsulatus ATCC 11166(T) (98.8 %), Rhodobacter maris JA276(T) (97 %), Rhodobacter aestuarii JA296(T) (96.7 %) and other members of the genus Rhodobacter (<96 %). However, strain JA737(T) showed 22-55 % DNA-DNA relatedness with the above type strains. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, strain JA737(T) represents a novel species of the genus Rhodobacter, for which the name Rhodobacter viridis sp. nov. is proposed. The type strain is JA737(T) ( = KCTC 15167(T) = MTCC 11105(T) = NBRC 108864(T)).
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Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream.
International journal of systematic and evolutionary microbiology, 2012Co-Authors: P Shalem Raj, Ch Sasikala, E V V Ramaprasad, S Vaseef, Ch V RamanaAbstract:A green phototrophic bacterium (strain JA737(T)), which was oval- to rod-shaped, Gram-negative and motile, was isolated from mud of a stream in the Western Ghats of India. Strain JA737(T) contained bacteriochlorophyll a, and the major carotenoid was neurosporene. The major quinone was Q-10 and the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. Phylogenetic analysis showed that the strain clustered with members of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strain JA737(T) had highest sequence similarity with Rhodobacter capsulatus ATCC 11166(T) (98.8 %), Rhodobacter maris JA276(T) (97 %), Rhodobacter aestuarii JA296(T) (96.7 %) and other members of the genus Rhodobacter (
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Rhodobacter johrii sp nov an endospore producing cryptic species isolated from semi arid tropical soils
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: K R Girija, Ch V Ramana, Chintalapati Sasikala, Cathrin Sproer, Shinichi Takaichi, Vera Thiel, Johannes F. ImhoffAbstract:An oval to rod shaped phototrophic purple nonsulfur bacterium, strain JA192T was isolated from an enrichment culture of a pasteurized rhizosphere soil sample of jowar crop collected from Godumakunta village, near Hyderabad, India. Strain JA192T is Gram-negative, motile and produces endospores. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain JA192T is closely related to Rhodobacter sphaeroides DSM 158T (99.9% sequence similarity), Rhodobacter megalophilus JA194T (99.8%) and Rhodobacter azotoformans JCM 9340T (98.1%) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA-DNA hybridization with Rba. sphaeroides DSM 158T, Rba. megalophilus JA194T and Rba. azotoformans JCM 9320T showed a relatedness of only 38-57% with respect to JA192T. On the basis of 16S rRNA gene sequence analysis, DNA-DNA hybridization data, morphological, physiological and chemotaxanomic characters, strain JA192T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter johrii sp. nov. is proposed. The type strain is JA192T (= DSM 18678T = JCM 14543T = MTCC 8172T).
Alastair G. Mcewan - One of the best experts on this subject based on the ideXlab platform.
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Asymmetric reduction of racemic sulfoxides by dimethyl sulfoxide reductases from Rhodobacter capsulatus, Escherichia coli and Proteus species.
Microbiology, 1998Co-Authors: Steven P. Hanlon, Anthony L. Shaw, D.l. Graham, Philip J. Hogan, Christopher David Reeve, Robert A Holt, Alastair G. McewanAbstract:The enantioselective reduction of racemic sulfoxides by dimethyl sulfoxide reductases from Rhodobacter capsulatus, Escherichia coli, Proteus mirabilis and Proteus vulgaris was investigated. Purified dimethyl sulfoxide reductase from Rhodobacter capsulatus catalysed the selective removal of (S)-methyl p-tolyl sulfoxide from a racemic mixture of methyl p-tolyl sulfoxide and resulted in an 88% recovery of enantiomerically pure (R)-methyl p-tolyl sulfoxide. Rhodobacter capsulatus was shown to be able to grow photoheterotrophically in the presence of certain chiral sulfoxides under conditions where a sulfoxide is needed as an electron sink. Whole cells of Rhodobacter capsulatus were shown to catalyse the enantioselective reduction of methyl p-tolyl sulfoxide, ethyl 2-pyridyl sulfoxide, methylthiomethyl methyl sulfoxide and methoxymethyl phenyl sulfoxide. Similarly, whole cells of Escherichia coli, Proteus mirabilis and Proteus vulgaris reduced these sulfoxides but with opposite enantioselectivity.
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Asymmetric reduction of racemic sulfoxides by dimethyl sulfoxide reductases from Rhodobacter capsulatus, Escherichia coli and Proteus species.
Microbiology, 1998Co-Authors: Steven P. Hanlon, Anthony L. Shaw, D.l. Graham, Philip J. Hogan, Christopher David Reeve, Robert A Holt, Alastair G. McewanAbstract:The enantioselective reduction of racemic sulfoxides by dimethyl sulfoxide reductases from Rhodobacter capsulatus, Escherichia coli, Proteus mirabilis and Proteus vulgaris was investigated. Purified dimethyl sulfoxide reductase from Rhodobacter capsulatus catalysed the selective removal of (S)-methyl p-tolyl sulfoxide from a racemic mixture of methyl p-tolyl sulfoxide and resulted in an 88% recovery of enantiomerically pure (R)-methyl p-tolyl sulfoxide. Rhodobacter capsulatus was shown to be able to grow photoheterotrophically in the presence of certain chiral sulfoxides under conditions where a sulfoxide is needed as an electron sink. Whole cells of Rhodobacter capsulatus were shown to catalyse the enantioselective reduction of methyl p-tolyl sulfoxide, ethyl 2-pyridyl sulfoxide, methylthiomethyl methyl sulfoxide and methoxymethyl phenyl sulfoxide. Similarly, whole cells of Escherichia coli, Proteus mirabilis and Proteus vulgaris reduced these sulfoxides but with opposite enantioselectivity.
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Cloning and sequence analysis of the dimethylsulfoxide reductase structural gene from Rhodobacter capsulatus
Biochimica et Biophysica Acta, 1996Co-Authors: Anthony L. Shaw, Graeme R. Hanson, Alastair G. McewanAbstract:The dimethylsulfoxide reductase structural gene (dorA) of Rhodobacter capsulatus was cloned from a λ expression library. The nucleotide sequence of the dorA gene was determined and it was found to encode a protein of 825 amino acids. Comparison of the deduced amino-acid sequence of DorA with N-terminal sequence of purified dimethylsulfoxide reductase from Rhodobacter capsulatus showed that the pre-protein possesses a 41-amino-acid N-terminal signal polypeptide. All of the conserved segments which have been described in bacterial enzymes which bind molybdopterin guanine dinucleotide (Berks, B.C., Ferguson, S.J., Moir, J.W.B. and Richardson, D.J. (1995) Biochim. Biophys. Acta 1232, 97-173) were identified in Rhodobacter capsulatus dimethylsulfoxide reductase.
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Phenotypic characterisation and genetic complementation of dimethylsulfoxide respiratory mutants of Rhodobacter sphaeroides and Rhodobacter capsulatus
FEMS microbiology letters, 1995Co-Authors: Tracey C. Bonnett, Paul A. Cobine, R. Elizabeth Sockett, Alastair G. McewanAbstract:Two chlorate resistant mutants of Rhodobacter sphaeroides were isolated which were deficient in dimethylsulfoxide reductase activity. Immunoblotting experiments showed that the phenotype of these mutants and that of Rhodobacter capsulatus strain DK9, a mutant unable to reduce dimethylsulfoxide, was correlated with low or undetectable levels of the dimethylsulfoxide reductase apoprotein. All three mutants were complemented by a cosmid from a library of Rhodobacter sphaeroides genomic DNA. Further genetic complementation analysis revealed that functions required for restoration of dimethylsulfoxide reductase activity in the Rhodobacter sphaeroides mutants were encoded on an 9 kb EcoR1 DNA fragment derived from this cosmid. Expression of this 9 kb DNA fragment in Escherichia coli showed that it encoded the dimethylsulfoxide reductase structural gene of Rhodobacter sphaeroides.
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The 44-kDa c-type cytochrome induced in Rhodobacter capsulatus during growth with dimethylsulphoxide as an electron acceptor is a cytochrome c peroxidase
Fems Microbiology Letters, 1992Co-Authors: Steven P. Hanlon, Robert A Holt, Alastair G. McewanAbstract:A 44-kDa c-type cytochrome was purified from membranes of Rhodobacter capsulatus. The cytochrome contained an ascorbate-reducible haem (α-max 556 nm) and a dithionite-reducible haem (α-max 552 nm) and had catalytic properties which indicated that it was a cytochrome c peroxidase. Increased levels of this cytochrome were observed when dimethylsulphoxide was present during phototrophic growth of cells but this was not observed when trimethylamine-N-oxide was present. The results indicate that the 44-kDa cytochrome is probably not directly involved in the dimethylsulphoxide/trimethylamine-N-oxide respiratory pathway of Rhodobacter capsulatus.
Ch Sasikala - One of the best experts on this subject based on the ideXlab platform.
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Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter.
Frontiers in microbiology, 2019Co-Authors: G. Suresh, Ch Sasikala, Tushar Lodha, B Indu, Ch V RamanaAbstract:The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.
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Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov.
International journal of systematic and evolutionary microbiology, 2017Co-Authors: G. Suresh, Ch Sasikala, B. Sailaja, A. Ashif, Bharti P. Dave, Ch V RamanaAbstract:Three strains (JA826T, JA912T and JA913), which were yellowish brown colour, rod to oval shaped, Gram-stain-negative, motile, phototrophic bacteria with a vesicular architecture of intracytoplasmic membranes, were isolated from different pond samples. The DNA G+C content of the three strains was between 64.6 and 65.5 mol%. The highest 16S rRNA gene sequence similarity of all three strains was with the type strains of the genus Rhodobacter sensu stricto in the family Rhodobacteraceae . Strain JA826T had highest sequence similarity with Rhodobacter maris JA276T (98.5 %), Rhodobacter viridis JA737T (97.5 %) and other members of the genus Rhodobacter (
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Rhodobacter viridis sp nov a phototrophic bacterium isolated from mud of a stream
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Shalem P Raj, Ch Sasikala, E V V Ramaprasad, S Vaseef, Ch V RamanaAbstract:A green phototrophic bacterium (strain JA737(T)), which was oval- to rod-shaped, Gram-negative and motile, was isolated from mud of a stream in the Western Ghats of India. Strain JA737(T) contained bacteriochlorophyll a, and the major carotenoid was neurosporene. The major quinone was Q-10 and the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. Phylogenetic analysis showed that the strain clustered with members of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strain JA737(T) had highest sequence similarity with Rhodobacter capsulatus ATCC 11166(T) (98.8 %), Rhodobacter maris JA276(T) (97 %), Rhodobacter aestuarii JA296(T) (96.7 %) and other members of the genus Rhodobacter (<96 %). However, strain JA737(T) showed 22-55 % DNA-DNA relatedness with the above type strains. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, strain JA737(T) represents a novel species of the genus Rhodobacter, for which the name Rhodobacter viridis sp. nov. is proposed. The type strain is JA737(T) ( = KCTC 15167(T) = MTCC 11105(T) = NBRC 108864(T)).
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Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream.
International journal of systematic and evolutionary microbiology, 2012Co-Authors: P Shalem Raj, Ch Sasikala, E V V Ramaprasad, S Vaseef, Ch V RamanaAbstract:A green phototrophic bacterium (strain JA737(T)), which was oval- to rod-shaped, Gram-negative and motile, was isolated from mud of a stream in the Western Ghats of India. Strain JA737(T) contained bacteriochlorophyll a, and the major carotenoid was neurosporene. The major quinone was Q-10 and the polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. Phylogenetic analysis showed that the strain clustered with members of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strain JA737(T) had highest sequence similarity with Rhodobacter capsulatus ATCC 11166(T) (98.8 %), Rhodobacter maris JA276(T) (97 %), Rhodobacter aestuarii JA296(T) (96.7 %) and other members of the genus Rhodobacter (
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Production of phenols and alkyl gallate esters by Rhodobacter sphaeroides OU5.
Current microbiology, 2009Co-Authors: Ranjith Kumavath, Ch V Ramana, Ch SasikalaAbstract:Rhodobacter sphaeroides OU5 grows phototrophically with generation doubling time of 18 h on l-phenylalanine when used as sole source of nitrogen. Phenols accumulated in the medium and gallate (0.5 mM) was identified as one of the major product. The others namely protocatechuate (0.2 mM) and caffeate (0.1 mM) and also three putative phenol alkyl esters were identified using Liquid chromatography–mass spectroscopy (LC–MS) analysis from the culture supernatant. Rhodobacter sphaeroides OU5 strain could explain its capability to produce the bioactive compounds during the growth. This study sheds production of bioactive and their biological exploring molecules.
Chunping Yang - One of the best experts on this subject based on the ideXlab platform.
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treatment of anaerobically digested swine wastewater by Rhodobacter blasticus and Rhodobacter capsulatus
Bioresource Technology, 2016Co-Authors: Huijun He, Zili Zhou, Chunping Yang, Xiang Li, Guangming ZengAbstract:Abstract Two strains of photosynthetic bacteria, Rhodobacter blasticus and Rhodobacter capsulatus, were used in this work to investigate the feasibility of using photosynthetic bacteria for the treatment of anaerobically digested swine wastewater. The effects of crucial factors which influence the pollutants removal efficiency were also examined. Results showed that anaerobically digested swine wastewater could be treated effectively by photosynthetic bacteria. The treatment efficiency was significantly higher by the mixed photosynthetic bacteria than that by any unitary bacterium. The optimal treatment condition by mixed bacteria was inoculation of 10.0% (v/v) of the two bacteria by 1:1, initial pH of 7.0 and initial chemical oxygen demand of 4800 mg L−1. Under these conditions, the removal rate of chemical oxygen demand was 83.3%, which was 19.3% higher than when using Rhodobacter blasticus or 10.6% higher than when using Rhodobacter capsulatus separately. This mixed photosynthetic bacteria achieved high chemical oxygen demand removal and cell yields.
Charles R Lovell - One of the best experts on this subject based on the ideXlab platform.
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seasonal dynamics of particle associated and free living marine proteobacteria in a salt marsh tidal creek as determined using fluorescence in situ hybridization
Environmental Microbiology, 2002Co-Authors: Hongyue Dang, Charles R LovellAbstract:Summary The seasonal distributions of salt marsh free-living and particle-associated bacteria belonging to three subdivisions of the Proteobacteria were determined by fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). More than 66% (median = 78%) of total bacterial cells that were stainable with the fluorescent DNA stain Yo-Pro-1 were also detected using the bacterial probe EUB338. The α-Proteobacteria, especially those from the marine Rhodobacter group, were abundant on suspended particles and as free-living cells all year round. The marine Rhodobacter group constituted more than 25% of the particle-associated bacteria and more than 18% of the free-living bacteria. Probes specific for three subgroups within the marine Rhodobacter group detected more than 49% of the total marine Rhodobacter group cells. These subgroups displayed different seasonal dynamics. The marine Rhodobacter group is clearly a widespread, diverse and important bacterial lineage in bacterioplankton and particle-associated assemblages in south-eastern United States salt marshes at all times of the year.
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numerical dominance and phylotype diversity of marine Rhodobacter species during early colonization of submerged surfaces in coastal marine waters as determined by 16s ribosomal dna sequence analysis and fluorescence in situ hybridization
Applied and Environmental Microbiology, 2002Co-Authors: Hongyue Dang, Charles R LovellAbstract:ABSTRACT Early stages of surface colonization in coastal marine waters appear to be dominated by the marine Rhodobacter group of the α subdivision of the division Proteobacteria (α-Proteobacteria). However, the quantitative contribution of this group to primary surface colonization has not been determined. In this study, glass microscope slides were incubated in a salt marsh tidal creek for 3 or 6 days. Colonizing bacteria on the slides were examined by fluorescence in situ hybridization by employing DNA probes targeting 16S or 23S rRNA to identify specific phylogenetic groups. Confocal laser scanning microscopy was then used to quantify and track the dynamics of bacterial primary colonists during the early stages of surface colonization and growth. More than 60% of the surface-colonizing bacteria detectable by fluorescence staining (Yo-Pro-1) could also be detected with the Bacteria domain probe EUB338. Archaea were not detected on the surfaces and did not appear to participate in surface colonization. Of the three subdivisions of the Proteobacteria examined, the α-Proteobacteria were the most abundant surface-colonizing organisms. More than 28% of the total bacterial cells and more than 40% of the cells detected by EUB338 on the surfaces were affiliated with the marine Rhodobacter group. Bacterial abundance increased significantly on the surfaces during short-term incubation, mainly due to the growth of the marine Rhodobacter group organisms. These results demonstrated the quantitative importance of the marine Rhodobacter group in colonization of surfaces in salt marsh waters and confirmed that at least during the early stages of colonization, this group dominated the surface-colonizing bacterial assemblage.
