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Akira Hiraishi - One of the best experts on this subject based on the ideXlab platform.

  • Rhodopseudomonas telluris sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.
    International journal of systematic and evolutionary microbiology, 2017
    Co-Authors: Akira Hiraishi, Keiko Okamura
    Abstract:

    A strain of anoxygenic phototrophic bacteria isolated from paddy soil (designated strain TUT3615T) was studied taxonomically in comparison with Rhodopseudomonas strain ATCC 17005 as its nearest phylogenetic relative. Strains TUT3615T and ATCC 17005 had budding rod-shaped cells and showed in vivo absorption maxima at 804 and 860 nm in the near infrared region, indicating the presence of bacteriochlorophyll a. The intracytoplasmic membrane system was of the lamellar type parallel to the cytoplasmic membrane. 16S rRNA gene sequence comparisons showed that strains TUT3615T and ATCC 17005 had a 99.7 % level of similarity to one another and were closest to Rhodopseudomonas palustris ATCC 17001T (98.6 % similarity) among the established species of the genus Rhodopseudomonas . Genomic DNA–DNA hybridization studies revealed that strains TUT3615T and ATCC 17005 had an average similarity level of 65 % to one another and of less than 40 % to the available type strains of Rhodopseudomonas species. Results of phenotypic studies showed that strains TUT3615T and ATCC 17005 could be differentiated from one another and from any previously described species of Rhodopseudomonas . The G+C contents of the genomic DNA of strain TUT3615T and ATCC 17005 were 66.3 and 66.5 mol%, respectively. Based on these data, we propose the name Rhodopseudomonas telluris sp. nov. for strain TUT3615T. The type strain is TUT3615T (=KCTC 23279T=NBRC 107609T). We suspend a proposal to reclassify strain ATCC 17005 as a novel species or subspecies until a genome-wide analysis provides more definite information on its taxonomic position.

  • Intrageneric relationships of members of the genus Rhodopseudomonas.
    The Journal of general and applied microbiology, 2009
    Co-Authors: Keiko Okamura, Koji Takata, Akira Hiraishi
    Abstract:

    The intrageneric structure of the genus Rhodopseudomonas was evaluated by studying sequence information on 16S rRNA genes, 16S-23S rRNA gene internal transcribed spacer (ITS) regions, and puf genes using 33 test strains. The topology of phylogenetic trees based on these sequences was similar to those of every other independent method for tree construction. These phylogenetic data indicated that the test strains were grouped into at least 7 clusters possibly at the species level. This was supported by genomic DNA-DNA similarities among 12 representative test strains selected from these clusters. Our molecular data confirmed that the currently available strains of Rhodopseudomonas (Rps.) palustris are genetically quite heterogeneous within the genus. For example, Rps. palustris strains DSM 123T and ATCC 17001T are different from each other at the species level despite their status as the type strain of the species. Rps. palustris strain ATCC 17005 and the full genome-sequenced strains BisA53, BisB18, BisB5, and HaA2 should be re-classified into different species from Rps. palustris or as novel species of the genus Rhodopseudomonas.

  • Full Paper Intrageneric relationships of members of the genus Rhodopseudomonas
    2009
    Co-Authors: Keiko Okamura, Koji Takata, Akira Hiraishi
    Abstract:

    The intrageneric structure of the genus Rhodopseudomonas was evaluated by studying sequence information on 16S rRNA genes, 16S�23S rRNA gene internal transcribed spacer (ITS) regions, and puf genes using 33 test strains. The topology of phylogenetic trees based on these sequences was similar to those of every other independent method for tree construction. These phylogenetic data indicated that the test strains were grouped into at least 7 clusters possibly at the species level. This was supported by genomic DNA-DNA similarities among 12 representative test strains selected from these clusters. Our molecular data confi rmed that the currently available strains of Rhodopseudomonas (Rps.) palustris are genetically quite heterogeneous within the genus. For example, Rps. palustris strains DSM 123 T and ATCC 17001 T are different from each other at the species level despite their status as the type strain of the species. Rps. palustris strain ATCC 17005 and the full genome-sequenced strains BisA53, BisB18, BisB5, and HaA2 should be re-classifi ed into different species from Rps. palustris or as novel species of the genus Rhodopseudomonas.

  • CHARACTERIZATION OF PHOTOTROPHIC PURPLE NONSULFUR BACTERIA FORMING COLORED MICROBIAL MATS IN A SWINE WASTEWATER DITCH
    Applied and environmental microbiology, 2006
    Co-Authors: Yoko Okubo, Hiroyuki Futamata, Akira Hiraishi
    Abstract:

    The community structure of pink-colored microbial mats naturally occurring in a swine wastewater ditch was studied by culture-independent biomarker and molecular methods as well as by conventional cultivation methods. The wastewater in the ditch contained acetate and propionate as the major carbon nutrients. Thin-section electron microscopy revealed that the microbial mats were dominated by rod-shaped cells containing intracytoplasmic membranes of the lamellar type. Smaller numbers of oval cells with vesicular internal membranes were also found. Spectroscopic analyses of the cell extract from the biomats showed the presence of bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Ubiquinone-10 was detected as the major quinone. A clone library of the photosynthetic gene, pufM, constructed from the bulk DNA of the biomats showed that all of the clones were derived from members of the genera Rhodobacter and Rhodopseudomonas. The dominant phototrophic bacteria from the microbial mats were isolated by cultivation methods and identified as being of the genera Rhodobacter and Rhodopseudomonas by studying 16S rRNA and pufM gene sequence information. Experiments of oxygen uptake with lower fatty acids revealed that the freshly collected microbial mats and the Rhodopseudomonas isolates had a wider spectrum of carbon utilization and a higher affinity for acetate than did the Rhodobacter isolates. These results demonstrate that the microbial mats were dominated by the purple nonsulfur bacteria of the genera Rhodobacter and Rhodopseudomonas, and the bioavailability of lower fatty acids in wastewater is a key factor allowing the formation of visible microbial mats with these phototrophs.

  • transfer of the bacteriochlorophyll b containing phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the genus blastochloris gen nov
    International Journal of Systematic and Evolutionary Microbiology, 1997
    Co-Authors: Akira Hiraishi
    Abstract:

    The phylogenetic positions of the bacteriochlorophyll (BChl) b-producing budding phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis were studied on the basis of 16S rRNA gene sequence information. These bacteria formed a tight cluster with the genus Rhodoplanes as a sister group within the alpha-2 subgroup of the Proteobacteria. Genomic DNA-DNA hybridization assays showed that R. viridis and R. sulfoviridis were closely related but were different species. Creation of the genus Blastochloris gen. nov. is proposed to accommodate these BChl b-producing species of phototrophic bacteria.

Ch V Ramana - One of the best experts on this subject based on the ideXlab platform.

  • Rhodopseudomonas pentothenatexigens sp. nov. and Rhodopseudomonas thermotolerans sp. nov., isolated from paddy soils
    International Journal of Systematic and Evolutionary Microbiology, 2013
    Co-Authors: B. Vinay Kumar, Ch Sasikala, E. V. V. Ramprasad, Ch V Ramana
    Abstract:

    Two strains (JA575T and JA576T) of orange- to pink-pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from paddy soils. Both strains contained bacteriochlorophyll a and carotenoids of spirilloxanthin series. Both strains had C18 : 1ω7c as the major cellular fatty acid, ubiquinone-10 (Q10) as the main quinone, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as polar lipids. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that both strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA575T and JA576T were genotypically (<35 % DNA–DNA relatedness) and phenotypically distinct from each other. Further, both strains showed less than 48 % DNA–DNA relatedness with the type strains of all recognized species of the genus Rhodopseudomonas . The molecular evidence is supported by phenotypic evidence. It is proposed that strains JA575T and JA576T be classified as representing two novel species of the genus Rhodopseudomonas with the species names Rhodopseudomonas pentothenatexigens sp. nov. and Rhodopseudomonas thermotolerans sp. nov., respectively. The type strains of the proposed novel species are JA575T ( = NBRC 108862T = KCTC15143T) and JA576T ( = NBRC 108863T = KCTC 15144T), respectively.

  • descriptions of Rhodopseudomonas parapalustris sp nov Rhodopseudomonas harwoodiae sp nov and Rhodopseudomonas pseudopalustris sp nov and emended description of Rhodopseudomonas palustris
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Venkata V Ramana, Kalyana S Chakravarthy, Shalem P Raj, Vinay B Kumar, E Shobha, E V V Ramaprasad, Ch Sasikala, Ch V Ramana
    Abstract:

    Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.

Johannes F. Imhoff - One of the best experts on this subject based on the ideXlab platform.

  • genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris dsm 123t as the authentic type strain of this species
    International Journal of Systematic and Evolutionary Microbiology, 2020
    Co-Authors: Johannes F. Imhoff, T E Meyer, John A. Kyndt
    Abstract:

    The genus Rhodopseudomonas , containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are collectively called Rhodopseudomonas palustris . The type species R. palustris and closely related species are the focus of this paper. The comparison of available genome sequences indicate that the following Rhodopseudomonas species are well recognized: R. palustris (strains ATH 2.1.6T=DSM 123T=NBRC 100419T and BisB5), Rhodopseudomonas rutila (strains R1T, DSM 126, CGA009, ATH 2.1.37, Eli 1980, ATCC 17001 and TIE1), Rhodopseudomonas pentothenatexigens JA575T and Rhodopseudomonas faecalis JCM 11668T. Other strains for which genome sequences are available are distinct from these four species. Evidence is presented that R. palustris strain ATH 2.1.6T–KCM as obtained directly from the van Niel collection by one of us (T.E.M.) is identical to the DSMZ deposit DSM 123T of ATH 2.1.6T, but not to the deposit at ATCC 17001. The amino acid sequences of the cytochromes C2 and C556 from R. palustris strain ATH 2.1.6T–KCM are in complete agreement with the translated genome sequences of R. palustris DSM 123T. In addition, the 16S rRNA gene sequence of R. palustris NBRC 100419T completely matches that of strain DSM 123T. In conclusion, the type strain of R. palustris ATH 2.1.6T is correctly represented by DSM 123T and NBRC 100419T. However, the deposit at ATCC 17001 has properties that do not conform with properties of authentic R. palustris , but rather indicate that this is a strain of R. rutila . The previously suggested assignment of the type strain of R. palustris DSM 123T to the new species R. pseudopalustris was incorrect because strain DSM 123T is the authentic type strain of R. palustris .

  • Taxonomic note: transfer of Rhodopseudomonas acidophila to the new genus Rhodoblastus as Rhodoblastus acidophilus comb. nov.
    2001
    Co-Authors: Johannes F. Imhoff
    Abstract:

    Rhodopseudomonas acidophila has unique properties among the phototrophic a-Proteobacteria and is quite distinct from the type species of Rhodopseudomonas, Rhodopseudomonas palustris. Therefore, the transfer of Rhodopseudomonas acidophila to Rhodoblastus acidophilus gen. nov., comb. nov., is proposed. This proposal is in accordance with other taxonomic reclassifications proposed previously and fully reflects the phylogenetic distance from Rhodopseudomonas palustris.

Jinyou Duan - One of the best experts on this subject based on the ideXlab platform.

  • Preparation and biological activities of an extracellular polysaccharide from Rhodopseudomonas palustris
    International Journal of Biological Macromolecules, 2019
    Co-Authors: Peng Zhang, Feifei Sun, Xiang Cheng, Shunchun Wang, Huiling Geng, Jinyou Duan
    Abstract:

    The photosynthetic bacterium, Rhodopseudomonas palustris has been widely used as probiotics in aquaculture, while the molecular basis underlying the probiotic properties of this organism remains largely unknown. In this study, a novel extracellular polysaccharides (RPEPS-30) extracted from the fermentation of Rhodopseudomonas palustris was characterized. Results illustrated that RPEPS-30 was an α-mannan with a molecular weight of 46.82 kDa, which possessed a backbone consisted of 1, 2-linked and 1, 4-linked mannose residues, with side chains composed of 1 → 6 linked and 1 → 2,6 linked mannose residues and substitution at O-6. The in vitro immunomodulatory tests revealed that RPEPS-30 could enhance phagocytic capacity, NO release and mRNA expression of cytokines in macrophages. In addition, RPEPS-30 was shown to promote the growth of resident beneficial gut microbiotasuch as Lactobacillus reuteri, Bacteroides thetaiotaomicron and Akkermansia muciniphila. These findings might help us to partially understand the molecular mechanism concerning the probiotic properties of Rhodopseudomonas palustris, in which the extracellular polysaccharide RPEPS-30 stimulated host immune response and favored the growth of specific benificial micriobiota in the gut.

John A. Kyndt - One of the best experts on this subject based on the ideXlab platform.

  • genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris dsm 123t as the authentic type strain of this species
    International Journal of Systematic and Evolutionary Microbiology, 2020
    Co-Authors: Johannes F. Imhoff, T E Meyer, John A. Kyndt
    Abstract:

    The genus Rhodopseudomonas , containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are collectively called Rhodopseudomonas palustris . The type species R. palustris and closely related species are the focus of this paper. The comparison of available genome sequences indicate that the following Rhodopseudomonas species are well recognized: R. palustris (strains ATH 2.1.6T=DSM 123T=NBRC 100419T and BisB5), Rhodopseudomonas rutila (strains R1T, DSM 126, CGA009, ATH 2.1.37, Eli 1980, ATCC 17001 and TIE1), Rhodopseudomonas pentothenatexigens JA575T and Rhodopseudomonas faecalis JCM 11668T. Other strains for which genome sequences are available are distinct from these four species. Evidence is presented that R. palustris strain ATH 2.1.6T–KCM as obtained directly from the van Niel collection by one of us (T.E.M.) is identical to the DSMZ deposit DSM 123T of ATH 2.1.6T, but not to the deposit at ATCC 17001. The amino acid sequences of the cytochromes C2 and C556 from R. palustris strain ATH 2.1.6T–KCM are in complete agreement with the translated genome sequences of R. palustris DSM 123T. In addition, the 16S rRNA gene sequence of R. palustris NBRC 100419T completely matches that of strain DSM 123T. In conclusion, the type strain of R. palustris ATH 2.1.6T is correctly represented by DSM 123T and NBRC 100419T. However, the deposit at ATCC 17001 has properties that do not conform with properties of authentic R. palustris , but rather indicate that this is a strain of R. rutila . The previously suggested assignment of the type strain of R. palustris DSM 123T to the new species R. pseudopalustris was incorrect because strain DSM 123T is the authentic type strain of R. palustris .

  • Draft Whole-Genome Sequence of the Purple Nonsulfur Photosynthetic Bacterium Rhodopseudomonas rutila R1.
    Microbiology resource announcements, 2018
    Co-Authors: Sydney Robertson, Amiera Rayyan, Terry E. Meyer, John A. Kyndt
    Abstract:

    Rhodopseudomonas species are purple nonsulfur bacteria found in many environments and known for their diverse metabolic capabilities. Here, we report the genome sequence of Rhodopseudomonas rutila type strain R1 and a whole-genome nucleotide comparison of related Rhodopseudomonas palustris species, suggesting the necessity for future reevaluation of the Rhodopseudomonas species differentiation.