Unique communities of anoxygenic phototrophic bacteria in saline lakes of Salar de Atacama (Chile): evidence for a new phylogenetic lineage of phototrophic Gammaproteobacteriafrom pufLMgene analyses (original) (raw)
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Rhodobacter ovatus sp. nov., a phototrophic alphaproteobacterium isolated from a polluted pond
International Journal of Systematic and Evolutionary Microbiology, 2008
A novel ovoid, phototrophic, purple non-sulfur bacterium was isolated in pure culture from a sample of sediment from an industrially polluted pond (Noor Mohammad Kunta) in Hyderabad, India. Strain JA234 T was found to be Gram-negative and non-motile and grew photoheterotrophically with a number of organic compounds serving as carbon source/electron donor. Photo-organoheterotrophic and chemo-organoheterotrophic growth were demonstrated. Biotin and thiamine were required for growth of strain JA234 T . Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA234 T is most closely related to Rhodobacter azotoformans (97.3 % sequence similarity) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA-DNA hybridization with Rba. azotoformans JCM 9340 T showed a relatedness of only 31.3 % with respect to strain JA234 T . On the basis of 16S rRNA gene sequence analysis, DNA-DNA hybridization data and morphological and physiological characteristics, strain JA234 T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter ovatus sp. nov. is proposed. The type strain is JA234 T (5JCM 14779 T 5CCUG 55049 T ).
Rhodoplanes serenus sp. nov., a purple non-sulfur bacterium isolated from pond water
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009
A bright pink to red-coloured, phototropic, purple non-sulfur bacterium, designated strain TUT3530 T , was isolated from pond water. Cells of the novel isolate were found to be Gram-negative, motile, budding rods. Cell extracts from phototrophically grown cultures had absorption maxima at 378, 482, 512, 550, 590, 800 and 850 nm, indicating the presence of bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The intracytoplasmic membrane system was of the lamellar type. Anaerobic photo-organotrophy with simple organic acids such as pyruvate was the preferred mode of growth. Aerobic growth at full atmospheric oxygen tension and anaerobic denitrifying growth in darkness were also possible. Photolithotrophic growth occurred with thiosulfate, but not with sulfide or hydrogen, as the electron donor. No growth factors were required. The major whole-cell fatty acid was C 18 : 1 v7c. The major quinones were ubiquinone-10 and rhodoquinone-10. A phylogenetic analysis based on 16S rRNA gene sequences and studies involving DNA-DNA hybridization demonstrated that strain TUT3530 T occupies a distinct taxonomic position within the genus Rhodoplanes. On the basis of these data, strain TUT3530 T represents a novel species of the genus Rhodoplanes, for which the name Rhodoplanes serenus sp. nov. is proposed. The type strain is TUT3530 T (5DSM 18633 T 5NBRC 102049 T ).
Two strains (JA643 T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10-15 6C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1-AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C 18 : 1 v7c (76-79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1-5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2-64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162 T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA-DNA hybridization with R. vannielii DSM 162 T. Strains JA643 T and JA755 shared .99 % 16S rRNA gene sequence similarity and were .85 % related on the basis of DNA-DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium, for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643 T (5KCTC 15219 T 5NBRC 109057 T). The family Hyphomicrobiaceae in the class Alphaproteo-bacteria contains three phototrophic genera: Blastochloris, Rhodomicrobium and Rhodoplanes. The genus Rhodomicro-bium can be distinguished from Blastochloris and Rhodo-planes mainly on the basis of cell morphology, including long prosthecae and a characteristic vegetative growth cycle. Rhodomicrobium vannielii (Duchow & Douglas, 1949) is the single recognized species of the genus Rhodomicrobium; in the present communication, we propose a novel species based on two strains (JA643 T and JA755) isolated from different geographical locations in India. Strain JA643 T was isolated from a freshwater stream sample collected from Udaipur in Himachal Pradesh [GPS of the sampling site is 32 u 439 30.550 N 76 u 399 55.450 E; altitude of 8970 feet (2734 m) above sea level], in the western Himalayas, India. Strain JA755 was isolated from a freshwater stream sample collected from Rottikadai town near the Annamalai hills [10u 359 N 76 u 979 E; altitude of 3500 feet (1067 m) above sea level] in the Western Ghats, Tamil Nadu, India. Both strains were isolated after enrichment in PE medium (Hanada et al., 1995) at pH 7.0, in fully filled 50 ml screw-capped bottles incubated under phototrophic (2500 lx) conditions at 30±2 u C for 15 days. Purification of the isolates and the media used for growth of the organisms are as previously described (Lakshmi et al., 2011a, b). Genomic DNA was extracted and purified according to the method of Marmur (1961) and the DNA G+C content of strains JA643 T and JA755 was 62.4 and 62.8 mol% as determined by HPLC (Mesbah et al., 1989). Cell material Abbreviation: FT-IR, Fourier transform infrared. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strains JA643 T and JA755 are FN995218 and HE863941, respectively.
Current Microbiology, 2019
A novel Gram-negative gamma-proteobacterium, non-sporulating motile, rod or coccus-shaped bacterium designated as strain PKS7 T was isolated from a sediment sample collected from Chilika Lake, Odisha, India and characterized taxonomically using a polyphasic approach. The major quinone was Q8 and major cellular fatty acids were C 16:0 , C 17:0 , C 15:1 w8c , C 17:1 w8c, C 12:0 3-OH. The chemotaxonomic features confirmed the isolate to be a member of genus Rheinheimera. 16SrRNA gene sequence of strain PKS7 T was closest in similarity to R. aquimaris SW-353 T (99.36% identity), R. muenzenbergensis E49 T (98.63%), R. nanhaiensis E407-8 T (98.35%), R. japonica KMM 9513 T (98.35%) and R. baltica DSM-14885 T (98.08%). The 16S rRNA gene sequence-based phylogenetic analysis and sequence similarity between the isolated strain and type strains also revealed its affiliation to genus Rheinheimera. DNA-DNA relatedness with closest type strain R. aquimaris SW-353 T was 25.0% (±3.40) and in silico DDH showed values in the range of 17.7-37.1% with the type strains of the genus Rheinheimera for which whole genome sequence are available. Strain PKS7 T was also distinguished by a multi-locus sequence analysis (MLST) by alingning gyrB gene sequences of the closest type strains of Rheinheimera. The draft genome of strain PKS7 T contained 32 contigs of total size 3,963,569 bp comprising of 3763 predicted coding sequences with a G + C content of 50.7 mol%. Comparision of phenotypic and genotypic data with its closest neighbours and closely related species confirm the strain PKS7 T to be recognised as a novel species within the genus Rheinheimera, for which the name Rheinheimera pleomorphica sp. nov. is proposed. The type strain is PKS7 T (= KCTC 42365 = JCM 30460).
Systematic and Applied Microbiology, 2008
The isolation of photoheterotrophic organism C3 from a saline microbial mat led to its taxonomic characterization. Strain C3 could be identified as a member of the species Rhodobium marinum due to the genetic and phenotypic similarities to the type strain of the species (DSM 2698 T). As a result of a taxonomic study, it was observed that the currently classified species of the genus formed two separate clades, each of them deserving genus status. Rhodobium orientis and Rhodobium gokarnense may be considered as true members of the genus Rhodobium, whereas R. marinum and Rhodobium pfennigii should be reclassified into a new genus. In the light of the genetic and phenotypic evidence observed, we propose that both latter species are reclassified within the new genus Afifella gen. nov., as species Afifella marina comb. nov., and Afifella pfennigii comb. nov., with Af. marina the type species of the genus. In addition, the taxonomic study has revealed that strain DSM 11549, identified as the type strain of the species Rhodopseudomonas julia, may represent a genomovar of Af. marina. The fact that the author of the first classification of R. julia indicates that the strains deposited in the German Collection for Microorganisms (DSM 11549) and American Collection of Type Cultures (ATCC 51105) do not correspond to the original description, makes the authenticity of the strains doubtful. Due to this reason, it is not proposed to reclassify the species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009
A Gram-negative, spiral-shaped, phototrophic, purple non-sulfur bacterial strain, designated JA145 T , was isolated from a freshwater habitat. Cells of strain JA145 T were motile by means of a monopolar flagellum. Intracellular photosynthetic membranes were of the stacked type. Bacteriochlorophyll a and the carotenoid lycopene and its glucosides were present as photosynthetic pigments. There was no vitamin requirement for strain JA145 T . The predominant cellular fatty acids were C 16 : 1 v7c/C 16 : 1 v6c (22.24 %), C 16 : 0 (22.97 %) and C 18 : 1 v7c (43.24 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA145 T clustered with species of the genus Phaeospirillum, in the class Alphaproteobacteria. The highest sequence similarities of strain JA145 T were found with the type strains of Phaeospirillum fulvum (96.12 %) and Phaeospirillum molischianum (96.19 %). Based on the 16S rRNA gene sequence analysis and the morphological and physiological characteristics, strain JA145 T is considered to represent a novel species, for which the name Phaeospirillum chandramohanii sp. nov. is proposed. The type strain is JA145 T (5JCM 14933 T 5KCTC 5703 T 5NBRC 104961 T ).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2008
Two strains of phototrophic, purple non-sulfur bacteria capable of growing at low temperatures (5 6C) were isolated from the Himalayas. The two strains showed positive phototaxis and grew over a relatively wide temperature range (5-40 6C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA194 T clustered with members of the genus Rhodobacter. Strain JA194 T showed highest 16S rRNA gene sequence similarity with Rhodobacter sphaeroides DSM 158 T (99 %). However, DNA-DNA hybridization experiments between Rba. sphaeroides DSM 158 T and strain JA194 T revealed a level of relatedness of only 67 %. The DNA base composition of strain JA194 T was 66.67 mol% G+C (by HPLC). Based on 16S rRNA gene sequence analysis, morphological, physiological, Fourier transform infrared fingerprinting and DNA-DNA hybridization studies, strain JA194 T (5KCTC 5602 T 5JCM 14598 T) is sufficiently different from other Rhodobacter species to merit its description as the type strain of a novel species, for which the name Rhodobacter megalophilus sp. nov. is proposed.