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1.
Int J Syst Evol Microbiol ; 66(12): 5167-5172, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27667642

ABSTRACT

A Gram-stain-positive, non-motile, rod-shaped bacterium (strain JC303T) isolated from a salt pan was identified based on 16S rRNA gene sequence analysis as a member of the genus Jeotgalibacillus. It was related most closely to Jeotgalibacillus salarius ASL-1T (99.1 % similarity), Jeotgalibacillusalimentarius YKJ-13T (97.9 %), Jeotgalibacillussoli JSM 081008 (97.9 %), Jeotgalibacillusmalaysiensis D5T (97.8 %), Jeotgalibacillusmarinus DSM 1297T (96.3 %), Jeotgalibacilluscampisalis SF-57T (96.1 %) and J. soli P9T (94.9 %). Genomic relatedness based on DNA-DNA hybridization of strain JC303T with the type strains of the closest related species was less than 40 %. Diphosphatidylglycerol, three aminophospholipids, an unidentified aminoglycolipid, two unidentified phospholipids and an unidentified lipid were the polar lipids of strain JC303T. Major (>10 %) fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0. Cell-wall amino acids contained peptidoglycan with l-lysine as the diagnostic diamino acid. Strain JC303T contained MK-7 as the predominant (96 %) menaquinone with the presence of a significant amount (4 %) of MK-8. The DNA G+C content was 43 mol%. On the basis of morphological, physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC303T is considered to represent a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus alkaliphilus sp. nov. is proposed. The type strain is JC303T (=KCTC 33662T=LMG 28756T). In addition, we propose to rename J. soli (Chen et al., 2010), an illegitimate homonym of the validly published name Jeotgalibacillus soli(Cunha et al., 2012) as Jeotgalibacillus terrae sp. nov. with type strain JSM 081008T (=DSM 22174T=KCTC 13528T).


Subject(s)
Phylogeny , Planococcaceae/classification , Sodium Chloride , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , Planococcaceae/genetics , Planococcaceae/isolation & purification , RNA, Ribosomal, 16S/genetics , Salinity , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
3.
Int J Syst Evol Microbiol ; 66(10): 3814-3820, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27381021

ABSTRACT

A Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA-DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTmwas >5 °C indicating that the strain represents a novel species of the genus Salinicoccus. Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccusamylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).


Subject(s)
Phylogeny , Salinity , Staphylococcaceae/classification , Amino Acids/chemistry , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Staphylococcaceae/genetics , Staphylococcaceae/isolation & purification , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
4.
Int J Syst Evol Microbiol ; 66(9): 3367-3371, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27260502

ABSTRACT

A reddish-brown-pigmented, phototrophic bacterium, designated strain JA877T, was isolated from a brown algae mat sample collected from Jalandhar beach, Gujarat, India. On the basis of the 16S rRNA gene sequence, strain JA877T belongs to the class Alphaproteobacteria and is closely related to the type strains Rhodovulum viride JA756T (99.0 %), Rhodovulum sulfidophilum Hansen W4T (98.9 %), Rhodovulumvisakhapatnamense JA181T (98.8 %),Rhodovulum kholense JA297T (97.5 %) and Rhodovulum salis JA746T (97.0). However, strain JA877T showed only 20-45 % relatedness with its phylogenetic neighbours and had a ∆Tm between 5.8 and 7.0 °C. The major respiratory quinone was ubiquinone-10 (Q10), and the polar lipid profile was composed of the major components phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, two unidentified sulfolipids and five unidentified lipids. The major fatty acids were C18 : 1ω5c, C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C18 : 0. The DNA G+C content was 64.5 mol%. On the basis of 16S rRNA gene sequence analysis, physiological data, and chemotaxonomic and molecular differences, strain JA877T is significantly different from other species of the genus Rhodovulum and represents a novel species, for which the name Rhodovulum algae sp. nov. is proposed. The type strain is JA877T (=LMG 29228T= KCTC 42963T).


Subject(s)
Phaeophyceae/microbiology , Phylogeny , Rhodovulum/classification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Lipids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Rhodovulum/genetics , Rhodovulum/isolation & purification , Sequence Analysis, DNA , Ubiquinone/chemistry
5.
Int J Syst Evol Microbiol ; 66(8): 2923-2928, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27129367

ABSTRACT

A Gram-stain-positive, endospore-forming, rod-shaped, facultatively anaerobic bacterium, designated as strain E3T, was isolated from groundnut seeds. Based on the 16S rRNA gene sequence analysis, strain E3T belongs to the genus Paenibacillus with Paenibacillus thailandensis S3-4AT (96.0 %), Paenibacillus xanthinilyticus 11N27T (95.7 %), Paenibacillus mendelii C/2T (95.7 %) and other members of the genus Paenibacillus (<95.5 %) as its closest phylogenetic neighbours. The DNA G+C content of strain E3T was 53 mol%. Strain E3T was positive for gelatin hydrolysis, ammonification, catalase, chitinase production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, HCN production, siderophore production, biofilm formation, and urea and starch hydrolysis. Strain E3T had phosphatidylethanolamine, diphosphotidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, two unidentified aminolipids and two unidentified lipids as polar lipids. Strain E3T had diploptene, deplopterol and bacteriohopaneterol as major hopanoids. anteiso-C15 : 0 was the predominant cellular fatty acid with significant proportions of iso-C16 : 0, C16 : 0, C17 : 0, anteiso-C17 : 0, C18 : 1ω9c and iso-C14 : 0. Strain E3T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. On the basis of physiological, biochemical, chemotaxonomic and molecular analysis, strain E3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus arachidis sp. nov. is proposed. The type strain is E3T (=KCTC 33574T=LMG 28417T).


Subject(s)
Arachis/microbiology , Paenibacillus/classification , Phylogeny , Seeds/microbiology , Bacterial Typing Techniques , Base Composition , Cell Wall/chemistry , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Nucleic Acid Hybridization , Paenibacillus/genetics , Paenibacillus/isolation & purification , Peptidoglycan/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
6.
Int J Syst Evol Microbiol ; 66(3): 1268-1274, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26738915

ABSTRACT

Twenty-three rod-shaped, endospore-forming, Gram-stain-positive, obligately anaerobic bacteria were isolated from different marine sediment samples of Gujarat. All 23 strains shared 16S rRNA gene sequence similarity of ∼100 %. Strain JC272T was designated the type strain and shared highest sequence similarity with Clostridium bifermentans ATCC 638T (99.8 %), Clostridium ghonii JCM 1400T (98.0 %), Clostridium sordellii ATCC 9714T (97.9 %) and other members of the genus Clostridium ( < 96.4 %). C16 : 0, C18 : 0, C17 : 0, C16 : 1ω9c and iso-C16 : 0 were the major (>5 %) fatty acids. Strain JC272T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified amino lipids. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) of strain JC272T with C. bifermentans ATCC 638T yielded values of 94.35 and 58.5 ± 2.8 %, respectively. The DNA G+C content of strain JC272T was 28.3 mol%. Strain JC272T together with C. bifermentans were found to fall outside Clostridium rRNA cluster I considered as Clostridium senso stricto. Based on ANI value, in-silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain JC272T represents a novel species of a new genus in the family Clostridiaceae, for which the name Paraclostridium benzoelyticum gen. nov., sp. nov. is proposed. The type strain is JC272T ( = KCTC 15476T = LMG 28745T). It is also proposed to transfer C. bifermentans to this new genus, as Paraclostridium bifermentans comb. nov. (type strain ATCC 638T = DSM 14991T = JCM 1386T). The genus Paeniclostridium gen. nov. is proposed to accommodate C. sordellii and C. ghonii as Paeniclostridium sordellii comb. nov. (type strain ATCC 9714T = LMG 15708T = JCM 3814T) and Paeniclostridium ghonii comb. nov. (type strain ATCC 25757T = DSM 15049T = JCM 1400T).

7.
Int J Syst Evol Microbiol ; 66(4): 1612-1619, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26704619

ABSTRACT

An obligately anaerobic spirochaete designated strain JC227T was isolated from the gut of a wood-eating cockroach, Cryptocercus punctulatus (Scudder), from the Rann of Kutch, Gujarat, India. Strain JC227T was Gram-stain-negative, mesophilic, halotolerant and alkaliphilic. Based on 16S rRNA gene sequence analysis, strain JC227T belongs to the genus Spirochaeta, with Spirochaeta sphaeroplastigenens JC133T (99.51%), S. odontotermitis JC202T (99.30%), S. alkalica Z-7491T (99.10%), S. americana (98.54%) and other members of the genus Spirochaeta (<92.7%) as its closest phylogenetic neighbours. However, DNA-DNA hybridization between strain JC227T and S. sphaeroplastigenens JC133T, S. odontotermitis JC202T, S. alkalica DSM 8900T and S. americana DSM 14872T was 62±2, 63, 58±2 and 48±4 %, respectively. Strain JC227T contained phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and six unidentified lipids. Summed feature C18:1ω7c/C18:1ω6c was the predominant cellular fatty acid, with significant proportions of C16:0, C14:0, C12:0, C15:1ω6c, C16:1ω5c, C16:1ω6c/C16:1ω7c and C17:0 2-OH. The DNA G+C content of strain JC227T was 55.5 mol%. On the basis of physiological, biochemical, chemotaxonomic (including metabolomic) and genomic differences from previously described taxa, strain JC227T can be differentiated from members of the genus Spirochaeta and represents a novel species of a new genus, for which the name Alkalispirochaeta cellulosivorans gen. nov., sp. nov. is proposed. The type strain of Alkalispirochaeta cellulosivorans is JC227T (=KCTC 15343T=NBRC 110105T). We also propose the reclassification of Spirochaeta sphaeroplastigenens, Spirochaeta odontotermitis, Spirochaeta alkalica and Spirochaeta americana as Alkalispirochaeta sphaeroplastigenens comb. nov. (type strain JC133T=KCTC 15220T=NBRC 109056T), Alkalispirochaeta odontotermitis comb. nov. (type strain JC202T=KCTC 15324T=NBRC 110104T), Alkalispirochaeta alkalica comb. nov. (type strain Z-7491T=DSM 8900T=ATCC 700262T) and Alkalispirochaeta americana comb. nov. (type strain ASpG1T=ATCC BAA-392T=DSM 14872T). The type species of Alkalispirochaeta gen. nov. is Alkalispirochaeta alkalica comb. nov.


Subject(s)
Cockroaches/microbiology , Phylogeny , Spirochaeta/classification , Animals , Bacterial Typing Techniques , Base Composition , Cellulose/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spirochaeta/genetics , Spirochaeta/isolation & purification , Wood
8.
Int J Syst Evol Microbiol ; 65(12): 4589-4594, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26377069

ABSTRACT

A Gram-stain-negative spirochaete (strain JC202T) was isolated from the gut of the termite Odontotermes obesus (Rambur) from Rann of Kutch, Gujarat, India. This strain was obligately anaerobic, mesophilic, halotolerant and required alkaline conditions for growth. Strain JC202T was resistant to rifampicin and kanamycin, but sensitive to gentamicin, tetracycline, ampicillin and chloramphenicol. Strain JC202T possessed phosphatidylglycerol, diphosphatidylglycerol, glycolipid and six unidentified lipids. C18 : 1ω7c was the predominant cellular fatty acid with significant proportions of C16 : 0, C18 : 1ω9c, C14 : 0, C18 : 0, C16 : 1ω5c, C18 : 1ω5c and C20 : 1ω9c. The DNA G+C content of strain JC202T was 59 mol%. Based on 16S rRNA gene sequence analysis, strain JC202T is considered to belong to the genus Spirochaeta with Spirochaeta sphaeroplastigenens JC133T (100 % similarity), Spirochaeta alkalica Z-7491T (99.92 %), Spirochaeta americana ATCC BAA-392T (99.47 %) and other members of the genus Spirochaeta ( < 93.83 %) as the closest phylogenetic neighbours. However, mean DNA-DNA hydridization values between strain JC202T and S. sphaeroplastigenens JC133T, S. alkalica DSM 8900T ( = Z-7491T) and S. americana DSM 14872T ( = ASpG1T) were 55 ± 2, 22 ± 3 and 32 ± 1 %, respectively. On the basis of physiological, biochemical, chemotaxonomic (including metabolome) and genomic differences from the previously described taxa, strain JC202T is differentiated from other members of the genus Spirochaeta and is considered to represent a novel species, for which the name Spirochaeta odontotermitis sp. nov. is proposed. The type strain is JC202T ( = KCTC 15324T = NBRC 110104T).


Subject(s)
Isoptera/microbiology , Phylogeny , Spirochaeta/classification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spirochaeta/genetics , Spirochaeta/isolation & purification
9.
Genome Announc ; 3(3)2015 Jun 11.
Article in English | MEDLINE | ID: mdl-26067979

ABSTRACT

We announce the draft genome sequence of Clostridium sp. JC272, isolated from a sediment sample collected from marine habitats of Gujarat, India. Clostridium sp. JC272 is an obligate anaerobe and has the ability to produce antimicrobial compounds. The genome sequence indicates the strain's capability of producing small peptides (microcins), which are potential novel antibiotics.

10.
Genome Announc ; 3(1)2015 Jan 22.
Article in English | MEDLINE | ID: mdl-25614577

ABSTRACT

We announce here the draft genome sequence of Spirochaeta sp. strain JC202 isolated from gut of a termite (Isoptera). The genome suggests that Spirochaeta sp. JC202 has the capability for natural conjugation with the help of fimbriae and pili. Experimental evidence and the genome sequence suggest that strain JC202 is capable of producing colicin V and a bacteriocin group of peptides in a specific interaction.

11.
Syst Appl Microbiol ; 38(2): 110-4, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25487950

ABSTRACT

Metagenome analysis of forty samples indicated a rich diversity of free living spirochaetes among Indian habitats. Only 2-3% of the total bacterial diversity was represented by spirochaetes with five distinct phylogenetic OTUs. A strain (JC230(T)) was brought to cultivation and its 16S rRNA gene sequence showed highest sequence similarity with that of Spirochaeta asiatica Z-7591(T) (90.78%). Genome sequence analysis of strain JC230(T) indicates the presence of 117 genes related to motility and chemotaxis. Strain JC230(T) is an obligate anaerobe. It is helical shaped, Gram-stain-negative and catalase and oxidase negative. Strain JC230(T) produces carotenoids and have all the genes related to carotenogenesis of spirilloxanthin series. Isoprenoid biosynthesis occurs through HMG-CoA (3-hydroxy-3-methylglutaryl-coenzyme A) pathway. Twelve bacterial haemoglobin and one flavohaemoglobin related genes are present in the genome of strain JC230(T). The genome of strain JC230(T) showed the presence of heavy metal resistance related genes of cobalt, zinc, cadmium and arsenic. Six genes related to colicin V and bacteriocin production cluster are present. Major (>2%) fatty acids were C12:0, C14:0, iso-C14:0, iso-C15:1H/C13:03OH, anteiso-C15:0, C16:0, and iso-C16:0. Strain JC230(T) contains diphosphatylglycerol, phosphatydilglycerol, phosphatydilethanolamine, unidentified phospholipid (PL1) and unidentified lipids (L1-7). G+C mol% of strain JC230(T) was 54.1%. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC230(T) as a representative of a new species in the genus Spirochaeta, for which the name Spirochaeta lutea sp. nov. is proposed. The type strain is JC230(T) (=KCTC 15387(T)=DSM 29074(T)).


Subject(s)
Spirochaeta/classification , Spirochaeta/isolation & purification , Bacteriocins/metabolism , Base Composition , Carotenoids/metabolism , Cluster Analysis , Cytosol/chemistry , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Environmental Microbiology , Fatty Acids/analysis , Genome, Bacterial , India , Metabolic Networks and Pathways/genetics , Molecular Sequence Data , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spirochaeta/genetics , Terpenes/metabolism
12.
DNA Res ; 21(6): 639-47, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25117430

ABSTRACT

Hopanoids are present in vast amounts as integral components of bacteria and plants with their primary function to strengthen rigidity of the plasma membrane. To establish their roles more precisely, we conducted sequencing of the whole genome of Rhodomicrobium udaipurense JA643(T) isolated from a fresh water stream of Udaipur in Himachal Pradesh, India, by using the Illumina HiSeq pair end chemistry of 2 × 100 bp platform. Determined genome showed a high degree of similarity to the genome of R. vannielii ATCC17100(T) and the 13.7 million reads generated a sequence of 3,649,277 bp possessing 3,611 putative genes. The genomic data were subsequently investigated with respect to genes involved in various features. The machinery required for the degradation of aromatic compounds and resistance to solvents as well as all that required for photosynthesis are present in this organism. Also, through extensive functional annotation, 18 genes involved in the biosynthesis of hopanoids are predicted, namely those responsible for the synthesis of diploptene, diplopterol, adenosylhopane, ribosylhopane, aminobacteriohopanetriol, glycosyl group containing hopanoids and unsaturated hopanoids. The hopanoid biosynthetic pathway was then inferred based on the genes identified and through experimental validation of individual hopanoid molecules. The genome data of R. udaipurense JA643(T) will be useful in understanding the functional features of hopanoids in this bacterium.


Subject(s)
Genome, Bacterial/physiology , Rhodomicrobium , Triterpenes/metabolism , Cell Membrane/genetics , Cell Membrane/metabolism , High-Throughput Nucleotide Sequencing , Molecular Sequence Annotation , Rhodomicrobium/genetics , Rhodomicrobium/metabolism
13.
Int J Syst Evol Microbiol ; 64(Pt 10): 3553-3558, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25061066

ABSTRACT

Two bacterial strains (JC109(T) and JC261) were isolated from a sediment sample collected from a shrimp cultivation pond in Tamil Nadu (India). Cells were Gram-stain-negative, motile rods. Both strains were positive for catalase and oxidase, hydrolysed Tween 80, and grew chemo-organoheterotrophically with an optimal pH of 6 (range pH 4-9) and at 30 °C (range 25-40 °C). Based on 16S rRNA gene sequence analysis, strains JC109(T) and JC261 were identified as belonging to the genus Alcanivorax with Alcanivorax dieselolei B-5(T) (sequence similarity values of 99.3 and 99.7%, respectively) and Alcanivorax balearicus MACL04(T) (sequence similarity values of 98.8 and 99.2%, respectively) as their closest phylogenetic neighbours. The 16S rRNA gene sequence similarity between strains JC109(T) and JC261 was 99.6%. The level of DNA-DNA relatedness between the two strains was 88%. Strain JC109(T) showed 31 ± 1 and 26 ± 2% DNA-DNA relatedness with A. dieselolei DSM 16502(T) and A. balearicus DSM 23776(T), respectively. The DNA G+C content of strains JC109(T) and JC261 was 54.5 and 53.4 mol%, respectively. Polar lipids of strain JC109(T) included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The major fatty acids were C10:0, C12:0, C16:0, C12:0 3-OH, C16:1ω7c, C18:1ω7c and C19:0 cyclo ω8c. Both strains could utilize diesel oil and a variety of xenobiotics as carbon and energy sources. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed the clear differentiation of strains JC109(T) and JC261 from all other members of the genus Alcanivorax. Strains JC109(T) and JC261 are thus considered to represent a novel species, for which the name Alcanivorax xenomutans sp. nov. is proposed. The type strain is JC109(T) ( = KCTC 23751(T) = NBRC 108843(T)).


Subject(s)
Alcanivoraceae/classification , Phylogeny , Ponds/microbiology , Water Microbiology , Alcanivoraceae/genetics , Alcanivoraceae/isolation & purification , Animals , Aquaculture , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Decapoda , Fatty Acids/chemistry , Geologic Sediments/microbiology , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spain
14.
Int J Syst Evol Microbiol ; 64(Pt 3): 957-962, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24425825

ABSTRACT

Two strains (JA746(T) and JA756(T)) having yellowish brown-to-green pigment were isolated from a solar saltern and a pink pond, respectively. While both strains were non-motile and shared the presence of bacteriochlorophyll-a, major cellular fatty acids (C18 : 1ω7c, C16 : 0, C18 : 0), quinone (Q-10), polar lipids and hopanoids, they differed from each other in their carotenoid composition. The G+C content of genomic DNA of strains JA746(T) and 756(T) was 62.4 and 63.3 mol%, respectively. The 16S rRNA gene-based EzTaxon-e blast search analysis of strains JA746(T) and 756(T) indicated highest sequence similarity with members of the genus Rhodovulum in the family Rhodobacteraceae of the class Alphaproteobacteria. Strain JA746(T) has high sequence similarities with Rhodovulum visakhapatnamense JA181(T) (97.3 %), Rhodovulum steppense A-20s(T) (97.3 %), Rhodovulum phaeolacus JA580(T) (97 %), Rhodovulum strictum MB-G2(T) (97 %) and other members of the genus Rhodovulum (<97 %). Strain JA756(T) has high sequence similarities with Rhodovulum visakhapatnamense JA181(T) (99.8 %), Rhodovulum sulfidophilum Hansen W4(T) (99.1 %), Rhodovulum kholense JA297(T) (97.9 %) and other members of the genus Rhodovulum (<97 %). The sequence similarity between strains JA746(T) and JA756(T) was 97.5 %. However, these strains are not closely related to each other or to their phylogenetic neighbours since the DNA-DNA reassociation values were less than 56 %. The genomic information was also supported by phenotypic and chemotaxonomic results, leading us to classify strains JA746(T) ( = NBRC 108898(T) = KCTC 15180(T)) and JA756(T) ( = NBRC 109122(T) = KCTC 15223(T)) as the type strains of two novel species of the genus Rhodovulum, for which the names Rhodovulum salis sp. nov. and Rhodovulum viride sp. nov. are proposed, respectively.


Subject(s)
Phylogeny , Ponds/microbiology , Rhodovulum/classification , Water Microbiology , Bacteriochlorophyll A/chemistry , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Rhodovulum/genetics , Rhodovulum/isolation & purification , Seawater , Sequence Analysis, DNA , Sodium Chloride , Ubiquinone/chemistry
15.
Int J Syst Evol Microbiol ; 63(Pt 12): 4484-4488, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23907221

ABSTRACT

The taxonomic position of strain MSSRFBL1(T), isolated from chickpea rhizosphere soil from Kannivadi, India, was determined. Strain MSSRFBL1(T) formed bluish black colonies, stained Gram-negative and was motile, aerobic, capable of fixing dinitrogen, oxidase-negative and catalase-positive. Q-10 was the major respiratory quinone. Major fatty acids of strain MSSRFBL1(T) were C18 : 1ω7c and C19 : 0cycloω8c. Minor amounts of C18 : 0, C12 : 0, C14 : 0 3-OH, C18 : 0 3-OH, C16 : 0, C16 : 1ω6c/C16 : 1ω7c, C17 : 0 3-OH and C20 : 1ω7c were also present. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine and two unidentified glycolipids. Bacteriohopane derivatives (BHD1 and 2), diplopterol, diploptene, bishomohopanediol, adenosylhopane and 2ß-methyl bacteriohopanetetrol were the major hopanoids of strain MSSRFBL1(T). The genomic DNA G+C content was 71 mol%. EzTaxon-e-based blast analysis of the 16S rRNA gene indicated the highest similarity of strain MSSRFBL1(T) to Ensifer adhaerens LMG 20216(T) (97.3 %) and other members of the genus Ensifer (<96.9 %) in the family Rhizobiaceae of the class Alphaproteobacteria. However, phylogenetic analysis based on 16S rRNA, recA, thrC and dnaK gene sequences showed distinct out-grouping from the recognized genera of the family Rhizobiaceae. Based on phenotypic, genotypic and chemotaxonomic characters, strain MSSRFBL1(T) represents a novel species in a new genus in the family Rhizobiaceae for which the name Ciceribacter lividus gen. nov., sp. nov. is proposed. The type strain of Ciceribacter lividus is MSSRFBL1(T) ( = DSM 25528(T) = KCTC 32403(T)).


Subject(s)
Alphaproteobacteria/classification , Cicer/microbiology , Phylogeny , Rhizosphere , Soil Microbiology , Alphaproteobacteria/genetics , Alphaproteobacteria/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genes, Bacterial , Glycolipids/chemistry , India , Molecular Sequence Data , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Triterpenes/chemistry , Ubiquinone/chemistry
16.
Int J Syst Evol Microbiol ; 63(Pt 12): 4524-4532, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23907224

ABSTRACT

Two bacterial strains (JC130(T) and JA747(T)) were isolated from dry soils of a solar saltern. Phylogenetic analysis showed that strain JA747(T) clustered with species of the genus Erythrobacter belonging to the family Erythrobacteraceae of the class Alphaproteobacteria in the phylum Proteobacteria, while strain JC130(T) clustered with species of the genus Pontibacter belonging to the family Cytophagaceae of the phylum Bacteroidetes. Based on 16S rRNA gene sequence analysis, strain JA747(T) had highest similarity with Erythrobacter gangjinensis K7-2(T) (96.7 %) and other members of the genus Erythrobacter (<96 %). Strain JC130(T) had highest sequence similarity with Pontibacter korlensis X14-1(T) (98.1 %), Pontibacter actiniarum KMM 6156(T) (96.9 %) and other members of the genus Pontibacter (<96 %). However, strain JC130(T) showed less than 32 % DNA reassociation value (based on DNA-DNA hybridization) with Pontibacter korlensis NRRL B-51097(T) ( = X14-1(T)) and Pontibacter actiniarum LMG 23027(T) ( = KMM 6156(T)). Strain JA747(T) was positive for catalase and oxidase activity and negative for nitrate reduction, and hydrolysis of starch and casein. Phosphatidylglycerol, diphostatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were the major polar lipids for strain JA747(T). C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C17 : 1ω6c and C16 : 0 were the major fatty acids of strain JA747(T). Strain JC130(T) was positive for catalase and oxidase, and negative for gelatinase and nitrate reduction. Phosphatidylethanolamine was the major polar lipid of strain JC130(T). Major fatty acids of strain JC130(T) were iso-C15 : 0 and summed feature 4 (anteiso-C17 : 1B/iso I). Based on the phenotypic, chemotaxonomic and molecular evidence presented, strains JA747(T) and JC130(T) are considered to represent two novel species of the genera Erythrobacter and Pontibacter, for which the names Erythrobacter odishensis sp. nov. (type strain JA747(T) = KCTC 23981(T) = NBRC 108930(T)) and Pontibacter odishensis sp. nov. (type strain JC130(T) = KCTC 23982(T) = LMG 26962(T)), respectively, are proposed. Emended descriptions of the genera Erythrobacter and Pontibacter are provided.


Subject(s)
Cytophagaceae/classification , Phylogeny , Soil Microbiology , Sphingomonadaceae/classification , Bacterial Typing Techniques , Cytophagaceae/genetics , Cytophagaceae/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , India , Molecular Sequence Data , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sphingomonadaceae/genetics , Sphingomonadaceae/isolation & purification , Triterpenes/chemistry , Ubiquinone/chemistry
17.
Int J Syst Evol Microbiol ; 63(Pt 9): 3457-3462, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23543498

ABSTRACT

Four bacterial strains (JC165(T), JC166(T), JC169 and JC170) were isolated from salt pan soils from a coastal region of Tamilnadu, India. They were obligately aerobic, pink- to red-pigmented, mesophilic, haloalkaliphiles having chemoorganoheterotrophic growth on various carbon sources and were catalase- and oxidase-positive. Phototrophic growth and bacteriochlorophyll a were absent in all four strains. Major carotenoids present were ß-carotene and rhodoxanthin. The main fatty acid in all strains was iso-C(15:0). The main polar lipids were phosphatidylethanolamine (PE) and phosphatidylcholine (PC) as well as a few unidentified lipids. Bacterial hopane derivatives and diplopterol (DPL) were detected in all four strains. Based on the 16S rRNA gene sequences, all four strains belong to the family Cyclobacteriaceae in the phylum Bacteroidetes. Strains JC165(T) and JC169 had a sequence similarity of 97.2% with Mongoliicoccus roseus MIM28(T), while strains JC166(T) and JC170 had a sequence similarity of 99.5% with Litoribacter ruber YIM CH208(T). Strains JC165(T)/JC169 and JC166(T)/JC170 had genomic DNA reassociation values (based on DNA-DNA hybridization) of 21 ± 2% and 23 ± 1% with M. roseus KCTC 19808(T) ( = MIM28(T)) and L. ruber KCTC 22899(T) ( = YIM CH208(T)), respectively, suggesting that they represented novel species. The reassociation values of >85% between strains JC165(T) and JC169, and JC166(T) and JC170 suggested they were strains of the same species. The genomic information was supported by phenotypic observations leading to the proposal of two novel species, Mongoliicoccus alkaliphilus sp. nov. (type strain, JC165(T) = KCTC 32210(T) =LMG 27255(T)) and Litoribacter alkaliphilus sp. nov. (type strain, JC166(T) = KCTC 32217(T) =LMG 27256(T)).


Subject(s)
Bacteroidetes/classification , Phylogeny , Sodium Chloride , Soil Microbiology , Bacterial Typing Techniques , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phosphatidylcholines/analysis , Phosphatidylethanolamines/analysis , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Triterpenes/analysis , Xanthophylls/analysis , beta Carotene/analysis
18.
Int J Syst Evol Microbiol ; 63(Pt 7): 2684-2689, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23291882

ABSTRACT

Two strains (JA643(T) and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10-15 °C) 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 C18 : 1ω7c (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) ( = KCTC 15219(T) = NBRC 109057(T)).


Subject(s)
Phylogeny , Rhodomicrobium/classification , Rivers/microbiology , Bacterial Typing Techniques , Bacteriochlorophyll A/analysis , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phospholipids/analysis , RNA, Ribosomal, 16S/genetics , Rhodomicrobium/genetics , Rhodomicrobium/isolation & purification , Sequence Analysis, DNA , Triterpenes/analysis
19.
Int J Syst Evol Microbiol ; 63(Pt 6): 2132-2137, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23104358

ABSTRACT

Two bacterial strains (JA744(T) and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18:1ω7c, C18:0 and C16:0, while minor amounts of C10:0 3-OH, C12:0, C12:0 3-OH, C14:0 and C16:0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75 ± 1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90%). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1(T) (96%) and other members of the genera Rhodobacter and Pseudorhodobacter (<96%). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744(T) (=KCTC 32158(T) =NBRC 108897(T)).


Subject(s)
Phylogeny , Rhodobacteraceae/classification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , India , Molecular Sequence Data , Nucleic Acid Hybridization , Phospholipids/analysis , RNA, Ribosomal, 16S/genetics , Rhodobacteraceae/genetics , Rhodobacteraceae/isolation & purification , Sequence Analysis, DNA , Triterpenes/analysis
20.
Int J Syst Evol Microbiol ; 63(Pt 6): 2338-2343, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23178725

ABSTRACT

Strain JC141(T) was isolated from an alkaline soil (pH 8.8) at Mau, Uttar Pradesh, India. Colonies were blue with a metallic sheen; cells stained Gram-negative, and were oxidase- and catalase-positive, but chitinase-negative. Major fatty acids were C16:1ω7c/C16:1ω6c, C16:0 and C18:0 with minor amounts of C10:0, C10:0 3-OH, C12:0, C14:0 and C18:1ω7c. Strain JC141(T) contained phosphatidylethanolamine and phosphatidylglycerol as major polar lipids, with minor amounts of diphosphatidylglycerol, unidentified aminolipids (AL1-3) and unidentified lipids (L1-4). A bacterial hopane derivative (BHD1) was the major hopanoid. Genomic DNA G+C content was 62.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC141(T) represents a member of the genus Vogesella within the family Neisseriaceae of the class Betaproteobacteria. Strain JC141(T) had a 16S rRNA gene sequence similarity of 98% with Vogesella indigofera ATCC 19706(T) and <96.5% with other members of the genus Vogesella. However, strain JC141(T) showed 45.8% relatedness (based on DNA-DNA hybridization) with V. indigofera LMG 6867(T) (=ATCC 19706(T)). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC141(T) as a representative of a novel species in the genus Vogesella, for which the name Vogesella alkaliphila sp. nov. is proposed. The type strain is JC141(T) (=KCTC 32041(T)=LMG 27066(T)). An emended description of the genus Vogesella is also proposed.


Subject(s)
Neisseriaceae/classification , Phylogeny , Soil Microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , India , Molecular Sequence Data , Neisseriaceae/genetics , Neisseriaceae/isolation & purification , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Triterpenes/analysis
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