L. Tushar

Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern

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.

Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern.

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)).

Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.).

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 2β-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)).

Erratum to Paraclostridium benzoelyticum gen. nov. sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii.

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).

Spirochaeta lutea sp. nov., isolated from marine habitats and emended description of the genus Spirochaeta.

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)).

Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis.

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 JA643T 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 ATCC17100T 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 JA643T will be useful in understanding the functional features of hopanoids in this bacterium.

Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

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)).

Rhodovulum salis sp. nov. and Rhodovulum viride sp. nov., phototrophic Alphaproteobacteria isolated from marine habitats.

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.

Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond.

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)).

Vogesella alkaliphila sp. nov., isolated from an alkaline soil, and emended description of the genus Vogesella.

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.