- Volume 68, Issue 1, 2018

A reddish pink-pigmented, Gram-stain-negative, aerobic and methylotrophic bacterial strain, designated strain IER25-16T, was isolated from a laboratory air conditioning system in the Republic of Korea. Cells were motile rods showing catalase- and oxidase-positive reactions. Strain IER25-16T grew at 10–40 °C (optimum, 30 °C), at pH 4.0–7.0 (optimum, pH 5.0–7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum, 0 %). The major respiratory quinone was ubiquinone-10 and ubiquinone-9 was also detected as the minor respiratory quinone. Summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) was detected as the predominant fatty acids. The genomic DNA G+C content of strain IER25-16T was 70.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain IER25-16T belonged to the genus Methylobacterium of the class Alphaproteobacteria . Strain IER25-16T was most closely related to Methylobacterium platani PMB02T (97.9 %), Methylobacterium aquaticum GR16T (97.9 %) and Methylobacterium tarhaniae N4211T (97.5 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain IER25-16T and M. platani , M. aquaticum and M. tarhaniae were 88.3, 88.8 and 89.6 % and 36.2, 37.3 and 39.3 %, respectively. The phenotypic and chemotaxonomic features and the phylogenetic inference clearly suggested that strain IER25-16T represents a novel species of the genus Methylobacterium , for which the name Methylobacterium frigidaeris sp. nov. is proposed. The type strain is strain IER25-16T (=KACC 19280T=JCM 32048T).

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated NF2-5-3T, was isolated from a paddy soil in Anseong city, Republic of Korea. This bacterium was characterized to determine its taxonomic position using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NF2-5-3T had a close relationship with, and was related most closely to, members of the genus Paraburkholderia , namely Paraburkholderia caribensis MWAP64T (98.8 % similarity), P. sabiae Br3407T (98.8 %), P. hospita LMG 20598T (98.5 %), P. terrae NBRC 100964T (98.3 %) and P. phymatum STM815T (98.1 %). Growth of strain NF2-5-3T occurred at 15–37 °C, at pH 6.0–8.0 and at NaCl concentrations of 0–2 % (w/v). The major respiratory quinone was ubiquinone 8 (Q-8) and the major fatty acids were C16 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C17 : 0 cyclo and C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, unidentified aminophospholipids, unidentified aminolipids and unidentified polar lipids. The G+C content of the genomic DNA was 64.2 mol%. DNA–DNA relatedness values between strain NF2-5-3T and its closest phylogenetic neighbours were much lower than 70 %. Strain NF2-5-3T could be differentiated phylogenetically and phenotypically from recognized species of the genus Paraburkholderia . The isolate therefore represents a novel species, for which the name Paraburkholderia azotifigens sp. nov. is proposed, with NF2-5-3T (=KACC 18968T=LMG 29961T) as the type strain.

We conducted a taxonomic study of two algicidal bacteria, designated strains Yeonmyeong 1-13T and Yeonmyeong 1-11, isolated from seawater off Geoje Island in the South Sea, Republic of Korea. The two novel strains were yellow-pigmented, halotolerant, Gram-stain-negative, strictly aerobic, non-spore-forming, rod-shaped bacteria. Both strains were able to grow at 5–39 °C, pH 5.0–10.0 and 0–11 % (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strains Yeonmyeong 1-13T and Yeonmyeong 1-11 belonged to the genus Stakelama and are closely related to Stakelama pacifica JLT832T (98.37% and 98.22 % sequence similarity, respectively). The pairwise sequence similarity between strains Yeonmyeong 1-13T and Yeonmyeong 1-11 was observed to be 99.50 %. In both strains, the only respiratory quinone was ubiquinone-10; the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid; the major fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0 2-OH. DNA G+C content values of strains Yeonmyeong 1-13T and Yeonmyeong 1-11 were 65.1% and 64.9 mol%, respectively. The DNA–DNA relatedness between Yeonmyeong 1-13T and S. pacifica DSM 25059T was 28.7 %, which falls below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain Yeonmyeong 1-13T from its closest phylogenetic neighbours. Thus, strains Yeonmyeong 1-13T and Yeonmyeong 1-11 represent a novel species of the genus Stakelama , for which the name Stakelama algicida sp. nov. is proposed. The type strain is Yeonmyeong 1-13T (=KEMB 9005-324T=JCM 31498T).

A Gram-stain-negative, non-endospore-producing, short-rod strain, KNDSS-Mac4T, was isolated from a downstream sediment sample of the river Ganges, Kanpur, India and studied by using the polyphasic taxonomic approach. 16S rRNA gene sequence analysis uncovered that the strain had similarity to species of the genus Thauera and formed a distinct phylogenetic cluster with Thauera humireducens KACC16524T. However, KNDSS-Mac4T showed closest phylogenetic affiliation to Thauera aminoaromatica DSM 14742T with 16S rRNA gene sequence similarity of 98.7 % followed by Thauera phenylacetica DSM 14743T (98.6 %), Thauera chlorobenzoica (98.2 %), T. humireducens KACC16524T (98.2 %), Thauera selenatis ATCC 55363T (98.2 %) and Thauera mechernichensis DSM 12266T (98.0 %). The digital DNA–DNA hybridization and average nucleotide identity values between strain KNDSS-Mac4T and the two most closely related taxa, T. aminoaromatica DSM 14742T and T. phenylacetica DSM 14743T, were 26.0, 26.7 and 84.0, 84.3 % respectively. Major lipids present were phosphatidylglycerol, three unknown aminophospholipids, phosphatidylmethylethanolamine, two unidentified lipids and Q-8 as the only ubiquonone. The major cellular fatty acids present were C16 : 1 ω6c/C16 : 1ω7c and C16 : 0. The DNA G+C content of strain KNDSS-Mac4T was 65.9 %. Based on data from phenotypic tests and the genotypic differences of strain KNDSS-Mac4T from its closest phylogenetic relatives, it is evident that this isolate should be regarded as a new species. It is proposed that strain KNDSS-Mac4T should be classified in the genus Thauera as a novel species, Thauera propionica sp. nov. The type strain is KNDSS-Mac4T (=KCTC 52820T=VTCC-B-910017T).

A Francisella -like bacterium, designated strain SYSU HZH-2T, was isolated from a water sample collected from Haizhu Lake, Guangzhou, China. The bacterium was fastidious, and required an exogenous source of l-cysteine for its growth on artificial media. Cells were Gram-stain-negative, coccobacilli, non-motile and non-spore-forming. The strain shared highest 16S rRNA gene sequence similarities with Cysteiniphilum litorale SYSU D3-2T (94.6 % identity), Fangia hongkongensis UST040201-002T (93.2 %) and Caedibacter taeniospiralis 51T (91.6 %). This strain possessed ubiquinone-8 as the respiratory quinone; diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the known polar lipids, and anteiso-C15 : 0 and C18 : 0 as the major fatty acids (>10 % of total fatty acids). The dendrograms based on 16S rRNA gene sequence analysis showed that it formed a separate cluster along with Cysteiniphilum litorale SYSU D3-2T, Caedibacter taeiniospiralis 51T and Fangia hongkongensis UST040201-002T. Based on the 16S rRNA gene sequence identity and differences in other phenotypic characteristics, the strain is considered to represent a novel species of a novel genus, for which the name Fastidiosibacter lacustris gen. nov., sp. nov. is proposed. The type strain of the type species Fastidiosibacter lacustris is SYSU HZH-2T (=NBRC 112274T = CGMCC 1.15950T). Additionally, the new taxon along with the genera Caedibacter , Cysteiniphilum and Fangia (family unassigned) were distinctly separated from the related families Francisellaceae , Piscirickettsiaceae and Thiotrichaeae in the phylogenetic trees. Therefore, we proposed a new family Fastidiosibacteraceae fam. nov. within the order Thiotrichales to accommodate these four genera.

A novel marine Gram-negative bacterium, designated strain GH1-23T, was isolated from a tidal mudflat sample collected at Dongmak seashore on Gangwha Island, Republic of Korea and its taxonomic position was determined through a polyphasic investigation. The bacterium was strictly aerobic, chemoheterotrophic, catalase- and oxidase-positive, consisted of non-motile rods and grew optimally at 30 °C, pH 7 and 1 % NaCl. The predominant cellular fatty acids were C18 : 1 ω7c and cyclo-C19 : 0 ω8c. The major isoprenoid quinone was Q-10. The major polar lipids were phosphatidylglycerol, a phosphoglycolipid and an aminolipid. Comparative 16S rRNA gene sequence analysis revealed that the isolate was closely related to members of the genus Maribius . The highest 16S rRNA gene sequence similarity was found to be 97.5 % to Maribius salinus followed by 97.4 % to Maribius pelagius ; levels of 16S rRNA gene sequence similarity between the novel strain and other representatives of family Rhodobacteraceae were <95.5 %. The DNA G+C content was 66.7 mol % and DNA–DNA relatedness values with the type strains of species of the genus Maribius were 33–39 %. Based on combined data from a polyphasic investigation, strain GH1-23T (=KCTC 52957T=DSM 104950T) represents a novel species of the genus Maribius , for which the name Maribius pontilimi sp. nov. is proposed.

During a study of oil-degrading bacteria, three yellow-coloured, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains Ktm-14T, Ktm-17 and Ktm-18, were isolated from oil-contaminated soil of Biratnagar, Morang, Nepal. The strains were able to grow at 15–37 °C, pH 4.5–10.0 and 0–2 % (w/v) NaCl concentration. Strains Ktm-14T, Ktm-17 and Ktm-18 were characterized by multiple taxonomic approaches. Based on 16S rRNA gene sequence analysis, strains Ktm-14T, Ktm-17 and Ktm-18 belonged to the genus Sphingopyxis and shared highest sequence similarity with Sphingopyxis ginsengisoli Gsoil 250T (98.94 %). The only respiratory quinone was ubiquinone-10 and the predominant polyamine was spermidine. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and sphingoglycolipids. The predominant fatty acids were C17 : 1ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The DNA G+C content values of strains Ktm-14T, Ktm-17 and Ktm-18 were 65.8, 65.9 and 65.6 mol%, respectively. The DNA–DNA relatedness between Ktm-14T and Ktm-17 and Ktm-18 were higher than 70 % but with closely related reference strains were less than 40 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain Ktm-14T from its closest phylogenetic neighbours. Thus, strain Ktm-14T represents a novel species of the genus Sphingopyxis , for which the name Sphingopyxis nepalensis sp. nov. is proposed. The type strain is Ktm-14T (=KEMB 9005-694T=KACC 19389T=JCM 32250T), and strains Ktm-17 and Ktm-18 represent two additional strains.

A Gram-stain-negative, rod-shaped Proteobacteria isolate, MBT G8648T, was obtained from an acid curd cheese called Quargel. The isolate was moderately salt tolerant and motile, with numerous peritrichous flagella. The 16S rRNA gene sequence analysis indicated that the strain belongs to the genus Halomonas , with 98.42 % 16S rRNA gene sequence similarity with Halomonas titanicae BH1T as nearest related neighbour. Further comparative sequence analysis of secA and gyrB genes, as well as physiological and biochemical tests, revealed that this bacterium formed a taxon well-separated from its nearest neighbours and other established Halomonas species. Thus, the strain represents a new species, for which the name Halomonas nigrificans sp. nov. is proposed, with strain MBT G8648T (=LMG 29097T =DSM 105749T) as type strain.

Strains previously identified as Klebsiella oxytoca phylogroup Ko6 were characterized by rpoB, gyrA and rrs gene sequencing, genome-sequence based average nucleotide identity analysis and their biochemical characteristics. rpoB and gyrA sequencing demonstrated that the Ko6 strains formed a well-demarcated sequence cluster related to, but distinct from, Klebsiella oxytoca (which includes strains previously labelled as K. oxytoca phylogroup Ko2) and Klebsiella michiganensis (Ko1). The average nucleotide identity values of Ko6 with K. oxytoca and K. michiganensis were 91.2 and 93.47 %, respectively. The inability to metabolize melezitose differentiated most of the Ko6 strains from K. oxytoca and K. michiganensis . Based on its genetic and phenotypic characteristics, we propose the name Klebsiella grimontii for the Ko6 sequence cluster, with strain 06D021T (=CIP111401T, DSM 105630T) as the type strain. Strains of Klebsiella grimontii were isolated from human blood cultures, wound infections, antibiotic-associated haemorrhagic colitis and faecal carriage.

A bacterial strain, designated ASS-1T, was isolated and identified from a sediment sample of the river Ganges, Allahabad, India. The strain was Gram-stain-negative, formed straw-yellow pigmented colonies, was strictly aerobic, motile with a single polar flagellum, and positive for oxidase and catalase. The major fatty acids were C16 : 1ω7c/ 16 : 1 C16 : 1ω6c, C18 : 1ω7c and C16 : 0. Sequence analysis based on the 16S rRNA gene revealed that strain ASS-1T showed high similarity to Pseudomonas guguanensis CC-G9AT (98.2 %), Pseudomonas alcaligenes ATCC 14909T (98.2 %), Pseudomonas oleovorans DSM 1045T (98.1 %), Pseudomonas indolxydans IPL-1T (98.1 %) and Pseudomonas toyotomiensis HT-3T (98.0 %). Analysis of its rpoB and rpoD housekeeping genes confirmed its phylogenetic affiliation and showed identities lower than 93 % with respect to the closest relatives. Phylogenetic analysis based on the 16S rRNA, rpoB, rpoD genes and the whole genome assigned it to the genus Pseudomonas . The results of digital DNA–DNA hybridization based on the genome-to-genome distance calculator and average nucleotide identity revealed low genome relatedness to its close phylogenetic neighbours (below the recommended thresholds of 70 and 95 %, respectively, for species delineation). Strain ASS-1T also differed from the related strains by some phenotypic characteristics, i.e. growth at pH 5.0 and 42 °C, starch and casein hydrolysis, and citrate utilization. Therefore, based on data obtained from phenotypic and genotypic analysis, it is evident that strain ASS-1T should be regarded as a novel species within the genus Pseudomonas , for which the name Pseudomonas fluvialis sp. nov. is proposed. The type strain is ASS-1T (=KCTC 52437T=CCM 8778T).

A Gram-stain-negative, rod-shaped bacterium, designated 157T, was isolated from seawater collected from the Philippine Sea. Cells of strain 157T grew in medium containing 0.5–10.0 % NaCl (w/v, optimum 3 %), at pH 6.0–8.5 (optimum 7.0) and at 15–40 °C (optimum 30 °C). Tweens 20, 40 and 80 as well as urea were hydrolysed. The 16S rRNA gene sequence of strain 157T had a high sequence similarity with respect to Pseudooceanicola marinus AZO-CT (97.2 %), and exhibited less than 97.0 % sequence similarity to other type strains of the species with validly published names. Phylogenetic analyses revealed that strain 157T fell within a cluster comprising the Pseudooceanicola species and formed a coherent clade with P. marinus AZO-CT and Pseudooceanicola antarcticus Ar-45T. Strain 157T exhibited average nucleotide identity values of 74.5 and 74.9 % to P. marinus LMG 23705T and P. antarcticus Ar-45T, respectively. In silico DNA–DNA hybridization analysis revealed that strain 157T shared 20.2 % DNA relatedness with P. marinus LMG 23705T and 20.6 % with P. antarcticus Ar-45T, respectively. The sole isoprenoid quinone was ubiquinone 10. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 0 cyclo ω8c, C16 : 0 2-OH and C16 : 0. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content was 64.6 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, it represents a novel species of the genus Pseudooceanicola , for which the name Pseudooceanicola lipolyticus is proposed. The type strain is 157T (=KCTC 52654T=MCCC 1K03317T). In addition, the description of the genus Pseudooceanicola is emended and Oceanicola flagellatus is reclassified as Pseudooceanicola flagellatus comb. nov., with the type strain DY470T (=CGMCC 1.12664T=LMG 27871T) proposed.

Two isolates of bacterial strains A15T and A17 were isolated from stream bank soil in Kyonggi University. Cells were aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, non-spore-forming, rod-shaped, opaque, and cream coloured. Both strains hydrolysed CM-cellulose. Strains were able to grow at 20–42 °C, pH 5.5–10.0 and at 1.5 % NaCl concentration (w/v). Indole test was positive. Analyses of phylogenetic trees based on its 16S rRNA gene sequences indicated that strain A15T formed a lineage within the family Rhodospirillaceae of the phylum Proteobacteria which was distinct from Ferrovibrio denitrificans S3T (98.4 % sequence similarity) and Ferrovibrio xuzhouensis LM-6T (97.4 %). The sole detected respiratory quinone was Q–10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The major cellular fatty acids were C19 : 0 cycloω8c, C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0cyclo and C12 : 0. The DNA G+C contents of strains A15T and A17 were 63.4 and 62.9 mol%, respectively. DNA–DNA relatedness between strain A15T and other two members of the genus Ferrovibrio ranged from 25 to 37 %. The polyphasic characterization revealed strains A15T and A17 represent a novel species in the genus Ferrovibrio , for which the name Ferrovibrio soli sp. nov. is proposed. The type strain is A15T (=KEMB 9005-522T=KACC 19102T=NBRC 112682T).

Strain Eup a-2T, isolated from the torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup a-2T were Gram-negative, aerobic and motile by three polar flagella and formed translucent colonies. Optimal growth occurred at 25 °C, pH 6–8 and in the presence of 2–4 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup a-2T belonged to the genus Litoribrevibacter and showed the highest levels of sequence similarity with respect to Litoribrevibacter albus Y32T (97.8 %). Strain Eup a-2T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the predominant fatty acids. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphophatidylglycerol. Genomic DNA G+C content of strain Eup a-2T was 49.1 mol%. The DNA–DNA hybridization value for strain Eup a-2T with L. albus Y32T was less than 30 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain Eup a-2T should be classified as a novel species of the genus Litoribrevibacter , for which the name Litoribrevibacter euphylliae sp. nov. is presented. The type strain is Eup a-2T (=BCRC 81004T=LMG 29725T=KCTC 52438T).

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.