- Volume 68, Issue 2, 2018

A novel aerobic, Gram-stain-positive, motile, moderately halophilic and coccoid bacterial strain, designated LCB217T, was isolated from a saline-alkali soil in north-western China and identified using a polyphasic taxonomic approach. Growth occurred with 3–15 % (w/v) NaCl (optimum 3–5 %), at 10–45 °C (optimum 30 °C) and at pH 7.0–9.0 (optimum pH 9.0). Strain LCB217T contained MK-7 and MK-8 as the predominant menaquinones and anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0 as the major fatty acids. The polar lipids from strain LCB217T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified phospholipid, one unidentified aminophospholipid and one unidentified lipid. The peptidoglycan type was A4α (l-Lys–d-Glu). Phylogenetic analysis of the 16S rRNA gene sequence showed that strain LCB217T belonged to the genus Planococcus and was closely related to the type strains Planococcus plakortidis AS/ASP6 (II)T (98.2 % similarity), Planococcus maitriensis S1T (97.7 %) and Planococcus salinarum ISL-16T (97.2 %). The G+C content of the genomic DNA was 49.4 mol%. DNA–DNA relatedness values between strain LCB217T and Planococcus plakortidis AS/ASP6 (II)T, Planococcus maitriensis S1T and Planococcus salinarum ISL-16T were 29.5, 38.1 and 39.5 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data, strain LCB217T represents a novel species of the genus Planococcus , for which the name Planococcus salinus sp. nov. is proposed. The type strain is LCB217T (=CGMCC 1.15685T=KCTC 33861T).

Strain Rs-Y01T was isolated from the gut of the wood-feeding subterranean termite Reticulitermes speratus. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain Rs-Y01T belonged to the genus Lactococcus and was most closely related to Lactococcus raffinolactis JCM 5706T with 98.1 % similarity in the 16S rRNA gene, followed by Lactococcus piscium JCM 16647T (97.2 %). Genomic comparisons of strain Rs-Y01T with L. raffinolactis JCM 5706Twere made using the Genome-to-Genome Distance Calculator and average nucleotide identity analysis (values indicated 29.2 and 84.6 %, respectively). Strain Rs-Y01T was a Gram-stain-positive, facultatively anaerobic, non-motile coco-bacilli and formed l-lactic acid. The sugar fermentation and enzyme reactions of strain Rs-Y01T differed from those of other species of the genus Lactococcus . The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 32.0 %), C16 : 0 (29.7 %) and C14 : 0 (18.1 %). Based on these characteristics, strain Rs-Y01T represents a novel species of the genus Lactococcus , for which the name Lactococcus reticulitermitis sp. nov. is proposed. The type strain is Rs-Y01T (=JCM 32106T=DSM 105715T).

Three strains, CLM-U50T, CLM-R50 and IVIC-Bov1, belonging to the genus Leptospira , were isolated in Venezuela from a patient with leptospirosis, a domestic rat (Rattus norvegicus) and a cow (Bos taurus), respectively. The initial characterisation of these strains based on the rrs gene (16S rRNA) suggested their designation as a novel species within the ‘intermediates’ group of the genus Leptospira . Further phylogenomic characterisation based on single copy core genes was consistent with their separation into a novel species. The average nucleotide identity between these three strains was >99 %, but below 89 % with respect to any previously described leptospiral species, also supporting their designation as a novel species. Given this evidence, these three isolates were considered to represent a novel species, for which the name Leptospira venezuelensis sp. nov. is proposed, with CLM-U50T (=CIP 111407T=DSM 105752T) as the type strain.

Chicory (Cichorium intybus) is a perennial plant (Asteraceae) that grows wild in pasture fields in Saudi Arabia. Chicory plants displaying symptoms typically induced by phytoplasmas, such as bushy phenotype and stunt, were observed in the Mulayda region, Qassim governorate, Saudi Arabia. In this study we examined samples taken from three symptomatic chicory plants and confirmed the presence of phytoplasma DNA. Analysis of the 16S rRNA-encoding sequences showed that the plants were infected with a phytoplasma from the pigeon pea witches’-broom group (16SrIX). Sequencing of the 16S rRNA-encoding gene and the partial cpn60 sequence, computer-simulated RFLP analysis, and phylogenetic analysis of both markers revealed that the phytoplasma identified was representative of a new 16SrIX-J and cpn60 UT IX-IJ subgroup. The present study identified chicory plants as a novel host for phytoplasma strains within the pigeon pea witches’-broom phytoplasma group, and expanded the known diversity of this group.

A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, transparent, motile and rod-shaped bacterium that was capable of fixing dinitrogen (designated strain A.slu09T), isolated from activated sludge, was characterized by a polyphasic approach to clarify its taxonomic position. Strain A.slu09T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain A.slu09T showed β-glucosidase activity, converting the major ginsenoside Rd to ginsenoside F2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A.slu09T belongs to the genus Ciceribacter of the family Rhizobiaceae and was most closely related to Ciceribacter lividus MSSRFBL1T (97.8 % similarity). The DNA G+C content was 67.2 mol%. The DNA–DNA hybridization value between strain A.slu09T and C. lividus KCTC 32403T was 16.9±1.17 %. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, aminophospholipid and two glycolipids, and one unknown phospholipid as a minor lipid. The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were C19 : 0 cyclo ω8c, C18 : 1 ω7c and/or C18 : 1ω6c (summed feature 8) and C18 : 0, a profile that supported the affiliation of A.slu09T to the genus Ciceribacter . Moreover, the physiological and biochemical characteristics and low level of DNA–DNA relatedness allowed the phenotypic and genotypic differentiation of strain A.slu09T from the recognized species of the genus Ciceribacter . Therefore, strain A.slu09T represents a novel species of the genus Ciceribacter , for which the name Ciceribacter azotifigens sp. nov. is proposed. The type strain is A.slu09T (=KACC 19080T=LMG 29962T).

Two novel bacterial strains (4M3-2T and 10-107-7) were isolated from poplar tree bark. The strains were Gram-stain-negative facultative aerobes, and produced short rods that were motile because of polar flagella. A phylogenetic tree was reconstructed based on 16S rRNA gene sequences indicating that the two novel strains are related to species of the genus Aureimonas and Aurantimonas . The two novel strains shared the highest 16S rRNA gene sequence similarities with Aureimonas frigidaquae CW5 7Y-4T (97.1 %) and A ureimonas altamirensis DSM 21988T (96.6 %)o. The lipids of the novel strain contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sulfoquinovosyl diacylglycerol. The presence of a distinct glycolipid (sulfoquinovosyl diacylglycerol) is an important chemotaxonomic feature used to distinguish between species of the genera, Aurantimonas and Aureimonas . Additionally, the DNA–DNA hybridization results indicated that the two novel strains represent a novel taxon distinct from Aureimonas frigidaquae . The results of the 16S rRNA gene sequence analysis, as well as the physiological and biochemical characteristics imply that the two novel strains should be assigned to a novel species, with the proposed name Aureimonas populi sp. nov. The type strain is 4M3-2T (=CFCC 11187T=KCTC 42087T).

A bacterial strain, 1-14T, was isolated from cyanobacterial aggregates in a eutrophic lake, Taihu Lake, China. Cells were observed to be slightly curved, rod-shaped, aerobic and Gram-stain-negative. Optimal growth occurred at pH 7.0 (range: 5.0–9.0), 28 °C (range: 20–32 °C) and 0 % (w/v) NaCl (range: 0–1.0 %) in R2A broth. No growth is observed at 37 °C. The cells were found to be positive for oxidase and catalase activities. The major respiratory quinone was ubiquinone Q-10. The major fatty acids (>10 %) were identified as C18 : 1ω6c/C18 : 1ω7c, C16 : 0 3-OH and C18 : 1 2-OH. The major polar lipids were found to consist of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine. Within the genus Niveispirillum , strain 1-14T was most closely related to Niveispirillum cyanobacteriorum TH16T (98.3 % 16S rRNA gene sequence similarity), followed by Niveispirillum irakense DSM 11586T (97.8 %) and Niveispirillum fermenti CC-LY736T (97.0 %). The genomic G+C content of strain 1-14T was 62.2 mol% based on total genome calculations. Genes coding for light-harvesting complexes LHI and LHII, and a photosynthetic reaction centre were detected in the genome. Average nucleotide identities and digital DNA–DNA hybridizations for complete genomes ranged from 76.4 to 83.5 and from 21.5 to 27.4 % between strain 1-14T and strains within the genus Niveispirillum . The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggested that strain 1-14T represents a novel species within the genus Niveispirillum , for which the name Niveispirillum lacus sp. nov. is proposed. The type strain is 1-14T (=CGMCC 1.12980T=LMG 28363T).

A novel bacterial strain, designated HSLHS2T, was isolated from the seawater of a tropical mangrove forest. Cells of strain HSLHS2T were found to be aerobic, Gram-stain-negative, non-flagellated, non-motile, short rods. Oxidase- and catalase-positive. Growth was observed at 5–40 °C (optimum, 35 °C), at pH 6.0–10.0 (optimum pH 8.0) and in 0–10 % NaCl (optimum 2 %, w/v). Strain HSLHS2T shared highest 16S rRNA gene sequence similarity with Celeribacter halophilus ZXM137T (95.4 %), but formed a distinct phyletic lineage and coherent phylogenetic cluster associated with Marivivens donghaensis AM-4T (95.1 %). The dominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The respiratory quinone was determined to be Q-10. The polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, four unidentified lipids, five unidentified phospholipids. The DNA G+C contents was 54.6 mol%. The combined genotypic and phenotypic data indicated that strain HSLHS2T represents a novel species of the genus Marivivens , for which the name Marivivens niveibacter sp. nov. is proposed. The type strain is HSLHS2T (=KCTC 52588T=MCCC 1A06712T).

A total of 29 strains mainly from guinea pigs were investigated by a polyphasic approach that included previously published data. The strains were classified as Bisgaard taxa 5 and 7 by comparison of phenotypic characteristics and the strains showed typical cultural characteristics for members of family Pasteurellaceae and the strains formed two monophyletic groups based on 16S rRNA gene sequence comparison. Partial rpoB sequence analysis as well as published data on DNA–DNA hybridization showed high genotypic relationships within both groups. A new genus with one species, Caviibacterium pharyngocola gen. nov., sp. nov., is proposed to accommodate members of taxon 5 of Bisgaard, whereas members of taxon 7 are proposed as Conservatibacter flavescens gen. nov., sp. nov. The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae . The type strain of Caviibacterium pharyngocola is 7.3T (=CCUG 16493T=DSM 105478T) and the type strain of Conservatibacter flavescens is 7.4T (=CCUG 24852T=DSM 105479T=HIM 794-7T), both were isolated from the pharynx of guinea pigs.

A Gram-stain-negative, aerobic, motile, flagellated rod-shaped bacterium, designated ST58-10T, was isolated from an estuarine sediment in the Republic of Korea. The strain was able to degrade benzene. Growth of strain ST58-10T was observed at 4–35 °C (optimum, 20–25 °C), pH 5–9 (optimum, pH 7–8) and 1–8 % NaCl (optimum, 3 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ST58-10T formed a phyletic lineage within the genus Marinobacterium of the family Oceanospirillaceae . Strain ST58-10T was most closely related to Marinobacterium profundum PAMC 27536T (99.6 %) and Marinobacterium rhizophilum CL-YJ9T (98.3 %), and to other members of the genus Marinobacterium (94.5–91.5 %). However, the mean value estimated by using the Genome-to-Genome Distance Calculator was 50.6±7.4 % with M. profundum PAMC 27536T and 30.9±2.8 with M. rhizophilum CL-YJ9T, respectively. An average nucleotide identity value was 89.0 % with M. profundum PAMC 27536T and 85.6 % with M. rhizophilum CL-YJ9T, respectively. The major fatty acids of strain ST58-10T were summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (comprising C18 : 1  ω7c/C18 : 1 ω6c), C16 : 0 and C10 : 0 3-OH, and contained ubiquinone (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, an unidentified glycolipid and an unidentified lipid were detected as polar lipids. The DNA G+C content of strain ST58-10T was 58.78 mol%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain ST58-10T represents a novel species of the genus Marinobacterium , for which the name Marinobacterium aestuarii sp. nov. is proposed. The type strain is ST58-10T (=KCTC 52193T=NBRC 112103T).

A novel rod-shaped, Gram-stain-negative, aerobic bacterium, designated S35T, was isolated from deep-sea sediment collected from the Pacmanus hydrothermal field, Manus Basin, Papua New Guinea. Strain S35T grew optimally at 28 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. 16S rRNA gene sequence analysis indicated that strain S35T shared 97.38–98.55% similarity with the type strains of Alteromonas lipolytica, Alteromonas mediterranea and Aestuariibacter halophilus . Phylogenetic analysis showed that strain S35T belonged to the genus Alteromonas. The strain contained ubiquinone-8 as the predominant respiratory lipoquinone. Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 were the major fatty acids. The DNA G+C content of strain S35T was 51.3 mol%. These results indicated that strain S35T represents a novel species of the genus Alteromonas, for which the name Alteromonas oceani sp. nov. (type strain S35T=KCTC 52449T=CGMCC 1.16029T) is proposed.

A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated JSSK-16T, was isolated from the place where the ocean and a freshwater spring meet at Jeju Island, South Korea. Strain JSSK-16T grew optimally at 30 °C, at pH 6.5–8.0 and in the presence of 2.0–4.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain JSSK-16T joined the clade comprising the type strains of Jannaschia species. Strain JSSK-16T exhibited 16S rRNA gene sequence similarity values of 97.5 and 97.1 % to the type strains of Jannaschia donghaensis and Jannaschia faecimaris , respectively, and of 94.1–96.6 % to the type strains of the other Jannaschia species. Strain JSSK-16T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C18 : 0 as the major fatty acids. The major polar lipids detected in strain JSSK-16T were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain JSSK-16T was 68.8 mol% and its DNA–DNA relatedness values with the type strains of J. donghaensis and J. faecimaris were 18 and 12, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain JSSK-16T is separated from recognized species of the genus Jannaschia . On the basis of the data presented, strain JSSK-16T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia confluentis sp. nov. is proposed. The type strain is JSSK-16T (=KACC 19436T=KCTC 62137T=NBRC 113018T).

Two dark pink pigmented bacterial strains (M3T and M11) were isolated from crude oil contaminated desert sand from Kuwait. Both strains were Gram-stain-negative and small-rod to oval-shaped bacteria. Strains M3T and M11 grew at 13–42 °C (optimum, 30–35 °C) and pH 6.5–9.0 (optimum, 7.0–7.5). No additional NaCl was required for the growth of both strains. The genomic DNA G+C content of strains M3T and M11 were 69.5 and 69.0 mol%, respectively. Both strains were closely related and the mean DNA–DNA hybridization value was 92±1 %. 16S rRNA gene sequence comparisons of both strains indicated that they belong to the genus Roseomonas . Strains M3T and M11 had a sequence similarity of 97.3 and 97.4 % with Roseomonas oryzae JC288T, respectively. Both strains had <97 % 16S rRNA gene sequence similarity with other members of the genus Roseomonas . Strain M3T showed 18±2 and 13±2 % reassociation (based on DNA–DNA hybridization) with R. oryzae KCTC 42542T and Roseomonas cervicalis KACC 11686T, respectively. The major cellular fatty acids (>5 %) were identified as C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c and C16 : 0 in both strains. Both strains showed diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-ethanolamine, phosphatidylcholine and unidentified glycolipid as major polar lipids. Based on distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa, we propose the classification of strains M3T and M11 as representative of a novel species in the genus Roseomonas , for which the name Roseomonas deserti sp. nov. is suggested. The type strain is M3T (=KEMB 2255-459T=JCM 31275T).

A Gram-stain-negative, aerobic, non-motile, rod-shaped, catalase-positive and oxidase-positive bacteria (THG-T61T), was isolated from rhizosphere of Hibiscus syriacus. Growth occurred at 10–37 °C (optimum 25–30 °C), at pH 5.0–9.0 (optimum 7.0) and in the presence of 0–2.0 % NaCl (optimum without NaCl supplement). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T61T were identified as Sphingomonas ginsengisoli KCTC 12630T (97.9 %), Sphingomonas jaspsi DSM 18422T (97.8 %), Sphingomonas astaxanthinifaciens NBRC 102146T (97.4 %), Sphingomonas sediminicola KCTC 12629T (97.2 %), ‘ Sphingomonas swuensis’ KCTC 12336 (97.1 %) and Sphingomonas daechungensis KCTC 23718T (96.9 %). The isoprenoid quinone was ubiquinone-10 (Q-10). The major fatty acids were C16 : 0, C17 : 1 ω6c, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified lipid, one unidentified phospholipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The polyamine was homospermidine. The DNA G+C content of strain THG-T61T was 65.6 mol%. The DNA–DNA relatedness values between strain THG-T61T and its closest reference strains were less than 49.2 %, which is lower than the threshold value of 70 %. Therefore, strain THG-T61T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas rhizophila sp. nov. is proposed. The type strain is THG-T61T (=KACC 19189T=CCTCC AB 2016245T).

A novel bacterial strain, A3T, was isolated from the intestines of the sea urchin Strongylocentrotus droebachiensis collected in Øresund, Denmark. The strain was Gram-reaction-negative, rod-shaped and facultatively anaerobic, and displayed growth at 5–25 °C (optimum 20 °C), pH 7–9 (optimum at pH 7) and 1–6 % (w/v) NaCl (optimum 3 %). Furthermore, strain A3T grew on agar, agarose, κ-carrageenan, alginate and laminarin as sole carbon source. Complete liquefaction of agar and κ-carrageenan was observed on solid plate media as a result of enzymatic activities. Major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The respiratory quinones were determined to be ubiquinones Q-8 (92 %) and Q-7 (8 %), and polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 36.9 mol%. Phylogenetical analyses based on the 16S rRNA gene showed that the bacterium was affiliated with the genus Colwellia within the Alteromonadaceae of the Gammaproteobacteria . The level of 16S rRNA gene sequence similarity between strain A3T and its closest relatives in the genus Colwellia ( C. psychrerythraea ATCC 27364T and C. asteriadis KMD 002T) was 97.5 %. The average nucleotide identity between strain A3T and other members of Colwellia was 78.6–80.5 %, and DNA–DNA hybridization prediction revealed values of less than 23 % relatedness between strain A3T and other Colwellia species. The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain A3T represents a novel species of the genus Colwellia , for which the name Colwellia echini sp. nov. is proposed. The type strain is A3T (=LMG 30125T=NCIMB 15095T).