- Volume 68, Issue 9, 2018

A novel bacterial strain, S-12T, of a member of the genus Phreatobacter was isolated from a cathode of a microbial fuel cell from Suwon City, South Korea. Cells were Gram-staining-negative, aerobic, non-sporulating rods, motile by means of a polar flagellum, and formed white round colonies. The strain grew at the range of 10–40 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum 7.0–8.0) and 0–1 % NaCl. The 16S rRNA gene sequence analysis showed the relatedness of S-12T to Phreatobacter stygius YC6-17T (98.2 %) and Phreatobacter oligotrophus PI_21T (98.1 %). The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified lipid. The major fatty acids were summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). The DNA G+C content was 69.3 mol%. On the basis of its differences from species of the genus Phreatobacter with validly published names, strain S-12T is identified as representing a novel species, for which the proposed name is Phreatobacter cathodiphilus sp. nov., with S-12T as the type strain (=KACC 18497T=JCM 31612T).

A Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated B093034T, was isolated from air at the foot of Xiangshan mountain, located in Beijing, China. Cells of strain B093034T were oxidase-negative and catalase-positive. Growth was observed at 4–41 °C, at pH 4.5–10.0 and at 0–7 % (w/v) NaCl. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c), C_16 : 0 and C_14 : 02-OH as the major fatty acids, sym-homospermidine as the major polyamine, and sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, aminolipid, two unidentified phospholipids and three unidentified polar lipids as the polar lipids. The DNA G+C content was 67.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B093034T grouped with members of the genus Sphingomonas and was closely related to Sphingomonas sanguinis IFO 13937T (96.49 % similarity), Sphingomonas pseudosanguinis G1-2T (96.37 %), Sphingomonas ginsenosidimutans Gsoil 1429T (95.99 %) and Sphingomonas endophytica YIM 65583T (95.78 %). On the basis of the polyphasic evidence presented here, strain B093034T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas aeria sp. nov. is proposed. The type strain is B093034T (=CFCC 13949T=LMG 30133T).

A novel Gram-negative bacterium, designated 4G11T, was isolated from the sea surface microlayer of a marine inlet. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity to Amylibacter ulvae KCTC 32465T (99.0 %). However, DNA–DNA hybridization values showed low DNA relatedness between strain 4G11T and its close phylogenetic neighbours, Amylibacter marinus NBRC 110140T (8.0±0.4 %) and Amylibacter ulvae KCTC 32465T (52.9±0.9 %). Strain 4G11T had C_18 : 1, C_16 : 0 and C_18 : 2 as the major fatty acids. The only isoprenoid quinone detected for strain 4G11T was ubiquinone-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, one unidentified polar lipid, one unidentified phospholipid and one unidentified aminolipid. The DNA G+C content of strain 4G11T was 50.0 mol%. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Amylibacter kogurei sp. nov. is proposed. The type strain of Amylibacter kogurei is 4G11T (KY463497=KCTC 52506T=NBRC 112428T).

Three bacterial isolates, designated W44T, W15 and W11, were isolated from the root of Oryza officinalis grown in Wuzhou, China. These isolates were Gram-negative, aerobic, motile and rod-shaped; demonstrated cellulase and urea activities; and formed cream-coloured colonies. The 16S rRNA gene sequence analysis indicated that the similarities between strain W44T and strains W15 and W11 were 100 %; all of them belonged to the genus Rhizobium and had the highest sequence similarity to Rhizobium rosettiformans W3T (98.7 %), followed by Rhizobium ipomoeae shin9-1T (98.2 %). Sequencing of housekeeping genes (recA, atpD, rpoB and glnA) of the novel isolates revealed similarities to members of established Rhizobium species to be less than 94.3 %. The values of DNA–DNA hybridization between strain W44T and the reference strains ( R. rosettiformans W3T and R. ipomoeae shin9-1T) were 41.3 and 29.2 %, respectively. The major cellular fatty acid of strain W44T was summed feature 8 (C_18 : 1ω9t and/or C_18 : 1ω9c and/or C_18 : 1ω7c). The polar lipid profile of strain W44T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified lipids and two unidentified aminophospholipids. The G+C content of strain W44T was 62.4 mol%. In nodulation tests, none of the three strains could induce nodule formation in Glycine max, Phaseolus vulgaris or Medicago sativa. The nodulation gene (nodA), nitrogenase reductase gene (nifH) and virulence gene (virC) were not detected by PCR in these strains. Based on the above results and phenotypic features, a novel species, Rhizobium wuzhouense sp. nov., is proposed, with strain W44T (=CCTCC AB 2017179T=GDMCC 1.1257T=KCTC 62194T) as the type strain.

Two rhizobial strains, BSA136T and BSA150, related to the genus Mesorhizobium were isolated from root nodules of Lotus tenuis grown in saline-alkaline lowlands soil from Argentina. These strains showed different repetitive element palindromic PCR fingerprinting patterns but shared more than 99 % sequence similarity for both 16S rRNA and recA genes. Despite the symbiotic nodC gene sequences of our strains being related to the canonical Lotus biovar species comprising Mesorhizobium loti and Mesorhizobium japonicum , the 16S rRNA phylogenetic marker suggests that their taxonomical identities are closely related to Mesorhizobium helmanticense , Mesorhizobium metallidurans , Mesorhizobium thianshanense, Mesorhizobium gobiense and Mesorhizobium tarimense . Multilocus sequence analysis performed with seven housekeeping genes confirmed that BSA136T belongs to a separate clade within the genus Mesorhizobium . The results of comparisons for in silico DNA–DNA hybridization and average nucleotide identity indexes between the genomes of BSA136T and closest-related Mesorhizobium species were below the threshold for species delineation. Phenotypic features differentiated BSA136T from its closest-related species. On the basis of our results, BSA136T and BSA150 can be considered to represent a novel species of the genus Mesorhizobium , for which the name Mesorhizobium sanjuanii sp. nov. is hereby proposed. The type strain of this species is BSA136T (=CECT 9305T=LMG 30060T), for which the draft genome sequence is available.

Two novel marine bacteria, designated strains CSC3H3T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10–40 °C, pH 5–10 and in the presence of 0–15 % (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira , and shared 97.5–98.3 % sequence similarity to all other validly type strains of the genus Thalassospira , and the highest similarity was to the type strain Thalassospira povalilytica Zumi 95T (98.3 %), followed by Thalassospira australica NP3b2T (98.2 %). The digital DNA–DNA hybridization value between the two strains was 80.4 %, while the values with T. povalilytica Zumi 95T and T. australica NP3b2T were only 20.5–20.7 % and 20.4–20.5 %, respectively. The two strains possess similar major cellular fatty acids including C_18 : 1ω7c, C_16 : 0, C_19 : 0ω8c cyclo, C_18 : 1 2-OH and C_17 : 0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3T (=MCCC 1A11786T=KCTC 62333T).

Three Gram-negative, non-spore-forming, rod-shaped and motile bacterial strains, designated MMS16-UL250T, MMS16-UL253T and MMS16-UL482T, were isolated from coastal seawater and subjected to taxonomic characterization. All isolates grew at 4–30 °C (optimum, 25 °C), at pH 6–10 (pH 7) and in the presence of up to 8 % NaCl (2.5–4.5 %). The 16S rRNA gene sequence similarities between the three isolates and Shewanella algicola St-6T, the closest species, were 98.1–99.2 %, and those among the isolates were 98.5–99.0 %. In the phylogenetic tree, MMS16-UL250T formed a cluster with S. algicola St-6T, but the DNA–DNA relatedness between the two strains was 28.8±1.5 %, thus confirming their separation at species level. The other two strains formed separate phylogenetic lines respectively. The main quinones for all strains were Q-7, Q-8, MK-7 and MMK-7, which is typical for Shewanella . The major polar lipids of all strains were phosphatidylglycerol and phosphatidylethanolamine, and the common major fatty acid was a summed feature consisting of C_16 : 1ω7c and/or C_16 : 1ω6c while the proportions varied among the three strains. The DNA G+C contents of the strains also varied between 42.1 and 43.7 mol%. Phenotypic properties distinguished each strain from S. algicola as well as from one another. Based on the polyphasic analysis, each strain is considered to represent a novel species of Shewanella , for which the names Shewanella saliphila sp. nov. (type strain, MMS16-UL250T=KCTC 62131T=JCM 32304T), Shewanella ulleungensis sp. nov. (type strain, MMS16-UL253T=KCTC 62130T=JCM 32305T) and Shewanella litoralis sp. nov. (type strain, MMS16-UL482T=KCTC 62129T=JCM 32306T) are proposed.

Published data on the genome sequences of Chromobacterium pseudoviolaceum LMG 3953T and Chromobacterium violaceum ATCC 12472T suggest that both isolates belong to the same species. Previous 16S rRNA gene sequence comparisons had demonstrated that these species share 99.9 % sequence similarity. Initial investigations of fatty acid patterns and substrate utilization had shown only a few differences between the type strains of both species. Despite the 47.5 % homology by DNA–DNA hybridization studies between these strains, in silico whole genome sequence comparisons have clearly demonstrated that OrthoANIu and Mash/MinHash values were >99.18 %. Molecular phylogeny based on the estimated phylogenetic positions of the published genome sequences of the two type strains, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analyses indicate that these strains are members of the same species. Due to priority of publication and validation of names, Chromobacterium pseudoviolaceum is reclassified as Chromobacterium violaceum .

A Gram-stain-negative, strictly aerobic, motile and rod-shaped bacterial strain, designated 102-Na3T, was isolated from sediment of Sinduri beach in Taean, Republic of Korea. Strain 102-Na3T grew optimally at 28–37 °C, at pH 7.0–11.0 and in the presence of 1–3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain 102-Na3T joined the clade comprising the type strains of Oceanimonas species. Strain 102-Na3T exhibited 16S rRNA gene sequence similarity values of 98.8, 98.3 and 98.0 % to the type strains of Oceanimonas doudoroffii MBIC1298T, Oceanimonas baumannii GB6T and Oceanimonas smirnovii 31-13T, respectively. Strain 102-Na3T contained summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c), summed feature 8 (comprising C_18 : 1ω7c and/or C_18 : 1ω6c), C_16 : 0 and C_12 : 0 as major fatty acids. The major quinone was ubiquinone-8. The polar lipids were composed of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 56.8 mol%. Strain 102-Na3T exhibited DNA–DNA relatedness values of 25.7, 21.7 and 14.8 % to the type strains of O. doudoroffii , O. baumannii and O. smirnovii , respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain 102-Na3T is separated from recognized species of the genus Oceanimonas . On the basis of the data presented, strain 102-Na3T (=KCTC 62271T=JCM 32358T=DSM 106032T) is considered the type strain of a novel species of the genus Oceanimonas , for which the name Oceanimonas marisflavi sp. nov. is proposed.

A Gram-stain-negative, non-spore-forming, motile and rod-shaped strain, z29T, was isolated from the active sludge of a municipal wastewater treatment plant at Wuhu, Anhui, PR China. Phylogenetic analysis of the 16S rRNA gene revealed that strain z29T is most closely related to the genus Arenimonas , showing the highest similarity to Arenimonas donghaensis HO3-R19T (97.14 %), Arenimonas aestuarii S2-21T (96.46 %), Arenimonas daejeonensis T7-07T (96.24 %) and Arenimonas taoyuanensis YN2-31AT (96.23 %). The only respiratory quinone of strain z29T was ubiquinone 8 (Q-8). The major cellular fatty acids (>10 %) were iso-C_15 : 0, iso-C_16 : 0 and summed feature 9 (iso-C_17 : 1ω9c and/or C_16 : 010-methyl). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was 70.2 mol%. Genomic comparison between strain z29T and Arenimonas donghaensis HO3-R19T revealed 83.72 % average nucleotide identity. Based on the phenotypic and chemotaxonomic results together with phylogenetical analysis, strain z29T is classified as representing a novel species of the genus Arenimonas , for which the name Arenimonas caeni sp. nov. is proposed. The type strain is z29T (=JCM 32091T=CCTCC AB 2017067T).

A Gram-negative, strictly aerobic, non-motile and short rod- or coccus-shaped bacterium, designated strain LYH11T, was isolated from a freshwater green alga Paulinella chromatophora. The strain grew at 5–37 °C (optimum, 30 °C) and pH 6–9 (pH 7) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LYH11T clearly belonged to the genus Kaistia of the family Rhizobiaceae . Strain LYH11T shared the highest 16S rRNA gene sequence similarity to Kaistia soli 5YN9-8T (98.3 %), Kaistia terrae 5YN3-3T (98.2 %), Kaistia geumhonensis B1-1T (97.8 %), Kaistia defluvii B6-12T (97.4 %) and Kaistia granuli Ko04T (97.2 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain LYH11T and K. soli 5YN9-8T, the closest Kaistia type strain, were 77.3 and 21.1 %, respectively. Major cellular fatty acids of strain LYH11T were cyclo-C_19 : 0 ω8c, summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c), iso-C_10 : 0, iso-C_17 : 0 3-OH, iso-C_17 : 1 ω5c and C_18 : 0. Strain LYH11T contained phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoaminolipid, an unidentified aminolipid, three unidentified phospholipids and five unidentified lipids as polar lipids. Ubiquinone-10 was the major respiratory quinone. The genomic DNA G+C content was 64.5 mol%. Based on the genotypic, chemotaxonomic and phenotypic analyses, strain LYH11T represents a novel species of the genus Kaistia , for which the name Kaistia algarum sp. nov. is proposed. The type strain is LYH11T (=KACC 19096T=JCM 31803T).

Two yeast strains (INY29 and INY13) representing a novel yeast species were isolated from the hypersaline marine environment of the Inland Sea, Qatar. Phylogenetic analysis based on the D1/D2 domains of the large subunit (LSU) regions and internal transcribed spacer (ITS1 and ITS2) regions showed that the two strains represent a single species in the genus Naganishia that is distinct from other species. These two strains were classified as members of the genus Naganishia and clustered in a strongly supported clade represented by Naganishia albidus in the Filobasidiales order in the phylogenetic tree drawn from ITS and D1/D2 sequences. The novel species was most closely related to the type strain of Naganishia cerealis but the two species differed by 1 % sequence divergence (four substitutions and one gap) in the D1/D2 domains and (five substitutions and one gap) in the ITS regions. In contrast to the closest relative, N. cerealis, the novel yeast species assimilated melibiose, glycerol, meso-erythritol, dl-lactate, methanol, propane 1-2-diol, butane 2-3-diol, and grew at 35 °C. The name Naganishia qatarensis sp. nov. is proposed to accommodate these strains, with INY29 as the holotype.