Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea

Pontibacter kalidii sp. nov., isolated from rhizosphere soil of Kalidium foliatum

A Gram-negative, aerobic, gliding motile, rod-shaped bacterium, designated XAAS-72T, was isolated from the rhizosphere soil of Kalidium foliatum sampled in the Xinjiang Uyghur Autonomous Region, PR China. Cells grew at 4-45 °C, pH 5.0-8.0 and 0-8% NaCl, with optimal growth at 20-30 °C, pH 6.0-7.0 and 1-2 % NaCl. Strain XAAS-72T is closely related to members of the genus Pontibacter, namely Pontibacter korlensis CCTCC AB 206081T (97.6%) and Pontibacter flavimaris ACCC 19859T (97.2 %), and <94.6 % related to other currently described Pontibacter strains. The average nucleotide identity values between XAAS-72T and P. korlensis CCTCC AB 206081T and P. flavimaris ACCC 19859T were 77.9 and 86.9 %, respectively; the corresponding digital DNA-DNA hybridization values were 21.7 and 31.8 %. Menaquinone-7 was the predominant respiratory menaquinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified glycolipids and five unidentified lipids. The major cellular fatty acids were summed feature 4 (containing iso-C17 : 1 I/anteiso-C17 : 1 B), summed feature 3 (containing C16 : 1  ω7c/C16 : 1  ω6c) and iso-C15 : 0. The genome length of strain XAAS-72T was 5 054 860 bp with a genomic DNA G+C content of 54.5 mol%. The phenotypic and genotypic data suggest that strain XAAS-72T represents a novel species of the genus Pontibacter, for which the name Pontibacter kalidii sp. nov. is proposed. The strain is XAAS-72T (CGMCC 16594T=KCTC 72095T).

Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales

Four Gram-staining-negative, aerobic, yellow-pigmented and rod-shaped bacteria, named strains BD1B2-1T, NT2B1T, YF14B1 and DM2B3-1, were isolated from four rhizosphere soil samples of banana in China. Comparison of the 16S rRNA gene sequences showed that all these strains were most closely related to an invalidly published species, 'Rhodocytophaga rosea' 172606-1, with similarities ranging from 87.7 to 88.0%. According to the phylogenomic analysis, the four strains were clustered in an independent lineage and closely related to the genus Rhodocytophaga. The genomic sizes of these strains were approximately 9.49-9.77 Mbp with the DNA G + C contents of 38.8-39.0 mol%. They all contained C16:1 ω5c, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids and menaquinone 7 as the only respiratory quinone. They all had phosphatidylethanolamine as the major polar lipids. Based on phenotypic and phylogenomic characteristics, the four strains should represent two novel species within a novel genus, for which the names Xanthocytophaga agilis gen. nov., sp. nov. (BD1B2-1T = GDMCC 1.2890T = JCM 35374T) and Xanthocytophaga flavus sp. nov. (NT2B1T = GDMCC 1.2889T = JCM 35375T) are proposed; the former is assigned as the type species of the novel genus Xanthocytophaga gen. nov. In addition, based on the phenotypic and phylogenomic data, we proposed to reclassify the existing genus Rhodocytophaga in the family Cytophagaceae into a novel family Rhodocytophagaceae fam. nov. The novel family consists of the type genus Rhodocytophaga and the novel genus Xanthocytophaga.

Fuscibacter oryzae gen. nov., sp. nov., a phosphate-solubilizing bacterium isolated from the rhizosphere of rice plant

An ovoid to rod shaped, white to brown pigmented, facultative anaerobic, mesophilic, non-phototrophic, Gram-staining-negative, non-motile, multiply by binary fission designated strain KVB23^T, which was isolated from root of rice plant, near Ilsan, South Korea, was investigated for its taxonomic position by polyphasic approach. Optimal growth was found to occur at 30˚C, at pH 6.5 and in the absence of NaCl on R2A. Phylogenetic analysis based on the 16S rRNA gene sequence of strain KVB23^T revealed that it formed a distinct lineage, as a separate deep branch within the family Rhodobacteriaceae, with < 96.5% sequence similarity to representatives of the genera Rhodobacter, Xinfangfangia, Tabrizicola, Falsirhodobacter, Haematobacter, Paenirhodobacter, Pseudorhodobacter and Pararhodobacter. Based in 16S rRNA sequences strain KVB23^T was most closely related to Tabrizicola fusiformis KCTC 62105 ^T (96.5%) and Rhodobacter thermarum KCTC 52712 ^T (96.2%). The draft genome of strain KVB23^T was 3.80 bp long with a DNA G + C content of 63.1%. Genome of strain KVB23^T harboured gene clusters for tryptophan and cobalamin biosynthesis. The strain contained Q-10 as the sole respiratory quinone. The predominant fatty acids were found to consist of C_16:0, C_18:0 and summed feature 8 (comprising C_18:1 ω7c and / or C_18:1 ω6). The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, seven unidentified phosphoglycolipids, two unidentified aminophosphoglycolipid, one unidentified glycolipid and four unidentified lipids. Phosphate-solubilizing bacteria have the ability to dissolve insoluble phosphates and enhance the soil fertility. Strain KVB23^T can solubilize calcium phosphate tribasic. Phosphate solubilizing and tryptophan biosynthesis property of strain KVB23^T could be a possible factor for the increase in growth of rice plant. Differential phenotypic, chemotaxonomic and genotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain KVB23^T was found to represent a novel genus in the Rhodobacteriaceae family, for which the name Fuscibacter oryzae gen. nov., sp. nov. is proposed, with the type strain KVB23^T(= KACC 21711 ^T = NBRC 114716 ^T).

Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis

A Gram-stain-negative, short-rod, aerobic, non-motile, red to pink-pigmented bacterium, designated Fur1T, was isolated from the dry spikelet clusters of a plant called Setaria viridis near Dongguk University. Phylogenetic analysis conducted based on 16S rRNA gene sequences indicated that strain Fur1T belonged to the genus Hymenobacter of the family Hymenobacteraceae . The 16S rRNA gene of Fur1T showed highest sequence similarity to those of Hymenobacter metalli KACC 17381T (97.5 %) and Hymenobacter marinus KACC 19042T (97.1 %). Growth occurred at 4–37 °C (optimum, 25–28 °C), up to 1.0 % NaCl (optimum, 0 %) and pH 5.5–9.0 (optimum, pH 6.0–7.5). The major fatty acids of strain Fur1T were identified as iso-C15 : 0, C16 : 1  ω5c, anteiso-C15 : 0, summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 4 (comprising anteiso-C17 : 1B and/or iso-C17 : 1I) as the major cellular fatty acids. The predominant respiratory quinone was identified as MK-7. The polar lipids were phosphatidylethanolamine, five unidentified aminophospholipids, two unidentified phospholipids, one unidentified glycolipid and one unidentified polar lipid. The genomic DNA G+C content based on the draft genome sequence was 58.7 mol%. DNA–DNA relatedness between strain Fur1T and its closest relative was below 70 %. Characterization based on phylogenetic, chemotaxonomic and phenotypic analyses clearly indicated that strain Fur1T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter setariae sp. nov. is proposed. The type strain is Fur1T (=KACC 19903T=NBRC=113691T).

Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail

A Gram-stain positive, short rod-shaped, aerobic, motile by means of gliding, yellow-pigmented actinobacterium, designated strain DD4a^T, was isolated from dry yellow foxtail. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DD4a^T is closely related to Amnibacterium soli MB78^T (98.4% similarity), Amnibacterium kyonggiense KSL51201-037^T (98.2%) and Amnibacterium endophyticum 1T4Z-3^T (97.43%). Strain DD4a^T forms yellow colonies on R2A agar medium. The peptidoglycan was found to contains diaminopimelic acid (which is a diagnostic cell wall diamino acid), alanine, glutamic acid and lysine. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids and an unidentified polar lipid were found to be present in strain DD4a^T. The major cellular fatty acids anteiso-C_15:0 (42.9%) and iso-C_16:0 (34.6%) were found in strain DD4a^T. The predominant respiratory quinones were found to be MK-11 and MK-12. The DNA G+C content of strain DD4a^T is 73.9 mol%. DNA-DNA relatedness of strain DD4a^T with A. soli MB78^T, A. kyonggiense KSL51201-037^T, and A. endophyticum 1T4Z-3^T were 53.3% (± 1.1%), 47.0% (± 0.5%), and 47.9% (± 0.9%), respectively. The digital DNA-DNA hybridisation and average nucleotide identity values between strain DD4a^T and A. kyonggiense KSL51201-037^T were determined to be 26.1% and 82.7%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, DD4a^T represents a novel member of the genus Amnibacterium, for which the name Amnibacterium setariae sp. nov., is proposed. The type strain of Amnibacterium setariae is DD4a^T (= KACC 19817^T = JCM 32878^T).