Arthrobacter mangrovi sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.

A novel actinobacterium, designated HIs16-36T, was isolated from the rhizosphere of a mangrove on Ishigaki Island, Okinawa, Japan, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HIs16-36T was closely related to the members of the genus Arthrobacter. The highest 16S rRNA gene sequence similarity was observed with Arthrobacter crystallopoietes (98.5 %), followed by Arthrobacter globiformis (97.2 %). The peptidoglycan of strain HIs16-36T was of the A4α type, with lysine as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-9(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two glycolipids. These chemotaxonomic features corresponded to those of the genus Arthrobacter. Meanwhile, the differences in some phenotypic characteristics, along with the results of average nucleotide identity and digital DNA-DNA hybridization analyses, indicated that strain HIs16-36T should be distinguished from the recognized species of the genus Arthrobacter. Therefore, strain HIs16-36T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter mangrovi sp. nov. is proposed. The type strain is HIs16-36T (=NBRC 112813T=TBRC 15750T).

Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov., isolated from the gut of larvae of Protaetia brevitarsis seulensis, reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and emended description of the genus Pseudolysinimonas.

Two bacterial strains, FWR-8T and CFWR-9T, were isolated from the gut of larvae of Protaetia brevitarsis seulensis that were raised at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Both strains were strictly aerobic, Gram-stain-positive and non-motile. Strain FWR-8T possessed the highest sequence similarity (98.7 %) to that of Protaetiibacter intestinalis 2DFWR-13T and the phylogenetic tree revealed that strain FWR-8T formed a cluster with Ptb. intestinalis 2DFWR-13T. Pseudolysinimonas kribbensis MSL-13T and Lysinimonas yzui N7XX-4T shared a high 16S rRNA gene sequence similarity (97.8 %) and formed a cluster adjacent to the cluster that included Ptb. intestinalis 2DFWR-13T. The 16S rRNA gene sequence of strain CFWR-9T exhibited the highest similarity (97.7 %) to that of Agromyces binzhouensis OAct353T and the phylogenetic tree indicated that strain CFWR-9T formed one independent cluster with A. binzhouensis OAct353T that was within the radius of the genus Agromyces. The peptidoglycan type, major fatty acids, major menaquinones and total polar lipids of strain FWR-8T were characterized as type B1, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, MK-15, MK-16 and MK-14, and diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid, respectively. Those from strain CFWR-9T were type B1, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, MK-11, MK-12 and MK-10, and diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid, respectively. Based on the phenotypic and genotypic data, strains FWR-8T and CFWR-9T each represent a novel species within the genera Protaetiibacter and Agromyces, respectively. For these species, the names Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov. have been proposed, with the type strains FWR-8T (=KACC 19322T=NBRC 113051T) and CFWR-9T (=KACC 19306T=NBRC 113046T), respectively. Our results also justify a reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and an emended description of the genus Pseudolysinimonas isprovided.

Lactococcus protaetiae sp. nov. and Xylanimonas protaetiae sp. nov., isolated from gut of larvae of Protaetia brevitarsis seulensis.

Two bacterial strains, designated 2DFWM-2T and FW10M-9T, were isolated from gut of larva of Protaetia brevitarsis seulensis grown at the National Institute of Agricultural Sciences, Wanju-gun, South Korea. 16S rRNA and rpoB gene sequences showed that strain 2DFWM-2T formed a separate branch with Lactococcus allomyrinae 1JSPR-7T in the genus Lactococcus, adjacent to a group of Lactococcus lactis subspecies. ANI and dDDH values between 2DFWM-2T and Lactococcus allomyrinae 1JSPR-7T were 93.30% and 53.20%, respectively. Based on the 16S rRNA gene sequence analysis, strain FW10M-9T was classified into the genus Xylanimonas revealing 96.9-98.5% sequence similarities with the Xylanimonas species. The ANI values of strain FW10M-9T with the closely species Xylanimonas pachnodae NBRC 107786T, Xylanimonas allomyrinae 2JSPR-7T, Isoptericola variabilis JCM 11754T and Xylanimonas cellulosilytica DSM 15894T was 81.5%, 81.2%, 81.0% and 84.1%, respectively, and the dDDH values estimated by GGDC was 24.3%, 24.3%, 29.3% and 28.1%, respectively. On the basis of the phenotypic and genotypic data, it is proposed that strain 2DFWM-2T represents a novel species of the genus Lactococcus, for which the name Lactococcus protaetiae sp. nov. is proposed, and the type strain is 2DFWM-2T (= KACC 19320T = NBRC 113069T). And, strain FW10M-9T represents a novel species of the genus Xylanimonas, for which the name Xylanimonas protaetiae sp. nov. is proposed, and the type strain is FW10M-9T (= KACC 19331T = NBRC 113053T).

Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis.

A Gram-stain-positive, strictly aerobic, polar flagellated, short rod-shaped bacterium, designated DFW100M-13T, was isolated from gut of the larva of Protaetia brevitarsis seulensis collected from Wanju-gun, South Korea. The growth range of NaCl concentration was 0-3 % (w/v) (optimally 0 % (w/v)), the temperature range for growth was 10-40 °C (optimally 28-30 °C), and the pH range for growth was pH 6.0-9.0 (optimally pH 7.0-8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DFW100M-13T had a high sequence similarity to members of the genus Microbacterium, having the highest similarity with Microbacterium luticocti DSM 19459T (97.7 %), Microbacterium rhizosphaerae CHO1T (97.1 %), and Microbacterium immunditiarum SK 18T (97.0 %), and formed a distinct lineage with Microbacterium luticocti DSM 19459T within the genus Microbacterium. A phylogenetic tree based on house-keeping genes also showed the result similar to the 16S rRNA gene-based tree. The main respiratory quinone (>10 %) was MK-11, MK-12 and MK-10, and the predominant cellular fatty acids (>10 %) were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, an inidentified glycolipid and an unidnetified lipid. The peptidoglycan type was supposed to be the B2ß with amino acids d-alanine, d-glutamic acid, glycine, l-homoserine and d-ornithine. The genomic DNA G+C content was 68.0 mol%. Based on the polyphasic taxonomic data, strain DFW100M-13T is considered to represent a novel species, for which the name Microbacterium protaetiae sp. nov. is proposed. The type strain is DFW100M-13T (=KACC 19323T=NBRC 113120T).

Gryllotalpicola protaetiae sp. nov., isolated from insect Protaetia brevitarsis seulensis, and emended descriptions of the genus Gryllotalpicola and the species Gryllotalpicola soli.

A bacterial strain, designated 2DFW10M-5T, was isolated from gut of the larva of Protaetia brevitarsis seulensis collected in the Republic of Korea. Cells of the strain were Gram-stain-positive, non-motile and rod-shaped. The strain grew at the range of 10-37 °C (optimum, 28-30 °C) and pH 4.0-8.0 (optimum, pH 7.0) and tolerated up to 1 % NaCl (w/v; optimum, 0 %) on Reasoner's 2A medium. It was catalase-positive and oxidase-negative. The 16S rRNA gene sequence of strain 2DFW10M-5T showed the highest similarity to Gryllotalpicola daejeonensis RU-04T (98.4 %), Gryllotalpicola soli KIS12-7T (98.2 %), Gryllotalpicola kribbensis PU-02T (97.5 %), Gryllotalpicola koreensis RU-16T (97.4 %) and Gryllotalpicola reticulitermitis TS-56T (97.2 %). The phylogenetic tree based on the 16S rRNA gene sequence revealed that strain 2DFW10M-5T fell into the radius of the genus Gryllotalpicola. The predominant fatty acid was ω-cyclohexyl-C17:0. The polar lipids of strain 2DFW10M-5T were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and two unidentified lipids. The detected isoprenoid quinones were MK-11 (61.0 %), MK-10 (33.7 %) and MK-12 (5.3 %). The peptidoglycan contained d- and l-alanine, d-glutamic acid, glycine, l-serine and d-lysine with l-lysine as the diamino acid. The DNA G+C content calculated from the genome sequence of strain 2DFW10M-5T was 69.2 mol%. On the basis of its genomic, phylogenetic and phenotypic properties and distinctiveness, strain 2DFW10M-5T represents a novel species of the genus Gryllotalpicola, for which the name Gryllotalpicola protaetiae sp. nov. is proposed. The type strain is 2DFW10M-5T (=KACC 19316T=NBRC 113049T).

Lactococcus allomyrinae sp. nov., isolated from gut of larvae of Allomyrina dichotoma.

Strain 1JSPR-7T, a facultatively anaerobic bacterium isolated from the gut of larvae of Allomyrina dichotoma raised in Wanju-gun, Republic of Korea, was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene and rpoB gene sequences showed that strain 1JSPR-7T fell within the genus Lactococcus, forming a compact cluster with the type strain of four subspecies of Lactococcus lactis and Lactococcus taiwanensis. The 16S rRNA gene sequence of strain 1JSPR-7T revealed the highest homology with L. lactissubsp. lactis JCM 5805T (97.3 %) and L. lactissubsp. hordniae NBRC 100931T (97.1 %), and the rpoB gene sequence showed the highest similarity to L. lactissubsp. cremoris DSM 20069T (91.4 %) and L. lactissubsp. tructae L105T (91.4 %). The average nucleotide identity and digital DNA-DNA hybridization values indicated that strain 1JSPR-7T was a novel species of the genus Lacococcus. The major fatty acids (>10 % of the total fatty acids) were summed feature 7 (unknown 18.846, C19 : 1ω6c and/or C19 : 0cyclo ω10c), C16 : 0 and C14 : 0, and the predominant menaquinone was MK-8 with MK-7 as a minor one. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and three unidentified glycolipids with diphosphatidylglycerol as the major one. The cell-wall peptidoglycan was of the A4α type with an interpeptide bridge comprising l-Lys-d-Asp. The DNA G+C content based on the whole genome sequences was 37.4 mol%. Based on the data obtained, strain 1JSPR-7T represents a novel species of the genus Lactococcus, for which the name Lactococcusallomyrinae sp. nov. is proposed. The type strain is 1JSPR-7T (=KACC 19319T=NBRC 113068T).

Protaetiibacter intestinalis gen. nov., of the family Microbacteriaceae, isolated from gut of Protaetia brevitarsis seulensis, reclassification of Lysinimonas kribbensis Jang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. and emended description of the genus Lysinimonas Jang et al. 2013.

A Gram-stain-positive, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, designated strain 2DFWR-13T, was isolated from gut of the larva of Protaetia brevitarsis seulensis, in the Republic of Korea. Strain 2DFWR-13T showed high sequence similarities to Lysinimonas kribbensis MSL-13T (97.7 %), Homoserinibacter gongjuensis 5GH26-15T (97.2 %), Microbacterium deminutum KV-483T (97.1 %) and Herbiconiux ginsengi CGMCC 4.3491T (97.1 %). The predominant fatty acids (>10 % of the total fatty acids) were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The major menaquinones were MK-13 and MK-12. The peptidoglycan type was type B2 with the diagnostic amino acid d-DAB. The N-acyl type of the murein was glycolyl. The polar lipids consisted of diphosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The DNA G+C content was 71.5 mol%. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics, we conclude that strain 2DFWR-13T represents a novel genus and species of the family Microbacteriaceae, for which the name Protaetiibacter intestinalis gen. nov., sp. nov. is proposed. The type strain of Protaetiibacter intestinalis is 2DFWR-13T (=KACC 19321T=NBRC 113050T). In addition, an emended description of the genus LysinimonasJang et al. 2013 and the reclassification of Lysinimonas kribbensisJang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. are proposed.

Litorihabitans aurantiacus gen. nov., sp. nov., an actinobacterium of the family Beutenbergiaceae isolated from beach sand.

A novel actinobacterium, designated HIsM16-52T, was isolated from beach sand collected from Ishigaki Island in Japan and its taxonomic position was investigated by a polyphasic approach. Strain HIsM16-52T contained both lysine and ornithine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and C14 : 0. The detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was determined to be 73.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIsM16-52T fell within the cluster of the family Beutenbergiaceae and formed a reliable cluster with the members of the genus Serinibacter. The highest 16S rRNA gene sequence similarities were obtained to species of the genus Serinibacter(97.8-97.9 %), followed by the genera Miniimonas (97.0 %), Beutenbergia (96.4 %) and Salana (95.9 %). However, strain HIsM16-52T differed from the members of the genus Serinibacter and the other genera within the family Beutenbergiaceae in terms of chemotaxonomic characteristics. Therefore, strain HIsM16-52T is concluded to represent a novel genus and species of the family Beutenbergiaceae, for which the name Litorihabitans aurantiacus gen. nov., sp. nov. is proposed. The type strain of L. aurantiacus is HIsM16-52T (=NBRC 112290T=TBRC 7759T).

Lactobacilus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter.

A rod-shaped, Gram-stain-positive, non-flagellated, facultatively anaerobic bacterium, designated SYF10-1aT, was isolated from Nuruk, a Korean traditional fermentation starter. It grew at 4-40 °C (optimum 37 °C), at pH 3.0-9.0 (optimum, pH 7.0) and with 0-5 % (w/v) NaCl. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain SYF10-1aT belonged to the genus Lactobacillus and showed the highest sequence similarity of 98.7 % to Lactobacillus crustorum LMG 23699T. A comparison of two housekeeping genes, pheS and rpoA, supported the suggestion that strain SYF10-1aT fell within the radius of the genus Lactobacillus, but was clearly separated from its closest related species. The average nucleotide identity value and digital DNA-DNA hybridization value between strain SYF10-1aT and the most closely related species,L. crustorum LMG 23699T, were 80.5 and 33.3 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1ω9c, C18 : 1ω7c and summed feature 3 (including iso-C15 : 0 2-OH and/or C16 : 1ω7c). Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminolipids and two unidentified glycolipids. The cell-wall peptidoglycan was of the A4α type with an interpeptide bridge comprising l-Lys-d-Asp. The DNA G+C content was 34.2 mol%. On the basis of this taxonomic study, strain SYF10-1aT represents a novel species within the genus Lactobacillus, for which the name Lactobacillus nuruki sp. nov. is proposed. The type strain is SYF10-1aT (=KACC 18726T=NBRC 112011T).

Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove.

A novel actinobacterium, designated HIr16-25T, was isolated from the rhizosphere soil of a mangrove growing on Iriomote Island in Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HIr16-25T fell within the cluster of the members of the genus Agromyces and the highest sequence similarity value was observed with Agromyces rhizospherae IFO 16236T (98.6%). Strain HIr16-25T possessed L-2,4-diaminobutyric acid as a diagnostic diamino acid of the peptidoglycan, and MK-12 and MK-11 as the predominant menaquinones. The major fatty acids were identified as iso-C16:0, anteiso-C15:0 and anteiso-C17:0 and the principal polar lipids were phosphatidylglycerol and one glycolipid. These chemotaxonomic features matched well those described for the members of the genus Agromyces. Meanwhile, the result of DNA-DNA hybridization and the presence of differential phenotypic characteristics between strain HIr16-25T and the type strain of A. rhizospherae indicated that strain HIr16-25T be classified as a novel species of the genus Agromyces. Therefore, we propose strain HIr16-25T to represent a novel species of the genus Agromyces, with the name Agromyces mangrovi sp. nov. The type strain is HIr16-25T (= NBRC 112812T = TBRC 7760T).

Lysinimicrobium sediminis sp. nov., an actinobacterium isolated from estuary sediment.

A novel Gram-stain-positive actinobacterium, designated HT7-17T, was isolated from a sediment sample collected from the estuary of the Tama River, Japan, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HT7-17T was closely related to members of the genus Lysinimicrobium, with a similarity range of 97.1-98.2 %. The peptidoglycan type of strain HT7-17T was A4α, the predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content was 69.9 mol%. These chemotaxonomic features corresponded to those of the genus Lysinimicrobium. Meanwhile, the differences in some phenotypic characteristics, along with the result of DNA-DNA hybridization, indicated that strain HT7-17T should be distinguished from the recognized species of the genus Lysinimicrobium. Therefore, strain HT7-17T represents a novel species of the genus Lysinimicrobium, for which the name Lysinimicrobium sediminis sp. nov. is proposed. The type strain is HT7-17T (=NBRC 112286T=TBRC 7037T).

Arenivirga flava gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a mangrove tidal flat.

A novel Gram-stain-positive actinobacterium, designated HIs16-32T, was isolated from a sand sample collected from a mangrove tidal flat in Japan and its taxonomic position was investigated by a polyphasic approach. The cells of strain HIs16-32T were Gram-stain-positive, rod-shaped, non-motile and non-endospore-forming. Strain HIs16-32T contained glutamic acid, glycine and lysine in the peptidoglycan; however, alanine was absent. Galactose and mannose were detected as cell-wall sugars. The isoprenoid quinones were identified as MK-11, MK-12 and MK-10, and the major fatty acids as anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was determined to be 72.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIs16-32T was related to members of the family Microbacteriaceae but did not form a reliable cluster with any known members of the family. The highest 16S rRNA gene sequence similarity values were obtained with species of the genera Herbiconiux(96.1-96.8 %), Plantibacter(96.5-96.7 %) and Schumannella (96.7 %). However, strain HIs16-32T was distinguishable from the phylogenetically related genera in terms of chemotaxonomic characteristics and phylogenetic relationship. Therefore, strain HIs16-32T is concluded to represent a novel genus and species of the family Microbacteriaceae, for which the name Arenivirga flava gen. nov., sp. nov. is proposed. The type strain of A. flava is HIs16-32T (=NBRC 112289T=TBRC 7038T).

Proposal of nine novel species of the genus Lysinimicrobium and emended description of the genus Lysinimicrobium.

Thirteen novel Gram-stain-positive bacteria were isolated from various samples collected from mangrove forests in Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence comparisons showed that the 13 isolates formed a single clade with Lysinimicrobium mangrovi HI08-69T, with a similarity range of 97.6-99.5 %. The peptidoglycan of the isolates was of the A4α type with an interpeptide bridge comprising Ser-Glu and an l-Ser residue at position 1 of the peptide subunit. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. These chemotaxonomic characteristics corresponded to those of the genus Lysinimicrobium. On the basis of the phenotypic and phylogenetic data, along with average nucleotide identity values among the isolates, we concluded that the 13 isolates should be assigned to the following nine novel species of the genus Lysinimicrobium: Lysinimicrobium aestuarii sp. nov. (type strain HI12-104T = NBRC 109392T = DSM 28144T), Lysinimicrobium flavum sp. nov. (type strain HI12-45T = NBRC 109391T = DSM 28150T), Lysinimicrobium gelatinilyticum sp. nov. (type strain HI12-44T = NBRC 109390T = DSM 28149T), Lysinimicrobium iriomotense sp. nov. (type strain HI12-143T = NBRC 109399T = DSM 28146T), Lysinimicrobium luteum sp. nov. (type strain HI12-123T = NBRC 109395T = DSM 28147T), Lysinimicrobium pelophilum sp. nov. (type strain HI12-111T = NBRC 109393T = DSM 28148T), Lysinimicrobium rhizosphaerae sp. nov. (type strain HI12-135T = NBRC 109397T = DSM 28152T), Lysinimicrobium soli sp. nov. (type strain HI12-122T = NBRC 109394T = DSM 28151T) and Lysinimicrobium subtropicum sp. nov. (type strain HI12-128T = NBRC 109396T = DSM 28145T). In addition, an emended description of the genus Lysinimicrobium is proposed.