- Volume 65, Issue Pt_3, 2015

A novel hyperthermophilic, anaerobic, archaeon was isolated from a terrestrial hot spring at Uzon Caldera, Kronotsky Nature Reserve, Kamchatka, Russia. The isolate, strain 1860T, grew optimally at 90–95 °C and pH 6.0–7.0. The cells were non-motile straight rods, 1.5–5.0 µm in length, covered with surface-layer lattice. Strain 1860T utilized complex proteinaceous compounds as electron donors and ferrihydrite, Fe(III) citrate, nitrate, thiosulfate, selenite, selenate and arsenate as electron acceptors for growth. The sequence of the 16S rRNA gene of strain 1860T had 97.9–98.7 % similarity with those of members of the genus Pyrobaculum . On the basis of its physiological properties and phylogenetic analyses including in silico genome to genome hybridization, the isolate is considered to represent a novel species, for which the name Pyrobaculum ferrireducens sp. nov. is proposed. The type strain is 1860T ( = DSM 28942T = VKM B-2856T).

The halophilic archaeal strain, YC82T, was isolated from Yuncheng salt lake in Shanxi, PR China. Cells from strain YC82T were Gram-stain negative, pleomorphic rods, which lysed in distilled water and formed light-red colonies on solid media. Strain YC82T grew at 25–50 °C (optimum 37 °C), in 1.4–4.8 M NaCl (optimum 2.0 M), in 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 6.0–9.5 (optimum pH 7.5). The major polar lipids of strain YC82T were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and three glycolipids, which were chromatographically identical to those of Haloarchaeobius iranensis IBRC-M 10013T and Haloarchaeobius litoreus CGMCC 1.10390T. 16S rRNA gene analysis revealed that strain YC82T had two dissimilar 16S rRNA genes and that it was phylogenetically related to Hab. iranensis IBRC-M 10013T (94.3–99.0 % nucleotide identity) and Hab. litoreus CGMCC 1.10390T (94.1–98.8 % nucleotide identity). The rpoB′ gene similarities between strain YC82T and Hab. iranensis IBRC-M 10013T and Hab. litoreus CGMCC 1.10390T were 96.5 % and 95.7 %, respectively. The DNA G+C content of strain YC82T was 63.7 mol%. Strain YC82T showed low DNA–DNA relatedness with Hab. iranensis IBRC-M 10013T and Hab. litoreus CGMCC 1.10390T. The phenotypic, chemotaxonomic and phylogenetic properties of strain YC82T ( = CGMCC 1.12232T = JCM 18644T) suggest that it represents a novel species of the genus Haloarchaeobius , for which the name Haloarchaeobius salinus sp. nov. is proposed. An emended description of the genus Haloarchaeobius is also presented.

A mesophilic, hydrogenotrophic methanogen, strain CYW4T, was isolated from deep-sea sediment obtained by the Ocean Researcher I cruiser, ORI-961, in 2011. The sediment was from the deformation front area offshore of south-western Taiwan. Here, seismic reflections indicated that methane hydrates were abundant. The methanogenic substrates utilized by strain CYW4T were formate and H2/CO2, but not acetate, secondary alcohols, methylamines, methanol and ethanol. Cells of strain CYW4T were non-motile, irregular cocci and 0.6–1.5 µm in diameter. The S-layer protein had an M r of 112 000. The optimum growth conditions were at 37 °C, pH 8.1 and 0.08 M NaCl. Growth of the strain was stimulated by acetate. The G+C content of the chromosomal DNA of strain CYW4T was 61 mol%. Phylogenetic analysis revealed that strain CYW4T was most closely related to Methanoculleus marisnigri JR1T (96.82 % 16S rRNA gene sequence similarity). Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is evident that strain CYW4T represents a novel species of the genus Methanoculleus , and the name Methanoculleus taiwanensis sp. nov. is proposed. The type strain is CYW4T ( = BCRC AR10043T = NBRC 110782T). The optical density of cultures of strain CYW4T dropped abruptly upon entering the stationary growth phase. During this time numerous particles of approximately 50 nm in diameter were observed on and around the cells. This suggests that strain CYW4T harbours a lytic virus that is induced in the stationary phase, which is of interest because only a few lytic viruses have been reported in methanogens.

A Gram-stain-positive bacterial isolate, strain 280/10T was isolated from the trachea of a white stork. The isolate was morphologically rod- to coccoid-shaped, non-motile and showed no oxidase activity. The highest 16S rRNA gene sequence similarity was found to the type strain of Corynebacterium ciconiae (97.3 % similarity) as the nearest relative of strain 280/10T, all other 16S rRNA gene sequence similarities to type strains of species of the genus Corynebacterium were below 94.2 %. Strain 280/10T had a quinone system consisting predominantly of menaquinone MK-8(H2), minor quantities of MK-9(H2) and small amounts of MK-8. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major compounds in the polar lipid profiles were diphosphatidylglycerol, phoshatidylglycerol, phosphatidylinositol and an acidic glycolipid. Two phosphatidylinositol-mannosides and several unidentified lipids were also present. The strain contained corynemycolic acids, while only small amounts of cellular polyamines were detected. Spermidine and spermine were predominant in the polyamine pattern of 280/10T and putrescine was present in moderate amounts. In the fatty acid profile C18 : 1ω9c, and C16 : 0 were predominant. The strain was distinguishable from C. ciconiae , which is the most closely related species. In conclusion, strain 280/10T is proposed to represent a novel species of the genus Corynebacterium with the name Corynebacterium trachiae sp. nov. and the type strain 280/10T ( = CIP 110796T = LMG 28214T).

The genus Clavibacter contains one recognized species, Clavibacter michiganensis . Clavibacter michiganensis is subdivided into subspecies based on host specificity and bacteriological characteristics, with Clavibacter michiganensis subsp. michiganensis causing bacterial canker of tomato. Clavibacter michiganensis subsp. michiganensis is often spread through contaminated seed leading to outbreaks of bacterial canker in tomato production areas worldwide. The frequent occurrence of non-pathogenic Clavibacter michiganensis subsp. michiganensis -like bacteria (CMB) is a concern for seed producers because Clavibacter michiganensis subsp. michiganensis is a quarantine organism and detection of a non-pathogenic variant may result in destruction of an otherwise healthy seed lot. A thorough biological and genetic characterization of these seed-associated CMB strains was performed using standard biochemical tests, cell wall analyses, metabolic profiling using Biolog, and single-gene and multilocus sequence analyses. Combined, these tests revealed two distinct populations of seed-associated members of the genus Clavibacter that differed from each other, as well as from all other described subspecies of Clavibacter michiganensis . DNA–DNA hybridization values are 70 % or higher, justifying placement into the single recognized species, C. michiganensis , but other analyses justify separate subspecies designations. Additionally, strains belonging to the genus Clavibacter isolated from pepper also represent a distinct population and warrant separate subspecies designation. On the basis of these data we propose subspecies designations for separate non-pathogenic subpopulations of Clavibacter michiganensis : Clavibacter michiganensis subsp. californiensis subsp. nov. and Clavibacter michiganensis subsp. chilensis subsp. nov. for seed-associated strains represented by C55T ( = ATCC BAA-2691T = CFBP 8216T) and ZUM3936T ( = ATCC BAA-2690T = CFBP 8217T), respectively. Recognition of separate subspecies is essential for improved international seed testing operations.

A Gram-staining-positive, aerobic organism, isolated from the Red Sea sponge Spheciospongia vagabunda was investigated to determine its taxonomic position. On the basis of results of 16S rRNA gene sequence analysis strain EG49T was most closely related to Actinokineospora cibodasensis and Actinokineospora baliensis (both 97.3 % similarity) and Actinokineospora diospyrosa and Actinokineospora auranticolor (both 97.0 % similarity). The 16S rRNA gene sequence similarity to all other species of the genus Actinokineospora was <97.0 %. The quinone system of strain EG49T contained the menaquinones MK-9(H4) (47 %), MK-9(H6) (27 %) and MK-9(H2) (15 %) in major amounts. Minor amounts of MK-7(H4) (2 %), MK-9(H0) (1 %), MK-9(H8) (3 %) and MK-10(H4) (3 %) were detected as well in addition to MK-8(H4), MK-8(H6), MK-10(H2) and MK-10(H6) (all <1 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine were predominant. Phosphatidylinositol-mannoside, two unidentified phospholipids and two glycoglipids as well as one aminoglycolipid, one aminolipid and one unidentified lipid were found in addition. The fatty acid profile was composed of mainly iso-branched fatty acids: iso-C16 : 0, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 1H. All these findings clearly supported the classification of the strain as representing a member of the genus Actinokineospora . In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain EG49T from the most closely related species of the genus Actinokineospora . Strain EG49T represents a novel species of the genus Actinokineospora , for which we propose the name Actinokineospora spheciospongiae sp. nov., with strain EG49T ( = DSM 45935T = CCM 8480T = LMG 27700T) as the type strain.

A novel actinomycete strain RY35-68T, isolated from a peat swamp forest soil sample in Rayong Province, Thailand, was characterized using a polyphasic approach. The strain belonged to the genus Actinomadura based on morphological and chemotaxonomic characteristics. Cell-wall analysis revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan layer. The diagnostic sugar in whole-cell hydrolysates was identified as madurose. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major cellular fatty acids were C16 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The genomic DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence similarity analysis, strain RY35-68T was closely related to the species Actinomadura atramentaria JCM 6250T (97.5 %). The value of DNA–DNA relatedness between strain RY35-68T and A. atramentaria JCM 6250T was 37.6–42.6 %. On the basis of its phenotypic characteristics and these results mentioned, this strain could be distinguished from the closely related type strain and represents a novel species of the genus Actinomadura , for which the name Actinomadura rayongensis sp. nov. (type strain RY35-68T = JCM 19830T = TISTR 2211T = PCU 332T) is proposed.

A Gram-stain positive, aerobic, non-motile actinobacterium, designated DSXY973T, was isolated from soil samples collected from Xinjiang desert using medium supplemented with resuscitation-promoting factor, and subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that DSXY973T belonged to the genus Arthrobacter and was most closely related to Arthrobacter oryzae JCM 15922T with 97.1 % similarity. The DNA G+C content was 67.6 %. Cells of strain DSXY973T mainly contained MK-9(H2), and the cell wall contained l-lysine as the primary diamino acid. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Strain DSXY973T was positive for catalase and negative for oxidase activity. On the basis of its phylogenetic position and phenotypic properties, strain DSXY973T represents a novel species of the genus Arthrobacter , for which the name Arthrobacter liuii sp. nov. is proposed. The type strain is DSXY973T ( = CGMCC1.12778T = JCM 19864T).

Strain DCY56T was isolated from a soil sample taken from a ginseng field. The strain was Gram-reaction positive, catalase-positive, oxidase-negative, aerobic and non-motile. Phylogenetic analysis, based on 16S rRNA gene sequence analysis, indicated that strain DCY56T belonged to the genus Microbacterium . The closest relatives were Microbacterium azadirachtae AI-S262T, Microbacterium aerolatum V-73T and Microbacterium phyllosphaerae DSM 13468T (98.0 %, 98.0 % and 97.5 % gene sequence similarity, respectively). The G+C content of the genomic DNA of strain DCY56T was 68.5 mol%. The DNA–DNA relatedness values between strain DCY56T and the most closely related type strains were lower than 36 %. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The predominant fatty acids contained iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The menaquinones were MK-12 and MK-13. The diagnostic diamino acid of strain DCY56T was ornithine. The dominant whole-cell sugars were glucose, rhamnose and ribose. The results of the genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrate that strain DCY56T represents a novel species within the genus Microbacterium , for which the name Microbacterium panaciterrae sp. nov. is proposed. The type strain is DCY56T ( = KCTC 19884T = JCM 17839T).

Strain MUSC 117T was isolated from mangrove soil of the Tanjung Lumpur forest in Pahang, Malaysia. This bacterium was yellowish-white pigmented, Gram-staining-positive, rod–coccus shaped and non-motile. On the basis of 16S rRNA gene sequence, strain MUSC 117T exhibited highest sequence similarity to Sinomonas atrocyanea DSM 20127T (98.0 %), Sinomonas albida LC13T (97.9 %) and Sinomonas soli CW 59T (97.8 %), and lower (<97.6 %) sequence similarity to other species of the genus Sinomonas . DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 27 %) between strain MUSC 117T and closely related species. Chemotaxonomically, the peptidoglycan type was A3α, containing the amino acids lysine, serine, glycine, alanine, glutamic acid and muramic acid. The whole-cell sugars detected were rhamnose, ribose, glucose, galactose and a smaller amount of mannose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and five unidentified glycolipids. The major fatty acids (>10.0 %) of the cell membrane were anteiso-C15 : 0 (39.4 %), C18 : 1ω7c (17.7 %), anteiso-C17 : 0 (17.2 %) and iso-C16 : 0 (11.4 %). The predominant respiratory quinones detected were MK-9(H2) and MK-9. The DNA G+C content was 67.3 mol%. A comparison of BOX-PCR fingerprints indicated that strain MUSC 117T represented a unique DNA profile. Results based on a polyphasic approach showed that strain MUSC 117T represents a novel species of the genus Sinomonas , for which the name Sinomonas humi sp. nov. is proposed. The type strain of Sinomonas humi sp. nov. is MUSC 117T ( = DSM 29362T = MCCC 1K00410T = NBRC 110653T).

A novel Gram-staining-positive, non-endospore-forming, aerobic bacterium, designated strain SJ5-4T, was isolated from seau-jeot, a traditional food that is made by fermentation of highly salted [approximately 25 % (w/v)] shrimp in Korea. Cells were moderately halophilic, non-motile cocci or short rods that showed catalase- and oxidase-positive reactions. Growth of strain SJ5-4T was observed at 15–40 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 6.5–7.0) and in the presence of 1–17 % (w/v) NaCl (optimum, 6 %). The major cellular fatty acids of strain SJ5-4T were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid, three glycolipids and an unidentified lipid were detected as the polar lipids. Strain SJ5-4T belonged to the exceptionally small group of strains within the order Micrococcales that show a peptidoglycan cross-linked according to the A-type but containing 2,4-diaminobutyric acid. The G+C content of the genomic DNA was 61.8 mol%. MK-7, MK-8 and MK-9 were detected as the isoprenoid quinones. Strain SJ5-4T was most closely related to members of the genus Nesterenkonia, with 16S rRNA gene sequence similarities of 93.1–94.8 %. However, phylogenetic inference based on 16S rRNA gene sequences showed that strain SJ5-4T formed a phyletic lineage distinct from members of the genus Nesterenkonia within the family Micrococcaceae . On the basis of its phenotypic and molecular features, strain SJ5-4T represents a novel genus and species of the family Micrococcaceae , for which the name Garicola koreensis gen. nov., sp. nov. is proposed. The type strain of Garicola koreensis is SJ5-4T ( = KACC 16909T = JCM 18572T = DSM 28238T).

During our previous studies we reclassified Clostridium coccoides and a number of misclassified ruminococci into a novel genus Blautia within the family Lachnospiraceae . However, the Rules of the Bacteriological Code currently require that the types of all species and subspecies with new names (including new combinations) be deposited in two different collections in two different countries. The type strain of Ruminococcus obeum was, at that period in time, only deposited in the American Type Culture Collection (ATCC) and a second independent deposit, as required by the Code, was not available. Consequently, the transfer of this species to the genus Blautia could not be made, because the resulting species name would not conform to the Rules governing the valid publication of species names and deposit of type material (Rules 27 and 30) and consequently would not be considered to be validly published. This resulted in a nomenclatural and taxonomic anomaly with R. obeum being phylogenetically placed among members of the genus Blautia with 16S rRNA gene sequence similarities of between 91.8 and 96.6 %. In order to rectify this unsatisfactory situation, through our discussions with the ATCC, the deposit of strain R. obeum ATCC 29174T to the DSMZ as strain number DSM 25238T was completed. Hence, the transfer of R. obeum to the genus Blautia as Blautia obeum comb. nov. is now proposed. The type strain is ATCC 29174T ( = DSM 25238T = KCTC 15206T).

An obligately anaerobic bacterium, designated strain GK12T, was isolated from an anaerobic digester in Fukagawa, Hokkaido Prefecture, Japan. The cells of strain GK12T were non-motile, non-spore-forming cocci that commonly occurred in chains. 16S rRNA gene sequence analysis revealed that strain GK12T was affiliated with the family Erysipelotrichaceae in the phylum Firmicutes and showed 91.8 % sequence similarity to the most closely related species, Faecalicoccus acidiformans . The strain grew at 30–50 °C (optimally at 40 °C) and at pH 5.5–8.5 (optimally at pH 7.5). The main end product of glucose fermentation was lactate. Yeast extract was required for growth. The strain contained C14 : 0, C14 : 0 1,1-dimethoxyalkane (DMA), C16 : 0 DMA and C18 : 0 DMA as the major cellular fatty acids (>10 % of the total). The polar lipid profile was composed of phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The whole-cell sugars were galactose, rhamnose and ribose. The cell-wall murein contained alanine, glutamic acid, lysine, serine and threonine, but not diaminopimelic acid. The G+C content of the genomic DNA was 47.7 mol%. Based on phenotypic, phylogenetic and chemotaxonomic properties, a novel genus and species, Catenisphaera adipataccumulans gen. nov., sp. nov., is proposed to accommodate strain GK12T ( = NBRC 108915T = DSM 25799T).

A Gram-reaction-positive, motile, thermophilic spore-forming strain, G1w1T, was isolated from a hot spring of the Valley of Geysers, Kamchatka (Russia). Based on data from the present polyphasic taxonomic study, including phylogenetic analysis of 16S rRNA and spo0A gene sequences, the strain is considered to represent a novel species of the genus Geobacillus , for which the name Geobacillus icigianus sp. nov. is proposed. The type strain is G1w1T ( = VKM B-2853T = DSM 28325T).

Three strains of an anaerobic, Gram-stain-positive coccobacillus were isolated from the intestines of mice. These strains shared 100 % similarity in their 16S rRNA gene sequences, but were distantly related to any described members of the family Lachnospiraceae (<94 %). The most closely related species with names that have standing in nomenclature were Robinsoniella peoriensis , Ruminococcus gnavus , Blautia producta and Clostridium xylanolyticum . Phylogenetic relationships based on 16S rRNA gene sequence analysis were confirmed by partial sequencing of hsp60 genes. The use of an in-house database search pipeline revealed that the new isolates are most prevalent in bovine gut samples when compared with human and mouse samples for Ruminococcus gnavus and B. producta . All three isolated strains shared similar cellular fatty acid patterns dominated by C16 : 0 methyl ester. Differences in the proportions of C12 : 0 methyl ester, C14 : 0 methyl ester and C18 : 1 cis-11 dimethyl acetal were observed when compared with phylogenetically neighbouring species. The major short-chain fatty acid produced by strain SRB-530-5-HT was acetic acid. This strain tested positive for utilization of d-fructose, d-galacturonic acid, d-malic acid, l-alanyl l-threonine and l-glutamic acid but was negative for utilization of amygdalin, arbutin, α-d-glucose, 3-methyl d-glucose and salicin, in contrast to the type strain of the closest related species Robinsoniella peoriensis . The isolates were not able to use mannitol for growth. Based on genotypic, phenotypic and chemotaxonomic characteristics, we propose to create the new genus and species Murimonas intestini gen. nov., sp. nov. to accommodate the three strains SRB-530-5-HT ( = DSM 26524T = CCUG 63391T) (the type strain of Murimonas intestini), SRB-509-4-S-H ( = DSM 27577 = CCUG 64595) and SRB-524-4-S-H ( = DSM 27578 = CCUG 64594).

An obligately anaerobic bacterial strain designated KC3T was isolated from a rice straw-degrading culture, for which soil of a Japanese rice field was used as the inoculum. Cells of strain KC3T were determined to be non-cellulolytic, Gram-stain-positive, non-motile, ellipsoidal, spore-forming rods, 0.8–1×4–25 µm. Endospores were formed at a terminal position in elongated cells (12–25 µm, mean 15 µm). The temperature range for growth was 20–50 °C, with an optimum at 37 °C. The pH range for growth was 5.0–7.5, with an optimum at pH 6.0 (slightly acidophilic). Strain KC3T fermented cellobiose to lactate, butyrate, acetate, formate, hydrogen and carbon dioxide. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and C19 : 0 cyclo 11,12 dimethylacetal. The DNA G+C content of strain KC3T was 37.5 mol%. 16S rRNA gene sequence analysis revealed that strain KC3T shared low sequence similarity (<93 %) with type strains of the genus Clostridium sensu stricto (Clostridium rRNA cluster I). Analyses of the DNA gyrase A and ATP synthase beta subunit sequences supported the affiliation of strain KC3T to the genus Clostridium sensu stricto. The evidence presented here indicates that strain KC3T represents a novel species of the genus Clostridium , for which the name Clostridium oryzae sp. nov. is proposed. The type strain of Clostridium oryzae is KC3T ( = DSM 28571T = NBRC 110163T).

A novel myxobacterium, MCy1366T (Ar1733), was isolated in 1981 from a soil sample collected from a region near Tokyo, Japan. It displayed general myxobacterial features like Gram-negative-staining, rod-shaped vegetative cells, gliding on solid surfaces, microbial lytic activity, fruiting-body-like aggregates and myxospore-like structures. The strain was mesophilic, aerobic and showed a chemoheterotrophic mode of nutrition. It was resistant to many antibiotics such as cephalosporin C, kanamycin, gentamicin, hygromycin B, polymyxin and bacitracin, and the key fatty acids of whole cell hydrolysates were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 0 2-OH. The genomic DNA G+C content of the novel strain was 65.6 mol%. The 16S rRNA gene sequence showed highest similarity (97.60 %) to ‘Stigmatella koreensis’ strain KYC-1019 (GenBank accession no. EF112185). Phylogenetic analysis based on 16S rRNA gene sequences and MALDI-TOF MS data revealed a novel branch in the family Myxococcaceae . DNA–DNA hybridization showed only 28 % relatedness between the novel strain and the closest recognized species, Corallococcus exiguus DSM 14696T (97 % 16S rRNA gene sequence similarity). A recent isolate from a soil sample collected in Switzerland, MCy10622, displayed 99.9 % 16S rRNA gene sequence similarity with strain MCy1366T and showed almost the same characteristics. Since some morphological features like fruiting-body-like aggregates were barely reproducible in the type strain, the newly isolated strain, MCy10622, was also intensively studied. On the basis of a comprehensive taxonomic study, we propose a novel genus and species, Aggregicoccus edonensis gen. nov., sp. nov., for strains MCy1366T and MCy10622. The type strain of the type species is MCy1366T ( = DSM 27872T = NCCB 100468T).