International Journal of Systematic and Evolutionary Microbiology

A thermotolerant, Gram-stain-positive, aerobic, sporangium-forming actinomycete, strain RA45T, was isolated from a desert region in Xinjiang Uigur Autonomous Region, north-western China. Comparative analysis of the 16S rRNA gene sequence and phenotypic characterization revealed that strain RA45T belonged phylogenetically to the family Pseudonocardiaceae of the suborder Pseudonocardineae. Strain RA45T showed more than 5 % 16S rRNA gene sequence divergence from recognized species of genera in the family Pseudonocardiaceae, forming a distinct lineage within the evolutionary radiation occupied by the genera Amycolatopsis, Prauserella, Thermocrispum, Saccharomonospora, Saccharopolyspora and Sciscionella, but distinct from each of them. The affiliation to the family was supported by the presence of suborder- and family-specific 16S rRNA signature nucleotides, a DNA G+C content of 69.9 mol%, the presence of meso-diaminopimelic acid, ribose, arabinose, glucose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes, the presence of menaquinone MK-9(H4) as the major respiratory lipoquinone, a lack of mycolic acids and the presence of an N-acetylated type of muramic acid. However, strain RA45T differed from known genera of the family in its polar lipid composition: the major phospholipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylmethylethanolamine, diphosphatidylglycerol, phospholipids of unknown structure and phospholipids of unknown structure containing glucosamine (phospholipid type IV). Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain RA45T is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Yuhushiella deserti gen. nov., sp. nov. is proposed. The type strain of Yuhushiella deserti is RA45T (=CGMCC 4.5579T =JCM 16584T).

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37T, was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37T stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37T had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C15 : 0 (41 %), iso-C14 : 0 3-OH and/or iso-C15 : 0 dimethyl acetal (21.6 %), iso-C13 : 0 (4.4 %), anteiso-C15 : 0 (3.9 %) and iso-C15 : 1 (2.8 %). Strain SOL3f37T grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2–8.1 (optimum pH 6.9). Strain SOL3f37T required at least 0.5 g NaCl l−1 and grew in the presence of NaCl concentrations up to 150 g l−1 (optimum 40 g l−1). Yeast extract (2 g l−1) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37T grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37T was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37T was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60T, 91.8 % with Thermohalobacter berrensis CTT3T and 91.7 % with Caloranaerobacter azorensis MV1087T. On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37T represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is proposed, with SOL3f37T (=DSM 21485T =JCM 15487T) as the type strain of Sporosalibacterium faouarense.

Five Gram-negative, facultatively anaerobic, non-spore-forming, coccoid rod-shaped bacterial isolates were obtained from infant formula and an infant formula production environment and were investigated by use of a polyphasic taxonomic study. Biochemical tests and partial rpoB gene sequence analysis of the five isolates revealed that they formed two distinct groups in the family Enterobacteriaceae, closely related to several species of the genera Pantoea and Erwinia, which indicated a phylogenetic position within the genus Pantoea or the genus Erwinia. Multilocus sequence analysis of concatenated partial atpD, gyrB, infB and rpoB gene sequences of two of the isolates suggested that they represented two novel species of the genus Pantoea, phylogenetically related most closely to Pantoea septica. The five isolates had general characteristics consistent with those of the genus Pantoea, and DNA–DNA hybridizations between two representatives and the type strains of their phylogenetically closest relatives based on comparative 16S rRNA gene sequence analysis showed that the isolates represented two novel genospecies. These two genospecies could be differentiated from each other based on fermentation of galacturonate, sorbitol and potassium 5-ketogluconate. They could be differentiated from phylogenetically related Pantoea species based on their ability to ferment lactose and to utilize β-gentiobiose and raffinose, their inability to ferment or utilize d-arabitol, and their inability to produce indole. On the basis of the results obtained, the five isolates are considered to represent two novel species of the genus Pantoea, for which the names Pantoea gaviniae sp. nov. (type strain A18/07T =LMG 25382T =DSM 22758T) and Pantoea calida sp. nov. (type strain 1400/07T =LMG 25383T =DSM 22759T) are proposed.

Two novel thermophilic and slightly acidophilic strains, Kam940Tand Kam1507b, which shared 99 % 16S rRNA gene sequence identity, were isolated from terrestrial hot springs of the Uzon caldera on the Kamchatka peninsula. Cells of both strains were non-motile, regular cocci. Growth was observed between 55 and 85 °C, with an optimum at 65–70 °C (doubling time, 6.1 h), and at pH 4.5–7.5, with optimum growth at pH 5.5–6.0. The isolates were strictly anaerobic organotrophs and grew on a narrow spectrum of energy-rich substrates, such as beef extract, gelatin, peptone, pyruvate, sucrose and yeast extract, with yields above 107cells ml−1. Sulfate, sulfite, thiosulfate and nitrate added as potential electron acceptors did not stimulate growth when tested with peptone. H2at 100 % in the gas phase inhibited growth on peptone. Glycerol dibiphytanyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl rings were present in the lipid fraction of isolate Kam940T. The G+C content of the genomic DNA of strain Kam940Twas 37 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates were archaea of the phylumCrenarchaeota, only distantly related to the cultured members of the classThermoprotei(no more than 89 % identity), and formed an independent lineage adjacent to the ordersDesulfurococcalesandAcidilobalesand clustering only with uncultured clones from hot springs of Yellowstone National Park and Iceland as the closest relatives. On the basis of their phylogenetic position and novel phenotypic features, isolates Kam940Tand Kam1507b are proposed to be assigned to a new genus and species,Fervidicoccus fontisgen. nov., sp. nov. The type strain ofFervidicoccus fontisis strain Kam940T(=DSM 19380T=VKM B-2539T). The phylogenetic data as well as phenotypic properties suggest that the novel crenarchaeotes form the basis of a new family,Fervidicoccaceaefam. nov., and order,Fervidicoccalesord. nov., within the classThermoprotei.

A moderately thermophilic chemoheterotrophic bacterium, strain Mat9-16T, was isolated from microbial mats developed in hot spring water streams from Yumata, Nagano, Japan. Cells of strain Mat9-16Twere strictly anaerobic, Gram-stain-negative, non-sporulating, non-motile and short to long rods (2.0–15.5 μm in length). Strain Mat9-16Tgrew fermentatively with optimum growth at 45 °C, pH 7.0–7.5 and 1 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene revealed that strain Mat9-16Twas affiliated with an uncultivated lineage, and the nearest cultivated neighbours were green sulfur bacteria belonging to the classChlorobeawith 77–83 % sequence similarity. However, strain Mat9-16Tcould not grow phototrophically and did not possess light-harvesting structures, morphologically and genetically, such as the chlorosomes of green sulfur bacteria. On the basis of phenotypic features and phylogenetic position, a novel genus and species are proposed for strain Mat9-16T, to be namedIgnavibacterium albumgen. nov., sp. nov. (=NBRC 101810T=DSM 19864T). We also propose to place the cultivated bacterial lineage accommodating the sole representative Mat9-16Tin a novel class,Ignavibacteriaclassis nov. In addition, we present a formal description of the phylum-level taxon‘Chlorobi’asChlorobiphyl. nov.

A novel halophilic actinomycete, designated strain YIM 93223T, was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 25–45 °C, at pH 6–8 and in the presence of 1–15 % (w/v) NaCl; no growth was observed in the absence of NaCl. Strain YIM 93223T contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids, and glucose and galactose as major whole-cell-wall sugars. Major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/iso-C15 : 0 2-OH. MK-8(H4) was the predominant menaquinone. The genomic DNA G+C content was 66.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93223T belongs to the genus Amycolatopsis. It shared highest 16S rRNA gene sequence similarity with Amycolatopsis palatopharyngis 1BDZT (96.6 %) and Amycolatopsis marina Ms392AT (96.4 %), but lower values (94.5–96.2 %) with the type strains of other recognized species of the genus Amycolatopsis. On the basis of the data from this polyphasic study, strain YIM 93223T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis halophila sp. nov. is proposed. The type strain is YIM 93223T (=DSM 45216T =KCTC 19403T).

An obligate anaerobic, Gram-staining-negative, mesophilic, cellulolytic bacterium, strain H1T, was isolated from the rumen content of yak. Cells were straight to slightly curved rods, 0.8–1.0×3.0–4.0 μm in size, non-motile and encapsulated with mucous materials. Elliptical and terminal spores that swelled the cells were produced occasionally. The strain grew at 25–45 °C (optimum, 38 °C) and pH 6.0–7.8 (optimum, pH 6.7). Cellulose, cellobiose, xylan, xylose and maltose were used as carbon and energy sources, but not glucose. Products from cellulose and cellobiose fermentation were formic acid, acetic acid, carbon dioxide and trace amounts of ethanol, lactic acid and succinic acid. The genomic DNA G+C content was 33.7±1.2 mol%. The predominant fatty acids were C16 : 0 (27.1 %), C14 : 0 (9.2 %) and iso-C16 : 0 (6.4%). Based on the 16S rRNA gene sequence analysis, strain H1T was affiliated to the clostridial rRNA cluster XIVb and showed the highest 16S rRNA gene sequence similarity to Clostridium lentocellum DSM 5427T (96.0 %). These two strains formed a distinct lineage of the family ‘Lachnospiraceae’. Based on data from this polyphasic taxonomic study, a new genus, Cellulosilyticum gen. nov., is proposed. Cellulosilyticum ruminicola sp. nov. is proposed for strain H1T. The type strain of Cellulosilyticum ruminicola sp. nov. is strain H1T (=CGMCC 1.5065T=JCM 14822T). Clostridium lentocellum was reclassified in the new genus as Cellulosilyticum lentocellum comb. nov. (type strain RHM5T=ATCC 49066T=DSM 5427T=NCIMB 11756T).

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

A moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain HRh1T, was obtained from mixed sediment samples from hypersaline chloride–sulfate lakes in the Kulunda Steppe, in south-western Siberia (Russia), using aerobic enrichment culture at 1 M NaCl with thiocyanate as substrate. Cells of the isolate were short, non-motile rods with a Gram-negative type of cell wall. The bacterium was an obligate aerobe capable of chemolithoautotrophic growth with thiocyanate and thiosulfate. With thiosulfate, it grew at NaCl concentrations of 0.2–3.0 M (optimum 0.5 M) and at pH 6.3–8.0 (optimum pH 7.3–7.5). During growth on thiocyanate, cyanate was identified as an intermediate. The dominant cellular fatty acids were C16 : 0and C18 : 1ω7. Phylogenetic analysis based on 16S rRNA gene sequencing placed the isolate in the classGammaproteobacteriaas an independent lineage, with an unclassified marine sulfur-oxidizing bacterium as the closest culturable relative (93 % sequence similarity). A singlecbbLgene (coding for the key enzyme of the Calvin–Benson cycle of autotrophic CO2assimilation) with relatively low similarity to any homologous genes found in chemolithoautotrophs was detected in strain HRh1T. On the basis of our phenotypic and phylogenetic analysis, the halophilic isolate is proposed to represent a new genus and novel species,Thiohalobacter thiocyanaticusgen. nov., sp. nov. The type strain ofThiohalobacter thiocyanaticusis HRh1T(=DSM 21152T=UNIQEM U249T).

A polyphasic study was undertaken to clarify the taxonomic position of endospore-forming strains 433-D9, 433-E17 and 121-X1. BOX-PCR-generated fingerprints indicated that they may be members of a single species. 16S rRNA gene sequence similarity demonstrated that a representative of this group, 433-D9, is affiliated closely with Bacillus arvi DSM 16317T (100 %), Bacillus arenosi DSM 16319T (99.8 %) and Bacillus neidei NRRL BD-87T (97.1 %). Sequence similarities revealed Bacillus pycnus NRRL NRS-1691T and several Kurthia species as the next nearest relatives. DNA–DNA hybridization results showed that strain 433-D9 is a member of B. arvi. Detection of l-Lys–d-Asp-based peptidoglycan in strain 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T was in agreement with their close relationship, but differentiated these strains from B. neidei NRRL BD-87T and B. pycnus NRRL NRS-1691T, for which l-Lys–d-Glu was reported. A similar quinone system was detected in strains 433-D9, 433-E17, 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T. This system, unusual for bacilli, consisted of the major compound menaquinone MK-8 (69–80 %) and moderate amounts of MK-7 (19–30 %). This observation was in contrast to the predominance of MK-7 of the closest relative B. pycnus NRRL NRS-1691T, as also reported for representatives of the closely related non-endospore-forming genus Kurthia. Strains 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T exhibited homogeneous and discriminative polar lipid profiles and fatty acid profiles consisting of major acids i-C15 : 0 and ai-C15 : 0 and moderate amounts of i-C17 : 1 ω10c and i-C17 : 1 I/ai-C17 : 1 B that discriminated them from closely related strains such as B. neidei NRRL BD-87T. On the basis of clear-cut discriminative chemotaxonomic markers, we propose strains 433-D9, 433-E17 and 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T to be reclassified within a separate genus. For this new taxon, we propose the name Viridibacillus gen. nov., and we propose the reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov. (the type species of Viridibacillus, with the type strain DSM 16317T =LMG 22165T), Viridibacillus arenosi comb. nov. (type strain DSM 16319T =LMG 22166T) and Viridibacillus neidei comb. nov. (type strain NRRL BD-87T =DSM 15031T =JCM 11077T).