Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants

Five Gram-stain-positive, aerobic, non-motile actinobacterial strains designated as CPCC 205763T, CPCC 203386T, CPCC 205716T, CPCC 203406T, and CPCC 203407 were obtained from different ecosystems associated with four kinds of Chinese traditional medicinal plants. The 16S rRNA gene sequences of these five strains showed closely related to members of the genus Herbiconiux of the family Microbacteriaceae, with the highest similarities of 97.4-99.7% to the four validly named species of Herbiconiux. In the phylogenetic trees based on 16S rRNA gene sequences and the core genome, these isolates clustered into the clade of the genus Herbiconiux within the lineage of the family Microbacteriaceae. The overall genome relatedness indexes (values of ANI and dDDH) and the phenotypic properties (morphological, physiological and chemotaxonomic characteristics) of these isolates, readily supported to affiliate them to the genus Herbiconiux, representing four novel species, with the isolates CPCC 203406T and CPCC 203407 being classified in the same species. For which the names Herbiconiux aconitum sp. nov. (type strain CPCC 205763T = I19A-01430T = CGMCC 1.60067T), Herbiconiux daphne sp. nov. (type strain CPCC 203386T = I10A-01569T = DSM 24546T = KCTC 19839T), Herbiconiux gentiana sp. nov. (type strain CPCC 205716T = I21A-01427T = CGMCC 1.60064T), and Herbiconiux oxytropis sp. nov. (type strain CPCC 203406T = I10A-02268T = DSM 24549T = KCTC 19840T) were proposed, respectively. In the genomes of these five strains, the putative encoding genes for amidase, endoglucanase, phosphatase, and superoxidative dismutase were retrieved, which were classified as biosynthetic genes/gene-clusters regarding plant growth-promotion (PGP) functions. The positive results from IAA-producing, cellulose-degrading and anti-oxidation experiments further approved their potential PGP bio-functions. Pangenome analysis of the genus Herbiconiux supported the polyphasic taxonomy results and confirmed their bio-function potential.

Characterization of three Stenotrophomonas strains isolated from different ecosystems and proposal of Stenotrophomonas mori sp. nov. and Stenotrophomonas lacuserhaii sp. nov

Stenotrophomonas spp. have primarily been reported as non-pathogenic, plant-probiotic bacteria, despite the presence of some opportunistic human pathogens in the genus. Here, three Gram-stain negative, rod-shaped, non-spore-forming bacteria, designated as strains CPCC 101365^T, CPCC 101269^T, and CPCC 101426 were isolated from surface-sterilized medicinal plant roots of a mulberry plant in Chuxiong of the Yunnan Province, freshwater from Erhai Lake in the Yunnan Province, and sandy soils in the Badain Jaran desert in Inner Mongolia Autonomous Region, China, respectively. The 16S rRNA gene sequences analysis of these isolates in comparison with sequences from the GenBank database indicated that they belong to the genus Stenotrophomonas, with nucleotide similarities of 96.52-99.92% to identified Stenotrophomonas members. Phylogenetic analysis based on 16S rRNA gene and genome sequences confirmed that the isolates are members of the genus Stenotrophomonas. Values for genomic average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; < 70%) indicated that strains CPCC 101365^T and CPCC 101269^T were well-differentiated from validly described Stenotrophomonas species, while strain CPCC 101426 shared high ANI (97.7%) and dDDH (78.3%) identity with its closest phylogenetic neighbor, Stenotrophomonas koreensis JCM 13256^T. The three genomes were approximately 3.1-4.0 Mbp in size and their G + C content ranged in 66.2-70.2%, with values slightly differing between CPCC 101365^T (3.4 Mbp; 70.2%), CPCC 101269^T (4.0 Mbp; 66.4%), and CPCC 101426 (3.1 Mbp; 66.2%). Genes encoding enzymes involved in the biosynthesis of indole-3-acetic acid (IAA) and siderophores were identified in the genomes of the three isolates, suggesting that these strains might serve roles as plant-growth promoting microorganisms. The polar lipid fractions of the three isolates primarily comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The predominant cellular fatty acid was iso-C₁₅: ₀, with moderate amounts of antesio-C_{15: 0}, iso-C_{11: 0}, iso C_{17: 1} ɷ9c/C_{16: 0} 10-methyl, iso-C_{14: 0}, and C_{16: 1} ɷ7c/C_{16: 1} ɷ6c. These results indicated that polyphasic characteristics of strains CPCC 101365^T and CPCC 101269^T differed from other identified Stenotrophomonas species and that strain CPCC 101426 was affiliated with the species Stenotrophomonas koreensis. Accordingly, two novel species of the genus Stenotrophomonas were consequently proposed, corresponding to Stenotrophomonas mori sp. nov. (type strain CPCC 101365^T = DY006^T = KCTC 82900^T) and Stenotrophomonas lacuserhaii sp. nov. (type strain CPCC 101269^T = K32^T = KCTC 82901^T).

Highlights

Members of the genus Stenotrophomonas, and particularly Stenotrophomonas maltophilia, are opportunistic human pathogens, but not enough research has evaluated the identification of environmental Stenotrophomonas spp. However, most Stenotrophomonas spp. serves as plant-probiotic bacteria.In this study, we obtained and characterized three Stenotrophomonas strains from different ecosystems. Based on phenotypic differences, chemotaxonomic properties, ANI and dDDH identity values, and phylogenetic analyses, two novel Stenotrophomonas species are proposed for the strains identified here. The encoding genes related to plant-growth promotion in the genomes of the newly recovered Stenotrophomonas spp. were retrieved. Follow-on experiments confirmed that these strains produced the important plant hormone IAA. Thus, these Stenotrophomonas spp. could considerably contribute to shaping and maintaining ecological stability in plant-associated environments, particularly while acting as plant-probiotic microorganisms.

Shinella lacus sp. nov., a novel microcystin-degrading alphaproteobacterium containing the bla carbapenemase gene

A Gram-stain-negative, rod-shaped, microcystin-degrading bacterium, designated as CPCC 100929T, was isolated from a fresh water reservoir in Sichuan Province, PR China. This isolate grew well at 4–37 °C and pH 6.0–8.0, with optimal growth at 28–32 °C and pH 7.0, respectively. The major cellular fatty acids were C18:1 ω7c/C18:1 ω6c, C16:0, C18:1 ω7c 11-methyl and C19:0 cyclo ω8c. The predominant respiratory quinone was Q-10. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine were detected in the polar lipids extraction. The 16S rRNA gene sequence of strain CPCC 100929T was closely related to those of members of the genus Shinella , with the highest similarity of 98.6 % to Shinella zoogloeoides DSM 287T and 97.4–98.4 % with other identified Shinella members. In the phylogenetic trees based on 16S rRNA gene sequences and the core-genes analysis, strain CPCC 100929T was included within the clade of the genus Shinella . The values of average nucleotide identity (81.4–86.7 %) and digital DNA–DNA hybridization (25.4–44.6 %) between strain CPCC 100929T and other Shinella species were all below the thresholds for bacterial species delineation, respectively. The genomic DNA G+C content of strain CPCC 100929T was 63.6 %. The genomic sequence analysis indicated that this species contained genes encoding peroxidase, bla carbapenemase and the key enzyme for microcystin bio degradation, as well as rich carbohydrate-active enzyme coding genes, which might endow the micro-organism with properties to adapt to diverse environments. Based on its phenotypic and genetic properties, we propose that strain CPCC 100929T (=T1A350T=KCTC 72957T) is the type strain of a novel species with the name Shinella lacus sp. nov.

Properties of Modestobacter deserti sp. nov., a Kind of Novel Phosphate-Solubilizing Actinobacteria Inhabited in the Desert Biological Soil Crusts

Three Gram-stain-positive, aerobic, motile actinobacterial strains designated as CPCC 205119^T, CPCC 205215, and CPCC 205251 were isolated from different biological soil crust samples collected from Tengger Desert, China. The 16S rRNA gene sequence comparison of these three strains showed they had almost identical 16S rRNA genes, which were closely related to members of the family Geodermatophilaceae, with the highest similarities of 96.3–97.3% to the species of Modestobacter. In the phylogenetic tree based on 16S rRNA gene sequences, these isolates clustered into a subclade next to the branch containing the species of Modestobacter lapidis and Modestobacter multiseptatus, within the lineage of the genus Modestobacter. The comparative genomic characteristics (values of ANI, dDDH, AAI, and POCP) and the phenotypic properties (morphological, physiological, and chemotaxonomic characteristics) of these isolates readily supported to affiliate them to the genus Modestobacter as a single separate species. For which, we proposed that the isolates CPCC 205119^T, CPCC 205215, and CPCC 205251 represent a novel species of the genus Modestobacter as Modestobacter deserti sp. nov. CPCC 205119^T (=I12A-02624=NBRC 113528^T=KCTC 49201^T) is the type strain. The genome of strain CPCC 205119^T consisted of one chromosome (4,843,235bp) containing 4,424 coding genes, 48 tRNA genes, five rRNA genes, three other ncRNA genes, and 101 pseudogenes, with G+C content of 74.7%. The whole-genome sequences analysis indicated that this species contained alkaline phosphatase genes (phoA/phoD), phosphate transport-related genes (phoU, phnC, phnD, phnE, phoB, phoH, phoP, phoR, pitH, ppk, pstA, pstB, pstC, and pstS), trehalose-phosphate synthase gene (otsA), trehalose 6-phosphate phosphatase gene (otsB) and other encoding genes for the properties that help the microorganisms to adapt to harsh environmental conditions prevalent in deserts. Strains of this species could solubilize tricalcium phosphate [Ca₃(PO₄)₂] and phytin, assimilate pyrophosphate, thiophosphate, dithiophosphate, phosphoenol pyruvate, 2-deoxy-d-glucose-6-phosphate, and cysteamine-S-phosphate.

Stenotrophomonas nematodicola sp. nov., isolated from Caenorhabditis elegans

A Gram stain-negative, coccoid rod-shaped, motile by gliding, facultatively aerobic bacterium, designated W5, was isolated from Caenorhabditis elegans samples in Baotianman Natural Reserve (33° 27' 47'' N; 111° 48' 32'' E), Nanyang, China. The isolate was characterized taxonomically using a polyphasic approach. The 16S rRNA gene of strain W5 exhibited 98.1-99.7% similarity to the 16S rRNA genes of members of the genus Stenotrophomonas, and < 98.0% similarities to those of other bacterial species in the family Lysobacteraceae. The most closely related strains were Stenotrophomonas rhizophila JCM 13333^T (99.7%) and Stenotrophomonas bentonitica DSM 103927^T (99.2%). The predominant respiratory quinone of the isolate is Q-8. The major fatty acids are iso-C_15:0 (38.2%) and antesio-C_15:0 (16.6%). The draft genome of strain W5 had a length of 4,402,751 bp and a DNA G + C content of 67.3 mol%. The ANI values between the draft genomes of strain W5 and its closest phylogenetic neighbors S. rhizophila JCM 1333^T and S. bentonitica DSM 103927^T were 84.7% and 85.0%, respectively. The DDH value between W5 and S. rhizophila JCM 13333^T was 30.8%, which was the highest DDH level. We propose that strain W5 represents a novel bacterial species with the name Stenotrophomonas nematodicola sp. nov. and W5 as the type strain. The type strain is W5 (= CPCC 101271^T = CGMCC 19401^T = KCTC XXX^T).

Actinokineospora xionganensis sp. nov., a filamentous actinomycete isolated from the lakeside soil of Baiyangdian

A novel actinomycete, strain HBU206404^T, belonging to the genus Actinokineospora, was isolated from the lakeside soil of Baiyangdian, in China. Cells grew at 9-37 °C (optimum temperature, 28 °C) and pH 6-9 (optimum, pH 7). Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan, and sugars present in whole-cell hydrolysates were arabinose, mannose, glucose and galactose. The predominant menaquinone was MK-9(H₄). The predominant cellular fatty acids (> 5%) of the strain HBU206404^T were iso-C_16:0 (21.5%), iso-C_15:0 (20.3%), C_16:1ω7c/C_16:1ω6c and/or C_16:1ω6c/C_16:1ω7c (15.0%), iso-C_17:0 (8.6%), C_16:0 (7.0%) and C_17:1ω8c (6.9%). The major polar lipids of the strain HBU206404^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, six unknown aminolipids, two unknown aminolipids and an unidentified lipid. The 16S rRNA gene sequence analysis indicated that the strain HBU206404^T was most closely related to Actinokineospora alba KCTC 19294^T (99.58%), but whole-genome comparisons, using average nucleotide identity (ANI) value (91.77%) and digital DNA-DNA hybridization (dDDH) value (60%), confirmed low genome relatedness. Nitrogen metabolism pathway was found in the genome of strain HBU206404^T which haboured nitrate reductase and nitrite reductase. Other phenotypic characteristics, such as ability to hydrolyze substances, enzyme activity, acid production from carbon source, etc., could also distinguish strain HBU206404^T from Actinokineospora alba KCTC 19294^T. On the basis of genetic and phenotypic evidence, strain HBU206404^T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora xionganensis sp. nov. is proposed. The type strain is HBU206404^T (= MCCC 1K04412^T = KCTC 49404^T).

Roseomonas harenae sp. nov., from desert gravel soil

A Gram-stain-negative, aerobic, non-motile, pink-pigmented, coccus bacterium, designated CPCC 101081^T, was isolated from a gravel soil sample collected from Badain Jara desert, PR China. Growth of the isolate occurred at 10-37 °C and pH 5.0-8.0, with optimal growth at 28-32 °C and pH 7.0, respectively. The major cellular fatty acids were summed feature 8 (C_18:1ω7c/C _18:1ω6c), summed feature 3 (C _16:1ω6c/C_16:1ω7c) and C_18:12-OH. Q-10 was detected as the main respiratory quinone. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an amino-containing lipid and an unidentified glycophospholipid were examined in the polar lipids extraction. The 16S rRNA gene sequence comparison of strain CPCC 101081^T with the available sequences in the GenBank database showed that the isolate was closely related to members of the genus Rosenomonas, with the highest similarity to Roseomonas rosea DSM 14916^T (97.4 %). In the phylogenetic trees based on 16S rRNA gene sequences and the core genomes, strain CPCC 101081^T was included within the clade of the genus Roseomonas, representing a species level, with the closest neighbor of R. rosea DSM 14916^T . The genomic DNA G+C content was 68.7 mol%. The average nucleotide identity and the digital DNA-DNA hybridization values between strain CPCC 101081^T and the related type strains of the genus Roseomonas were all far lower than the cut-off values for definition species. On the basis of above phenotypic and genotypic characteristics, strain CPCC 101081^T is proposed to represent a novel species of the genus Roseomonas with the name Roseomonas harenae sp. nov. strain CPCC 101081^T (=KCTC 62852^T=NBRC 113512^T) is the type strain of the species.

Saccharopolyspora coralli sp. nov. a novel actinobacterium isolated from the stony coral Porites

A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain E2A^T, was isolated from a coral sample and examined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain E2A^T formed a distinct phyletic lineage in the genus Saccharopolyspora and was closely related to S. cavernae CCTCC AA 2012022^T (96.4 %) and S. lacisalsi CCTCC AA 2010012^T (95.3 %). The isolate grew at 15-35 °C, pH 5-12 and in the presence of 1-16 % (w/v) NaCl. The cell-wall diamino acid was meso-DAP. Major fatty acids identified were iso-C_15 : 0, iso-C_16 : 0 and C_17 : 1  ω8c. The predominant menaquinone was MK-9(H₄). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unidentified aminolipid. The genomic DNA G+C content was 68.6 mol%. Based on the data from the polyphasic taxonomic study reported here, strain E2A^T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora coralli sp. nov. is proposed. The type strain is E2A^T=(JCM 31844^T=MCCC 1A17150^T).

Roseomonas vastitatis sp. nov. isolated from Badain Jaran desert in China

A Gram-stain-negative, non-motile, coccobacillus-shaped bacterium, designated CPCC 101021^T, was isolated from a sandy soil sample collected from Badain Jaran desert, China. Its 16S rRNA gene sequence was closely related to those of members of the genus Roseomonas, showing high similarities with Roseomonas hibiscisoli THG-N2.22^T (98.0 %), Roseomonas oryzae KCTC 42542^T (97.9 %), Roseomonas rhizosphaerae YW11^T (97.9 %) and Roseomonas suffusca S1^T (97.8 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 101021^T formed a distinct subclade with R. oryzae KCTC 42542^T within the genus Roseomonas. Growth of the isolate occurred at 15-37 °C and pH 6.0-8.5, with optimal growth at 30 °C and pH 7.0. The major cellular fatty acids were C_18 : 1ω7c, summed feature 8 (C_16 : 1ω7c/C_16 : 1ω6c), summed feature 3 (C_16 : 1ω6c/C_16 : 1ω7c) and C_16 : 0ω6c. Q-10 was detected as the main component in the respiratory quinone system, with Q-9 as a minor component. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid were found in the polar lipid profile. The genomic DNA G+C content was 68.7 mol%. The average nucleotide identity was 84.6 % when comparing the draft genome sequences of strain CPCC 101021^T with R. oryzae KCTC 42542^T. On the basis of genotypic, chemotaxonomic and phenotypic characteristics, strain CPCC 101021^T is proposed to represent a novel species of the genus Roseomonas with the name Roseomonas vastitatis sp. nov. Strain CPCC 101021^T (=J1A743^T=KCTC 62043^T) is the type strain of the species.

Desertihabitans aurantiacus gen. nov., sp. nov., a novel member of the family Propionibacteriaceae

The taxonomic position of an actinobacterium isolated from a desert soil sample collected from Badain Jaran Desert, designated as CPCC 204711^T, was established using a polyphasic approach. Cells of the isolate were Gram-staining-positive, aerobic, non-motile cocci. Good growth was observed at 28 °C (range 20-40 °C), pH 7.0 (range pH 6.0-8.0) and 0-1 % NaCl concentration (range 0-5 %, w/v). Galactose, arabinose and ribose were detected as the sugar compositions in the whole cell hydrolysates. The peptidoglycan type was A3gamma (ll-Dpm-Gly). MK-9(H4) was detected as the predominant menaquinone, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, several unidentified glycolipids, and one unidentified amino-glycolipid were detected as the major polar lipids. The predominant fatty acid was anteiso-C15 : 0. The genomic DNA G+C content was 73.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204711^T affiliated to the family Propionibacteriaceae, in which the strain formed a distinct phylogenetic lineage next to the genus Mariniluteicoccus, with the highest 16S rRNA gene sequence similarity of 96.0 % to Mariniluteicoccus endophyticus YIM 2617^T. Both phylogenetic analysis and phenotypic characteristics supported that strain CPCC 204711^T represents a novel species of a new genus in the family Propionibacteriaceae, for which the name Desertihabitans aurantiacus gen. nov., sp. nov. is proposed, with CPCC 204711^T (=KCTC 39977^T=DSM 105431^T) as the type strain.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla

A Gram-positive bacterium originating from the surface-sterilized leaf of Paris polyphylla var. yunnanensis (Franch.) was characterized by using a polyphasic approach. The isolate formed yellow, smooth, circular colonies on nutrient agar with 0.2 % starch (NSA). Cells were non-motile, non-sporulating, irregular rods or cocci. Strain CPCC 203535^T had the highest 16S rRNA gene sequence similarity to the type strain of Ornithinimicrobium kibberense (96.9 %) and formed the deepest branch in the genus Ornithinimicrobium in the neighbour-joining (NJ) phylogenetic tree based on 16S rRNA gene sequences. The major menaquinones of strain CPCC 203535^T were MK-8(H4), MK-8(H2) and MK-8. The peptidoglycan contained ornithine as the diagnostic diamino acid. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI) and unknown lipid (UL). The major fatty acids iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 were consistent with the fatty acid patterns reported for members of the genus Ornithinimicrobium. The DNA G+C composition is 71.4 mol%. The results of physiological and biochemical tests allowed phenotypic differentiation of strain CPCC 203535^T from its closest phylogenetic species in the genus Ornithinimicrobium. Strain CPCC 203535^T represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium flavum sp. nov. is proposed, with CPCC 203535^T (=NBRC 109452 ^T=KCTC 29164^T) as the type strain.

Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.)

A Gram-stain-positive, non-spore-forming actinobacterial strain, designated CPCC 204077^T, was isolated from the surface-sterilized root of a medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The peptidoglycan type of strain CPCC 204077^T was detected as A4α with an l-Lys-l-Ser-d-Asp interpeptide bridge. Galactose, glucose, rhamnose and ribose were the sugar compositions in the whole-cell hydrolysates. MK-8(H4) was the only menaquinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phospholipid and one unidentified glycolipid. The major fatty acid was iso-C16 : 0. The genomic DNA G+C content was 71.0 mol%. The phylogenetic tree based on 16S rRNA gene sequences showed that strain CPCC 204077^T stood for a distinct lineage within the family Dermacoccaceaealongside the genera Branchiibius, Demetria and Barrientosiimonas, with the highest 16S rRNA gene sequence similarities to Branchiibius hedensis Mer 29717^T (95.0 %), Calidifontibacter indicus PC IW02^T (95.0 %), Barrientosiimonas humi 39^T (94.9 %) and Demetria terragena HKI 0089^T (94.7 %), and less than 94.7 % sequence similarities to all other species. Signature nucleotides in the 16S rRNA sequence showed that the strain contained the Dermacoccaceaefamily-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. Combining the genotypic and phenotypic analyses, we propose that strain CPCC 204077^T represents a novel species of a new genus in the family Dermacoccaceae with the name Allobranchiibius huperziae gen. nov., sp. nov. Strain CPCC 204077^T (=NBRC 110719^T=DSM 29531^T) is the type strain of the type species.

Saccharopolyspora spongiae sp. nov., a novel actinomycete isolated from the marine sponge Scopalina ruetzleri (Wiedenmayer, 1977)

A novel marine actinomycete, designated strain CMAA 1452T, was isolated from the sponge Scopalina ruetzleri collected from Saint Peter and Saint Paul Archipelago, in Brazil, and subjected to a polyphasic taxonomic investigation. The organism formed a distinct phyletic line in the Saccharopolyspora 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Saccharopolyspora dendranthemae KLBMP 1305T (99.5% 16S rRNA gene sequence similarity) and shared similarities of 99.3, 99.2 and 99.0 % with 'Saccharopolyspora endophytica' YIM 61095, Saccharopolyspora tripterygii YIM 65359T and 'Saccharopolyspora pathumthaniensis' S582, respectively. DNA-DNA relatedness values between the isolate and its closest phylogenetic neighbours, namely S. dendranthemae KLBMP 1305T, 'S. endophytica' YIM 61095 and S. tripterygii YIM 65359T, were 53.5, 25.8 and 53.2 %, respectively. Strain CMAA 1452T was also distinguished from the type strains of these species using a range of phenotypic features. On the basis of these results, it is proposed that strain CMAA 1452T (=DSM 103218T=NRRL B-65384T) merits recognition as the type strain of a novel Saccharopolyspora species, Saccharopolyspora spongiae sp. nov.

Actinophytocola xanthii sp. nov., an actinomycete isolated from rhizosphere soil of the plant Xanthium sibiricum

A novel actinomycete strain, 11-183T, was isolated from the rhizosphere soil of Xanthium sibiricum, which was collected in Tangshan, Hebei, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain 11-183T formed a clade within the genus Actinophytocola, with a maximum similarity of 98.44 % to Actinophytocola xinjiangensis QAIII60T, followed by 97.76 % similarity to Actinophytocola sediminis YIM M13705T. The average nucleotide identity and digital DNA-DNA hybridization values differed by 79.24 and 23.4 %, respectively, between strain 11-183T and Actinophytocolaxinjiangensis QAIII60T. Strain 11-183T grew well on N-Z-amine agar, and it produced a scant, white aerial mycelium. The isolate formed pale yellow to brown-black colonies and a dense, non-fragmented, branched substrate mycelium, and produced aerial hyphae on which nodular spore chains formed. Growth was observed at salinities ranging from 0 to 2 %, at pH values ranging from pH 6.5 to 8.0 and at temperatures ranging from 15 to 37 °C. The cell-wall amino acids included meso-diaminopimelic acid. Whole cell hydrolysates contained galactose and glucose. The principal fatty acids were iso-C16 : 0, iso-C16 : 1 H and C17 : 1ω6c. Diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine were the diagnostic phospholipids. The isoprenoid quinones included MK-9(H4) and MK-10(H4). The G+C content of the genomic DNA was 71.7 mol%. Based on the genotypic and phenotypic data, we conclude that strain 11-183T belongs to a novel species of the genus Actinophytocola. The name proposed for the novel species is Actinophytocola xanthii sp. nov., with the type strain 11-183T (=KCTC 39690T= MCCC 1K02062T).

Paenibacillus eucommiae sp. nov., isolated from a traditional Chinese medicinal herbal plant, Eucommia ulmoides Oliver

The taxonomic status of a novel bacterium, designated strain CPCC 100226T, isolated from a traditional Chinese medicinal herbal plant, Eucommia ulmoides Oliver, was characterized by using a polyphasic approach. The aerobic isolate formed pale white colonies on tryptic soy agar. Cells were Gram-stain-positive, rod-shaped, motile and endospore-forming. Chemotaxonomic investigations revealed the presence of meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant menaquinone, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids, and the strain had a phospholipid pattern of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and unidentified aminophospholipids. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus aestuarii DSM 23861T with 95.1 % similarity. The G+C content of the genomic DNA was 47.9 mol%. On the basis of the genotypic and phenotypic data, the isolate is considered to represent a novel species of the genus Paenibacillus. The name proposed for this taxon is Paenibacillus eucommiae sp. nov. with CPCC 100226T (=DSM 26048T=KCTC 33054T) as the type strain.

Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard)

The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, C16 : 1ω9c, iso-C16 : 1 and C16 : 0. The genomic DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204279T should be placed in the family Pseudonocardiaceae, in which the strain formed a distinct lineage next to the genus Actinophytocola. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained the Pseudonocardiaceae family-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis and phenotypic characteristics supported the conclusion that strain CPCC 204279T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Herbihabitans rhizosphaerae gen. nov., sp. nov. is proposed. Strain CPCC 204279T (=NBRC 111774T=DSM 101727T) is the type strain of the type species.

Actinorectispora indica gen. nov., sp. nov. isolated from soil, a member of the family Pseudonocardiaceae

The taxonomic positions of three Gram-stain-positive, aerobic strains, designated YIM 75722, 75726 and 75728^T, and isolated from a soil sample collected from Kurnool of Andhra Pradesh province, India, were assessed using a polyphasic approach. Growth was observed at pH 7.0-10.0 (optimum pH 7.0), 15-28 °C (optimum 28 °C) and 0-8 % (w/v) NaCl (grew without NaCl). Strains showed cylindrical spores with straight-chain morphology on aerial mycelium, but did not reveal sporangium-like structures or fragmentation of the substrate mycelium. Whole-cell hydrolysates of all strains contained galactose and ribose as the diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H₄); MK-9 (H₆) and MK-10 (H₄) were present in smaller amounts. The phospholipid pattern consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were i-C_15 : 0, ai-C_15 : 0, i-C_17 : 0 and ai-C_17 : 0. The genomic DNA G+C content was 68.0 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain YIM 75728^T should be placed within the family Pseudonocardiaceae, in which the strain formed a distinct lineage. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data support the conclusion that strain YIM 75728^T represents a novel species of a novel genus of the family Pseudonocardiaceae for which the name Actinorectispora indica gen. nov., sp. nov., is proposed. Strain YIM 75728^T ( = DSM 45410^T = CCTCC AA 209065^T) is the type strain of Actinorectispora indica. Strain YIM 75728^T was considered as the type strain over the other two strains based on the highest sequence read length of the strain.

Saccharopolyspora halotolerans sp. nov., a halophilic actinomycete isolated from a hypersaline lake

A novel actinomycete strain, designated TRM 45123T, was isolated from a hypersaline habitat in Xinjiang Province (40° 20′ N 90° 49′ E), north-west China. The isolate was characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain TRM 45123T belonged to the genus Saccharopolyspora and was closely related to Saccharopolyspora gloriosae (96.7 % similarity). The G+C content of the DNA was 69.07 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and anteiso-C15 : 0. On the basis of the evidence from this polyphasic study, a novel species, Saccharopolyspora halotolerans sp. nov., is proposed. The type strain of Saccharopolyspora halotolerans is TRM 45123T ( = CCTCC AA 2013006T = DSM 45990T).

Actinophytocola gilvus sp. nov., isolated from desert soil crusts, and emended description of the genus Actinophytocola Indananda et al. 2010

An actinomycete strain, designated I12A-02593(T), was isolated from a desert soil crust sample collected in the Shapotou region of Tengger Desert, north-west China. The isolate grew well on International Streptomyces Project (ISP) media 2, 3, 5 and 7, YS and Bennett's agar; it produced spherical bodies and formed clumps on the aerial mycelia on ISP 5 agar plates. Chemotaxonomically, the strain contained meso-diaminopimelic acid as the diagnostic diamino acid, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, MK-9(H4) as the sole isoprenoid quinone, and iso-C16 : 0, iso-C16 : 0 2-OH and iso-C16 : 1 H as the major cellular fatty acids, without mycolic acids. The profile of the phospholipids mainly comprised diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The genomic DNA G+C content was 70.1 mol%. The 16S rRNA gene sequence of strain I12A-02593(T) exhibited 96.4-97.4 % similarities with members of the genus Actinophytocola. In the phylogenetic tree based on 16S rRNA gene sequences, the isolate formed a robust cluster with Actinophytocola oryzae NBRC 105245(T), Aactinophytocola timorensis NBRC 105524(T), Actinophytocola corallina NBRC 105525(T), Actinophytocola burenkhanensis NBRC 105883(T)and Actinophytocola xinjiangensis NBRC 106673(T). DNA-DNA hybridization values between strain I12A-02593(T) and the five species of the genus Actinophytocola were all less than 70 %. On the basis of the polyphasic taxonomy evidence, a novel species of the genus Actinophytocola is proposed, with the name Actinophytocola gilvus sp. nov. The type strain is I12A-02593(T) ( = CPCC 203543(T) = DSM 45828(T) = NBRC 109453(T) = KCTC 29165(T)). An emended description of the genus Actinophytocola is also provided.

Saccharopolyspora indica sp. nov., an actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis)

A novel actinomycete strain, designated VRC122T, was isolated from a Callistemon citrinus rhizosphere sample collected from New Delhi, India, and its taxonomic status was determined by using a polyphasic approach. Strain VRC122T was a Gram-stain-positive, aerobic, non-motile, non-acid–alcohol-fast strain. Phylogenetic analysis based on 16S rRNA gene sequences showed the strain was placed in a well-separated sub-branch within the genus Saccharopolyspora . The highest levels of 16S rRNA gene sequence similarity were found with Saccharopolyspora hirsuta subsp. kobensis JCM 9109T (98.71 %), Saccharopolyspora antimicrobica I05-00074T (98.69 %) and Saccharopolyspora jiangxiensis W12T (98.66 %); 16S rRNA gene sequence similarities with type strains of all other species of the genus Saccharopolyspora were below 98 %. Chemosystematic studies revealed that it contained meso-diaminopimelic acid. Arabinose and galactose were the predominant whole-cell sugars. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine. MK-9(H6) was the predominant menaquinone. C14 : 0, C16 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C15 : 0, anteiso-C17 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major cellular fatty acids. The G+C content of the genomic DNA was 69.5 mol%. The results of DNA–DNA hybridization (30 %, 22 % and 25 %, respectively) with type strains of the above-mentioned species, in combination with differences in physiological and biochemical data supported that strain VRC122T represents a novel species of the genus Saccharopolyspora , for which the name Saccharopolyspora indica sp. nov., is proposed. The type strain is VRC122T ( = KCTC 29208T = MTCC 11564T = MCC 2206T = ATCC BAA-2551T).

Roseivivax roseus sp. nov., an alphaproteobacterium isolated from a solar saltern soil sample

A pink, Gram-stain-negative, motile, halotolerant bacterium with subpolar flagellum, designated strain BH87090T, was isolated from a saline soil sample collected from the south-west coastal area of South Korea (125° 58′ 58.08″ E 34° 45′ 37.32″ N). The isolate formed opaque pink to red colonies on marine agar plates at 30 °C. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sulfoquinovosyl diacylglycerol, phosphatidylcholine and one unidentified phospholipid. The sole respiratory quinone was ubiquinone-10 (Q-10). The major cellular fatty acids were C18 : 1ω7c, C19 : 0 cyclo ω8c, C16 : 0 and 11-methyl C18 : 1ω7c. The genomic DNA G+C content was 61.8 mol%. These chemotaxonomic characteristics were all consistent with specific properties of the genus Roseivivax . Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate affiliated to the cluster with members of the genus Roseivivax in the Roseobacter clade, which suggested that the strain belonged to the genus Roseivivax . However, the low 16S rRNA gene similarities (93.5–95.3 %) of strain BH87090T with all the members of the genus Roseivivax indicated that it represented a novel species of the genus Roseivivax . On the basis of phenotypic and genotypic data, strain BH87090T should be classified as a novel species of the genus Roseivivax . The name Roseivivax roseus sp. nov. is proposed, with strain BH87090T ( = DSM 23042T = KCTC 22650T) as the type strain.

Paratrechina longicornis ants in a tropical dry forest harbor specific Actinobacteria diversity

The diversity of Actinobacteria associated with Paratrechina longicornis, an ant species that prefers a high protein diet, in a subtropical dry forest (Guánica, Puerto Rico) was determined by culture methods and by 16S rDNA clone libraries. The results of both methodologies were integrated to obtain a broader view of the diversity. Streptomyces, Actinomadura, Nocardia, Ornithinimicrobium, Tsukamurella, Brevibacterium, Saccharopolyspora, Nocardioides, Microbacterium, Leifsonia, Pseudonocardia, Corynebacterium, Geodermatophilus, Amycolatopsis, and Nonomuraea were found associated with the ants. The genera Streptomyces and Actinomadura were the most abundant. Also, the diversity of Actinobacteria associated with the soil surrounding the nest was determined using 16S rDNA clone libraries. In total, 27 genera of Actinobacteria were associated with the nest soils. A dominant genus was not observed in any of the soil samples. We compared statistically the Actinobacteria communities among P. longicornis nests and each nest with its surrounding soil using the clone libraries data. We established that the communities associated with the ants were consistent and significantly different from those found in the soil in which the ants live.

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant

Two actinobacterial strains, CPCC 203464(T) and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464(T) and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia. Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464(T) and CPCC 203448 to the genus Williamsia. The DNA-DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia. The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464(T) ( = DSM 45741(T) = KCTC 29118(T)) as the type strain.

Themoanaerobacterium calidifontis sp. nov., a novel anaerobic, thermophilic, ethanol-producing bacterium from hot springs in China

A novel thermophilic Gram staining positive strain Rx1 was isolated from hot springs in Baoshan of Yunnan Province, China. The strain was characterized as a hemicellulose-decomposing obligate anaerobe bacterium that is rod-shaped (diameter: 0.5–0.7 μm; length: 2.0–6.7 μm), spore-forming, and motile. Its growth temperature range is 38–68 °C (optimum 50–55 °C) and pH range is 4.5–8.0 (optimum 7.0). The maximum tolerance concentration of NaCl was 3 %. Rx1 converted thiosulfate to elemental sulfur and reduced sulfite to hydrogen sulfide. The bacterium grew by utilizing xylan and starch, as well as a wide range of monosaccharide and polysaccharides, including glucose and xylose. The main products of fermentation were ethanol, lactate, acetate, CO₂, and H₂. The maximum xylanase activity in the culture supernatant after 30 h of incubation at 55 °C was 16.2 U/ml. Rx1 DNA G + C content was 36 mol %. 16S rRNA gene sequence analysis indicated that strain Rx1 belonged to the genus Thermoanaerobacterium of the family ‘Thermoanaerobacteriaceae’ (Firmicutes), with Thermoanaerobacterium aciditolerans 761–119 (99.2 % 16S rRNA gene sequence similarity) being its closest relative. DNA–DNA hybridization between Rx1 and T. aciditolerans 761–119 showed 36 % relatedness. Based on its physiological and biochemical tests and DNA–DNA hybridization analyses, the isolate is considered to represent a novel species in the genus Thermoanaerobacterium, for which the name Thermoanaerobacterium calidifontis sp. nov. is proposed, with the type strain is Rx1 (=JCM 18270 = CCTCC M 2011109).

Allonocardiopsis opalescens gen. nov., sp. nov., a new member of the suborder Streptosporangineae , from the surface-sterilized fruit of a medicinal plant

An endophytic actinomycete, designated strain I10A-01259T, was isolated from a surface-sterilized fruit of Lonicera maackii (Rupr.) Maxim., a medicinal plant, which was collected from a suburb of Beijing, China. Whole-cell hydrolysates of the isolate contained galactose and meso-diaminopimelic acid. The predominant phospholipids were phosphatidylglycerol and diphosphatidylglycerol; the menaquinones consisted mainly of MK-9, MK-11 and MK-12, with a minor amount of MK-10. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Comparative analysis of 16S rRNA gene sequences indicated that strain I10A-01259T was most closely related to Nocardiopsis arabia S186T (93.2 % sequence similarity), Thermobifida halotolerans YIM 90462T (93.0 %) and other strains of genera within the families Nocardiopsaceae and Thermomonosporaceae . On the phylogenetic tree based on 16S rRNA gene sequences, strain I10A-01259T fell within the radius of the suborder Streptosporangineae , in which the strain formed a distinct lineage next to the genera of the families Nocardiopsaceae and Thermomonosporaceae . Based on the data from our polyphasic taxonomic study, a novel genus and species, Allonocardiopsis opalescens gen. nov., sp. nov., are proposed within the suborder Streptosporangineae . The type strain of Allonocardiopsis opalescens is strain I10A-01259T ( = CPCC 203428T  = DSM 45601T  = KCTC 19844T).

Cultivation-independent methods applied to the microbial prospection of oil and gas in soil from a sedimentary basin in Brazil

The upper parts of oil field structures may leak gas which is supposed to be indirectly detected by the soil bacterial populations. Such microorganisms are capable of consuming this gas, supporting the Microbial Prospection of Oil and Gas (MPOG) methodology. The goal of the present work was to characterize microbial communities involved in short-chain alkane metabolism, namely methane, ethane and propane, in samples from a petroliferous (P) soil through clone libraries of the 16S rRNA gene of the Domains Bacteria and Archaea and the catabolic gene coding for the soluble di-iron monooxygenase (SDIMO) enzyme alpha subunit. The microbial community presented high abundance of the bacterial phylum Actinobacteria, which represented 53% of total clones, and the Crenarchaeota group I.1b from the Archaea Domain. The analysis of the catabolic genes revealed the occurrence of seven Operational Protein Families (OPF) and higher richness (Chao = 7; Ace = 7.5) and diversity (Shannon = 1.09) in P soil when compared with a non-petroliferous (Np) soil (Chao = 2; Ace = 0, Shannon = 0.44). Clones related to the ethene monooxygenase (EtnC) and methane monooxygenase (MmoX) coding genes occurred only in P soil, which also presented higher levels of methane and lower levels of ethane and propane, revealed by short-chain hydrocarbon measures. Real-time PCR results suggested that the SDIMO genes occur in very low abundance in the soil samples under study. Further investigations on SDIMOs genes in natural environments are necessary to unravel their still uncharted diversity and to provide reliable tools for the prospection of degrading populations.

Saccharopolyspora pathumthaniensis sp. nov., a novel actinomycetes isolated from termite guts (Speculitermes sp.)

Morphological and chemotaxonomic characterization of actinomycete strain S582 isolated from the gut of a termite (Speculitermes sp.) in Pathum Thani Province, Thailand, clearly demonstrated that this strain is a member of the genus Saccharopolyspora. 16S rDNA sequence analysis for the strain supported the assignment of the strain to the genus Saccharopolyspora. The similarity value of sequences between this strain and the closely related species Saccharopolyspora endophytica was 99.5%. The DNA G+C content was 70.2 mol%. DNA-DNA hybridization results (53.3%) and some physiological and biochemical properties indicated that strain S582(T) was distinguished from the phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain S582(T) should be a new species in the genus Saccharopolyspora and the name Saccharopolyspora pathumthaniensis sp. nov. is proposed for the strain. The type strain is S582(T) (=NBRC 104112(T) =BCC 28624(T)).

Sinosporangium album gen. nov., sp. nov., a new member of the suborder Streptosporangineae

A Gram-positive, aerobic, non-motile actinobacterium, designated strain 6014T, was isolated from a soil sample collected from Qinghai province, north-west China, and subjected to a polyphasic taxonomic study. The isolate formed elementary branching hyphae and abundant aerial mycelia with globose sporangia on ISP 4 and R2A media. Whole-cell hydrolysates of strain 6014T contained arabinose, galactose and ribose as diagnostic sugars and meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipids consisted of phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, N-acetylglucosamine-containing phospholipids, two unknown phospholipids and an unknown glycolipid. The menaquinone system contained MK-9(H2) and MK-9(H4). The major fatty acids were C14 : 0, i-C15 : 0, C16 : 0 and 10-methyl-C16 : 1. The genomic DNA G+C content of the isolate was 69.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6014T fell within the radius of the suborder Streptosporangineae, in which the strain formed a distinct lineage next to genera of the family Streptosporangiaceae. Based on data from this polyphasic study, strain 6014T can be readily distinguished from previously described organisms and represents a member of a novel species within a new genus in the suborder Streptosporangineae. The name Sinosporangium album gen. nov., sp. nov. is proposed with 6014T (=DSM 45181T =KCTC 19655T) as the type strain.

Amycolatopsis xylanica sp. nov., isolated from soil

An actinomycete, designated CPCC 202699T, was isolated from soil in Qinghai province, China, and its taxonomic status was established. Strain CPCC 202699Tcontainedmeso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, a phospholipid pattern consisting mainly of phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine, MK-9(H4) as the predominant menaquinone and iso-C16 : 0(18.8 %), iso-C15 : 0(18.1 %), iso-C14 : 0(14.2 %), C16 : 1cis9 (10.9 %) and C17 : 1cis9 (10.3 %) as the major fatty acids. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 202699Tformed a separate branch within the genusAmycolatopsis. However, strain CPCC 202699Tshowed low 16S rRNA gene sequence similarities (<97.0 %) with type strains of species with validly published names in the genusAmycolatopsis. On the basis of genotypic and phenotypic differences from the closest phylogenetic neighbours of strain CPCC 202699T, a novel species,Amycolatopsis xylanicasp. nov., is proposed. The type strain is CPCC 202699T(=DSM 45285T=KCTC 19581T=CCM 7627T).

Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9 %) and Saccharopolyspora spinosa DSM 44228T (98.5 %). However, these strains shared low levels of DNA–DNA relatedness (<26 %). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16 : 0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).

Saccharopolyspora gloriosae sp. nov., an endophytic actinomycete isolated from the stem of Gloriosa superba L

A Gram-stain-positive, aerobic actinomycete, strain YIM 60513T, was isolated from the stem of Gloriosa superba L. collected from tropical rainforest at Xishuangbanna, Yunnan Province, south-west China. 16S rRNA gene sequence analysis indicated that strain YIM 60513T belonged to the genus Saccharopolyspora and was closely related to Saccharopolyspora gregorii NCIB 12823T (99.1 % similarity) and Saccharopolyspora cebuensis SPE 10-1T (97.3 % similarity). Data for the predominant quinone [MK-9(H4)], major fatty acids (iso-C16 : 0, anteiso-C17 : 0 and C17 : 1 cis9) and G+C content of the genomic DNA (71.6 mol%) were similar to those for members of the genus Saccharopolyspora. The level of DNA–DNA relatedness between strain YIM 60513T and S. gregorii NCIB 12823T was 43 %. The combination of phylogenetic analysis, phenotypic differences, chemotaxonomic characteristics and DNA–DNA hybridization data supported the view that strain YIM 60513T should be distinguished from S. gregorii NCIB 12823T and S. cebuensis SPE 10-1T. Strain YIM 60513T therefore represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora gloriosae sp. nov. is proposed. The type strain is YIM 60513T (=KCTC 19243T =CCTCC AA 207006T).

Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant

A novel actinobacterial strain, designated CPCC 201356(T), was isolated from a rhizosphere soil sample of the medicinal plant Astragalus membranaceus and subjected to a polyphasic taxonomic analysis. Good growth occurred at 20-32 °C, at pH 7.0-7.5 and with 0-1 % (w/v) NaCl. Colonies on R2A and ISP 2 agar were light red to red, round and lacked aerial mycelium; cells adhered to the agar. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H(4)) and MK-9. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids were iso-C(16 : 0), iso-C(15 : 0) and C(17 : 1)ω8c. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CPCC 201356(T) belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch with Geodermatophilus obscurus DSM 43160(T). The organism showed 16S rRNA gene sequence similarity of 97.7 % with G. obscurus DSM 43160(T). DNA-DNA hybridization between strain CPCC 201356(T) and G. obscurus DSM 43160(T) was 17.4 %. On the basis of evidence from this polyphasic taxonomic study, a novel species, Geodermatophilus ruber sp. nov., is proposed; the type strain is CPCC 201356(T) (=DSM 45317(T) =CCM 7619(T)).

Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil

The taxonomic position of a Gram-stain-positive, aerobic strain, designated 03-9939(T), isolated from a soil sample collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain 03-9939(T) contained galactose and ribose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were iso-C(16 : 0) (61.5 %) and iso-C(16 : 1) H (11.6 %). The genomic DNA G+C content was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 03-9939(T) should be placed within the family Actinosynnemataceae, in which the strain formed a distinct lineage. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data supported the conclusion that strain 03-9939(T) represents a novel species in a new genus of the family Actinosynnemataceae, for which the name Alloactinosynnema album gen. nov., sp. nov. is proposed. Strain 03-9939(T) (=DSM 45114(T) =KCTC 19294(T) =CCM 7461(T)) is the type strain of Alloactinosynnema album.

Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma

The taxonomic status of a bacterium isolated from a patient with bronchial carcinoma was established using a polyphasic taxonomic approach. The strain had morphological and chemotaxonomic characteristics consistent with those of members of the genus Saccharopolyspora. The generic assignment was confirmed by comparative analysis of the 16S rRNA gene sequence, which showed that the strain constituted a distinct phyletic line, displaying 93.5-96.9 % sequence similarity with respect to members of the genus Saccharopolyspora. The isolate was distinguished from the type strains of recognized members of the genus Saccharopolyspora by means of various biochemical tests. The genotypic and phenotypic data obtained demonstrated that strain IMMIB L-1070(T) represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora rosea sp. nov. is proposed. The type strain is IMMIB L-1070(T) (=DSM 45226(T)=CCUG 56401(T)).