Paenibacillus swuensis sp. nov., a bacterium isolated from soil

Strain DY6^T, a Gram-positive endospore-forming motile rod-shaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6^T revealed that strain DY6^T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6^T were found with Paenibacillus gansuensis B518^T (97.9%), P. chitinolyticus IFO 15660^T (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173^T (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C_15:0 (38.7%) and C_16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6^T (=KCTC 33026^T =JCM 18491^T) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.     

Paenibacillus marinisediminis sp. nov., a bacterium isolated from marine sediment

A Gram-negative, nonmotile, endospore-forming, rod-shaped bacterial strain LHW35^T, which belonged to the genus Paenibacillus, was isolated from marine sediment collected from the south coast of the Republic of Korea. A phylogenetic analysis of 16S rRNA gene sequences indicated that strain LHW35^T was most closely related to Paenibacillus taiwanensis G-soil-2-3^T (97.2% similarity). The optimal growth conditions for strain LHW35^T were 37°C, pH 6.0, and 0% (w/v) NaCl. The main isoprenoid quinone was menaquinone-7 (MK-7) and the major polyamine was spermidine. The diamino acid present in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acids were anteiso-C_15:0 and C_16:0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified amino-hospholipids, unidentified phospholipids, and unidentified polar lipids. A DNA-DNA hybridization experiment using the type strain of P. taiwanensis indicated <40% relatedness. The DNA G+C content was 45.0 mol%. Based on these phylogenetic, genomic, and phenotypic analyses, strain LHW35^T should be classified as a novel species within the genus Paenibacillus, for which the name Paenibacillus marinisediminis sp. nov. is proposed. The type strain is LHW35^T (=KACC 16317^T =JCM 17886^T).     

Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean

A Gram-positive, rod-shaped bacterium, designated strain SCSIO N0306^T, was isolated from an abyssal sediment sample collected from the Indian Ocean. The isolate was found to grow optimally at 0–2 % (w/v) NaCl, pH 7.0 and 30 °C. Comparative analysis of the 16S rRNA gene sequence showed that the isolate SCSIO N0306^T belongs phylogenetically to the genus Paenibacillus, and to be most closely related to P. algorifonticola XJ259^T (with 95.47 % sequence similarity), sharing less than 95.0 % sequence similarity with all other taxa of this genus. Chemotaxonomic analysis revealed MK-7 as the major isoprenoid quinone, the DNA G+C content was determined to be 45.5 mol%, and anteiso-C_15:0, C_16:0, and iso-C_15:0 were identified as the major fatty acids. On the basis of this polyphasic taxonomic data, isolate SCSIO N0306^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus abyssi sp. nov. is proposed. The type strain is SCSIO N0306^T (= DSM 26238^T = CGMCC 1.12987^T).     

Paenibacillus sinensis sp. nov., a nitrogen-fixing species isolated from plant rhizospheres

Two strains HN-1^T and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1^T and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472^T and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1^T with P. stellifer DSM 14472^T was 90.69, which was below the recommended threshold value (<?95–96% ANI). The dDDH showed 42.1% relatedness between strain HN-1^T and P. stellifer DSM 14472^T, which was lower than the recommended threshold value (dDDH?<?70%). The strain HN-1^T contain anteiso-C_15:0 as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472^T, strain HN-1^T or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1^T or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1^T (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively.

     

Paenibacillus hordei sp. nov., isolated from naked barley in Korea

A Gram-staining positive, facultative aerobic bacterium, designated strain RH-N24^T, was isolated from naked barley in South Korea. Cells of the isolate were observed to be motile rods by means of peritrichous flagella and showed catalase-positive and oxidase-negative reactions. Growth of strain RH-N24^T was observed at 4–40 °C (optimum: 35–37 °C) and at pH 5.0–9.0 (optimum: pH 6.0–7.0). Chemotaxonomic data (major isoprenoid quinone: MK-7; DNA G + C content: 53.5 mol %; cell wall type: A1γ-meso-diaminopimelic acid; major fatty acids: anteiso-CB_15:0 and CB_16:0B) supported the affiliation of the isolate to the genus Paenibacillus. The major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences also supported the conclusion that strain RH-N24^T belonged to the genus Paenibacillus. Comparative 16S rRNA gene sequence analysis showed that strain RH-N24^T was most closely related to Paenibacillus hunanensis FeL05^T and Paenibacillus illinoisensis NRRL NRS-1356^T with similarities of 94.64 and 94.54 %, respectively. On the basis of phenotypic and molecular properties, strain RH-N24^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus hordei sp. nov. is proposed. The type strain is RH-N24^T (=KACC 15511^T = JCM 17570^T).     

Arthrobacter enclensis sp. nov., isolated from sediment sample

A novel bacterial strain designated as NIO-1008^T was isolated from marine sediments sample in Chorao Island India. Cells of the strains were gram positive and non-motile, displayed a rod–coccus life cycle and formed cream to light grey colonies on nutrient agar. Strain NIO-1008^T had the chemotaxonomic markers that were consistent for classification in the genus Arthrobacter, i.e. MK-9(H₂) (50.3 %), as the major menaquinone, and the minor amount of MK-7 (H₂-27.5 %), MK-8 (H₄-11.6 %) and MK-8 (H₂-10.4 %). anteiso-C_15:0, iso-C_15:0, iso-C_16:0 and C_15:0 were the predominant fatty acids. Galactose, glucose and rhamnose are the cell-wall sugars, and DNA G+C content was 61.3 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains were most similar to Arthrobacter equi IMMIB L-1606^T, Arthrobacter chlorophenolicus DSM 12829^T, Arthrobacter defluvii KCTC 19209^T and Arthrobacter niigatensis CCTCC AB 206012^T with 98.5, 98.4, 98.0 and 97.8 %, respectively, and formed a separate lineage. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that strains NIO-1008^T represent a novel species within the genus Arthrobacter, for which the name Arthrobacter enclensis sp. nov., is proposed. The type strain is NIO-1008^T = (NCIM 5488^T = DSM 25279^T).     

Paenibacillus beijingensis sp. nov., a nitrogen-fixing species isolated from wheat rhizosphere soil

A novel nitrogen-fixing bacterium, BJ-18^T, was isolated from wheat rhizosphere soil. Strain BJ-18^T was observed to be Gram-positive, facultatively anaerobic, motile and rod-shaped (0.4–0.9 μm × 2.0–2.9 μm). Phylogenetic analysis based on a partial nifH gene sequence and an assay for nitrogenase activity showed its nitrogen-fixing capacity. Phylogenetic analysis based on full 16S rRNA gene sequences suggested that strain BJ-18^T is a member of the genus Paenibacillus. High similarity of 16S rRNA gene sequence was found between BJ-18^T and Paenibacillus peoriae DSM 8320^T (99.05 %), Paenibacillus jamilae DSM 13815^T (98.86 %), Paenibacillus brasiliensis DSM 13188^T (98.55 %), Paenibacillus polymyxa DSM 36^T (98.74 %), Paenibacillus terrae DSM 15891^T (97.99 %) and Paenibacillus kribbensis JCM 11465^T (97.92 %), whereas the similarity was below 96.0 % between BJ-18^T and the other Paenibacillus species. DNA–DNA relatedness between strain BJ-18^T and P. peoriae DSM 8320^T, P. jamilae DSM 13815^T, P. brasiliensis DSM 13188^T, P. polymyxa DSM 36^T, P. kribbensis JCM 11465^T and P. terrae DSM 15891^T was determined to be 43.6 ± 2.7, 34.2 ± 5.3, 47.9 ± 6.6, 36.8 ± 3.5, 27.4 ± 4.3 and 23.6 ± 4.1 % respectively. The DNA G+C content of BJ-18^T was determined to be 45.8 mol %. The major fatty acid was identified as anteiso-C_15:0 (67.1 %). The polar lipids present in strain BJ-18^T were identified as diphosphatidylglycerol, phosphatidyl methylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The phenotypic and genotypic characteristics, and DNA–DNA relatedness data, suggest that BJ-18^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus beijingensis sp. nov. (Type strain BJ-18^T=DSM25425^T=CGMCC 1.12045^T) is proposed.     

Bacillus enclensis sp. nov., isolated from sediment sample

A novel bacterial strain, designated SGD-1123^T was isolated from Chorao Island, in Goa Province, India. The strain was found to be able to grow at 15–42 °C, pH 5–12 and 0–12 % (w/v) NaCl. The whole cell hydrolysates were found to contain meso-diaminopimelic acid, galactose and arabinose. The major fatty acids were identified as iso-C_15:0 and anteiso-C_15:0, MK-7 was identified as the predominant menaquinone and the predominant polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. The genomic DNA G+C content was determined to be 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate within the genus Bacillus and further revealed that strain SGD-1123^T had highest sequence similarity with Bacillus aquimaris, and forms a separate clade with its closest relatives i.e. B. aquimaris, Bacillus vietnamensis and Bacillus marisflavi, with which it shares 94.5, 94.1 and 94.1 % similarity respectively. The phylogenetic, chemotaxonomic and phenotypic analyses indicated that strain SGD-1123^T represents a novel species within the genus Bacillus, for which the name Bacillus enclensis is proposed. The type strain is SGD-1123^T (NCIM 5450^T=CCTCC AB 2011125^T).     

Ruminococcus luti sp. nov., isolated from a human faecal sample

A strain of an unidentified strictly anoxic, gram-postive, non-motile Ruminococcus-like bacterium was isolated from a human faecal sample. The organism used carbohydrates as fermentable substrates, produced acetate, succinate, and hydrogen as the major products of glucose metabolism, and possessed a G + C content of 43.3 mol%. The morphological and biochemical characteristics of the organism were consistent with its assignment to the genus Ruminococcus but it did not correspond to any recognized species of this genus. Comparative 16S rRNA gene sequencing showed the unidentified bacterium represents a previously unrecognised sub-line within the Clostridium coccoides rRNA group of organisms. The nearest relative of the unknown bacterium corresponded to Ruminococcus obeum but a 16S rRNA sequence divergence value of >3% demonstrated it represents a different species. Based on the presented findings a new species, Ruminococcus luti, is described. The type strain of Ruminococcus luti is BInIX(T) (DSM 14534T, CCUG 45635T).     

Kocuria sediminis sp. nov., isolated from a marine sediment sample

A Gram-positive, pinkish-orange pigmented, coccoid strain, FCS-11^T was isolated from a marine sediment sample taken from Kochi fort area, Kerala, India and subjected to polyphasic taxonomic study. The 16S rRNA gene sequence of the strain was determined and the results of 16S rRNA gene sequence analysis showed that the strain FCS-11^T should be assigned to the genus Kocuria. The chemotaxonomic data supported this taxonomic placement i.e. menaquinones MK-7(H₂), MK-8(H₂) and MK-9(H₂); major fatty acids anteiso C15:0 and iso-C15:0 and phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG) as major polar lipids. Further phylogenetic analysis of the 16S rRNA gene sequence confirmed that the strain FCS-11^T belonged to the genus Kocuria and is closely related to Kocuria turfanensis MTCC 10790^T (99.4%) followed by Kocuria polaris MTCC 3702^T (98.2%), Kocuria rosea MTCC 2522^T (98.2%), Kocuria flava MTCC 10971^T (98.2%), Kocuria aegyptia MTCC 10791^T (98.0%), Kocuria himachalensis MTCC 7020^T (97.5%) and Kocuria atrinae MTCC 10972^T (97.1%). However, the DNA–DNA hybridisation values obtained between strain FCS-11^T and other related strains were well below the threshold that is required for the proposal of a novel species. The G+C content of the genomic DNA was 60.7 mol%. The phenotypic and genotypic data showed that the strain FCS-11^T merits the recognition as a representative of a novel species of the genus Kocuria. It is proposed that the isolate should be classified in the genus Kocuria as a novel species, Kocuria sediminis sp. nov. The type strain is FCS-11^T (= MTCC 10969^T = JCM 17929^T).     

Clostridium asparagiforme sp. nov., isolated from a human faecal sample

An obligatory anaerobic, Gram-positive, rod-shaped organism was isolated from faeces of a healthy human donor. It was characterized using biochemical, phenotypic and molecular taxonomic methods. The organism produced acetate, lactate, and ethanol as the major products of glucose fermentation. The G + C content was 53 mol%. Based on comparative 16S rRNA gene sequencing, the unidentified bacterium is a member of the Clostridium subphylum of the Gram-positive bacteria, and most closely related to species of the Clostridium coccoides cluster (rRNA cluster XIVa) [M.D. Collins et al., The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations, Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Clostridium bolteae and Clostridium clostridioforme were identified as the most closely related described species. A 16S rRNA sequence divergence value of > 3% suggested that the isolate represents a new species. This was also supported by the gyrase-encoding gyrB gene sequences. Based on these findings, we propose the novel bacterium from human faeces to be classified as a new species, Clostridium asparagiforme. The type strain of C. asparagiforme is N6 (DSM 15981 and CCUG 48471).     

Paenibacillus beijingensis sp. nov., a novel nitrogen-fixing species isolated from jujube garden soil

A novel Gram-positive, rod-shaped, motile, spore-forming, nitrogen-fixing bacterium, designated strain 7188^T, was isolated from jujube rhizosphere soil in Beijing, China. The strain grew at 4–40 °C and pH 6–12, with an optimum of 30 °C and pH 7.0, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 7188^T is a member of the genus Paenibacillus. Levels of 16S rRNA gene sequence similarities between strain 7188^T and the type strains of all recognized members of the genus Paenibacillus were below 96 %. The major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0 and C_16:0. The predominant menaquinone was MK-7. The DNA G+C content of strain 7188^T was 60.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminophospholipids. The diamino acid in the cell wall peptidoglycan is meso-diaminopimelic acid. On the basis of these results, strain 7188^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus beijingensis sp. nov. is proposed. The type strain is 7188^T (=ACCC 03082^T = DSM 24997^T).