- Volume 66, Issue 10, 2016
Volume 66, Issue 10, 2016
- New taxa
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- Firmicutes and related organisms
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Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater
A Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9T was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9T were rod shaped with dimensions of 0.3×(1–10) µm and stained Gram-negative. Strain Z9T grew within the temperature range 20–60 °C (optimum at 30–40 °C), between pH 5 and 8 (optimum 5.2–5.8) and under salt concentrations of 1–5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI) when H2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S0). The G+C content of the DNA from strain Z9T was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9T showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus , T. fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9T represents a novel species within the genus Tepidibacillus , for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9T (=ATCC BAA-2644T=DSM 103037T).
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Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum
More LessMore than 100 isolates of a Gram-stain-negative, curved rod-shaped, so far uncultured bacterium were isolated from chicken caecal content. The strains were obligate anaerobes which formed endospores. They were catalase-positive, cytochrome-oxidase-negative and did not hydrolyse aesculin. The detected predominant metabolic end product in reinforced clostridial bedium broth was acetate. The DNA G+C content was 62.2 mol%. The cell fatty acid composition was dominated by C15 : 0 iso, C15 : 0 anteiso, C16 : 0, C13 : 0 iso, C14 : 0 iso and C16 : 0 DMA. Analysis of the 16S rRNA gene sequences of the novel isolates showed 99 % similarity to each other. Phylogenetically they are placed in Clostridium cluster IV. They exhibited 99 % 16S rRNA gene sequence similarity to uncultured bacterial clone SJTU_C_03_83 (GenBank accession no. EF404038.1) and to three other so far uncultured strains. The closest related type strains, Hydrogenoanaerobacterium saccharovorans SW51T and Anaerotruncus colihominis WAL 14565T, exhibited a 16S rRNA gene sequence divergence of at least 8 % to the newly described isolates. In addition, morphological and biochemical characteristics allowed differentiation of the novel isolates from these and other related and validly published species, including Clostridium methylpentosum and Acetanaerobacterium elongatum . Therefore, a new genus, Harryflintia gen. nov., is proposed for the isolated hitherto unknown strains with V20-281aT (=DSM 100433T =CECT 8892T) as the type strain of its type species, Harryflintia acetispora gen. nov., sp. nov.
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Reclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces
More LessA Gram-positive-staining, coccoid-shaped, non-motile, asporogenous, obligately anaerobic and butyrate-producing bacterium was recovered from a healthy human’s faeces. The organism was isolated by the enrichment culture technique using yeast extract-casein hydrolysate-fatty acids broth supplemented with 0.5 % mucin. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the novel strain should be classified as a member of the Eubacterium desmolans -related cluster in the family Ruminococcaceae . Furthermore, this analysis demonstrated that the type strains of Butyricicoccus pullicaecorum (95.6 %) and Eubacterium desmolans (94.7 %) were the closest phylogenetic neighbours to strain YIT 12789T. However, DNA‒DNA reassociation values with these closest strains were less than 20 %. On the basis of the phenotypic, genotypic and chemotaxonomic features, the novel coccoid-shaped bacterium should be designated as a representative of a novel species of the genus Butyricicoccus , for which the name Butyricicoccus faecihominis sp. nov. is proposed. The type strain is YIT 12789T (=JCM 31056T=DSM 100989T). It is also proposed that Eubacterium desmolans be reclassified in the genus Butyricicoccus as Butyricicoccus desmolans comb. nov.
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Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor
More LessPhylogenetic studies were performed on a group of novel Gram-stain-positive, anaerobic, non-sporulating rod-shaped bacteria isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene sequence comparison indicated that the isolates SD1DT, SD1G, SD1I and RK1P share 100 % sequence identity, and are most closely related to Herbinix hemicellulosilytica T3/55T with which they share a 16S rRNA gene sequence similarity of 96.4 %. As a representative of the whole group of isolates, strain SD1DT was further characterized. Strain SD1DT was catalase-negative, indole-negative, and produced acetate, ethanol, butyric acid and hydrogen as major end-products during fermentative cellobiose utilization. Cells are rod-shaped, growing optimally at 40–65 °C and pH 6.5–8.5. The major cellular fatty acids (>10 %) were C19 : 0 cyc 9,10 dimethyl acetal, C16 : 0 and C14 : 0. The DNA G+C content was 35.1 mol%. Due to the genetic and phenotypic differences to the most closely affiliated species, the isolates represent a novel species of the genus Herbinix within the family Lachnospiraceae , for which the name Herbinix luporum sp. nov. is proposed. The type strain is SD1DT(=DSM 100831T=CECT 8959T).
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Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China
Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9T and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus . They are most closely related to Streptococcus thoraltensis CIP 105518T based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9T forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis . In silico DNA–DNA hybridization of HTS9T showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518T. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA–DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus ), we propose with confidence that strains HTS9T and HTS12 should be classified as representing a novel species of the genus Streptococcus , Streptococcus halotolerans sp. nov. The type strain is HTS9T (=DSM 101996T=CGMCC1.15532T). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.
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Oceanobacillus longus sp. nov., a moderately halophilic bacterium isolated from a salt lake
A Gram-stain-positive, endospore-forming, long rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain T9BT, was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain T9BT were motile and produced colonies with a brown pigment. Growth occurred between 1.0 and 20 % (w/v) NaCl and the isolate grew optimally at 5.0 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, while it was able to grow over pH and temperature ranges of pH 6.0–9.0 and 25–45 °C. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain T9BT is a member of the genus Oceanobacillus . The closest relative to this strain was Oceanobacillus rekensis PT-11T with a similarity of 97.4 %, followed by Oceanobacillus profundus CL-MP28T and Oceanobacillus polygoni SA9T with 97.3 and 97.1 % similarity, respectively. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The polar lipids of strain T9BT consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and one aminoglycolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 42.9 mol%. Phylogenetic analysis, DNA–DNA hybridization data and phenotypic characteristics allowed strain T9BT to be differentiated from other members of the genus Oceanobacillus . A novel species, Oceanobacillus longus sp. nov., is therefore proposed to accommodate this strain. The type strain is T9BT (=IBRC-M 10703T=LMG 29250T).
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- Other bacteria
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Thermodesulfatator autotrophicus sp. nov., a thermophilic sulfate-reducing bacterium from the Indian Ocean
More LessA novel sulfate-reducing bacterium, strain S606T, was isolated from a sulfide sample collected at a depth of 2764 m from a deep-sea vent chimney wall in the Indian Ocean. Phylogenetic 16S rRNA gene sequence analyses placed strain S606T within the genus Thermodesulfatator , with highest sequence similarity of 98.2 % to Thermodesulfatator indicus DSM 15286T, followed by Thermodesulfatator atlanticus AT1325T (97.4 %). The average nucleotide identity (ANI) values between S606T and the two other type strains (T. indicus DSM 15286T and T. atlanticus AT1325T) were 79.2 % and 71.5 %, respectively. The digital DNA–DNA hybridization estimate values between S606T and these two type strains were 22.7±2.4 % and 18.1±2.3 %, respectively. Cells were Gram-stain-negative, anaerobic, motile rods (1–1.8×0.5–0.7 µm). The novel isolate grew at NaCl concentrations ranging from 1.5 to 4.5 % (optimum 2.5–3 %), from pH 5.5 to 8 (optimum 6.5–7.0) and at temperatures between 50 and 80 °C (optimum 65–70 °C). S606T grew chemolithoautotrophically in an H2/CO2 atmosphere (80 : 20, v/v; 200 kPa), used sulfate as a terminal electron acceptor, but not sulfur, sulfite nor thiosulfate. The predominant fatty acids were C16 : 0 (24.2 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1 ω7c, 26.3 %), C18 : 0 (22.2 %) and C18 : 1ω9c (9.2 %). The DNA G+C content of the chromosomal DNA was 43.1 mol%. The combined genotypic, chemotaxonomic and phenotypic traits show that S606T should be described as representing a novel species of the genus Thermodesulfatator , for which the name Thermodesulfatator autotrophicus sp. nov. is proposed. The type strain is S606T (=DSM 101864T=MCCC 1A01871T).
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- Proteobacteria
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Sulfitobacter faviae sp. nov., isolated from the coral Favia veroni
More LessThree closely related, non-sporulating, aerobic, Gram-stain-negative, motile, rod-shaped isolates (S5-53T, S6-62 and S6-64) were obtained from mucus of corals Favia veroni from the Andaman Sea, India. Colonies grown on marine agar were small, circular and cream-coloured. Heterotrophic growth was observed at 10–40 °C and pH 6–10; optimum growth occurred at 25–30 °C and pH 7–8. 16S rRNA gene sequence analysis confirmed the isolates belonged to the genus Sulfitobacter and the three isolates shared more than 99 % pairwise sequence similarity. Strain S5-53T shared highest 16S rRNA gene sequence similarity of 98.43 % with Sulfitobacter dubius KMM 3554T. DNA–DNA relatedness among the three isolates was above 70 % whereas strain S5-53T showed less than 70 % relatedness with the type strains of closely related species. The DNA G+C content of strain S5-53T was 61 mol%. It contained phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Predominant fatty acids included C18 : 1 ω7c, C18 : 1 ω7c 11-methyl, C16 : 0 and C10 : 0 3-OH. Q10 was the major respiratory quinone. Based on this polyphasic analysis, the new isolates (S5-53T, S6-62 and S6-64) are considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter faviae sp. nov. is proposed. The type strain is S5-53T(=JCM 31093T=LMG 29156T).
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Roseomonas rubra sp. nov., isolated from lagoon sediments
More LessA novel Gram-stain-negative, coccus to oval-shaped, non-motile bacterium, designated strain S5T, was isolated from lagoon sediments collected from North Carolina, USA. Strain S5T was able to grow at 12–45 °C (optima, 30–37 °C) and at pH 6.3–9.0 (optima, 6.5–7.5). No added NaCl was required for growth of strain S5T. Strain S5T was positive for catalase and oxidase activity. C18 : 1 ω6c/C18 : 1 ω7c, C16 : 1 ω6c/C16 : 1 ω7c and C16 : 0 were predominant fatty acids with minor amounts of C8 : 0 3-OH, C14 : 0, C16 : 0 3-OH, C18 : 1 2-OH, C14 : 1 ω5c, C16 : 1 ω5c and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were major polar lipids. Minor amounts of an unidentified amino lipid and three unidentified lipids were also detected. The G+C content of the genomic DNA was 73.5 mol%. 16S rRNA gene sequence comparisons indicated that strain S5T represents a member of the genus Roseomonas within the family Acetobacteraceae of the class Alphaproteobacteria . Strain S5T had a sequence similarity of 97.80 % with Roseomonas rhizosphaerae YW11T, 97.69 % with Roseomonas aestuarii JC17T and <97 % with other members of the genus Roseomonas . However, strain S5T showed only 45.2±2 and 17±2 % relatedness (based on DNA–DNA hybridization) with R . rhizosphaerae KACC 17225T (=YW11T) and R . aestuarii KCTC 22692T (=JC17T), respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain S5T as a representative of a novel species in the genus Roseomonas , for which the name Roseomonas rubra sp. nov. is proposed. The type strain is S5T (=KEMB 563-468T=JCM 31177T).
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Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment
More LessA Gram-stain-negative, moderately halophilic bacterium, designated strain CPS11T, was isolated from the sediment of a solar pond located in Shinan, Korea. Strain CPS11T was a strictly aerobic, motile, straight rod-shaped bacterium that grew at pH 5.0–9.0 (optimum, pH 7.0–8.0), at 10–37 °C (optimum, 28 °C) and at salinities of 1–20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CPS11T belonged to the genus Halomonas , with sequence similarity of 98.5–94.3 % to existing type strains, showing highest sequence similarity to Halomonas fontilapidosi 5CRT (98.5 %), Halomonas ventosae Al12T (98.5 %), Halomonas campaniensis 5AGT (98.2 %), Halomonas huangheensis BJGMM-B45T (98.0 %), Halomonas alimentaria YKJ-16T (98.0 %), Halomonas mongoliensis Z-7009T (97.8 %), Halomonas shengliensis SL014B-85T (97.5 %) and Halomonas cupida DSM 4740T (97.5 %). The predominant ubiquinone was Q-9. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C17 : 0 cyclo, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, an unknown phospholipid and unknown lipids. The DNA G+C content of this novel isolate was 64.3 mol%. Levels of DNA–DNA relatedness between strain CPS11T and the type strains of ten other species of the genus ranged from 50 to 21 %. On the basis of the polyphasic analysis conducted in this study, strain CPS11T represents a novel species of the genus Halomonas , for which the name Halomonas sediminicola sp. nov. is proposed. The type strain is CPS11T(=KACC 18262T=NBRC 110636T).
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Chromobacterium rhizoryzae sp. nov., isolated from rice roots
A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryzasativa) in Hubei Province. Cells of LAM1188T were Gram-stain-negative and motile. The temperature and pH ranges for growth were 15–40 °C (optimum: 30 °C) and pH 5–10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium , and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98.7 % and 97.3 % sequence similarity, respectively. The values of DNA–DNA hybridization between LAM1188T and C. haemolyticum JCM 14163T and C. aquaticum CCUG 55175T were 54.0±2.1 % and 44.0±1.2 %, respectively. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and four unidentified lipids. The respiratory quinone was ubiquinone Q-8. The DNA G+C content was 64.1 mol% as determined by the Tm method. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain LAM1188T is suggested to represent a novel species of the genus Chromobacterium, for which the name Chromobacte riumrhizoryzae sp. nov. is proposed. The type strain is LAM1188T (=ACCC 19900T=JCM 31180T).
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Acinetobacter pragensis sp. nov., found in soil and water ecosystems
More LessThis study aimed to define the taxonomic status of a novel, phenetically distinct group of seven strains belonging to the genus Acinetobacter , which were isolated from environmental soil and water samples collected in Central Bohemia, Czech Republic. Comparative sequence analyses of the 16S rRNA, gyrB and rpoB genes showed that all these strains formed respective tight clusters (intracluster sequence similarities of ≥99.8, ≥98.1 and ≥98.3 %, respectively), which were distant from all known Acinetobacter species (≤98.2, ≤84.0 and ≤88.9 %, respectively). The average nucleotide identity and digital DNA–DNA hybridization values (≤83.5 and ≤27.4 %, respectively) between the whole-genome sequence of a group representative (strain ANC 4149T) and those of known taxa were far below the thresholds used to discriminate between bacterial species. The seven strains also formed a tight and distinct cluster based on the genus-wide comparison of whole-cell mass fingerprints generated by matrix-assisted laser desorption/ionization time-of-flight MS and could be distinguished from all other members of the genus Acinetobacter by the combination of their ability to assimilate glutarate and l-tartrate and inability to grow at 37 °C and on l-aspartate. It is concluded that the seven strains represent a novel species for which the name Acinetobacter pragensis sp. nov. is proposed. The type strain is ANC 4149T (=CCM 8637T=CCUG 67962T=CNCTC 7530T).
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Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio
More LessA novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae , but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to Desulfovibrio portus MSL79T (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2T (96.11 %), Desulfovibrio piezophilus C1TLV30T (96.04 %) and Desulfovibrio profundus DSM 11384T (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2–6×0.4–0.6 µm). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5–7) and at temperatures between 9 and 40 °C (optimum 30–35 °C). J2T was piezophilic, growing optimally at 10 MPa (range 0–30 MPa). J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C17 : 0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T represents a novel species of a novel genus in the family Desulfovibrionaceae , for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.
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Sphingobium hydrophobicum sp. nov., a hydrophobic bacterium isolated from electronic-waste-contaminated sediment
More LessFour hydrophobic bacteria were isolated from sediment at Guiyu, an electronic-waste recycling site in southeastern China. The isolates had high cell surface hydrophobicity with microbial-adhesion-to-hydrocarbon score of 71.4 %. 16S rRNA gene sequences of the strains all showed highest similarity to the hydrophilic Sphingobium xenophagum DSM 6383T (99.9 % 16S rRNA gene sequence similarity), followed by Sphingobium czechense DSM 25410T (97.1 %). However, DNA–DNA hybridization revealed that the isolates and S. xenophagum DSM 6383T exhibited low DNA–DNA relatedness with a hybridization value of 54.5±0.5 %. The genomic DNA G+C content was 64.2 mol% and the predominant quinone was ubiquinone Q-10. Spermidine was the major polyamine component. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c, C16 : 0, C14 : 0 2-OH and C14 : 0. In contrast to its closest relative S. xenophagum DSM 6383T, the isolates had a much higher proportion of C16 : 0 and C14 : 0 and a much lower proportion of C18 : 1ω9t. Sphingoglycolipid was present and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylmonomethylethanolamine were detected in the polar lipid pattern. Phosphatidyldimethylethanolamine and phosphatidylcholine, which are present in S. xenophagum DSM 6383T, were not detected in the isolates. Results of DNA–DNA relatedness, cell surface hydrophobicity, fatty acids, polar lipids, and biochemical and physiological properties reveal that the isolates represent a novel species of the genus Sphingobium , for which the name Sphingobium hydrophobicum sp. nov. is proposed. The type strain is C1T (=CCTCC AB 2015198T=KCTC 42740T).
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Martelella suaedae sp. nov. and Martelella limonii sp. nov., isolated from the root of halophytes
More LessTwo Gram-stain-negative, aerobic and endophytic bacterial strains, designated YC7033T and YC7034T, were isolated from the roots of halophytes (Suaeda maritime and Limonium tetragonum, respectively) inhabiting tidal flats of the Sacheon area, Korea. The phylogenetic analyses of 16S rRNA gene sequences showed that the two strains were closely related to Martelella endophytica YC6887T, Martelella mangrovi BM9-1T, Martelella radicis BM5-7T and Martelella mediterranea DSM 17316T at 97.6–99.1 % similarity. Sequence similarities with the type strains of another closely related genus, Rhizobium , were lower than 95.0 %. Both strains contained ubiquinone-10 (Q-10) as the major respiratory quinone system. The G+C contents of the genomic DNA of strains YC7033T and YC7034T were 52.8 and 62.2 mol%, respectively. The major fatty acids of both strain YC7033T and strain YC7034T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C19 : 0 cyclo ω8c. On the basis of phylogenetic analysis, and biochemical and phenotypic characteristics, strains YC7033T and YC7034T represent two novel species of the genus Martelella , for which the names Martelella suaedae sp. nov. (type strain: YC7033T=KACC 17175T=NBRC 109440T) and Martelella limonii sp. nov. (type strain: YC7034T=KACC 17176T=NBRC 109441T) are proposed, respectively.
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Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands
More LessThe taxonomic position of a novel bacterial strain, designated C3T, isolated from hydrocarbon-contaminated desert sands was determined. Strain C3T was a Gram-stain-negative, rod- to curved-rod-shaped and non-motile bacterium. It was able to grow at 4–45 °C (optima, 28– 35 °C) and at pH 6.1–8.8 (optima, 6.9–7.7). No added NaCl was required for growth of strain C3T and it tolerated up to 3.5 % (w/v) NaCl with optimal growth with 0.5–1.5 %. Catalase and oxidase were positive. C18 : 1 ω6c/C18 : 1 ω7c, C16 : 0, C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 0 I and C18 : 1 ω7c 11-methyl were predominant fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine were major polar lipids. The genomic DNA G+C content was 65.4 mol%. 16S rRNA gene sequence comparisons indicated that strain C3T represents a member of the genus Shinella within the family Rhizobiaceae of the class Alphaproteobacteria . Strain C3Tshowed a 16S rRNA gene sequence similarity of 98.39 % with Shinella kummerowiae CCBAU 25048T, 98.37 % with Shinella granuli Ch06T, 98.17 % with Shinella zoogloeoides I-16-MT, 97.74 % with Shinella fusca DC-196T, 97.46 % with Shinella yambaruensis MS4T and <96.68 % with other members of the family Rhizobiaceae . DNA–DNA hybridization values between strain C3T and the type strains of the nearest species were clearly below the 70 % threshold for species delineation. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain C3T as a representative of a novel species in the genus Shinella , for which the name Shinella curvata sp. nov. is proposed. The type strain is C3T (=KEMB 2255-446T=JCM 31239T).
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Devosia confluentis sp. nov., isolated from the junction between the ocean and a freshwater lake, and reclassification of two Vasilyevaea species as Devosia enhydra comb. nov. and Devosia mishustinii comb. nov.
More LessA Gram-stain-negative, aerobic, non-flagellated and pleomorphic bacterium, designated HJR-2T, was isolated from a junction between the ocean and a freshwater lake on the East Sea, South Korea. It grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 0–1.5 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain HJR-2T clustered with the type strains of Vasilyevaea enhydra and Vasilyevaea mishustinii and this cluster fell within the clade comprising the type strains of Devosia species. Strain HJR-2T exhibited 16S rRNA gene sequence similarity values of 97.2 and 97.0 % to the type strains of V. enhydra and V. mishustinii , respectively, and 93.9–96.2 % to the type strains of Devosia species. Strain HJR-2T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0 as major fatty acids. Major polar lipids of strain HJR-2T were phosphatidylglycerol and two unidentified glycolipids. The DNA G+C content was 66.0 mol% and its mean DNA–DNA relatedness values with the type strains of V. enhydra and V. mishustinii were 11–17 %. Differential phenotypic properties, together with its phylo genetic and genetic distinctiveness, revealed that strain HJR-2T is separated from V. enhydra , V. mishustinii and Devosia species. On the basis of the data presented, strain HJR-2T (=KCTC 52211T=NBRC 112271T) is considered to be the type strain of a novel species of the genus Devosia , for which the name Devosia confluentis sp. nov. is proposed. In this study, it is also proposed that V. enhydra and V. mishustinii be reclassified as members of the genus Devosia .
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Skermanella rosea sp. nov., isolated from hydrocarbon-contaminated desert sands
More LessA novel Gram-stain-negative, small rod-shaped, motile strain, designated M1T, was isolated from hydrocarbon-contaminated desert sands collected from Kuwait. M1T grew at 12–45 °C, pH 6.1–8.8 and 0–4.5 % (w/v) NaCl concentration. Casein, Tween-20 and Tween-80 were hydrolyzed while starch, urea, chitin, DNA and carboxymethyl-cellulose were not hydrolyzed by M1T. C18 : 1ω6c/C18 : 1ω7c, C16 : 0 and C12 : 0 aldehyde were predominant fatty acids with minor amounts of iso-C16 : 1I/C14 : 0 3-OH, C16 : 0 3-OH, C18 : 0, C16 : 1ω6c/C16 : 1ω7c, C16 : 1ω11c and C18 : 1ω9c. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phosphatidylcholine (PC) were the major polar lipids. Minor amounts of unidentified aminolipids (AL1–2), unidentified phospholipids (PL1–2) and unidentified lipids (L1–4) were also detected. Genomic G+C content was 69.5 mol%. Comparisons of 16S rRNA gene sequence indicate that M1T represent a member of the genus Skermanella in the family Rhodospirillaceae of the class Alphaproteobacteria . M1T has a sequence similarity of 97.5 % with Skermanella aerolata 5416T-32T, 96.7 % with Skermanella stibiiresistens SB22T and <95.7 % with the other two species of the genus Skermanella . DNA–DNA hybridization values between M1T and the type strains of the most closely related species were clearly below the 70 % threshold. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain M1T as a representative of a novel species in the genus Skermanella , for which the name Skermanella rosea sp. nov. is proposed. The type strain is M1T (=KEMB 2255-458T=JCM 31276T).
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Altererythrobacter confluentis sp. nov., isolated from water of an estuary environment
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated KEM-4T, was isolated from water of an estuary environment on the Yellow Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain KEM-4T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 1.0–2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain KEM-4T fell within the clade comprising the type strains of species of the genus Altererythrobacter , clustering with the type strains of Altererythrobacter aestiaquae, Altererythrobacter gangjinensis and Altererythrobacter luteolus, showing 95.0–96.5 % sequence similarity. Sequences similarities to the type strains of the other species of the genus Altererythrobacter were 93.1–95.1 %. Strain KEM-4T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C17 : 1ω6c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain KEM-4T was 59.5 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain KEM-4T is separated from species of the genus Altererythrobacter with validly published names. On the basis of the data presented, strain KEM-4T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter confluentissp. nov. is proposed. The type strain is KEM-4T (=KCTC 52259T=NBRC 112305T).
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Lysobacter erysipheiresistens sp. nov., an antagonist of powdery mildew, isolated from tobacco-cultivated soil
More LessA bacterial strain, RS-LYSO-3T, was isolated from tobacco-cultivated soil, collected near Chuxiong, Yunnan province, southwestern China. RS-LYSO-3T could effectively inhibit the invasion of powdery mildew on tobacco. The colonies of RS-LYSO-3T were pale yellow, and its cells were Gram-stain-negative and rod-shaped, with 68 mol% DNA G+C content. Gene sequence analysis for its 16S rRNA gene revealed the highest similarity (97.78 %) with that of Lysobacter spongiicolaKMM 329T. Chemotaxonomic data showed that RS-LYSO-3T possesses a quinone system with Q-8, and iso-C16 : 0, summed feature 9 and iso-C15 : 0 as the predominant fatty acids, all of which support the affiliation of RS-LYSO-3T to the genus Lysobacter . The results of DNA–DNA hybridization, physiological and biochemical tests clearly proved that RS-LYSO-3T is a representative of a novel species of the genus Lysobacter , for which the name Lysobacter erysipheresistens sp. nov. is proposed. The type strain is RS-LYSO-3T (=CCIC 23922T=JCM 31042T).
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