- Volume 65, Issue Pt_12, 2015
Volume 65, Issue Pt_12, 2015
- NEW TAXA
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- Proteobacteria
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Sphingomonas hengshuiensis sp. nov., isolated from lake wetland
A polyphasic taxonomic study was undertaken to establish the status of a novel bacterium, designated strain WHSC-8T, which was isolated from soil of Hengshui Lake Wetland Reserve in Hebei province, northern China. Colonies of this strain were yellow and cells were rod-shaped, polar-flagellated and obligately aerobic, exhibiting negative Gram reaction. The strain was able to grow at 0–1 % (w/v) NaCl, pH 5–10 and 20–35 °C, with optimal growth occurring at pH 7.0 and 28 °C without NaCl. Chemotaxonomic data revealed that strain WHSC-8T possesses ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids, and sym-homospermidine as the major polyamine. Sphingomonadaceae-specific sphingoglycolipid was detected in the polar lipid patterns. The G+C content of the genomic DNA was 68.7 mol%. All of the above characters corroborated the assignment of the novel strain to the genus Sphingomonas. Strain WHSC-8T shared less than 97.0 % 16S rRNA gene sequence similarity with the type strains of other species of the genus Sphingomonas, except for Sphingomonas asaccharolytica DSM 10564T (97.5 %). The low DNA–DNA relatedness value and distinct phenotypic and chemotaxonomic characteristics distinguished strain WHSC-8T from closely related species of the genus Sphingomonas. Therefore, strain WHSC-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas hengshuiensis sp. nov. is proposed. The type strain is WHSC-8T ( = KCTC 42455T = CCTCC AB 2015265T).
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Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut
Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.
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Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand
More LessA red-pigmented bacterium producing a metallic green sheen, designated strain JC333T, was isolated from a sand sample collected from Shivrajpur–Kachigad beach, Gujarat, India. Phylogenetic analyses based on the 16S rRNA gene sequence of strain JC333T showed highest sequence similarity to Zooshikella ganghwensis JC2044T (99.24 %) and less than 91.94 % similarity with other members of the class Gammaproteobacteria. DNA–DNA hybridizations between JC333T and Z. ganghwensis JC2044T showed low relatedness values of 19 ± 1.3 % (reciprocal 21 ± 2.2 %). The major respiratory quinone was ubiquinone-9 (Q9) and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The presence of C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C18 : 1ω7c and C12 : 0 as major fatty acids supported the affiliation of strain JC333T to the genus Zooshikella. Prodigiosin, cycloprodigiosin and eight other prodigiosin analogues were the pigments of JC333T. Characterization based on 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, and polar lipid and fatty acid compositions revealed that JC333T represents a novel species of the genus Zooshikella, for which the name Zooshikella marina sp. nov. is proposed. The type strain is JC333T ( = KCTC 42659T = LMG 28823T).
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Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii
A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).
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Roseovarius scapharcae sp. nov., isolated from ark shell Scapharca broughtonii
More LessA Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated MA4-5T, was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. The novel strain grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences showed that strain MA4-5T forms a coherent cluster with the type strains of Roseovarius albus, Roseovarius aestuarii and Roseovarius nubinhibens, sharing 97.0–99.2 % sequence similarity. It exhibited 16S rRNA gene sequence similarity of 93.1–96.1 % to the type strains of other Roseovarius species. Strain MA4-5T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain MA4-5T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA4-5T was 53.8 mol% and its mean DNA–DNA relatedness values with the type strains of R. albus, R. aestuarii and R. nubinhibens were 11–26 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, indicated that strain MA4-5T is separate from recognized species of the genus Roseovarius. On the basis of the data presented, strain MA4-5T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius scapharcae sp. nov. is proposed. The type strain is MA4-5T ( = KCTC 42703T = NBRC 111226T).
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Thalassotalea marina sp. nov., isolated from a marine recirculating aquaculture system, reclassification of Thalassomonas eurytherma as Thalassotalea eurytherma comb. nov. and emended description of the genus Thalassotalea
More LessA Gram-stain-negative, facultatively anaerobic bacterium, strain QBLM2T, was isolated from rearing water of a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated through a polyphasic approach. Cells of strain QBLM2T were non-spore-forming rods, motile by means of a single polar flagellum. Positive for oxidase and catalase. Growth occurred at 15–40 °C (optimum 30 °C), at pH 6.5–10.5 (optimum pH 7.5–8.5) and in the presence of 0–5.0 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QBLM2T formed a distinct lineage within the genus Thalassotalea and exhibited sequence similarities of 94.5–96.3 % to members of the genus Thalassotalea. The predominant fatty acids (>10 %) were C17 : 1ω8c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the major ubiquinone. The DNA G+C content was 37.1 mol%. Based on the data above, strain QBLM2T is considered to represent a novel species of the genus Thalassotalea, for which the name Thalassotalea marina sp. nov. is proposed. The type strain is QBLM2T ( = CGMCC 1.12814T = KCTC 42731T). Phylogenetic analyses indicated that Thalassomonas eurytherma Za6a-12T fell within the genus Thalassotalea, so it is reclassified as Thalassotalea eurytherma comb. nov. and the description of the genus Thalassotalea is emended.
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Burkholderia dipogonis sp. nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia
Seven strains, ICMP 19430T, ICMP 19429, ICMP 19431, WSM4637, WSM4638, WSM4639 and WSM4640, were isolated from nitrogen-fixing nodules on roots of the invasive South African legume Dipogon lignosus (subfamily Papilionoideae, tribe Phaseoleae) in New Zealand and Western Australia, and their taxonomic positions were investigated by using a polyphasic approach. All seven strains grew at 10–37 °C (optimum, 25–30 °C), at pH 4.0–9.0 (optimum, pH 6.0–7.0) and with 0–2 % (w/v) NaCl (optimum growth in the absence of NaCl). On the basis of 16S rRNA gene sequence analysis, the strains showed 99.0–99.5 % sequence similarity to the closest type strain, Burkholderia phytofirmans PsJNT, and 98.4–99.7 % sequence similarity to Burkholderia caledonica LMG 19076T. The predominant fatty acids were C18 : 1ω7c (21.0 % of the total fatty acids in strain ICMP 19430T), C16 : 0 (19.1 %), C17 : 0 cyclo (18.9 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.7 %) and C19 : 0 cyclo ω8c (7.5 %). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was Q-8 and the DNA G+C content of strain ICMP 19430T was 63.2 mol%. The DNA–DNA relatedness of the novel strains with respect to the closest neighbouring members of the genus Burkholderia was 55 % or less. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data, these strains represent a novel symbiotic species in the genus Burkholderia, for which the name Burkholderia dipogonis sp. nov. is proposed, with the type strain ICMP 19430T ( = LMG 28415T = HAMBI 3637T).
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Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil
Strain RIPI 110T was isolated from a soil sample collected from an oil-contaminated site on Siri Island, Persian Gulf, Iran. Cells of the novel isolate were Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped. Cells divided asymmetrically by budding and formed rosette-like clusters. The optimum pH and temperature for growth were pH 7 and 30 °C, while the strain was able to grow at pH 5.5–8 and 15–35 °C. Strain RIPI 110T utilized only complex carbon sources and pyruvate as the sole carbon source and could not grow under photoautotrophic conditions. The highest 16S rRNA gene sequence similarities, 93.9, 93.9 and 93.5 %, were obtained with Variibacter gotjawalensis GJW-30T, Rhodoplanes roseus 941T and Rhodoplanes elegans AS130T, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipid analyses revealed that strain RIPI 110T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid and four unknown phospholipids. Ubiquinone-10 was the predominant quinone component. The DNA G+C content was 59.4 mol%. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, the novel isolate could not be classified in any recognized genera. Strain RIPI 110T is thus considered to represent a novel species of a new genus within the order Rhizobiales, for which the name Pseudorhodoplanes sinuspersici gen. nov., sp. nov. is proposed. The type strain of the type species is RIPI 110T ( = IBRC-M 10770T = CECT 8374T).
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Gibbsiella papilionis Kim et al. 2013 is a later heterotypic synonym of Gibbsiella dentisursi Saito et al. 2013
More LessSynonymy of Gibbsiella dentisursi DSM 23818T ( = NUM 1720T) and Gibbsiella papilionis JCM 18389T ( = LEN33T) was suspected following multilocus sequence analysis (MLSA) of both type strains in a previous classification study, where they were found to share >99.6 % gene sequence similarity. The taxonomic relationship between these two strains was re-examined here using a polyphasic approach. A DNA–DNA hybridization value of 98 % confirmed that the two type strains belong to a single taxon, while the phenotypic profiles were found to be nearly identical. Therefore we propose Gibbsiella papilionis as a later heterotypic synonym of Gibbsiella dentisursi, with the type strain as NUM 1720T ( = DSM 23818T = JCM 17201T).
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Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil
More LessA Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0–10.8 (optimum, pH 8.5), at 10–55 °C (optimum, 28 °C) and at salinities of 0–23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA–DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T).
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Luteimonas soli sp. nov., isolated from farmland soil
A yellow-pigmented bacterial strain, designated Y2T, was isolated from farmland soil in Bengbu, Anhui province, China. Cells of strain Y2T were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Strain Y2T grew optimally at pH 7.0, 30 °C and in the presence of 2 % (w/v) NaCl. The DNA G+C content was 68.9 mol%. The major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C11 : 0 3-OH and iso-C11 : 0. The major respiratory quinone was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain Y2T was most closely related to Luteimonas mephitis B1953/27.1T (99.1 % 16S rRNA gene sequence similarity), followed by Luteimonas lutimaris G3T (98.6 %), Luteimonas abyssi XH031T (96.2 %) and Luteimonas aquatica RIB1-20T (96.0 %). Strain Y2T exhibited low DNA–DNA relatedness with Luteimonas mephitis B1953/27.1T (43.6 ± 0.5 %) and Luteimonas lutimaris G3T (43.9 ± 2.1 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain Y2T represents a novel species of the genus Luteimonas, for which the name Luteimonas soli sp. nov. is proposed. The type strain is Y2T ( = ACCC 19799T = KCTC 42441T).
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Novel environmental species isolated from the plaster wall surface of mural paintings in the Takamatsuzuka tumulus: Bordetella muralis sp. nov., Bordetella tumulicola sp. nov. and Bordetella tumbae sp. nov.
More LessTen strains of Gram-stain-negative, non-spore-forming, non-motile coccobacilli were isolated from the plaster wall surface of 1300-year-old mural paintings inside the stone chamber of the Takamatsuzuka tumulus in Asuka village (Asuka-mura), Nara Prefecture, Japan. Based on 16S rRNA gene sequence analysis of the isolates, they belonged to the proteobacterial genus Bordetella (class Betaproteobacteria) and could be separated into three groups representing novel lineages within the genus Bordetella. Three isolates were selected, one from each group, and identified carefully using a polyphasic approach. The isolates were characterized by the presence of Q-8 as their major ubiquinone system and C16 : 0 (30.0–41.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.1–27.0 %) and C17 : 0 cyclo (10.8–23.8 %) as the predominant fatty acids. The major hydroxy fatty acids were C12 : 0 2-OH and C14 : 0 2-OH. The DNA G+C content was 59.6–60.0 mol%. DNA–DNA hybridization tests confirmed that the isolates represented three separate novel species, for which the names Bordetella muralis sp. nov. (type strain T6220-3-2bT = JCM 30931T = NCIMB 15006T), Bordetella tumulicola sp. nov. (type strain T6517-1-4bT = JCM 30935T = NCIMB 15007T) and Bordetella tumbae sp. nov. (type strain T6713-1-3bT = JCM 30934T = NCIMB 15008T) are proposed. These results support previous evidence that members of the genus Bordetella exist in the environment and may be ubiquitous in soil and/or water.
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Roseomonas oryzicola sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.)
More LessA Gram-stain-negative, coccobacilli-shaped bacterium, designated YC6724T, was isolated from the rhizosphere of rice in Jinju, Korea. The taxonomy of strain YC6724T was studied using a polyphasic approach. Strain YC6724T grew optimally at 30 °C and pH 7.0–8.0. Comparative 16S rRNA gene sequence analyses showed that the strain was most closely related to Roseomonas soli 5N26T (98.4 % 16S rRNA gene sequence similarity), Roseomonas lacus TH-G33T (97.3 %) and Roseomonas terrae DS-48T (97.3 %). Sequence similarities with other species of the genus Roseomonas with validly published names were lower than 94.0 %. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain YC6724T formed a distinct phyletic lineage within the genus Roseomonas. Strain YC6724T had DNA–DNA relatedness values of 16.6 %, 44.0 % and 33.2 % with R. soli KACC 16376T, R. terrae KACC 12677T and R. lacus KACC 11678T, respectively. The predominant fatty acids of strain YC6724T were C18 : 1ω7c and/or C18 : 1ω6c, C16 : 0 and C18 : 1 2-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown lipids. The G+C content of the genomic DNA was 70.5 mol% and the major quinone was Q-10. Strain YC6724T contained spermidine as the major polyamine. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain YC6724T represents a novel species of the genus Roseomonas, for which the name Roseomonas oryzicola sp. nov. is proposed. The type strain is YC6724T ( = KCTC 22478T = NBRC 109439T).
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Marinobacter confluentis sp. nov., a lipolytic bacterium isolated from a junction between the ocean and a freshwater lake
More LessA Gram-stain-negative, motile, aerobic and rod-shaped bacterium, designated HJM-18T, was isolated from the place where the ocean and a freshwater lake meet at Hwajinpo, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain HJM-18T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 1.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain HJM-18T belonged to the genus Marinobacter. Strain HJM-18T exhibited 16S rRNA gene sequence similarity values of 97.05–98.22 % to the type strains of Marinobacter algicola, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter salarius, Marinobacter salsuginis, Marinobacter guineae and Marinobacter gudaonensis and of 93.21–96.98 % to the type strains of the other species of the genus Marinobacter. Strain HJM-18T contained Q-9 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω9c as the major fatty acids. The major polar lipids detected in strain HJM-18T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminophospholipid. The DNA G+C content was 58 mol% and the mean DNA–DNA relatedness values with the type strains of the seven phylogenetically related species of the genus Marinobacter were 10–27 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain HJM-18T is separated from recognized species of the genus Marinobacter. On the basis of the data presented, strain HJM-18T represents a novel species of the genus Marinobacter, for which the name Marinobacter confluentis sp. nov. is proposed. The type strain is HJM-18T ( = KCTC 42705T = NBRC 111223T).
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Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses
More LessEight strains of symbiotic bacteria from root nodules of local races of cowpea (Vigna unguiculata) and Bambara groundnut (Vigna subterranea) grown on subsistence farmers’ fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus Bradyrhizobium. To clarify their taxonomic status, these strains were further characterized using a polyphasic approach. In phylogenetic analysis of the 16S rRNA gene sequence the novel group was most closely related to Bradyrhizobium iriomotense EK05T and Bradyrhizobium ingae BR 10250T, and to ‘Bradyrhizobium arachidis’ CCBAU 051107 in the ITS sequence analysis. Phylogenetic analysis of concatenated glnII-recA-rpoB-dnaK sequences placed the strains in a lineage distinct from named species of the genus Bradyrhizobium. The species status was validated by results of DNA–DNA hybridization. Phylogenetic analysis of nifH and nodC genes placed the novel strains in a group with ’B. arachidis’ CCBAU 051107. The combination of phenotypic characteristics from several tests including carbon source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain 14-3T induces effective nodules on Vigna subterranea, Vigna unguiculata, Arachis hypogaea and Lablab purpureus. Based on the data presented, it is concluded that the strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium kavangense sp. nov. is proposed. The type strain is 14-3T [ = DSM 100299T = LMG 28790T = NTCCM 0012T (Windhoek)]. The DNA G+C content of strain 14-3T is 63.8 mol% (T m ).
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Pelistega suis sp. nov., isolated from domestic and wild animals
Biochemical and molecular genetic studies were performed on three novel Gram-stain-negative, catalase- and oxidase-positive, bacilli-shaped organisms isolated from the tonsils of two pigs and one wild boar. The micro-organism was identified as a species of the genus Pelistega based on its cellular morphological and biochemical tests. The closest phylogenetic relative of the novel bacilli was Pelistega indica HM-7T (98.2 % 16S rRNA gene sequence similarity to the type strain). groEL and gyrB sequence analysis showed interspecies divergence from the closest 16S rRNA gene phylogenetic relative, P. indica of 87.0.% and 69 %, respectively. The polyamine pattern contains predominantly putrescine and 2-hydroxyputrescine. The major quinone is ubiquinone Q-8 and in the polar lipid profile, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid are predominant. The novel bacterial isolate can be distinguished from P. indica by several biochemical characteristics, such as the production of l-pyrrolydonil arylamidase but not gamma-glutamyl-transferase, and the utilization of different carbon sources. Based on both phenotypic and phylogenetic findings, the novel bacterium is classified as representing a novel species of the genus Pelistega, for which the name Pelistega suis sp. nov. is proposed. The type strain is 3340-03T ( = CECT 8400T = CCUG 64465T).
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- Bacteroidetes
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Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir
More LessA Gram-stain-negative, non-motile and yellow-pigmented bacterium, designated HME8275T, was isolated from freshwater in Korea. The major fatty acids of strain HME8275T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and iso-C15 : 0. The only respiratory quinone was MK-7. Polar lipid analysis showed phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content of strain HME8275T was 37.6 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8275T formed a lineage within the family Cytophagaceae and was related to Lacihabitans soyangensis HME6675T (92.6 % 16S rRNA gene sequence similarity), Leadbetterella byssophila 4M15T (89.0 %), Fluviimonas pallidilutea TQQ6T (89.7 %) and Emticicia oligotrophica GPTSA100-15T (89.8 %). On the basis of the evidence presented in this study, strain HME8275T represents a novel species of a new genus in the family Cytophagaceae, for which the name Taeseokella kangwonensis, gen. nov., sp. nov. is proposed. The type strain of the type species is HME8275T ( = KACC 16933T = CECT 8198T).
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Variovorax gossypii sp. nov., isolated from Gossypium hirsutum
More LessA beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).
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Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken
Three strains of anaerobic Gram-stain-negative, short to longer rod-shaped bacteria isolated from the caecum of chicken in Indonesia were studied using a polyphasic taxonomic approach. These strains belonged to the genus Bacteroides, based on sequence analysis of 16S rRNA and hsp60 (groEL) genes, with similarities of 93.2–94.1 and 89.8–90.8 %, respectively, to the closest recognized species, Bacteroides coprocola JCM 17929T. Sugar fermentation and enzyme characteristics, cellular fatty acid profiles, menaquinone profiles and metabolic end products were also investigated. Furthermore, DNA–DNA hybridization studies confirmed that the three novel strains are different from the closest related species. The strains were also found to be distinct from each other on the basis of ribotype profiles. The DNA G+C contents of the three strains were 41.1–41.8 mol%. Based on phenotypic and phylogenetic characteristics, a novel species, Bacteroides caecigallinarum sp. nov., is proposed (type strain C13EG111T = LIPI12-4-Ck773T = JSAT12-4-Ck773T = InaCC B455T = NBRC 110959T).
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Tenacibaculum holothuriorum sp. nov., isolated from the sea cucumber Apostichopus japonicus intestine
More LessA novel bacterial strain, designated S2-2T, was isolated from the intestine of a sea cucumber Apostichopus japonicus in Xiapu, Fujian province, China. Strain S2-2T was found to be aerobic, Gram-stain-negative, pale yellow, rod-shaped, oxidase- and catalase-positive. Growth occurred at 15–36 °C (optimum, 25–32 °C), in the presence of 2–7% sea salt (w/v, optimum, 3–5%) and at pH 6–9 (optimum, pH 7.0). The isolate was able to hydrolyse gelatin, casein and DNA, but unable to degrade Tween 20, 40 and 80, starch and cellulose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-2T represented a member of the genus Tenacibaculum, with highest sequence similarity to Tenacibaculum aiptasiae a4T (96.9% similarity), followed by Tenacibaculum xiamenense WJ-1T (96.5% similarity) and showed lower similarities (93.3–95.9%) with other members of the genus Tenacibaculum. The major cellular fatty acids were summed feature 3 (comprising C16 : 1ω6c/C16 : 1ω7c, 33.8%), iso-C15 : 0 (13.7%), iso-C15 : 1G (8.6%), iso-C15 : 0 3-OH (5.3%) and C15 : 0 3-OH (5.1%). The DNA G+C content of the chromosomal DNA was determined to be 31.8 mol%. The respiratory quinone was determined to be MK-6. Phosphatidylethanolamine, phosphatidylglycerol, one unknown aminophospholipid, one unknown phospholipid, one unknown glycolipid and five unknown lipids were detected as major polar lipids. Hence, the combined genotypic and phenotypic data indicated that strain S2-2T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculum holothuriorum sp. nov. is proposed. The type strain is S2-2T ( = MCCC 1A09872T = LMG 27758T).
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Belliella marina sp. nov., isolated from seawater
More LessA Gram-stain-negative, rod-shaped bacterium, strain SW112T, was isolated from a seawater sample collected from the Indian Ocean. The strain was strictly aerobic and catalase- and oxidase-positive. Strain SW112T grew at 4–42 °C (optimum 30 °C), at pH 5.5–9.5 (optimum pH 7.5) and in the presence of 0–9.0 % (w/v) NaCl (optimum 2.0–3.0 %). The predominant cellular fatty acids were iso-C15 : 0 (29.7 %), iso-C17 : 03-OH (14.3 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 15.1 %). The major menaquinone was menaquinone-7 and the major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of strain SW112T was 39 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SW112T was related to members of the genus Belliella, showing the highest similarity with Belliella aquatica TS-T86Tand Belliella baltica DSM 15883T (96.5 % and 96.4 % sequence similarity, respectively). On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that strain SW112T represents a novel species of the genus Belliella, for which the name Belliella marina sp. nov. is proposed. The type strain is SW112T ( = CGMCC 1.15180T = KCTC 33694T).
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Emticicia aquatica sp. nov., a species of the family Cytophagaceae isolated from fresh water
More LessA Gram-staining-negative, non-gliding, orange-pigmented bacterial strain, designated HMF2925T, was isolated from fresh water in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HMF2925T formed a distinct lineage within the genus Emticicia. Strain HMF2925T was closely related to Emticicia oligotrophica DSM 17448T (95.5 %) and Emticicia ginsengisoli Gsoil 085T (94.1 %). The major fatty acids of strain HMF2925T were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0, C16 : 1ω5c and C16 : 0.The major polar lipids of strain HMF2925T were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, two unidentified amino lipids and three unidentified polar lipids. The DNA G+C content of strain HMF2925T was 36.5 mol%. On the basis of the evidence presented in this study, strain HMF2925T represents a novel species of the genus Emticicia, for which the name Emticicia aquatica sp. nov. is proposed. The type strain is HMF2925T ( = KCTC 42574T = CECT 8858T).
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Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea
Four brown-alga-degrading, Gram-stain-negative, aerobic, non-flagellated, gliding and rod-shaped bacteria, designated LMG 28520T, LMG 28521, LMG 28522 and LMG 28523, were isolated from the gut of the abalone Haliotis gigantea obtained in Japan. The four isolates had identical random amplified polymorphic DNA patterns and grew optimally at 25 °C, at pH 6.0–9.0 and in the presence of 1.0–4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences placed the isolates in the genus Formosa with Formosa algae and Formosa arctica as closest neighbours. LMG 28520T and LMG 28522 showed 100 % DNA–DNA relatedness to each other, 16–17 % towards F. algae LMG 28216T and 17–20 % towards F. arctica LMG 28318T; they could be differentiated phenotypically from these established species. The predominant fatty acids of isolates LMG 28520T and LMG 28522 were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G and iso-C15 : 0. Isolate LMG 28520T contained menaquinone-6 (MK-6) as the major respiratory quinone and phosphatidylethanolamine, two unknown aminolipids and an unknown lipid as the major polar lipids. The DNA G+C content was 34.4 mol% for LMG 28520T and 35.5 mol% for LMG 28522. On the basis of their phylogenetic and genetic distinctiveness, and differential phenotypic properties, the four isolates are considered to represent a novel species of the genus Formosa, for which the name Formosa haliotis sp. nov. is proposed. The type strain is LMG 28520T ( = NBRC 111189T).
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Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata
More LessA Gram-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).
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Hymenobacter terrenus sp. nov., isolated from biological soil crusts
More LessA Gram-stain-negative, non-spore-forming, short rod-shaped, non-motile, light-pink bacterial strain, MIMtkLc17T, was isolated from biological soil crusts collected in Liangcheng, Inner Mongolia. Growth of strain MIMtkLc17T was observed at 2–35 °C and in the presence of 1% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences showed that sequence similarities between strain MIMtkLc17T and the type strains of species of the genus Hymenobacter ranged from 89.93% to 96.49%. Strain MIMtkLc17T can secrete mass polysaccharide. The major fatty acids of strain MIMtkLc17T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 1ω5c and summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B). The sole respiratory quinone was menaquinone MK-7. The G+C content of the chromosomal DNA was 57.8 mol%. The results of phylogenetic, chemotaxonomic and phenotypic characterization indicated that strain MIMtkLc17T can be distinguished from all known species of the genus Hymenobacter and represents a novel species of this genus, for which the name Hymenobacter terrenus sp. nov. is proposed. The type strain is MIMtkLc17T ( = MCCC 1K00507T = KCTC 42636T).
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Croceitalea litorea sp. nov., isolated from seashore sand
Strain CBA3205T is a Gram-stain-negative, non-motile and rod-shaped bacterium that was isolated from the seashore sand of Jeju Island in South Korea. Based on the phylogenetic analysis, the most closed related species was Croceitalea eckloniae DOKDO 025T, with 94.8 % sequence similarity for the 16S rRNA gene. Strain CBA3205T was observed to grow optimally at 25–30 °C and at pH 8.5 in the presence of 2–3 % (w/v) NaCl. The major fatty acids of strain CBA3205T were iso-C15 : 0, iso-C15 : 1 G, and iso-C17 : 0 3-OH. The major respiratory quinone was MK-6 and the major polar lipids were two unidentified amino-group-containing phospholipids and an unidentified polar lipid. The G+C content of the genomic DNA of strain CBA3205T was 62.5 mol%. Based on the phenotypic, genotypic and phylogenetic analyses, strain CBA3205T was considered to be a novel species belonging to the genus Croceitalea within the family Flavobacteriaceae, for which the name Croceitalea litorea sp. nov. is proposed. The type strain is CBA3205T ( = KACC 17669T = JCM 19531T).
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Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces
Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism. The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0 fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 (in a 1 : 1 ratio) and the predominant menaquinone was MK-11. The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627T and 177T placed these bacteria in the genera Alistipes (family Rikenellaceae) and Coprobacter (family Porphyromonadaceae), respectively.
On the basis of the phenotypic and genotypic properties of strains 627T and 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the names Alistipes inops sp. nov. (type strain 627T = DSM 28863T = VKM B-2859T) and Coprobacter secundus sp. nov. (type strain 177T = DSM 28864T = VKM B-2857T) are proposed.
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Chitinophaga dinghuensis sp. nov., isolated from soil
More LessA Gram-reaction-negative, aerobic, non-motile bacterial strain, DHOC24T, was isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOC24T underwent a shape change during the course of culture from long filamentous cells (10–30 × 0.4–0.5 μm) at 2 days to coccobacilli (0.5–1.0 × 0.7–1.0 μm) at 15 days after inoculation. It grew optimally at 28–33 °C and pH 6.5–7.5. The major quinone of strainDHOC24T was MK-7, the main fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH and the DNA G+C content was 43.1 mol%. On the basis of 16S rRNA gene sequence analysis, the strain was found to be affiliated with members of the genus Chitinophaga, but was clearly separated from established species of the genus. Strain DHOC24T was most closely related to Chitinophaga jiangningensis JN53T (98.3 % 16S rRNA gene sequence similarity) and Chitinophaga terrae KP01T (97.9 %). DNA–DNA hybridization study showed relatively low relatedness values (32.1 %) of strain DHOC24T with C. jiangningensis JN53T. The phenotypic, chemotaxonomic and phylogenetic data showed that strain DHOC24T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga dinghuensis sp. nov. is proposed. The type strain is DHOC24T ( = CGMCC 1.12995T = DSM 29821T).
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Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae
A Gram-stain-negative, aerobic, proteorhodopsin-containing, orange, rod-shaped bacterium, designated SAORIC-234T, was isolated from deep seawater in the Pacific Ocean. 16S rRNA gene sequence analysis revealed that the strain could be affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and shared less than 94.6 % similarity with other species of the family with validly published names. The phenotypic characteristics of this novel isolate, such as growth properties and enzyme activities, could be differentiated from those of other species. The strain was non-motile, oxidase-positive and catalase-negative. The G+C content of the genomic DNA was determined to be 34.8 mol% and menaquinone-6 (MK-6) was the predominant isoprenoid quinone. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids comprised phosphatidylethanolamine, three unknown aminolipids and three unknown lipids. On the basis of the taxonomic data collected in this study, it was concluded that strain SAORIC-234T represents a novel genus and species in the family Flavobacteriaceae, for which the name Aurantivirga profunda gen. nov., sp. nov. is proposed. The type strain of the type species, Aurantivirga profunda sp. nov., is SAORIC-234T ( = NBRC 110606T = KACC 18400T).
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Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus
More LessA Gram-stain-negative, yellow, motile by gliding, filamentous bacterium, designated SR 2-06T, was isolated from surface-sterilized root of garden cosmos. 16S rRNA gene sequence analysis indicated that SR 2-06T was related most closely to Filimonas lacunae YT21T of the family Chitinophagaceae at a sequence similarity of 96.90 %, while levels of similarity to other related taxa were less than 93.08 %. Strain SR 2-06T exhibited similar features to F. lacunae in that it contained MK-7 as the major respiratory quinone, and iso-C15 : 1 G, iso-C15 : 0 and a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c as the major fatty acids. However, strain SR 2-06T was distinguished from F. lacunae using a combination of physiological and biochemical properties. The cellular polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids, an unknown phospholipid and unidentified polar lipids. The DNA G+C content was 46.0 mol%. The phenotypic and phylogenetic evidence clearly indicates that strain SR 2-06T represents a novel species of the genus Filimonas, for which the name Filimonas endophytica sp. nov. is proposed. The type strain is SR 2-06T ( = KCTC 42060T = JCM 19844T).
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Flavisolibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from soil used for cultivating ginseng
More LessA Gram-reaction-negative, aerobic, non-motile and rod-shaped bacterial strain designated Gsoil 636T was isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea and its taxonomic position was investigated using a polyphasic approach. Gsoil 636T grew at 18–30 °C and at pH 6.0–8.0 on R2A medium. Gsoil 636T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (ones of the dominant active components of ginseng) to F2. On the basis of 16S rRNA gene sequence similarity, Gsoil 636T was shown to belong to the family Chitinophagaceae and to be related to Flavisolibacter ginsengiterrae Gsoil 492T (96.7 % sequence similarity), Flavisolibacter ginsengisoli Gsoil 643T (96.6 %) and Flavisolibacter rigui 02SUJ3T (96.6 %). The G+C content of the genomic DNA was 48.9 %. The predominant respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. DNA and chemotaxonomic data supported the affiliation of Gsoil 636T to the genus Flavisolibacter. Gsoil 636T could be differentiated genotypically and phenotypically from the species of the genus Flavisolibacter with validly published names. The isolate therefore represents a novel species, for which the name Flavisolibacter ginsenosidimutans sp. nov. is proposed, with the type strain Gsoil 636T (KCTC 22818T = JCM 18197T = KACC 14277T).
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- Other bacteria
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Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01
An anaerobic, saccharolytic bacterial strain designated GLS2T was isolated from aggregates of the psychrotolerant archaeon Methanosarcina mazei strain JL01 isolated from arctic permafrost. Bacterial cells were non-motile, spherical, ovoid and annular with diameter 0.2–4 μm. They were chemoorganoheterotrophs using a wide range of mono-, di- and trisaccharides as carbon and energy sources. The novel isolate required yeast extract and vitamins for growth. The bacteria exhibited resistance to a number of β-lactam antibiotics, rifampicin, streptomycin and vancomycin. Optimum growth was observed between 30 and 34 °C, at pH 6.8–7.5 and with 1–2 g NaCl l− 1. Isolate GLS2T was a strict anaerobe but it tolerated oxygen exposure. On the basis of 16S rRNA gene sequence similarity, strain GLS2T was shown to belong to the genus Sphaerochaeta within the family Spirochaetaceae. Its closest relatives were Sphaerochaeta globosa BuddyT (99.3 % 16S rRNA gene sequence similarity) and Sphaerochaeta pleomorpha GrapesT (95.4 % similarity). The G+C content of DNA was 47.2 mol%. The level of DNA–DNA hybridization between strains GLS2T and BuddyT was 34.7 ± 8.8 %. Major polar lipids were phosphoglycolipids, phospholipids and glycolipids; major fatty acids were C14 : 0, C16 : 0, C16 : 0 3-OH, C16 : 0 dimethyl acetal (DMA), C16 : 1n8 and C16 : 1 DMA; respiratory quinones were not detected. The results of DNA–DNA hybridization, physiological and biochemical tests demonstrated genotypic and phenotypic differentiation of strain GLS2T from the four species of the genus Sphaerochaeta with validly published names that allowed its separation into a new lineage at the species level. Strain GLS2T therefore represents a novel species, for which the name Sphaerochaeta associata sp. nov. is proposed, with the type strain GLS2T ( = DSM 26261T = VKM B-2742T).
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Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus
An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2T, was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2T grew at 53–76 °C and at pH 5.9–8.2. The DNA G+C content was 58.4 mol%. The major fatty acids were 12-methyl C18 : 0 and C18 : 0. Polar lipids were all linked to long-chain 1,2-diols, and comprised 2-acylalkyldiol-1-O-phosphoinositol (diolPI), 2-acylalkyldiol-1-O-phosphoacylmannoside (diolP-acylMan), 2-acylalkyldiol-1-O-phosphoinositol acylmannoside (diolPI-acylMan) and 2-acylalkyldiol-1-O-phosphoinositol mannoside (diolPI-Man). Strain WKT50.2T utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2T was observed on protein derivatives. WKT50.2T was sensitive to ampicillin, chloramphenicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2T belonged to the class Thermomicrobia within the phylum Chloroflexi, and was most closely related to Thermorudis peleae KI4T (99.6% similarity). DNA–DNA hybridization between WKT50.2T and Thermorudis peleae DSM 27169T was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2T from Thermorudis peleae KI4T and other members of the Thermomicrobia. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2T represents a novel species, for which the name Thermorudis pharmacophila sp. nov. is proposed, with the type strain WKT50.2T ( = DSM 26011T = ICMP 20042T). Emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus are also proposed, and include the description of a novel respiratory quinone, MK-8 2,3-epoxide (23%), in Thermomicrobium roseum.
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Hypnocyclicus thermotrophus gen. nov., sp. nov. isolated from a microbial mat in a hydrothermal vent field
More LessThe bacterial strain, IR-2T, was isolated from a microbial mat sampled near a hydrothermal vent in the Greenland Sea. Phylogenetic analysis, based on the 16S rRNA gene, showed that the closest relatives of IR-2T were Ilyobacter tartaricus, Ilyobacter insuetus, Propionigenium modestum and Fusobacterium varium (91 % 16S rRNA gene sequence similarity). The cells of the novel strain were Gram-stain-negative and pleomorphic; changing from long motile rods to non-motile ring structures during the growth cycle. Growth occurred at 20–55 °C (optimally at 48 °C), with 1–6 % (w/v) NaCl (optimally with 2 %), and at pH 5.3–8.0 (optimally at pH 6.0–8.0). The strain had obligate fermentative growth on various sugars and yeast extract. The DNA G+C content of strain IR-2T was 25.7 mol%. The cell sugars comprised mainly ribose, mannose and glucose, while the main polar lipids were glycolipids, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. The fatty acid content of strain IR-2 was dominated by saturated and unsaturated iso-branched or anteiso-branched forms. Strain IR-2 represents a novel genus and species, for which the name Hypnocyclicus thermotrophus gen. nov., sp. nov. is proposed. The type strain is IR-2T ( = DSM 100055 = JCM 30901).
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Spirochaeta odontotermitis sp. nov., an obligately anaerobic, cellulolytic, halotolerant, alkaliphilic spirochaete isolated from the termite Odontotermes obesus (Rambur) gut
More LessA Gram-stain-negative spirochaete (strain JC202T) was isolated from the gut of the termite Odontotermes obesus (Rambur) from Rann of Kutch, Gujarat, India. This strain was obligately anaerobic, mesophilic, halotolerant and required alkaline conditions for growth. Strain JC202T was resistant to rifampicin and kanamycin, but sensitive to gentamicin, tetracycline, ampicillin and chloramphenicol. Strain JC202T possessed phosphatidylglycerol, diphosphatidylglycerol, glycolipid and six unidentified lipids. C18 : 1ω7c was the predominant cellular fatty acid with significant proportions of C16 : 0, C18 : 1ω9c, C14 : 0, C18 : 0, C16 : 1ω5c, C18 : 1ω5c and C20 : 1ω9c. The DNA G+C content of strain JC202T was 59 mol%. Based on 16S rRNA gene sequence analysis, strain JC202T is considered to belong to the genus Spirochaeta with Spirochaeta sphaeroplastigenens JC133T (100 % similarity), Spirochaeta alkalica Z-7491T (99.92 %), Spirochaeta americana ATCC BAA-392T (99.47 %) and other members of the genus Spirochaeta ( < 93.83 %) as the closest phylogenetic neighbours. However, mean DNA–DNA hydridization values between strain JC202T and S. sphaeroplastigenens JC133T, S. alkalica DSM 8900T ( = Z-7491T) and S. americana DSM 14872T ( = ASpG1T) were 55 ± 2, 22 ± 3 and 32 ± 1 %, respectively. On the basis of physiological, biochemical, chemotaxonomic (including metabolome) and genomic differences from the previously described taxa, strain JC202T is differentiated from other members of the genus Spirochaeta and is considered to represent a novel species, for which the name Spirochaeta odontotermitis sp. nov. is proposed. The type strain is JC202T ( = KCTC 15324T = NBRC 110104T).
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Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring
More LessAn obligately thermophilic, chemolithotrophic, microaerophilic bacterium, designated strain GBS1T, was isolated from the water column of Great Boiling Spring, Nevada, USA. Thiosulfate was required for growth. Although capable of autotrophy, growth of GBS1T was enhanced in the presence of acetate, peptone or Casamino acids. Growth occurred at 70–85 °C with an optimum at 80 °C, at pH 6.50–7.75 with an optimum at pH 7.25, with 0.5–8 % oxygen with an optimum at 1–2 % and with ≤ 200 mM NaCl. The doubling time under optimal growth conditions was 1.3 h, with a final mean cell density of 6.2 ± 0.5 × 107 cells ml− 1. Non-motile, rod-shaped cells 1.4–2.4 × 0.4–0.6 μm in size occurred singly or in pairs. The major cellular fatty acids (>5 % of the total) were C20 : 1ω9c, C18 : 0, C16 : 0 and C20 : 0. Phylogenetic analysis of the GBS1T 16S rRNA gene sequence indicated an affiliation with Thermocrinis ruber and other species of the genus Thermocrinis, but determination of 16S rRNA gene sequence similarity ( ≤ 97.10 %) and in silico estimated DNA–DNA hybridization values ( ≤ 18.4 %) with the type strains of recognized Thermocrinis species indicate that the novel strain is distinct from described species. Based on phenotypic, genotypic and phylogenetic characteristics, a novel species, Thermocrinis jamiesonii sp. nov., is proposed, with GBS1T ( = JCM 19133T = DSM 27162T) as the type strain.
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Streptobacillus notomytis sp. nov., isolated from a spinifex hopping mouse (Notomys alexis Thomas, 1922), and emended description of Streptobacillus Levaditi et al. 1925, Eisenberg et al. 2015 emend.
A pleomorphic, Gram-negative, rod-shaped, indole-, oxidase- and catalase-negative, non-spore-forming, non-motile bacterium was isolated in 1979 from the heart of a spinifex hopping mouse (Notomys alexis Thomas, 1922) with septicaemia and stored as Streptobacillus moniliformis in the strain collection of the Animal Health Laboratory, South Perth, Western Australia (AHL 370-1), as well as under CCUG 12425. On the basis of 16S rRNA gene sequence analyses, the strain was assigned to the genus Streptobacillus, with 99.4 % sequence similarity to the type strain of Streptobacillus moniliformis, 95.6 % sequence similarity to the type strain of Streptobacillus hongkongensis and 99.0 % sequence similarity to the type strain of Streptobacillus felis. The clear differentiation of strain AHL 370-1T from Streptobacillus moniliformis, Streptobacillus hongkongensis and Streptobacillus felis was also supported by rpoB, groEL and recA nucleotide and amino acid sequence analysis. Average nucleotide identity was 87.16 % between strain AHL 370-1T and Streptobacillus moniliformis DSM 12112T. Physiological data confirmed the allocation of strain AHL 370-1T to the family Leptotrichiaceae, considering the very similar profiles of enzyme activities and fatty acids compared to closely related species. Within the genus Streptobacillus, isolate AHL 370-1T could also be separated unambiguously from the type strains of Streptobacillus moniliformis, Streptobacillus hongkongensis and Streptobacillus felis by MALDI-TOF mass spectrometry. Two further strains (KWG2 and KWG24) isolated from asymptomatic black rats in Japan were highly similar to AHL 370-1T. On the basis of these data, we propose the novel species Streptobacillus notomytis sp. nov., with the type strain AHL 370-1T ( = CCUG 12425T = DSM 100026T = CCM 8593T = EF 12425T).
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Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant
More LessA strictly anaerobic, Gram-stain-positive, non-spore-forming, rod-shaped bacterial strain, designated BS-1T, was isolated from an anaerobic digestion reactor during a study of bacteria utilizing galactitol as the carbon source. Its cells were 0.3–0.5 μm × 2–4 μm, and they grew at 35–45 °C and at pH 6.0–8.0. Strain BS-1T produced H2, CO2, ethanol, acetic acid, butyric acid and caproic acid as metabolic end products of anaerobic fermentation. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain BS-1T represented a novel bacterial genus within the family Ruminococcaceae, Clostridium Cluster IV. The type strains that were most closely related to strain BS-1T were Clostridium sporosphaeroides KCTC 5598T (94.5 %), Clostridium leptum KCTC 5155T (94.3 %), Ruminococcus bromii ATCC 27255T (92.1 %) and Ethanoligenens harbinense YUAN-3T (91.9 %). Strain BS-1T had 17.6 % and 20.9 % DNA–DNA relatedness values with C. sporosphaeroides DSM 1294T and C. leptum DSM 753T, respectively. The major components of the cellular fatty acids were C16 : 0 dimethyl aldehyde (DMA) (22.1 %), C16 : 0 aldehyde (14.1 %) and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA; 10.0 %). The genomic DNA G+C content was 50.0 mol%. Phenotypic and phylogenetic characteristics allowed strain BS-1T to be clearly distinguished from other taxa of the genus Clostridium Cluster IV. On the basis of these data, the isolate is considered to represent a novel genus and novel species within Clostridium Cluster IV, for which the name Caproiciproducens galactitolivorans gen. nov., sp. nov. is proposed. The type species is BS-1T ( = JCM 30532T and KCCM 43048T).
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- Eukaryotic micro-organisms
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Description and phylogenetic position of Corlissina maricaensis gen. nov., sp. nov. (Karyorelictea, Geleiidae), a novel interstitial ciliate from Brazil, with redefinition of the family Geleiidae
More LessCorlissina maricaensis gen. nov., sp. nov. was obtained from samples of sediment collected in a brackish lagoon of Maricá city, Rio de Janeiro state, Brazil. The morphological description was based on live observations, after protargol staining, and scanning electron microscopy. The novel species has a cylindrical body shape that is slightly contractile, 230–550 × 35–65 μm, a cytoplasm with many globular inclusions, one row of irregular cortical granules between each somatic kinety, approximately 40–62 somatic kineties, two globular macronuclei measuring 9–24 μm and one micronucleus of approximately 4–9 μm. A subapical oral cavity was approximately 20–80 × 9–25 μm, with an adoral zone on the left side of the buccal field, which was composed of 32–60 polykineties and a paroral at the right side that was composed of 40–57 short polykineties. The new genus is distinguished from other geleiids by a loop-shaped posterior end of the paroral ciliature, made up of two rows of short polykineties, and the oralization of the central superior kinety (K0i), forming a row of dikinetids that borders the adoral zone internally, followed by several rows of monokinetids. In the phylogenetic analyses, the novel species was recovered as the sister group of Parduczia orbis with full support values based on 18S rRNA gene sequences. This work also indicates some problems in the definitions of the Geleiidae and proposes a new diagnosis for this karyorelictid family.
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Morphological and phylogenetic studies on three members of the genus Pseudochilodonopsis (Ciliophora, Cyrtophoria) isolated from brackish waters in China, including a novel species, Pseudochilodonopsis quadrivacuolata sp. nov.
More LessThree cyrtophorian ciliates isolated from brackish biotopes in China, Pseudochilodonopsis quadrivacuolata sp. nov., Pseudochilodonopsis fluviatilis Foissner, 1988 and Pseudochilodonopsis mutabilis Foissner, 1981 , were investigated using living observation and protargol-staining methods. P. quadrivacuolata sp. nov. can be characterized as follows: cell size 50–70 × 30–40 μm in vivo; body oval with posterior end rounded; four tetragonally positioned contractile vacuoles; 12–15 nematodesmal rods; five right and six left somatic kineties; terminal fragment positioned apically on dorsal side, consisting of 11–14 basal bodies; four or five fragments in preoral kinety. P. fluviatilis and P. mutabilis were generally consistent with previous descriptions. In addition, a brief revision and a key to Pseudochilodonopsis are presented. The small-subunit (SSU) rRNA gene was also sequenced to support the identification of these species. Phylogenetic analyses based on molecular data indicate that the genera Pseudochilodonopsis and Chilodonella are closely related and both are well outlined; that is, all known congeners for which SSU rRNA gene sequence data are available group together, forming the core part of the family Chilodonellidae.
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Yamadazyma riverae sp. nov., a yeast species isolated from plant materials
Nine strains of a novel yeast species were isolated from rotting wood, tree bark, ant nests or living as endophytes in leaves of Vellozia gigantea. Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species was related to Candida insectorum in the Yamadazyma clade. The novel species differed from closely related species by 10 and 11 substitutions in the ITS region and the D1/D2 domains of the large subunit of the rRNA gene, respectively. The species is heterothallic and forms asci with one to two hat-shaped ascospores. The name Yamadazyma riverae sp. nov. is proposed for the novel species. The type strain is UFMG-CM-Y444T ( = CBS 14121T) and the allotype strain is TT12 ( = CBS 14098 = UFMG-CM-Y577). The Mycobank number is MB 813221.
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Starmera pilosocereana sp. nov., a yeast isolated from necrotic tissue of cacti in a sandy coastal dune ecosystem
More LessTwo strains of a novel cactophilic yeast species were isolated from the columnar cactus Pilosocereus arrabidae in a sand dune ecosystem in Rio de Janeiro, Brazil. Phylogenetic analysis of sequences of the large subunit rRNA gene D1/D2 domains showed that the strains represent a sister species to Starmera caribaea, from which it differs by 21 nt substitutions and two indels. The novel species is heterothallic and the asci are deliquescent with the formation of two to four hat-shaped ascospores. The name Starmera pilosocereana sp. nov. is proposed for the species. The type strain is UFMG-CM-Y316T ( = CBS 13266T) and the allotype is UFMG-CM-Y346a ( = CBS 13265). The Mycobank number is MB 810683. In addition, Candida stellimalicola belonging to the Starmera clade, is reassigned to Starmera as a new combination.
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Description of Diutina gen. nov., Diutina siamensis, f.a. sp. nov., and reassignment of Candida catenulata, Candida mesorugosa, Candida neorugosa, Candida pseudorugosa, Candida ranongensis, Candida rugosa and Candida scorzettiae to the genus Diutina
Three strains (DMKU-RE28, DMKU-RE43T and DMKU-RE123) of a novel anamorphic yeast species were isolated from rice leaf tissue collected in Thailand. DNA sequence analysis demonstrated that the species forms a sister pair with Candida ranongensis CBS 10861T but differs by 24–30 substitutions in the LSU rRNA gene D1/D2 domains and 30–35 substitutions in the ITS region. A phylogenetic analysis based on both the small and the large rRNA gene subunits confirmed this connection and demonstrated the presence of a clade that also includes Candida catenulata, Candida mesorugosa, Candida neorugosa, Candida pseudorugosa, Candida rugosa and Candida scorzettiae. The clade is not closely affiliated to any known teleomorphic genus, and forms a well-separated lineage from currently recognized genera of the Saccharomycetales. Hence, the genus Diutina gen. nov. is proposed to accommodate members of the clade, including Diutina siamensis f.a. sp. nov. and the preceding seven Candida species. The type strain is DMKU-RE43T ( = CBS 13388T = BCC 61183T = NBRC 109695T).
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Morphology and molecular phylogeny of Pleuronema orientale spec. nov. and Pleuronema paucisaetosum spec. nov. (Ciliophora, Scuticociliata) from Hangzhou Bay, China
More LessTwo novel species, Pleuronema orientale spec. nov. and Pleuronema paucisaetosum spec. nov., isolated from coastal waters of Hangzhou Bay, China, were investigated with standard methods. Pleuronema orientale is characterized as follows: size in vivo 95–135 × 50–85 μm; usually one spherical macronucleus; 12–15 prolonged caudal cilia; two or three preoral kineties and 42–50 somatic kineties; membranelle 1 (M1) about 20 % of the anterior fragment of membranelle 2 (M2a) in length, consisting of three longitudinal rows of kinetosomes; posterior end of M2a hook-like; membranelle 3 (M3) three-rowed. Pleuronema paucisaetosum is characterized as follows: size in vivo about 55–85 × 25–55 μm; four or five preoral kineties and 21–23 somatic kineties; posterior end of M2a hook-like; M3 three-rowed. The small-subunit rRNA gene was sequenced for both species. Phylogenetic analyses revealed that P. orientale is most closely related to Pleuronema puytoraci and that P. paucisaetosum is sister to Pleuronema grolierei and Pleuronema setigerum (GenBank accession no. JX310015). With the inclusion of the two new sequences, the monophyly of the genus Pleuronema is not supported.
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- ICSP Matters
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Alicyclobacillus fodiniaquatilis sp. nov., isolated from acid mine water
Two novel, Gram-stain-variable, moderately thermophilic, acidophilic, rod-shaped, endospore-forming bacteria, G45-16T and G45-17, were isolated from acid mine water of Zijin copper mine in Fujian Province, China. Phylogenetic analysis of 16S rRNA gene sequences showed that they were closely related to Alicyclobacillus acidoterrestris ATCC 49025T with sequence similarities of 96.8 %. Cells grew aerobically at 20–45 °C (optimum, 40 °C), at pH 2.5–5.5 (optimum, pH 3.5) and in the presence of 0–4.0 % (w/v) NaCl. Strains contained MK-7 as the major menaquinone and the major cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 51.3 and 49.8 mol% (T m) for G45-16T and G45-17, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with their relatives and DNA–DNA relatedness values, it is concluded that strains G45-16T and G45-17 represent a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus fodiniaquatilis sp. nov. is proposed; the type strain is G45-16T ( = CGMCC 1.15049T = NBRC 111483T).
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Volumes and issues
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