- Volume 64, Issue Pt_8, 2014
Volume 64, Issue Pt_8, 2014
- Notification List
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 64, part 5, of the IJSEM
More LessThis listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Archaea
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Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota
A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76T, was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6–0.9 µm and possessed archaella and archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas of high and low electron density, as well as tubule-like structures. Strain EN76T had an S-layer with p3 symmetry, so far only reported for members of the Sulfolobales . Crenarchaeol was the major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids. The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively. The genome of strain EN76T had a DNA G+C content of 52.7 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain EN76T is affiliated with the recently proposed phylum Thaumarchaeota , sharing 85 % 16S rRNA gene sequence identity with the closest cultivated relative ‘Candidatus Nitrosopumilus maritimus’ SCM1, a marine ammonia-oxidizing archaeon, and a maximum of 81 % 16S rRNA gene sequence identity with members of the phyla Crenarchaeota and Euryarchaeota and any of the other recently proposed phyla (e.g. ‘Korarchaeota’ and ‘Aigarchaeota’). We propose the name Nitrososphaera viennensis gen. nov., sp. nov. to accommodate strain EN76T. The type strain of Nitrososphaera viennensis is strain EN76T ( = DSM 26422T = JMC 19564T). Additionally, we propose the family Nitrososphaeraceae fam. nov., the order Nitrososphaerales ord. nov. and the class Nitrososphaeria classis nov.
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- Actinobacteria
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Streptomyces graminifolii sp. nov., isolated from bamboo (Sasa borealis) litter
More LessThe taxonomic position of strain JL-22T, isolated from litter of a bamboo (Sasa borealis) forest, was determined using a polyphasic approach. The organism had phenotypic and morphological properties consistent with it being a member of the genus Streptomyces . Phylogenetic analysis of the 16S rRNA gene sequence showed that strain JL-22T was closely related to Streptomyces prunicolor NRRL B-12281T (99.2 %), Streptomyces galilaeus JCM 4757T (99.0 %) and Streptomyces chartreusis NBRC 12753T (99.0 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain JL-22T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Based on phenotypic and genotypic data, strain JL-22T represents a novel species of the genus Streptomyces , for which the name Streptomyces graminifolii sp. nov. is proposed. The type strain is JL-22T ( = KACC 17180T = NBRC 109806T).
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Luteococcus sediminum sp. nov., isolated from deep subseafloor sediment of the South Pacific Gyre
More LessA Gram-stain-positive, strictly aerobic, coccus-shaped, non-motile, yellow-pigmented bacterium, designated strain XH208T, was isolated from a deep subseafloor sediment sample collected from the South Pacific Gyre (41° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH208T belonged to the genus Luteococcus and showed the highest 16S rRNA gene sequence similarities with Luteococcus peritonei CCUG 38120T (96.9 %), Luteococcus japonicus DSM 10546T (95.4 %) and Luteococcus sanguinis CCUG 33897T (95.2 %). The DNA G+C content of strain XH208T was 66.9 mol%. The cell wall of strain XH208T possessed a type A3γ peptidoglycan (ll-diaminopimelic acid–glycine), and ribose, glucose and galactose as the major whole-cell sugars. The major fatty acids were C17 : 1ω8c, C17 : 1ω6c, and C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3). The major respiratory quinone was menaquinone MK-9(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. On the basis of data from the polyphasic analysis, strain XH208T is considered to represent a novel species in the genus Luteococcus , for which the name Luteococcus sediminum sp. nov. is proposed. The type strain is XH208T ( = DSM 27277T = JCM 19259T).
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Streptomyces chumphonensis sp. nov., isolated from marine sediments
Two actinomycete strains, KK1-2T and CPB4-7, were isolated from marine sediments collected in Chumphon province, Thailand. Chumphon province, Thailand. Their taxonomic positions were determined using a polyphasic approach. The morphological, cultural and chemotaxonomic characteristics of these isolates were consistent with the classification of the strains as representing a member of the genus Streptomyces . They contained ll-diaminopimelic acid in their cell wall peptidoglycan; the whole-cell sugars were ribose and glucose. The predominant menaquinones were MK9-(H6) and MK9-(H8). The major polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. On the basis of 16S rRNA gene sequence similarity studies, these isolates were determined to be closely related to Streptomyces xinghaiensis JCM 16958T (98.2 %), Streptomyces rimosus subsp. paromomycinus JCM 4541T (98.1 %), Streptomyces sclerotialus JCM 4828T (98.1 %) and Streptomyces flocculus JCM 4476T (98.0 %). The G+C contents of the genomic DNA of strains KK1-2T and CPB4-7 were 73.3 and 74.2 mol%, respectively. They could be clearly distinguished from the related type strains by a low DNA–DNA relatedness and phenotypic differences. On the basis of these results, these strains represent a novel species of the genus Streptomyces , for which the name Streptomyces chumphonensis sp. nov. (type strain KK1-2T = JCM 18522T = TISTR 2106T = PCU 330T) is proposed.
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Rhodococcus enclensis sp. nov., a novel member of the genus Rhodococcus
A novel actinobacterial strain, designated, NIO-1009T, was isolated from a marine sediment sample collected from Chorao Island, Goa, India. Phylogenetic analysis comparisons based on 16S rRNA gene sequences between strain NIO-1009T and other members of the genus Rhodococcus revealed that strain NIO-1009T had the closest sequence similarity to Rhodococcus kroppenstedtii DSM 44908T and Rhodococcus corynebacterioides DSM 20151T with 99.2 and 99.1 %, respectively. Furthermore, DNA–DNA hybridization results showed that R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T were 39.5 (3.0 %) and 41.7 (2.0 %) with strain NIO-1009T, respectively, which were well below the 70 % limit for any novel species proposal. Phylogenetically strain NIO-1009T forms a stable clade with and R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T with 100 % bootstrap values. Strain NIO-1009T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the cell wall sugars. The major fatty acids were C16 : 0, C18 : 1ω9c, C16 : 1(ω6c and/or ω7c) and 10-methyl C18 : 0. The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 66.9 mol%. The phenotypic and genotypic data showed that strain NIO-1009T warrants recognition as a novel species of the genus Rhodococcus for which the name Rhodococcus enclensis sp. nov., is proposed; the type strain is NIO-1009T ( = NCIM 5452T = DSM 45688T).
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Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan
An actinomycete strain, K12-0602T, was isolated from the root of a Helleborus orientalis plant in Japan. The 16S rRNA gene sequence of strain K12-0602T showed that it had a close relationship with members of the family Micromonosporaceae and the 16S rRNA gene sequence similarity values between strain K12-0602T and type strains of type species of 27 genera belonging to the family Micromonosporaceae were below 96.2 %. MK-9 (H4) and MK-9 (H6) were detected as major menaquinones, and galactose, xylose, mannose and ribose were present in the whole-cell hydrolysate. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were iso-C15 : 0, iso-C16 : 0, C17 : 1ω9c and anteiso-C17 : 0. Phosphatidylethanolamine was detected as the phospholipid corresponding to phospholipid type II. The G+C content of the genomic DNA was 67 mol%. Analyses of the cell-wall peptidoglycan by TLC and LC/MS showed that it was composed of alanine, glycine, hydroxylglutamic acid and an unknown amino acid, which was subsequently determined to be 3,4-dihydroxydiaminopimelic acid using instrumental analyses, including NMR and mass spectrometry. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strain K12-0602T represents a novel species of a new genus in the family Micromonosporaceae , for which the name Rhizocola hellebori gen. nov., sp. nov. is proposed. The type strain of the type species is K12-0602T ( = NBRC 109834T = DSM 45988T). This is the first report, to our knowledge, of 3,4-dihydroxydiaminopimelic acid being found as a diamino acid in bacterial cell-wall peptidoglycan.
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Nocardioides nanhaiensis sp. nov., an actinobacterium isolated from a marine sediment sample
A rod- to coccus-shaped, non-spore-forming actinobacterium, strain YIM M13091T, was isolated from a marine sediment sample collected from the South China Sea and examined by a polyphasic approach to clarify its taxonomic position. This Gram-staining-positive, aerobic actinobacterium did not produce substrate mycelium and aerial hyphae, and no diffusible pigments were produced on the media tested. The optimum growth occurred at 30 °C, 1 % (w/v) NaCl and pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Nocardioides , with low levels (≤96.2 %) of sequence similarity with respect to Nocardioides kribbensis KSL-2T and other members of the genus Nocardioides . Whole-organism hydrolysates of the strain contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4), with MK-8 in a minor amount. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, hydroxyphosphatidylinositol and phosphatidylcholine, were the main polar lipids detected, while iso-C16 : 0 and C18 : 1ω9c were the major fatty acids. The G+C content of the genomic DNA was 68.5 mol%. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a member of the genus Nocardioides , and the name Nocardioides nanhaiensis sp. nov. (Type strain YIM M13091T = JCM 18127T = CCTCC AA 2011020T) is proposed for the novel species.
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Conyzicola lurida gen. nov., sp. nov., isolated from the root of Conyza canadensis
More LessA novel Gram-stain-positive, non-spore-forming, pale yellow, irregular rod-shaped bacterium designated strain HWE2-01T was isolated from the surface-sterilized root of horseweed (Conyza canadensis). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HWE2-01T belongs to the family Microbacteriaceae and showed sequence similarity levels of 97.1–97.7 % with species of the genus Salinibacterium , 95.9–97.6 % with species of the genus Leifsonia and 97.1 % with Homoserinimonas aerilata . The highest sequence similarity (97.7 %) was with Salinibacterium xinjiangense 0543T. The genomic DNA G+C content of the novel strain was 68.1 mol%. The predominant cellular fatty acid of strain HWE2-01T was anteiso-C15 : 0, major menaquinones were MK-10, MK-9 and MK-11, and diagnostic polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The peptidoglycan of the novel strain contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The cell-wall sugars of strain HWE2-01T were galactose, mannose and rhamnose. The murein was of the acetyl type. Based on the results of the phenotypic and phylogenetic analysis, strain HWE2-01T differed in some respects from other members of the family Microbacteriaceae . Therefore, strain HWE2-01T is proposed to represent a novel species of a new genus in the family Microbacteriaceae with the name Conyzicola lurida gen. nov., sp. nov. (type strain = HWE2-01T = KCTC 29231T = JCM 19257T).
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Halopolyspora alba gen. nov., sp. nov., isolated from sediment
A novel halophilic, filamentous actinomycete, designated strain AFM 10251T, was isolated from a sediment sample collected from the Dead Sea, Israel. The isolate grew with 10–35 % multi-salts, and did not grow without NaCl or MgCl2. The isolate formed a white aerial mycelium, and long chains of arthrospores with more than 10 spores per chain. The spores were spherical or oval with warty surfaces, and sterile mycelium was present between individual spores. The isolate contained meso-diaminopimelic acid and a small proportion of ll-diaminopimelic acid as cell-wall diamino acids, and galactose and arabinose as whole-cell sugars. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. Major fatty acids were iso-C16 : 0, iso-C17 : 0, iso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain AFM 10251T was 66.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM 10251T and the genus Actinopolyspora formed a distinct lineage. Analysis of the secondary structures of variable areas of the 16S rRNA gene showed that strain AFM 10251T was different from all recognized species of the genus Actinopolyspora and members of the family Pseudonocardiaceae . Analysis of the signature nucleotides of the 16S rRNA gene showed that strain AFM 10251T and Actinopolyspora halophila formed a single group, but with base pair differences at positions 127 : 234 and 183 : 194. On the basis of analysis of chemical and molecular characteristics, strain AFM 10251T is considered to represent a novel species of a new genus in the family Actinopolysporaceae , for which the name Halopolyspora alba gen. nov., sp. nov. is proposed. The type strain of Halopolyspora alba is AFM 10251T ( = DSM 45976T = CGMCC 4.7114T).
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Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus)
More LessSix Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (Callithrix jacchus). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a ‘Y’ shape. Strains MRM 3/1T and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1T showed a peptidoglycan type unique among members of the genus Bifidobacterium . The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, hsp60, clpC and rpoB gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1T and MRM 4/2 had the highest similarities to Bifidobacterium scardovii DSM 13734T (94.6 %) and Bifidobacterium stellenboschense DSM 23968T (94.5 %). Analysis of hsp60 showed that both strains were closely related to B. stellenboschense DSM 23968T (97.5 % similarity); however, despite this high degree of similarity, our isolates could be distinguished from B. stellenboschense DSM 23968T by low levels of DNA–DNA relatedness (30.4 % with MRM 3/1T). Strains MRM 3/1T and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus Bifidobacterium than to other genera in the family Bifidobacteriaceae . On the basis of these results, strains MRM 3/1T and MRM 4/2 represent a novel species within the genus Bifidobacterium , for which the name Bifidobacterium aesculapii sp. nov. is proposed; the type strain is MRM 3/1T ( = DSM 26737T = JCM 18761T).
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Sinosporangium siamense sp. nov., isolated from soil and emended description of the genus Sinosporangium
An actinomycetes strain A-T 1946T that developed spherical sporangia containing non-motile spores on aerial mycelia was isolated from dry deciduous forest soil in Thailand. 16S rRNA gene sequence analysis indicated that strain A-T 1946T belongs to the genus Sinosporangium , being closely related to Sinosporangium album 6014T (98.8 % sequence similarity). The DNA–DNA relatedness values were 43.7–50.9 %, which were significantly below 70 % and differentiated strain A-T 1946T from the closest species. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained rhamnose, ribose, madurose and glucose. The predominant menaquinone was MK-9(H2). The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol-mannoside, N-acetylglucosamine-containing phospholipids, two unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were unsaturated C16 : 1 and C17 : 1, and saturated C16 : 0 and 10-methyl-C17 : 0. Following an evaluation of phenotypic, chemotaxonomic and genotypic characteristics, the isolate is proposed to represent a novel species of genus Sinosporangium to be named Sinosporangium siamense sp. nov. The type strain is A-T 1946T ( = BCC 29081T = NBRC 109515T). An emended description of the genus Sinosporangium is also provided.
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Actinophytocola sediminis sp. nov., an actinomycete isolated from a marine sediment
A novel actinomycete strain, designated YIM M13705T, was isolated from a marine sediment sample of the South China Sea and its characteristics were determined by a polyphasic approach. The slowly growing, Gram-stain-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced on the media tested. At maturity, spore chains were formed on aerial hyphae and substrate mycelium was not fragmented. Whole-cell hydrolysates of the strain contained meso-diaminopimelic acid and galactose, glucose, ribose and rhamnose. The predominant menaquinones were MK-9(H4) and MK-10(H2). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and ninhydrin-positive phosphoglycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 68.2 mol%. On the basis of 16S rRNA gene sequence, the strain was shown to be most closely related to species of the genus Actinophytocola . DNA–DNA hybridization relatedness values (<70 %) of the isolate with its closest neighbour Actinophytocola xinjiangensis QAIII60T supported classification of the isolate as a representative of a novel species. On the basis of phylogenetic analysis, and phenotypic and genotypic data, it is concluded that the new isolate belongs to a novel species of the genus Actinophytocola , for which the name Actinophytocola sediminis sp. nov. (type strain YIM M13705T = DSM 45939T = BCRC 16956T) is proposed.
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Geodermatophilus brasiliensis sp. nov., isolated from Brazilian soil
A Gram-reaction-positive bacterial isolate, designated Tü 6233T, with rudimentary, coral-pink vegetative mycelium that formed neither aerial mycelium nor spores, was isolated from a Brazilian soil sample. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus . Cell-wall hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose as the diagnostic sugar. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 1ω8c and the predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, an unknown glycophospholipid and an unknown phospholipid. The DNA G+C content of the strain was 75.4 mol%. The 16S rRNA gene sequence identity with members of the genus Geodermatophilus was 94.2–98.7 %. Based on phenotypic, chemotaxonomic and phylogenetic data, strain Tü 6233T is proposed to represent a novel species, Geodermatophilus brasiliensis sp. nov., with the type strain Tü 6233T ( = DSM 44526T = CECT 8402T).
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- Firmicutes and Related Organisms
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Enterococcus olivae sp. nov., isolated from Spanish-style green-olive fermentations
Six strains of a hitherto unknown, Gram-stain-positive coccus were recovered from samples of Spanish-style green-olive fermentations. The 16S rRNA gene sequences from these isolates shared 98.7 % and 98.5 % of their nucleotide positions with those from Enterococcus saccharolyticus subsp. taiwanensis 812T and from E. saccharolyticus subsp. saccharolyticus ATCC 43076T, respectively. The sequence of the rpoA gene in the isolates was 95 % similar to that of E. saccharolyticus CECT 4309T ( = ATCC 43076T). The 16S rRNA and rpoA gene phylogenies revealed that the isolates grouped in a statistically well-supported cluster separate from E. saccharolyticus . Enzyme activity profiles as well as fermentation patterns differentiated the novel bacteria from other members of the Enterococcus genus. Finally, phenotypic, genotypic and phylogenetic data supported the identification of a novel species of the genus Enterococcus , for which the name Enterococcus olivae sp. nov. is proposed. The type strain is IGG16.11T ( = CECT 8063T = DSM 25431T).
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Lysinibacillus halotolerans sp. nov., isolated from saline-alkaline soil
A novel aerobic, halotolerant bacterium, designated strain LAM612T, was isolated from saline-alkaline soil samples from Lingxian County, Shandong Province, China. Cells of strain LAM612T were Gram-reaction-positive, endospore-forming, motile and rod-shaped. The optimal temperature and pH for growth were 35 °C and pH 6.0, respectively. Strain LAM612T could grow in the presence of up to 10 % (w/v) NaCl. The genomic DNA G+C conten was 36.4 mol% as detected by the T m method. Comparative analysis of 16S rRNA gene sequences revealed that LAM612T was closely related to Lysinibacillus sinduriensis KACC 16611T (98.0 %), L. chungkukjangi KACC 16626T (97.5 %), L. massiliensis KCTC 13178T (97.4 %), L. xylanilyticus KACC 15113T (97.2 %), L. macroides DSM 54T (97.0 %) and L. manganicus DSM 26584T (96.5 %). The DNA–DNA hybridization values between strain LAM612T and its closest relatives ranged from 20.6 % to 41.9 %. The major fatty acids of strain LAM612T were iso-C15 : 0 (40.8 %), iso-C16 : 0 (15.2 %) and anteiso-C15 : 0 (10.8 %). The cell-wall peptidoglycan content was A4α (l-Lys–d-Asp). The predominant menaquinone was MK-7 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, five unknown glycolipids and an unknown lipid. Based on the DNA–DNA hybridization results and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM612T could be distinguished from the recognized species of the genus Lysinibacillus , and was suggested to represent a novel species of this genus, for which the name Lysinibacillus halotolerans sp. nov. is proposed. The type strain is LAM612T ( = ACCC 00718T = JCM 19611T).
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Lactobacillus bombi sp. nov., from the digestive tract of laboratory-reared bumblebee queens (Bombus terrestris)
More LessThree bacterial strains belonging to the genus Lactobacillus were isolated from the digestive tracts of laboratory-reared bumblebee queens (Bombus terrestris) using MRS agar under anaerobic conditions. The isolates were identified according to 16S rRNA gene sequence analysis as undescribed members of the genus Lactobacillus , with the highest 16S rRNA gene sequence similarity (96.9 %) to the uncharacterized bacterial strain Lactobacillus sp. Mboho2r2 isolated from the stomach of a European honeybee (Apis mellifera). Lactobacillus tucceti was found to be the closest related species with a validly published name, with 92.9 % 16S rRNA gene sequence similarity to the type strain. However, phylogenetic analyses based on different markers revealed that this species is phylogenetically very distant from the novel strains. The DNA G+C content of the proposed type strain BTLCH M1/2T is 37.8 mol%. The fatty acids C19 : 1ω6c and/or C19 : 0 cyclo ω10c/19ω6, C18 : 1ω9c and C16 : 0 were predominant in all strains. Diphosphatidylglycerol, phosphatidylglycerol, a phospholipid, seven glycolipids and two phosphoglycolipids were detected in the novel strains. Growth was observed at 47 °C. The peptidoglycan type A4α l-Lys–d-Asp was determined for strain BTLCH M1/2T. Genotypic characteristics and phylogenetic analyses based on the phylogenetic markers hsp60, pheS, rpoA and tuf as well as phenotypic characteristics and the results of chemotaxonomic analyses confirmed that the new isolates belong to a novel species of the genus Lactobacillus , for which the name Lactobacillus bombi sp. nov. is proposed. The type strain is BTLCH M1/2T ( = DSM 26517T = CCM 8440T).
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Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium
Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1T, ACB7T and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7T grew weakly on sucrose only. The growth temperature range was 30–42 °C with optimum growth at 37 °C. Major metabolic fermentation end products of strain ACB1T were acetate and lactate; the only product of strains ACB7T and ACB8 was acetate. Major fatty acids of strain ACB1T were C14 : 0, C16 : 0, C16 : 1ω7c dimethyl aldehyde (DMA) and C18 : 1ω7c DMA. Major fatty acids of strain ACB7T were C12 : 0, C14 : 0, C16 : 0, C16 : 1ω7c and C16 : 1ω7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. Genomic DNA G+C content varied from 42 to 43.3 % between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1T, ACB8 and ACB7T formed two separate branches within the genus Oribacterium , with 98.1–98.6 % sequence similarity to the type strain of the type species, Oribacterium sinus . Predicted DNA–DNA hybridization values between strains ACB1T, ACB8, ACB7T and O. sinus F0268 were <70 %. Based on distinct genotypic and phenotypic characteristics, strains ACB1T and ACB8, and strain ACB7T are considered to represent two distinct species of the genus Oribacterium , for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1T ( = DSM 24637T = HM-481T = ATCC BAA-2638T) and ACB7T ( = DSM 24638T = HM-482T = ATCC BAA-2639T), respectively.
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Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium
A novel strictly anaerobic, halotolerant, organotrophic bacterium, strain P3M-3T, was isolated from a microbial mat formed under the flow of hot water emerging from a 2775 m-deep well in Tomsk region (western Siberia, Russia). Cells of strain P3M-3T were straight and curved rods, 0.2–0.4 µm in width and 1.5–20 µm in length. Strain P3M-3T grew optimally at 37 °C, pH 7.0–7.5 and in a NaCl concentration of 15 g l−1. Under optimum growth conditions, the doubling time was 1 h. The isolate was able to ferment a variety of mono-, di- and polysaccharides, including microcrystalline cellulose. Acetate, ethanol, H2 and CO2 were the main products of glucose fermentation. The DNA G+C content was 33.4 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-3T was a member of family Lachnospiraceae , whose representatives are also found in Clostridium cluster XIVa. 16S rRNA gene sequence similarity with Clostridium jejuense HY-35-12T, the closest relative, was 93.9 %. A novel genus and species, Mobilitalea sibirica gen. nov., sp. nov., are proposed based on phylogenetic analysis and physiological properties of the novel isolate. The type strain of the type species is P3M-3T ( = DSM 26468T = VKM B-2804T).
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Paenibacillus selenii sp. nov., isolated from selenium mineral soil
More LessStrain W126T, a Gram-reaction-positive, spore-forming, rod-shaped, facultatively anaerobic bacterium, motile by means of peritrichous flagella, was isolated from selenium mineral soil in Hubei province of China. 16S rRNA gene sequence analysis demonstrated that this isolate belonged to the genus Paenibacillus , with 97.9 % sequence similarity to Paenibacillus anaericanus MH21T, while compared with the other species of the genus Paenibacillus , the 16S rRNA gene sequence similarities were less than 96.0 %. DNA–DNA hybridization between strain W126T and Paenibacillus anaericanus DSM 15890T was 24 %. The major isoprenoid menaquinone was menaquinone-7. Anteiso-C15 : 0 was the major fatty acid. The DNA G+C content was 42.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. Strain W126T contained A1γ-meso-diaminopimelic acid in the cell-wall peptidoglycan. The phenotypic, chemotaxonomic and genotypic data indicate that strain W126T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus selenii sp. nov. is proposed. The type strain is W126T ( = KCTC 33420T = CCTCC AB 2014003T).
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Thermotolerant Bacillus kokeshiiformis sp. nov. isolated from marine animal resources compost
More LessA novel Gram-staining-positive, endospore-forming, rod-shaped, facultatively anaerobic, thermotolerant bacterium, designated strain MO-04T, was isolated from a marine animal resources (MAR) compost. The 16S rRNA gene sequence of strain MO-04T showed 99.4 % similarity with Bacillus thermolactis R-6488T, 94.1 % similarity with Bacillus thermoamylovorans CNCM I-1378T, 93.3 % similarity with Bacillus humi LMG 22167T, 93.2 % similarity with Bacillus niacini IFO 15566T and the similarities with other species were less than 93 %. DNA–DNA relatedness between strain MO-04T and B. thermolactis DSM 23332T was 45 %. The DNA G+C content of strain MO-04T was 33.4 mol%, comparatively lower than that of B. thermolactis R-6488T (35.0 mol%). Strain MO-04T grew at 35–61 °C (optimum 50 °C), pH 4.5–9.0 (optimum pH 7.2) and tolerated up to 8.0 % (w/v) NaCl (optimum 2 %). The MO-04T cell wall peptidoglycan type was meso-2,6-diaminopimelic acid, and the major fatty acids were C16 : 1, C14 : 1, C17 : 0 and C17 : 1. The major polar lipids were represented by diphosphatidylglycerol and phosphatidylglycerol and two unidentified phospholipids. The analysed polyphasic data presented here clearly indicate that the isolate MO-04T is considered to represent a novel species within the genus Bacillus for which the name Bacillus kokeshiiformis sp. nov. is proposed. The type strain of B. kokeshiiformis is MO-04T ( = JCM 19325T = KCTC 33163T).
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Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge
More LessA Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, aerobic bacterial strain, designated BUT-2T, was isolated from activated sludge of one herbicide-manufacturing wastewater-treatment facility in Kunshan, Jiangsu province, China, and subjected to polyphasic taxonomic studies. Analysis of the 16S rRNA gene sequence indicated that strain BUT-2T shared the highest similarity with Chryseomicrobium amylolyticum (98.98 %), followed by Chryseomicrobium imtechense (98.88 %), with less than 96 % similarlity to members of the genera Paenisporosarcina , Planococcus , Sporosarcina and Planomicrobium . Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain BUT-2T clustered with C. amylolyticum JC16T and C. imtechense MW10T, occupying a distinct phylogenetic position. The major fatty acid (>10 % of total fatty acids) type of strain BUT-2T was iso-C15 : 0. The quinone system comprised menaquinone MK-7 (77.8 %), MK-6 (11.9 %) and MK-8 (10.3 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and some unidentified phospholipids. The cell-wall peptidoglycan type of strain BUT-2T was l-Orn-d-Glu. The genomic DNA G+C content of strain BUT-2T was 48.5 mol%. Furthermore, the DNA–DNA relatedness in hybridization experiments against the reference strain was lower than 70 %, confirming that strain BUT-2T did not belong to previously described species of the genus Chryseomicrobium . On the basis of its morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strain BUT-2T is considered to represent a novel species of the genus Chryseomicrobium , for which the name Chryseomicrobium aureum sp. nov. is proposed. The type strain is BUT-2T ( = CCTCC AB2013082T = KACC 17219T).
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Planomicrobium soli sp. nov., isolated from soil
Xiaonan Luo, Jianli Zhang, Dai Li, Yuhua Xin, Di Xin and Lei FanA Gram-staining-positive bacterium, designated strain XN13T, was isolated from a soil sample collected from ALaShan National Geological Park in Inner Mongolia Autonomous Region, China and subjected to a taxonomic study using a polyphasic approach. Strain XN13T was found to have a range of chemical and morphological properties consistent with its classification in the genus Planomicrobium . Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain XN13T was related to members of the genus Planomicrobium . The closest phylogenetic relatives were Planomicrobium okeanokoites NBRC 12536T, Planomicrobium koreense JG07T, Planomicrobium mcmeekinii S23F2T and Planomicrobium flavidum ISL-41T with 98.2 %, 97.8 %, 97.8 % and 97.7 % 16S rRNA gene sequence similarity, respectively. The major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0 and C16 : 1ω11c. The predominant menaquinones were MK-8 and MK-7. The DNA G+C content was 40.3 mol%. The DNA–DNA relatedness values between strain XN13T and Planomicrobium okeanokoites KCTC 3672T, Planomicrobium koreense KCTC 3684T, P. mcmeekinii CGMCC 1.2724T, Planomicrobium flavidum KCTC 13261T, Planomicrobium chinense CGMCC 1.3454T and Planomicrobium glaciei CGMCC 1.6846T were 36 %, 30 %, 34 %, 29 %, 30 % and 31 %, respectively. The organism is different from recognized species of the genus Planomicrobium in several phenotypic characteristics. On the basis of phenotypic and genotypic properties, strain XN13T represents a novel species of the genus Planomicrobium , for which the name Planomicrobium soli sp. nov. is proposed. The type strain is XN13T ( = CGMCC 1.12259T = KCTC 33047T).
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Proposal of Effusibacillus lacus gen. nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov.
More LessA novel thermophilic, facultatively anaerobic bacterium, strain skLN1T, was isolated from the sediment of a freshwater lake in Japan. Cells of strain skLN1T were rod-shaped and Gram-stain-variable. A KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH was pH 7.25–7.50 and the optimum temperature was 50–52 °C. The G+C content of the genomic DNA was 50.8 mol%. Nitrate was reduced to nitrite. Alicyclic fatty acids were not detected, and branched-chain fatty acids were major components in the cellular fatty acid profile. MK-7 was the predominant respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strain was related most closely to Alicyclobacillus consociatus CCUG 53762T (95 % similarity). This analysis also showed that the monophyly of the genus Alicyclobacillus had been lost. On the basis of phylogenetic and phenotypic characterization, Effusibacillus lacus gen. nov., sp. nov. is proposed. The type strain of Effusibacillus lacus is skLN1T ( = NBRC 109614T = DSM 27172T). It is also proposed that Alicyclobacillus pohliae and Alicyclobacillus consociatus should be reclassified to the genus Effusibacillus as Effusibacillus pohliae comb. nov. and Effusibacillus consociatus comb. nov., respectively.
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Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks
A Gram-stain-positive, aerobic, endospore-forming, moderately halophilic rod, designated strain R1T, was isolated from rice husks and subjected to a taxonomic study using a polyphasic approach. Strain R1T produced spherical or ellipsoidal endospores at a subterminal position in swollen sporangia, and was catalase- and oxidase-positive. The isolate grew optimally at 37 °C and pH 6.0–7.0, and could grow in the presence of up to 9 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R1T belongs to the genus Bacillus . The closest relatives of strain R1T were Bacillus subtilis subsp. subtilis NCIB 3610T, Bacillus aquimaris TF-12T, and Bacillus marisflavi TF-11T, with 16S rRNA gene sequence similarities of 96.0 %, 98.4 %, and 98.7 %, respectively. DNA–DNA relatedness values between the isolate and the reference strains were ≤42±3 %. The predominant menaquinones were MK-5 (50 %) and MK-7 (50 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0 (48.6 %) and anteiso-C15 : 0 (20.6 %), and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analyses and chemotaxonomic and phenotypic characteristics, it is concluded that strain R1T represents a novel species of the genus Bacillus , for which we propose the name Bacillus oryzaecorticis sp. nov. The type strain is R1T ( = KACC 17217T = KCCM 90231T = JCM 19602T).
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Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor
More LessA novel anaerobic, mesophilic, hydrogen-producing bacterium, designated strain M2/40T, was isolated from a mesophilic, two-phase, laboratory-scale biogas reactor fed continuously with maize silage supplemented with 5 % wheat straw. 16S rRNA gene sequence comparison revealed an affiliation to the genus Clostridium sensu stricto (cluster I of the clostridia), with Clostridium cellulovorans as the closest characterized species, showing 93.8 % sequence similarity to the type strain. Cells of strain M2/40T were rods to elongated filamentous rods that showed variable Gram staining. Optimal growth occurred at 35 °C and at pH 7. Grown on glucose, the main fermentation products were H2, CO2, formate, lactate and propionate. The DNA G+C content was 29.6 mol%. The major fatty acids (>10 %) were C16 : 0, summed feature 10 (C18 : 1ω11c/ω9t/ω6t and/or unknown ECL 17.834) and C18 : 1ω11c dimethylacetal. Based on phenotypic, chemotaxonomic and phylogenetic differences, strain M2/40T represents a novel species within the genus Clostridium , for which we propose the name Clostridium bornimense sp. nov. The type strain is M2/40T ( = DSM 25664T = CECT 8097T).
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Bacillus fengqiuensis sp. nov., isolated from a typical sandy loam soil under long-term fertilization
More LessA Gram-staining-positive, endospore-forming, moderately alkaliphilic bacterium, strain NPK15T, was isolated from a typical sandy loam soil under long-term NPK fertilization in northern China and was subjected to a polyphasic taxonomic study. The diamino acid of the cell-wall peptidoglycan of strain NPK15T was found to be meso-diaminopimelic acid and the cell-wall sugars were xylose, glucose and traces of mannose. The only respiratory quinone found in strain NPK15T was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, C16 : 0 and C16 : 1ω6c/C16 : 1ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis of the strain based on its 16S rRNA gene sequence showed that it was related most closely to ‘ Bacillus thaonhiensis ’ KACC 17216 (99.59 %), B. songklensis KCTC 13881T (99.52 %) and B. abyssalis CCTCC AB 2012074T (99.00 %). DNA–DNA hybridization results indicated that the strain was distinct from other species of the genus Bacillus , the degree of relatedness being 35.4 % with B. abyssalis CCTCC AB 2012074T, 39.7 % with B. songklensis KCTC 13881T and 51.2 % with ‘ B. thaonhiensis ’ KACC 17216. The DNA G+C content of strain NPK15T was 45.5 mol%. Phenotypic, chemotaxonomic and molecular analyses identified strain NPK15T as a member of a novel species of the genus Bacillus , for which the name Bacillus fengqiuensis sp. nov. is proposed. The type strain is NPK15T ( = DSM 26745T = CCTCC AB 2013156T).
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Paenibacillus dongdonensis sp. nov., isolated from rhizospheric soil of Elymus tsukushiensis
More LessA Gram-staining-positive, endospore-forming and rod-shaped bacterial strain, designated KUDC0114T, was isolated from rhizospheric soil of Elymus tsukushiensis from Dongdo Island, one of the largest of the Dokdo Islands, South Korea. The strain displayed optimal growth at 37 °C, pH 8.5 in the absence of NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain KUDC0114T represented a member of the genus Paenibacillus and was most closely related to Paenibacillus taichungensis BCRC 17757T (98.46 %). The cell-wall peptidoglycan was A1γ type, and the predominant quinone was menaquinone-7 (MK-7). The major cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA–DNA hybridization of strain KUDC0114T with nine other strains indicated less than 23 % relatedness, and its DNA G+C content was 44.30 mol%. Based on genomic, phenotypic and phylogenetic analyses, KUDC0114T should be classified as representing novel species within the genus Paenibacillus . The name Paenibacillus dongdonensis sp. nov. is proposed. The type strain is KUDC0114T ( = DSM27607T = KCTC33221T).
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Lactobacillus furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles
More LessTwo strains of lactic acid bacteria, Nu27T and Nu29, were isolated from Nukadoko, rice bran paste for Japanese pickles. The isolates were Gram-stain-positive, rod-shaped, catalase-negative, non-motile and facultatively anaerobic lactic acid bacteria. The isolates showed identical 16S rRNA gene sequences. The closest relatives to strain Nu27T based on 16S rRNA gene sequence similarities were Lactobacillus versmoldensis KU-3T (98.9 % 16S rRNA gene sequence similarity), Lactobacillus nodensis iz4bT (96.3 %) and Lactobacillus tucceti CECT 5290T (97.2 %). DNA–DNA relatedness values revealed genotype separation of the two isolates from the above three species. Based on the physiological, biochemical and genotypic characteristics provided, the isolates represent a novel species of the genus Lactobacillus , for which name is Lactobacillus furfuricola proposed. The type strain is Nu 27T ( = JCM 18764T = NRIC 0900T = DSM 27174T).
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- Proteobacteria
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Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment
More LessStrain CMB17T was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25–30 °C, pH 6.5–7 and 0.5–1 % (w/v) NaCl. The major fatty acid was C18 : 1ω7c (87.59 %), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17T is most closely related to Paracoccus stylophorae KTW-16T (96.7 %), P. solventivorans DSM 6637T (96.4 %) and P. saliphilus YIM 90738T (96.4 %). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17T is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17T = JCM 18467T = DSM 26170T = CGMCC 1.12681T).
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Thiophaeococcus fuscus sp. nov., isolated from a lagoon
More LessA brown-coloured bacterium, designated strain JA633T, was purified from a photoheterotrophic enrichment culture obtained from black sand of a lagoon. Cells of strain JA633T were coccoid–spherical, Gram-stain-negative and motile by means of polar flagella. Strain JA633T had an obligate requirement for NaCl and could tolerate up to 4 % (w/v) NaCl. Internal photosynthetic membranes were present as vesicles. Photo-organoheterotrophy was the only growth mode observed. Strain JA633T contained bacteriochlorophyll a and a major (>85 %) unidentified carotenoid of the spirilloxanthin series. Thiamine and p-aminobenzoic acid were required for growth. Major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphotidylcholine and an unknown aminophospholipid were the major polar lipids in strain JA633T. The DNA G+C content of strain JA633T was 64.5 mol%. Strain JA633T shared highest 16S rRNA gene sequence similarity with the type strains of Thiorhodococcus kakinadensis (96.9 %), Thiophaeococcus mangrovi (96.3 %) and Thiorhodococcus bheemlicus (96.2 %), which belonged to the class Gammaproteobacteria . However, phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA633T formed a separate clade along with Thiophaeococcus mangrovi JA304T whereas the members of the genus Thiorhodococcus remained as two distinct phylogenetic lineages. Based on morphological, physiological, chemotaxonomic and molecular evidence, strain JA633T was significantly different from the type strain of Thiophaeococcus mangrovi of the family Chromatiaceae . It is thus proposed that the strain be classified as a representative of a novel species, for which the name Thiophaeococcus fuscus sp. nov. is proposed. The type strain is JA633T ( = KCTC 15337T = NBRC 109958T).
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Litoreibacter ascidiaceicola sp. nov., isolated from the golden sea squirt Halocynthia aurantium
More LessA Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated RSS4-C1T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. The novel strain grew optimally at 25 °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 revealed that strain RSS4-C1T fell within the clade comprising the type strains of species of the genus Litoreibacter . Strain RSS4-C1T exhibited the highest 16S rRNA gene sequence similarity (99.6 %) to the type strain of Litoreibacter albidus and sequence similarities of 96.5–98.5 % to type strains of other recognized species of the genus Litoreibacter . Strain RSS4-C1T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl-C18 : 1ω7c as the major fatty acids. The major polar lipids of strain RSS4-C1T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain RSS4-C1T was 58.0 mol% and its DNA–DNA relatedness values with type strains of four species of the genus Litoreibacter were 21–34 %. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain RSS4-C1T is distinct from other species of the genus Litoreibacter . On the basis of the data presented, strain RSS4-C1T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter ascidiaceicola sp. nov. is proposed. The type strain is RSS4-C1T ( = KCTC 42050T = CECT 8539T).
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Sphingorhabdus arenilitoris sp. nov., isolated from a coastal sand, and reclassification of Sphingopyxis rigui as Sphingorhabdus rigui comb. nov. and Sphingopyxis wooponensis as Sphingorhabdus wooponensis comb. nov.
More LessA Gram-stain-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated GJR-7T, was isolated from coastal sand of the South Sea of South Korea. Strain GJR-7T grew optimally at 30 °C, at pH 7.0–7.5 and without NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GJR-7T clustered with the type strains of Sphingopyxis wooponensis , Sphingopyxis rigui and Sphingorhabdus planktonica , with which it exhibited 16S rRNA gene sequence similarity values of 96.0–96.3 %. Sequence similarities to the type strains of other recognized species were less than 95.5 %. Strain GJR-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, 11-methyl C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) or C14 : 0 2-OH. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain GJR-7T was 55.5 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, revealed that strain GJR-7T is separated from the type strains of Sphingopyxis wooponensis , Sphingopyxis rigui and Sphingorhabdus planktonica . On the basis of the data presented, strain GJR-7T is considered to represent a novel species of the genus Sphingorhabdus , for which the name Sphingorhabdus arenilitoris sp. nov. is proposed. The type strain is GJR-7T ( = KCTC 42051T = CECT 8531T). It is also proposed that Sphingopyxis wooponensis and Sphingopyxis rigui should be reclassified as members of the genus Sphingorhabdus .
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Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov.
A light-pink-pigmented, microaerophilic bacterium was obtained from a methanotrophic consortium enriched from acidic Sphagnum peat and designated strain Pf56T. Cells of this bacterium were Gram-negative, non-motile, thick curved rods that contained a vesicular intracytoplasmic membrane system characteristic of some purple non-sulfur alphaproteobacteria. The absorption spectrum of acetone/methanol extracts of cells grown in the light showed maxima at 363, 475, 505, 601 and 770 nm; the peaks at 363 and 770 nm are characteristic of bacteriochlorophyll a. However, in contrast to purple non-sulfur bacteria, strain Pf56T was unable to grow phototrophically under anoxic conditions in the light. Best growth occurred on some sugars and organic acids under micro-oxic conditions by means of fermentation. The fermentation products were propionate, acetate and hydrogen. Slow chemo-organotrophic growth was also observed under fully oxic conditions. Light stimulated growth. C1 substrates were not utilized. Strain Pf56T grew at pH 4.0–7.0 (optimum pH 5.5–6.5) and at 15–30 °C (optimum 22–28 °C). The major cellular fatty acids were 19 : 0 cyclo ω8c and 18 : 1ω7c; quinones were represented by ubiquinone Q-10. The G+C content of the DNA was 70.0 mol%. Strain Pf56 displays 93.6–94.7 and 92.7–93.7 % 16S rRNA gene sequence similarity to members of the families Methylocystaceae and Beijerinckiaceae , respectively, and belongs to a large cluster of environmental sequences retrieved from various wetlands and forest soils in cultivation-independent studies. Phenotypic, genotypic and chemotaxonomic characteristics of strain Pf56T suggest that it represents a novel genus and species of bacteriochlorophyll a-containing fermentative bacteria, for which the name Roseiarcus fermentans gen. nov., sp. nov. is proposed. Strain Pf56T ( = DSM 24875T = VKM B-2876T) is the type strain of Roseiarcus fermentans, and is also the first characterized member of a novel family within the class Alphaproteobacteria , Roseiarcaceae fam. nov.
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Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide–degrading bacterium isolated from activated sludge
Strain BUT-14T, a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90 % of butachlor, acetochlor and alachlor (100 mg l−1) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14T was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821T (97.9 %), N. naphthalenivorans KACC 15258T (97.4 %), N. pentaromativorans JCM 12182T (97.4 %) and N. barchaimii DSM 25411T (97.1 %) and lower (<97 %) sequence similarities to all other species of the genus Novosphingobium . Chemotaxonomic analysis revealed that strain BUT-14T possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C18 : 1ω7c (46.9 %), C17 : 1ω6c (17.9 %), summed feature 3, C14 : 0 2-OH (4.4 %), C15 : 0 2-OH (3.1 %) and C16 : 0 (5.51 %) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14T showed low DNA–DNA relatedness with N. soli DSM 22821T (41.5±2.9 %), N. naphthalenivorans JCM 12182T (49.2±4.2 %), N. pentaromativorans KACC 12295T (53.2±1.9 %) and N. barchaimii DSM 25411 (51.2±4.5 %). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization supports the suggestion that strain BUT-14T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14T ( = CCTCC AB 2013086T = KACC 17147T = JCM 19923T).
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Loktanella variabilis sp. nov., isolated from a tidal flat
More LessTwo Gram-negative, aerobic and rod-shaped or ovoid bacterial strains with different colony colours (greyish yellow and moderate orange), designated J-MR2-YT and J-MR2-O, were isolated from a tidal flat in the South Sea of South Korea. The two novel strains grew optimally at 35–37 °C. Strains J-MR2-YT and J-MR2-O showed no difference in their 16S rRNA gene sequences, and the mean DNA–DNA relatedness between them was 94 %. Phylogenetic trees based on 16S rRNA gene sequences revealed that strains J-MR2-YT and J-MR2-O clustered consistently with the type strains of Loktanella soesokkakensis , L. hongkongensis and L. cinnabarina , with which it exhibited 97.83–99.06 % sequence similarity. Sequence similarities to the type strains of the other recognized species of the genus Loktanella were 94.01–96.26 %. Both strains contained Q-10 as the predominant ubiquinone, C18 : 1ω7c as the major fatty acid and phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminolipid as the major polar lipids. The DNA G+C contents of strains J-MR2-YT and J-MR2-O were 68.1 and 68.4 mol%, respectively, and DNA–DNA relatedness values with the type strains of L. soesokkakensis , L. hongkongensis and L. cinnabarina were 19–37 %. Differential phenotypic properties, together with their phylogenetic and genetic distinctiveness, revealed that the two novel strains are separated from other species of the genus Loktanella . On the basis of the data presented, strains J-MR2-YT and J-MR2-O are proposed to represent a novel species of the genus Loktanella , for which the name Loktanella variabilis sp. nov. is proposed. The type strain is J-MR2-YT ( = KCTC 42074T = CECT 8572T).
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Boseongicola aestuarii gen. nov., sp. nov., isolated from a tidal flat sediment
More LessA Gram-stain-negative, aerobic, non-motile and pleomorphic (coccoid, ovoid or rod-shaped) bacterial strain, BS-W15T, isolated from a tidal flat sediment at Boseong in South Korea, was characterized taxonomically. Strain BS-W15T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W15T joined the cluster comprising the type strains of Profundibacterium mesophilum , Hwanghaeicola aestuarii , M. pelagius and M. salinus , showing 93.5–96.4 % sequence similarities. Strain BS-W15T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain BS-W15T contained phosphatidylcholine and phosphatidylglycerol as major components, differentiating it from those of the type strains of P. mesophilum , H. aestuarii , M. pelagius and M. salinus . The DNA G+C content of strain BS-W15T was 58.7 mol%. The differential phenotypic properties, together with the phylogenetic and chemotaxonomic data, demonstrate that strain BS-W15T is distinct from type strains of P. mesophilum , H. aestuarii , M. pelagius and M. salinus . On the basis of the data presented, strain BS-W15T is considered to represent a novel genus and species, for which the name Boseongicola aestuarii gen. nov., sp. nov. is proposed. The type strain is BS-W15T ( = KCTC 32576T = CECT 8489T).
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Devosia pacifica sp. nov., isolated from deep-sea sediment
More LessA novel bacterial strain, NH131T, was isolated from deep-sea sediment of South China Sea. Cells were strictly aerobic, Gram-stain negative, short rod-shaped and motile with a single lateral flagellum. Strain NH131T grew optimally at pH 6.5–7.0 and 25–30 °C. 16S rRNA gene sequence analysis revealed that strain NH131T belonged to the genus Devosia , sharing the highest sequence similarity with the type strain, Devosia geojensis BD-c194T (96.2 %). The predominant fatty acids were C18 : 1ω7c, 11-methyl C18 : 1ω7c, C18 : 0 and C16 : 0. Ubiquinone 10 was the predominant ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, three glycolipids and two unknown lipids. The DNA G+C content of strain NH131T was 63.0 mol%. On the basis of the results of polyphasic identification, it is suggested that strain NH131T represents a novel species of the genus Devosia for which the name Devosia pacifica sp. nov. is proposed. The type strain is NH131T ( = JCM 19305T = KCTC 32437T).
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Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.
More LessA Gram-stain-negative bacterial strain, 10-17T, was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 10-17T was phylogenetically related to Enterobacter hormaechei CIP 103441T, Enterobacter cancerogenus LMG 2693T, Enterobacter asburiae JCM 6051T, Enterobacter mori LMG 25706T, Enterobacter ludwigii EN-119T and Leclercia adecarboxylata LMG 2803T, having 99.5 %, 99.3 %, 98.7 %, 98.5 %, 98.4 % and 98.4 % 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17T ( = LMG 27195T = NCIMB 14836T = CCUG 62994T). Enterobacter sacchari Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1T( = CGMCC 1.12102T = LMG 26783T).
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Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan
More LessAn aerobic, Gram-stain-negative, agarolytic rod-shaped bacterium, designated KMM 9504T, was isolated from a sediment sample collected from the seashore of the Sea of Japan. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9504T belonged to the genus Simiduia as it was most closely related to Simiduia areninigrae KCTC 23293T (97.3 % sequence similarity). Strain KMM 9504T was characterized by the major ubiquinone Q-8, and by the predominance of C16 : 1ω7c, C17 : 1ω8c, followed by C16 : 0, C15 : 0, C17 : 0 and C12 : 1 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid, unknown phospholipids, and unknown lipids. Based on the distinctive phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results, it is concluded that strain KMM 9504T represents a novel species of the genus Simiduia , for which the name Simiduia litorea sp. nov. is proposed. The type strain of the species is strain KMM 9504T ( = NRIC 0917T = JCM 19759T).
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Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes
More LessPolyvinyl-alcohol-degrading bacteria were isolated from the fruit of a grape in Yokosuka, Japan. The isolated strain, Zumi 37T, was a Gram-stain-negative, rod-shaped, motile, non-spore-forming and strictly aerobic chemo-organotroph, showing optimal growth at pH 7.5, 30 °C and 0.1 % (w/v) NaCl. The major respiratory quinone was Q-8. The predominant fatty acids were iso-C15 : 0, C16 : 0 and C16 : 1ω7c. The major polyamines were homospermidine and putrescine. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of the novel strain was 64.2 mol%. 16S rRNA gene sequence comparison revealed that strain Zumi 37T belongs to the family Sinobacteraceae within the class Gammaproteobacteria . Steroidobacter denitrificans DSM 18526T was the most closely related species with a validly published name, with 98.0 % similarity based on 16S rRNA gene sequence comparison (and showed less than 87.5 % sequence similarity to members of the genera Alkanibacter , Fontimonas , Hydrocarboniphaga , Nevskia and Solimonas with known 16S rRNA gene sequences). Phenotypes for growth under aerobic conditions and on complex media and major fatty acid composition, differed greatly from those of with comparatively high 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain Zumi 37T represents a novel species in a new genus for which the name Povalibacter uvarum gen. nov., sp. nov. is proposed. The type strain of the type species is Zumi 37T ( = JCM 18749T = DSM 26723T).
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Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007
A Gram-staining-negative, non-pigmented, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, devoid of bacteriochlorophyll, designated strain CC-AMW-ET, was isolated from surface seawater off the coast at Kending, Taiwan. Strain CC-AMW-ET shared 95.7 and 93.9 % 16S rRNA gene sequence similarity, respectively, with the type strains of the type species of the genera Donghicola ( Donghicola eburneus SW-277T) and Roseovarius ( Roseovarius tolerans EL-172T). The predominant (>75 % of the total) fatty acid was summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminolipid. In addition, moderate amounts of an unidentified lipid and trace amounts of an unidentified phospholipid were detected. The DNA G+C content was 67.9 mol%. Ubiquinone Q-10 was the sole respiratory quinone. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics (in particular its polar lipid pattern), we conclude that strain CC-AMW-ET represents a novel genus and species of the family Rhodobacteraceae , for which the name Youngimonas vesicularis gen. nov., sp. nov. is proposed. The type strain of Youngimonas vesicularis is CC-AMW-ET ( = JCM 18819T = BCRC 80549T). In addition, an emended description of the genus Donghicola Yoon et al. 2007 and the reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. (type strain Y-2T = MCCC 1A00107T = LMG 24574T = CGMCC 1.7081T) are proposed.
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Fulvimonas yonginensis sp. nov., isolated from greenhouse soil, and emended description of the genus Fulvimonas
More LessA novel strain, designated 5GHs31-2T, was isolated from a greenhouse soil sample collected from Yongin city, South Korea. Cells of strain 5GHs31-2T were Gram-stain-negative, rod-shaped, polar flagellated and yellow-pigmented. The isolate was aerobic, catalase-negative and oxidase-positive and grew optimally at 28–30 °C and pH 7.0. Strain 5GHs31-2T revealed the highest 16S rRNA gene sequence similarities with Fulvimonas soli LMG 19981T (97.6 %), Dyella thiooxydans ATSB10T (97.5 %) and Frateuria terrea VA24T (97.4 %). Furthermore, the neighbour-joining tree showed that strain 5GHs31-2T was a representative of a member of the genus Fulvimonas . Strain 5GHs31-2T contained iso-C16 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0 and iso-C17 : 0 as the major fatty acids, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an aminolipid as the main polar lipids and Q-8 as the predominant quinone. The genomic DNA G+C content of 5GHs31-2T was 73.0 mol%. According to DNA–DNA hybridization experiments, DNA–DNA relatedness values between strain 5GHs31-2T and its closest phylogenetic neighbours were below 70 %. Based on the taxonomic data, strain 5GHs31-2T represents a novel species of the genus Fulvimonas , for which the name Fulvimonas yonginensis sp. nov. is proposed. The type strain is 5GHs31-2T ( = KACC 16952T = DSM 28344T).
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Paracoccus lutimaris sp. nov., isolated from a tidal flat sediment
More LessA Gram-negative, coccoid or oval-shaped and gliding bacterial strain, designated HDM-25T, belonging to the Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HDM-25T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HDM-25T fell within the clade comprising the species of the genus Paracoccus , clustering with the type strain of Paracoccus aminophilus , with which it exhibited the highest 16S rRNA gene sequence similarity (97.7 %). The 16S rRNA gene sequence similarity between strain HDM-25T and the type strains of the other species of Paracoccus was 93.6–97.0 %. The DNA G+C content was 65.9 mol% and the mean DNA–DNA relatedness between strain HDM-25T and the type strain of P. aminophilus was 10.7±2.7 % (9.9±4.0 %, reciprocal analysis). Strain HDM-25T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain HDM-25T is distinguishable from other species of the genus Paracoccus . On the basis of the data presented, strain HDM-25T is considered to represent a novel species of the genus Paracoccus , for which the name Paracoccus lutimaris sp. nov. is proposed. The type strain is HDM-25T ( = KCTC 42007T = CECT 8525T).
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Amphiplicatus metriothermophilus gen. nov., sp. nov., a thermotolerant alphaproteobacterium isolated from a hot spring
More LessA thermotolerant, Gram-strain-negative, non-spore-forming and strictly aerobic bacterium, designated GU51T, was isolated from Guhai hot spring in Jimsar county, Xinjiang province, north-west China. Each cell of strain GU51T consisted of an oval body and two symmetrical long (3–6 µm) prosthecae. The strain moved by polar flagellum. Oxidase and catalase were produced. Strain GU51T grew within the ranges of 37–65 °C (optimum 48–50 °C), 0.5–7.5 % (w/v) NaCl (optimum 2–3 %) and pH 6.0–9.0 (optimum pH 7.5). The major respiratory quinone detected was ubiquinone 10 (U-10) and the genomic DNA G+C content was 66.7±0.4 mol%. Major fatty acids (>5 %) were C16 : 0, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The polar lipids consisted of diphosphatidylglycerol, five glycolipids, phosphatidylglycerol and an unknown phospholipid. Phylogenetic analysis showed the closest relatives of strain GU51T were members of the genus Parvularcula with 92.3 % 16S rRNA gene sequence similarity. On the basis of this polyphasic taxonomic characterization, it is suggested that strain GU51T represents a novel species of a new genus in the family ‘ Parvularculaceae ’, for which the name Amphiplicatus metriothermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is GU51T ( = CGMCC 1.12710T = JCM 19779T).
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Roseibium aquae sp. nov., isolated from a saline lake
More LessA Gram-staining-negative bacterium, strain DSG-S4-2T, was isolated from Dasugan Lake, a saline lake (salinity 3.1 %, w/v) in Qaidam basin, Qinghai, China and its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S4-2T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–3.8 µm long and motile by means of a single polar flagellum. Strain DSG-S4-2T was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. PufLM and coxL genes were present, bacteriochlorophyll a (BChl a) and a carotenoid pigment were produced. Growth was observed in the presence of 0–8.0 % (w/v) NaCl (optimum, 1.0–2.0 %), at 20–40 °C (optimum, 35 °C) and pH 6.5–10.5 (optimum, pH 7.5–8.0). Strain DSG-S4-2T contained Q-10 as the sole respiratory quinone. The polar lipids contained two aminolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sulphoquinovosyldiacylglyceride, phosphatidylcholine and some unknown phospholipids, like the other members of the genus Roseibium . The predominant fatty acid (>70 %) was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 61.4 mol% (determined from melting temperature). Phylogenetic trees (neighbour-joining, maximum-likelihood and maximum-parsimony) based on 16S rRNA gene sequences showed that strain DSG-S4-2T was associated with the members of the genus Roseibium , with highest 16S rRNA gene sequence similarity to Roseibium denhamense OCh 254T (96.3 %) and Roseibium hamelinense OCh 368T (96.3 %). Based on the data presented above, it is concluded that strain DSG-S4-2T represents a novel species of the genus Roseibium , for which the name Roseibium aquae sp. nov. is proposed. The type strain is DSG-S4-2T ( = CGMCC 1.12426T = JCM 19310T).
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Campylobacter corcagiensis sp. nov., isolated from faeces of captive lion-tailed macaques (Macaca silenus)
More LessAn investigation of the prevalence of Campylobacter ureolyticus in a variety of animals led to the identification of the strain CIT 045T, in the faeces of captive lion-tailed macaques (Macaca silenus). Originally, believed to be Campylobacter ureolyticus based on the colony morphology and positive urease test, analysis of 16S rRNA and hsp60 gene sequences of this isolate revealed that the strain differs significantly from other species of the genus Campylobacter described to date. Species-specific primers for 16S rRNA and hsp60 genes were designed and used to identify two additional strains isolated from faeces samples from other macaques. Nucleotide sequence analysis of the 16S rRNA and hsp60 genes revealed ≤95 % and ≤82 % sequence similarity to recognized species of the genus Campylobacter respectively. All three isolates formed a distinct group within the genus Campylobacter based on their 16S rRNA and hsp60 sequences and matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) profiles. The unique species status was further supported by phenotypic characteristics of the isolates. All isolates were found to be oxidase-, catalase- and urease-positive, they grew well at 37 °C and 42 °C and produced H2S on TSI (triple-sugar iron) and SIM (sulfide indole motility) media. The name Campylobacter corcagiensis sp. nov. is proposed for this novel species, with the strain CIT 045T as the type strain CIT 045T ( = LMG 27932T, CCUG 64942T).
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Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed
More LessA novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBMT, was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBMT were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBMT was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16–37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBMT, but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBMT grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C15 : 0 and C18 : 1ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBMT into a distinct lineage within the class Deltaproteobacteria . The closest, cultivated phylogenetic relative of strain SCBMT was Desulfarculus baarsii DSM 2075T, with only 91.7 % 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBMT represents a novel genus and species of sulfate-reducing bacteria, for which the name Desulfocarbo indianensis gen. nov., sp. nov. is proposed. The type strain of Desulfocarbo indianensis is SCBMT ( = DSM 28127T = JCM 19826T). Desulfocarbo is the second genus of the order Desulfarculales .
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- Bacteroidetes
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Roseivivax marinus sp. nov., isolated from deep water
More LessA Gram-stain-negative, strictly aerobic, non-motile, cream, long rod-shaped bacterium, designated strain ZL136T, was isolated from deep water of the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain belonged to the genus Roseivivax with highest sequence similarity to Roseivivax halodurans OCh 239T (97.0 %), followed by Roseivivax isoporae sw-2T (96.9 %). Growth occurred at 4–37 °C (optimum 32 °C), pH 6.0–10.0 (optimum 8.0) and in the presence of 0–12 % (w/v) NaCl (optimum 3–4 %) in marine broth 2216. Strain ZL136T did not produce bacteriochlorophyll a. The predominant fatty acids were C18 : 1ω7c and/or C18 : 1ω6c, C18 : 0, C16 : 0 and 11-methyl C18 : 1ω7c. The major polar lipids of ZL136T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified lipid. The major respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content of strain ZL136T was 67.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain ZL136T was classified as a representative of a novel species in the genus of Roseivivax , for which the name Roseivivax marinus sp. nov. is proposed. The type strain is ZL136T ( = JCM 19386T = KCTC 32470T).
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Chitinophaga ginsengihumi sp. nov., isolated from soil of ginseng rhizosphere
More LessA novel strain designated SR18T was isolated from the rhizosphere soil of a ginseng in Korea. Cells were Gram-staining-negative, motile by gliding, catalase-positive and oxidase-negative, non-spore-forming rods. The isolate grew aerobically at 15–45 °C (optimum 28 °C), pH 5.5–7.5 (optimum pH 7.0) and with 0–3.0 % (w/v) NaCl (optimum 1.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SR18T belongs to the genus Chitinophaga with sequence similarity of 97.2 % and 97.0 % to Chitinophaga japonensis 758T and Chitinophaga rupis CS5-B1T, respectively. Similarity to other species of the genus Chitinophaga was 92.8–95.5 %. The predominant menaquinone was MK-7. Major fatty acids were iso-C15 : 0 and C16 : 1ω5c. The polar lipids included phosphatidylethanolamine, unidentified phospholipids, unknown aminolipids and unknown lipids. The genomic DNA G+C content was 45.3 mol%. DNA–DNA relatedness between strain SR18T and C. japonensis NBRC 16041T was 29–32 %. On the basis of polyphasic analysis from this study, strain SR18T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga ginsengihumi sp. nov. is proposed. The type strain is SR18T ( = KACC 17604T = NBRC 109832T).
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Volumes and issues
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Volume 74 (2024)
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