scholarly journals Terrisporobacter petrolearius sp. nov., isolated from an oilfield petroleum reservoir

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3522-3526 ◽  
Author(s):  
Yu Deng ◽  
Xiang Guo ◽  
Yanwei Wang ◽  
Mingxiong He ◽  
Kedong Ma ◽  
...  

A Gram-staining-positive, spore-forming, strictly anaerobic bacterium, designated strain LAM0A37T, was isolated from enrichment samples collected from a petroleum reservoir in Shengli oilfield. Cells of strain LAM0A37T were rod-shaped and motile by peritrichous flagella. The optimal temperature and pH for growth were 40 °C and 7.0–7.5, respectively. The strain did not require NaCl for growth but tolerated up to 3 % (w/v) NaCl. Strain LAM0A37T was able to utilize glucose, fructose, maltose, xylose, sorbitol, cellobiose, melibiose and melezitose as sole carbon sources. Sulfite was used as an electron acceptor. The main products of glucose fermentation were acetate and CO2. The predominant fatty acid was C16 : 0 (23.6 %). The main polar lipid profile comprised of five glycolipids, six phospholipids and two lipids. No menaquinone was detected. The genomic DNA G+C content was 27.1 ± 0.2 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate was a member of the genus Terrisporobacter, and was most closely related to Terrisporobacter glycolicus JCM 1401T and Terrisporobacter mayombei DSM 6539T with 98.3 % 16S rRNA gene sequence similarity to both. DNA–DNA hybridization values between strain LAM0A37T and type strains of Terrisporobacter glycolicus and Terrisporobacter mayombei were 45.6 ± 0.3 % and 38.3 ± 0.4 %, respectively. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0A37T is suggested to represent a novel species of the genus Terrisporobacter, for which the name Terrisporobacter petrolearius sp. nov. is proposed. The type strain is LAM0A37T ( = ACCC 00740T = JCM 19845T).

Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.


2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).


2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4839-4844 ◽  
Author(s):  
Eu Jin Chung ◽  
Hwan Sik Yoon ◽  
Kyung Hyun Kim ◽  
Che Ok Jeon ◽  
Young Ryun Chung

A 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).


2011 ◽  
Vol 61 (2) ◽  
pp. 384-391 ◽  
Author(s):  
Wolfgang Eder ◽  
Gerhard Wanner ◽  
Wolfgang Ludwig ◽  
Hans-Jürgen Busse ◽  
Frank Ziemke-Kägeler ◽  
...  

A Gram-negative, oxidase- and catalase-positive, flagellated, rod-shaped bacterium, designated strain EM 1T, was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belonged to the family Oxalobacteraceae within the class Betaproteobacteria; the closest phylogenetic relative was Undibacterium pigrum DSM 19792T (96.7 % gene sequence similarity). The new isolate could be distinguished from the type strain of U. pigrum DSM 19792T (=CCUG 49009T=CIP 109318T) and from strain CCUG 49012T, which has been described as a second genomovar of this species, on the basis of genotypic data and several phenotypic properties. An S-layer was present in the cell envelope in U. pigrum DSM 19792T, but was absent in strains EM 1T and CCUG 49012T. Test conditions were established that enabled strain CCUG 49012T to be distinguished from U. pigrum DSM 19792T. As found for U. pigrum, the main fatty acids of strains EM 1T and CCUG 49012T were summed feature 3 (including unsaturated C16 : 1 ω7c), straight-chain C16 : 0 and unsaturated C18 : 1 ω7c (low percentage in strain CCUG 49012T), and C10 : 0 3-OH was the sole hydroxylated fatty acid. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile was mainly composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. In contrast to U. pigrum and strain CCUG 49012T, where ubiquinone Q8 was reported as the sole quinone component, the quinone system of strain EM 1T consisted of ubiquinone Q-8 (64 %) and Q-7 (36 %). The 16S rRNA gene sequence similarity, the polar lipid profile and the absence of C12-hydroxylated fatty acids all indicated that strain EM 1T was affiliated with the genus Undibacterium. 16S rRNA gene sequence similarity values lower than 97.0 % and several differentiating phenotypic traits demonstrated that strain EM 1T represents a novel species for which the name Undibacterium oligocarboniphilum sp. nov. is proposed (type strain EM 1T=DSM 21777T=CCUG 57265T). In addition, based on previously published results and this study, a separate species, Undibacterium parvum sp. nov., is proposed with strain CCUG 49012T (=DSM 23061T=CIP 109317T) as the type strain.


2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4495-4502 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yi-Ling Chen ◽  
Wen-Ming Chen

A bacterial strain designated TNR-2T was isolated from spring water in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-2T were aerobic, Gram-stain-negative, straight rods, motile by a single polar flagellum and containing poly-β-hydroxybutyrate. The cells were covered by large capsules and formed yellow colonies. Growth occurred at 15–37 °C (optimum, 20–30 °C), with 0–1.0 % NaCl (optimum, 0–0.1 %) and at pH 5.0–8.0 (optimum, pH 6.0). According to a phylogenetic tree based on 16S rRNA gene sequence analysis, strain TNR-2T belonged to the genus Sphingomonas and clustered with Sphingomonas alpina S8-3T, with which it shared the highest 16S rRNA gene sequence similarity (95.6 %). The major fatty acids (>10 %) of strain TNR-2T were C18 : 1ω7c, C17 : 1ω6c and C16 : 0. The DNA G+C content was 62.8 mol%. The major isoprenoid quinone was Q-10. The major polyamine was homospermidine. The polar lipid profile consisted of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, two uncharacterized glycolipids and an uncharacterized phospholipid. Phenotypic characteristics of the novel strain differed from those of the closest related species of the genus Sphingomonas. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TNR-2T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas fonticola sp. nov. is proposed. The type strain is TNR-2T ( = BCRC 80539T = LMG 27384T = KCTC 32258T).


2011 ◽  
Vol 61 (10) ◽  
pp. 2348-2352 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
H.-J. Busse ◽  
Chiu-Chung Young ◽  
W.-A. Lai ◽  
...  

A Gram-staining-positive coccus, designated CC-SPL15-2T, was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2T belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352T (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351T (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which supported the affiliation of strain CC-SPL15-2T to the genus Salinicoccus. DNA–DNA relatedness between strain CC-SPL15-2T and S. hispanicus CCUG 43288T was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2T from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2T be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2T ( = DSM 23267T  = CCM 7756T).


2007 ◽  
Vol 57 (6) ◽  
pp. 1315-1317 ◽  
Author(s):  
Seil Kim ◽  
Hyunyoung Jeong ◽  
Jongsik Chun

A strictly anaerobic, halophilic, motile, endospore-forming, rod-shaped bacterium, designated strain HY-45-18T, was isolated from a sediment sample of a tidal flat in Korea. The isolate produced butyric acid, propionic acid, glycerol and H2 as fermentation end products from glucose. Strain HY-45-18T is halophilic as it was unable to grow in the absence of sea salts. A 16S rRNA gene sequence analysis clearly indicated that the tidal flat isolate is a member of cluster I of the order Clostridiales, which contains the type species of Clostridium, Clostridium butyricum. The closest phylogenetic neighbour of strain HY-45-18T was Clostridium ganghwense KCTC 5146T (96.5 % 16S rRNA gene sequence similarity). Several phenotypic characteristics can be readily used to differentiate the isolate from phylogenetically related clostridia. Therefore, strain HY-45-18T represents a novel species of the genus Clostridium, for which the name Clostridium aestuarii sp. nov. is proposed. The type strain is HY-45-18T (=IMSNU 40129T=KCTC 5147T=JCM 13194T).


2006 ◽  
Vol 56 (7) ◽  
pp. 1621-1629 ◽  
Author(s):  
Yuji Sekiguchi ◽  
Hiroyuki Imachi ◽  
Ambar Susilorukmi ◽  
Mizuho Muramatsu ◽  
Akiyoshi Ohashi ◽  
...  

Three anaerobic, moderately thermophilic, syntrophic primary alcohol- and lactate-degrading microbes, designated strains JLT, JE and OL, were isolated from sludges of thermophilic (55 °C) digesters that decomposed either municipal solid wastes or sewage sludge. The strains were strictly anaerobic organisms. All three strains grew at 25–60 °C and pH 5.5–8.5 and optimum growth was observed at 45–50 °C and pH 6.0–7.0. The three organisms grew chemo-organotrophically on a number of carbohydrates in the presence of yeast extract. In co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus, all strains could utilize ethanol, glycerol and lactate syntrophically for growth, although these compounds were not metabolized in pure culture without additional external electron acceptors. All strains could reduce thiosulphate. Quinones were not detected. The DNA G+C contents of strains JLT, JE and OL were 38.0, 37.3 and 37.7 mol%, respectively. Major cellular fatty acids of the strains were iso-C15 : 0, C16 : 0 and unsaturated species of C15 : 1. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belong to a deeply branched lineage of the phylum Firmicutes; the most closely related species was Thermovenabulum ferriorganovorum (16S rRNA gene sequence similarity of 88 %). The three strains were phylogenetically very closely related to each other (99–100 % 16S rRNA gene sequence similarity) and were physiologically and chemotaxonomically similar. These genetic and phenotypic properties suggest that the strains should be classified as representatives of a novel species and genus; the name Tepidanaerobacter syntrophicus gen. nov., sp. nov. is proposed. The type strain of Tepidanaerobacter syntrophicus is strain JLT (=JCM 12098T=NBRC 100060T=DSM 15584T).


2011 ◽  
Vol 61 (11) ◽  
pp. 2702-2705 ◽  
Author(s):  
P. Kämpfer ◽  
S. Wellner ◽  
K. Lohse ◽  
N. Lodders ◽  
K. Martin

A Gram-positive-staining, non-endospore-forming actinobacterium, designated C7T, was isolated from the leaf surface of Trifolium repens. On the basis of 16S rRNA gene sequence analysis, strain C7T was shown to belong to the genus Williamsia and was most closely related to Williamsia maris SJS0289/JS1T (98.0 % 16S rRNA gene sequence similarity), Williamsia deligens IMMIB RIV-956T (96.4 %) and Williamsia serinedens IMMIB SR-4T (95.7 %). The quinone system consisted predominantly of the menaquinones MK-9(H2), MK-8(H2) and MK-7(H2). The major components in the polar lipid profile were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1ω7c, C16 : 0, C18 : 0, C18 : 1ω9c and tuberculostearic acid, supported the affiliation of strain C7T with the genus Williamsia. Physiological and biochemical analysis revealed clear differences between strain C7T and its closest phylogenetic neighbours. Therefore, strain C7T represents a novel species, for which the name Williamsia phyllosphaerae sp. nov. is proposed. The type strain is C7T ( = CCUG 60465T = CCM 7855T).


2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3352-3358 ◽  
Author(s):  
Om Prakash ◽  
Yogesh Nimonkar ◽  
Ankita Vaishampayan ◽  
Mrinal Mishra ◽  
Shreyas Kumbhare ◽  
...  

A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase β subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase β subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA–DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17  : 0 cyclo, C19  : 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T. The polar lipid profile mainly comprised phospholipids. The DNA G+C content was 59.1 mol%. Thus, based on the findings of the current study, strain 29Y89BT showed clear delineations from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T, and is thus considered to represent a novel species of the genus Pantoea, for which the name Pantoea intestinalis sp. nov. is proposed. The type strain is 29Y89BT ( = DSM 28113T = MCC 2554T).


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