scholarly journals Pseudodesulfovibrio sediminis sp. nov., a Mesophilic and Neutrophilic Sulfate-reducing Bacterium Isolated From Sediment of a Brackish Lake

2021 ◽  
Author(s):  
Ayaka Takahashi ◽  
Hisaya Kojima ◽  
Miho Watanabe ◽  
Manabu Fukui
Keyword(s):  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Brackish Lake ◽  
Phenotypic Properties ◽  
Circular Chromosome ◽  
Sulfate Reducing ◽  
Optimum Growth Temperature ◽  
Reducing Conditions ◽  
Fermentative Growth ◽  
Ph Range

Abstract A novel mesophilic and neutrophilic sulfate-reducing bacterium, strain SF6T, was isolated from sediment of a brackish lake in Japan. Cells of strain SF6T were motile and rod-shaped with length of 1.2–2.5 μm and width of 0.6–0.9 μm. Growth was observed at 10–37°C with an optimum growth temperature of 28°C. The pH range for growth was 5.8–8.2 with an optimum pH of 7.0. The most predominant fatty acid was anteiso-C15 : 0. Under sulfate-reducing conditions, strain SF6T utilized formate, lactate, ethanol and glucose as growth substrate. Chemolithoautotrophic growth on H2 was also observed. Fermentative growth occurred on pyruvate. As electron acceptor, sulfate, sulfite, thiosulfate and nitrate supported heterotrophic growth of the strain. The complete genome of strain SF6T is composed of a circular chromosome with length of 3.8 Mbp and G + C content of 54 mol%. Analyses of the 16S rRNA gene and whole genome sequence indicated that strain SF6T belongs to the genus Pseudodesulfovibrio but distinct form all existing species in the genus. On the basis of its genomic and phenotypic properties, strain SF6T (= DSM111931T = NBRC 114895T) is proposed as the type strain of a new species, with name of Pseudodesulfovibrio sediminis sp. nov.

scholarly journals Methyloradius Palustris Gen. Nov., Sp. Nov., a Methanol-oxidizing Bacterium Isolated From Snow

2021 ◽  
Author(s):  
Takeshi Miyadera ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
Phylogenetic Analyses ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Circular Chromosome ◽  
Optimum Growth Temperature ◽  
The Family ◽  
Bacterium Strain ◽  
Ph Range ◽  
A New Species

Abstract A novel methylotrophic bacterium, strain Zm11 T , was isolated from reddish brown snow collected in a moor in Japan. Cells of the isolate were Gram-stain-negative, motile and rod-shaped (0.6-0.7×1.2-2.7 μm). Growth was observed at 5–32°C with an optimum growth temperature of 25–28°C. The pH range for growth was 5.4–7.8 with an optimum pH of 6.8. The strain utilized only methanol as carbon and energy sources for aerobic growth. The major cellular fatty acids (>40% of total) were summed feature 3 (C 16:1 ω 7 c and/or C 16:1 ω 6 c ) and C 16 : 0 . The predominant quinone was Q-8. The complete genome of strain Zm11 T is composed of a circular chromosome (2,800,413 bp), with G + C content of 46.4 mol%. Phylogenetic analyses were conducted based on the 16S rRNA gene sequence and conserved proteins encoded in the genome. The results of analyses indicate that strain Zm11 T is a member of the family Methylophilaceae but does not belong to any existing genus. On the basis of its genomic and phenotypic properties, strain Zm11 T (= DSM111909 T = NBRC114766 T ) is proposed as the type strain of a new species in a new genus, Methyloradius palustris gen. nov., sp. nov.

Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge

2004 ◽  
Vol 54 (1) ◽  
pp. 227-233 ◽  
Author(s):  
H. Moussard ◽  
S. L'Haridon ◽  
B. J. Tindall ◽  
A. Banta ◽  
P. Schumann ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Central Indian Ridge ◽  
Sulfate Reducing ◽  
The Family ◽  
Fermentative Growth ◽  
Bacterium Strain ◽  
Indian Ridge ◽  
Ph Range

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812T, was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55–80 °C, with an optimum at 70 °C. The NaCl concentration range for growth was 10–35 g l−1, with an optimum at 25 g l−1. The pH range for growth was 6–6·7, with an optimum at approximately pH 6·25. H2 and CO2 were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812T were similar to those of Thermodesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the family Thermodesulfobacteriaceae (similarity values of less than 90 %). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812T could be distinguished from Thermodesulfobacterium commune, the type species of the type genus of the family Thermodesulfobacteriaceae. Finally, the G+C content of the genomic DNA of strain CIR29812T (46·0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812T represents a novel species of a new genus, Thermodesulfatator, of which Thermodesulfatator indicus is the type species. The type strain is CIR29812T (=DSM 15286T=JCM 11887T).

scholarly journals Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park

2009 ◽  
Vol 76 (4) ◽  
pp. 1014-1020 ◽  
Author(s):  
Scott D. Hamilton-Brehm ◽  
Jennifer J. Mosher ◽  
Tatiana Vishnivetskaya ◽  
Mircea Podar ◽  
Sue Carroll ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Optimal Growth ◽  
Small Subunit ◽  
Rrna Gene ◽  
Cellulolytic Bacterium ◽  
Small Subunit Rrna ◽  
Phenotypic Properties ◽  
Fermentative Growth ◽  
Ph Range

ABSTRACT A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47T, was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram-positive rod approximately 2 μm long by 0.2 μm wide and grew at temperatures between 55 and 85°C, with the optimum at 78°C. The pH range for growth was 6.0 to 8.0, with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rate at 0.75 h−1. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass, and Populus. OB47T was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbitol, carboxymethylcellulose, and casein. Yeast extract stimulated growth, and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H2, and CO2, although lactate and ethanol were produced in 5-liter batch fermentations. The G+C content of the DNA was 35 mol%, and sequence analysis of the small subunit rRNA gene placed OB47T within the genus Caldicellulosiruptor. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated Caldicellulosiruptor obsidiansis sp. nov. and OB47 is the type strain (ATCC BAA-2073).

scholarly journals Desulfotomaculum thermosubterraneum sp. nov., a thermophilic sulfate-reducer isolated from an underground mine located in a geothermally active area

2006 ◽  
Vol 56 (11) ◽  
pp. 2603-2608 ◽  
Author(s):  
Anna H. Kaksonen ◽  
Stefan Spring ◽  
Peter Schumann ◽  
Reiner M. Kroppenstedt ◽  
Jaakko A. Puhakka
Keyword(s):  
Dimethyl Acetal ◽  
Underground Mine ◽  
Active Area ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Sequence Comparisons ◽  
Sulfate Reducing ◽  
Fermentative Growth ◽  
Lactate And Pyruvate ◽  
Ph Range

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from an underground mine in a geothermally active area in Japan. Cells of this strain, designated RL50JIIIT, were rod-shaped and motile. The temperature range for growth was 50–72 °C (optimum growth at 61–66 °C) and the pH range was 6.4–7.8 (optimum at pH 7.2–7.4). Strain RL50JIIIT tolerated up to 1.5 % NaCl, but optimum growth occurred in the presence of 0–1 % NaCl. Electron acceptors utilized were sulfate, sulfite, thiosulfate and elemental sulfur. Electron donors utilized were H2 in the presence of CO2, alanine, various carboxylic acids and alcohols. Fermentative growth occurred on lactate and pyruvate. The cell wall contained mesodiaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone 7 (MK-7). Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0 DMA (dimethyl acetal), iso-C15 : 0 DMA and iso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed 98.7 % similarity with Desulfotomaculum solfataricum DSM 14956T. However, DNA–DNA hybridization experiments with Desulfotomaculum kuznetsovii, Desulfotomaculum luciae and D. solfataricum and the G+C content of the DNA (54.4 mol%) allowed the differentiation of strain RL50JIIIT from the recognized species of the genus Desulfotomaculum. Strain RL50JIIIT therefore represents a novel species, for which the name Desulfotomaculum thermosubterraneum sp. nov. is proposed. The type strain is RL50JIIIT (=DSM 16057T=JCM 13837T).

Litorilinea aerophila gen. nov., sp. nov., an aerobic member of the class Caldilineae , phylum Chloroflexi , isolated from an intertidal hot spring

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1149-1154 ◽  
Author(s):  
Varsha Kale ◽  
Snædís H. Björnsdóttir ◽  
Ólafur H. Friðjónsson ◽  
Sólveig K. Pétursdóttir ◽  
Sesselja Ómarsdóttir ◽  
...  
Keyword(s):  
Type Species ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Fermentative Growth ◽  
Distinct Lineage ◽  
Ph Range

A thermophilic, aerobic, Gram-stain-negative, filamentous bacterium, strain PRI-4131T, was isolated from an intertidal hot spring in Isafjardardjup, NW Iceland. The strain grew chemo-organotrophically on various carbohydrates. The temperature range for growth was 40–65 °C (optimum 55 °C), the pH range was pH 6.5–9.0 (optimum pH 7.0) and the NaCl range was 0–3 % (w/v) (optimum 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRI-4131T represented a distinct lineage within the class Caldilineae of the phylum Chloroflexi. The highest levels of sequence similarity, about 91 %, were with Caldilinea aerophila STL-6-O1T and Caldilinea tarbellica D1-25-10-4T. Fermentative growth was not observed for strain PRI-4131T, which, in addition to other characteristics, distinguished it from the two Caldilinea species. Owing to both phylogenetic and phenotypic differences from the described members of the class Caldilineae , we propose to accommodate strain PRI-4131T in a novel species in a new genus, Litorilinea aerophila gen. nov., sp. nov. The type strain of Litorilinea aerophila is PRI-4131T ( = DSM 25763T  = ATCC BAA-2444T).

Pontivivens ytuae sp. nov., isolated from deep sea sediment of the Mariana Trench

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Zhen Wang ◽  
Rong-bin Du ◽  
Qing-lei Sun ◽  
Yuan-yuan Sun ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Circular Chromosome ◽  
Mariana Trench ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

A Gram-stain-negative, light pink-coloured, rod-shaped, flagellated and facultative anaerobic bacterial strain, designated MT2928T, was isolated from deep-sea sediment collected from the Mariana Trench. Growth of strain MT2928T occurred optimally at 28 °C, pH 8.0–9.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT2928T belongs to the genus Pontivivens and has the highest sequence similarity to Pontivivens insulae GYSW-23T (96.6 %). Genomic analysis indicated that strain MT2928T contains a circular chromosome of 4 199 362 bp with G+C content of 67.2 mol%. The strain did not produce bacteriochlorophyll a, but produced carotenoid. The predominant respiratory quinone of MT2928T was ubiquinone-10. The polar lipids of MT2928T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and two unidentified phospholipids. The major fatty acids of strain MT2928T contained summed feature 8 (C18 : 1  ω7c or/and C18 : 1  ω6c), C18 : 0 and summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH). On the basis of phylogenetic, physiological, biochemical and other phenotypic properties, strain MT2928T represents a novel species of the genus Pontivivens , and the name Pontivivens ytuae sp. nov. is proposed with the type species MT2928T (=MCCC 1K05575T=JCM 34320T).

scholarly journals Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan

2007 ◽  
Vol 57 (1) ◽  
pp. 98-102 ◽  
Author(s):  
Anna H. Kaksonen ◽  
Stefan Spring ◽  
Peter Schumann ◽  
Reiner M. Kroppenstedt ◽  
Jaakko A. Puhakka
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Underground Mine ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Sulfate Reducer ◽  
Sulfate Reducing ◽  
Fermentative Growth ◽  
Lactate And Pyruvate

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIVT, was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61–80 °C (optimum at 69–72 °C) and pH 6.4–7.9 (optimum at pH 6.8–7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIVT utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H2 in the presence of CO2, and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. Strain RL80JIVT was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490T (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259T (90.0 % similarity). Strain RL80JIVT is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIVT (=DSM 16036T=JCM 13928T).

scholarly journals Urechidicola croceus gen. nov., sp. nov., a member of the family Flavobacteriaceae

2020 ◽  
Vol 70 (3) ◽  
pp. 1751-1757 ◽  
Author(s):  
Su-Kyoung Shin ◽  
Hana Yi
Keyword(s):  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Urechis Unicinctus ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, rod-shaped, non-flagellated, non-gliding, aerobic bacterial strain, designated LPB0138T, was isolated from a marine spoon worm (Urechis unicinctus). The strain LPB0138T contains a circular chromosome of 3.43 Mb with a DNA G+C content of 30.4 mol%. The genome includes 2987 protein-coding genes and two copies of rRNA operons. The 16S rRNA gene sequence analysis showed that the isolate occurred within a clade containing only members of the family Flavobacteriaceae . The highest sequence similarity was observed with the genus Lutibacter (93.0–94.3 %), but the phylogenetic leaf of the new isolate did not belong to any of the genera known in the family Flavobacteriaceae . The low sequence similarity and the phylogenetic tree topology implied the novel generic status of the new isolate. The phenotypic properties of the strain LPB0138T also differentiated this isolate from its neighbour genera by showing a distinctive fatty acid composition, unique polar lipids profile, and low DNA G+C content. The LPB0138T strain contained menaquinone 6 as the isoprenoid quinone; iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH, and iso-C17 : 0 3-OH as the major fatty acids; and phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, and unidentified lipids as the major polar lipids. Based on the polyphasic taxonomic data obtained, the LPB0138T strain is considered to represent a novel species in a novel genus of the family Flavobacteriaceae, for which the name Urechidicola croceus gen. nov., sp. nov. was proposed. The type strain is LPB0138T (=KACC 18889T;=JCM 31563T).

scholarly journals Butyribacter intestini gen. nov., sp. nov., a butyric acid-producing bacterium of the family Lachnospiraceae isolated from the human faeces, and reclassification of Acetivibrio ethanolgignens as Acetanaerobacter ethanolgignens gen. nov., comb. nov

2020 ◽  
Author(s):  
Wenbin Xue ◽  
Xiaoqian Lin ◽  
Mei Lv ◽  
Guangwen Luo ◽  
Ying Dai ◽  
...  
Keyword(s):  
Butyric Acid ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Human Faeces ◽  
Obligate Anaerobic

AbstractA novel, non-motile, Gram-stain-positive, non-spore-forming, obligate anaerobic bacterium, designated strain TF01-11T, was isolated from human faeces. The isolate was characterized by phylogenetic and phenotypic properties, as well as by determination of its whole genome sequence. The growth temperature and pH ranges were 30–42 °C and 6.0–8.5, respectively. The end products of glucose fermentation were butyric acid and a small amount of acetic acid. The genome was estimated to be 3.61Mbp with G+C content of 36.79 mol%. Genes related to biosynthesis of diaminopimelic acid, polar lipids, polyamines, teichoic and lipoteichoic acids were present. The predominant fatty acids were C16:0 (37.9 %), C14:0 (16.4 %), C13:0 OH/iso-C15:1 H (11.1 %) and C18:1ω9c (10.6 %). Phylogenetic analyses based on 16S rRNA gene sequences, the isolate was a member of family Lachnospiraceae, with the highest sequence similarity to the type strain of Roseburia intestinalis DSM 14610T at 92.18 % followed by Acetivibrio ethanolgignens ATCC 33324T at 91.99 %. The average nucleotide identity (ANI) calculated for the genomes between strain TF01-11T and these closest relatives were 70.5 % and 68.1 %. Based on results of phenotypic characteristics and genotypic properties presented in this study, strain TF01-11T represent a novel species in a new genus, for which the name Butyribacter intestini gen. nov., sp. nov. is proposed. The type strain of the type species is TF01-11T (CGMCC 1.5203T = CGMCC 10984T = DSM 105140T). In addition, Acetivibrio ethanolgignens is proposed to be reclassified as Acetanaerobacter ethanolgignens gen. nov., comb. nov.

scholarly journals Glaesserella australis sp. nov., isolated from the lungs of pigs

2020 ◽  
Vol 70 (6) ◽  
pp. 3686-3692 ◽  
Author(s):  
Conny Turni ◽  
Yunchen Wu ◽  
Lida Omaleki ◽  
Nhan Giang ◽  
P.J. Blackall ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Dna Renaturation

Twenty-nine isolates of an unknown haemophilic organism were isolated from the lungs of pigs from 14 farms in Australia. Phylogenetic analyses based on the 16S rRNA gene, recN and rpoA showed a monophyletic group that was most closely related to Glaesserella parasuis and [ Actinobacillus ] indolicus. Whole genome sequence analysis indicated that the Glaesserella parasuis and this group, using the type strain HS4635T for comparison, showed a similarity of 30.9 % DNA–DNA renaturation. The isolates were Gram-stain-negative, NAD-dependent, CAMP-negative and were oxidase-positive, catalase-negative and produced indole but not urease. The isolates could be separated from all currently recognized haemophilic and non-haemophilic members of the family Pastuerellaceae. Key phenotypic properties were the production of indole, the lack of urease activity, production of β-galactosidase but not α-fucosidase, acid formation from (−)-d-arabinose, (+)-d-galactose, maltose and trehalose and a failure to produce acid from (−)-d-mannitol. Taken together, these data indicate that the isolates belong to a novel species for which the name Glaesserella australis sp. nov. is proposed. The type strain is HS4635T (=CCUG 71931T and LMG 30645T).

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