scholarly journals Thermoproteus thermophilus sp. nov., a hyperthermophilic crenarchaeon isolated from solfataric soil

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2507-2510 ◽  
Author(s):  
Kyung June Yim ◽  
Hye Seon Song ◽  
Jong-Soon Choi ◽  
Seong Woon Roh
Keyword(s):  
Yeast Extract ◽  
Carbon Sources ◽  
Optimal Growth ◽  
The Philippines ◽  
Rrna Gene ◽  
Mayon Volcano ◽  
Thermoproteus Tenax ◽  
Casamino Acids ◽  
Genotypic Characteristics ◽  
The 16S Rrna Gene

A hyperthermophilic crenarchaeon, designated strain CBA1502T, was isolated from volcanic soil in the Mayon volcano in the Philippines. The 16S rRNA gene sequence of strain CBA1502T was most closely related to that of Thermoproteus uzoniensis DSM 5263T (99.2 % similarity) and Thermoproteus tenax Kra 1T (99.0 %). The organism grew at 75–90 °C and pH 4.0–6.0 and in the presence of 0–0.5 % (w/v) NaCl, with optimal growth at 85 °C and pH 5.0. Strain CBA1502T utilized d-arabinose, beef extract, Casamino acids, formate, fumarate, peptone, pyruvate, trimethylamine and yeast extract as energy substrates, and d-arabinose, formate, pyruvate and yeast extract as carbon sources. Fumarate, sulfate, sulfur and thiosulfate functioned as electron acceptors, but not ferric chloride, nitrate, malate or oxidized glutathione. DNA–DNA hybridization studies showed that there was less than 46.1 % relatedness between strain CBA1502T and other members of the genus Thermoproteus. The DNA G+C content of strain CBA1502T was 62.0 mol%. We conclude that, according to its phylogenetic, phenotypic and genotypic characteristics, strain CBA1502T represents a novel species of the genus Thermoproteus, and propose the name Thermoproteus thermophilus sp. nov., with the type strain CBA1502T ( = ATCC BAA-2416T = JCM 17229T).

scholarly journals Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3597-3602 ◽  
Author(s):  
Van Hong Thi Pham ◽  
Seung-Woo Jeong ◽  
Jaisoo Kim
Keyword(s):  
Contaminated Soil ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Optimal Growth ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Degrading Bacterium ◽  
Genotypic Characteristics ◽  
Type Strains

Strain NHI-1T is a Gram-negative, motile, non-spore-forming bacterium isolated from oil-contaminated soil in South Korea. The strain was able to grow by using gasoline, diesel and kerosene as energy and carbon sources. After incubation for 14 days, cells (1 g l− 1) degraded approximately 58 % of oil present at concentration of 1500 p.p.m. at pH 8 and 28 °C. Strain NHI-1T grew well under aerobic conditions, with optimal growth at pH 7–9 and 28 °C–37 °C but grew poorly in the presence of ≥ 0.5 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest relatives of strain NHI-1T were Aquabacterium fontiphilum CS-6T (97.96 % sequence similarity), Aquabacterium parvum B6T (96.39 %), Aquabacterium commune B8T (95.76 %), Aquabacterium limnoticum ABP-4T (95.72 %) and Aquabacterium citratiphilum B4T (95.25 %). DNA–DNA relatedness was 41–53 % between strain NHI-1T and its closest type strains. The major fatty acids present in strain NHI-1T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 44.5 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c, 21.5 %) and C16 : 0 (16.2 %), and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol and uncharacterized aminophospholipids. Strain NHI-1T was distinguishable from other members of genus Aquabacterium based on phenotypic, chemotaxonomic and genotypic characteristics. Therefore, strain NHI-1T represents a novel species of the genus Aquabacterium for which the name Aquabacterium olei sp. nov. is proposed. The type strain is NHI-1T ( = KEMB 9005-082T =  KACC 18244T = NBRC 110486T).

scholarly journals Vulcanisaeta thermophila sp. nov., a hyperthermophilic and acidophilic crenarchaeon isolated from solfataric soil

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 201-205 ◽  
Author(s):  
Kyung June Yim ◽  
In-Tae Cha ◽  
Jin-Kyu Rhee ◽  
Hye Seon Song ◽  
Dong-Wook Hyun ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
The Philippines ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Mayon Volcano ◽  
Final Electron ◽  
The Republic ◽  
Ph Range

An anaerobic, rod-shaped, hyperthermophilic and acidophilic crenarchaeon, designated strain CBA1501T, was isolated from solfataric soil of the Mayon volcano in the Republic of the Philippines. Phylogenetic analysis showed that strain CBA1501T is affiliated with the genus Vulcanisaeta in the phylum Crenarchaeota . DNA sequence similarities between the 16S rRNA gene of strain CBA1501T and those of Vulcanisaeta distributa IC-017T and Vulcanisaeta souniana IC-059T were 98.5 and 97.4 %, respectively. Strain CBA1501T grew between 75–90 °C, over a pH range of 4.0–6.0 and in the presence of 0–1.0 % (w/v) NaCl, with optimal growth occurring at 85 °C, pH 5.0, and with 0 % (w/v) NaCl. Fumarate, malate, oxidized glutathione, sulfur and thiosulfate were used as final electron acceptors, but FeCl3, nitrate and sulfate were not. The DNA G+C content of strain CBA1501T was 43.1 mol%. On the basis of polyphasic taxonomic analysis, strain CBA1501T represents a novel species of the genus Vulcanisaeta in the phylum Crenarchaeota , for which we propose the name Vulcanisaeta thermophila sp. nov. The type strain is CBA1501T ( = ATCC BAA-2415T = JCM 17228T).

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3400-3406 ◽  
Author(s):  
Xun Zhou ◽  
Guan Nan Guo ◽  
Le Qi Wang ◽  
Su Lan Bai ◽  
Chun Li Li ◽  
...  
Keyword(s):  
Physcomitrella Patens ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Beijing China ◽  
The 16S Rrna Gene

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain XBT, was isolated from Physcomitrella patens growing in Beijing, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inferences. The novel strain was spore-forming, motile, catalase-negative and weakly oxidase-positive. Optimal growth of strain XBT occurred at 28°C and pH 7.0–7.5. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unidentified components, including one phospholipid, two aminophospholipids, three glycolipids, one aminolipid and one lipid. The predominant isoprenoid quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acid components (>5 %) were anteiso-C15 : 0 (51.2 %), anteiso-C17 : 0 (20.6 %), iso-C16 : 0 (8.3 %) and C16 : 0 (6.7 %). The G+C content of the genomic DNA was 53.3 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain XBT fell within the evolutionary distances encompassed by the genus Paenibacillus; its closest phylogenetic neighbour was Paenibacillus yonginensis DCY84T (96.6 %). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain XBT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus physcomitrellae sp. nov., is proposed. The type strain is XBT ( = CGMCC 1.15044T = DSM 29851T).

Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4675-4682 ◽  
Author(s):  
Jessica K. Cole ◽  
Brandon A. Gieler ◽  
Devon L. Heisler ◽  
Maryknoll M. Palisoc ◽  
Amanda J. Williams ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Casamino Acids ◽  
Ph Range ◽  
Dense Liquid ◽  
Cellulose Filter

Several closely related, thermophilic and cellulolytic bacterial strains, designated JKG1T, JKG2, JKG3, JKG4 and JKG5, were isolated from a cellulolytic enrichment (corn stover) incubated in the water column of Great Boiling Spring, NV. Strain JKG1T had cells of diameter 0.7–0.9 µm and length ~2.0 µm that formed non-branched, multicellular filaments reaching >300 µm. Spores were not formed and dense liquid cultures were red. The temperature range for growth was 45–65 °C, with an optimum of 55 °C. The pH range for growth was pH 5.6–9.0, with an optimum of pH 7.5. JKG1T grew as an aerobic heterotroph, utilizing glucose, sucrose, xylose, arabinose, cellobiose, CM-cellulose, filter paper, microcrystalline cellulose, xylan, starch, Casamino acids, tryptone, peptone, yeast extract, acetate, citrate, lactate, pyruvate and glycerol as sole carbon sources, and was not observed to photosynthesize. The cells stained Gram-negative. Phylogenetic analysis using 16S rRNA gene sequences placed the new isolates in the class Chloroflexia , but distant from other cultivated members, with the highest sequence identity of 82.5 % to Roseiflexus castenholzii . The major quinone was menaquinone-9; no ubiquinones were detected. The major cellular fatty acids (>5 %) were C18 : 0, anteiso-C17 : 0, iso-C18 : 0, iso-C17 : 0, C16 : 0, iso-C16 : 0 and C17 : 0. The peptidoglycan amino acids were alanine, ornithine, glutamic acid, serine and asparagine. Whole-cell sugars included mannose, rhamnose, glucose, galactose, ribose, arabinose and xylose. Morphological, phylogenetic and chemotaxonomic results suggest that JKG1T is representative of a new lineage within the class Chloroflexia , which we propose to designate Kallotenue papyrolyticum gen. nov., sp. nov., Kallotenuaceae fam. nov., Kallotenuales ord. nov. The type strain of Kallotenue papyrolyticum gen. nov., sp. nov. is JKG1T ( = DSM 26889T = JCM 19132T).

scholarly journals Characterization a Novel Butyric Acid-Producing Bacterium Collinsella aerofaciens Subsp. Shenzhenensis Subsp. Nov.

2019 ◽  
Vol 7 (3) ◽  
pp. 78 ◽  
Author(s):  
Panpan Qin ◽  
Yuanqiang Zou ◽  
Ying Dai ◽  
Guangwen Luo ◽  
Xiaowei Zhang ◽  
...  
Keyword(s):  
Butyric Acid ◽  
Dna Hybridization ◽  
Type Strain ◽  
Inflammatory Diseases ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Human Gut ◽  
Positive Growth ◽  
The 16S Rrna Gene

Butyrate-producing bacteria can biosynthesize butyrate and alleviate inflammatory diseases. However, few studies have reported that the genus Collinsella has the ability to produce butyric acid. Here, our study depicts a Collinsella strain, which is a rod-shaped obligate anaerobe that is able to produce butyric acid. This microorganism was isolated from a human gut, and the optimal growth conditions were found to be 37 °C on PYG medium with pH 6.5. The 16S rRNA gene sequence demonstrated that this microorganism shared 99.93% similarity with C. aerofaciens ATCC 25986T, which was higher than the threshold (98.65%) for differentiating two species. Digital DNA–DNA hybridization and average nucleotide identity values also supported that this microorganism belonged to the species C. aerofaciens. Distinct phenotypic characteristics between TF06-26 and the type strain of C. aerofaciens, such as the fermentation of D-lactose, D-fructose and D-maltose, positive growth under pH 5 and 0.2% (w/v) cholate, suggested this strain was a novel subspecies. Comparative genome analysis revealed that butyric acid kinase and phosphate butyryltransferase enzymes were coded exclusively by this strain, indicating a specific butyric acid-producing function of this C. aerofaciens subspecies within the genus Collinsella. Thus, Collinsella aerofaciens subsp. shenzhenensis subsp. nov. was proposed, with set strain TF06-26T (=CGMCC 1.5216T = DSM 105138T) as the type strain.

scholarly journals Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents

2004 ◽  
Vol 54 (1) ◽  
pp. 175-181 ◽  
Author(s):  
Costantino Vetriani ◽  
Mark D. Speck ◽  
Susan V. Ellor ◽  
Richard A. Lutz ◽  
Valentin Starovoytov
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
East Pacific ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

scholarly journals Nautilia nitratireducens sp. nov., a thermophilic, anaerobic, chemosynthetic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent

2010 ◽  
Vol 60 (5) ◽  
pp. 1182-1186 ◽  
Author(s):  
Ileana Pérez-Rodríguez ◽  
Jessica Ricci ◽  
James W. Voordeckers ◽  
Valentin Starovoytov ◽  
Costantino Vetriani
Keyword(s):  
Gas Phase ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
East Pacific ◽  
Optimum Ph ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemosynthetic bacterium, designated strain MB-1T, was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at  ° 50′ N 10 ° 17′ W. The cells were Gram-negative-staining rods, approximately 1–1.5 μm long and 0.3–0.5 μm wide. Strain MB-1T grew at 25–65 °C (optimum 55 °C), with 10–35 g NaCl l−1 (optimum 20 g l−1) and at pH 4.5–8.5 (optimum pH 7.0). Generation time under optimal conditions was 45.6 min. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Nitrate was used as the electron acceptor, with resulting production of ammonium. Thiosulfate, sulfur and selenate were also used as electron acceptors. No growth was observed in the presence of lactate, peptone or tryptone. Chemo-organotrophic growth occurred in the presence of acetate, formate, Casamino acids, sucrose, galactose and yeast extract under a N2/CO2 gas phase. The G+C content of the genomic DNA was 36.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Nautilia profundicola AmHT, Nautilia abyssi PH1209T and Nautilia lithotrophica 525T (95, 94 and 93 % sequence identity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Nautilia, Nautilia nitratireducens sp. nov. The type strain is MB-1T (=DSM 22087T =JCM 15746T).

scholarly journals Thermovenabulum gondwanense sp. nov., a thermophilic anaerobic Fe(III)-reducing bacterium isolated from microbial mats thriving in a Great Artesian Basin bore runoff channel

2010 ◽  
Vol 60 (5) ◽  
pp. 1079-1084 ◽  
Author(s):  
Christopher D. Ogg ◽  
Anthony C. Greene ◽  
Bharat K. C. Patel
Keyword(s):  
Yeast Extract ◽  
Microbial Mats ◽  
Wide Spectrum ◽  
Thermal Waters ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Phylogenetic Distance ◽  
Artesian Basin ◽  
Great Artesian Basin ◽  
Casamino Acids

A strictly anaerobic, thermophilic bacterium, designated strain R270T, was isolated from microbial mats thriving in the thermal waters (66 °C) of a Great Artesian Basin bore (registered no. 17263) runoff channel. Cells of strain R270T were straight to slightly curved rods (3.50–6.00×0.75–1.00 μm) that stained Gram-positive, but possessed a Gram-negative cell-wall ultrastructure. Strain R270T grew optimally in tryptone-yeast extract-Casamino acids medium at 65 °C (growth temperature range between 50 and 70 °C) and at pH 7.0 (growth pH range between 6.0 and 9.0). In the presence of 0.02 and 0.10 % yeast extract, pyruvate and Casamino acids were the only substrates fermented from a wide spectrum of substrates tested. Fe(III), Mn(IV), thiosulfate and elemental sulfur were used as electron acceptors in the presence 0.2 % yeast extract, but not sulfate, sulfite, nitrate, nitrite or fumarate. Growth of strain R270T increased in the presence of Fe(III), which was reduced in the presence of peptone, tryptone, Casamino acids, amyl media, starch, pyruvate, H2 and CO2, but not in the presence of acetate, lactate, propionate, formate, benzoate, glycerol or ethanol. Growth and Fe(III) reduction were inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and 2 % NaCl (w/v). The DNA G+C content of strain R270T was 41±1 mol% (T m) and phylogenetic analysis of the 16S rRNA gene indicated that this isolate was closely related to Thermovenabulum ferriorganovorum DSM 14006T (similarity value of 96.1 %) within the family ‘Thermoanaerobacteraceae’, class ‘Clostridia’, phylum ‘Firmicutes’. On the basis of the phylogenetic distance separating the two, together with differences in a number of key phenotypic characteristics, strain R270T represents a novel species of the genus Thermovenabulum, for which the name Thermovenabulum gondwanense sp. nov. is proposed; the type strain is R270T (=KCTC 5616T=DSM 21133T).

Sign in / Sign up

Export Citation Format

Share Document