scholarly journals Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan

2005 ◽  
Vol 55 (5) ◽  
pp. 1877-1884 ◽  
Author(s):  
Jun Tsubota ◽  
Bulat Ts. Eshinimaev ◽  
Valentina N. Khmelenina ◽  
Yuri A. Trotsenko
Keyword(s):  
Sequence Analysis ◽  
Hot Spring ◽  
Methane Monooxygenase ◽  
Comparative Sequence Analysis ◽  
Rrna Gene ◽  
Type I ◽  
Particulate Methane Monooxygenase ◽  
Moderately Thermophilic ◽  
Ribulose Monophosphate Pathway ◽  
Genotypic Characteristics

A novel moderately thermophilic methanotroph, strain MYHTT, was isolated from a hot spring in Japan. The isolate grew on methane or methanol at 37–67 °C, and optimally at 57–59 °C. It was found to be a Gram-negative aerobe, with colourless colonies of non-motile coccoid cells, possessing type I intracytoplasmic membranes and regularly arranged surface layers of linear (p2) symmetry. Strain MYHTT expressed only the particulate methane monooxygenase and employed the ribulose monophosphate pathway for formaldehyde assimilation. It is a neutrophilic and halotolerant organism capable of growth at pH 6·5–7·5 (optimum pH 6·8) and in up to 3 % NaCl (optimum 0·5–1 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that strain MYHTT is most closely related to the thermophilic undescribed methanotroph ‘Methylothermus’ HB (91 % identity) and the novel halophilic methanotroph Methylohalobius crimeensis 10KiT (90 % identity). Comparative sequence analysis of particulate methane monooxygenase (pmoA) genes also confirmed the clustering of strain MYHTT with ‘Methylothermus’ HB and Methylohalobius crimeensis 10KiT (98 and 92 % derived amino acid sequence identity, respectively). The DNA G+C content was 62·5 mol%. The major cellular fatty acids were C16 : 0 (37·2 %) and C18 : 1 ω9c (35·2 %) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. On the basis of comparative phenotypic and genotypic characteristics, a new genus and species, Methylothermus thermalis gen. nov., sp. nov., is proposed, with MYHTT as the type strain (=VKM B-2345T=IPOD FERM P-19714T).

Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field

2011 ◽  
Vol 61 (11) ◽  
pp. 2568-2572 ◽  
Author(s):  
Estefanía Geymonat ◽  
Lucía Ferrando ◽  
Silvana E. Tarlera
Keyword(s):  
Paddy Field ◽  
Sequence Similarity ◽  
Rice Paddy ◽  
Cellular Fatty Acid ◽  
Comparative Sequence Analysis ◽  
Rrna Gene ◽  
Type I ◽  
Methylococcus Capsulatus ◽  
Rice Paddy Field ◽  
Moderately Thermophilic

A novel methanotroph, designated strain E10T, was isolated from a rice paddy field in Uruguay. Strain E10T grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30–35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2T (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10T formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14LT, respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C16 : 0 (62.05 %). Thus, strain E10T ( = JCM 16910T  = DSM 23452T) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed.

Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2538-2544 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
P. D. Rekha ◽  
H.-J. Busse ◽  
C.-C. Young ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gene Sequence ◽  
Hot Spring ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157T, and a lower sequence similarity to all other species of the genus Ruegeria . Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus Ruegeria . Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus Ruegeria , for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).

scholarly journals Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

2011 ◽  
Vol 61 (7) ◽  
pp. 1544-1548 ◽  
Author(s):  
P. D. Rekha ◽  
Chiu-Chung Young ◽  
Peter Kämpfer ◽  
Karin Martin ◽  
A. B. Arun ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic ◽  
Gene Sequence Analysis

A beige-coloured, Gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1T, was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94 % sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C18 : 1ω7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1T was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1T represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp. nov., is proposed. The type strain of the type species is CC-MHSW-1T ( = JCM 15068T = CCM 7767T).

scholarly journals Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from hot spring sediment

2010 ◽  
Vol 60 (4) ◽  
pp. 861-865 ◽  
Author(s):  
Digvijay Panday ◽  
Subrata K. Das
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic ◽  
Gene Sequence Analysis

A moderately thermophilic bacterial strain (HT4T) isolated from a hot spring sediment was characterized phenotypically and phylogenetically. Cells were Gram-negative, aerobic, non-sporulating, rod-shaped and motile by means of a single polar flagellum. Both oxidase and catalase activities were positive. Heterotrophic growth was observed at pH 6.0–8.5 and at 20–50 °C; optimum growth occurred at pH 7.5–8.0 and 37–42 °C. The major cellular fatty acids were C14 : 0 3-OH, C18 : 0 3-OH, C18 : 1 2-OH, C18 : 1 ω7c and C19 : 0 cyclo ω8c. The DNA G+C content of strain HT4T was 67.8 mol%.16S rRNA gene sequence analysis indicated that strain HT4T clustered within the radiation of the genus Chelatococcus and showed 99.0 % similarity with Chelatococcus daeguensis CCUG 54519T and 96 % similarity with Chelatococcus asaccharovorans DSM 6462T. However, levels of DNA–DNA relatedness between strain HT4T and Chelatococcus daeguensis CCUG 54519T and Chelatococcus asaccharovorans DSM 6462T were 52 and 20 %, respectively. On the basis of the phenotypic, physiological and chemotaxonomic data, 16S rRNA gene sequence analysis and DNA–DNA hybridization results, strain HT4T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus sambhunathii sp. nov. is proposed. The type strain is HT4T (=DSM 18167T=JCM 14988T).

scholarly journals A Novel Moderately Thermophilic Type Ib Methanotroph Isolated from an Alkaline Thermal Spring in the Ethiopian Rift Valley

2020 ◽  
Vol 8 (2) ◽  
pp. 250 ◽  
Author(s):  
Tajul Islam ◽  
Amare Gessesse ◽  
Antonio Garcia-Moyano ◽  
J. Colin Murrell ◽  
Lise Øvreås
Keyword(s):  
Rift Valley ◽  
Methane Monooxygenase ◽  
Thermal Spring ◽  
Substantial Contribution ◽  
Ethiopian Rift ◽  
Type I ◽  
Methylococcus Capsulatus ◽  
Biological Reduction ◽  
Moderately Thermophilic ◽  
The Family

Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel moderately thermophilic Methylococcus-like Type Ib methanotroph recovered from an alkaline thermal spring (55.4 °C and pH 8.82) in the Ethiopian Rift Valley. The isolate, designated LS7-MC, most probably represents a novel species of a new genus in the family Methylococcaceae of the class Gammaproteobacteria. The 16S rRNA gene phylogeny indicated that strain LS7-MC is distantly related to the closest described relative, Methylococcus capsulatus (92.7% sequence identity). Growth was observed at temperatures of 30–60 °C (optimal, 51–55 °C), and the cells possessed Type I intracellular membrane (ICM). The comparison of the pmoA gene sequences showed that the strain was most closely related to M. capsulatus (87.8%). Soluble methane monooxygenase (sMMO) was not detected, signifying the biological oxidation process from methane to methanol by the particulate methane monooxygenase (pMMO). The other functional genes mxaF, cbbL and nifH were detected by PCR. To our knowledge, the new strain is the first isolated moderately thermophilic methanotroph from an alkaline thermal spring of the family Methylococcaceae. Furthermore, LS7-MC represents a previously unrecognized biological methane sink in thermal habitats, expanding our knowledge of its ecological role in methane cycling and aerobic methanotrophy.

Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 109-113 ◽  
Author(s):  
Zhao-Ming Gao ◽  
Xin Liu ◽  
Xi-Ying Zhang ◽  
Ling-Wei Ruan
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Anaerobic Bacterium ◽  
Hot Spring ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
The Family

A moderately thermophilic and strictly anaerobic bacterium, designated HS1T, was isolated from offshore hot spring sediment in Xiamen, China. Cells were Gram-negative, catalase-positive, oxidase-negative, slender and flexible rods without flagella. The strain could grow at 35–55 °C (optimum at 50 °C) and in 1–8 % NaCl (w/v; optimum 2–4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HS1T was affiliated with the family Marinilabiliaceae and shared a distant relationship with the previously described genera. The isolate was most closely related to Anaerophaga thermohalophila Fru22T with 16S rRNA gene sequence similarity of 92.4 %, followed by the other members of the family Marinilabiliaceae with 88.7–91.1 % similarity. The dominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE) and an unknown polar lipid. The genomic DNA G+C content was 38.7 mol%. Besides the phylogenetically distant relationship, strain HS1T was obviously distinguished from the most closely related genera in several phenotypic properties including colony colour and pigment production, optimal temperature, optimal NaCl, relation to O2, bicarbonate/carbonate requirement, catalase activity, nitrate reduction, fermentation products and cellular fatty acid profile. Based on the phenotypic and phylogenetic data, strain HS1T represents a novel species of a new genus, for which the name Thermophagus xiamenensis gen. nov., sp. nov. is proposed. The type strain of the type species is HS1T ( = DSM 19012T = CGMCCC 1.5071T).

scholarly journals Thiomonas islandica sp. nov., a moderately thermophilic, hydrogen- and sulfur-oxidizing betaproteobacterium isolated from a hot spring

2011 ◽  
Vol 61 (1) ◽  
pp. 132-137 ◽  
Author(s):  
Hildur Vésteinsdóttir ◽  
Dagný B. Reynisdóttir ◽  
Johann Örlygsson
Keyword(s):  
Dna Hybridization ◽  
Hot Spring ◽  
Distinct Species ◽  
Rrna Gene ◽  
Heterotrophic Growth ◽  
Moderately Thermophilic ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Chemolithotrophic Growth ◽  
Sulfur Oxidizing

A novel, hydrogen- and sulfur-oxidizing bacterium, designated strain 6CT, was isolated from a hot spring in Graendalur, south-western Iceland. Cells of this organism were Gram-reaction-negative, rod-shaped and motile. The strain grew aerobically and was capable of chemolithotrophic growth on thiosulfate and hydrogen, heterotrophic growth on pyruvate, oxalate, acetate and on glutamate in the presence of yeast extract and mixotrophic growth on several organic compounds, thiosulfate and/or hydrogen. During growth on thiosulfate, the final product was sulfate, resulting in a drop in pH from 6.8 to 2.7. Heterotrophic growth on pyruvate was observed at pH 4–7 (optimum pH 4) and 35–50 °C (optimum 45 °C). The DNA G+C content was 65.2 mol%. As determined by 16S rRNA gene sequence analysis, strain 6CT represents a distinct species belonging to the class Betaproteobacteria and is most closely related to Thiomonas intermedia DSM 18155T and Thiomonas perometabolis DSM 18570T. DNA–DNA hybridization between strain 6CT and Thiomonas intermedia DSM 18155T and Thiomonas perometabolis DSM 18570T gave relatedness values below 32 %. These results, together with physiological characteristics, showed that strain 6CT represents a novel species within the genus Thiomonas, for which the name Thiomonas islandica sp. nov. is proposed. The type strain is 6CT (=DSM 21436T =JCM 16107T).

scholarly journals Structure of the 5′ Nontranslated Region of the Coxsackievirus B3 Genome:Chemical Modification and Comparative Sequence Analysis

2006 ◽  
Vol 81 (2) ◽  
pp. 650-668 ◽  
Author(s):  
Jennifer M. Bailey ◽  
William E. Tapprich
Keyword(s):  
Sequence Analysis ◽  
Viral Genome ◽  
Type I Diabetes ◽  
Coxsackievirus B3 ◽  
Comparative Sequence Analysis ◽  
Type I ◽  
Comparative Sequence ◽  
Chemical Probing ◽  
Nontranslated Region ◽  
Tertiary Interactions

ABSTRACT Coxsackievirus B3 (CVB3) is a picornavirus which causes myocarditis and pancreatitis and may play a role in type I diabetes. The viral genome is a single 7,400-nucleotide polyadenylated RNA encoding 11 proteins in a single open reading frame. The 5′ end of the viral genome contains a highly structured nontranslated region (5′NTR) which folds to form an internal ribosome entry site (IRES) as well as structures responsible for genome replication, both of which are critical for virulence. A structural model of the CVB3 5′NTR, generated primarily by comparative sequence analysis and energy minimization, shows seven domains (I to VII). While this model provides a preliminary basis for structural analysis, the model lacks comprehensive experimental validation. Here we provide experimental evidence from chemical modification analysis to determine the structure of the CVB3 5′NTR. Chemical probing results show that the theoretical model for the CVB3 5′NTR is largely, but not completely, supported experimentally. In combination with our chemical probing data, we have used the RNASTRUCTURE algorithm and sequence comparison of 105 enterovirus sequences to provide evidence for novel secondary and tertiary interactions. A comprehensive examination of secondary structure is discussed, along with new evidence for tertiary interactions. These include a loop E motif in domain III and a long-range pairing interaction that links domain II to domain V. The results of our work provide mechanistic insight into key functional elements in the cloverleaf and IRES, thereby establishing a base of structural information from which to interpret experiments with CVB3 and other picornaviruses.

Fonticella tunisiensis gen. nov., sp. nov., isolated from a hot spring

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 1947-1950 ◽  
Author(s):  
Belkis Fraj ◽  
Wajdi Ben Hania ◽  
Anne Postec ◽  
Moktar Hamdi ◽  
Bernard Ollivier ◽  
...  
Keyword(s):  
Type Species ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Fermentation Products ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Nitrate And Nitrite

A strictly anaerobic, moderately thermophilic, halotolerant rod, designated BELH25T, was isolated from a water sample of a Tunisian hot spring. Cells were non-motile, 2–6 µm long and 0.4–0.6 µm wide, appearing singly or in pairs. The isolate grew at 45–70 °C (optimum 55 °C), at pH 6.2–8.0 (optimum pH 7.0) and with 0–4 % NaCl (optimum 0–2.0 %). Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain BELH25T used cellobiose, fructose, galactose, glucose, maltose, mannose, sucrose, starch and yeast extract as electron donors. The main fermentation products from glucose metabolism were formate, acetate, ethanol and CO2. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and anteiso-C15 : 0. The DNA G+C content was 37.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain BELH25T was most closely related to Caloramator viterbiensis JW/MS-VS5T and Fervidicella metallireducens AeBT (92.2 and 92.1 % sequence similarity, respectively), and the isolate was positioned approximately equidistantly between these genera. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain BELH25T is proposed to be a member of a novel species of a novel genus within the order Clostridiales , family Clostridiaceae , for which the name Fonticella tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is BELH25T ( = DSM 24455T = JCM 17559T).

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