scholarly journals Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity

2004 ◽  
Vol 54 (6) ◽  
pp. 2297-2300 ◽  
Author(s):  
Yumiko Kodama ◽  
Kazuya Watanabe
Keyword(s):  
Crude Oil ◽  
Electron Acceptor ◽  
Rrna Gene ◽  
Microaerobic Condition ◽  
Facultatively Anaerobic ◽  
Oil Storage ◽  
Novel Genus And Species ◽  
Thiomicrospira Denitrificans ◽  
Sulfur Oxidizing ◽  
Bacterium Strain

A facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain YK-1T, was isolated from an underground crude-oil storage cavity at Kuji in Iwate, Japan. The cells were motile, curved rods and had a single polar flagellum. Optimum growth occurred in a low-strength salt medium at pH 7·0 and 25 °C. It utilized sulfide, elemental sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use nitrite. Oxygen also served as the electron acceptor under the microaerobic condition (O2 in the head space 1 %). It did not grow on sugars, organic acids or hydrocarbons as carbon and energy sources. The DNA G+C content of strain YK-1T was 45 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that its closest relative was Thiomicrospira denitrificans in the ‘Epsilonproteobacteria’, albeit with low homology (90 %). On the basis of physiological and phylogenetic data, strain YK-1T should be classified into a novel genus and species, for which the name Sulfuricurvum kujiense gen. nov., sp. nov. is proposed. The type strain is YK-1T (=JCM 11577T=MBIC 06352T=ATCC BAA-921T).

scholarly journals Sulfurospirillum cavolei sp. nov., a facultatively anaerobic sulfur-reducing bacterium isolated from an underground crude oil storage cavity

2007 ◽  
Vol 57 (4) ◽  
pp. 827-831 ◽  
Author(s):  
Yumiko Kodama ◽  
Le Thu Ha ◽  
Kazuya Watanabe
Keyword(s):  
Carbon Source ◽  
Crude Oil ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Facultatively Anaerobic ◽  
Oil Storage ◽  
Curved Rods

A novel facultatively anaerobic sulfur-reducing bacterium, designated strain Phe91T, was isolated from petroleum-contaminated groundwater in an underground crude oil storage cavity at Kuji in Iwate, Japan. Cells of strain Phe91T were slightly curved rods with single polar flagella. Optimum growth was observed at pH 7.0 and 30 °C. The novel strain utilized elemental sulfur, thiosulfate, sulfite, dithionite, arsenate, nitrate and DMSO as electron acceptors with lactate as an energy and carbon source, but nitrite was not utilized. Microaerophilic growth was also observed. Fumarate, pyruvate, lactate, malate, succinate, hydrogen (with acetate as a carbon source) and formate (with acetate) could serve as electron donors. Fumarate, pyruvate and malate were fermented. The DNA G+C content was 42.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Phe91T was affiliated with the genus Sulfurospirillum in the class Epsilonproteobacteria and was most closely related to Sulfurospirillum deleyianum (sequence similarity 97 %). However, the DNA–DNA hybridization value between strain Phe91T and S. deleyianum was only 14 %. Based on the physiological and phylogenetic data, Phe91T should be classified as a representative of a novel species in the genus Sulfurospirillum; the name Sulfurospirillum cavolei sp. nov. is proposed, with Phe91T (=JCM 13918T=DSM 18149T) as the type strain.

scholarly journals Isolation and Characterization of a Sulfur-Oxidizing Chemolithotroph Growing on Crude Oil under Anaerobic Conditions

2003 ◽  
Vol 69 (1) ◽  
pp. 107-112 ◽  
Author(s):  
Yumiko Kodama ◽  
Kazuya Watanabe
Keyword(s):  
Crude Oil ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Anaerobic Conditions ◽  
Molecular Approaches ◽  
Oil Storage ◽  
Isolation And Characterization ◽  
Inorganic Medium ◽  
Sulfur Oxidizing ◽  
Microaerobic Conditions

ABSTRACT Molecular approaches have shown that a group of bacteria (called cluster 1 bacteria) affiliated with the ε subclass of the class Proteobacteria constituted major populations in underground crude-oil storage cavities. In order to unveil their physiology and ecological niche, this study isolated bacterial strains (exemplified by strain YK-1) affiliated with the cluster 1 bacteria from an oil storage cavity at Kuji in Iwate, Japan. 16S rRNA gene sequence analysis indicated that its closest relative was Thiomicrospira denitrificans (90% identity). Growth experiments under anaerobic conditions showed that strain YK-1 was a sulfur-oxidizing obligate chemolithotroph utilizing sulfide, elemental sulfur, thiosulfate, and hydrogen as electron donors and nitrate as an electron acceptor. Oxygen also supported its growth only under microaerobic conditions. Strain YK-1 could not grow on nitrite, and nitrite was the final product of nitrate reduction. Neither sugars, organic acids (including acetate), nor hydrocarbons could serve as carbon and energy sources. A typical stoichiometry of its energy metabolism followed an equation: S2− + 4NO3 − → SO4 2− + 4NO2 − (ΔG 0 = −534 kJ mol−1). In a difference from other anaerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 1% NaCl was negligible. When YK-1 was grown anaerobically in a sulfur-depleted inorganic medium overlaid with crude oil, sulfate was produced, corresponding to its growth. On the contrary, YK-1 could not utilize crude oil as a carbon source. These results suggest that the cluster 1 bacteria yielded energy for growth in oil storage cavities by oxidizing petroleum sulfur compounds. Based on its physiology, ecological interactions with other members of the groundwater community are discussed.

scholarly journals Flavicella marina gen. nov., sp. nov., a carotenoid-producing bacterium from surface seawater

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 799-804 ◽  
Author(s):  
Maki Teramoto ◽  
Miyuki Nishijima
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Novel Genus And Species ◽  
Bacterium Strain ◽  
Kochi Prefecture ◽  
Type Strains

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped or spherical bacterium, strain 2A-7T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced a pigment(s), the absorption spectrum of which closely resembled that of β-carotene. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and clustered distantly with the type strains of species of the genus Lutibacter (up to 93.9 % similarity). The DNA G+C content was 34.1 mol%. The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-7T represents a novel genus and species, for which the name Flavicella marina gen. nov., sp. nov. is proposed. The type strain of Flavicella marina is 2A-7T ( = NBRC 110145T = KCTC 42197T).

scholarly journals Moorella humiferrea sp. nov., a thermophilic, anaerobic bacterium capable of growth via electron shuttling between humic acid and Fe(III)

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 613-617 ◽  
Author(s):  
Y. N. Nepomnyashchaya ◽  
G. B. Slobodkina ◽  
R. V. Baslerov ◽  
N. A. Chernyh ◽  
E. A. Bonch-Osmolovskaya ◽  
...  
Keyword(s):  
Humic Acid ◽  
Electron Acceptor ◽  
Type Strain ◽  
Kamchatka Peninsula ◽  
Alginate Beads ◽  
Rrna Gene ◽  
Electron Shuttling ◽  
Bacterium Strain ◽  
Hydrothermal Spring ◽  
Ph Range

An anaerobic, thermophilic, spore-forming bacterium (strain 64-FGQT) was isolated from a terrestrial hydrothermal spring from the Kamchatka peninsula, Russia. This strain utilized lactate as an electron donor, insoluble poorly crystalline Fe(III) oxide incorporated into alginate beads as a potential electron acceptor and 9,10-anthraquinone-2,6-disulfonate (AQDS) as an electron-shuttling compound. Vegetative cells of strain 64-FGQT were Gram-stain-positive, peritrichously flagellated, motile, straight rods, 0.3–0.5 µm in diameter and 2.0–5.0 µm long, growing singly or forming short chains. Cells formed round refractive endospores in terminal swollen sporangia. The temperature range for growth was 46–70 °C, with an optimum at 65 °C. The pH range for growth was 5.5–8.5, with an optimum at pH 7.0. The substrates utilized by strain 64-FGQT in the presence of AQDS as an electron acceptor included lactate, malate, succinate, glycerol and yeast extract. The strain fermented galactose, fructose, maltose, sucrose, pyruvate and peptone. Strain 64-FGQT used AQDS, humic acid, thiosulfate, nitrate and perchlorate as electron acceptors for growth. Fe(III) was not directly reduced, but strain 64-FGQT was able to grow and reduce Fe(III) oxide in the presence of small amounts of AQDS or humic acid as electron-shuttling compounds. The G+C content of the DNA of strain 64-FGQT was 51 mol%. 16S rRNA gene sequence analysis placed the isolate in the genus Moorella, with the type strain of Moorella glycerini as its closest relative (97.2 % similarity). Based on phylogenetic analysis and physiological characteristics, strain 64-FGQT is considered to represent a novel species of the genus Moorella, for which the name Moorella humiferrea sp. nov. is proposed; the type strain is 64-FGQT ( = DSM 23265T = VKM B-2603T).

scholarly journals Haloargentinum marplatensis gen. nov., sp. nov., a novel extremely halophilic bacterium isolated from salted-ripened anchovy (Engraulis anchoita)

2020 ◽  
Author(s):  
Silvina Perez ◽  
Margarita Gomila ◽  
Silvia Elena Murialdo ◽  
Irene Mabel Ameztoy ◽  
Narjol Gonzalez-Escalona ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Strain ◽  
Close Relationships ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Gram Negative ◽  
Novel Genus And Species ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

ABSTRACTA facultative aerobic, Gram-negative, motile, non-endospore forming and extremely halophilic bacterium, strain 11aii⊺, isolated from salted-ripened anchovy, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA gene revealed close relationships to species of the genera Lentibacillus and Virgibacillus (94.2% similarity). The organism grew optimally in the presence of 20-35 % NaCl. The major fatty acids of strain 11aii⊺ were C16:0 (42.1%) and anteiso-C15:0 (31.2%) and also presented iso-C16:0 (11.0%), anteiso-C17:0 (10.4%) and C18:0 (5.2%). Based on data presented here, strain 11aii⊺ is considered to represent a novel genus and species, for which the name Haloargentinum marplatensis gen. nov. sp. nov. is proposed with the strain 11aii⊺ as type strain.

scholarly journals Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ‘Verrucomicrobia’, isolated from a sponge (Porifera)

2006 ◽  
Vol 56 (9) ◽  
pp. 2119-2124 ◽  
Author(s):  
Matthias Scheuermayer ◽  
Tobias A. M. Gulder ◽  
Gerhard Bringmann ◽  
Ute Hentschel
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Ph Values ◽  
Novel Genus And Species ◽  
Bacterium Strain

A marine bacterium, strain Pol012T, was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum ‘Verrucomicrobia’. Strain Pol012T was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 °C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012T was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012T is the first marine pure-culture representative of ‘Verrucomicrobia’ subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012T (=DSM 177716T=CIP 108984T).

scholarly journals Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment

2010 ◽  
Vol 60 (8) ◽  
pp. 1832-1836 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova ◽  
Valery V. Mikhailov
Keyword(s):  
Sequence Similarity ◽  
Phospholipid Fatty Acid ◽  
Fatty Acid Analysis ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Phylogenetic Distance ◽  
Separate Branch ◽  
Novel Genus And Species ◽  
Bacterium Strain

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1 ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1 ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).

scholarly journals Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments

2004 ◽  
Vol 54 (5) ◽  
pp. 1477-1482 ◽  
Author(s):  
Fumio Inagaki ◽  
Ken Takai ◽  
Kenneth H. Nealson ◽  
Koki Horikoshi
Keyword(s):  
Okinawa Trough ◽  
Cold Seep ◽  
Molecular Characteristics ◽  
Rrna Gene ◽  
Sulfur Oxidizing ◽  
Bacterium Strain ◽  
Gas Bubbling ◽  
Ph Range ◽  
Environmental Sequences ◽  
The 16S Rrna Gene

A novel mesophilic sulfur- and thiosulfate-oxidizing bacterium, strain 42BKTT, was isolated from the gas-bubbling sediment at the Iheya North hydrothermal system in the mid-Okinawa Trough, Japan. The isolate was a Gram-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 10–40 °C (optimum 28–30 °C) and in the pH range 5·0–9·0 (optimum 6·5–7·0). Strain 42BKTT grew chemolithoautotrophically with elemental sulfur or thiosulfate as a sole electron donor and oxygen (optimum 5 % in gas phase) or nitrate as an electron acceptor. The G+C content of the genomic DNA was 48·0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the previously uncultivated Group F within the ε-Proteobacteria, which includes phylotypes of vent epibiont and environmental sequences from global deep-sea cold seep and hydrothermal vent fields. On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus, Sulfurovum lithotrophicum gen. nov., sp. nov., is proposed. The type strain is 42BKTT (=ATCC BAA-797T=JCM 12117T).

Halomonas xianhensis sp. nov., a moderately halophilic bacterium isolated from a saline soil contaminated with crude oil

2012 ◽  
Vol 62 (1) ◽  
pp. 173-178 ◽  
Author(s):  
Baisuo Zhao ◽  
Hui Wang ◽  
Xinwei Mao ◽  
Ruirui Li ◽  
Yun-Jiao Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Crude Oil ◽  
Saline Soil ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium ◽  
Bacterium Strain

A Gram-negative, aerobic, short rod-shaped and non-motile bacterium, strain A-1T, was isolated from a saline soil contaminated with crude oil in Xianhe, Shangdong Province, China. Strain A-1T formed yellow colonies, was moderately halophilic and grew with 0.05–27.5 % (w/v) total salts (optimum 5–8 %), at 10–42 °C (optimum 30 °C) and at pH 5.5–9.0 (optimum pH 7.2). The dominant fatty acids (>5 %) were C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c, C19 : 0 cyclo ω8c and C12 : 0 3-OH and the predominant ubiquinone was Q-9. The genomic DNA G+C content was 67.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A-1T belonged to the genus Halomonas in the class Gammaproteobacteria. The closest relatives were Halomonas lutea YIM 91125T (97.7 % 16S rRNA gene sequence similarity), H. muralis LMG 20969T (95.6 %), H. pantelleriensis AAPT (95.5 %) and H. kribbensis BH843T (95.2 %). DNA–DNA relatedness between strain A-1T and H. lutea CCTCC AB 206093T was 27±3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain A-1T should be placed in the genus Halomonas as a representative of a novel species. The name Halomonas xianhensis sp. nov. is proposed, with strain A-1T ( = CGMCC 1.6848T  = JCM 14849T) as the type strain.

Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil

2011 ◽  
Vol 61 (8) ◽  
pp. 1767-1775 ◽  
Author(s):  
Man Cai ◽  
Lu Wang ◽  
Hua Cai ◽  
Yan Li ◽  
Ya-Nan Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Crude Oil ◽  
Type Strain ◽  
Saline Soil ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Positive Staining ◽  
Facultatively Anaerobic

Four bacterial strains, SL014B-41A4T, SL014B-20A1T, SL014B-76A1 and SL014B-79A, isolated from a crude oil-contaminated saline soil of Shengli Oilfield, China, were investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL014B-41A4T belonged to the genus Salinarimonas in the order Rhizobiales, with the highest sequence similarity with Salinarimonas rosea YIM YD3T (98.3 %). The DNA–DNA relatedness of strain SL014B-41A4T to S. rosea YIM YD3T was 27.03±3.0 %. Strain SL014B-41A4T was Gram-negative staining, facultatively anaerobic and produced deep red pigment in artificial seawater medium. Cells of strain SL014B-41A4T were rod-shaped (0.6–4.0×1.25–25 µm), motile with a single polar flagellum and often formed branches. The strain contained Q-10 as the predominant respiratory ubiquinone and C18 : 1ω7c (57.5 %), C16 : 0 (16.4 %) and 10-methyl C19 : 0 (9.1 %) as the major fatty acids. Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were actinobacteria and belonged to the genus Tessaracoccus in the family Propionibacteriaceae of the order Actinomycetales with the highest 16S rRNA gene sequence similarities with Tessaracoccus flavescens SST-39T (96.4 %), Tessaracoccus lubricantis KISS-17SeT (96.2 %) and Tessaracoccus bendigoensis Ben 106T (94.7 %). Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were Gram-positive staining, facultatively anaerobic, non-endospore-forming, non-motile, acid-fast and oval to rod-shaped (0.48×0.5–1.0 µm). These three novel strains had ll-diaminopimelic acid (DAP) as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-9(H4) as the only menaquinone and anteiso-C15 : 0 (67.11–76.14 %) as the major cellular fatty acid. The G+C contents of the genomic DNA of strain SL014B-41A4T and strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were 67.68 mol% and 65.65–67.17 mol%, respectively. Based on phenotypic and genotypic characteristics, strain SL014B-41A4T represents a novel species of the genus Salinarimonas, for which the name Salinarimonas ramus is proposed, with strain SL014B-41A4T ( = DSM 22962T = CGMCC 1.9161T) as the type strain. Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus oleiagri is proposed, with strain SL014B-20A1T ( = DSM 22955T = CGMCC 1.9159T) as the type strain.

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