Deferrisoma camini gen. nov., sp. nov., a moderately thermophilic, dissimilatory iron(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in the Deltaproteobacteria

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2463-2468 ◽  
Author(s):  
G. B. Slobodkina ◽  
A.-L. Reysenbach ◽  
A. N. Panteleeva ◽  
N. A. Kostrikina ◽  
I. D. Wagner ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Electron Donors ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Ph Range

A moderately thermophilic, anaerobic, dissimilatory iron(III)-reducing bacterium (strain S3R1T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Centre in the Pacific Ocean at a depth of about 2150 m. Cells of strain S3R1T were ovals to short rods with a single polar flagellum, Gram-stain-negative, 0.5–0.6 µm in diameter and 0.8–1.3 µm long, growing singly or in pairs. The temperature range for growth was 36–62 °C, with an optimum at 50 °C. The pH range for growth was 5.5–7.5, with an optimum at pH 6.5. Growth of strain S3R1T was observed at NaCl concentrations ranging from 1.0 to 5.0 % (w/v), with an optimum at 2.0–2.5 % (w/v). The isolate used acetate, fumarate, malate, maleinate, succinate, propanol, palmitate, stearate, peptone and yeast extract as electron donors for growth and iron(III) reduction. All electron donors were oxidized completely to CO2 and H2O. Iron(III) (in the form of ferrihydrite, ferric citrate or ferric nitrilotriacetate) and elemental sulfur (S0) were the electron acceptors that supported growth. The DNA G+C content was 64.4 mol%. Results of 16S rRNA gene sequence analysis showed that the novel bacterium was related to representatives of the orders Desulfuromonadales and Syntrophobacterales with 84–86 % sequence similarity and formed a distinct phylogenetic branch in the Deltaproteobacteria . On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the new isolate represents the sole species of a novel genus, Deferrisoma camini gen. nov., sp. nov. The type strain of Deferrisoma camini is S3R1T ( = DSM 24185T  = VKM B-2672T).

scholarly journals Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2084-2088 ◽  
Author(s):  
Lijing Jiang ◽  
Hongxiu Xu ◽  
Zongze Shao ◽  
Minnan Long
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Type Species ◽  
Marine Bacterium ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, strictly aerobic, chemoheterotrophic marine bacterium, designated 20V17T, was isolated from a deep-sea hydrothermal vent chimney collected from the South-west Indian Ridge. Cells of strain 20V17T were motile, short rods, 1.2–1.8 µm in length and 0.5–0.7 µm in width. Growth was observed at between 20 and 37 °C (optimum 25 °C–28 °C), pH 5.0 and 8.0 (optimum pH 7.0) and 0.5 and 8 % (w/v) NaCl (optimum 1.5–2.0 % NaCl). The major fatty acids were C18 : 1ω7c (74.4 %), C19 : 0 cyclo ω8c (11 %), C18 : 0 (5.1 %) and C18 : 0 3-OH (2.8 %), and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and four unidentified phospholipids. Ubiquinone 10 was the major quinone. The G+C content of genomic DNA was 66.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 20V17T belonged to the genus Defluviimonas and shared 96.5 and 96.1 % sequence similarity with Defluviimonas denitrificans D9-3T and Defluviimonas aestuarii BS14T, respectively. On the basis of the taxonomic data obtained in this study, strain 20V17T represents a novel species of the genus Defluviimonas , for which the name Defluviimonas indica sp. nov. is proposed. The type strain is 20V17T (CGMCC 1.10859T = JCM 17871T = MCCC 1A01802T).

scholarly journals Reclassification of Desulfobacterium anilini as Desulfatiglans anilini comb. nov. within Desulfatiglans gen. nov., and description of a 4-chlorophenol-degrading sulfate-reducing bacterium, Desulfatiglans parachlorophenolica sp. nov.

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3081-3086 ◽  
Author(s):  
Daisuke Suzuki ◽  
Zhiling Li ◽  
Xinxin Cui ◽  
Chunfung Zhang ◽  
Arata Katayama
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Electron Acceptors ◽  
Electron Donors ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (DST), isolated from river sediment contaminated with volatile organic compounds, was characterized phenotypically and phylogenetically. Cells were Gram-reaction-negative, non-motile short rods. For growth, optimum NaCl concentration was 0.9 g l−1, optimum temperature was 30 °C and optimum pH was 7.2. Strain DST utilized phenol, benzoate, 4-hydroxybenzoate, 4-methylphenol, 4-chlorophenol, acetate, butyrate and pyruvate as electron donors for sulfate reduction. Electron donors were completely oxidized. Strain DST did not utilize sulfite, thiosulfate or nitrate as electron acceptors. The genomic DNA G+C content of strain DST was 58.9 mol%. Major cellular fatty acids were iso-C14 : 0, anteiso-C15 : 0 and C18 : 1ω7c. Phylogenetic analyses based on the 16S rRNA gene indicated its closest relatives were strains of Desulfobacterium anilini (about 98–99 % sequence similarity) but the DNA–DNA hybridization value with Desulfobacterium anilini Ani1T was around 40 %. Although strain DST and its relatives shared most phenotypic and chemotaxonomic characteristics, the utilization of 4-chlorophenol, the range of electron acceptors and the optimum growth conditions differed. Strain DST is closely related to strains of Desulfobacterium anilini , but constitutes a different species within the genus. Based on phylogeny, phenotypic characteristics and chemotaxonomic characteristics, strain DST and Desulfobacterium anilini were clearly different from strains of other species of the genus Desulfobacterium . We thus propose the reclassification of Desulfobacterium anilini within a new genus, Desulfatiglans gen. nov., as Desulfatiglans anilini comb. nov. We also propose Desulfatiglans parachlorophenolica sp. nov. to accommodate strain DST. The type strain is DST ( = JCM 19179T = DSM 27197T).

scholarly journals Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 359-364 ◽  
Author(s):  
Shuhui Li ◽  
Kai Tang ◽  
Keshao Liu ◽  
Nianzhi Jiao
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Deep Sea Water ◽  
Link Type ◽  
Novel Genus And Species ◽  
Family Rhodobacteraceae

A bacterial strain, JLT2016T, was isolated from a sample of South-eastern Pacific deep-sea water. Cells were Gram-stain-negative, aerobic, devoid of flagella, motile by gliding and rod-shaped. Colonies were mucoid and cream. Growth occurred at 1.0–11.0 % (w/v) NaCl, 10–40 °C and pH 4.0–9.0. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (60.5 %), C19 : 0 cyclo ω8c (10.9 %) and C16 : 0 (9.0 %). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two sphingoglycolipids. The DNA G+C content was 67.1 mol%. The closest relative of strain JLT2016T was Salipiger mucosus A3T (96.7 % 16S rRNA gene sequence similarity). The results of phylogenetic analyses with different treeing algorithms indicated that this strain belonged to the Roseobacter clade in the order Rhodobacterales . Based on polyphasic analysis, strain JLT2016T is considered to represent a novel genus and species, for which the name Thiobacimonas profunda gen. nov., sp. nov. is proposed. The type strain is JLT2016T ( = LMG 27365T = CGMCC 1.12377T).

Dissulfuribacter thermophilus gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating, deeply branching deltaproteobacterium from a deep-sea hydrothermal vent

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 1967-1971 ◽  
Author(s):  
A. I. Slobodkin ◽  
A.-L. Reysenbach ◽  
G. B. Slobodkina ◽  
T. V. Kolganova ◽  
N. A. Kostrikina ◽  
...  
Keyword(s):  
Energy Source ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Elemental Sulfur ◽  
Phylogenetic Analyses ◽  
Spreading Center ◽  
Rrna Gene ◽  
Content Type ◽  
Physiological Properties ◽  
Ph Range

A thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S69T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center and Valu Fa Ridge, Pacific Ocean, at a depth of 1910 m using anoxic medium with elemental sulfur as the only energy source. Cells of strain S69T were Gram-negative short rods, 0.4–0.6 µm in diameter and 1.0–2.5 µm in length, motile with a single polar flagellum. The temperature range for growth was 28–70 °C, with an optimum at 61 °C. The pH range for growth was 5.6–7.9, with optimum growth at pH 6.8. Growth of strain S69T was observed at NaCl concentrations ranging from 0.9 to 5.0 %, with an optimum at 1.8–2.7 (w/v). Strain S69T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline Fe(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S69T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor either with H2 or with organic electron donors. Analysis of the 16S rRNA gene sequence revealed that the isolate formed a distinct phylogenetic branch within the Deltaproteobacteria . On the basis of its physiological properties and results of phylogenetic analyses, strain S69T is considered to represent a novel species of a new genus, for which the name Dissulfuribacter thermophilus gen. nov., sp. nov. is proposed. The type strain of Dissulfuribacter thermophilus is S69T ( = DSM 25762T = VKM B-2760T).

Chitinophaga rhizophila sp. nov., isolated from rhizosphere soil of banana

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Xian-Jiao Zhang ◽  
Guang-Da Feng ◽  
Fan Yang ◽  
Honghui Zhu ◽  
Qing Yao
Keyword(s):  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Ph Range

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as strain B61T, was isolated from rhizosphere soil of banana collected from Dongguan, Guangdong Province, PR China. Growth occurred at 15–40 °C, within a pH range of pH 6.0–9.0. Results of 16S rRNA gene sequence similarity and phylogenetic analyses showed that strain B61T was most closely related to ‘Chitinophaga agri’ KACC 21303 (98.9 %) and Chitinophaga pinensis DSM 2588T (98.8 %). The genome size was 7.6 Mb with a G+C content of 45.2 mol%. The genome-inferred average nucleotide identity values between strain B61T and two closely related strains were 79.2 and 79.3 %, respectively, with corresponding digital DNA–DNA hybridization values of 22.3 and 22.6 %. The major fatty acids of the novel strain were iso-C15:0, C16:1 ω5c and iso-C17:0 3-OH and the sole respiratory quinone was menaquinone 7 (MK-7). The polar lipids consisted of phosphatidylethanolamine, five unidentified aminolipids, four unidentified glycolipids and six unidentified lipids. The phenotypic and phylogenetic results clearly supported that strain B61T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga rhizophila, sp. nov. is proposed, with the type strain B61T (=GDMCC 1.2608T=KCTC 82856T).

scholarly journals Mizugakiibacter sediminis gen. nov., sp. nov., isolated from a freshwater lake

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3983-3987 ◽  
Author(s):  
Hisaya Kojima ◽  
Riho Tokizawa ◽  
Manabu Fukui
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Phenotypic Properties ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Ph Range

A novel, moderately thermophilic, bacterial strain (skMP5T) was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. Growth was observed at temperatures ranging from 25 to 52 °C, with optimum growth observed at 48–50 °C. The pH range for growth was pH 5.0–8.2, with optimum growth at pH 6.0–7.0. The G+C content of genomic DNA was 72 mol%. The major components in the fatty acid profile were iso-C17 : 0 and iso-C17 : 1ω9c. The predominant isoprenoid quinone of the strain was ubiquinone Q-8. The strain was facultatively anaerobic, and reduced nitrate to nitrite under anoxic conditions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was a member of the family Xanthomonadaceae within the class Gammaproteobacteria , showing highest sequence similarity with Tahibacter aquaticus RaM5-2 (93.6 %) and Metallibacterium scheffleri DKE6T (93.3 %). On the basis of phylogenetic and phenotypic properties, strain skMP5T represents a novel species of a new genus, Mizugakiibacter sediminis gen. nov., sp. nov. The type strain of the type species is skMP5T ( = DSM 27098T = NBRC 109608T).

Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2565-2571 ◽  
Author(s):  
A. I. Slobodkin ◽  
A.-L. Reysenbach ◽  
G. B. Slobodkina ◽  
R. V. Baslerov ◽  
N. A. Kostrikina ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Elemental Sulfur ◽  
Phylogenetic Analyses ◽  
Spreading Center ◽  
Rrna Gene ◽  
Content Type ◽  
Physiological Properties ◽  
Bacterium Strain ◽  
Ph Range

An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean, at a depth of 1910 m. Cells of strain S95T were oval to short Gram-negative rods, 0.5–0.6 µm in diameter and 1.0–1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50–92 °C, with an optimum at 74 °C. The pH range for growth was 5.5–8.0, with an optimum at pH 7.0. Growth of strain S95T was observed at NaCl concentrations ranging from 1.5 to 3.5 % (w/v). Strain S95T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline iron(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylum Thermodesulfobacteria . On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents the sole species of a new genus, Thermosulfurimonas dismutans gen. nov., sp. nov.; S95T ( = DSM 24515T = VKM B-2683T) is the type strain of the type species. This is the first description of a thermophilic micro-organism that disproportionates elemental sulfur.

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).

scholarly journals Nesterenkonia alkaliphila sp. nov., an alkaliphilic, halotolerant actinobacteria isolated from the western Pacific Ocean

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 516-521 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yubian Zhang ◽  
Xijie Yin ◽  
Shuang Wang
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Western Pacific ◽  
Rrna Gene ◽  
Western Pacific Ocean ◽  
Content Type ◽  
Link Type ◽  
The Western Pacific

A Gram-staining-positive, aerobic, motile and non-spore-forming actinobacteria, designated strain F10T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Nesterenkonia . Strain F10T shared highest 16S rRNA gene sequence similarity of 96.8 % with Nesterenkonia aethiopica DSM 17733T, followed by Nesterenkonia xinjiangensis YIM 70097T (96.7 %) and Nesterenkonia alba CAAS 252T (96.6 %). The organism grew at 4–50 °C, at pH 7.0–12.0 and in the presence of 0–12 % (w/v) NaCl, with optimal growth occurring at 40 °C, at pH 9.0 and in the presence of 1 % (w/v) NaCl. The peptidoglycan type was A4(alpha), l-Lys–Gly–l-Glu. The polar lipid profile of strain F10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and two unknown lipids. The isolate contained MK-9 (92 %) and MK-8 (5.8 %) as the major components of the menaquinone system, and anteiso-C17 : 0 (50.9 %) and anteiso-C15 : 0 (29.8 %) as the predominant fatty acids. The G+C content of the genomic DNA of strain F10T was 66.2 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain F10T represents a novel species of the genus Nesterenkonia for which the name Nesterenkonia alkaliphila sp. nov. is proposed. The type strain is F10T ( = LMG 28112T = CGMCC 1.12781T = JCM 19766T = MCCC 1A09946T).

Aquimarina megaterium sp. nov., isolated from seawater

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 122-127 ◽  
Author(s):  
Tong Yu ◽  
Zenghu Zhang ◽  
Xiaoyang Fan ◽  
Xiaochong Shi ◽  
Xiao-Hua Zhang
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Gliding Motility ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Integrated Ocean Drilling Program

A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated XH134T, was isolated from surface seawater of the South Pacific Gyre (45° 58′ S 163° 11′ W) during the Integrated Ocean Drilling Program Expedition 329. The major respiratory quinone of strain XH134T was MK-6. The dominant fatty acids of strain XH134T were iso-C15 : 0, iso-C15 : 1 G, C16 : 1ω6c and/or C16 : 1ω7c, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c. The polar lipids of strain XH134T comprised phosphatidylethanolamine, one unknown aminolipid and three unknown polar lipids. The DNA G+C content of strain XH134T was 32.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina macrocephali JAMB N27T with 96.9 % sequence similarity. A number of phenotypic characteristics distinguished strain XH134T from described members of the genus Aquimarina . On the basis of combined phenotypic and phylogenetic analyses, strain XH134T represents a novel species of the genus Aquimarina , for which the name Aquimarina megaterium sp. nov. is proposed. The type strain is XH134T ( = CGMCC 1.12186T = JCM 18215T).

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