scholarly journals Sulfurisoma sediminicola gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1587-1592 ◽  
Author(s):  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Sulfur Oxidation ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel facultatively autotrophic bacterium, strain BSN1T was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. As sole energy sources for autotrophic growth, the strain oxidized thiosulfate, elemental sulfur and hydrogen. Strain BSN1T was a facultative anaerobe utilizing nitrate as an electron acceptor. Growth was observed at temperatures lower than 34 °C, and the optimum growth was observed at 30–32 °C. The range of pH for growth was pH 6.8–8.8, and the optimum pH was pH 7.8–8.1. The optimum growth of the isolate occurred at concentrations of NaCl less than 50 mM. The G+C content of genomic DNA was 67 mol%. The major component in the fatty acid profile of strain BSN1T grown on fumarate was summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria , and it showed the highest sequence similarity with Georgfuchsia toluolica G5G6T (96.2 %). Phylogenetic analyses were also performed on genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain BSN1T ( = DSM 26916T = NBRC 109412T) is proposed as the type strain of a novel species of a novel genus, Sulfurisoma sediminicola gen. nov., sp. nov.

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).

scholarly journals Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake

2010 ◽  
Vol 60 (12) ◽  
pp. 2862-2866 ◽  
Author(s):  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
Carbon Fixation ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Sulfur Oxidation ◽  
Freshwater Lake ◽  
Nitrate Respiration ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Phenotypic Properties ◽  
Sulfur Oxidizing

A novel facultatively anaerobic, sulfur-oxidizing bacterium, strain skB26T, was isolated from anoxic water of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-negative. Strain skB26T oxidized elemental sulfur and thiosulfate to sulfate as sole energy sources. Strain skB26T was microaerobic and could also utilize nitrate as an electron acceptor, reducing it to nitrogen. Growth was observed at temperatures below 28 °C; optimum growth was observed at 22 °C. The pH range for growth was 6.0–9.0, and the optimum pH was 7.5–8.0. Optimum growth of the isolate was observed in medium without NaCl, and no growth was observed in medium containing more than 220 mM NaCl. The G+C content of genomic DNA was around 59 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain was a member of the class Betaproteobacteria, and the closest cultivated relative was ‘Thiobacillus plumbophilus’ DSM 6690, with 93 % sequence similarity. Phylogenetic analyses were also performed using sequences of genes involved in sulfur oxidation, inorganic carbon fixation and nitrate respiration. On the basis of its phylogenetic and phenotypic properties, strain skB26T (=NBRC 105220T =DSM 22764T) is proposed as the type strain of a novel species of a new genus, Sulfuricella denitrificans gen. nov., sp. nov.

scholarly journals Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 86-92 ◽  
Author(s):  
O. A. Podosokorskaya ◽  
E. A. Bonch-Osmolovskaya ◽  
A. A. Novikov ◽  
T. V. Kolganova ◽  
I. V. Kublanov
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Hot Water ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Deep Well ◽  
Physiological Properties ◽  
Tomsk Region ◽  
Bacterium Strain

A novel obligately anaerobic, mesophilic, organotrophic bacterium, strain P3M-1T, was isolated from a microbial mat formed in a wooden bath filled with hot water emerging from a 2775 m-deep well in the Tomsk region of western Siberia, Russia. Cells of strain P3M-1T were rod-shaped, 0.3–0.7 µm in width and formed multicellullar filaments that reached up to 400 µm in length. Strain P3M-1T grew optimally at 42–45 °C, pH 7.5–8.0, and with 0.1% (w/v) NaCl. Under optimal conditions, the doubling time was 6 h. The isolate was able to ferment a variety of proteinaceous substrates and sugars, including microcrystalline cellulose. Acetate, ethanol and H2 were the main products of glucose fermentation. The genomic DNA G+C content was 55 mol%. 16S rRNA gene sequence-based phylogenetic analyses showed that strain P3M-1T was a member of the class Anaerolinea , with 92.8 % sequence similarity to Levilinea saccharolytica KIBI-1T. Based on phylogenetic analysis and physiological properties, strain P3M-1T represents a novel species in a new genus, for which the name Ornatilinea apprima gen. nov., sp. nov. is proposed; the type strain of O. apprima is P3M-1T ( = DSM 23815T = VKM B-2669T).

scholarly journals Sulfuriferula multivorans gen. nov., sp. nov., isolated from a freshwater lake, reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov., and description of Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1504-1508 ◽  
Author(s):  
Tomohiro Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Phenotypic Properties ◽  
Content Type ◽  
Nacl Concentration ◽  
Bacterium Strain ◽  
Ph Range

A sulfur-oxidizing bacterium, strain TTNT, was isolated from a Thioploca sample obtained from a freshwater lake in Japan. The isolate shared 97.1 % 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, ‘Thiobacillus plumbophilus’ Gro7T. Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTNT grew over a temperature range of 8–32 °C (optimum 22–25 °C), an NaCl concentration range of 0–133.3 mM (optimum 0–3.3 mM) and a pH range of 5.3–8.6 (optimum pH 6.4–7.0). Strain TTNT was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTNT represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTNT ( = NBRC 110683T = DSM 29343T). Along with this, the reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov. (type strain Gro7T = NBRC 107929T = DSM 6690T) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.

scholarly journals Aquirufa rosea sp. nov., isolated from a freshwater lake

2020 ◽  
Vol 70 (5) ◽  
pp. 3145-3153 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Tzu-Ying Chen ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A bacterial strain designated CAR-16T was isolated from a freshwater lake in Taiwan and characterized using the polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed rose-colored colonies. Optimal growth occurred at 30 °C, pH 7 and with 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that CAR-16T represented a member of the family Cytophagaceae and formed a phylogenetic lineage in the genus Aquirufa . CAR-16T was most closely related to Aquirufa nivalisilvae 59G-WUEMPELT with a 99.7 % 16S rRNA gene sequence similarity. CAR-16T showed 71.2–79.5 % average nucleotide identity and 17.8–21.7 % digital DNA–DNA hybridization identity with the strains of other species of the genus Aquirufa . The major fatty acids of strain CAR-16T were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c and/or iso-C15 : 0 2-OH). The polar lipid profile consisted of a mixture of phosphatidylethanolamine and several uncharacterized aminophospholipids, phospholipids and lipids. The major isoprenoid quinone was MK-7. The genomic DNA G+C content of CAR-16T was 38.8 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, CAR-16T should be classified as representing a novel species of the genus Aquirufa , for which the name Aquirufa rosea sp. nov. is proposed. The type strain is CAR-16T (=BCRC 81153T=LMG 30923T=KCTC 62869T).

Pseudorhodobacter wandonensis sp. nov., isolated from wood falls, and emended description of the genus Pseudorhodobacter

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1479-1484 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Soo-Young Lee ◽  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated WT-MW11T, was isolated from wood falls on the coast of Wando, an island of South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain WT-MW11T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2.0–3.0 % (w/v) NaCl. Bacteriochlorophyll a was not produced. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WT-MW11T clustered with Pseudorhodobacter ferrugineus IAM 12616T and Pseudorhodobacter aquimaris HDW-19T, with which it exhibited 16S rRNA gene sequence similarity values of 97.9 and 95.5 %, respectively. Strain WT-MW11T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain WT-MW11T was similar to those of P. ferrugineus JCM 20687T and P. aquimaris HDW-19T. The DNA G+C content of strain WT-MW11T was 61.6 mol% and its mean DNA–DNA relatedness value with P. ferrugineus JCM 20687T was 12.3 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WT-MW11T was distinguishable from the two recognized species of the genus Pseudorhodobacter . On the basis of the data presented, strain WT-MW11T is considered to represent a novel species of the genus Pseudorhodobacter , for which the name Pseudorhodobacter wandonensis sp. nov. is proposed. The type strain is WT-MW11T ( = KCTC 23672T = CCUG 61506T). The description of the genus Pseudorhodobacter is emended.

scholarly journals Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1086-1091 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Wei-Cheng Huang ◽  
Chih-Yu Cheng ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A facultatively anaerobic, chitinolytic bacterium, strain KL-9T, was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9T were Gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15–40 °C (optimum, 30–37 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9T was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9T formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria , being most closely related to members of the genera Leeia , Chitinimonas , Silvimonas and Andreprevotia . Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9T is thus considered to represent a novel species of a new genus within the class Betaproteobacteria , for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9T ( = BCRC 80168T = LMG 25530T).

Olleya namhaensis sp. nov., isolated from wood falls, and emended description of the genus Olleya Mancuso Nichols et al. 2005 emend. Lee et al. 2010

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1610-1615 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-stain-negative, non-flagellated, gliding, rod-shaped bacterial strain, designated WT-MY15T, was isolated from wood falls in the South Sea in Korea and subjected to a polyphasic taxonomic study. Strain WT-MY15T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WT-MY15T clustered with the type strains of two Olleya species, exhibiting 16S rRNA gene sequence similarity values of 97.7–98.1 %. Strain WT-MY15T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain WT-MY15T were similar to those of Olleya aquimaris L-4T and Olleya marilimosa CIP 108537T. The DNA G+C content of strain WT-MY15T was 42.8 mol% and its mean DNA–DNA relatedness values with O. aquimaris L-4T and O. marilimosa CIP 108537T were 8.3 and 5.6 %, respectively. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WT-MY15T is separate from the two recognized species of the genus Olleya . On the basis of the data presented, strain WT-MY15T is considered to represent a novel species of the genus Olleya , for which the name Olleya namhaensis sp. nov. is proposed. The type strain is WT-MY15T ( = KCTC 23673T = CCUG 61507T). An emended description of the genus Olleya is also presented.

Tropicimonas sediminicola sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2424-2429 ◽  
Author(s):  
Na-Ri Shin ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Bora Yun ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97T, was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97T was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1–2 % (w/v) NaCl and at pH 7–8. The main cellular fatty acids were C16 : 0, C18 : 1ω7c, C12 : 0 3-OH and cyclo-C19 : 0ω8c. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97T belongs to the genus Tropicimonas , with highest sequence similarity to Tropicimonas aquimaris DPG-21T (99.0 %). The DNA G+C content of strain M97T was 68.5 mol%. Mean DNA–DNA relatedness between strain M97T and T. aquimaris DPG-21T was 46±10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97T is considered to represent a novel species of the genus Tropicimonas , for which the name Tropicimonas sediminicola sp. nov. is proposed. The type strain is M97T ( = KACC 15544T = JCM 17731T).

scholarly journals Muricauda beolgyonensis sp. nov., isolated from a tidal flat

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1134-1139 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Type Strains

The taxonomic position of a Gram-staining-negative, non-motile, rod-shaped bacterium, strain BB-My12T, which was isolated from a sediment sample collected from a tidal flat in Korea, was investigated by using a polyphasic approach. Strain BB-My12T grew optimally at 37 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain BB-My12T fell within the cluster comprising species of the genus Muricauda and appeared most similar to the type strains of Muricauda aquimarina , Muricauda lutimaris and Muricauda ruestringensis (97.5–97.6 % sequence similarity). The DNA G+C content was 45.0 mol%. Strain BB-My12T contained MK-6 as the predominant menaquinone and iso-C15 : 1, iso-C17 : 0 3-OH and iso-C15 : 0 as the major cellular fatty acids. The polar lipids of strain BB-My12T were phosphatidylethanolamine and four unidentified lipids. The DNA–DNA relatedness values between strain BB-My12T and the type strains of the three species of the genus Muricauda that appeared most closely related were in the range 5–7 %. The genetic distinctiveness and some phenotypic properties indicated that strain BB-My12T did not belong to any established species of the genus Muricauda . Strain BB-My12T is therefore considered to represent a novel species of the genus Muricauda , for which the name Muricauda beolgyonensis sp. nov. is proposed. The type strain is BB-My12T ( = KCTC 23501T  = CCUG 60800T).

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