Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1926-1931 ◽  
Author(s):  
T. N. R. Srinivas ◽  
P. Vishnu Vardhan Reddy ◽  
Z. Begum ◽  
P. Manasa ◽  
S. Shivaji
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Sequence Similarity ◽  
The Arctic ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Svalbard Archipelago ◽  
Content Type ◽  
Link Type

A novel Gram-staining-negative, coccoid, non-motile bacterium, designated strain V1-41T, was isolated from a sample of marine sediment collected, at a depth of 200 m, from Kongsfjorden (an inlet on the west coast of Spitsbergen, an island that forms part of the Svalbard archipelago in the Arctic Ocean). The strain formed cream–brown colonies on marine agar. Cells of the novel strain were positive in tests for catalase, oxidase, lysine decarboxylase and ornithine decarboxylase activities but negative for gelatinase and lipase activities. They hydrolysed aesculin, starch and urea, but not casein or DNA. Most of the cellular fatty acids were medium-chain and saturated (37.1 %) or long-chain and unsaturated (27.8 %), with C12 : 0 (37.1 %), C18:1ω7c, and summed features 2 (19.3%) and 3 (24.1%) predominating. The major respiratory quinone was Q-8. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, four unidentified phospholipids and one other unidentified lipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain’s closest known relatives were Oceanisphaera litoralis DSM 15406T (98.5 % sequence similarity) and Oceanisphaera donghaensis BL1T (98.3 %). In DNA–DNA hybridizations, however, the levels of relatedness between strain V1-41T and O. litoralis DSM 15406T and between the novel strain and O. donghaensis DSM 17589T were found to be only 19 % and 29 %, respectively. Based on these low levels of similarity at the DNA–DNA level and the phenotypic and chemotaxonomic differences from O. litoralis DSM 15406T and O. donghaensis DSM 17589T, strain V1-41T represents a novel species of the genus Oceanisphaera for which the name Oceanisphaera arctica sp. nov. is proposed. The type strain is V1-41T ( = CCUG 58690T = KCTC 23013T = NBRC 106171T).

Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1639-1645 ◽  
Author(s):  
Lei Zhang ◽  
Xihui Shen ◽  
Yingbao Liu ◽  
Shiqing Li
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
The Family

A Gram-staining-negative, rod-shaped, gliding and pale-pink-pigmented bacterium, designated strain ZLM-10T, was isolated from a soil sample collected from an arid area in Xinjiang province, China, and characterized in a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30–37 °C and in the presence of 2 % (w/v) sea salts. The only respiratory quinone detected was MK-7 and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified aminophospholipids. The DNA G+C content was 45.4 mol%. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZLM-10T was a member of the phylum Bacteroidetes and appeared most closely related to Cesiribacter roseus 311T (90.2 % sequence similarity), Marivirga sericea LMG 13021T (89.2 %), Cesiribacter andamanensis AMV16T (89.1 %) and Marivirga tractuosa DSM 4126T (89.1 %). On the basis of phenotypic and genotypic data and phylogenetic inference, strain ZLM-10T should be classified as a novel species of a new genus in the family Flammeovirgaceae , for which the name Nafulsella turpanensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZLM-10T ( = CCTCC AB 208222T = KCTC 23983T).

scholarly journals Alkalicaulis satelles gen. nov., sp. nov., a novel haloalkaliphile isolated from a laboratory culture cyanobacterium Geitlerinema species and proposals of Maricaulaceae fam. nov., Robiginitomaculaceae fam. nov., Maricaulales ord. nov. and Hyphomonadales ord. nov.

2020 ◽  
Author(s):  
Vadim Kevbrin ◽  
Yulia Boltyanskaya ◽  
Veronika Koziaeva ◽  
Maria Uzun ◽  
Denis Grouzdev
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A prosthecate bacterial strain, designated G-192T, was isolated from decaying biomass of a haloalkaliphilic cyanobacterium Geitlerinema sp. Z-T0701. The cells were aerobic, Gram-negative, non-endospore-forming and dimorphic, occurring either as sessile bacteria with a characteristic stalk or as motile flagellated cells. The strain utilized a limited range of substrates, mostly peptonaceous, but was able to degrade whole proteins. Growth occurred at 5–46 °C (optimum, 35–40 °C), pH 7.3–10.3 (optimum, pH 8.0–9.0), 0–14 % NaCl (v/w; optimum, 2.0–6.0 %, v/w). The G+C content of the genomic DNA of strain G-192T was 66.8%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain G-192T formed a distinct evolutionary lineage within the family Hyphomonadaceae . Strain G-192T showed the highest 16S rRNA sequence similarity to Glycocaulis profundi ZYF765T (95.2%), Oceanicaulis stylophorae GISW-4T (94.2%) and Marinicauda salina WD6-1T (95.5%). The major cellular fatty acids (>5% of the total) were C18:1 ω9c, C18:0 and 11-methyl-C18:1 ω7c. The major polar lipids were glycolipids and phospholipids. The only respiratory quinone was ubiquinone-10 (Q-10). Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain G-192T represents a novel species of a new genus, for which the name Alkalicaulis satelles gen. nov., sp. nov. is proposed. The type strain is G-192T (=VKM B-3306T=KCTC 72746T). The strain is the first representative of the stalked bacteria associated with a haloalkaliphilic cyanobacterium. Based on phylogenomic indices and phenotypic data, it is proposed to evolve two novel families Maricaulaceae fam. nov. and Robiginitomaculaceae fam. nov. out of the current family Hyphomonadaceae . In addition, it is proposed to place the first two families in the novel order Maricaulales ord. nov. and novel order Hyphomonadales ord. nov. is proposed to accommodate the family Hyphomonadaceae .

Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1259-1264 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A bacterial strain, isolated from a sample of reef-building coral (Isopora palifera) collected off the coast of southern Taiwan, was characterized using a polyphasic taxonomic approach. The strain, designated sw-2T, was Gram-staining-negative, aerobic, rod-shaped and motile, with subpolar flagella, and formed greyish pink colonies. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain sw-2T was most closely related to Roseivivax halodurans Och 239T (97.4 % sequence similarity) and Roseivivax halotolerans Och 210T (96.4 %). The novel strain did not require NaCl for growth and exhibited optimal growth at 35–40 °C, at pH 7.5–8.0 and with 3–7 % (w/v) NaCl. It produced bacteriochlorophyll a under aerobic conditions. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 63.7 %) predominated in the cellular fatty acid profile. The novel strain’s major respiratory quinone was ubiquinone Q-10 and its genomic DNA G+C content was 68.8 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sulfo-quinovosyl diacylglycerol and three uncharacterized phospholipids. The level of DNA–DNA relatedness between strain sw-2T and Roseivivax halodurans Och 239T was only 15.0 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from all established species of the genus Roseivivax . Based on the genotypic, phenotypic and chemotaxonomic data, strain sw-2T represents a novel species in the genus Roseivivax , for which the name Roseivivax isoporae sp. nov. is proposed. The type strain is sw-2T ( = LMG 25204T = BCRC 17966T).

Erythrobacter jejuensis sp. nov., isolated from seawater

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1421-1426 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative, yellow-pigmented, non-motile, strictly aerobic, rod-shaped bacterium, designated strain CNU001T, was isolated from seawater collected on the coast of Jeju Island, South Korea, and subjected to a polyphasic taxonomic study. The temperature, pH and NaCl ranges for growth were 10–30 °C, pH 6.0–10.0 and 2.0–5.0 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNU001T belonged to the genus Erythrobacter in the family Erythrobacteraceae , with Erythrobacter longus DSM 6997T (96.6 % sequence similarity), Erythrobacter gaetbuli SW-161T (96.3 %), Erythrobacter vulgaris 022 2-10T (96.2 %), Erythrobacter nanhaisediminis T30T (96.1 %) and other members of the genus Erythrobacter (<96.0 %) identified as the novel strain’s closest relatives. The major cellular fatty acids were C18 : 1ω7c and C17 : 1ω6c. The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid and six other unidentified lipids. The major respiratory quinone was ubiquinone-10 (UQ-10) and the genomic DNA G+C content of the novel strain was 58.9 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU001T represents a novel species within the genus Erythrobacter , for which the name Erythrobacter jejuensis sp. nov. is proposed. The type strain is CNU001T ( = KCTC 23090T  = JCM 16677T).

Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter , Pedobacter heparinus , Pedobacter daechungensis , Pedobacter terricola , Pedobacter glucosidilyticus and Pedobacter lentus

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1963-1969 ◽  
Author(s):  
Zhichao Zhou ◽  
Fan Jiang ◽  
Shaohua Wang ◽  
Fang Peng ◽  
Jun Dai ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Arctic Region ◽  
The Arctic ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Arctic Soil

A Gram-stain-negative, short rod-shaped, motile (by gliding) bacterial strain, designated A12T, was isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. The temperature, NaCl and pH ranges for growth were 4–25 °C (optimum, 18 °C), 0–2 % (optimum, 0 %) and pH 6–9 (optimum, pH 7). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate belonged to the genus Pedobacter and showed highest sequence similarity (94.4 %) to Pedobacter daechungensis KCTC 12637T. The DNA G+C content (38.3 mol%), polar lipid profile, presence of sphingolipid, MK-7 as the only respiratory quinone, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids supported the allocation of strain A12T to the genus Pedobacter as a representative of a novel species, for which the name Pedobacter arcticus sp. nov. is proposed. The type strain is A12T ( = CCTCC AB 2010223T = NRRL B-59457T). Emended descriptions of the genus Pedobacter and of Pedobacter heparinus , Pedobacter daechungensis , Pedobacter terricola , Pedobacter glucosidilyticus and Pedobacter lentus are also given.

scholarly journals Kineobactrum salinum sp. nov., isolated from marine sediment

2020 ◽  
Author(s):  
Minji Kim ◽  
In-Tae Cha ◽  
Ki-Eun Lee ◽  
Byoung-Hee Lee ◽  
Soo-Je Park
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Polyphasic Characterization

Strain M2T, isolated from marine sediment collected at Jeju Island, was an aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, rod-shaped bacterium that formed circular, raised, yellow colonies. Strain M2T grew at 15–42 °C, pH 5.5–9.0 and with 1–9 % (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain M2T was closely related to Kineobactrum sediminis F02T (98.0 % sequence similarity). Ubiquinone-8 was determined to be the sole respiratory quinone. Summed feature 3 (C16 : 1  ω6c/C16 : 1  ω7c) and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) were identified as the predominant fatty acids. The DNA G+C content and digital DNA–DNA relatedness between strain M2T and K. sediminis F02T were 60.7 mol% and 19.5 %, respectively. Phosphatidylglycerol and phosphatidylethanolamine were identified as the major polar lipids. Thus, polyphasic characterization revealed that strain M2T represents a novel species in the genus Kineobactrum , for which the name Kineobactrum salinum sp. nov. is proposed. The type strain is M2T (=KCTC 72815T=VTCC 910108T).

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).

Description of Sphingobium psychrophilum sp. nov., a cold-adapted bacterium isolated from Arctic soil

2021 ◽  
Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
The Arctic ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
Arctic Soil

A yellow-coloured, Gram-stain-negative, non-sporulating, psychrotolerant and motile bacterium, designated AR-3-1T, was isolated from the Arctic soil of Cambridge Bay, Nunavut, Canada. Strain AR-3-1T could grow at 4–32 °C and pH 5.0– 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain AR-3-1T formed a lineage within the family Sphingomonadaceae and clustered as a member of the genus Sphingobium . The closest members within this genus were Sphingobium cupriresistens CU4T (98.1 % sequence similarity), Sphingobium vermicomposti VC-230T (97.6 %) and Sphingobium lactosutens DS20T (97.5 %). The only respiratory quinone was the ubiquinone Q-10. Spermidine was the predominant polyamine. The principal cellular fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (iso-C15  : 0 2-OH and/or C16  : 1 ω7c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid and phosphoglycolipid. The DNA G+C content was 63.1 %. The average nucleotide identity and in silico DNA–DNA hybridization relatedness values between strain AR-3-1T and its most closely related genus members were ≤89.6 and 39.6 %, respectively. The genome was 5 162 327 bp long, with 83 scaffolds and 4824 protein-coding genes. The genome showed six putative biosynthetic gene clusters responsible for various secondary metabolites. Based on this polyphasic study, strain AR-3-1T represents a novel species within the genus Sphingobium , for which the name Sphingobium psychrophilum sp. nov. is proposed. The type strain is AR-3-1T (=KACC 21613T=NBRC 114604T).

scholarly journals Roseovarius arcticus sp. nov., a bacterium isolated from Arctic marine sediment

2020 ◽  
Vol 70 (3) ◽  
pp. 2072-2078 ◽  
Author(s):  
Lu Lu ◽  
Yumin Zhang ◽  
Xiaoya Peng ◽  
Jia Liu ◽  
Kun Qin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Polar Lipid ◽  
Type Species ◽  
Sequence Similarity ◽  
The Arctic ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

An aerobic, Gram-stain-negative, motile, rod or long-rod-shaped bacterial isolate, strain MK6-18T, was isolated from a marine sediment sample from Kongsfjorden, Arctic. The bacterium grew optimally at 20 °C, pH 7.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MK6-18T belonged to the genus Roseovarius . Its closest phylogenetic neighbour was Roseovarius nanhaiticus NH52JT showing 96.97 % 16S rRNA gene sequence similarity. The genome of strain MK6-18T is 4.2 Mb long in size with a G+C content of 59.5 mol%. The average nucleotide identity value between the genomes of strain MK6-18T and Roseovarius nanhaiticus NH52JT, was 78.0 %. Similar to other species of the genus Roseovarius , strain MK6-18T had ubiquinone 10 as the predominant ubiquinone and C12 : 0, C16 : 0, summed feature 3 (C16 : 1ω7c/ω6c) and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine; one unidentified polar lipid, one unidentified aminolipid and one unidentified lipid were also detected. This is the first time that a member of the genus Roseovarius has been isolated from the Arctic, which may promote the study of the distribution characteristics and environmental adaptability of this genus. On the basis of the data provided here, strain MK6-18T should be classed as representing a novel species of the genus Roseovarius , for which the name Roseovarius arcticus sp. nov. is proposed. The type strain is MK6-18T (=CCTCC AB 2018219T=KCTC 72187T).

scholarly journals Aquitalea aquatilis sp. nov., isolated from Jungwon waterfall

2020 ◽  
Vol 70 (9) ◽  
pp. 4903-4907 ◽  
Author(s):  
Hien T.T. Ngo ◽  
HongYong Kim ◽  
Huan Trinh ◽  
Tae-Hoo Yi
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, facultative anaerobic, motile, short rods and yellow-pigmented bacterium, designated strain THG-DN7.12T, was isolated from water collected at Jungwon waterfall on Yongmun mountain, Republic of Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN7.12T was found to be most closely related to Aquitalea denitrificans 5YN1-3T (98.9 % sequence similarity), Aquitalea magnusonii TRO-001DR8T (98.7 %) and Aquitalea pelogenes P1297T (98.0 %). The DNA–DNA relatedness between strain THG-DN7.12T and its phylogenetically closest neighbours was below 70.0 %. The strain's DNA G+C content was 59.7 mol%. The major polar lipid was found to be phosphatidylethanolamine. Summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0 were identified as the major fatty acids. Ubiquinone Q-8 was detected as the only respiratory quinone. These data supported the affiliation of strain THG-DN7.12T to the genus Aquitalea . Strain THG-DN7.12T was distinguished from related Aquitalea species by physiological and biochemical tests. Therefore, the novel isolate represents a novel species, for which the name Aquitalea aquatilis sp. nov. is proposed, with THG-DN7.12T as the type strain (=KACC 18847T=CCTCC AB 2016185T).

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