Marinicauda pacifica gen. nov., sp. nov., a prosthecate alphaproteobacterium of the family Hyphomonadaceae isolated from deep seawater

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2248-2253 ◽  
Author(s):  
Xi-Ying Zhang ◽  
Guo-Wei Li ◽  
Chun-Sheng Wang ◽  
Yan-Jiao Zhang ◽  
Xue-Wei Xu ◽  
...  

A marine prosthecate bacterium, designated strain P-1 km-3T, was isolated from deep seawater from the Pacific. Cells of strain P-1 km-3T were Gram-stain-negative, aerobic, catalase- and oxidase-positive, dimorphic rods with a single polar prostheca or flagellum. The strain hydrolysed gelatin and grew at 6–40 °C (optimum, 30 °C) and with 0.5–12 % (w/v) NaCl (optimum, 2 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain P-1 km-3T belonged to the family Hyphomonadaceae in the class Alphaproteobacteria and represented a separate lineage, located between the genera Oceanicaulis and Woodsholea . Sequence similarities of strain P-1 km-3T with type strains of species of the genera Oceanicaulis and Woodsholea were 93.2–93.9 %. The predominant cellular fatty acids in strain P-1 km-3T were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c, C17 : 0 and C19 : 0 cyclo ω8c. The major respiratory quinone of strain P-1 km-3T was Q-10. The polar lipids of strain P-1 km-3T comprised glucuronopyranosyldiglyceride (GUDG), monoglycosyldiglyceride (MGDG), sulfo-quinovosyl diacylglycerol (SQDG), phosphatidylglycerol (PG), an unidentified phospholipid (PL) and an unidentified lipid (L). The genomic DNA G+C content of strain P-1 km-3T was 66.0 mol%. On the basis of the polyphasic data presented in this study, strain P-1 km-3T is proposed to represent a novel species in a new genus, Marinicauda pacifica gen. nov., sp. nov., within the family Hyphomonadaceae . The type strain of the type species is P-1 km-3T ( = KACC 16526T = CGMCC 1.11031T).

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1766-1770 ◽  
Author(s):  
Joon Yong Kim ◽  
Jina Lee ◽  
Na-Ri Shin ◽  
Ji-Hyun Yun ◽  
Tae Woong Whon ◽  
...  

A novel Gram-stain-negative, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain C7T, was isolated from the gut of the butterfly Sasakia charonda. Strain C7T grew optimally at 20–25 °C, at pH 7–8 and with 1 % (w/v) NaCl. The strain was negative for oxidase activity but positive for catalase activity. The 16S rRNA gene sequences of strain C7T and Orbus hercynius CN3T shared 96.8 % similarity. The major fatty acids identified were C14 : 0, C16 : 0, C18 : 1ω7c and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C7T were phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid and two unidentified aminophospholipids. The G+C content of the genomic DNA extracted from strain C7T was 32.1 mol%. Taken together, the phenotypic, genotypic and phylogenetic analyses indicate that strain C7T represents a novel species of the genus Orbus , for which the name Orbus sasakiae sp. nov. is proposed. The type strain is C7T ( = KACC 16544T = JCM 18050T). An emended description of the genus Orbus is provided.


Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).


2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4484-4488 ◽  
Author(s):  
R. Kathiravan ◽  
S. Jegan ◽  
V. Ganga ◽  
V. R. Prabavathy ◽  
L. Tushar ◽  
...  

The taxonomic position of strain MSSRFBL1T, isolated from chickpea rhizosphere soil from Kannivadi, India, was determined. Strain MSSRFBL1T formed bluish black colonies, stained Gram-negative and was motile, aerobic, capable of fixing dinitrogen, oxidase-negative and catalase-positive. Q-10 was the major respiratory quinone. Major fatty acids of strain MSSRFBL1T were C18 : 1ω7c and C19 : 0cycloω8c. Minor amounts of C18 : 0, C12 : 0, C14 : 0 3-OH, C18 : 0 3-OH, C16 : 0, C16 : 1ω6c/C16 : 1ω7c, C17 : 0 3-OH and C20 : 1ω7c were also present. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine and two unidentified glycolipids. Bacteriohopane derivatives (BHD1 and 2), diplopterol, diploptene, bishomohopanediol, adenosylhopane and 2β-methyl bacteriohopanetetrol were the major hopanoids of strain MSSRFBL1T. The genomic DNA G+C content was 71 mol%. EzTaxon-e-based blast analysis of the 16S rRNA gene indicated the highest similarity of strain MSSRFBL1T to Ensifer adhaerens LMG 20216T (97.3 %) and other members of the genus Ensifer (<96.9 %) in the family Rhizobiaceae of the class Alphaproteobacteria . However, phylogenetic analysis based on 16S rRNA, recA, thrC and dnaK gene sequences showed distinct out-grouping from the recognized genera of the family Rhizobiaceae . Based on phenotypic, genotypic and chemotaxonomic characters, strain MSSRFBL1T represents a novel species in a new genus in the family Rhizobiaceae for which the name Ciceribacter lividus gen. nov., sp. nov. is proposed. The type strain of Ciceribacter lividus is MSSRFBL1T ( = DSM 25528T = KCTC 32403T).


2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1528-1535 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sun Ja Cho ◽  
Suk Min Kim ◽  
Sun Bok Lee

A Gram-staining-negative, strictly aerobic, non-motile, yellow-pigmented bacterium, designated strain M091T, was isolated from seawater at Damupo beach in Pohang, Republic of Korea, and investigated using a polyphasic taxonomic approach. The novel strain grew optimally at 25 °C, pH 7.0–8.0, and in the presence of 3 % (w/v) NaCl. In a phylogenetic analysis based on 16S rRNA gene sequences, strain M091T formed a lineage within the family Flavobacteriaceae that was distinct from the most closely related genera of Flaviramulus (95.1 % sequence similarity), Algibacter (94.9–93.9 %), Mariniflexile (94.8–94.2 %), Winogradskyella (94.8–93.2 %), Lacinutrix (94.7–93.8 %) and Tamlana (94.7–92.9 %). The polar lipid profile of the novel strain comprised phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and seven unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (20.5 %), iso-C17 : 0 3-OH (15.4 %), iso-C15 : 0 3-OH (12.4 %), C15 : 0 (10.9 %) and iso-C15 : 1 G (9.9 %). The genomic DNA G+C content of strain M091T was 34.4 mol% and the major respiratory quinone was MK-6. Based on phenotypic and genotypic data, strain M091T represents a new genus and novel species in the family Flavobacteriaceae , for which the name Postechiella marina gen. nov., sp. nov. is proposed. The type strain of the type species is M091T ( = KCTC 23537T = JCM 17630T).


Author(s):  
Yanzhu Zhang ◽  
Shufen He ◽  
Liufei Shi ◽  
Yang Liu ◽  
Deqiang Mao ◽  
...  

An aerobic Gram-stain-negative, curved rod-shaped and non-spore-forming bacterial strain (NBU2194T) was isolated from seawater collected in an intertidal zone in Ningbo, Zhejiang Province, PR China. It was motile though a single polar flagellum and grew at 20–42 °C (optimum, 30 °C), in 0–2.0 % NaCl (0 %, w/v) and at pH 5.0–9.0 (pH 6.0–7.0). The sole respiratory quinone was ubiquinone-8. The major cellular fatty acids were C16 : 0, C16 : 1  ω7c and/or C16 : 1  ω6c. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and two unidentified aminophosphoglycolipids. A phylogenetic analysis based on 16S rRNA gene sequences and 65 genomic core genes showed that strain NBU2194T formed a distinct lineage in the family Alteromonadaceae . The genome of strain NBU2194T was 4 913 533 bp with a DNA G+C content of 43.9 mol% and coded 3895 genes, 12 rRNA genes and 47 tRNA genes. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain NBU2194T and related species of Alteromonadaceae were below the threshold limit for prokaryotic species delineation. NBU2194T could be distinguished from other genera in the family Alteromonadaceae based on phenotypic, chemotaxonomic and genomic characteristics. On the basis of the polyphasic taxonomic evidence collected in this study, strain NBU2194T is considered to represent a novel genus and species in the family Alteromonadaceae , for which the name Paraneptunicella aestuarii is proposed. The type strain is NBU2194T (=KCTC 82442T=GDMCC 1.2217T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1105-1110 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Hyun-Myung Oh ◽  
Sang-Jin Kim ◽  
Jung-Hyun Lee ◽  
...  

A Gram-stain-negative, aerobic, rod-shaped, non-motile and orange-coloured marine bacterium, YH207T, was isolated from a tidal flat at Yeongheung-do on the coast of the Yellow Sea, Korea. 16S rRNA gene sequence analysis revealed that strain YH207T was affiliated with the family Cryomorphaceae and showed highest similarity to Brumimicrobium glaciale IC156T (95.4 %). Growth was observed at 11–36 °C, at pH 6.5–10.0 and with 0.4–7.0 % NaCl. The predominant cellular fatty acids when grown at 20 °C were iso-C15 : 0 (44.2 %), iso-C15 : 1 G (34.3 %), iso-C17 : 0 3-OH (8.7 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c; 2.3 %). The major respiratory quinone was MK-6. Phosphatidylethanolamine, phosphatidylglycerol, three unidentified lipids, three unidentified aminophospholipids, one unidentified phospholipid, four unidentified aminolipids and three unidentified glycolipids were identified as major polar lipids. The DNA G+C content was 34.3 mol%. On the basis of the data from our polyphasic taxonomic study, strain YH207T should be classified in a novel species in the genus Brumimicrobium , for which the name Brumimicrobium mesophilum sp. nov. is proposed. The type strain is YH207T ( = KCCM 42331T  = JCM 14063T). Emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale Bowman et al. 2003 are also given.


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 274-279 ◽  
Author(s):  
T. N. R. Srinivas ◽  
T. B. Kailash ◽  
Pinnaka Anil Kumar

A novel Gram-negative, rod-shaped, motile bacterium, designated strain AK13T, was isolated from a sediment sample collected from mangrove of Namkhana, Sunderbans, West Bengal, India. Strain AK13T was positive for oxidase, DNase and lipase activities and negative for catalase, gelatinase, ornithine decarboxylase, lysine decarboxylase, nitrate reductase, aesculinase and urease activities. The fatty acids were dominated by iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C16 : 0, iso-C17 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strain AK13T contained Q-8 as the major respiratory quinone and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids, one unidentified glycolipid and one unidentified lipid as the polar lipids. The DNA G+C content of strain AK13T was 55.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the type strain of Silanimonas lenta , of the family Xanthomonadaceae (phylum Proteobacteria ), was the closest neighbour of strain AK13T, with 95.2 % sequence similarity. Other members of the family showed sequence similarities <94.4 %. Based on the phenotypic characteristics and phylogenetic inference, strain AK13T is proposed as a member of a novel species of the genus Silanimonas , Silanimonas mangrovi sp. nov.; the type strain is AK13T ( = MTCC 11082T  = DSM 24914T). An emended description of the genus Silanimonas is also provided.


2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 11-14 ◽  
Author(s):  
Gavin J. Humphreys ◽  
Angela Oates ◽  
Ruth G. Ledder ◽  
Andrew J. McBain

An aerobic, Gram-stain-negative, non-motile coccus, designated strain GVCNT2T, was isolated from the tonsils of a healthy adult female. Cells were oxidase- and catalase-positive, positive for the production of esterase (C4), esterase lipase (C8) and leucine arylamidase, and weakly positive for naphthol-AS-BI-phosphohydrolase and alkaline phosphatase. Cells were also capable of hydrolysing DNA. Growth was observed at 20–37 °C and in the presence of up to 1.5 % NaCl. Phylogenetic analysis of near full-length 16S rRNA gene sequences indicated that the strain exhibited closest sequence similarity to Moraxella boevrei ATCC 700022T (94.68 %) and an uncultured, unspeciated bacterial clone (strain S12-08; 99 %). The major fatty acids were C18 : 1ω9c, C18 : 0, C16 : 0 and C16 : 1ω6c/C16 : 1ω7c. The DNA G+C content of strain GVCNT2T was 40.7 mol%. The major respiratory quinone identified was Q-8. Strain GVCNT2T exhibited a comparable phenotypic profile to other members of the genus Moraxella but could be distinguished based on its ability to produce acid (weakly) from d-glucose, melibiose, l-arabinose and rhamnose and on its ability to hydrolyse DNA. On the basis of phenotypic and phylogenetic differences from other members of the family Moraxellaceae , strain GVCNT2T is considered to represent a novel species of a new genus, for which the name Faucicola mancuniensis gen. nov., sp. nov. is proposed. The type strain of Faucicola mancuniensis is GVCNT2T ( = DSM 28411T = NCIMB 14946T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2101-2107 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sun Ja Cho ◽  
Suk Min Kim ◽  
Sun Bok Lee

A novel bacterium, designated strain F028-2T, was isolated from seawater at Damupo beach in Pohang, Korea, and investigated in a taxonomic study using a polyphasic approach. This novel strain was strictly aerobic, non-motile, Gram-stain-negative and rod-shaped, and occasionally formed aggregates. The temperature, pH and NaCl ranges for growth were 4–30 °C, pH 6.5–9.0 and 1–7 % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F028-2T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria , and was closely related to members of the genera Sagittula and Antarctobacter with 96.3–96.4 % sequence similarities. The polar lipid profile of strain F028-2T comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and six unidentified lipids. The predominant cellular fatty acids were C18 : 1ω7c and C12 : 1 3-OH. The genomic DNA G+C content of strain F028-2T was 61.6 mol% and the major respiratory quinone was Q-10. Based on phenotypic, phylogenetic and genotypic data, strain F028-2T is considered to represent a novel species in the genus Sagittula , for which the name Sagittula marina sp. nov. is proposed. The type strain is F028-2T ( = KCTC 23543T = JCM 17627T). An emended description of the genus Sagittula is also proposed.


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 533-539 ◽  
Author(s):  
Asif Hameed ◽  
Mariyam Shahina ◽  
Shih-Yao Lin ◽  
Wei-An Lai ◽  
You-Cheng Liu ◽  
...  

A Gram-staining-negative, orange-pigmented, strictly aerobic, carotenoid-producing, rod-shaped, non-flagellated, non-spore-forming bacterium, motile by gliding, designated strain CC-AMO-30DT, was isolated from surface seawater collected near Taichung harbour, Taiwan. Strain CC-AMO-30DT shared pairwise 16S rRNA gene sequence similarities of 94.8, 93.7 and 92.5 % with the type strains of the type species of the genera Joostella , Pustulibacterium and Galbibacter , respectively, and formed a distinct monophyletic lineage in phylogenetic trees. The major fatty acids (≥5 % of total) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of phosphatidylethanolamine, four unidentified lipids, two unidentified aminolipids and an unidentified phospholipid. The major polyamine was the triamine sym-homospermidine. The DNA G+C content was 47.1 mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMO-30DT represents a novel genus and species of the family Flavobacteriaceae , for which the name Robertkochia marina gen. nov., sp. nov. is proposed; the type strain of the type species Robertkochia marina is CC-AMO-30DT ( = JCM 18552T = BCRC 80469T). Emended descriptions of the genera Joostella and Galbibacter are also proposed.


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