Neiella marina gen. nov., sp. nov., isolated from the sea cucumber Apostichopus japonicus

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1597-1601 ◽  
Author(s):  
Zong-Jun Du ◽  
Ting-Ting Miao ◽  
Alejandro P. Rooney ◽  
Qian-Qian Liu ◽  
Guan-Jun Chen

A novel strain, designated J221T, was isolated from the intestine of a sea cucumber, Apostichopus japonicus, collected from earthen ponds in Qingdao, China. The strain was Gram-negative, oxidase-positive, aerobic, rod-shaped and motile by means of one to several polar flagella. Growth of strain J221T was observed at temperatures between 10 and 40 °C with optimum growth between 25 and 28 °C. The pH range for growth was 5.0–9.0 with optimum growth at pH 7.5–8.0. The dominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 29.04 %), C16 : 0 (28.93 %) and C18 : 1ω7c (26.15 %). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Diphosphatidylglycerol, an unknown aminolipid and an unknown aminophospholipid were present in moderate to minor amounts in the polar lipid profile. Strain J221T had Q-8 as the major respiratory quinone. The DNA G+C content of strain J221T was 46.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J221T is a member of the Gammaproteobacteria . It formed a distinct phyletic line with less than 91 % sequence similarity to any species within previously recognized genera. On the basis of this polyphasic taxonomic study, strain J221T should be classified as a representative of a novel species of a new genus, for which the name Neiella marina gen. nov., sp. nov. is proposed. The type strain of Neiella marina is J221T ( = CGMCC 1.10130T = NRRL B-51319T).

Author(s):  
Xinyin Zhang ◽  
Zhicheng Wu ◽  
Cen Yan ◽  
Can Chen ◽  
Gang Zheng ◽  
...  

A Gram-stain-positive, rod-shaped, strictly aerobic bacterial strain (Y6T) was isolated from a sewage sludge sample collected from a fisheries processing factory in Zhoushan, Zhejiang Province, PR China. The growth range of NaCl concentration was 0–6.0 % (w/v), with an optimum at 3.0 % (w/v). The temperature range for growth was 10–42 °C, with an optimum at 37 °C. The pH range for growth was pH 7.0–10.0, with an optimum at pH 9.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y6T belonged to the genus Nocardioides and showed the highest sequence similarity of 97.8 % to Nocardioides jishulii dk3136T. The average nucleotide identity and in silico DNA–DNA hybridization values between strain Y6T and the reference strains were 76.9–81.2 % and 20.6–23.6 %, respectively. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-8(H4) and the predominant cellular fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and C18 : 1  ω9c. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified phospholipids, three unidentified aminolipids and five unidentified lipids. The peptidoglycan was ll-2,6-diaminopimelic acid. On the basis of the phenotypic, genotypic, phylogenetic and chemotaxonomic features, strain Y6T is considered to represent a novel species, for which the name Nocardioides malaquae sp. nov. is proposed. The type strain is Y6T (=KCTC 49504T=MCCC 1K04765T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5355-5362 ◽  
Author(s):  
Heeyoung Kang ◽  
Inseong Cha ◽  
Haneul Kim ◽  
Kiseong Joh

Two novel strains (HMF3257T and HMF4905T), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus Spirosoma by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 1 ω5c, while strains HMF3257T and HMF4905T contained a moderately high amount of C16 : 0 and iso-C15 : 0, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257T consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905T consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257T and HMF4905T were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257T and HMF4905T are closely related to Spirosoma migulaei 15J9-8T (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257T and HMF4905T was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257T and HMF4905T represent two novel members within the genus Spirosoma , for which the names Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. are proposed, respectively. The type strain of S. telluris is HMF3257T (=KCTC 62463T=NBRC 112670T) and type strain of S. arboris is HMF4905T (=KCTC 72779T=NBRC 114270T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).


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).


2020 ◽  
Vol 70 (5) ◽  
pp. 3323-3327 ◽  
Author(s):  
Qian Wang ◽  
Sheng-Dong Cai ◽  
Jie Liu ◽  
De-Chao Zhang

The Gram-strain-negative, rod-shaped, facultatively anaerobic, non-motile bacterial strain, designated S1-10T, was isolated from marine sediment. Strain S1-10T grew at 4–42 °C (optimally at 30–35 °C), at pH 7.0–10 (optimally at pH 9) and in the presence of 0.5–8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-10T was related to the genus Aequorivita and had highest 16S rRNA gene sequence similarity to Aequorivita viscosa 8-1bT (97.7%). The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G+C content of strain S1-10T was 34.6 mol%. The polar lipid profile of strain S1-10T contained phosphatidylethanolamine, two aminolipids, two glycolipids, one phosphoglycolipid and three unidentified polar lipids. In addition, the maximum values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain S1-10T and A. viscosa CGMCC 1.11023T were 15.4 and 75.7 %, respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain S1-10T is the representative of a novel species of the genus Aequorivita , for which we propose the name Aequorivita sinensis sp. nov. (type strain S1-10T=CGMCC 1.12579T=JCM 19789T). We also propose that Vitellibacter todarodis and Vitellibacter aquimaris should be transferred into genus Aequorivita and be named Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov., respectively. The type strain of Aequorivita todarodis comb. nov. is MYP2-2T (= KCTC 62141T= NBRC 113025T) and the type strain of Aequorivita aquimaris comb. nov. is D-24T (=KCTC 42708T=DSM 101732T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3234-3240 ◽  
Author(s):  
Sihui Zhang ◽  
Xiaoxia Wang ◽  
Jing Yang ◽  
Shan Lu ◽  
Xin-He Lai ◽  
...  

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144T and 4053, were isolated from leaves of Lamiophlomis rotata on the Qinghai–Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner’s 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144T belonged to the genus Nocardioides and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were Nocardioides litoris DSM 103718T (98.4 %), Nocardioides rubriscoriae DSM 23986T (98.2%) and Nocardioides plantarum DSM 11054T (97.8 %). The genome of strain S-1144T showed less than 70 % digital DNA–DNA hybridization and < 95–96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144T was 73.5 mol%. MK-8(H4) was the predominant respiratory quinone (96.0 %) and llLL-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1  ω8c, C17 : 0 and C18 : 1  ω9c. On the basis of obtained data, strain S-1144T represented a novel species of the genus Nocardioides , for which the name Nocardioides dongxiaopingii sp. nov. is proposed. The type strain is S-1144T (=CGMCC 4.7568T=JCM 33469T).


2020 ◽  
Vol 70 (11) ◽  
pp. 5627-5633 ◽  
Author(s):  
Yong Li ◽  
Shengkun Wang ◽  
Ju-pu Chang ◽  
Dan-ran Bian ◽  
Li-min Guo ◽  
...  

Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas . The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18 : 1  ω7c and/or C18 : 1  ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15 : 0, C16 : 1  ω7c and/or C16 : 1  ω6c and iso-C17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium . The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3459-3466 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yang-Shun Lin ◽  
Jhen-Ci Chen ◽  
Soon-Wo Kwon ◽  
Wen-Ming Chen

A bacterial strain designated CMJ-15T was isolated from a freshwater shrimp culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain CMJ-15T were facultatively anaerobic, Gram-stain-negative and motile by a single polar flagellum and formed light-yellow colonies. Growth occurred at 20–40 °C (optimum, 25–30 °C), with 0–0.7 % NaCl (optimum, 0–0.2 %) and at pH 5.0–9.0 (optimum, pH 6.0–7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CMJ-15T belonged to the genus Undibacterium and its closest neighbour was Undibacterium oligocarboniphilum EM 1T, with sequence similarity of 96.3 %. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The polyamine profile was composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. The major respiratory quinone was Q-8 and the DNA G+C content was 52.2 mol%. On the basis of these phylogenetic and phenotypic data, strain CMJ-15T should be classified as representing a novel species, for which the name Undibacterium squillarum sp. nov. is proposed. The type strain is CMJ-15T ( = BCRC 80404T = LMG 26892T = KCTC 23917T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 667-672 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Miroslava Sedlackova ◽  
Ales Hampl ◽  
...  

A yellow-pigmented bacterial strain, designated LL02T, was isolated from hexachlorocyclohexane-contaminated soil from Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL02T occupied a distinct phylogenetic position in the genus Novosphingobium and showed the highest sequence similarity with Novosphingobium resinovorum NCIMB 8767T (98.59 %). DNA–DNA relatedness between strain LL02T and its closest phylogenetic neighbours was <70 %, which indicated that strain LL02T represented a novel species of the genus Novosphingobium . The DNA G+C content of strain LL02T was 67.72±0 mol%. The major respiratory quinone was ubiquinone Q-10. The polar lipid profile of the isolate corresponded to those reported for other members of the genus Novosphingobium (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipids), thus supporting its classification in the genus. Spermidine was the major polyamine. The major fatty acids were summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c; 40.13 %), summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 31.09 %) and C14 : 0 2-OH (23.16 %). The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished the isolate from its closest phylogenetic neighbours. Thus, strain LL02T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium barchaimii sp. nov. is proposed. The type strain is LL02T ( = CCM 7980T  = DSM 25411T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1457-1463 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu

A bacterial strain designated Ruye-90T was isolated from a freshwater tilapiine cichlid fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Strain Ruye-90T was Gram-negative, aerobic, yellow-coloured, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at 4–30 °C (optimum, 20–30 °C), at pH 7.0–9.0 (optimum, pH 8.0–9.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-90T belonged to the genus Rheinheimera and its most closely related neighbour was Rheinheimera tangshanensis JA3-B52T with sequence similarity of 97.5 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 41.3 %), C16 : 0 (19.3 %), C18 : 1ω7c (8.4 %) and C12 : 0 3-OH (7.0 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 49.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, aminolipid and two uncharacterized phospholipids. The DNA–DNA relatedness of strain Ruye-90T with respect to recognized members of the genus Rheinheimera was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Ruye-90T represents a novel species in the genus Rheinheimera , for which the name Rheinheimera tilapiae sp. nov. is proposed. The type strain is Ruye-90T ( = LMG 26339T = BCRC 80263T = KCTC 23315T).


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