scholarly journals Sunxiuqinia indica sp. nov., isolated from deep sea

2020 ◽  
Vol 70 (7) ◽  
pp. 4186-4192 ◽  
Author(s):  
Jianyang Li ◽  
Mingming Qi ◽  
Qiliang Lai ◽  
Guangyi Wang ◽  
Zongze Shao
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sea Water ◽  
Novel Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Normal Metabolism ◽  
Gene Similarity

A Gram-stain-negative, facultative anaerobic, red-pigmented, rod-shaped and non-motile strain (RC1_OXG_1FT) was isolated from deep sea water of the Indian Ocean. It was able to grow at pH 5–8 (optimum, pH 7), at 5–37 °C (optimum, 30 °C), and at salinity (% NaCl, w/v) of 0.5–5 % (optimum, 1–2 %). Catalase- and oxidase-positive. It had highest 16S rRNA gene similarity (96.7 %) to ‘ Sunxiuqinia dokdonensis ’ DH1T, followed by Sunxiuqinia faeciviva JAM-BA0302T (96.6 %), Sunxiuqinia elliptica CGMCC 1.9156T (96.2 %), Sunxiuqinia rutila HG677T (96.0 %) and species (less than 92.3 %) of other genera. It belongs to the genus Sunxiuqinia within the phylum Bacteroidetes , based on the phylogenetic analysis. The results of digital DNA–DNA hybridization and average nucleotide identity analyses indicated that the strain belonged to a novel species. Its genome size is 5,250, 885 bp, with DNA G+C content of 40.5 mol%. Genome analysis revealed that the strain possessed many genes involved in polysaccharide degradation, especially hemicellulose degradation, indicating that the strain could maintain its normal metabolism by using recalcitrant organic matter in the oligotrophic deep sea environment. Its principal fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the major polar lipids were phosphatidylethanolamine, two unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. The isoprenoid quinone was MK-7. Based on the phenotypic, chemotaxonomic and genotypic data, the strain represents a novel species within the genus Sunxiuqinia , for which the name Sunxiuqinia indica sp. nov. is proposed. The type strain is RC1_OXG_1FT (=MCCC 1A13858T=KCTC 62805T).

scholarly journals Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean

2019 ◽  
Vol 69 (4) ◽  
pp. 932-936 ◽  
Author(s):  
Qiliang Lai ◽  
Xiupian Liu ◽  
Jun Yuan ◽  
Shuchen Xie ◽  
Zongze Shao
Keyword(s):  
Indian Ocean ◽  
Deep Sea ◽  
Type Species ◽  
Sea Water ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Content Type ◽  
Deep Sea Water ◽  
Link Type ◽  
The Indian Ocean

A taxonomic study was carried out on strain CIC4N-9T, which was isolated from deep-sea water of the Indian Ocean. The bacterium was Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0–9% and at temperatures of 4–41 °C. The isolate was able to degrade gelatin but not aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CIC4N-9T belonged to the genus Pararhodobacter , with the highest sequence similarity to the only recognized species, Pararhodobacter aggregans D1-19T (96.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain CIC4N-9T and P. aggregans D1-19T were 80.4 and 23.0 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C18 : 1ω7c 11-methyl, C18 : 0 and C17 : 0. The G+C content of the chromosomal DNA was 66.8 mol%. The sole respiratory quinone was determined to be Q-10. Phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unknown phospholipids, four unknown aminolipids and one unknown polar lipid were present. The combined genotypic and phenotypic data show that strain CIC4N-9T represents a novel species within the genus Pararhodobacter , for which the name Pararhodobacter marinus sp. nov. is proposed. The type strain is CIC4N-9T (=MCCC 1A01225T=KCTC 52336T).

Flavobacterium jumunjinense sp. nov., isolated from a lagoon, and emended descriptions of Flavobacterium cheniae , Flavobacterium dongtanense and Flavobacterium gelidilacus

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3937-3943 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Distinct Lineage ◽  
Motile By Gliding

A Gram-staining-negative, yellow-pigmented bacterial strain, motile by gliding, designated HME7102T, was isolated from lagoon water in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HME7102T formed a distinct lineage within the genus Flavobacterium . Strain HME7102T was closely related to Flavobacterium cheniae NJ-26T (94.5 %), Flavobacterium dongtanense LW30T (94.4 %) and Flavobacterium gelidilacus LMG 21477T (94.2 %). The major fatty acids of strain HME7102T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The DNA G+C content of strain HME7102T was 36.5 mol%. On the basis of the evidence presented in this study, strain HME7102T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium jumunjinense sp. nov. is proposed. The type strain is HME7102T ( = KCTC 23618T = CECT 7955T). Emended descriptions of F. cheniae , F. dongtanense and F. gelidilacus are also proposed.

Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
Shan Lu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Similarity

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320T/zg-336, zg-917T/zg-910 and zg-913T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320T/zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353T (97.51 %), zg-917T/zg-910 to Corynebacterium coyleae DSM 44184T (98.68 %), and zg-913T/zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2–64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320T vs. Corynebacterium auriscanis CIP 106629T, Corynebacterium resistens DSM 45100T and Corynebacterium suicordis DSM 45110T); 24.4/82.3% and 23.7/81.3 % (zg-917T vs. C. coyleae DSM 44184T and Corynebacterium jeddahense JCBT); 26.8/83.7% and 27.7/84.4 % (zg-913T vs. Corynebacterium mucifaciens ATCC 700355T and C. afermentans subsp. lipophilum CCUG 32105T). The three novel species had C16 : 0, C18 : 0, C18 : 1  ω9c and C18 : 0 ante/C18 : 2  ω6,9c as the major cellular fatty acids; MK-8(H2) in strain zg-917T and MK-9(H2) in strains zg-320T and zg-913T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35–37 °C, 0.5 % (w/v) NaCl and pH 7.0–8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320T = GDMCC 1.1719T = JCM 34106T), Corynebacterium lujinxingii sp. nov. (zg-917T = GDMCC 1.1707T = JCM 34094T) and Corynebacterium wankanglinii sp. nov. (zg-913T = GDMCC 1.1706T = JCM 34398T).

Identification of Haloactinobacterium kanbiaonis sp. nov. and Ruania zhangjianzhongii sp. nov., two novel species of the family Ruaniaceae isolated from faeces of bats (Hipposideros spp.)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Mingchao Xu ◽  
Yan Dai ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Gene Similarity

Two pairs of aerobic, Gram-stain-positive, rod-shaped strains (HY164T/HY044, HY168T/HY211) were isolated from bat faecal samples. Strains HY164T and HY044 were motile with a polar flagellum, and had 16S rRNA gene similarity of 95.1–98.6 % to Haloactinobacterium album YIM 93306T and Haloactinobacterium glacieicola T3246-1T; strains HY168T and HY211 were most similar to Ruania albidiflava DSM 18029T (96.6 %). Phylogenetic trees based on 16S rRNA gene and whole genome sequences revealed affiliation of strains HY164T and HY168T to the family Ruaniaceae , representing novel lineages in the genera Haloactinobacterium and Ruania , respectively, which was also supported by the results for average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). For all isolates, the principal cellular fatty acids were anteiso-C15 : 0 and iso-C14 : 0. HY164T and HY168T had MK-8(H4) as the predominant isoprenoid quinone, diphosphatidylglycerol, phosphatidylglycerol, several unidentified phospholipids and glycolipids as common polar lipids while the latter strain additionally contained one unidentified aminophospholipid and one unidentified phosphoglycolipid. Besides sharing alanine, glutamic acid and lysine with HY164T, HY168T additionally contained 2,4-diaminobutyric acid in the cell-wall peptidoglycan. The whole-cell sugars of HY164T were ribose and rhamnose, while HY168T only included the latter. The DNA G+C contents of HY164T and HY168T were 71.0 and 69.1 mol%, respectively. Combining the polyphasic taxonomic data, HY164T (=CGMCC 4.7606T=JCM 33464T) is classified as representing a novel species of the genus Haloactinobacterium with the proposed name Haloactinobacterium kanbiaonis sp. nov., and HY168T (=CGMCC 1.16970T=JCM 33465T) is proposed to represent a novel species of the genus Ruania with the name Ruania zhangjianzhongii sp. nov.

Cellulomonas marina sp. nov., isolated from deep-sea water

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3014-3018 ◽  
Author(s):  
Limin Zhang ◽  
Lijun Xi ◽  
Danheng Qiu ◽  
Lei Song ◽  
Xin Dai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Deep Sea ◽  
Type Species ◽  
Sea Water ◽  
Rrna Gene ◽  
Southwest Indian Ocean ◽  
Content Type ◽  
Deep Sea Water ◽  
Link Type ◽  
Physiological And Biochemical Characteristics

A bacterial strain FXJ8.089T was isolated from deep-sea water collected from the southwest Indian Ocean (49° 39′ E 37° 47′ S) at a depth of 2800 m, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FXJ8.089T belonged to the genus Cellulomonas and had the highest similarities with Cellulomonas oligotrophica (96.9 %) and Cellulomonas aerilata (96.6 %). It contained MK-9(H4) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol and phosphatidylinositol mannosides. The cell-wall peptidoglycan type was A4β with an interpeptide bridge l-Orn–d-Glu. The cell-wall sugars were glucose, mannose and ribose. The DNA G+C content was 70.3 mol%. The strain also showed a number of physiological and biochemical characteristics that were distinct from the closely related species. Based on phenotypic and genotypic data, strain FXJ8.089T ( = CGMCC 4.6945T = DSM 24960T) represents a novel species of the genus Cellulomonas , for which the name Cellulomonas marina sp. nov. is proposed.

Alcanivorax marinus sp. nov., isolated from deep-sea water

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4428-4432 ◽  
Author(s):  
Qiliang Lai ◽  
Jianning Wang ◽  
Li Gu ◽  
Tianling Zheng ◽  
Zongze Shao
Keyword(s):  
16S Rrna ◽  
Deep Sea ◽  
Type Species ◽  
Sea Water ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Content Type ◽  
Deep Sea Water ◽  
Link Type ◽  
Degrading Bacteria

A taxonomic study was carried out on strain R8-12T, which was isolated from deep-sea water of the Indian Ocean during the screening of oil-degrading bacteria. The isolate was Gram-stain-negative, oxidase and catalase-positive. Growth was observed at salinities from 0.5 to 15 % (optimum 3 %), at pH from 6–10 (optimum 7–8) and at temperatures from 10 to 42 °C (optimum 28 °C). On the basis of 16S rRNA gene sequence similarity, strain R8-12T was shown to belong to the genus Alcanivorax and to be related to Alcanivorax venustensis DSM 13974T (97.2 %), A. dieselolei B-5T (95.0 %), A. balearicus MACL04T (94.6 %), A. hongdengensis A-11-3T (94.3 %), A. jadensis T9T (93.8 %), A. borkumensis SK2T (93.7 %) and A. pacificus W11-5T (93.7 %). The gyrB sequence similarities between R8-12T and other species of the genus Alcanivorax ranged from 77.9 % to 86.9 %. The major fatty acids were C16 : 0 (31.8 %), C18 : 1ω7c (20.3 %), C19 : 0ω8c cyclo (15.8 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (8.9 %). The polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two aminolipids (AL1–AL2) and two phospholipids (PL1–PL2). Three alkane hydroxylase (alkB) genes were identified in the genome. The G+C content of the chromosomal DNA was 66.1 mol%. DNA–DNA hybridization showed that strain R8-12T and A. venustensis DSM 13974T had a DNA–DNA relatedness of 63±3 %. According to its phenotypic features and fatty acid composition as well as the 16S rRNA and gyrB gene sequences, the novel strain represents a member of the genus Alcanivorax , but could be easily distinguished from all other known species of the genus Alcanivorax described to date. The name Alcanivorax marinus sp. nov. is proposed, with the type strain R8-12T ( = MCCC 1A00382T = LMG 24621T = CCTCC AB 208234T).

Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 905-912 ◽  
Author(s):  
Yeon-Ju Kim ◽  
Ngoc-Lan Nguyen ◽  
Hang-Yeon Weon ◽  
Deok-Chun Yang
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative bacterium, designated DCY13T, was isolated from soil of a ginseng field in South Korea. Comparative analysis of 16S rRNA gene sequences showed that strain DCY13T shared the highest sequence similarity (95.0 %) with Sediminibacterium salmoneum NBRC 103935T and 87.6–91.4 % sequence similarity with other members of the family Chitinophagaceae . Cells were non-spore-forming rods, catalase- and oxidase-positive, motile by gliding and facultatively anaerobic. The only respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G. The G+C content of the genomic DNA was 47.5±1.0 mol%. In addition to phosphatidylethanolamine, the major polar lipids were two unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The major cell-wall sugars were ribose, xylose and galactose. It is proposed that strain DCY13T represents a novel species in the genus Sediminibacterium , for which the name Sediminibacterium ginsengisoli sp. nov. is proposed. The type strain is DCY13T ( = KCTC 12833T  = JCM 15794T  = DSM 22335T). Emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum are also proposed.

scholarly journals Alteromonas profundi sp. nov., isolated from the Indian Ocean

2020 ◽  
Vol 70 (8) ◽  
pp. 4531-4536 ◽  
Author(s):  
Xudong Shen ◽  
Sidong Zhu ◽  
Bingxia Dong ◽  
Yong Chen ◽  
Zehao Xue ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Type Species ◽  
Sea Water ◽  
Novel Species ◽  
Core Gene ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
The Indian Ocean

A Gram-staining-negative bacterium, designated 345S023T, was isolated from a sea water sample from the Indian Ocean. The results of 16S rRNA gene sequence analysis revealed that 345S023T represents a member of the genus Alteromonas , with closely related type strains Alteromonas fortis 1T (98.7 %), Alteromonas hispanica F-32T (98.6 %) and Alteromonas genovensis LMG 24078T (98.6 %). Up-to-date bacterial core gene set analysis revealed that 345S023T formed a phyletic lineage with Alteromonas australica H 17T. The case for 345S023T representing a novel species was supported by genomic results. Pairwise in silico DNA–DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. Strain 345S023T contains ubiquinone-8 (Q-8) as the sole isoprenoid quinone, summed featured 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the dominant cellular fatty acids (>10 %), and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain 345S023T consisted of a 4.4 Mb chromosome with a DNA G+C content of 44.4 %. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Alteromonas profundi sp. nov. The type strain is 345S023T(=JCM 33893T=MCCC 1K04570T).

scholarly journals Chryseoglobus indicus sp. nov., isolated from deep sea water

2020 ◽  
Author(s):  
Shengxiang Pei ◽  
Fuquan Xie ◽  
Wenjing Wang ◽  
Shuang Zhang ◽  
Gaiyun Zhang
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sea Water ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Deep Sea Water ◽  
Link Type ◽  
The Indian Ocean

A novel Gram-stain-positive, motile, aerobic, non-spore-forming and slender rod-shaped actinobacterium, designated strain CTD02-10-2T, was isolated from deep sea water of the Indian Ocean. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CTD02-10-2T was grouped into a separated branch with Chryseoglobus frigidaquae JCM 14730T (98.4 % nucleotide sequence identity). The respiratory quinones were menaquinones with 11, 12, 13 and 14 isoprene units and anteiso-C15 : 0, iso-C16 : 0, anteiso-C15 : 1 A and anteiso-C17 : 0 were the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unknown glycolipids. The genome of strain CTD02-10-2T was 2.59 Mb, with a DNA G+C content of 69.6 mol% and contained genes involved in the biosynthesis of alkylresorcinol, ansamycin, and carotenoids. In silico DNA–DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between strain CTD02-10-2T and C. frigidaquae JCM 14730T were clearly below the thresholds used for the delineation of a new species. Based on its morphological and chemotaxonomic characteristics, as well as genotypic data, strain CTD02-10-2T was classified as a novel species of the genus Chryseoglobus , for which the name Chryseoglobus indicus sp. nov. is proposed. The type strain is CTD02-10-2T (=JCM 33842T=MCCC 1A16619T).

Cyclobacterium jeungdonense sp. nov., isolated from a solar saltern

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 11-15 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Seung Bum Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Solar Saltern ◽  
16S Rrna Gene Sequences ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Distinct Lineage

A horseshoe-shaped, orange-pigmented strain, HMD3055T, was isolated from a solar saltern in Korea. Strain HMD3055T grew optimally at 25 °C and with a salt concentration of 3–5 %. The predominant quinone of strain HMD3055T was menaquinone (MK)-7. The major fatty acids of strain HMD3055T were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The polar lipids of HMD3055T consisted of phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and five unidentified polar lipids. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD3055T formed a distinct lineage within the genus Cyclobacterium . Strain HMD3055T was closely related to Cyclobacterium lianum (95.8 %), Cyclobacterium lianum HY9T (95.8 %), C. marinum DSM 745T (93.2 %) and C. amurskyense KMM6143T (92.6 %) form a distinct lineage from other members of the genus Cyclobacterium . The DNA G+C content of strain HMD3055T was 45.6 mol%. On the basis of the evidence presented in this study, it is concluded that strain HMD3055T represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium jeungdonense sp. nov. is proposed. The type strain is HMD3055T ( = KCTC 23150T = CECT 7706T).

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