scholarly journals Leekyejoonella antrihumi gen. nov., sp. nov., a new member of the family Dermacoccaceae isolated from a cave soil

2020 ◽  
Vol 70 (5) ◽  
pp. 3340-3347 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Peter Schumann ◽  
Gwanpil Song
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Rrna Gene ◽  
The Novel ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A novel Gram-stain-positive, actinobacterial strain, designated C5-26T, was isolated from soil from a natural cave in Jeju, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The organism was aerobic, and cells were non-spore-forming, non-motile cocci that occurred singly, in pairs, in triplets, in tetrads, in short chains or in irregular clusters. Colonies of the cells were circular, convex, entire and white. The peptidoglycan type was A4α with an l-Ser–d-Asp interpeptide bridge. The whole-cell sugars comprised glucose, rhamnose, mannose, arabinose, galactose and ribose. The major menaquinone was MK-8(H4). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The major fatty acids were iso-C16 : 0 and iso-C16 : 1 h. The size of the draft genome was 5.32 Mbp with depth of coverage of 161×. The G+C content of the genomic DNA was 67.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel isolate belonged to the family Dermacoccaceae and formed a distinct subcluster at the base of the radiation of the genus Luteipulveratus . Highest sequence similarities of the novel isolate were found to the type strains of Luteipulveratus halotolerans (96.2 %), Branchiibius hedensis (95.4 %), Luteipulveratus mongoliensis (95.4 %) and Branchiibius cervicis (95.3 %). The whole genome-based phylogeny supported the novelty of the isolate at the genus level in the family Dermacoccaceae . On the basis of data from this polyphasic study, strain C5-26T (=KCTC 39632T=DSM 108676T) represents a novel species of a new genus in the family Dermacoccaceae , for which the name Leekyejoonella antrihumi gen. nov., sp. nov. is proposed.

Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Sequence Similarities

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).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

scholarly journals Bacillus acidinfaciens sp. nov., isolated from farmland soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1075-1080 ◽  
Author(s):  
Leni Sun ◽  
Yan Chen ◽  
Wei Tian ◽  
Lunguang Yao ◽  
Zhaojin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Farmland Soil

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).

Fertoeibacter niger gen. nov., sp. nov. a novel alkaliphilic bacterium of the family Rhodobacteraceae

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Sára Szuróczki ◽  
Gorkhmaz Abbaszade ◽  
Dominika Buni ◽  
Károly Bóka ◽  
Peter Schumann ◽  
...  
Keyword(s):  
Type Species ◽  
Draft Genome ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Unidentified Phospholipid ◽  
Polar Lipid Profile ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
The Family

Three Gram-stain-negative, non-motile, oxidase- and catalase-positive, rod-shaped, black, facultative phototrophic bacterial strains, RG-N-1aT, DMA-N-7a and RA-N-9 were isolated from the water sample from Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Rhodobacteraceae and their closest relatives are Tabrizicola piscis K13M18T (96.32%) followed by Cypionkella psychrotolerans PAMC 27389T (96.25%). The novel bacterial strains prefer alkaline environments and grow optimally at 23–33 °C in the presence of NaCl (1–2 w/v%). Bacteriochlorophyll a was detected. Cells contained exclusively ubiquinone Q-10. The major cellular fatty acids were C18 : 1ω7c, C19 : 1iso ω5c, C18 : 0 3-OH and C18 : 1ω7c 11-methyl. The polar lipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid and four unidentified lipids. The assembled draft genome of RG-N-1aT had 33 contigs with N50 values 315 027 nt, 96× genome coverage, total length of 4 326 551 bp and a DNA G+C content of 64.9%. Genome-based calculations (genome-to-genome distance and DNA G+C percentage) and pairwise amino acid identity (AAI <73.5%) indicate that RG-N-1aT represents a novel genus. RG-N-1aT (=DSM 108317T=NCAIM B.02647T) is suggested as the type strain of a novel genus and species in the family Rhodobacteraceae , for which the name Fertoeibacter niger gen. nov., sp. nov. is proposed.

scholarly journals Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., isolated from the soil of a hay meadow

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1908-1913 ◽  
Author(s):  
Byung-Yong Kim ◽  
Xiaoying Rong ◽  
Tiago D. Zucchi ◽  
Avinash N. V. Bonda ◽  
Ying Huang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Morphological Properties ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Respective Type ◽  
Type Strains

The taxonomic positions of three streptomycetes isolated from a soil sample from a hay meadow were determined using a polyphasic approach. The isolates had chemical and morphological properties typical of the genus Streptomyces and, in phylogenetic analyses based on 16S rRNA gene sequences, formed a distinct subclade that was most closely related to the Streptomyces prasinus subclade. DNA–DNA relatedness studies showed that the novel strains belonged to three different genomic species. The novel strains could be distinguished from one another and from the type strains of the species classified in the S. prasinus subclade using a combination of genotypic and phenotypic properties. On the basis of these data, it is proposed that the novel strains be assigned to the genus Streptomyces as Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., with BK119T ( = KACC 21001T  = CGMCC 4.5797T), BK128T ( = KACC 21002T  = CGMCC 4.5799T) and BK138T ( = KACC 20904T  = CGMCC 4.5800T) as the respective type strains.

scholarly journals Novosphingobium silvae sp. nov., isolated from subtropical forest soil

2020 ◽  
Vol 70 (4) ◽  
pp. 2901-2906 ◽  
Author(s):  
Guang-Da Feng ◽  
Wendi Chen ◽  
Jun Zhang ◽  
Yong-Hong Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Subtropical Forest ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A novel bacterial strain, designated FGD1T, was isolated from subtropical forest soil of the Nanling National Forest Park located in Guangdong Province, P.R. China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FGD1T was most closely related to Novosphingobium lindaniclasticum DSM 25049T (98.8 %), followed by N. barchaimii DSM 25411T (98.7 %), N. guangzhouense DSM 32207T (98.2 %), N. panipatense DSM 22890T (98.1 %) and other species of Novosphingobium (<98 %). The draft genome sequence was 4.58 Mb in length with a G+C content of 65.1 mol%. The calculated average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain FGD1T and closely related type strains were 77.7‒79.6 % and 21.7–22.9 %, respectively. Major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C14 : 0 2-OH and C16 : 0. The predominant respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Polar lipids were composed of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and lipid. The polyphasic taxonomic results indicated that strain FGD1T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium silvae sp. nov. is proposed. The type strain is FGD1T (=GDMCC 1.1761T=KACC 21283T).

Chitinophaga silvatica sp. nov., isolated from forest soil, and reclassification of Chitinophaga extrema as a later heterotypic synonym of Chitinophaga solisilvae

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yuxin Yao ◽  
Xinhua Zhong ◽  
Huixian Li ◽  
Weilin Fan ◽  
Qi Xiang ◽  
...  
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Biosphere Reserve ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A novel bacterial strain, designated K2CV101002-2T, was isolated from forest soil collected at Dinghushan Biosphere Reserve, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that it belonged to the genus Chitinophaga and was most closely related to Chitinophaga terrae KP01T (99.0 %), followed by Chitinophaga extrema Mgbs1T (98.3 %) and Chitinophaga solisilvae O9T (98.1 %). The draft genome sequence was 6.8 Mb long with a relative low G+C content of 39.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the novel strain and closely related type strains were 71.4‒76.2 % and 18.4‒19.6 %, respectively. Meanwhile the corresponding values between C. extrema Mgbs1T and C. solisilvae O9T were 98.6 and 88.1 %, respectively. The novel strain contained iso-C15:0, C16:1 ω5c and iso-C17:0 3-OH as the major fatty acids and MK-7 as the predominant respiratory quinone. The polyphasic study clearly supported that strain K2CV101002-2T represents a new species of the genus Chitinophaga , for which the name Chtinophaga silvatica sp. nov. (type strain K2CV101002-2T=GDMCC 1.1288T=JCM 32696T) is proposed. In addition, Chitinophaga extrema Goh et al. 2020 should be taken as a later heterotypic synonym of Chitinophaga solisilvae Ping et al. 2020.

Tamlicoccus marinus gen. nov., sp. nov., isolated from seawater

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 1951-1954 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Unknown Phospholipid ◽  
Type Strains ◽  
Cellular Fatty Acid Profile

A novel actinobacterial strain was isolated from a seawater sample collected on Mara Island, Jeju, Republic of Korea. Cells of this organism were aerobic, Gram-positive, non-spore-forming, non-motile cocci that occurred singly or in pairs. Colonies were circular, smooth, convex and white–cream in colour. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Dermacoccaceae and formed a monophyletic clade between the type strains of Demetria terragena (96.8 % similarity) and Branchiibius hedensis (95.2 % similarity). The cell-wall peptidoglycan contained l-lysine, alanine, aspartic acid, glutamic acid, glycine and serine, indicating that the isolate possessed peptidoglycan type A4α. The whole-cell sugars were galactose, glucose, mannose, xylose, arabinose, ribose and rhamnose. The major menaquinone was MK-8(H4). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and five unknown lipids. The cellular fatty acid profile was represented by large amounts of iso-methyl branched and monounsaturated iso- and anteiso-methyl branched acids, along with the presence of a diagnostic 10-methyl acid. The G+C content of the DNA was 71 mol%. On the basis of data from polyphasic analyses presented here, strain MSW-24T is considered to represent a novel species of a new genus in the family Dermacoccaceae , for which the name Tamlicoccus marinus gen. nov., sp. nov. is proposed. The type strain of Tamlicoccus marinus is MSW-24T ( = KCTC 19485T = DSM 21415T).

scholarly journals Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae

2020 ◽  
Vol 70 (3) ◽  
pp. 2108-2114 ◽  
Author(s):  
Sára Szuróczki ◽  
Gorkhmaz Abbaszade ◽  
Attila Szabó ◽  
Károly Bóka ◽  
Peter Schumann ◽  
...  
Keyword(s):  
Bacterial Strain ◽  
Type Species ◽  
Draft Genome ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Isoprenoid Quinones

The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family Verrucomicrobiaceae of the phylum Verrucomicrobia , and its closest relatives are Verrucomicrobium spinosum DSM 4136T (94.38 %) and Roseimicrobium gellanilyticum DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22–28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family Verrucomicrobiaceae , for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.

Maribrevibacterium harenarium gen. nov., sp. nov., represented by a marine strain of the family Oceanospirillaceae

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Kunlian Mo ◽  
Qingjuan Wu ◽  
Yonghua Hu ◽  
Huiqin Huang
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-stain-negative, non-motile, facultatively anaerobic, short rod-shaped bacterium, designated HB171799T, was isolated from seacoast sandy soil collected at Qishui Bay, Hainan, PR China. The chemotaxonomic analysis revealed that the respiratory quinones were Q-8 and Q-7, and the major cellular fatty acids were summed feature 8 (comprising C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C18 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The size of the draft genome was 3.68 Mb with a DNA G+C content of 48.0 mol%. Results of phylogenetic analyses based on 16S rRNA gene and genome sequences showed that the novel isolate belonged to the family Oceanospirillaceae and formed a distinct subcluster at the base of the radiation of the genus Marinomonas . The highest sequence similarity (96.0 %) of the novel isolate was found to the type strains of Marinomonas fungiae JCM 18476T and Marinomonas ostreistagni DSM23425T. The whole genome-based phylogeny and differences in cellular fatty acids and polar lipids readily distinguished strain HB171799T from all the closely related validly published type strains. Strain HB171799T is therefore suggested to represent a novel species of a new genus in the family Oceanospirillaceae , for which the name Maribrevibacterium harenarium gen. nov., sp. nov. is proposed. The type strain is HB171799T (=CGMCC 1.16727T=JCM 33332T).

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