scholarly journals Muricauda oceani sp. nov., isolated from the East Pacific Ocean

2020 ◽  
Vol 70 (6) ◽  
pp. 3839-3844 ◽  
Author(s):  
Bingxia Dong ◽  
Sidong Zhu ◽  
Ting Chen ◽  
Na Ren ◽  
Xiunuan Chen ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Core Gene ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
East Pacific ◽  
Gene Sequence Analysis ◽  
East Pacific Ocean

A Gram-stain-negative bacterium, designated strain 501str8T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain 501str8T belonged to the genus Muricauda , with closely related type strains Muricauda aquimarina SW-63T (98.5 %), Muricauda lutimaris SMK-108T (98.3 %) and Muricauda ruestringensis B1T (97.9 %). Up-to-date bacterial core gene set analysis revealed that strain 501str8T represented one independent lineage with M. aquimarina SW-63T. The average nucleotide identity values of strain 501str8T with M. aquimarina SW-63T and M. lutimaris SMK-108T were 80.2 and 81.3 %, respectively. In silico DNA–DNA hybridization values between strain 501str8T and M. aquimarina SW-63T and M. lutimaris SMK-108T were 22.8 and 32.9 %, respectively. The predominant isoprenoid quinone was menaquinone-6, and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G were the dominant cellular fatty acids. The G+C content of the genomic DNA was 42.8 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain 501str8T could be differentiated from closely related species. Therefore, we propose that strain 501str8T represents a novel species of the genus Muricauda , for which the name Muricauda oceani sp. nov. is suggested. The type strain is 501str8T (=JCM 33902T=MCCC 1K04567T).

Muricauda sediminis sp. nov., isolated from western Pacific Ocean sediment

2021 ◽  
Author(s):  
Sidong Zhu ◽  
Zehao Xue ◽  
Yizhe Huang ◽  
Xiunuan Chen ◽  
Na Ren ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Western Pacific ◽  
Rrna Gene ◽  
Western Pacific Ocean ◽  
Phenotypic Properties ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Ocean Sediment

A Gram-stain-negative bacterium, designated strain 40Bstr401T, was isolated from a sediment sample collected from the western Pacific Ocean. Analysis of its 16S rRNA gene sequence revealed that strain 40Bstr401T belongs to the genus Muricauda and is closely related to type strains Muricauda antarctica Ar-22T (98.2 %), Muricauda taeanensis 105T (98.2 %) and Muricauda beolgyonensis BB-My12T (97.4 %). The average nucleotide identity values for 40Bstr401T with M. antarctica Ar-22T and M. taeanensis 105T are 79.3 % and 78.8 %, respectively. The in silico DNA–DNA hybridization values between strain 40Bstr401T and M. antarctica Ar-22T and M. taeanensis 105T are 26.7 and 26.6 %, respectively. The major isoprenoid quinone of 40Bstr401T is MK-6, and iso-C17 : 0 3-OH and iso-C15 : 0 are the dominant cellular fatty acids. The major polar lipids are phosphatidylethanolamine, four unidentified amino lipids and two unidentified lipids. The G+C content of the genomic DNA is 42.9 mol%. Its phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, indicate that strain 40Bstr401T can be differentiated from closely related species. Therefore, we propose strain 40Bstr401T represents a novel species in the genus Muricauda , for which the name Muricauda sediminis sp. nov. is suggested. The type strain is 40Bstr401T (=MCCC 1K04568T=KCTC 82139T).

scholarly journals Nesterenkonia alkaliphila sp. nov., an alkaliphilic, halotolerant actinobacteria isolated from the western Pacific Ocean

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 516-521 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yubian Zhang ◽  
Xijie Yin ◽  
Shuang Wang
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Western Pacific ◽  
Rrna Gene ◽  
Western Pacific Ocean ◽  
Content Type ◽  
Link Type ◽  
The Western Pacific

A Gram-staining-positive, aerobic, motile and non-spore-forming actinobacteria, designated strain F10T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Nesterenkonia . Strain F10T shared highest 16S rRNA gene sequence similarity of 96.8 % with Nesterenkonia aethiopica DSM 17733T, followed by Nesterenkonia xinjiangensis YIM 70097T (96.7 %) and Nesterenkonia alba CAAS 252T (96.6 %). The organism grew at 4–50 °C, at pH 7.0–12.0 and in the presence of 0–12 % (w/v) NaCl, with optimal growth occurring at 40 °C, at pH 9.0 and in the presence of 1 % (w/v) NaCl. The peptidoglycan type was A4(alpha), l-Lys–Gly–l-Glu. The polar lipid profile of strain F10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and two unknown lipids. The isolate contained MK-9 (92 %) and MK-8 (5.8 %) as the major components of the menaquinone system, and anteiso-C17 : 0 (50.9 %) and anteiso-C15 : 0 (29.8 %) as the predominant fatty acids. The G+C content of the genomic DNA of strain F10T was 66.2 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain F10T represents a novel species of the genus Nesterenkonia for which the name Nesterenkonia alkaliphila sp. nov. is proposed. The type strain is F10T ( = LMG 28112T = CGMCC 1.12781T = JCM 19766T = MCCC 1A09946T).

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

scholarly journals Actinomadura geliboluensis sp. nov., isolated from soil

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 2011-2017 ◽  
Author(s):  
Anil Sazak ◽  
Mustafa Camas ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk ◽  
Nevzat Sahin
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Acid Type ◽  
Gene Sequence Analysis ◽  
Taxonomic Approach

A novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).

Rhizobium changzhiense sp. nov., isolated from effective nodules of Vicia sativa L. in North China

2021 ◽  
Author(s):  
Junjie Zhang ◽  
Shanshan Peng ◽  
Mitchell Andrews ◽  
Chunzeng Liu ◽  
Yimin Shang ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Vicia Sativa ◽  
Common Vetch ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Rhizobial Species ◽  
Distinct Lineage ◽  
Type Strains

Three fast-growing rhizobial strains isolated from effective nodules of common vetch (Vicia sativa L.) were characterized using a polyphasic approach. All three strains were assigned to the genus Rhizobium on the basis of the results of 16S rRNA gene sequence analysis. Phylogenetic analysis based on concatenated atpD-recA genes separated the strains into a distinct lineage represented by WYCCWR 11279T, which showed average nucleotide identity values of 95.40 and 93.61 % with the most similar phylogenetic type strains of Rhizobium sophorae CCBAU 03386T and Rhizobium laguerreae FB TT, respectively. The digital DNA–DNA hybridization relatedness values between WYCCWR 11279T and the closest related type strains were less than 70 %. Therefore, a novel rhizobial species is proposed, Rhizobium changzhiense sp. nov., and strain WYCCWR 11279T (=HAMBI 3709T=LMG 31534T) is designated as the type strain for the novel species.

Novosphingobium decolorationis sp. nov., an aniline blue-decolourizing bacterium isolated from East Pacific sediment

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Xiunuan Chen ◽  
Bingxia Dong ◽  
Ting Chen ◽  
Na Ren ◽  
Jing Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Aniline Blue ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
East Pacific ◽  
Type Strains

Aniline blue-decolourizing bacterial strain 502str22T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22T belongs to the genus Novosphingobium , with closely related type strains ‘ Novosphingobium profundi ’ F72T (97.6%), N. mathurense SM117T (97.1%) and N. arvoryzae Jyi-02T (97.0%). Digital DNA–DNA hybridization and average nucleotide identity values between strain 502str22T and closely related type strains were 20.3–24.8% and 74.1–81.9%, respectively. The major cellular fatty acid (>10%) was C18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22T (=KCTC 82134T= MCCC 1K04799 T).

scholarly journals Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1786-1793 ◽  
Author(s):  
Wallace Rafael Souza ◽  
Rafael Eduardo Silva ◽  
Michael Goodfellow ◽  
Kanungnid Busarakam ◽  
Fernanda Sales Figueiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

scholarly journals Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1348-1353 ◽  
Author(s):  
Hui-xian Wu ◽  
Pok Yui Lai ◽  
On On Lee ◽  
Xiao-jian Zhou ◽  
Li Miao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Red Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248T, was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248T fell within the genus Erythrobacter . Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.3 % (with Erythrobacter gangjinensis ) to 98.2 % (with Erythrobacter citreus ). However, levels of DNA–DNA relatedness between strain UST081027-248T and the type strains of closely related species were below 70 %. Optimal growth of the isolate occurred in the presence of 2.0 % NaCl, at pH 8.0–9.0 and at 28–36 °C. The isolate did not produce bacteriochlorophyll a. The predominant cellular fatty acids were C17 : 1ω6c, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C15 : 0 2-OH. The genomic DNA G+C content of strain UST081027-248T was 60.4 mol%. Phenotypic properties and phylogenetic distinctiveness clearly indicated that strain UST081027-248T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter pelagi sp. nov. is proposed. The type strain is UST081027-248T ( = JCM 17468T = NRRL 59511T).

scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Agromyces humi sp. nov., actinobacterium isolated from farm soil

2020 ◽  
Vol 70 (9) ◽  
pp. 5032-5039 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Phyletic Line ◽  
Phylogenomic Analyses ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and at salinities of 0–4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA–DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces . The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 :  0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces , for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).

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