Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Shahina Akter ◽  
Jong-Hyun Park ◽  
M. Mizanur Rahman ◽  
Md. Amdadul Huq
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Draft Genome ◽  
Rrna Genes ◽  
Physiological Data ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis

A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1–0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20–37 °C, at pH 5.0–8.5 and at 0–2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57T (97.7 % similarity), Niastella koreensis GR20-10T (97.1 %) and Niastella yeongjuensis GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-29T and three closely related type strains were in the range of 78.2–83.2 % and 22.1–27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of DNA–DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29T represents a novel species within the genus Niastella , for which the name Niastella soli sp. nov. is proposed, with MAH-29T (=KACC 19969T=CGMCC 1.16606T) as the type strain.

Frateuria flava sp. nov., isolated from soil

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Shahina Akter ◽  
Sun-Young Lee ◽  
Md. Amdadul Huq
Keyword(s):  
Type Species ◽  
Draft Genome ◽  
Nutrient Agar ◽  
Rrna Genes ◽  
Physiological Data ◽  
Trna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8–3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13T was found to be able to grow at 20–40 °C, at pH 5.0–10.0 and with 0–1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515T (98.2% similarity), Dyella thiooxydans ATSB10T (98.2 %), Frateuria defendens HyOGT (97.9 %), Rhodanobacter glycinis MO64T (97.8 %) and Frateuria aurantia DSM 6220T (97.8 %). The novel strain MAH-13T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAH-13T and five closely related type strains were in the range of 73.7–85.5 % and 20.7–30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13T represents a novel species within the genus Frateuria , for which the name Frateuria flava sp. nov. is proposed, with MAH-13T (=KACC 19743T=CGMCC 1.13655T) as the type strain.

scholarly journals Ramlibacter pinisoli sp. nov., a novel bacterial species isolated from pine garden soil

2020 ◽  
Vol 70 (11) ◽  
pp. 5841-5847 ◽  
Author(s):  
Shahina Akter ◽  
Kihong N. A. M. ◽  
Sun-Young Lee ◽  
Sung-Kwon Moon ◽  
Changsun Choi ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Nutrient Agar ◽  
Rrna Genes ◽  
Garden Soil ◽  
Physiological Data ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis

A Gram-stain-negative, aerobic, non-motile and rod- or coccoid-shaped novel bacterial strain, designated MAH-25T, was isolated from soil sampled in a pine garden. The colonies were observed to be light pink-coloured, smooth, spherical and 1–2 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-25T was found to be able to grow at 15–35 °C, at pH 5.0–8.0 and at 0–2.0 % NaCl. Cell growth occurred on Reasoner's 2A agar and nutrient agar. The strain was found to be positive in both oxidase and catalase tests. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Ramlibacter and closely related to Ramlibacter solisilvae 5-10T (98.0 % similarity), Ramlibacter henchirensis TMB834T (97.7 %), Ramlibacter tataouinensis TTB310T (97.6 %) and Ramlibacter rhizophilus YS3.2.7T (97.3 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-25T and the four closely related type strains were in the range of 78.8–81.3 % and 22.3–24.1 %, respectively. The novel strain MAH-25T has a draft genome size of 5 505 957 bp (11 contigs), annotated with 5210 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content was determined to be 70.3 mol%. The predominant isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were identified as C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of DNA–DNA hybridization, genotypic analysis, chemotaxonomic and physiological data, strain MAH-25T represents a novel species within the genus Ramlibacter , for which the name Ramlibacter pinisoli sp. nov. is proposed, with MAH-25T (=KACC 19839T=CGMCC1.13660T) as the type strain.

Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Md. Amdadul Huq ◽  
Muhammad Zubair Siddiqi ◽  
Sri Renukadevi Balusamy ◽  
M. Mizanur Rahman ◽  
Md Ashrafudoulla ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Content Type ◽  
Link Type ◽  
Pine Tree ◽  
The Family

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7–1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10–40 °C, at pH 6.0–9.0 and with 0–1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria–Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae . Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26T represents a novel species of a novel genus of the family Chitinophagaceae , for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26T (=KACC 19749T=CGMCC 1.13701T).

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

2021 ◽  
Author(s):  
Sinchan Banerjee ◽  
András Táncsics ◽  
Erika Tóth ◽  
Fruzsina Révész ◽  
Károly Bóka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Enrichment Culture ◽  
Draft Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Para Xylene

A benzene, para- and meta-xylene-degrading Gram-stain-negative, aerobic, yellow-pigmented bacterium, designated as D2P1T, was isolated from a para-xylene-degrading enrichment culture. Phylogenetic analyses based on 16S rRNA genes showed that D2P1T shares a distinct phyletic lineage within the genus Hydrogenophaga and shows highest 16S rRNA gene sequence similarity to Hydrogenophaga taeniospiralis NBRC 102512T (99.2 %) and Hydrogenophaga palleronii NBRC 102513T (98.3 %). The draft genome sequence of D2P1T is 5.63 Mb long and the genomic DNA G+C content is 65.5 %. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed low genomic relatedness to its closest relatives (OrthoANI <86 %; dDDH <30 %). D2P1T contains ubiquinone 8 (Q-8) as the only respiratory quinone and phospholipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol as major polar lipids. The main whole-cell fatty acids of D2P1T are summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). The polyphasic taxonomic results indicated that strain D2P1T represents a novel species of the genus Hydrogenophaga , for which the name Hydrogenophaga aromaticivorans sp. nov. is proposed. The type strain is D2P1T (=LMG 31780T=NCAIM B 02655T).

scholarly journals Streptosporangium jomthongense sp. nov., an actinomycete isolated from rhizospheric soil and emendation of the genus Streptosporangium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2400-2406 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Watanalai Panbangred ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 30EHST, was isolated from the rhizospheric soil under an elephant ear plant (Caladium bicolor) in Jomthong district, Bangkok, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 30EHST fell within the cluster of the genus Streptosporangium . Chemical composition analysis confirmed that the strain represented a member of the genus Streptosporangium even though this strain produced a tightly packed single spore on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain 30EHST was most closely related to Streptosporangium fragile NBRC 14311T (98.1 %), Streptosporangium carneum NBRC 15562T (97.8 %) and Streptosporangium violaceochromogenes NBRC 15560T (97.4 %). The DNA–DNA hybridization relatedness values between strain 30EHST and the above three strains were below 70 %. Based on combined data for phylogenetic analysis, DNA–DNA hybridization relatedness and physiological characteristics, it was concluded that strain 30EHST should be classified as representing a novel species of the genus Streptosporangium . We propose the name Streptosporangium jomthongense sp. nov., with the type strain 30EHST ( = BCC 53154T = NBRC 110047T). An emended description of the genus Streptosporangium is also proposed.

Actinokineospora bangkokensis sp. nov., isolated from rhizospheric soil

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2655-2660 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Yōko Takahashi ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 44EHWT, was isolated from rhizospheric soil under an Elephant ear plant (Colocasia esculenta) in Bangkok, Thailand. Strain 44EHWT produced long branching hyphae and abundant aerial mycelia with chains of rod-shaped spores. Whole-cell hydrolysates contained galactose, glucose, arabinose, ribose, mannose and rhamnose as diagnostic sugars. meso-Diaminopimelic acid was the diamino acid and glycine, alanine and glutamic acid were present in the cell-wall peptidoglycan with the acyl type of the peptidoglycan being acetyl. Phospholipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids and diphosphatidylglycerol, as well as other unknown phospholipids; however, no mycolic acids were detected. The predominant menaquinone observed was MK-9(H4) and major fatty acids were iso-C16 : 0 and 2-OH iso-C16 : 0. The G+C content of genomic DNA was 74 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate was most similar to Actinokineospora enzanensis NBRC 16517T. However, DNA–DNA hybridization revealed a low relatedness between this isolate and A. enzanensis NBRC 16517T, indicating that this isolate represented a novel species in the genus Actinokineospora . On the basis of 16S rRNA gene sequence analysis, phenotypic characteristics and DNA–DNA hybridization data, we propose that strain 44EHWT represents a novel species in the genus Actinokineospora , Actinokineospora bangkokensis. The type strain is 44EHWT ( = BCC 53155T = NBRC 108932T).

Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2607-2611 ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Joon Yong Kim ◽  
Ji-Hyun Yun ◽  
Dong-Wook Hyun ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Intestinal Tract ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis ◽  
Emended Description

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33T, was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33T grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33T contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33T was most closely related to Gibbsiella quercinecans FRB 97T and Gibbsiella dentisursi NUM 1720T, with 98.7 % similarities. DNA–DNA hybridization experiments indicated less than 40.7±2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97T. The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33T represents a novel species within the genus Gibbsiella , for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33T ( = KACC 16707T = JCM 18389T). An emended description of the genus Gibbsiella is also proposed.

Bacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 855-860 ◽  
Author(s):  
Ngoc-Lan Nguyen ◽  
Yeon-Ju Kim ◽  
Van-An Hoang ◽  
Jin Woo Min ◽  
Zhi-qi Liang ◽  
...  
Keyword(s):  
Type Species ◽  
Physiological Data ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Optimum Growth Temperature ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Genotypic Analysis ◽  
Bacillus Niacini

A novel bacterial strain DCY53T was isolated from a soil sample from a ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, endospore-forming and motile with flagella. The strain was aerobic, catalase- and oxidase-positive, optimum growth temperature and pH were 30–37 °C and 6.0–7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY53T was shown to belong to the genus Bacillus and the closest phylogenetic relatives were Bacillus pocheonensis KCTC 13943T (98.3 %), Bacillus bataviensis LMG 21833T (98.0 %), Bacillus soli LMG 21838T (97.9 %), Bacillus drentensis LMG 21831T (97.8 %), Bacillus niacini DSM 2923T (97.8 %), Bacillus novalis LMG 21837T (97.7 %), Bacillus vireti LMG 21834T (97.6 %) and Bacillus fumarioli LMG 17489T (97.3 %). The DNA G+C content was 43.6 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The DNA–DNA relatedness with closest relatives was below 55 %. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY53T represented a novel species within the genus Bacillus , for which we propose the name Bacillus ginsengisoli. The type strain is DCY53T ( = KCTC 13945T = JCM 17335T).

scholarly journals Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample

2020 ◽  
Vol 70 (7) ◽  
pp. 4151-4157 ◽  
Author(s):  
Shahina Akter ◽  
Md. Amdadul Huq
Keyword(s):  
Soil Sample ◽  
Type Species ◽  
Draft Genome ◽  
Nutrient Agar ◽  
Rrna Genes ◽  
Garden Soil ◽  
Tween 20 ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A novel bacterial strain, designated MAH-6T, was isolated from a garden soil sample. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The colonies were light yellow, smooth, circular and 0.6–1.2 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-6T grew at 15–35 °C, at pH 5.0–7.0 and with 0–0.5 % NaCl. Cell growth occurred on nutrient agar and Reasoner's 2A (R2A) agar. The strain was positive for both catalase and oxidase tests. Cells were able to hydrolyse starch, aesculin, Tween 20 and Tween 80. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and was most closely related to Sphingomonas polyaromaticivorans B2-7T (98.2 % sequence similarity), Sphingomonas oligoaromativorans SY-6T (96.9 %) and Sphingomonas morindae NBD5T (96.6 %). The novel strain MAH-6T has a draft genome size of 4 370 740 bp (28 contigs), annotated with 4199 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content of the strain was determined to be 66.2 mol% and the predominant isoprenoid quinone is Q-10. The major fatty acids were identified as summed feature 8 (comprising C18 : 1  ω7c and/or C18 : 1  ω6c), C14 : 0 2OH and C16 : 0. The main polar lipids were phosphatidylcholine, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the results of phenotypic, genotypic, chemotaxonomic and DNA–DNA hybridization studies, strain MAH-6T represents a novel species, for which the name Sphingomonas chungangi sp. nov. is proposed, with MAH-6T as the type strain (=KACC 19292T=CGMCC1.13654T).

Permianibacter fluminis sp. nov., isolated from a freshwater stream

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Miri S. Park ◽  
Jaeho Song ◽  
Jaeho Chang ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Freshwater Stream

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated as IMCC34836T, was isolated from a freshwater stream. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34836T was most closely related to Permianibacter aggregans HW001T (of the family Pseudomonadaceae ) with 95.6 % sequence similarity and formed a robust clade with P. aggregans HW001T. The draft genome sequence of strain IMCC34836T was 4.4 Mbp in size with 59.1 mol% DNA G+C content. Average nucleotide identity and digital DNA–DNA hybridization values between strain IMCC34836T and P. aggregans HW001T were 71.2 and 22.0 %, respectively, indicating that the new strain represents a novel species. The strain contained iso-C15 : 0, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 1 10-methyl) as the major fatty acids and harboured phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids as major polar lipids. The isoprenoid quinone detected in the strain was ubiquinone-8. Based on the phylogenetic and phenotypic characteristics, strain IMCC34836T is considered to represent a novel species of the genus Permianibacter , for which the name Permianibacter fluminis sp. nov. is proposed. The type strain is IMCC34836T (=KACC 21755T=NBRC 114416T).

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