Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium

Author(s):  
Yingning Wang ◽  
Fang Ma ◽  
Jixian Yang ◽  
Haijuan Guo ◽  
Delin Su

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter , for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

Author(s):  
Si Chen ◽  
Mengyuan He ◽  
Qiliang Lai ◽  
Ying Xu ◽  
Chenjing Shang

A taxonomic study was carried out on strain SHC163T, which was isolated from the gut of Onchidium reevesii. The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0–4.0 % NaCl and at temperatures of 15–35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163T belonged to the genus Jannaschia , with the highest sequence similarity to Jannaschia seosinensis CL-SP26T (97.9%), followed by Jannaschia faecimaris DSM 100420T (97.8 %), Jannaschia rubra CECT 5088T (97.5%) and eight species of the genus Jannaschia (94.7−97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA–DNA hybridization estimate values between strain SHC163T and the type strains of the genus Jannaschia were 64.33−79.78 %, 71.0−78.4 % and 19.2−21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c, 56.5 %), C18 : 1  ω7c 11-methyl (23.1 %), C18 : 0 (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163T represents a novel species within the genus Jannaschia , for which the name Jannaschia marina sp. nov. is proposed, with the type strain SHC163T (=MCCC 1K04032T=KCTC 72524T).


Author(s):  
Minchung Kang ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Taegun Seo

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11T (97.0 %), Sphingomonas edaphi DAC4T (96.8 %), Sphingomonas xanthus AE3T (96.5 %) and Sphingomonas oryziterrae YC6722T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3T grew at 7–50 °C (optimum, 30–35 °C), pH 5.0–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3T and its reference strains with publicly available genomes were 17.9–18.9 %, 72.0–75.3 % and 63.3–76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas . The type strain is sand1-3T (=KCTC 82358T=NBRC 114538T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3528-3533 ◽  
Author(s):  
Yan-lin Zhong ◽  
Xun-Ke Sun ◽  
Jian-Gang Hui ◽  
Hui-ling Teng ◽  
Zong-Jun Du

A Gram-stain-negative, rod-shaped, facultative anaerobic bacterium, designated strain 3539T, was isolated from coastal sediment of Weihai, PR China. Optimal growth occurred at 28 °C, pH 7.5–8.0 and in the presence of 3.0 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 3539T formed a robust clade with members of the genus Marinicella and was closely related to Marinicella litoralis JCM 16154T, Marinicella sediminis F2T and Marinicella pacifica sw153T with 97.7, 96.2 and 95.4 % sequence similarity, respectively. The average amino acid identity, percentage of conserved proteins, average nucleotide identity and digital DNA–DNA hybridization values between strain 3539T and M. litoralis JCM 16154T were 64.9, 68.3, 72.8 and 18.9 %, respectively. The genomic DNA G+C content of strain 3539T was 42.0 mol%. The dominant respiratory quinone was ubiquinone-8, and the major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). The polar lipids of strain 3539T consisted of phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified lipid and three unidentified phospholipids. Based on the combination of phylogenetic, phenotypic and chemotaxonomic data, strain 3539T is considered to represent a novel species within the genus Marinicella in he family Alcanivoracaceae , for which the name Marinicella rhabdoformis sp. nov. is proposed. The type strain of the new species is 3539T (=KCTC 72414T=MCCC 1H00388T).


2020 ◽  
Vol 70 (12) ◽  
pp. 6133-6141 ◽  
Author(s):  
Chan-Yeong Park ◽  
Seong-Jun Chun ◽  
Chunzhi Jin ◽  
Ve Van Le ◽  
Yingshun Cui ◽  
...  

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile, and rod-shaped bacterium, strain ETT8T was isolated from a chemostat culture of microalga Ettlia sp. YC001. Optimal growth was with 0–2% NaCl and at 25–37 °C on R2A medium. Phylogenetic analysis based on the 16S rRNA gene and genome sequence showed that strain ETT8T belongs to the genus Tabrizicola , with the close neighbours being T. sediminis DRYC-M-16T (98.1 %), T. alkalilacus DJCT (97.6 %), T. fusiformis SY72T (96.9 %), T. piscis K13M18T (96.8 %), and T. aquatica RCRI19T (96.5 %). The genomic comparison of strain ETT8T with type species in the genus Tabrizicola was analysed using the genome-to-genome distance calculator (GGDC), average nucleotide identity (ANI), and average amino acid identity (AAI) (values indicated ≤17.7, ≤75.4 and ≤71.9 %, respectively). The genomic DNA G+C content of strain ETT8T was 64.4 %, plus C18 : 1  ω6c and C18 : 0-iso were the major fatty acids and Q-10 the major respiratory quinone. Strain ETT8T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine aminolipid, and four unidentified lipids as the major polar lipids. Based on the chemotaxonomic, genotypic, and phenotype results, strain ETT8T was recognized as a novel species of the genus Tabrizicola for which the name Tabrizicola algicola sp. nov. is proposed. The type strain is ETT8T (=KCTC 72206T=JCM 31893T=MCC 4339T).


2020 ◽  
Vol 70 (7) ◽  
pp. 4245-4249 ◽  
Author(s):  
kun-lian Mo ◽  
Ling Wang ◽  
Qing-juan Wu ◽  
Lin Ye ◽  
Xing-di Liu ◽  
...  

A Gram-stain-negative, short-rod-shaped and pink-pigmented bacterial strain (HB172049T) was isolated from mangrove sediment. Cells grew at 10–45 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0.5–9.0 % (w/v) NaCl (optimum, 2–5 %). Analysis of the 16S rRNA gene sequence revealed that the isolate had highest sequence similarities to Pontibacter mucosus DSM 100162T (96.5 %) and Pontibacter korlensis X14-1T (96.5 %). The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between the isolate and its close neighbours were, respectively, less than 80.1, 81.7 and 23.2 %. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-7 and the predominant cellular fatty acids were summed feature 4 and iso-C15 : 0 (42.2 and 24.6 %, respectively). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified polar lipids. The genomic DNA G+C content was 52.6 mol%. Based on polyphasic taxonomic characterization, it is proposed that strain HB172049T belongs to the genus Pontibacter and represents a novel species, for which the name Pontibacter mangrovi sp. nov. is proposed. The type strain is HB172049T (=CGMCC 1.16729T=JCM 33333T).


Author(s):  
Adeline Lum Nde ◽  
George Charimba ◽  
Arina Hitzeroth ◽  
Lize Oosthuizen ◽  
Laurinda Steyn ◽  
...  

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic, yellow-pigmented bacterium was isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic taxonomy study was used to describe and name the bacterial isolate, strain 1_F178T. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain 1_F178T was a member of the genus Chryseobacterium and was closely related to Chryseobacterium jejuense (99.1%) and Chryseobacterium nakagawai (98.7%). Overall genome similarity metrics (average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity) revealed greatest similarity to the C. jejuense and C. nakagawai type strains but were below the threshold for species delineation. Genome sequencing revealed a genome size of 6.18 Mbp and a G+C content of 35.6 mol%. The major respiratory quinone and most abundant polar lipid of strain 1_F178T were menaquinone-6 and phosphatidylethanolamine, respectively. Strain 1_F178T had a typical fatty acid composition for Chryseobacterium species. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic data, strain 1_F178T constitutes a novel species of Chryseobacterium , for which the name Chryseobacterium pennae sp. nov. is proposed. The type strain is 1_F178T (=LMG 30779T=KCTC 62759T).


Author(s):  
Qi Yin ◽  
Jinyou Liang ◽  
Xiaoli Zheng ◽  
Yu Wang ◽  
Zhi-Man Song ◽  
...  

A novel symbiotic bacterium, designated strain XY-114T, was isolated from the cerata of an Onchidium marine invertebrate species collected in the South China Sea. Strain XY-114T was an aerobic, Gram-stain-negative, non-motile and short rod-shaped bacterium (0.5–0.8 µm wide and 1.0–1.5 µm long) without flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XY-114T belonged to the genus Algibacter with the highest similarity of 97.2 % to the closest phylogenetic relative Algibacter aestuarii KYW371T. Cells grew at 15–37 °C (optimum, 30 °C), at pH 5.5–9.0 (optimum 7.0–8.0) and at NaCl concentrations of 0.5–5.0 % (w/v; optimum 1.5–3.0 %). The major fatty acids (>10 %) were summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was MK-6. Flexirubin-type pigments were absent. The genome size of strain XY-114T was 3.4 Mbp, with 34.9 mol% of DNA G+C content. The average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values between strain XY-114T and A. aestuarii KYW371T were 74.5 %, 17.0±1.8 % and 73.9 %. Characterization based on phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain XY-114T represents a novel species of the genus Algibacter , for which the name Algibacter onchidii sp. nov. is proposed. The type strain is XY-114T (=KCTC 72217T=MCCC 1K03606T).


2020 ◽  
Vol 70 (6) ◽  
pp. 3816-3823 ◽  
Author(s):  
Hui Zhang ◽  
Lian Xu ◽  
Jin-Xin Zhang ◽  
Ji-Quan Sun

A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10–40 °C (optimum, 35 °C), pH 5.0–9.0 (optimum, pH 8.0) and 0–12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with Sphingomonas turrisvirgatae MCT13T and Sphingomonas koreensis JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to S. koreensis JSS-26T and S. turrisvirgatae MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C17 : 1  ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of strain XS-10T with S. turrisvirgatae MCT13T and S. koreensis JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).


2020 ◽  
Vol 70 (9) ◽  
pp. 4920-4926 ◽  
Author(s):  
So Muramatsu ◽  
Masataka Kanamuro ◽  
Yuki Sato-Takabe ◽  
Setsuko Hirose ◽  
Yuki Muramatsu ◽  
...  

An obligate aerobic and bacteriochlorophyll a-containing bacterium, designated strain AI77T, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77T is a member of the genus Roseobacter and closely related to Roseobacter ponti MM-7T (97.8 %), Roseobacter denitrificans OCh 114T (97.3 %) and Roseobacter litoralis OCh 149T (97.3 %). The G+C content of strain AI77T was 61.0 mol%. The average amino acid identity values of the genome in strain AI77T with those in R. denitrificans OCh 114T and R. litoralis OCh 149T were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA–DNA hybridization values of strain AI77T with the type strains R. denitrificans OCh 114T and R. litoralis OCh 149T were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and saturated fatty acid C16 : 0. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77T represents a new species of the genus Roseobacter , for which we propose the name Roseobacter cerasinus sp. nov.; the type strain is AI77T (=DSM 110091T=NBRC 114115T).


2020 ◽  
Vol 70 (8) ◽  
pp. 4502-4507 ◽  
Author(s):  
Chao Sun ◽  
Xiang Zeng ◽  
Qiliang Lai ◽  
Zhaoshou Wang ◽  
Zongze Shao

An alkali lignin-degrading, Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated BM_7T, was isolated from mangrove sediment of the supralittoral zone in the Jiulong river estuary, PR China. The cells of strain BM_7T were 0.4–0.6 µm wide and 1.0–8.5 µm long. Oxidase and catalase activities were positive. Strain BM_7T could grow at 10–37 °C (optimum, 25–28 °C), at pH 6.0–8.0 (optimum, pH 7.0) and in the presence of 0.5–6 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BM_7T belonged to the genus Mangrovibacterium of the family Prolixibacteraceae . It showed the highest similarity to Mangrovibacterium diazotrophicum JCM 19152T (96.8 %), followed by Mangrovibacterium marinum KCTC 42253T (96.1%). The values of average nucleotide identity and DNA–DNA hybridization were calculated as 76.9, 24.3 and 76.1, 17.4 % between strain BM_7T with M. diazotrophicum JCM 19152T and M. marinum KCTC 42253T, respectively. The major respiratory quinone of strain BM_7T was MK-7. The polar lipids were detected as phosphatidylethanolamine, three unidentified phospholipids and four unidentified aminolipids. The dominant fatty acids consisted of iso-C15 : 0, anteiso-C15 : 0, C15 : 1  ω6c, iso-C17 : 0 3-OH, C17 : 1  ω6c, C17 : 0 3-OH and C17 : 0. The genome size of strain BM_7T is 5.6 Mb, with G+C content of 43.4 mol%. Based on the phylogenetic and phenotypic characteristics, strain BM_7T was considered to represent a novel species of the genus Mangrovibacterium , and the name Mangrovibacterium lignilyticum sp. nov. is proposed. The type strain is BM_7T (=MCCC 1A15882T=KCTC 72696T).


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