scholarly journals Sinorhodobacter populi sp. nov., isolated from the symptomatic bark tissue of Populus × euramericana canker

2019 ◽  
Vol 69 (4) ◽  
pp. 1220-1224 ◽  
Author(s):  
Guan-tang Xu ◽  
Chungen Piao ◽  
Ju-pu Chang ◽  
Li-min Guo ◽  
Xu-qi Yang ◽  
...  
Keyword(s):  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Positive Growth ◽  
Bark Tissue ◽  
Type Strains ◽  
The 16S Rrna Gene

We isolated five novel bacterial strains from symptomatic bark tissue of Populus × euramericana canker that were Gram-stain-negative, non-motile, aerobic oxidase-negative and catalase-positive. Growth occurred at 10–41 °C and at pH 5.0–7.0, with optimum growth at 30 °C and pH 7.0. Additionally, growth occurred in conditions of 0–5 % (w/v) salinity, but not above 7 % NaCl. The 16S rRNA gene sequences of the novel strains shared the highest similarity with Sinorhodobacter ferrireducens SgZ-3T (97.1 %). The average nucleotide identity values between the novel strains and two type strains (S.inorhodobacter ferrireducens CCTCC AB2012026T and ‘ S inorhodobacter hungdaonensis’ CGMCC 1.12963T) were 78.4–78.9 %, which were lower than the proposed species boundary cut-off (95–96 %). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified lipid and phosphatidylcholine. The main respiratory quinone was Q-10, and major fatty acids were C18 : 1ω7c and/or C18 : 1 ω6c. Based on data from a polyphasic taxonomy study, the novel strains represent a novel species of the genus Sinorhodobacter , for which the name Sinorhodobacter populi sp. nov. is proposed. The type strain is sk2b1T (=CFCC 14580T=KCTC 52802T).

scholarly journals Skermanella pratensis sp. nov., isolated from meadow soil, and emended description of the genus Skermanella

2020 ◽  
Vol 70 (3) ◽  
pp. 1605-1609 ◽  
Author(s):  
Qiannan Guo ◽  
Zhengfu Zhou ◽  
Lijuan Zhang ◽  
Chen Zhang ◽  
Ming Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Meadow Soil ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Pr China ◽  
The 16S Rrna Gene

A novel Gram-stain-negative, light pink-coloured, short rod-shaped, designated strain W17T, was isolated from a meadow soil sample collected from Xinjiang, PR China. The 16S rRNA gene sequence analysis indicated that strain W17T was related most closely to Skermanella rosea M1T (98.72 %) and Skermanella mucosa 8-14-6T (98.44 %). However, strain W17T showed a low level of DNA–DNA relatedness to S. rosea M1T (32.4±2.6 %) and S. mucosa 8-14-6T (33.5±0.1 %). The genome size of the novel strain was 5.87 Mb and the genomic DNA G+C content was 67.27 mol%. The only respiratory quinone of strain W17T was Q-10. Diphosphatidylglycerol, phosphatidylglycerol. phosphatidylethanolamine and phosphatidylcholine were the major polar lipids. The predominant cellular fatty acids were C18 : 1ω6c and/or C18 : 1ω7c (48.53 %), C16 : 0 (20.88 %) and C18 : 0 (14.92 %). The phylogenetic, phenotypic and chemotaxonomic data showed that strain W17T represents a novel species of the genus Skermanella , for which the name Skermanella pratensis sp. nov. is proposed. The type strain is W17T (=GDMCC 1.1392T=KCTC 62434T).

scholarly journals Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes

2020 ◽  
Vol 70 (5) ◽  
pp. 3361-3373 ◽  
Author(s):  
Xiao-meng Lv ◽  
Min Yang ◽  
Li-rong Dai ◽  
Bo Tu ◽  
Chen Chang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Shengli Oilfield ◽  
Methanothermobacter Thermautotrophicus ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and Methanothermobacter thermautotrophicus ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of Desulfitibacter alkalitolerans , Calderihabitans maritimus and members of the genus Moorella . Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family Peptococcaceae were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.

Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yeonjae Yoo ◽  
Dongjun Kim ◽  
Hanbyul Lee ◽  
Jong Seong Khim ◽  
Bogun Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Marine Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Salt Flat ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, pale yellow-coloured, rod-shaped marine bacterium designated strain YJ-S2-02T was isolated from salt flat sediment sampled in Yongyu-do, Republic of Korea. Strain YJ-S2-02T grew at pH 6.0–9.0 (optimum, pH 7.0), 10–40 °C (optimum, 30 °C) and with optimum 1 % (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain YJ-S2-02T was closely related to Novosphingobium naphthalenivorans NBRC 102051T (97.8 %) followed by Novosphingobium mathurense SM117T (97.5 %), Novosphingobium indicum H25T (97.3 %), Novosphingobium pentaromativorans US6-1T (96.8 %), Novosphingobium fontis STM-14T (96.6 %), Novosphingobium endophyticum EGI60015T (96.5 %), Novosphingobium naphthae D39T (96.5 %) and Novosphingobium malaysiense MUSC 273T (95.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between YJ-S2-02T and related type strains were 77.0–77.9 % and 19.1–24.0 %. Strain YJ-S2-02T was characterized as having Q-10 as the predominant respiratory quinone and the principal fatty acids (>10 %) were summed feature 8 (C18 : 1  ω6c/ω7c, 20.7 %), C18 : 3  ω6c (16.3 %) and C17 : 1  ω6c (11.8 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingolipids and two unidentified lipids. The DNA G+C content of strain YJ-S2-02T was 65.6 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S2-02T should be classified as representing a novel species within the genus Novosphingobium , for which name Novosphingobium aureum is proposed, with the type strain YJ-S2-02T (=KACC 21677T =KCTC 72891T=JCM 33996T).

Dyadobacter tibetensis sp. nov., isolated from glacial ice core

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3636-3639 ◽  
Author(s):  
Liang Shen ◽  
Yongqin Liu ◽  
Tandong Yao ◽  
Ninglian Wang ◽  
Baiqing Xu ◽  
...  
Keyword(s):  
Ice Core ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
The Novel ◽  
Phenotypic Data ◽  
Glacial Ice ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, designated Y620-1T, was isolated from a glacier on the Tibetan Plateau, China. The 16S rRNA gene sequence of the novel isolate shared 93.6–95.1 % similarity with type strains of species of the genus Dyadobacter . The major fatty acids of strain Y620-1T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone and polar lipid were MK-7 and phosphatidylethanolamine (PE), respectively. The DNA G+C content was 44.4±0.3 mol% (T m). Flexirubin-type pigment was produced. The novel isolate was classified in the genus Dyadobacter , but a number of phenotypic characteristics distinguished the novel isolate from type strains of species of the genus Dyadobacter . From these genotypic and phenotypic data, it is evident that strain Y620-1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter tibetensis sp. nov. is proposed. The type strain is Y620-1T ( = JCM 18589T = CGMCC 1.12215T).

scholarly journals Cohnella arctica sp. nov., isolated from Arctic tundra soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 817-821 ◽  
Author(s):  
Fan Jiang ◽  
Jun Dai ◽  
Yang Wang ◽  
Xiuqing Xue ◽  
Mengbo Xu ◽  
...  
Keyword(s):  
Rrna Gene ◽  
Tundra Soil ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Major Respiratory Quinone ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A psychrotolerant Gram-reaction-negative, rod-shaped and orange-pigmented bacterium, designated strain M9-62T, which was motile by means of peritrichous flagella, was isolated from tundra soil sampled near Ny-Ålesund, Svalbard Islands, Norway (78° N). Growth occurred at 4–30 °C (optimum, 25 °C) and pH 5.0–8.0 (optimum, pH 6.0–7.0). Analysis of the 16S rRNA gene sequence of strain M9-62T placed it in the genus Cohnella ; sequence similarities of the isolate with type strains of members of related genera ranged from 92.0 to 96.3 %. Strain M9-62T contained anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (7.5 %) and C16 : 0 (6.1 %) as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol as the main polar lipids. The major respiratory quinone was MK-7 and the DNA G+C content was 50.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain M9-62T is considered to represent a novel species of the genus Cohnella , for which the name Cohnella arctica sp. nov. is proposed; the type strain is M9-62T ( = CCTCC AB 2010228T = NRRL B-59459T).

Mycetocola zhadangensis sp. nov., isolated from snow

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3375-3378 ◽  
Author(s):  
Liang Shen ◽  
Yongqin Liu ◽  
Tandong Yao ◽  
Shichang Kang ◽  
Yanan Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
Isoprenoid Quinones ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-stain-positive, aerobic, short rod-shaped bacterium, strain ZD1-4T, was isolated from the Zhadang Glacier snow pit. The 16S rRNA gene sequence of the isolate showed highest similarity (98.8 %) to that of Mycetocola manganoxydans MB1-14T. The major fatty acids of strain ZD1-4T were anteiso-C15 : 0, C16 : 0, C18 : 0 and anteiso-C17 : 0. It possessed diphosphatidylglycerol as one of the major polar lipids, and MK-10 and MK-11 as the predominant isoprenoid quinones. The DNA G+C content of strain ZD1-4T was 63.8±0.2 mol% (T m). A number of phenotypic characteristics distinguished this bacterium from the type strains of other species of the genus Mycetocola . Moreover, the novel isolate showed only approximately 50 % DNA–DNA relatedness with M. manganoxydans MB1-14T. According to these genotypic and phenotypic data, it is evident that strain ZD1-4T represents a novel species of the genus Mycetocola , for which the name Mycetocola zhadangensis sp. nov. is proposed. The type strain is ZD1-4T ( = KACC 16570T = CGMCC 1.12042T).

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

scholarly journals Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities

2020 ◽  
Vol 70 (4) ◽  
pp. 2537-2553 ◽  
Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim
Keyword(s):  
Type Strain ◽  
Antioxidant Activities ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Strictly Aerobic ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Arctic Soil ◽  
Type Strains

Fifteen isolates of the genus Pedobacter were obtained from Arctic soil samples. All isolates were Gram-stain-negative and rod-shaped. Cells were strictly aerobic, psychrotolerant and grew optimally at 15–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all the isolated strains formed a lineage within the family Sphingobacteriaceae and clustered as members of the genus Pedobacter . The sole respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (iso-C15 : 02-OH/C16 : 1ω7c/ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of the novel strains was 33.9–41.8 mol%. In addition, the average nucleotide identity and in silico DNA–DNA hybridization relatedness values between the novel type strains and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, phylogenetic and phylogenomic analyses, the isolated strains represent novel species in the genus Pedobacter , for which the names Pedobacter cryotolerans sp. nov. (type strain AR-2-6T=KEMB 9005-717T=KACC 19998T=NBRC 113826T), Pedobacter cryophilus sp. nov. (type strain AR-3-17T=KEMB 9005-718T=KACC 19999T=NBRC 113827T), Pedobacter frigiditerrae sp. nov. (type strain RP-1-13T=KEMB 9005-720T=KACC 21147T=NBRC 113829T), Pedobacter psychroterrae sp. nov. (type strain RP-1-14T=KEMB 9005-721T=KACC 21148T=NBRC 113830T), Pedobacter hiemivivus sp. nov. (type strain RP-3-8T=KEMB 9005-724T=KACC 21152T=NBRC 113833T), Pedobacter frigidisoli sp. nov. (type strain RP-3-11T=KEMB 9005-725T=KACC 21153T=NBRC 113927T), Pedobacter frigoris sp. nov. (type strain RP-3-15T=KEMB 9005-726T=KACC 21154T=NBRC 113834T), Pedobacter psychrodurus sp. nov. (type strain RP-3-21T=KEMB 9005-728T=KACC 21156T=NBRC 113835T) and Pedobacter polaris sp. nov. (type strain RP-3-22T=KEMB 9005-729T=KACC 21157T=NBRC 113836T) are proposed.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

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