scholarly journals Arthrobacter nanjingensis sp. nov., a mineral-weathering bacterium isolated from forest soil

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 365-369 ◽  
Author(s):  
Zhi Huang ◽  
Yuan Yuan Bao ◽  
Tong Tong Yuan ◽  
Guo Xiang Wang ◽  
Lin Yan He ◽  
...  
Keyword(s):  
Cell Wall ◽  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, non-motile, rod- or coccoid-shaped actinobacterium, designated strain A33T, was isolated from a forest soil sample from Nanjing, Jiangsu Province, PR China. The strain grew optimally at 30 °C, pH 7.0 and with 3 % NaCl (w/v). Phylogenetic analysis of the strain, based on 16S rRNA gene sequences, showed that it was most closely related to Arthrobacter woluwensis (98.4 % sequence similarity), Arthrobacter humicola (97.5 %), Arthrobacter globiformis (97.4 %), Arthrobacter oryzae (97.3 %) and Arthrobacter cupressi (97.0 %). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0; MK-9(H2) was the predominant respiratory quinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and three glycolipids. Cell-wall analysis revealed that the peptidoglycan type was A3α, based on l-lysine-l-alanine; the cell-wall sugars were galactose and mannose. The genomic G+C content of strain A33T was 66.8 mol%. The low DNA–DNA relatedness values between strain A33T and recognized species of the genus Arthrobacter and many phenotypic properties supported the classification of strain A33T as a representative of a novel species of the genus Arthrobacter , for which the name Arthrobacter nanjingensis sp. nov. is proposed. The type strain is A33T ( = CCTCC AB 2014069T = DSM 28237T).

Dyella jiangningensis sp. nov., a γ-proteobacterium isolated from the surface of potassium-bearing rock

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3154-3157 ◽  
Author(s):  
Fei Zhao ◽  
Xin-qi Guo ◽  
Peng Wang ◽  
Lin-yan He ◽  
Zhi Huang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Many

A Gram-stain-negative, aerobic, motile with one polar flagellum γ-proteobacterium, designated strain SBZ3-12T, was isolated from surfaces of weathered potassic trachyte. Phylogenetic analysis of this strain based on 16S rRNA gene sequences showed that it was most closely related to Dyella japonica XD53T (97.9 % 16S rRNA gene sequence similarity), Dyella terrae JS14-6T (97.7 %), Dyella soli JS12-10T (97.5 %) and Dyella koreensis BB4T (97.0 %). The DNA G+C content of strain SBZ3-12T was 64.0 mol%. In addition, iso-C17 : 1ω9c, iso-C15 : 0 and iso-C16 : 0 were the major cellular fatty acids and ubiquinone Q-8 was the predominant respiratory quinone. The low DNA–DNA relatedness values between strain SBZ3-12T and recognized species of the genus Dyella and the many phenotypic properties supported the classification of strain SBZ3-12T as a representative of a novel species of the genus Dyella , for which the name Dyella jiangningensis sp. nov. is proposed. The type strain is SBZ3-12T ( = CCTCC AB 2012160T = KACC 16539T = DSM 26119T).

Reyranella soli sp. nov., isolated from forest soil, and emended description of the genus Reyranella Pagnier et al. 2011

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3164-3167 ◽  
Author(s):  
Soo-Jin Kim ◽  
Jae-Hyung Ahn ◽  
Tae-Hyung Lee ◽  
Hang-Yeon Weon ◽  
Seung-Beom Hong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated KIS14-15T, was isolated from forest soil of Baengnyeong Island in the Yellow Sea in Korea and its taxonomic position was investigated by using a polyphasic study. Strain KIS14-15T grew optimally at 30 °C, at pH 6.0–7.0 and without NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain KIS14-15T formed a cluster with the strains of Reyranella massiliensis with a bootstrap resampling value of 100 %. Strain KIS14-15T exhibited 16S rRNA gene sequence similarity values of 98.0 % to R. massiliensis 521T and of less than 89 % to the type strains of other taxa. The mean level of DNA–DNA relatedness between strain KIS14-15T and R. massiliensis KACC 16548T was 21 % (reciprocal, 24 %). The predominant ubiquinone found in strain KIS14-15T and R. massiliensis KACC 16548T was ubiquinone-10 (Q-10). The predominant fatty acids of strain KIS14-15T and R. massiliensis KACC 16548T were C18 : 1ω7c, C18 : 1 2-OH and 11-methyl C18 : 1ω7c. Total polar lipids of strain KIS14-15T were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown aminolipid and one unknown lipid. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain KIS14-15T is distinguishable from R. massiliensis . On the basis of the data presented, strain KIS14-15T is considered to represent a novel species of the genus Reyranella , for which the name Reyranella soli sp. nov. is proposed. The type strain is KIS14-15T ( = KACC 13034T = NBRC 108950T).

Myroides xuanwuensis sp. nov., a mineral-weathering bacterium isolated from forest soil

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 621-624 ◽  
Author(s):  
Zhen-Dong Zhang ◽  
Lin-Yan He ◽  
Zhi Huang ◽  
Xia-Fang Sheng
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Myroides Odoratimimus

A Gram-reaction-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium, designated strain TH-19T, was isolated from a forest soil sample in Jiangsu province, China. On the basis of 16S rRNA gene sequence similarity, strain TH-19T was shown to belong to the genus Myroides , a member of the phylum Bacteroidetes , and was related to Myroides odoratimimus LMG 4029T (98.7 % similarity), Myroides profundi D25T (98.2 %) and Myroides marinus JS-08T (97.5 %). Strain TH-19T contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain TH-19T was 37.2 mol%. The DNA–DNA relatedness values of strain TH-19T with Myroides odoratimimus JCM 7460T, Myroides profundi D25T and Myroides marinus JS-08T were below 70 %. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain TH-19T represents a novel species of the genus Myroides , for which the name Myroides xuanwuensis sp. nov. is proposed. The type strain is TH-19T ( = CCTCC AB 2013145T = JCM 19200T).

Paraburkholderia flava sp. nov., isolated from cool temperate forest soil

2020 ◽  
Vol 70 (4) ◽  
pp. 2509-2514 ◽  
Author(s):  
Ngoc Hoang Trinh ◽  
Jaisoo Kim
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic and short rod-shaped bacterial strain, designated LD6T, was isolated from a forest soil sample in Suwon, Gyeonggi-do, Republic of Korea. Strain LD6T grew at 10–37 °C (optimal temperature, 28 °C), and tolerated pH 8.0 and 2 % (w/v) NaCl. Strain LD6T was related most closely to members of the genus Paraburkholderia , namely Paraburkholderia azotifigens NF2-5-3T (98.2 % 16S rRNA gene sequence similarity), P. megapolitana A3T (97.9 %), P. ginsengiterrae DCY85T (97.9 %) and P. caribensis MWAP64T (97.7 %). The strain grew well on R2A agar, tryptone soya agar, Mueller-Hinton agar and nutrient agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and glycolipid. The major respiratory quinone was ubiquinone 8 (Q-8). The main fatty acids were C17 : 0 cyclo, C16 : 0, C16 : 0 3-OH, C19 : 0 cyclo ω8c and C12 : 0. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.4 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain LD6T and its reference type strains ranged from 80.3 to 82.4%, and from 23.7 to 33.7%, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain LD6T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Paraburkholderia . Therefore, strain LD6T is considered to represent a novel species, for which the name Paraburkholderia flava sp. nov. is proposed. The type strain is LD6T (=KACC 21387T=JCM 33640T).

Chitinophaga jiangningensis sp. nov., a mineral-weathering bacterium

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 260-265 ◽  
Author(s):  
Qi Wang ◽  
Cheng Cheng ◽  
Lin-Yan He ◽  
Zhi Huang ◽  
Xia-Fang Sheng
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, rod-shaped bacterial strain, JN53T, was isolated from the surfaces of weathered rock (potassic trachyte) from Nanjing, Jiangsu Province, PR China. Strain JN53T grew optimally at 30 °C, pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JN53T belonged to the genus Chitinophaga in the family Chitinophagaceae . It was most closely related to Chitinophaga terrae KP01T (97.3 % 16S rRNA gene sequence similarity), Chitinophaga eiseniae YC6729T (96.3 %). Strain JN53T contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The main fatty acids of strain JN53T were iso-C15 : 0, C16 : 1ω5c, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 0 3-OH and C16 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids and unknown lipids. The total DNA G+C content of strain JN53T was 49.7 mol%. The low level of DNA–DNA relatedness to other species of the genus Chitinophaga and the many phenotypic properties that distinguished strain JN53T from recognized species of this genus demonstrated that isolate JN53T should be classified as representing a novel species of the genus Chitinophaga , for which the name Chitinophaga jiangningensis sp. nov. is proposed. The type strain is JN53T ( = CCTCC AB 2013166T = JCM 19354T).

scholarly journals Zoogloea dura sp. nov., a N2-fixing bacterium isolated from forest soil and emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera

2020 ◽  
Vol 70 (10) ◽  
pp. 5312-5318 ◽  
Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Type Strains ◽  
Zoogloea Ramigera

A motile, Gram-stain-negative, rod-shaped bacterium, designated G-4-1-14T, was obtained from forest soil sampled at Gwanggyo mountain, Gyeonggi-do, Republic of Korea. Cells were colourless, aerobic, grew optimally at 28–35 °C and hydrolysed DNA and casein. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-4-1-14T formed a lineage within the genus Zoogloea . The closest members were Zoogloea resiniphila ATCC 70068T (98.6 % sequence similarity), Zoogloea caeni EMB43T (98.2 %), Zoogloea oryzae A-7T (97.7 %), Zoogloea ramigera IAM 12136T (96.9 %) and Zoogloea oleivorans BucT (96.2 %). The major respiratory quinone was ubiquinone-8 and the principal polar lipids were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The predominant cellular fatty acids were summed feature 3 (iso-C15 :0 2-OH/C16  : 1 ω7c) and C16 : 0. The DNA G+C content was 65.9 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain G-4-1-14T and other type strains were ≤81.6 and ≤24.9 %, respectively, which are below the species demarcation thresholds. Based on the results of phenotypic, phylogenetic and genomic analyses, strain G-4-1-14T represents a novel species in the genus Zoogloea , for which the name Zoogloea dura sp. nov. is proposed. The type strain is G-4-1-14T (=KACC 21618T=NBRC 114358T). In addition, we propose emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera .

Pseudonocardia xishanensis sp. nov., an endophytic actinomycete isolated from the roots of Artemisia annua L.

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2395-2399 ◽  
Author(s):  
Guo-Zhen Zhao ◽  
Jie Li ◽  
Wen-Yong Zhu ◽  
Da-Qiao Wei ◽  
Jin-Li Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Artemisia Annua ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Endophytic Actinomycete ◽  
Link Type

A Gram-positive, non-motile, endophytic actinomycete, designated strain YIM 63638T, was isolated from the surface-sterilized roots of Artemisia annua L. The isolate grew optimally with 1–3 % (w/v) NaCl, at pH 6.0–7.0 and at 20–37 °C. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belonged to the genus Pseudonocardia and showed highest sequence similarity with Pseudonocardia oroxyli D10T (98.9 %), Pseudonocardia ailaonensis YIM 45505T (98.3 %) and Pseudonocardia halophobica IMSNU 21327T (98.0 %). Phylogenetic distance from other type strains of species with validly published names within the genus Pseudonocardia was greater than 2.3 %. Strain YIM 63638T had a genomic DNA G+C content of 72.1 mol% and MK-8(H4) as the predominant respiratory quinone. The major fatty acids were iso-C16 : 0 (36.32 %) and 10-methyl-C16 : 0 (19.78 %). On the basis of phenotypic properties and phylogenetic distinctiveness, strain YIM 63638T represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia xishanensis sp. nov. is proposed. The type strain is YIM 63638T ( = JCM 17906T  = KCTC 29005T).

scholarly journals Novosphingobium kunmingense sp. nov., isolated from a phosphate mine

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2324-2329 ◽  
Author(s):  
Fuhong Xie ◽  
Shujing Quan ◽  
Dehai Liu ◽  
Weihong He ◽  
Yanan Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Western China ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Phosphate Mine

A yellow-pigmented, Gram-stain-negative, strictly aerobic, rod-shaped, round-ended bacterium, designated strain 18-11HKT, was isolated from a phosphate mine situated in the suburb of Kunming in Yunnan province in south-western China. The taxonomic status of this strain was evaluated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, strain 18-11HKT was shown to belong to the genus Novosphingobium , showing the highest levels of sequence similarity with respect to ‘Novosphingobium ginsenosidimutans’ FW-6 (97.2 %), Novosphingobium subterraneum DSM 12447T (96.7 %), Novosphingobium aromaticivorans DSM 12444T (96.7 %) and Novosphingobium tardaugens DSM 16702T (96.3 %). Strain 18-11HKT had a genomic DNA G+C content of 65.3 mol% and Q-10 as the predominant respiratory quinone. DNA–DNA hybridizations of strain 18-11HKT with N. subterraneum DSM 12447T, N. aromaticivorans DSM 12444T and N. tardaugens DSM 16702T showed low relatedness values of 29.6, 33.5 and 32.3 %, respectively. The predominant fatty acids of strain 18-11HKT were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0, and the major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile revealed the presence of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified lipids. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain 18-11HKT represents a novel species of the genus Novosphingobium , for which the name Novosphingobium kunmingense sp. nov. is proposed. The type strain is 18-11HKT ( = CGMCC 1.12274T = DSM 25975T).

scholarly journals Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil

2020 ◽  
Vol 70 (9) ◽  
pp. 4966-4977 ◽  
Author(s):  
Selma Vieira ◽  
Javier Pascual ◽  
Christian Boedeker ◽  
Alicia Geppert ◽  
Thomas Riedel ◽  
...  
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Major Respiratory Quinone ◽  
Prosthecate Bacteria

The family Caulobacteraceae comprises prosthecate bacteria with a dimorphic cell cycle and also non-prosthecate bacteria. Cells of all described species divide by binary fission. Strain 0127_4T was isolated from forest soil in Baden Württemberg (Germany) and determined to be the first representative of the family Caulobacteraceae which divided by budding. Cells of strain 0127_4T were Gram-negative, rod-shaped, prosthecate, motile by means of a polar flagellum, non-spore-forming and non-capsulated. The strain formed small white colonies and grew aerobically and chemo-organotrophically utilizing organic acids, amino acids and proteinaceous substrates. 16S rRNA gene sequence analysis indicated that this bacterium was related to Aquidulcibacter paucihalophilus TH1-2T and Asprobacter aquaticus DRW22-8T with 91.3 and 89.7% sequence similarity, respectively. Four unidentified glycolipids were detected as the major polar lipids and, unlike all described members of the family Caulobacteraceae , phosphatidylglycerol was absent. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c/C16 : 0 10-methyl), C16 : 0 and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). The major respiratory quinone was Q-10. The G+C content of the genomic DNA was 63.5 %. Based on the present taxonomic characterization, strain 0127_4T represents a novel species of a new genus, Terricaulis silvestris gen. nov., sp. nov. The type strain of Terricaulis silvestris is 0127_4T (=DSM 104635T=CECT 9243T).

Chitinophaga fulva sp. nov., isolated from forest soil

2021 ◽  
Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim
Keyword(s):  
Forest Soil ◽  
Type Species ◽  
Sequence Similarity ◽  
Mountain Forest ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Nacl Concentration

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and yellow-coloured bacterium designated strain G-6-1-13T was isolated from Gwanggyo mountain forest soil. Strain G-6-1-13T could grow at 15–40 °C (optimum, 20–32 °C), pH 4.5–10.5 (optimum, pH 6.0–9.0), at 2 % (w/v) NaCl concentration, and produced flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain G-6-1-13T formed a lineage within the genus Chitinophaga that was distinct from other species of the genus. Closest member was Chitinophaga varians 10–7 W-9003T (98.6 % sequence similarity) followed by C. eiseniae DSM 22224T (98.4 %), C. qingshengii JN246T (97.6 %) and C. terrae KP01T (97.4%). The major cellular fatty acids were iso-C15 : 0, C16 : 1  ω5c, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω6c). MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content of strain G-6-1-13T was 48.7 mol%. Average nucleotide identity and in silico DNA–DNA hybridization were below the species threshold. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characterization, G-6-1-13T represents a novel species in the genus Chitinophaga , for which the name Chitinophaga fulva sp. nov. is proposed. The type strain is G-6-1-13T (=KACC 21624T=NBRC 114361T).

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