Pontibacter ramchanderi sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2829-2834 ◽  
Author(s):  
Amit Kumar Singh ◽  
Nidhi Garg ◽  
Naseer Sangwan ◽  
Vivek Negi ◽  
Roshan Kumar ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Soil Sediment ◽  
Genotypic Characteristics ◽  
Sequence Similarities

A Gram-stain-negative, motile, red pigmented, rod-shaped bacterium, designated strain LP43T, was isolated from hexachlorocyclohexane (HCH)-contaminated soil sediment (Lucknow, India). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate formed a cluster with the genus Pontibacter in the phylum Bacteroidetes with sequence similarities ranging from 92.9 to 97.0 % with species of the genus Pontibacter . The DNA G+C content of strain LP43T was 59.1 mol%. The polar lipid profile of strain LP43T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, unknown aminolipids and unknown polar lipids. Strain LP43T contained MK-7 as the predominant menaquinone and sym-homospermidine as the major polyamine. The major cellular fatty acids of strain LP43T were, iso-C15 : 0 (15.74 %), iso-C15 : 0 3-OH (7.57 %), iso-C17 : 0 3-OH (7.32 %), summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B) (31.22 %) and summed feature 8 (C18 : 1ω7c/ C18 : 1ω6c) (7.60 %). Based on the results of DNA–DNA hybridization and phenotypic and genotypic characteristics, strain LP43T represents a novel species of the genus Pontibacter , for which the name Pontibacter ramchanderi is proposed. The type strain is LP43T ( = CCM 8406T = MCC 2019T).

scholarly journals Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 562-569 ◽  
Author(s):  
Hong Cheng ◽  
Shun Zhang ◽  
Ying-Yi Huo ◽  
Xia-Wei Jiang ◽  
Xin-Qi Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Hydrolysis Of ◽  
Sequence Similarities

A taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus Gilvimarinus . ‘Gilvimarinus agarilyticus’ KCTC 23325 and Gilvimarinus chinensis QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus Gilvimarinus , for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus Gilvimarinus is also presented.

scholarly journals Novosphingobium ovatum sp. nov., isolated from a freshwater mesocosm

2020 ◽  
Vol 70 (10) ◽  
pp. 5243-5254 ◽  
Author(s):  
Wen-Ming Chen ◽  
Cheng-Ye Cai ◽  
Der-Shyan Sheu ◽  
Jyh-Ming Tsai ◽  
Shih-Yi Sheu
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph

A bacterial strain, designated FSY-8T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20–40 °C (optimum, 30–37 °C) and pH 5–7 (optimum, pH 6) and in the presence of 0–0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8T were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8T formed a phylogenetic lineage in the genus Novosphingobium . Strain FSY-8T showed 71.6–77.2 % average nucleotide identity and 19.9–22.8 % digital DNA–DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8T should be classified in a novel species of the genus Novosphingobium , for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8T (=BCRC 81051T=LMG 30053T=KCTC 52812T).

scholarly journals Gynuella sunshinyii gen. nov., sp. nov., an antifungal rhizobacterium isolated from a halophyte, Carex scabrifolia Steud

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1038-1043 ◽  
Author(s):  
Eu Jin Chung ◽  
Jeong Ae Park ◽  
Che Ok Jeon ◽  
Young Ryun Chung
Keyword(s):  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Sequence Similarities

An antifungal bacterial strain, designated YC6258T, was isolated from the rhizosphere of a halophyte (Carex scabrifolia Steud.) growing in a tidal flat area of Namhae Island, Korea. Cells of the strain were Gram-stain-negative, facultatively anaerobic, moderately halophilic, rod-shaped and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YC6258T formed a phyletic lineage distinct from members of the most closely related genera, Saccharospirillum and Reinekea, with less than 91.2 % sequence similarities. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and Summed feature 3 (C16 : 1ω7c/ C16 : 1ω6c). The quinone system of strain YC6258T consisted mainly of ubiquinone Q-8. The polar lipid profile exhibited phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unknown lipids. The DNA G+C content was 48.9 mol%. Based on the phylogenetic and phenotypic characteristics, strain YC6258T should be classified as a representative of a novel species in a novel genus for which the name Gynuella sunshinyii gen. nov., sp. nov. is proposed. The type strain is YC6258T (KCCM 43015T = NBRC 109345T).

scholarly journals Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov.

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1697-1702 ◽  
Author(s):  
Guang-Da Feng ◽  
Song-Zhen Yang ◽  
Yong-Hong Wang ◽  
Xiu-Xiu Zhang ◽  
Guo-Zhen Zhao ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Lead Zinc ◽  
Pr China ◽  
Sequence Similarities

A Gram-stain-negative bacterial strain, designated 9NM-8T, was isolated from an abandoned lead-zinc ore in Mei county, Meizhou, Guangdong province, PR China. The isolate was orange-pigmented, aerobic, oxidase- and catalase-positive, motile with lophotrichous flagella and rod-shaped. Strain 9NM-8T grew optimally at pH 7.0 and 30 °C and in the absence of NaCl on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 9NM-8T belongs to the genus Sphingomonas , with highest sequence similarities to Sphingomonas azotifigens KACC 14484T (96.1 %), Sphingomonas trueperi DSM 7225T (96.0 %) and Sphingomonas pituitosa DSM 13101T (95.6 %). Strain 9NM-8T contained Q-10 as the predominant ubiquinone. The major fatty acids included C18 : 1ω7c, C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and 11-methyl C18 : 1ω7c. The DNA G+C content was 69.6±1.3 mol%. The major component in the polyamine pattern was sym-homospermidine and the polar lipid profile contained sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and two unidentified phospholipids. Based on comparative analysis of physiological, chemotaxonomic and phylogenetic characteristics, strain 9NM-8T should be considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas guangdongensis sp. nov. is proposed. The type strain is 9NM-8T ( = GIMCC 1.653T = CGMCC 1.12672T = DSM 27570T).

scholarly journals Ornithinicoccus soli sp. nov., isolated from farmland soil

2020 ◽  
Vol 70 (3) ◽  
pp. 1793-1799 ◽  
Author(s):  
Wan-Kui Jiang ◽  
Qin-Qin Gao ◽  
Lu Zhang ◽  
Gao-Jie Sun ◽  
Ming-Liang Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Farmland Soil ◽  
Diamino Acid

A Gram-stain-positive, aerobic, non-motile and coccoid-shaped bacterium, designated XNB-1T, was isolated from farmland soil in Taian, Shandong province, China. Strain XNB-1T contained iso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn←Gly(1, 2)←d-Glu. The polar lipid profile of strain XNB-1T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone of strain XNB-1T was MK-8(H4) and the DNA G+C content was 70.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XNB-1T belonged to the genus Ornithinicoccus , and shared the highest similarity with Ornithinicoccus hortensis HKI 0125T (96.0 %), followed by Ornithinicoccus halotolerans EGI 80423T (95.5 %). Genome-based analysis of average nucleotide identity of strain XNB-1T with O. hortensis HKI 0125T and O. halotolerans EGI 80423T yielded values of 73.1 and 73.3 %, respectively, while the digital DNA–DNA hybridization values were 19.5 and 19.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain XNB-1T is considered to represent a novel species of the genus Ornithinicoccus , for which the name Ornithinicoccus soli sp. nov. is proposed. The type strain is XNB-1T (=CCTCC AB 2019099T=KCTC 49259T).

Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 723-728 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Fazlurrahman Khan ◽  
Miroslava Sedlackova ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Dump Site ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A yellow-pigmented bacterial strain, designated LL01T, was isolated from hexachlorocyclohexane (HCH)-contaminated soil at Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL01T occupied a distinct phylogenetic position in the Sphingobium cluster, showing highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.5 %). The DNA G+C content of strain LL01T was 66.1 mol%. The predominant respiratory pigment was ubiquinone Q-10. The polar lipid profile of strain LL01T also corresponded to those reported for other Sphingobium species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipids), supporting its identification as a member of the genus Sphingobium . Spermidine was the major polyamine observed. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain LL01T from closely related species of the genus Sphingobium . Therefore, strain LL01T represents a novel species of the genus Sphingobium , for which the name Sphingobium czechense sp. nov. is proposed (type strain LL01T = CCM 7979T = DSM 25410T).

Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1692-1697 ◽  
Author(s):  
Yasuko Yoneda ◽  
Takashi Yoshida ◽  
Satoshi Kawaichi ◽  
Takashi Daifuku ◽  
Keiji Takabe ◽  
...  
Keyword(s):  
Elemental Sulfur ◽  
Hot Spring ◽  
Novel Species ◽  
Ferric Citrate ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarities

A novel anaerobic, Fe(III)-reducing, hydrogenogenic, carboxydotrophic bacterium, designated strain Ug1T, was isolated from a volcanic acidic hot spring in southern Kyushu Island, Japan. Cells of the isolate were rod-shaped (1.0–3.0 µm long) and motile due to peritrichous flagella. Strain Ug1T grew chemolithoautotrophically on CO (100 % in the gas phase) with reduction of ferric citrate, amorphous iron (III) oxide, 9,10-anthraquinone 2,6-disulfonate, thiosulfate or elemental sulfur. No carboxydotrophic growth occurred with sulfate, sulfite, nitrate or fumarate as electron acceptor. During growth on CO, H2 and CO2 were produced. Growth occurred on molecular hydrogen as an energy source and carbon dioxide as a sole carbon source. Growth was observed on various organic compounds under an N2 atmosphere with the reduction of ferric iron. The temperature range for carboxydotrophic growth was 50–70 °C, with an optimum at 65 °C. The pH25 °C range for growth was 4.6–8.6, with an optimum between 6.0 and 6.5. The doubling time under optimum conditions using CO with ferric citrate was 1.5 h. The DNA G+C content was 42.2 mol%. Analysis of 16S rRNA gene sequences demonstrated that this strain belongs to the thermophilic carboxydotrophic bacterial genus Carboxydothermus , with sequence similarities of 94.1–96.6 % to members of this genus. The isolate can be distinguished from other members of the genus Carboxydothermus by its ability to grow with elemental sulfur or thiosulfate coupled to CO oxidation. On the basis of phylogenetic analysis and unique physiological features, the isolate represents a novel species of the genus Carboxydothermus for which the name Carboxydothermus pertinax sp. nov. is proposed; the type strain of the novel species is Ug1T ( = DSM 23698T = NBRC 107576T).

Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Antonio Castellano-Hinojosa ◽  
David Correa-Galeote ◽  
Martha-Helena Ramírez-Bahena ◽  
Germán Tortosa ◽  
Jesús González-López ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to ‘ A. deltaense ’ YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium . Whole genome average nucleotide identity and digital DNA–DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10–42 °C, pH 5.0–10.0 and with 0.0–0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium , for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).

Streptomyces graminilatus sp. nov., isolated from bamboo litter

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 528-532 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Sequence Similarities

A Gram-stain-positive, novel actinobacterium, designated strain JL-6T, was isolated from the litter of a bamboo (Sasa borealis) forest in Damyang, Korea. Strain JL-6T had white‐grey, smooth, cylindrical spores that were borne in straight, long spore-chains. The novel strain grew aerobically at 15–28 °C (optimum, 28 °C), pH 4.0–8.0 (optimum, pH 5.5) and with 0–1.5 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. The predominant menaquinones were MK-9(H6) and MK-9(H8). Whole-cell hydrolysates mainly contained glucose and ribose. Phosphatidylinositol and phosphatidylcholine were the diagnostic phospholipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JL-6T belonged to the genus Streptomyces with sequence similarities ranging from 97.3 % to 98.3 %. However, DNA–DNA hybridization between JL-6T and the closest related strain, Streptomyces turgidiscabies , ATCC 700248T and other closely related species in the genus Streptomyces showed <50 % relatedness. Based on these observations, strain JL-6T is proposed to represent a novel species of the genus Streptomyces , for which the name Streptomyces graminilatus sp. nov. is proposed. The type strain is JL-6T ( = KACC 16470T = NBRC 108882T).

Methylobacterium tarhaniae sp. nov., isolated from arid soil

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2823-2828 ◽  
Author(s):  
Aysel Veyisoglu ◽  
Mustafa Camas ◽  
Demet Tatar ◽  
Kiymet Guven ◽  
Anil Sazak ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Arid Soil ◽  
Link Type ◽  
Hybridization Data

A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211T, isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211T belonged to the genus Methylobacterium . Strain N4211T was most closely related to Methylobacterium aquaticum GR16T (98.56 %), Methylobacterium platani PMB02T (97.95 %) and Methylobacterium variabile GR3T (97.2 %), and the phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C18 : 1 cis11/t9/t6). The DNA G+C content was 67.3 mol%. DNA–DNA relatedness of strain N4211T and the most closely related strains M. aquaticum DSM 16371T and M. platani KCTC 12901T were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA–DNA hybridization data, strain N4211T is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium tarhaniae sp. nov. is proposed. The type strain is N4211T( = KCTC 23615T = DSM 25844T).

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