Dyadobacter subterraneus sp. nov., isolated from hydrocarbon-polluted groundwater from an oil refinery in Hungary

Szabó, István; Al-Omari, Jafar; Szerdahelyi, Gábor Soma; Radó, Júlia; Kaszab, Edit; Táncsics, Andräs; Szoboszlay, Sándor; Kriszt, Balázs

doi:10.1099/ijsem.0.004916

Cited by 8 publications

(5 citation statements)

References 31 publications

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“…The sole isoprenoid quinone detected in strain U1 T was MK-7, which is in good agreement with the results that members of the genus Dyadobacter contain MK-7 as the major isoprenoid quinone [2–11, 13, 14]. The major cellular fatty acids (>5 % of the total fatty acids) of strain U1 T were iso-C 15 : 0 (20.0 %), C 16 : 0 (10.0 %), C 16 : 1 ω5 c (8.6 %) and summed feature 3 (comprising C 16 : 1 ω 6 c and/or C 16 : 1 ω7 c , 43.6 %).…”

Section: Chemotaxonomic Analysissupporting

confidence: 88%

“…The genome size of strain U1 T was 7 688 kb, and 6419 total genes, 6330 coding sequences (CDSs), 39 tRNA genes for 20 amino acid synthesis, and four complete rRNA operons (16S, 23S, 5S) were identified. The DNA G+C content of strain U1 T based on the genome sequence was 45.5 mol%, which was within the range (40.0–51.3 mol%) of the G+C contents of Dyadobacter species [1–14]. The general genomic features of strain U1 T were compared with those of closely related reference strains ().…”

Section: Genome Features and Phylogeny Of Whole Genome Sequencesmentioning

confidence: 93%

“…Cells of the genus Dyadobacter produce mucoid and yellow-coloured flexirubin-type pigments. Members of the genus Dyadobacter have been isolated from a diverse range of environments, including soil (arctic, forest, rose rhizosphere, and ginseng field) [2][3][4][5][6][7], plants (maize root and surface-sterilized Zea mays stems) [1,8], sediment (subsurface, lake, and sewage) [9][10][11], water (fresh and hydrocarbon-polluted ground water) [12,13], and seawater [14]. During an investigation of bacteria associated with plastic biodegradation, we isolated a putative novel species of the genus Dyadobacter, designated strain U1 T , from a plastic waste landfill site and taxonomically characterized the strain using a polyphasic approach.…”

Section: Introductionmentioning

confidence: 99%

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Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil

Kim

Kyeong

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10–37 °C (optimum, 25–30 °C) and pH 6.0–9.0 (optimum, pH 8.0), and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Strain U1T contained iso-C15 : 0, C16 : 0, C16 : 1 ω5c and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus Dyadobacter . Strain U1T has the highest 16S rRNA sequence similarity to Dyadobacter bucti QTA69T (97.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain U1T and D. bucti QTA69T were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).

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Section: Chemotaxonomic Analysissupporting

confidence: 88%

Section: Genome Features and Phylogeny Of Whole Genome Sequencesmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil

Kim

Kyeong

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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“…Leaf182. The macrobrevin is the recently described antibiotic derived from trans-acyltransferase polyketide synthase [30]; one gene cluster encoding T1PKS, which is an enzyme complexes that produce polyketides [31]; one gene cluster encoding terpene, which relates to biosynthesis for hydrocarbon groups that contained C 5 H 8 as the basic construct [32]; one RiPP-like cluster, which is a cluster consist of peptides that produced by ribosome [33]; and one gene cluster encoding NAGGN that is involved in adaptation to osmotic stress [34]. The genomic region of the BGC, showing details such as smBCG type, most similar known cluster and the numbers of core biosynthetic genes and additional biosynthetic genes, is provided in Table S3.…”

Section: Genome Featuresmentioning

confidence: 99%

Roseibium limicola sp. nov., isolated from tidal mudflat

Weerawongwiwat

Kim

Yoon

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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A novel bacterium, designated strain CAU 1637T, was isolated from a tidal mudflat. Cells of strain CAU 1637T were Gram-stain-negative, aerobic, motile with single flagellum and rod-shaped. The optimum conditions for growth were observed at 30 °C, pH 6.0 and in the presence of 2 % (w/v) NaCl. The respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1637T was closely related to the genus Roseibium , with the highest similarity to Roseibium aestuarii NRBC 112946T (97.4 %), followed by Roseibium hamelinense NRBC 16783T (96.8 %), Roseibium aquae JCM 19310T (96.4 %), Roseibium sediminis KCTC 52373T (95.8 %) and Roseibium denhamense JCM 10543T (95.3 %). The predominant cellular fatty acids were C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity values between the novel isolate and related strains ranged from 71.0 to 76.4 %, and the DNA−DNA hybridization values ranged from 19.3 to 20.3 %. The G+C content was 58.4 mol% and the whole-genome size was 4.6 Mb, which included 17 contigs and 3931 protein-coding genes. Based on the taxonomic data, strain CAU 1637T represents a novel species of the genus Roseibium , for which the name Roseibium limicola sp. nov. is proposed. The type strain is CAU 1637T (=KCTC 82429T=MCCC 1K06080T).

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“…The DNA G+C content approximately ranges from 40.0 to 51.3 %. At the time of writing, the genus Dyadobacter comprises 24 species with validly published names (https://lpsn.dsmz.de/genus/ dyadobacter) originally isolated from various natural environments including plant materials [1,3,4], soil [2,[5][6][7][8][9][10][11][12], water [13][14][15], desert sand [16], sediment [17][18][19][20] and glacial ice [21,22].…”

Section: Introductionmentioning

confidence: 99%

Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov., and Dyadobacter fanqingshengii sp. nov., isolated from soil of the Qinghai-Tibetan Plateau

Gui

Cheng

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Six novel bacterial strains, designated CY22T, CY357, LJ419T, LJ53, CY399T and CY107 were isolated from soil samples collected from the Qinghai–Tibetan Plateau, PR China. Cells were aerobic, rod-shaped, yellow-pigmented, catalase- and oxidase-positive, Gram-stain-negative, non-motile and non-spore-forming. All strains were psychrotolerant and could grow at 0 °C. The results of phylogenetic and phylogenomic analyses, based on 16S rRNA gene sequences and core genomic genes, indicated that the three strain pairs (CY22T/CY357, LJ419T/LJ53 and CY399T/CY107) were closely related to members of the genus Dyadobacter and clustered tightly with two species with validly published names, Dyadobacter alkalitolerans 12116T and Dyadobacter psychrophilus BZ26T. Values of digital DNA–DNA hybridization between genome sequences of the isolates and other strains from the GenBank database in the genus Dyadobacter were far below the 70.0 % threshold. The genomic DNA G+C content of these six strains ranged from 45.2 to 45.8 %. The major cellular fatty acids of all six strains were iso-C15 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). MK-7 was the only respiratory quinone, and phosphatidylethanolamine was the predominant polar lipid for strains CY22T, LJ419T and CY399T. On the basis of the phenotypic, phylogenetic and genomic evidence presented, these six strains represent three novel members of the genus Dyadobacter , for which the names Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov. and Dyadobacter fanqingshengii sp. nov. are proposed. The type strains are CY22T (= GDMCC 1.3045T = KCTC 92299T), LJ419T (= GDMCC 1.2872T = JCM 33794T) and CY399T (= GDMCC 1.3052T = KCTC 92306T), respectively.

show abstract

Dyadobacter subterraneus sp. nov., isolated from hydrocarbon-polluted groundwater from an oil refinery in Hungary

Cited by 8 publications

References 31 publications

Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil

Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil

Roseibium limicola sp. nov., isolated from tidal mudflat

Dyadobacter chenhuakuii sp. nov., Dyadobacter chenwenxiniae sp. nov., and Dyadobacter fanqingshengii sp. nov., isolated from soil of the Qinghai-Tibetan Plateau

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