Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus

Zhang, Yongping; Peng, Xiaoya; Qin, Kun; Liu, Jia; Xu, Qiang; Niu, Jingjing; Zheng, Yufeng; Peng, Fang

doi:10.1099/ijsem.0.005103

Cited by 10 publications

(6 citation statements)

References 41 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%

“…Comparison of phenotype characteristics of strain U1 T and related type strains of the genus Dyadobacter Strains: 1, U1 T (this study); 2, D. bucti KCTC 72024 T[9]; 3, D. flavalbus NBRC 113854 T[10]; 4, D. alkalitolerans DSM 23607 T[3]; 5, D. psychrophilus DSM 22270 T ; 6, D. fermentans KACC 15354 T[1]. All strains are positive for the following characteristics: hydrolysis* of aesculin (w) and enzyme activity* of leucine arylamidase, alkaline phosphatase, valine arylamidase, acid phosphatase, αgalactosidase, αglucosidase, β-glucosidase, Nacetyl-β-glucosaminidase, αmannosidase, β-galactosidase, esterase (C4) (w) and esterase lipase (C8) (w).…”

mentioning

confidence: 98%

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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%

mentioning

confidence: 98%

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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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“…All tested microorganisms were acquired from China Center for Type Culture Collection (CCTCC), Wuhan, Hubei, China. The fungi were identified as described in 3.1, while bacteria were identified as described earlier ( Zhang et al., 2021 ). The culture mediums of the tested microorganisms were listed in Table S1 .…”

Section: Methodsmentioning

confidence: 99%

Identification and functional studies of microbial volatile organic compounds produced by Arctic flower yeasts

Niu

Li²,

Zhang³

et al. 2023

Front. Plant Sci.

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Microbial volatile organic compounds (mVOCs) can serve as a communication channel among microorganisms, insects and plants, making them important in ecosystem. In order to understand the possible role of mVOCs in Arctic ecology, the microbes in Arctic flowers and their mVOCs and effects on plants were investigated. This study aims to isolate different yeast species from the flowers of five Arctic plant species and further to explore the function of mVOCs emitted by these microbes to plant. It was found that the composition and amount of mVOCs produced by the isolated yeasts were considerably affected by changes in incubation temperature. When the incubation temperature rose, the species of alcohols, aldehydes, esters, organic acids, and ketones increased, but substances specific to low temperature decreased or disappeared. When yeasts were co-cultured with Arabidopsis thaliana without any direct contact, mVOCs produced by the isolated yeasts inhibited the seed germination of A. thaliana at low temperatures; however, the mVOCs promoted the chlorophyll content, fresh weight, root weight and flowering rate of Arabidopsis plants. Although the overall growth-promoting effect of yeast mVOCs was higher at 20°C than at 10°C, the growth-promoting effect on roots, flowers and chlorophyll was highest at 10°C. When cultured at 10°C, the mVOCs produced by Cystofilobasidium capitatum A37, Cryptococcus sp. D41, and Sporidiobolus salmonicolor D27 had the highest growth-promoting effects on the root, flowering rate and chlorophyll content of Arabidopsis, respectively. In the co-culture system, some new mVOCs were detected, such as hendecane, tetradecane, and 1-hexanol that have been proven to promote plant growth. In addition, mVOCs of the isolated Arctic yeasts could inhibit the growth of several microorganisms, especially filamentous fungi. It was the first time to prove that mVOCs produced by the isolated yeasts had varying effects on plant growth at different incubating temperatures, providing a reference for the interactions between microorganisms and plants and their possible responses to climate change in the Arctic area. Moreover, the characteristics of promoting plant growth and inhibiting microbial growth by mVOCs of Arctic yeasts would lay a foundation for potential applications in the future.

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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.

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Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus

Cited by 10 publications

References 41 publications

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

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

Identification and functional studies of microbial volatile organic compounds produced by Arctic flower yeasts

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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