Novosphingobium silvae sp. nov., isolated from subtropical forest soil

Feng, Guang-Da; Chen, Wen-Di; Zhang, Jun; Wang, Yonghong; Liu, Yang; Yang, Zhihui; Zhu, Honghui

doi:10.1099/ijsem.0.004115

Cited by 7 publications

(2 citation statements)

References 36 publications

(37 reference statements)

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“…Members of genus Novosphingobium are characterized as Gram-negative, rod-shaped, non-spore-forming and aerobic bacteria. Species of the genus Novosphingobium have been isolated from various habitats, including soil, seawater, sediment, activated sludge, oil-contaminated soil and hexachlorocyclohexane-contaminated soil [3][4][5][6][7], while several species of the genus have been isolated from rhizosphere and plants including Novosphingobium rhizosphaerae, Novosphingobium pokkalii, Novosphingobium arabidopsis, Novosphingobium oryzae, Novosphingobium gossypii, Novosphingobium endophyticum and Novosphingobium fluoreni [8][9][10][11][12][13][14]. During a study of microbial diversity and plant growth-promoting endophytic bacteria in Thailand, strain Sx8-5 T was isolated from stem of peacock ginger (Kaempferia marginata Carey) and characterized using polyphasic analysis, including phenotypic characteristics, ubiquinone, cellular fatty acid, polar lipid and genomic comparisons.…”

Section: Introductionmentioning

confidence: 99%

Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey

Sitlaothaworn

Yukphan

Budsabun

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming and yellow-pigment-producing bacterium, designated as Sx8-5T, was isolated from stem tissue of Kaempferia marginata Carey in Kanchanaburi Province, Thailand. The strain exhibited tricalcium phosphate solubilizing activity. Its taxonomic position was investigated using a polyphasic approach. Sx8-5T grew at 25–37 °C (optimum 30 °C), pH 6–9 (optimum 7) and with 0 and 1% NaCl (optimum 0 %). According to the 16S rRNA gene phylogeny, Sx8-5T represents a member of genus Novosphingobium and shared the highest sequence similarities to Novosphingobium barchaimii LL02T of 99.4 % and shared sequence similarities with other species of the genus Novosphingobium of less than 99.4 %. The whole-genome size was 5.7 Mb, comprised of one contig, with a DNA G+C content of 66 %. The average nucleotide identity using BLASTn (ANIb) or MUMMER (ANIm) values for whole genome comparisons between Sx8-5T and Novosphingobium barchaimii LL02T and six closely related type strains were 72.33–82.14 % and 83.82–87.38 %, respectively, and the digital DNA–DNA hybridization (dDDH) values ranged from 21.0 to 28.6% when compared with the type strains of the members of the genus Novosphingobium . Major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), respectively. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unidentified phospholipids and unidentified polar lipids. The major isoprenoid quinone was Q-10. According to results obtained using a polyphasic approach, Sx8-5T represents a novel species of the genus Novosphingobium , the name Novosphingobium kaempferiae sp. nov. is proposed. The type strain is Sx8-5T (=JCM 35076T =TBRC 15600T).

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Section: Introductionmentioning

confidence: 99%

Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey

Sitlaothaworn

Yukphan

Budsabun

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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“…At present, 56 species names of the genus Novosphingobium have been validly published, and the type species is Novosphingobium capsulatum (https://lpsn.dsmz.de/genus/novosphingobium) [4]. The species of Novosphingobium were isolated from various environments, such as soil [5][6][7][8][9], water [10][11][12], animals [13], plants [14][15][16][17][18] and sediments [19]. Novosphingobium species are aerobic, rod-shaped, Gram-stain-negative, yellow-pigmented or whitish-brown and take ubiquinone-10 (Q-10) as their primary isoprenoid quinone, sphingoglycolipid as their distinctive polar lipid, and 2-hydroxymyristic acid (C 14 : 0 2OH) as their major OPEN ACCESS 2-hydroxy fatty acid [1].…”

Section: Introductionmentioning

confidence: 99%

Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant

Lü

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus Novosphingobium . The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of Novosphingobium species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1 ω7c, C18 : 0, C16 : 1 ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of Novosphingobium , for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.

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Erythrobacteraceae

Xu,

Zhang

2023

Bergey's Manual of Systematics of Archaea and Bacteria

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E.ry.thro.bac.te.ra'ceae. N.L. masc. n. Erythrobacter , type genus of the family; L. fem. pl. n. suff. ‐ aceae , ending to denote a family; N.L. fem. pl. n. Erythrobacteraceae , the Erythrobacter family. Pseudomonadota / Alphaproteobacteria / Sphingomonadales / Erythrobacteraceae Cells are Gram‐stain‐negative rods, cocci, or ellipsoids. Several species are motile. Aerobic or facultatively anaerobic. The dominant respiratory quinone is ubiquinone‐10 (Q‐10). The major polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and glycosphingolipid (SGL). The cellular fatty acid profiles are dominated by unsaturated fatty acids including heptadecenoic acid (C 17 : 1 ) and octadecenoic acid (C 18 : 1 ). The family forms a monophyletic cluster in neighbor‐joining phylogenetic analyses of the 16S rRNA gene, while its genus discriminations are based on phylogenomic and genomic similarity analysis. It currently accommodates 19 genera. Members of the family Erythrobacteraceae were isolated from various habitats, including marine, terrestrial and freshwater environments. DNA G + C content (mol%) : 54–74 (by genome, HPLC or T m ). Type genus : Erythrobacter Shiba and Simidu 1982 VP .

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Novosphingobium silvae sp. nov., isolated from subtropical forest soil

Cited by 7 publications

References 36 publications

Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey

Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey

Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant

Erythrobacteraceae

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