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<p>Three endophytic <i>Sphingobium</i> strains, WW5<sup>T</sup>, 11R-BB, and HT1-2<sup>T</sup>, were isolated from <i>Salix sitchensis</i> stems, <i>Populus trichocarpa</i> roots, and <i>Pluchea carolinensis</i> shoots, respectively, growing on nutrient-limited rock substrates undergoing primary succession. Cells are Gram-negative, strictly aerobic, rod-shaped, catalase-positive, and motile by a single flagellum. Colonies formed within 2–3&#xa0;days on nitrogen-limited combined carbon medium (NLCCM) and mannitol-glutamate/Luria (MGL) media. Growth occurred at 25–35&#xa0;°C (optimum 30–32.5&#xa0;°C), pH 5–8, and up to 2% NaCl for strains WW5<sup>T</sup> and 11R-BB and 3% for strain HT1-2<sup>T</sup>. Cellular fatty acid profiles were dominated by C<sub>18:1</sub> ω7c and C<sub>16:1</sub> ω7c. The predominant respiratory quinone was ubiquinone-10, and the principal polar lipids were phosphatidylethanolamine, sphingoglycolipids, and phosphatidylglycerol. Hybrid genome assemblies ranged from 5.49–5.72&#xa0;Mb with 64.0–64.2&#xa0;mol% GC, and 5404–5635 coding sequences. The 16S rRNA gene sequences of strains WW5<sup>T</sup>, 11R-BB, and HT-12<sup>T</sup> showed 99.5–99.9% identity to <i>S. yanoikuyae</i> JCM 7371<sup>T</sup>, but formed a separate lineage in neighbor-joining, maximum-likelihood, and maximum-parsimony trees. Pairwise digital DNA–DNA hybridization (dDDH; 99.8%), average nucleotide identity based on BLAST (ANIb; 99.98%), and alignment fraction (AF; 99.5%) indicate that strains WW5<sup>T</sup> and 11R-BB are conspecific and represent the same subspecies. Strain HT1-2<sup>T</sup> showed lower relatedness (70% dDDH; 95.05–95.31% ANIb; 76–79% AF) but was more closely related to strains WW5<sup>T</sup> and 11R-BB than to <i>S. yanoikuyae</i> JCM 7371<sup>T</sup>, supporting its placement as a subspecies within the same species as strains WW5<sup>T</sup> and 11R-BB. Based on phylogenomic, genomic, and phenotypic evidence, these strains constitute a novel species, <i>Sphingobium salicis</i> sp. nov., with the strain WW5<sup>T</sup> (DSM 120182<sup>T</sup>, NCCB 101075<sup>T</sup>) designated as the type strain.</p>

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Sphingobium salicis sp. nov., a novel endophyte with two subspecies from pioneer plants growing on primary substrates

  • 期刊论文

  • 发表日期：

    2025年12月19日

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  • Robert J. Tournay,
  • John L. Freeman,
  • Misha Levish,
  • Douglas Baker,
  • Andrea Firrincieli,
  • Sharon L. Doty

摘要

Three endophytic Sphingobium strains, WW5T, 11R-BB, and HT1-2T, were isolated from Salix sitchensis stems, Populus trichocarpa roots, and Pluchea carolinensis shoots, respectively, growing on nutrient-limited rock substrates undergoing primary succession. Cells are Gram-negative, strictly aerobic, rod-shaped, catalase-positive, and motile by a single flagellum. Colonies formed within 2–3 days on nitrogen-limited combined carbon medium (NLCCM) and mannitol-glutamate/Luria (MGL) media. Growth occurred at 25–35 °C (optimum 30–32.5 °C), pH 5–8, and up to 2% NaCl for strains WW5T and 11R-BB and 3% for strain HT1-2T. Cellular fatty acid profiles were dominated by C18:1 ω7c and C16:1 ω7c. The predominant respiratory quinone was ubiquinone-10, and the principal polar lipids were phosphatidylethanolamine, sphingoglycolipids, and phosphatidylglycerol. Hybrid genome assemblies ranged from 5.49–5.72 Mb with 64.0–64.2 mol% GC, and 5404–5635 coding sequences. The 16S rRNA gene sequences of strains WW5T, 11R-BB, and HT-12T showed 99.5–99.9% identity to S. yanoikuyae JCM 7371T, but formed a separate lineage in neighbor-joining, maximum-likelihood, and maximum-parsimony trees. Pairwise digital DNA–DNA hybridization (dDDH; 99.8%), average nucleotide identity based on BLAST (ANIb; 99.98%), and alignment fraction (AF; 99.5%) indicate that strains WW5T and 11R-BB are conspecific and represent the same subspecies. Strain HT1-2T showed lower relatedness (70% dDDH; 95.05–95.31% ANIb; 76–79% AF) but was more closely related to strains WW5T and 11R-BB than to S. yanoikuyae JCM 7371T, supporting its placement as a subspecies within the same species as strains WW5T and 11R-BB. Based on phylogenomic, genomic, and phenotypic evidence, these strains constitute a novel species, Sphingobium salicis sp. nov., with the strain WW5T (DSM 120182T, NCCB 101075T) designated as the type strain.