Successful seed germination and seedling growth in orchids require an association with mycorrhizal fungi. An endophytic Fusarium fungal strain YZU 172038 exhibiting plant growth-promoting (PGP) ability was isolated from the roots of Spiranthes sinensis (Orchidaceae). The harboring endohyphal bacteria were detected in the hypha by SYTO-9 fluorescent nucleic acid staining, fluorescence in situ hybridization (FISH), and PCR amplification of the 16S rDNA gene’s region. Consequently, one endohyphal bacterium (EHB) – a strain YZSR384 was isolated and identified as Bacillus subtilis based on morphology, phylogenetic analysis, and genomic information. The results indicated that the strain YZSR384 could significantly promote the growth of rice roots and shoots similar to its host fungus. Its indole acetic acid (IAA) production reached a maximum of 23.361 μg/ml on the sixth day after inoculation. The genome annotation revealed several genes involved in PGP traits, including the clusters of genes encoding the IAA (trpABCDEFS), the siderophores (entABCE), and the dissolving phosphate (pstABCS and phoABDHPR). As an EHB, B. subtilis was first isolated from endophytic Fusarium acuminatum from S. sinensis.
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