Integrated metagenomics and metabolomics reveal the dynamic mechanism in the rhizosphere soil of <i>Morus alba</i> L. and <i>Fraxinus mandshurica</i> Rupr. with <i>Inonotus hispidus</i>

<i>Inonotus hispidus</i> is a medicinal fungus that grows on <i>Morus alba</i> L., <i>Fraxinus mandshurica</i> Rupr., and <i>Ziziphus jujuba</i> Mill. However, there have been no reports on the comparative study of microbial diversity and metabolites in the rhizosphere soil of different tree species, specifically <i>M. alba</i> and <i>F. mandshurica</i>, growing with <i>I. hispidus</i>. Therefore, this study conducts a multi-omics joint analysis utilizing metagenomics and metabolomics to explore the differences in the synergistic mechanisms between different hosts of <i>I. hispidus</i>. Using metagenomics technology, a total of 177 phyla and 2,651 genera were identified as significantly different. At both the phylum and genus levels, Actinomycetota and Pseudomonadota as well as <i>Solirubrobacter</i> and <i>Bradyrhizobium</i> emerged as the predominant phyla and genera, respectively. In the Kyoto Encyclopedia of Genes and Genomes database, carbohydrate and amino acid metabolisms were identified as the primary metabolic pathways. Differential analysis of these metabolic pathways revealed that glucokinase and pyruvate kinase were downregulated. Additionally, metabolomics analysis identified 558 differential metabolites, with tyrosine metabolism being the foremost metabolic pathway involved. This pathway included five differential metabolites, among which salidroside, 3,4-dihydroxyphenylpropanoate, rosmarinate, and homovanillate were significantly upregulated in <i>M. alba</i> in association with <i>I. hispidus</i>. Furthermore, correlation analysis indicated that <i>Enhydrobacter</i> was positively correlated with 10 differential metabolites, while <i>Gaiella</i>, <i>Haladaptatus</i>, <i>Jiangella</i>, and <i>Prauserella</i> showed negative correlations. This study lays a solid foundation for elucidating the interactions between <i>I. hispidus</i> and its hosts, as well as for the effective utilization of <i>I. hispidus</i> resources across different tree species.IMPORTANCE<i>Inonotus hispidus</i>, which is traditionally recognized as the authentic source of the medicinal fungus, primarily grows on <i>Morus alba</i> L. It is commonly found in ancient regions along the Yellow River, including Linqing, Xiajin, and Wudi in Shandong, as well as Chengde in Hebei Province and Aksu in Xinjiang. In traditional Chinese medicine, it is known as "Sanghuang" and has a long history of medicinal use. In addition to <i>M. alba</i>, <i>I. hispidus</i> also grows on other broad-leaved species, such as <i>Ulmus macrocarpa</i>, <i>Acer truncatum</i>, and <i>Fraxinus mandshurica</i>. The lack of fundamental research on its multi-host and -source diversity has hindered its industrial development and medicinal value. Consequently, this study employs metagenomics and metabolomics to investigate the rhizosphere soil microbial diversity and differential metabolites associated with the different host plants of <i>I. hispidus</i>, specifically <i>M. alba</i> and <i>F. mandshurica</i>, with the aim of providing a reference for its resource conservation and development.