Plant developmental stage drives the assembly and functional adaptability of endophytic microbial communities

The results showed that plant developmental stage explained the large variation in endophytic bacterial and fungal communities in <i>A. muelleri</i> and that multiple microbial attributes (e.g., α, β-diversity, community composition, and bacterial and fungal ecological networks) are driven by the developmental state of <i>A. muelleri</i>. Metagenomic analyses further indicated that the four stages after rooting have higher microbial functional diversity. Microbial functional genes involved in cell wall/membrane/envelope biogenesis, inorganic ion transport and metabolism, and carbon degradation were abundant in <i>A. muelleri</i> seeds from Stage 1 to Stage 3 (before rooting). From Stage 4 to Stage 7 (after rooting), microbial functional genes involved in the carbon, nitrogen and phosphorus cycles, starch and sucrose metabolism, and energy production and conversion were more abundant. Coincidentally, more abundant Proteobacteria, and Basidiomycota taxa related to carbon degradation were found in stages 1-3, while more <i>Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium</i> and <i>Stenotrophomonas</i> taxa associated with nitrogen cycling and plant growth promotion were observed in stages 4-7. These findings have greatly improved our basic understanding of the assembly and functional adaptability of the endophytic microbiome during <i>A. muelleri</i> plant development and are helpful for the mining, development and utilization of functional microbial resources.