Microbial assembly among plant parts of a tropical tree in different habitats and seasons

Microorganisms are exhibited in every environment, but their role in the ecosystem and host association remains to be understood. Microbiome research highlights environmental filtering as a factor shaping microbial communities in terrestrial ecosystems. We analyzed bacterial and fungal communities in flowers, leaves, branches, trunks, roots, and soil of wild and rice field-grown <i>Bombax ceiba</i> under different seasons using the recent advanced techniques of 16S rRNA and ITS rRNA amplicon pyrosequencing, respectively. Our findings revealed variation in microbial communities across different plant parts and heights (flower, leaf, branch, trunk, roots, and soil). NMDS and hierarchical clustering (Bray-Curtis dis) analysis revealed that bacterial and fungal communities related to endophytic (within plant tissue) and epiphytic (external plant surfaces) niches of above and below-ground parts significantly differed due to seasonal variation in rice and wild habitats. Moreover, seasonal variation significantly affected the number of shared OTUs and bacterial and fungal taxa across all plant parts in both habitats. The spring season significantly influenced microbial diversity, assembly, and correlation networks in plant parts, with the most potent effects in the rice field compared to the wild habitat of <i>Bombax ceiba</i>, influencing flowering and boosting Firmicutes abundance. Wild habitats possessed higher functional diversity than rice-grown fields in spring and autumn across all plant parts, indicating their strong relation with different environments. The outcomes of the present study revealed that seasonal changes across various habitats dynamically shape the plant microbiome, suggesting distinct ecological roles (e.g., nutrient cycling, pathogen suppression, and stress tolerance) for bacterial and fungal communities in various niches.IMPORTANCEThis study shows that seasonal variation and habitat type (wild vs rice field) significantly influence the diversity, composition, and assembly of bacterial and fungal communities in different plant parts of <i>Bombax ceiba</i>. By analyzing both endophytic and epiphytic niches across above- and below-ground compartments, it reveals the spatial complexity of plant microbiomes. Wild habitats support greater stability to microbiome and their functions as compared with rice fields, particularly in spring, indicating that land-use practices affect microbiome structure and function. The study gives the details on how the compositions of microbiomes associated with plants change with season, which can impart insight into sustainable crop-management strategies, as well as conservation measures.