Different assembly mechanisms between prokaryotic and fungal communities in grassland plants and soil

Microorganisms play pivotal roles in plant growth and health. However, it remains unclear whether distinct mechanisms govern the assembly of prokaryotic and fungal communities across plant compartments and soils in grasslands. Microbial communities in plant compartments (phyllosphere, leaf endosphere, rhizosphere and root endosphere) and bulk soil of multiple plants from different grasslands were investigated through amplicon sequencing of the 16S rRNA gene and ITS fragment. The results showed that the rhizosphere harbored the most diverse fungal communities, while the alpha diversities of prokaryotic communities did not exhibit a significant difference between the rhizosphere and bulk soil. Moreover, prokaryotic communities across different compartments were subjected to strong selection effects. For instance, there was strong phylogenetic turnover of prokaryotic communities from bulk soil or phyllosphere (two sources of leaf endophyte) to the leaf endosphere. Conversely, fungal communities were affected by strong stochastic effects. Fungi in plant compartments (especially the phyllosphere) were more impacted by geographical characteristics and their interactions with plant genotypes than prokaryotes. Additionally, strong homogeneous selections on the prokaryotes between the phyllosphere and rhizosphere highlighted similar adaptative mechanisms of prokaryotes between the underground and aboveground plant surfaces. The differences between fungi and prokaryotes in plant compartments are closely linked to their functional traits related with fitness for plant niches. In summary, distinct mechanisms shape prokaryotic and fungal communities in grassland plant compartments. This research provides significant insights into the community assembly mechanisms of prokaryotes and fungi in grassland plant compartments and ambient soil.