LAUSR

Microorganisms play essential roles in soil-ecosystem multifunctionality. However, the contribution of their community assembly processes, composition, diversity, and keystone species to ecosystem multifunctionality is unclear, especially in tea-plantation ecosystems. In order to assess the effects of various intercropping patterns (tea-plant monoculture and tea plants, respectively, intercropped with soybean, soybean—milk vetch, soybean—red clover, and soybean—smooth vetch) on soil rare and abundant taxa, a field experiment was carried out. We found that tea plantation intercropping with legumes improved the soil-ecosystem multifunctionality by altering the soil environment, and ultimately benefited nutrient absorption and quality improvement of tea leaves. Whether it was in bacteria or fungi, rare taxa had a higher proportion of deterministic processes in community assembly than abundant taxa. Additionally, intercropping practices changed the soil environment, and rare bacterial taxa were assembled and shifted from variable selection to homogeneous dispersal. Intercropping practices significantly changed the bacterial and fungal communities’ composition, and rare taxa had higher α-diversity than abundant taxa. Increasing legume species in intercropping practice enhanced community dissimilarity to the tea monoculture by affecting soil pH, ammonium nitrogen, and nitrate nitrogen. Rare bacterial and fungal β-diversity exhibited stronger positive relationships with ecosystem multifunctionality (both average and multi-threshold approaches) compared to the corresponding abundant taxa. Furthermore, ecosystem multifunctionality under different intercropping practices was closely related to the keystone rare operational taxonomic units, especially rare bacterial species of Chloroflexi. Our results emphasize the disparate feedbacks of rare and abundant taxa to diverse intercropping practices, as well as the important connection between rare bacterial taxa and ecosystem multifunctionality.