Roots alter soil microbial diversity and interkingdom interactions in diversified agricultural landscapes

The complex interactions between plant roots and soil microorganisms are, broadly, well described. Yet the patterns of microbe-microbe interaction and their association with the root functional traits are less known especially in plant communities at the edges of agricultural landscapes. To address this gap, we measured the active soil microbial communities with and without the presence of plant roots, using in situ root exclusions, in four plant communities at the edges of agricultural fields: undisturbed natural deciduous forests (FOREST1), coniferous forests (FOREST2), rehabilitated agroforests (AGROFOREST) and perennial herbaceous grass buffers (GRASS). Amplicon-based analysis of 16S rRNA and ITS transcripts was used to evaluate soil bacterial, archaeal and fungal communities, and their interactions, with 'roots' and with 'no roots'. Plants roots were measured for a suite of functional traits and explored in association with microbial community composition. Significant differences in bacterial and archaeal but not fungal diversity were observed between soil plots with 'roots' and with 'no roots'. Network analysis illustrated intra and inter kingdoms co-occurrence patterns respond to the presence of plant roots, with GRASS exhibiting distinct patterns in comparison to tree-dominated soils. A shift in microbial hub from bacterial to fungal was observed with the exclusion of roots; Planctomycetes (OM190)_10 was replaced by Archaeorhizomyces in AGROFOREST site. Microbial taxa strongly correlate with root traits especially specific root length, root diameter and root tissue density indicating root traits are predictors of microbial community composition. This study validates the vital role of root traits in predicting plant-microbe interactions and highlights the key role of fungi in microbial interkingdom interactions when roots are absent. These findings have significant ecosystem level implications, with the rising interest in associated biodiversity in and at the edges of agricultural landscapes, this work suggests that plant community selection for specific root traits may drive microbial community structure and ecosystem services.