Distinct Planting Patterns Shape the Network and Assembly of Root‑Associated Microbiome in Subsequent Crops

Abstract

Soil legacy effects of previous crops alter the plant-soil interactions, which is an aspect of our general interest in crop rotation. However, the microbial mechanism underlying this effect in subsequent crop root-associated compartments remains unclear. This study investigated the effects of planting patterns (four-year continuous spring maize [MM], three-year wheat and one-year maize rotation [WM], and three-year potato and one-year maize rotation [PM]) on the microbial composition and structure of root-associated compartments, how distinct previous crops affect microbial co-occurrence patterns, and the assembly mechanism of root-associated compartments in subsequent crops to regulate microbiome habitat. WM and PM altered the composition and structure of bacterial and fungal communities in the three compartments compared with MM. The responses of the co-occurrence patterns of the microbial communities to different planting patterns varied. Specific planting pattern-sensitive ASVs (psASVs) were enriched in specific modules of each co-occurrence treatment network. The psASVs in the roots in MM showed lower degrees of co-occurrence than those in WM or PM. Planting patterns can also regulate the assembly patterns of fungi in the bulk soil, rhizosphere, and roots in subsequent crops; however, stochastic processes are a real force in the assembly of microbial communities. Compared with MM, the stochasticity of bacterial assembly decreased under WM and PM but increased for fungi. WM and PM also increased the homogenized dispersal of fungal assemblies in the roots. Therefore, soil heritage should not be ignored when discussing microbiome recruitment strategies and co-occurrence patterns in root-associated compartments. This study provides valuable information on microbial management strategies to maintain soil health.

Keywords: root-associated compartments, co-occurrence network, microbial community assembly, planting patterns