Biogeography and ecological processes affecting root-associated bacterial communities in soybean fields across China

Highlights: • Bacterial communities in bulk soil, soybean rhizosphere and endosphere were compared. • High–throughput sequencing was performed on an Illumina HiSeq 2500 platform. • Environmental rather than spatial factors governed bacterial community turnover. • Edaphic factors were more important than climatic factors for community turnover. • Bacteria in the three compartments displayed different biogeographic patterns. Root-associated bacteria have profound effects on plant health and productivity, but their biogeographic patterns across large spatial scales remain poorly understood. Here, we used high–throughput sequencing to compare the bacterial distributions in the bulk soil, rhizosphere, and endosphere across 51 soybean fields in China. Environmental variables were more important than spatial variables, and edaphic variables were more important than climatic variables, for governing bacterial community turnover in each soil-root compartment. Both bacterial richness and community turnover were significantly correlated with different environmental and spatial variables among the three compartments. Their different spatial autocorrelation ranges for bacteria suggested distinct bacterial biogeographic patterns were present. The distributions of nearest taxon index (NTI) showed that deterministic processes dominated local bacterial communities, while its importance decreased from the bulk soil to the endosphere. These results provide new insights into the assembly of root–associated bacterial communities at a continental scale.