Long-Term Rice and Green Manure Rotation Alters the Endophytic Bacterial Communities of the Rice Root

This study focuses on the effects of long-term rice rotated with milk vetch being as green manure on the composition of bacteria in rice roots. The endophytic bacterial communities in rice roots of the rice–rice–milk vetch (R-R-MV) and the rice–rice–winter fallow (R-R-WF) crop rotations with a 28-year research history were investigated using combined culture-dependent and culture-independent methods. It was found that the endophytic bacterial population in rice roots with the green manure was significantly higher than that of without it. There were 169 and 77 strains of endophytic bacteria that were isolated from rice roots of the R-R-MV and the R-R-WF, respectively. The 16S rRNA gene analysis shows that the 77 R-R-WF bacteria belong to 15 species of 14 genera while the other 169 R-R-MV bacteria belong to 21 species of 19 genera, in which Herbaspirillum and Cedecea were two mutually dominant populations and Burkholderia, Pseudomonas, Sphingomonas, and Pantoea accounted for large proportions of the endophytic bacteria in rice roots through R-R-MV rotation. The analysis of 16S rDNA clone libraries showed that the Shannon–Weaver diversity index of endophytic bacteria in R-R-MV approximates that in R-R-WF rotation, whereas the richness indexes of Chao 1 and ACE in R-R-MV rotation system were significantly higher than those in R-R-WF rotation. The diversity of endophytic bacteria was richer in R-R-MV. Both the culture-dependent and the culture-independent method revealed significant effect of long-term different tillage systems on the microbial community.