Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system

As an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.