Depth effects on bacterial community assembly processes in paddy soils

Bacterial communities in soil play a key role in carbon (C) and nutrient cycling. Unravelling how bacterial community assemble and distribute with soil depth is a prerequisite for understanding microbial functions, nutrient cycling and management. Twenty-six rice fields in a typical red soil area in a wet subtropical climate were sampled in the topsoil (0-10 and 10-20 cm) and subsoil (20-40 cm). Physico-chemical soil properties, quantitative fluorescence PCR and high-throughput sequencing were used to analyse the V4 region of 16S rDNA. The rRNA operon copy number and alpha diversity decreased continuously with soil depth because of reduced access to carbon, energy, oxygen and nutrients. The relative abundance of the dominant phyla Proteobacteria and Actinobacteria decreased with increasing soil depth, whereas the opposite trend was observed for the phylum Nitrospirae. The interaction intensity between taxa increased with depth, as limited carbon and nutrients in the undisturbed subsoil lead to the cooccurrence of taxa with similar ecological niches that cooperated to reduce functional redundancy. The higher modularity of the bacterial network in the topsoil is associated with greater environmental perturbations (flooding, fertilization, etc.) to maintain the robustness of the microbial community. Bacterial community assembly processes were stochastic up to 40 cm, but ecological drift was the predominant process in the topsoil, whereas dispersal limitation was dominant in the subsoil. The contribution of abiotic factors (e.g. nutrient and iron contents) and biotic factors (taxa-taxa interactions) as well as dispersal limitations to bacterial community assembly was depth specific. Concluding, the basic principles of bacterial community assembly were evaluated for the first time for a broad range of paddy soils.

Automated summary

Bacterial communities in soil play a critical role in carbon and nutrient cycling. This study investigated the assembly and distribution of bacterial communities at different soil depths. The results showed that bacterial diversity and abundance decreased with soil depth due to limited access to carbon and nutrients. The relative abundance of different phyla also varied with soil depth. The study also found that ecological interactions between bacterial taxa increased with depth, leading to reduced functional redundancy. The study provides valuable insights into the assembly processes of bacterial communities in different soil depths.