Shifts in bacterial community composition increase with depth in three soil types from paddy fields in China

Bacterial community distribution along soil depth gradients is currently poorly understood at the large scale. We selected three typical paddy soils in three regions from north to south in China to investigate the vertical distribution (0-100 cm) of the bacterial community by Illumina MiSeq amplicon sequencing and identify its drivers. Results indicated that the dominant bacterial phyla in paddy soils were Chloroflexi, Acidobacteria, and Proteobacteria. The four diversity indices of the bacterial community all increased at depths of 0-20 cm, then gradually decreased at depths of 20-100 cm. Linear discriminant analysis effect size showed that some bacterial taxa displayed significant differences in relative abundance among different depth gradients. Some bacterial taxa (such as phyla Chloroflexi, Bacteroidetes, and Nitrospirae; classes Alphaproteobacteria, Betaproteobacteria, and Anaerolineae; and genera Candidatus Koribacter and Rhodoplanes) had a high relative abundance at depths of 0-20 cm. Other taxa (belonging to classes Deltaproteobacteria and Gammaproteobacteria and to genera Geobacter and Acinetobacter) had a high relative abundance at depths of 80-100 cm. Non-metric multidimensional scaling analysis indicated that the soil bacterial community structure clearly changed with region and soil depth, and the shifts in bacterial community composition increased with depth in three paddy soils. Variance partitioning analysis showed that geographic distance had more effect on bacterial community distribution than environmental variables in deeper soil (20-100 cm) at a large scale. In addition, distance-based redundancy analysis suggested that soil total carbon and nitrogen contents were strongly associated with the vertical distribution of the bacterial community in paddy soil.