Limited effects of depth (0–80 cm) on communities of archaea, bacteria and fungi in paddy soil profiles

Most current microbial studies in paddy soils have focused on the top (0–20 cm) layer where rice roots are concentrated. To better understand the vertical distribution of microorganisms in paddy soils, we investigated the abundances, diversities and community compositions of archaea, bacteria and fungi in six geographically and climatically distinct paddy soil profiles from 0–80-cm depth. Although microbial abundances and operational taxonomic unit (OTU) diversities largely decreased with soil depth, only the community composition of archaea (not bacteria or fungi) was associated with soil depth, echoing that only one archaeal OTU, but no bacterial or fungal OTUs, differed significantly in relative abundance between depth intervals. Mean annual temperature, precipitation and soil iron and manganese concentrations were significantly correlated with the ordinations of microbial communities for all three domains. Besides these common environmental factors, bacterial and archaeal community structures were also influenced by soil chloride and sulphate concentrations, whereas the concentrations of organic matter and total nitrogen were important explanatory factors for the variation in fungal community composition. Further analyses on putative bacterial functions showed significant differences between sampling sites rather than depth intervals, and suggested that bacterial OTUs that significantly varied in relative abundance across sampling sites might be functionally related to organic matter decomposition, sulphur oxidation and reduction, as well as nitrate reduction. Altogether, in the studied paddy soil profiles, the community composition and putative functions of bacteria were largely the same between different vertical layers, each with a thickness of 20 cm. This study suggests that the community compositions of archaea, bacteria and fungi are mainly driven by different soil chemical properties rather than soil depth, which could be linked to the ecological traits of the three microbial domains.