Bacterial succession in paddy soils derived from different parent materials

Abstract

Purpose: Soils derived from different parent materials are known to support quite distinct indigenous community structures. Crop cultivation is also an important factor regulating bacterial community structure in soils. However, the extent to which the soil parent material imposes limits on the diversity of organisms present and the extent to which cropping practices are able to supplant the effects of soil parent materials are largely unknown. Materials and methods: Five ancient paddy soils developed on three different parent materials were collected from the major rice production regions in southern China. The 16S rRNA genes were amplified from each soil DNA sample and then analyzed using Tag-pyrosequencing and terminal restriction fragment length polymorphism (T-RFLP) to characterize bacterial communities and their relative abundance. Total bacterial abundance was determined by 16S rRNA gene quantitative PCR (qPCR). Canonical correspondence analysis (CCA) was used to investigate the relationship between the bacterial distribution and soil properties. Results and discussion: Cluster analysis of the T-RFLP and pyrosequencing data indicated that although the bacterial communities in the surface layers (0–20 cm) could be distinguished from those recovered from depths of 20–40 and 40–60 cm in all soils, the bacterial community structures in soils with similar parent materials clustered regardless of soil depth. Bacteria of the phylum Proteobacteria dominated in all soils with significantly higher proportions in the top soils. The relative abundances of Chloroflexi and Acidobacteria were closely associated with the soil parent material. This suggested that the changes in bacterial community compositions induced by rice cultivation did not mask those determined by soil parent material. CCA indicated that soil pH, available Mn, and total K and Fe contents explained most of the variance in bacterial distribution due to differences in parent materials. qPCR revealed that the bacterial abundance in top soils (0–20 cm) also varied with parent material. Conclusions: The nature of the parent material is an important factor in determining soil bacterial community structure, and although long-term rice cultivation resulted in shifts in this structure, the community retained characteristics of the original populations.