This paper aimed to clarify the effect of farmland flooding on the soil environment of continuous pepper cropping, and to provide the technical basis for reducing the soil sickness caused by continuous pepper cropping.

In this experiment, the flooded and non-flooded soil of continuous cropped pepper in Hexian County of Anhui Province were analyzed, with non-flooded soil as control. The determination of chemical property and microbial community structure in soil with flowing analyser, qPCRand Illumina MiSeq sequencing explored the effect of flooding on the soil. Besides, the pepper was used as plant material to explore the effects of flooded and non-flooded soil on seed germination and seedling growth by the Petri dish method.

Soil flooding significantly decreased the soil EC value, organic matter, nitrate N, ammonium N, available K, and Olsen P. Quantitative PCR analysis showed that soil flooding significantly increased the bacterial community abundance (P<0.05), however decreased that of the fungal communities. Illumina MiSeq sequencing showed that the soil flooding significantly increased the relative abundances of Actinobacteria and Myxococcota, which decreased the Firmicutes and Mortierellomycota at phylum level. The soil flooding decreased the relative abundance of potential pathogenic fungi, such as Fusarium spp., positive correlation with nitrate N. The soil flooding increased potential Azotobacter, including Azoarcus, Gemmatimonas, Sideroxydans, Candidatus_Solibacter, Bryobacter, Sideroxydans spp. and plant-beneficial potential such as Aspergillus and Acremonium spp., which were negatively correlated with nitrate N. The soil microbial community structure and composition was significantly affected by soil nitrate N. In petri dish, the seed germination rate, seeding fresh weight and root length of peppers planted in flooded soil were significantly higher than those in non-flooded soil.

Soil flooding significantly reduced the EC value and abundance of potentially pathogenic microbial community and increased the abundance of potentially beneficial bacterial, but significantly reduced the content of available nutrients. At the same time, Soil flooding was conducive to the seed germination and seedling growth and alleviated the pepper continuous cropping obstacles.