Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China

Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genusPaenibacillus,as well as the fungal genusMortierellawere significantly enriched, while the potentially pathogenic fungal genusFusariumwas significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.

Automated summary

The practice of tomato-rice rotation in subtropical and tropical regions in China enhances crop productivity and suppresses soil-borne plant pathogens. Over two years of experimentation, it was found that beneficial bacterial and fungal communities increased significantly, while potentially pathogenic fungi decreased. Soil acidification was improved and soil total phosphorus was identified as a key factor influencing microbial communities.