Contrasting ecological communities in rice paddy fields under conventional and no-fertilizer farming practices

Global crop production is essential for providing energy and nutrients to humans, with rice ( Oryza sativa ) being one of the most important crops globally. However, agricultural systems contribute substantially to greenhouse gas emissions and other environmental challenges, making it crucial to find sustainable methods for crop production that minimize environmental impacts. Paddy fields serve as habitats for numerous species and ecological communities, which play a critical role in rice performance and can be leveraged to promote sustainable crop production. In this study, we conducted extensive field monitoring of two rice paddy fields in Kyoto Prefecture, Japan, where a rice variety, Hinohikari , was cultivated, to investigate how ecological communities influence rice growth and yields under two contrasting farming practices: conventional farming and no-fertilizer farming. The no-fertilizer paddy field has been maintained without fertilizers and pesticides since 1951, yet it still maintains sufficient grain yields. We have three objectives in this study: (1) to monitor rice growth and ecological dynamics to create a comprehensive ecological time series using quantitative eDNA metabarcoding and complementary monitoring methods, (2) to identify ecological variables that causally affect rice performance and quantify these effects using nonlinear time series analysis, and (3) to examine the effects of the two farming practices on ecological variables and rice performance in real paddy fields. As expected, the no-fertilizer paddy field showed lower rice growth and yields but still produced 40–50% of the yields of the conventional field. Ecological monitoring revealed contrasting ecological communities between the two fields, particularly among plant species on the paddy ridges and microbial taxa. Our causal detection analysis indicated that 25 taxa had statistically significant causal influences on rice performance indicators such as growth, SPAD readings, or the number of rice stems. While the per-abundance influences of the causal taxa were largely similar in both paddy fields, their abundances were different between the two paddy fields, contributing to the differences in the overall effects of these taxa on the rice performance indicators. These findings suggest that the abundance of causal taxa, along with nutrient conditions, may drive differences in rice growth between the two paddy fields.