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, but agricultural systems contribute substantially to environmental issues, making it crucial to find sustainable methods for 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. We had three objectives: (1) to monitor rice growth and ecological dynamics to create a comprehensive ecological time series using quantitative environmental DNA metabarcoding and complementary monitoring methods, (2) to identify ecological variables that causally affect rice performance using nonlinear time series analysis, and (3) to examine the effects of the two farming practices on ecological variables and rice performance. 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. Twenty-five taxa had statistically clear causal influences on rice performance. While the per-abundance influences of the causal taxa were largely similar in both paddy fields, their abundances were different, contributing to the differences in the overall effects of these taxa on the rice performance. These findings suggest that the abundance of causal taxa, along with nutrient conditions, may have driven differences in rice growth between the two paddy fields.