Rice–fish coculture system enhances paddy soil fertility, bacterial network stability and keystone taxa diversity

High-input, modern rice farming (MRF) has caused severe soil degradation worldwide, necessitating a transition towards more sustainable practices. The traditional rice–fish coculture (RFC) and manure fertilization (Manure) may provide valuable insights to this transition. However, it remains elusive how long-term agricultural conversion influences microbial community structure, soil fertility, and food supply. Here, we performed six-year conversions of MRF to either RFC or Manure in a hilly area of Sichuan (China). We found that agricultural conversions exerted a greater impact than rice growing stages on bacterial community structure. The RFC bacterial network exhibited the highest modularity and robustness, but also harbored the most diverse keystone taxa, followed by Manure. In contrast, MRF displayed network properties that are characteristic of unstable communities. Importantly, RFC also exhibited the greatest capability in improving the preservation of soil organic carbon, nitrogen, and phosphorus, and has significantly increased soil pH (> 1.5 units). Yet, adopting traditional practices, particularly Manure, decreased rice yields, but fish harvested in RFC could offset the decrease in rice yield. Our field study highlights bacterial network structure and keystone taxa diversity as possible indicators for agriculture sustainability, but also incentivizes the integration of traditional RFC in developing novel sustainable agricultural practices.