Physiology-informed LSTM framework integrating crop model and Sentinel-2 time series for rice nitrogen status estimation

Accurate assessment of plant dry matter (PDM) and plant N accumulation (PNA) provides essential indicators for precision nitrogen (N) management in rice production. However, purely data-driven models struggle to generalize due to the spatial scarcity of ground-truth physiological data. To address this, a physiology-informed long short-term memory (PI-LSTM) framework was developed for robust regional N diagnosis and variable-rate fertilization. First, the model was pretrained to internalize crop growth dynamics using a DSSAT-based simulation library, which spanned 2000 representative fields and 700 management scenarios to provide physiologically consistent pseudo-labels. Subsequently, the framework was fine-tuned using multi-year field observations (2020, 2023, 2024), Sentinel-2 time-series data, and meteorological inputs. The proposed LSTM framework outperformed conventional machine learning approaches in estimating PDM and PNA, achieving five-fold cross-validation R² values of 0.87 and 0.83, respectively. Based on these biophysical estimations, the N nutrition index (NNI) diagnosis achieved a 67.3% overall classification accuracy. Furthermore, by integrating the critical N dilution curve, the critical PNA and accumulated N deficiency (AND) were quantified, which served as the basis for developing the AND-based N recommendation algorithm (ANDA). Finally, variable-rate topdressing field experiments conducted across seven sites in 2024 and 2025 demonstrated that the ANDA reduced N input by 13.4% compared with farmers’ practices, while maintaining or increasing yield and improving N partial factor productivity by 18.6%. This study provides a reliable, physically consistent decision-support framework for regional-scale precision N management.