Fully Organic Agroforestry Practices in Rice Cultivation: Effects on Soil Bacterial Microbiota, Soil Health and Grain Quality

Introduction: Sustainable practices are increasingly recognised for benefiting soil biodiversity, health, and overall grain quality. This study examined a unique rice agroecosystem adopting fully organic practices and agroforestry through a seasonal characterisation of soil bacterial microbiota and physicochemical parameters. Furthermore, the first nutritional characterisation of an heirloom rice variety was provided, explicitly detailing how the soil biodiversity and parameters influence the grain quality. Materials and Methods: Following the rice growth cycle, soil bacterial microbiota were studied through a metabarcoding approach on environmental DNA. Soil physicochemical properties were determined with standardised protocols and an FT‐IR analysis on the labile and recalcitrant carbon. Besides, the grain nutritional profile was obtained using standardised kits and protocols, while grain protein quantification was performed by combining SDS‐PAGE assay and MALDI‐TOF mass spectrometry. Results: Microbiota profiling highlighted the cover crops field's role in hosting functionally important bacteria, in support of the subsequent rice cultivation. Taxonomical and functional diversity significantly increased across the rice growing season, peaking at flowering, a delicate physiological phase directly impacting crop yields. Soil ROC, OM and flooding conditions primarily drove the bacteria community dissimilarity inter‐stages (R2 = 0.637). The sustainable practices employed for rice cultivation (i.e., green mulching, zero external inputs) led to a stabilisation of TOC and OM, increased available labile C, and to a carbon sequestration at the end of the growing season (7%), besides soil N and P conservation. Correlation analysis showed that CEC, C/N and bacterial diversity mainly influenced the carbohydrate fraction of the rice grain, with an indirect effect on the protein content. Conclusion: Through a multidisciplinary approach, this study highlights that sustainable rice cultivation provides vital ecosystem services by positively affecting bacterial biodiversity, nutrient cycling, and grain quality. These sustainable practices represent an evidence‐based strategy to achieve global Sustainable Development Goals and to redesign rice agriculture.