The Fungal World of Mangrove Swamp Rice_Insights into Guinea-Bissau Crop Cycle

Rice is a staple crop in Guinea-Bissau, where mangrove swamp rice (MSR) cultivation represents a unique and culturally significant production system. Despite its importance for food security and livelihoods, little is known about the fungal communities affecting MSR, particularly in West Africa. This study applied ITS based metabarcoding, complemented by field disease prospection, to characterize rice phyllosphere fungal communities across three major MSR producing regions (Cacheu, Oio, Tombali) along the crop cycle. Results show that community composition is jointly shaped by regional climate, plant developmental stage, and disease status. Wetter southern region and later growth stages supported more diverse and balanced communities, while drier northern regions and early vegetative stages were dominated by opportunistic fungi. A core microbiome was shared across all conditions, but several high-risk pathogens, including Bipolaris oryzae (brown spot), Pyricularia oryzae (blast), and Ustilaginoidea virens (false smut), were detected for the first time in MSR and in Guinea-Bissau. Field prospection confirmed B. oryzae (brown spot) as the dominant and most severe causal agent, with incidence increasing from vegetative to ripening stages. Opportunistic colonization by Aspergillus was also noted on ripening grains, highlighting storage related risks. At the same time, potential beneficial fungi such as Hannaella phetchabunensis were consistently detected, suggesting the possibility of microbiome mediated disease suppression. These findings demonstrate that MSR fungal communities share a core microbiome across regions and crop conditions, with implications for integrated disease management. Monitoring fungal biomarkers, recognizing growth stage specific risks, and maintaining beneficial taxa may enhance sustainable rice production in low-input mangrove system.