Temporal Turnover of Aquatic Fungal Communities Driven by Water Quality Changes in FLOCponics Japanese Eel Aquaculture System

FLOCponics systems combine biofloc-based aquaculture with nutrient recycling and are considered sustainable for intensive aquaculture. However, fungal community dynamics in these systems and their links to water quality remain poorly understood. In this study, we examined temporal changes in fungal communities in a FLOCponics system-based Japanese eel aquaculture by integrating metabarcoding with weekly water quality monitoring. Electrical conductivity (EC), nitrite, and pH displayed significant temporal variation, whereas other water quality parameters remained stable. Metabarcoding yielded 217 fungal operational taxonomic units across all samples. Alpha diversity indices exhibited no significant differences among weeks, indicating stable richness and evenness. In contrast, beta diversity analyses revealed consistent temporal shifts in fungal community composition with time exerting a significant effect after accounting for tank identity. Community changes were significantly EC-associated, with associations to nitrite and nitrate. Variation partitioning indicated that time and water quality primarily explained variation through their overlapping contribution rather than independent effects. Beta diversity decomposition revealed that temporal differences were driven primarily by species replacement rather than nestedness. Environmentally responsive taxa were mainly composed of Rozellomycota, with fewer Ascomycota, including <i>Metapochonia</i>. These results demonstrate structured short-term temporal fungal community reassembly in FLOCponics systems and highlight fungal turnover as a potential indicator of water quality-linked microbial dynamics in sustainable aquaculture.