Metagenomic insights into feasibility of agricultural wastes on optimizing water quality and natural bait by regulating microbial loop

Effective screening feed substitutes for improving water quality in aquaculture systems has become a trending research topic now. In this study, three typical organic agricultural wastes, including sugar cane bagasse (SC), coconut shell powder (CS), and corn cob powder (CC), were selected to evaluate their potential roles on the optimization of water quality and natural bait compared to aquafeeds. Fish feed resulted in the highest growth rate of fish but the worst water quality. Organic detritus addition markedly improved the water quality, especially soluble reactive phosphorus (SRP, decrease of 56–61%) and ammonium (decrease of 16% in SC, 47% in CC). Specially, SC induced core microbes to mediate nutrients transformation and recycling (N2-fixation, ammonification, nitrification, dissimilatory nitrate reduction to ammonia and organic nutrients decomposition), which facilitated the primary productivity based on their positive relationships. This further reduced the available nutrients (especially SRP) in the water and built a mutually beneficial microbial loop. In addition, SC addition increased the abundance of genes involved in amino acids biosynthesis pathways, photosynthesis, and carbon fixation. These results led to energy transfer to higher trophic levels. The addition of CC had a better effect than SC in terms of lower nitrogen levels and a higher fish growth rate (19% in CC, 5% in SC). However, low temperatures and carbon accumulation jointly drive the anaerobic decomposition, resulting in unhealthy microbial loops and low fish growth rates. In contrast to the direct consumption of fish feed, organic detritus can induce more natural bait to provide food for fish by regulating the microbial loop, as showed by the microbial community composition in the water and fish gut. To comprehensively assess water quality, natural bait, and fish growth and quality, certain organic detritus should be considered as an auxiliary material to partially replace feed for healthy and sustainable aquaculture systems.