Ecological functioning of aquaculture systems: effects of species interactions, feed inputs, and nutrient processing

Abstract

Aquaculture has rapidly expanded in recent decades, becoming a key contributor to global food security and animal protein production. However, its sustainability depends on a better understanding of the biological, behavioral, and biogeochemical processes that regulate production efficiency and environmental impacts in farming systems. This study integrates complementary approaches to investigate how species traits, feed inputs, and nutrient pathways interact to shape freshwater aquaculture systems. First, we evaluated fish development, behavior, and water quality under different production strategies, demonstrating that species interactions influence growth performance, spatial distribution, and key environmental parameters. These results highlight the importance of species composition and behavioral dynamics in determining both productivity and system functioning. Second, we investigated the role of feed as a driver of carbon dynamics, focusing on the decomposition of uneaten feed and its contribution to greenhouse gas emissions. Our results show that feed characteristics strongly regulate decomposition rates and associated CO₂ and CH₄ production, emphasizing the importance of feed properties and management in controlling carbon emissions in aquaculture systems. Finally, we assessed nutrient dynamics following feed ingestion by quantifying the partitioning between dissolved and particulate pathways. We demonstrate that most nutrients are rapidly transferred to the dissolved pool through excretion and microbial processes, while only a limited fraction is exported as particulate waste. This partitioning plays a central role in shaping water quality and nutrient availability within the system. Together, these findings demonstrate that aquaculture systems are structured by the interaction between species-specific traits, feed inputs, and nutrient processing pathways. By linking biological, behavioral, and biogeochemical processes, this study provides a more integrated understanding of aquaculture functioning and supports the development of more efficient and environmentally sustainable production strategies.