From Waste to Resource: Alkaline Protease Converts Aquaculture Sediment into Plant-Bioavailable Nutrients—Metabolomic and Agronomic Evidence

Aquaculture sediment accumulation poses an environmental challenge yet offers a resource recovery opportunity. This study innovatively employs alkaline protease hydrolysis to convert sediments from three origins, largemouth bass ( Micropterus salmoides ) pond, Nile tilapia ( Oreochromis niloticus ) pond, and largemouth bass farm tailwater treatment area, into liquid organic fertilizers evaluated through metabolomics and agronomic trials. Sediment characterization revealed high total nitrogen (536.02–530.12 mg/kg) and phosphorus (747.97–649.13 mg/kg). Enzymatic treatment (pH 8.3, 45°C, 3 h) significantly enhanced nutrient bioavailability, with metabolomics showing marked enrichment of plant-available compounds such as L-glutamate (log₂FC ≥ 3.2). Pot trials with baby bok choy ( Brassica rapa var. glabra Regel ) demonstrated improved growth, with the bass-sediment-derived fertilizer yielding the best results (plant height: 6.6 cm; growth rate: 31.64%). Pathway analysis indicated significant enrichment in amino acid biosynthesis and carbon metabolism ( P < 0.05). These results indicate that hydrolysates from alkaline protease treatment of sediments derived from high-protein-demand fish ponds exhibit stronger plant growth-promoting effects; however, hydrolysates from other sediment sources may possess distinct bioactivities. This work presents a green, efficient strategy for valorizing aquaculture waste, advancing the circular bioeconomy. • Alkaline protease first applied to aquaculture sediments, releasing plant-available nutrients. • Metabolomics identifies enriched key metabolites (e.g., L-glutamate) with clear mechanisms. • Enzyme-treated fertilizer boosts pak choi growth vs. control. • Converts sediment waste into high-value biofertilizer for sustainable agriculture. • Native sediment bacteria enhance enzymatic hydrolysis efficiency.