Study on the nutrient spatiotemporal changes and multi-habitat microbial succession in a decoupled largemouth bass–garlic chive aquaponics system

The decoupled aquaponics system was an important model of circular agriculture and represents a mature circular agricultural framework, yet integrated studies simultaneously tracking nitrogen, phosphorus, potassium and microbial communities in water, sediment, substrate and fish gut remain scarce. To address this gap, we conducted a three-month continuous monitoring (July to September 2024) of a triplicate indoor decoupled aquaponics system combining largemouth bass ( Micropterus salmoides ) and garlic chives ( Allium tuberosum ) in northern Chinese greenhouses. Nutrient dynamics (total nitrogen, TN; total phosphorus, TP; total potassium, TK) were quantified monthly in aquaculture water, sedimentation tank mud and cultivation substrate, while microbial community structure, succession and putative functions were characterized via 16S rRNA amplicon sequencing, canonical correspondence analysis (CCA), variance partitioning analysis (VPA) and PICRUSt2 functional prediction. The results were as follows: (1) The three modules formed a characteristic “water transport → mud accumulated → substrate consumption” nutrient cascade, with nutrient reserves ordered as mud > substrate > water. (2) TN in water increased by 237.60% over the cultivation period, indicating a latent risk of eutrophication. Microbial communities exhibited strong habitat partitioning, with Proteobacteria as the shared dominant phylum across environmental media, while fish gut harbored a temporally dynamic assemblage shifting from Fusobacteriota (83.11% in July) to Firmicutes (73.31% in September), forming a distinct “environmental versus host” bistable zonation. (3) VPA revealed that TN and TP synergistically regulated mud microbiota (27.70% interaction), whereas TK independently structured substrate communities (19.95% independent contribution), ranking as the strongest single-nutrient driver (K > N > P). (4) PICRUSt2-based functional prediction indicated metabolism as the core function across all habitats, with complementary profiles—sediment for nutrient sensing, substrate for stable transformation, water for temporal adaptation, and gut for host-specific nutrition. These provide species-specific nutrient–microbe linkage data, synchronous four-habitat temporal dynamics, and quantitative partitioning of N/P/K effects, offering actionable baselines for structural optimization, seasonal nutrient regulation and targeted microbial modification in decoupled aquaponics facilities.