| dc.description.abstract | Growing demand for food, water scarcity, and the need for circular and resource-efficient production systems have increased interest in aquaponics as a sustainable method for simultaneous fish and crop production. By integrating aquaculture and hydroponics, aquaponics can recover nutrients from fish waste while reducing water use and fertilizer inputs. However, commercial adoption remains limited due to unstable productivity, incomplete understanding of nutrient use efficiency, and limited knowledge of how system design influences microbial ecology and long-term performance. In particular, critical knowledge gaps remain regarding how design decisions, such as hydraulic configuration and fish-tank light exposure, affect nutrient cycling, microbial community structure, fish productivity, plant performance, root-zone health, and overall system reliability in media-based biofloc aquaponic systems. This dissertation addressed these gaps through a series of replicated, long-term studies conducted over a three-year experimental campaign evaluating the effects of system coupling versus decoupling and photoautotrophic versus heterotrophic conditions on fish, plants, microbial communities, and nutrient dynamics in aquaponic systems producing tilapia and cherry tomato.
The first component evaluated the combined effects of fish-tank illumination and hydraulic configuration on aquaponic productivity in the first year of the experiment (2023). Illumination increased fish yield by 21%, while hydraulic coupling increased fish yield by 22%, largely due to the contribution of algal biofloc as a supplemental food source and improved water clarity in coupled systems. Plant performance showed a tradeoff between nutrient availability and solids accumulation. In one production cycle, coupled systems produced 44.5% higher yields due to higher nutrient availability, whereas in a subsequent cycle, decoupled systems outperformed coupled systems by 26%, yielding 1711 g per plant, due to reduced sludge accumulation and improved root-zone conditions. Importantly, illumination did not negatively affect plant growth and, in some cases, improved yield. These results highlight that while coupling enhances nutrient retention, excessive solids accumulation can limit plant performance.
The second component examined how system design shaped microbial communities and their functional roles in the second year of the experiment (2024). Coupled systems retained higher nutrient concentrations but supported less diverse microbial communities, whereas decoupled systems promoted greater microbial diversity and higher abundance of plant growth-promoting bacteria. For example, putative siderophore-producing Streptomyces reached 1.16% relative abundance in decoupled systems compared to 0.068% in coupled systems, corresponding to increased iron and zinc availability in plants. However, decoupled systems also exhibited unstable nitrification, with ammonium-N concentrations reaching 20 mg L⁻¹, which likely negatively affected plant productivity. Putative pathogens such as Pythium graminicola and Xiphinema rivesi were associated with plant stress and wilting under certain conditions. These findings demonstrate that system design influences not only microbial composition but also the balance between beneficial and harmful organisms, directly affecting plant health and system performance.
The third component focused on long-term system reliability and root-zone disorders. Plant wilt in media-based systems was primarily driven by sludge accumulation and poor drainage, which created hypoxic root-zone conditions and reduced yields by 21% in affected systems. System modifications, including improved solids removal and controlled irrigation, significantly enhanced performance; however, some failures persisted. Root-zone analysis showed that wilted plants exhibited lower dissolved oxygen levels (65% lower) and trends toward higher relative abundance of putative pathogens and parasitic organisms (Pythium graminicola and Xiphinema rives). These results indicate that long-term aquaponic stability depends on both effective solids management and maintaining a balanced root-zone microbiome.
The fourth component evaluated tilapia production and biofloc quality under different design conditions over a two-year production. Illuminated systems developed photoautotrophic biofloc communities dominated by algae, which improved nutritional quality, including higher protein, lipid content, and essential fatty acids. These changes enhanced fish growth, with light-coupled systems achieving the highest biomass (up to 581 g) and improved feed conversion ratios. Importantly, illumination did not promote off-flavor compounds, as cyanobacteria remained below 0.03% and geosmin/MIB concentrations remained below sensory detection thresholds. These findings demonstrate that light exposure can be used strategically to enhance fish productivity without compromising product quality.
The final component quantified the fate of feed-derived nitrogen and phosphorus across two fish growth stages and experimental treatments. Nutrient partitioning was strongly influenced by fish size, with 30.0–34.4% of feed nitrogen recovered in fish biomass in 2025 compared to 10.2–15.6% in 2024, along with approximately 50% lower nitrogen loss in 2025. Photoautotrophic systems retained a greater fraction of nitrogen and phosphorus in measurable pools (solids and water) and exhibited reduced loss, indicating improved internal recycling. Plant uptake remained relatively consistent across treatments, accounting for approximately 6–11% of nitrogen and 7–12% of phosphorus, with the highest recovery observed in heterotrophic-coupled systems. These results highlight that while aquaponics is often described as a circular system, nutrient recovery efficiency depends strongly on fish growth stage, microbial regime and hydraulic configuration.
Overall, this dissertation demonstrates that aquaponic system performance is governed by interactions among hydraulic design, fish-tank illumination, microbial community structure, and solids management. Photoautotrophic conditions and hydraulic coupling enhance fish productivity and nutrient recovery, while plant performance is more strongly influenced by root-zone conditions and microbial balance. By linking system design to microbial processes, nutrient cycling, and biological performance, this work provides a mechanistic foundation for improving the stability, productivity, and resource efficiency of aquaponic systems and supports their advancement within controlled-environment agriculture and circular food production systems. | en_US |
