Stable isotope ratios, carbon (δ¹³C) and nitrogen (δ¹⁵N), and fatty acids validated the trophic connection between farmed fish in a commercial nearshore fish farm and sea cucumbers in the Mediterranean Sea. This dual tracer approach evaluated organic matter transfer in integrated multi-trophic aquaculture (IMTA) and the ability of sea cucumbers to incorporate fish farm waste (fish faeces and uneaten artificial fish feed) into their tissue. Between October 2018 and September 2019, Holothuria (Roweothuria) poli Delle Chiaje, 1824, co-cultured at IMTA sites directly below one of the commercial fish cage , at 10 m and 25 m from the selected fish cage, and at two reference sites over 800 m from the fish farm. Sea cucumbers were sampled from each site in February, May and September, except at 0 m due to mass mortalities recorded here in the first month of study. Isotopic mixing models revealed that fish farm organic waste was the dominant dietary source for H. poli in IMTA at 10 m and 25 m from the cage. The contribution of marine plant-derived organic matter, Posidonia oceanica leaves and rhizomes, was least important. The isotopic signatures of sea cucumber tissues at reference sites were not explained by the sampled food resources. Importantly, fatty acid profiling revealed a high abundance of individual terrestrial plant fatty acids, such as oleic (18:1n-9), linoleic (18:2n-6) and eicosenoic (20:1n-9) acids in sea cucumber tissue at 10 m and 25 m from the fish cage, presumably linked to the terrestrial plant oil content of the fish feeds. At the reference sites, sea cucumber tissues were characterised by higher relative abundance of arachidonic acid (20:4n-6) acid, and the natural marine-based eicosapentaenoic (20:5n-3) and docosahexaenoic (22:6n-3) acids. These analyses revealed important differences in the composition of H. poli between the IMTA and reference locations, driven by aquaculture-derived waste near fish cages. Moreover, this study revealed temporal variation in food availability and quality, and possible differences in the physiological responses of H. poli. Stable isotope analysis and fatty acid profiling provided complementary evidence for the important dietary preferences of H. poli and validated the potential of sea cucumbers to uptake aquaculture organic waste as part of inshore fish-sea cucumber IMTA. It reveals the important implications that an established trophic link has on the viability of using sea cucumbers for the development of IMTA and the sustainable expansion of aquaculture.

The role of seagrasses in providing a complex habitat for marine organisms is globally documented; however, few studies have investigated the trophic incorporation of endemic Mediterranean Posidonia oceanica into marine food webs. Meadows of P. oceanica are declining due to climate change and anthropogenic pressures, emphasising the need to determine its contribution in local trophic dynamics. We investigated whether benthic marine invertebrate (BMI) and fish consumers assimilate carbon directly from P. oceanica seagrass or other sources along the seagrass meadow margins in Malta. We sampled and analysed the δ¹³C and δ¹⁵N isotope values of P. oceanica, particulate organic matter (POM), macroalgae, 14 invertebrate taxa, and 10 fishes at three locations marginal to P. oceanica seagrass meadows. Stable isotope ratios were significantly different between all taxa (F₂₆ = 17.37, R² = 0.68, p < 0.01) and locations (F₂ = 34.22, R² = 0.10, p < 0.01). The source, invertebrate, and fishes were enriched in both ¹³C and ¹⁵N at Baħar iċ-Ċagħaq relative to the other locations, L’Aħrax and Golden Bay, likely due to the increased effluent. Stable isotope mixing models were somewhat confounded as POM and macroalgae had similar δ¹³C and δ¹⁵N values at each site, hampering efforts to define the resource use of the sampled taxa. However, Posidonia oceanica made the lowest contribution for both consumer groups at all locations, consistent with the results of other Mediterranean studies, suggesting that P. oceanica does not contribute significantly to the diet of consumers at seagrass meadow margins within Maltese waters.

In real-world situations, marine fish farms accommodate multiple fish species and cohorts within the farm, leading to diverse farm layouts influenced by cage dimensions, configurations, and intricate arrangements. These cage management practices are essential to meet production demands, however, farm-level complexities can impact model predictions of waste deposition and benthic impact near fish cages. This is of particular importance when the cages are used for integrated multi-trophic aquaculture (IMTA) with benthic feeders, where this waste not only affects environmental conditions but also provides a potential food source. The Cage Aquaculture Particulate Output and Transport (CAPOT) model incorporated multiple species, cohorts, and cage arrangements to estimate waste distribution from a commercial fish farm in the Mediterranean between October 2018 and July 2019. This spreadsheet model estimated dispersion for individual fish cages using a grid resolution of 5 m x 5 m. The study categorized discrete production periods for each fish cage every month, aligning with intermittent changes in biomass and food inputs due to different cage management practices throughout production. This approach facilitated the use of detailed input data and enhanced model representativeness by considering variations in cage biomass, food types, settling velocities, and configurations. Model outputs, represented in contour plots, indicated higher deposition directly below fish cages that varied monthly throughout fish production cycles. Deposition footprints reflected changes in cage biomass, food inputs, and farm-level practices reflecting this real-world scenario where aquaculture does not follow a production continuum. Moreover, cohort dynamics and cage movements associated with the cage management practices of the fish farm influenced the quantity and fate of wastes distributed around fish cages, revealing variability in deposition footprints. Clearly, these findings have important implications for the design of benthic IMTA systems, with species such as sea cucumber and polychaetes. Variability in waste deposition creates challenges in identifying where the benthic organisms should be placed to allow optimal uptake of waste to meet their food requirements and increase survivability. Evidently, models have an important role to play and this study emphasizes the need for representative input data to describe actual food inputs, cage biomass changes, and management practices for more representative farm-scale modelling and essentially to improve particulate waste management. To effectively mitigate benthic impacts through IMTA, models must quantify and resolve particulate waste distribution and impact around fish farms to maintain a balanced system with net removal of wastes. Resolving farm-level complexities provides vital information about the variability of food availability and quality for extractive organisms that helps improve recycling of organic wastes in integrated systems, demanding a more representative modelling approach.