# From Feed to Fish--Nutrients' Fate in Aquaculture Systems
## 2 Materials and Methods  
To answer our research questions, we searched literature from the past 40 years, aiming to include the 20 years prior to the rapid increase in fish production as well as recent research. In April 2020, the search was performed in Scopus, ScienceDirect, and Web of Science using advanced searches, with combinations of the following search terms together with the Boolean operators AND and OR: fish pond OR \"fishpond\" AND freshwater AND carbon AND nitrogen AND phosphorus and \"nutrient budget\" AND aquaculture found in the papers' titles or keywords. The search results from the platforms were saved in BibTeX format and exported to the software State of the Art through Systematic Review (StArt version 2.3.4.2), where the papers were sorted. Based on the papers' abstracts, we first selected all papers that reported nutrient fluxes, concentrations in at least one pond compartment (inlet, pond, and outlet), and the fish species cultivated. We did not include papers that focused on the aquaculture of species other than fish (for instance, algae, crustaceans, mollusks, and shellfish), papers that focused on marine and brackish systems, nor, for instance, review papers without original data. Other papers that lacked data providing insight into the ponds' nutrient budgets tended to focus on specific biological groups within the ponds (e.g., bacteria, algae, plants, and animal communities) or aquaculture systems other than ponds (e.g., net cages) (Figure 1). A Sankey plot, obtained using the software JMP(r) 17 (trial version) with the Enhanced Sankey Plot extension, was used to display the interactions among cultivation systems and fish species. Our search yielded 1267 papers; 65 were duplicated, and 1112 papers were rejected. Of these, 606 papers did not focus on freshwater fish cultivation, and within fish aquaculture, 506 papers did not follow the inclusion criteria and were classified as follows: focusing on the biology of the fish rather than on the nutrient budget (113), aquaculture not involving fish (85), papers on marine or brackish systems (81), papers without original data (224), and aquaculture carried out in freshwater systems other than excavated earthen ponds (e.g., reservoirs, rivers, or natural lakes) (19). Finally, we also excluded papers in which the input data were based solely on qualitative data obtained from interviews (two) that were not included in our review. Figure 1: Flow chart of the paper search, selection, and data extraction. We retrieved data on carbon, nitrogen, and phosphorus fluxes from the various sources (inputs) as well as the different losses (outputs). Next, we calculated the contribution of different nutrient sources to the total nutrient input to the fishponds and the contribution of the different output terms to the total output. As water used to fill the ponds can be an important nutrient source, we accounted for rainwater and inlet water separately. Inlet water can include more diverse sources, including runoff, groundwater, rivers, streams, lakes, irrigation canals, effluents from mines, reservoirs and other fishponds, and domestic sewage. Furthermore, we give an overview of the multiple nutrient loss pathways. Particulate matter entering the ponds, including organic and inorganic matter in the inlet water, uneaten feed, feces, within-pond primary production, as well as leaves and other material falling into the water, may settle at the pond bottom. When sedimentation rates are higher than sediment mineralization, this leads to the accumulation of organic matter in the pond bottoms. We also identified pathways that were often not quantified (e.g., infiltration and gas efflux). Gas efflux can be measured as ammonia volatilization and diffusive and ebullitive pathways of nitrogen and carbon. We pay special attention to the assimilation of nutrients by the cultivated species, as this is the targeted endpoint of the nutrients added to the fishponds and ultimately impacts its marketability and the sustainability of the aquaculture practice.