The production of food for a growing world population is a great challenge. In particular, protein and the long-chain n-3 fatty acids, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), which exert a series of potential health effects, are scarce resources in the context of global food security. Fish from wild capture and aquaculture production cannot meet the current demand for EPA and DHA; therefore, a supplementation with alternative sources is crucial. Specific microalgae species have been shown to be a lucrative source of EPA, DHA, and protein, in particular, the oleaginous microalgae Nannochloropsis sp. and Phaeodactylum tricornutum. This study aimed to compare different cultivation scenarios of Nannochloropsis sp. and P. tricornutum with the production of aquaculture and capture fish as traditional sources of EPA and DHA in terms of environmental impacts. Scenarios included borosilicate glass and acrylic glass as photobioreactor (PBR) materials, two different tube diameters, and three different cultivation seasons. In these scenarios, carbon dioxide was modeled as an avoided burden. Additionally, all scenarios were modeled with the burdens resulting from carbon dioxide production. Environmental impacts of selected fish species were obtained from systematic literature research. Life cycle assessment following ISO 14040/44 was used to analyze the global warming potential, acidification, eutrophication, cumulative energy demand, water footprint, and land use. The system boundaries were set from “cradle-to-store,” where the target store is located in Germany. Microalgae biomass as a source of EPA, DHA, and protein was found to have similar or lower environmental impacts than fish fillet from wild capture and aquaculture production when carbon dioxide was modeled as an avoided burden. Microalgae production that included the full burden of carbon dioxide production still caused similar or lower environmental impacts than aquaculture fish. It was found that the distinct microalgae species can significantly influence the results if the comparison is conducted based on nutritional values. Regarding the recommended daily intake of 250–500 mg EPA+DHA, microalgae are an advisable source of nutrients to lessen the environmental pressure on marine ecosystems.
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