The largest cost in aquafeed production is protein, with fishmeal (USD $2,200/tonne FAO., 2024) being the primary source due to its palatability, amino acid composition, lipid profile, and other essential nutrient content. However, factors like cost, scalability, and sustainability persuade companies to substitute protein with poultry meal, blood meal, and soybean meal. While these alternatives contribute to a circular economy and supply some essential amino acids, they are not scalable and often result in poor-quality feed ingredients (Idenyi et al., 2022).

Microalgae contain essential amino acids comparable to or surpassing that of common animal-based proteins like eggs (Wells et al., 2017). Most species relevant to aquaculture provide all essential amino acids, including Arginine, Tyrosine and Taurine, which are important for marine animal development (Zhang et al., 2023). Protein content varies by species ( Table 1 ) but may be increased by cultivating under nitrogen supplementation, low salinity, increased CO2, and by harvesting during the exponential phase (Geada et al., 2021).

Given the high variability in microalgae protein content, it is essential to standardise quantification methods and ensure reported values are directly relevant to practical applications. Since microalgae contain non-protein nitrogen, conversion should use N x 4.78 rather than the traditionally used N x 6.25 (Geada et al., 2021). Additionally, reporting the essential amino acid index (EAAI) would enable cross-species comparisons of protein quality for use in aquaculture.

As fish oil (USD $7,700/tonne (FAO., 2024) is a high-value commodity in aquafeed, many commercial feeds use cheaper terrestrial alternatives such as vegetable oils, e.g. linseed, palm, and soybean. While these can maintain similar food conversion ratios (FCR) and specific growth rates (SGR) in many fish species (Hodar et al., 2020), excessive substitution can lead to deficiencies in essential fatty acids, compromising the health benefits to humans while leading to physiological and immunological disorders in fish (Rahman et al., 2024). Microalgae are among the few primary producers capable of de novo synthesis of ω-3 PUFAs, making them a promising and sustainable alternative to fish oil in aquafeed formulations.

Increased photoautotrophic lipid production has been reported under optimised abiotic conditions for many microalgae species, with dry weight levels reaching up to 70%, and ω-3 PUFA content reaching as high as 50% of total lipids (Sun et al., 2018). The rapid oxidation of PUFAs means their optimal accumulation occurs in environments with low oxidative damage. High light, high temperature, high salinity and late harvesting stage all negatively affect ω-3 PUFA productivity in most microalgae species (Sun et al., 2018). To enhance lipid accumulation in industry-scale production, nitrogen (N) limitation is commonly used in a two-stage cultivation process: the first stage focuses on biomass productivity under N-replete conditions, while the second is N-deplete to enhance lipid production (Liyanaarachchi et al., 2021).

Bioactives in microalgae include both macronutrients and secondary metabolites such as pigments, phenolic compounds, vitamins, and minerals. Investigating the synergistic effects of these compounds may guide future aquafeed formulation strategies. A key feature of microalgae bioactives is their antioxidative capacity.

Technological advances in upstream cultivation have great potential, especially across two key fields: metabolic engineering and species-specific strain selection. These advancements will ultimately reduce costs by optimising productivity, improving the accumulation of high-value metabolites, and meeting species-specific nutritional requirements.

Metabolic engineering refers to the enhancement of a targeted metabolic pathway’s efficiency. In microalgae, increased metabolite production, stress resilience, photosynthetic efficiency and even carbon sequestration have been achieved. Robust tools for metabolic engineering include: adaptive laboratory evolution (ALE), genome editing, chemical elicitors (e.g. phytohormones), and co-cultivation strategies (e.g. with bacteria or another microalgae).

Adaptive Laboratory Evolution (ALE) subjects microalgae to a defined stress condition over successive generations. This drives the evolution of genetic variants that can adapt readily, resulting in highly refined strains with enhanced metabolic pathways. For example, stimulating carotenoid production using ALE in microalgae is usually linked to photoprotective pathways. Parkes et al. (2022) enhanced astaxanthin production in three Haematococcus species using blue light, which upregulates the psy, pds, dgat1 and dgat2d gene pathways- precursors for xanthophyll cycle pigments. D. salina and P. tricornutum exposed to a combination of red (75%) and blue (25%) LED light resulted in 3.3-fold higher β-carotene, and 2-fold higher fucoxanthin content, respectively (Fu et al., 2013; Yi et al., 2015). Interestingly, similar increases in astaxanthin production have been observed with ALE under salinity stress, nitrogen deprivation, and glucose supplementation in Haematococcus pluvialis and Chromochloris Zofingiensis (Lu et al., 2021). Recent advancements include the strategic design of multi-factor ALE to enhance microalgae tolerance to multiple stressors for practical applications, along with machine learning models to identify optimal evolutionary endpoints (B. Zhang et al., 2021).

Gene editing is extremely efficient when focused on targeted biosynthesis pathways such as fatty acid production e.g., N. gaditana enhanced from 20% (wild-type) to 40-55% (mutant) in N-replete conditions (Ajjawi et al., 2017). However, ALE might be advantageous over gene editing for enhancing adaptations such as stress tolerance, as these adaptations are typically mediated polygenically. Furthermore, genetically modified microalgae are subject to ethical and regulatory concerns, especially for use as a feedstock. In this respect, biocontainment of mutants can be physically ensured using closed systems such as photobioreactors, as well as biochemical assurances that work under ‘lock-and-key’ methods, such as synthetic auxotrophy and conditional lethality, which can be further explored in Sebesta et al. (2022). Overall, gene editing technology remains highly optimal for the biofuels and bioplastics sectors.

Recent research aimed at enhancing lipid accumulation for aquafeed for large-scale applications focuses on co-cultivation strategies, especially with the phytobiome, the community of bacteria that interact with the extracellular polymeric substances excreted by algae. Co-culturing I. galbana with Marinobacter sp. (Wang et al., 2022; Xu et al., 2024) and Bacillus jeotgali (Xu et al., 2024) enhanced DHA and EPA production, upregulating desaturase genes associated with PUFA biosynthesis. These bacteria create a less oxidative environment through mechanisms such as gas exchange, secretion of phytohormone and quorum signalling compounds, nutrient acquisition, antibiotic production, and degradation of organic matter (Wang et al., 2022).

Use of elicitors such as phytohormones and quorum signalling compounds that influence microbial consortia behaviour also show great potential for regulating axenic cultures, particularly in photobioreactors. Although more research is needed to determine their effects on different algal strains and to identify phytohormone receptors. Preliminary findings are promising with increases in high-value metabolites, specific growth, and stress tolerance reported (Han et al., 2018).

The genetic diversity of microalgae is expected to expand alongside advances in metabolic engineering. To support the deployment of elite strains across environmental conditions, high-throughput screening technologies are being developed to catalogue complex phenotypic data. Microalgal phenomics aims to emulate existing plant and yeast phenomics databases by constructing a searchable library of phenotypic traits, enabling researchers to identify shared characteristics and distinguish the roles of seemingly redundant gene copies (Fabris et al., 2020). In aquaculture, phenotypic traits such as the nutritional and bioactive content but also digestibility of microalgae could be mapped to specific animal models. This approach would allow strain development to target specific nutritional gaps in key aquaculture species across varying environments.

High production and processing costs have limited the scalability of microalgae-based feeds; however, biotechnological advances in the field of metabolic engineering now allow for greater strain diversification, enabling optimised production in wastewater systems, saline environments, and non-arable land. While recent photobioreactor technologies can improve productivity and reduce biofouling and contamination, downstream costs associated with harvesting and pre-treatment remain significant. As algal growth and metabolite production are intrinsically linked in a complex system, incorporating a biorefinery at the algae production site increases economic feasibility in three key ways. First, it enables full automation from seeding to extraction. Second, it allows for the integration of advanced control systems such as artificial intelligence to dynamically adjust abiotic conditions to optimise metabolite yield. Third, co-locating the biorefinery with the production reduces costs associated with transport and facilitates recycling waste streams such as CO2 emissions generated during production (Lim et al., 2022; Samoraj et al., 2024).

Technological advances in downstream processing have significant potential for enhancing microalgae utilization in aquaculture, particularly through improved hydrolysis methods that maximize nutrient bioavailability, while reducing costs.

Hydrolysis techniques can significantly improve nutrient bioavailability of aquafeeds for aquaculture species. For example, apparent digestibility coefficients (ADCs) for microalgae proteins in fish can range from 60-85% depending on species and processing method, with mechanical cell disruption typically improving protein ADCs by 10-20%, compared to untreated biomass (Ahmad et al., 2022; Rahman Shah et al., 2018). The use of chemical treatments like acid/alkaline hydrolysis, thermal processing via extrusion, and ultrasonification also demonstrate effectiveness in improving protein digestibility (Sirohi et al., 2021). However, these come at high capital and operational costs. Therefore it is vital that more cost-effective treatments are explored.

Promising “Green methods” show that bacteria can also mediate downstream processing steps including flocculation (Yee et al., 2021) as well as hydrolytic treatment of cell wall during fermentation (Barati et al., 2021), increasing their digestibility in aquafeed (Ali et al., 2024). A better understanding of algae-bacteria interactions could also benefit open raceway farms and waste-water based cultivation systems, where contamination is unavoidable. By providing necessary prebiotics and probiotics to the medium, the enrichment of production-stage bacteria could significantly reduce costs (Úbeda et al., 2017). This synergistic approach may also enhance aquaculture health by inhibiting pathogens during circular cultivation (Smahajcsik et al., 2025).