Microalgae as an Eco-Friendly and Functional Ingredient for Sustainable Aquafeed

Abstract

Aquaculture is the fastest-growing food production sector and plays a pivotal role in global food security. However, the reliance on conventional fishmeal and fish oil in aquafeeds raises sustainability concerns due to overfishing, high costs, and ecological burden. This review explores the valorisation of microalgae as a sustainable and functional alternative for aquafeed development. Microalgae are rich in proteins, polyunsaturated fatty acids, bioactive compounds, and pigments that support aquatic animal growth, immunity, and product quality. We critically examine the integration of green technologies, including cultivation systems, biomass harvesting, and eco-friendly extraction methods for optimising microalgal biomass and bioactive recovery. The review also discusses recent innovations in bioremediation and circular aquaculture systems, highlighting the role of microalgae in reducing nutrient discharge, carbon footprint, and operational cost. Challenges such as scalability, digestibility, and economic feasibility are also addressed, providing insight into pathways toward industrial adoption. This review aims to provide an updated and holistic perspective on microalgae-based aquafeeds in advancing sustainable aquaculture practices.

1. Introduction

Aquaculture has become the dominant source of aquatic animal production, contributing 57% (94.4 million tonnes) of global fish consumption for direct human use in 2022, according to the FAO’s latest report [1]. Of the total 223.2 million tonnes of aquatic production, 89% was intended for food and the remainder for non-food uses, mainly fishmeal (FM) and fish oil (FO) [1]. The demand for commercial feed, on which nearly 70% of global aquaculture depends, is growing more rapidly than the industry itself [2]. This trend underscores the critical need for sustainable feed management, which contributes to approximately 60% of total production costs, for long-term economic viability [3,4].

Efficient feed systems are vital for optimising the feed conversion ratio (FCR) and minimising environmental impact. These strategies involve species-specific nutritional formulations considering protein–energy balance, fish size, feeding frequency, water quality, and oxygen levels [2,5,6]. While FM and FO remain gold standards for aquafeed due to their digestibility and high concentrations of long-chain polyunsaturated fatty acids (LC-PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), their environmental sustainability, escalating cost, and dwindling availability have prompted a global search for alternatives [1,7,8].

Consequently, there has been a significant shift in research focusing towards incorporating novel and sustainable feed ingredients such as single-cell proteins, plant-derived compounds, and notably microalgae [9,10]. Their integration into circular aquaculture models supports wastewater remediation, reduces greenhouse gas emissions, and enhances nutrient recycling, making them promising candidates for future aquafeeds [11].

Furthermore, global initiatives such as the Sustainable New Ingredients to Promote Health (SNIPH) under GAIN (Green Aquaculture Intensification in Europe) work with countries across the globe (UK, India, Tanzania, and Kenya) to develop fish feed using indigenous materials, including macrophytes, algae, and microbes [12]. This strategy simultaneously addresses aquafeed sustainability and global public health concerns.

The selection of ingredients for feed formulation is subject to several aspects, ranging from nutrient density, digestibility, palatability, environmental impact, cost-effectiveness, and market availability. These are summarised in Figure 1, which outlines the key considerations in aquafeed ingredient selection [11,13,14,15].

These factors represent essential checkpoints in designing nutritionally balanced and environmentally responsible aquafeeds. Nutrient density is vital to ensure optimal growth and health across diverse aquaculture species [16]. Digestibility and palatability significantly affect voluntary feed intake and feed conversion efficiency, which are crucial for performance and economic feasibility [17]. Environmental concerns have gained prominence due to the increasing need to reduce nutrient loading, greenhouse gas emissions, and reliance on wild fish resources for FM and FO production [18]. Given that feed can account for up to 60% of total production costs, cost-effectiveness is a critical consideration in sustaining large-scale operations [4]. Market availability, including regional accessibility and supply chain stability, also shapes the practicality of ingredient adoption [19]. In this context, microalgae have gained attention due to their high protein content, essential fatty acids, and bioactive compounds, along with their capacity to grow in various systems, such as wastewater-based and closed-loop platforms [5,20]. The integration of green technology in feed production, ranging from cultivation and harvesting to bioactive compound extraction, has further improved the feasibility of microalgae in aquafeed industrial output [21]. As summarised in Figure 1, these interconnected aspects provide the rationale for advancing microalgae as sustainable feed ingredients in modern aquaculture.

Considering these multifaceted factors in feed formulation and the emerging role of microalgae as sustainable ingredients, this review was undertaken to evaluate their full potential. Therefore, this review aims to critically assess the nutritional and functional potential of microalgae in aquafeeds, highlight recent advancements in green technologies applied in their cultivation and bioactive extraction, address challenges related to scalability, bioavailability, and cost-effectiveness, and explore the role of microalgae in circular aquaculture systems and bioremediation. Through this comprehensive analysis, we provide a current perspective on how microalgae, when supported by technological innovation and ecosystem-based practices, can contribute to the development of sustainable aquafeed.

2. Microalgae as Aquaculture Feed

Microalgae have garnered increasing attention as a sustainable alternative to conventional FM and FO due to their high nutritional value, rapid biomass productivity, and minimal land and freshwater requirements [19]. In alignment with the FAO’s Blue Transformation Roadmap, microalgae are well-positioned to support sustainable aquatic food growth, enhance ecological resilience, and address feed-related bottlenecks in aquaculture [1].

Various microalgal species are rich sources of proteins, polyunsaturated fatty acids (PUFAs), carbohydrates, pigments, vitamins, and minerals, making them ideal candidates for both nutritional and functional feed formulations [22,23,24]. These bioactive compounds not only promote growth but also improve feed conversion efficiency, immunity, and stress resistance in farmed species [25].

2.1. Bioactive and Nutritional Components from Microalgae for Functional Aquafeed Applications

2.1.1. Protein

Microalgae such as Spirulina sp., Chlorella sp., Dunaliella sp., Chlamydomonas sp., Scenedesmus sp., and Isochrysis sp. are generally rich in protein content (40–55%), with all the essential amino acids required for aquatic life [26]. The partial or total replacement of FM by microalgae in the aquaculture feed for their protein and energy sources did not negatively affect, but at times enhanced, the growth rate and weight gain of several aquatic species compared with the control group, such as in Pacific white shrimp (Litopenaeus vannamei), rainbow trout (Oncorhynchus mykiss) [27], juvenile turbot (Scophthalmus maximus L.) [28], juvenile steelhead (O. mykiss) [29], and juvenile gilthead seabream (Sparus aurata) [30]. Apart from that, protein from microalgae can boost the immune system of aquatic life, as shown by a study using Spirulina platensis, which exhibited increased immunity in white shrimp by increasing haemocytes, an important component of the immune system, functioning in phagocytosis [31]. A dietary intervention using 10–15% of Nannochloropsis oculata in Nile tilapia (Oreochromis niloticus) juvenile feeds showed a significant decrease in the cumulative mortality rate when exposed to a pathogenic strain of Aeromonas veronii bacteria, compared with the control [32].

2.1.2. Fatty Acids

Microalgae are rich in omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFAs), including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and docosapentaenoic acid (DPA) [33]. Microalgae rich in PUFAs can be achieved through mutagenesis, selective breeding, or genetic modifications to enhance biomass production and increase biosynthesis of the PUFAs [22]. Most fish cannot synthesise them de novo and can only acquire and accumulate them via their diet [34]. These fatty acids are important in fish diets, especially in farmed fish species, particularly Atlantic salmon (Salmo salar L.), as dietary n-3 LC-PUFAs play multiple essential roles in fish physiology and health. For instance, EPA and DHA are critical for neural development, fillet quality, and early growth, particularly in the formation of brain retinal tissues, improve innate immune activity, and reduce plasma corticosteroid levels under stress [35,36,37]. Among the microalgae species reported for their high PUFAs, including Nannochloropsis sp., Schizochytrium sp., Phaeodactylum sp., and Isochrysis sp. Zakaria et al. [34] highlighted that Nannochloropsis oceanica and Crypthecodinium cohnii are especially rich in EPA and DHA, respectively, making them suitable candidates for FO replacement in aquafeeds [34]. Schizochytrium sp. has been shown to be as a promising FO substitute in diets for juvenile Atlantic salmon (Salmo salar), significantly improving DHA digestibility [15]. In a more recent study, partial (50%) replacement of FO with Schizochytrium sp.-derived algal oil enhanced mucosal barrier functions in the intestine, skin, and gills, increased mucous cell density, and upregulated mucin and antimicrobial peptide gene expression without compromising salinity tolerance. These findings reinforce the functional value of microalgal lipids in promoting fish health while supporting sustainable aquafeed development [25]. Furthermore, an effective complete replacement of FO with two commercial oils from microalgae and in combination with other cost-effective lipid sources (poultry and rapeseed oils) for gilthead seabream (S. aurata) juveniles, was reported, showing that growth performance was unaffected and the nutritional quality of the fish products was maintained [38]. Microalgae cultivation can be optimised for PUFA production through selective breeding, nutrient management, and controlled environmental conditions, further enhancing their applicability in sustainable aquafeed development [34]. Thus, microalgae represent a reliable and functional lipid source that not only fulfils the physiological requirements of farmed aquatic species but also promotes their health, resilience, and fillet quality.

2.1.3. Carbohydrates

Microalgae contain carbohydrates, which are made up of glucose, sugars, starch, and various polysaccharides, which comprise up to 50% of their dry weight due to the high efficiency of their photosynthesis process [39]. Species such as Tetraselmis subcordiformis, Chlamydomonas reinhardtii, and Chlorella vulgaris exhibit higher starch content, ranging from 30% to 49% [40]. In contrast, fibre, a complex carbohydrate, ranges from 5% to 18% in microalgae [41]. Unlike terrestrial plants, microalgal fibre lacks lignin and contains lower hemicellulose levels, which suggests better digestibility [42]. Species such as Spirulina sp. and C. vulgaris have lower fibre contents (8.5% and 5.6%, respectively), while higher fibre levels are reported in Nannochloropsis, Tetraselmis, Tisochrysis, and Phaeodactylum species [42].

Polysaccharides, particularly the sulphated exopolysaccharides from several microalgae, have been reported to exhibit various beneficial effects, which include antiviral, antioxidant, anti-inflammatory, anti-tumour, hypolipidaemic, and hypoglycaemic properties, anti-adhesive agents, and anticoagulant and antithrombotic activity [43]. Moreover, water-soluble polysaccharides rich in (β1→3, β1→4)-glucans, (α1→3), (α1→4)-mannans, and anionic sulphated heterorhamnans also showed immunostimulatory activity, enhancing specific mechanisms of innate and adaptive immune responses [44].

2.1.4. Pigment Components

There are three classes of pigments in microalgae, namely carotenoids (carotenes and xanthophylls), chlorophylls (a, b, and c), and phycobiliproteins [45]. Among the three classes of pigments, carotenoids have been extensively used in the aquaculture field. Carotenoids act as pigment agents, offering a desirable pink or red colour to salmonids and other farmed aquatic life. Aquatic life fed with xanthophyll carotenoids such as Astaxanthin-producing microalgae (e.g., Haematococcus pluvialis) demonstrated improved growth performance, reproduction, and obvious colour changes in their flesh or muscle [46]. The greenlip abalone (Haliotis laevigata Donovan) showed changes in colour after being fed with several macroalgae and Spirulina sp. [47]. European sea bass (Dicentrarchus labrax) fed with a combination of dried Tisochrysis lutea and Tetraselmis suecica containing xanthophyll carotenoids changed towards grey-greenness at the dorsal part of the fish skin, with a slight tendency towards redness [48]. Shrimps tend to be redder in colour and the content of astaxanthins (free and esterified) were found to be higher in the group fed with H. pluvialis compared to the control, indicating the replacement of microalgae meal could be a good source of pigmentation as well as a source of protein [49]. Porphyridium cruentum showed better results for pigmentation, weight gain, and feed conversion ratio on ornamental fish, Tomato Clownfish (Amphiprion frenatus), compared to Nannochloropsis oculata and the control group [50]. In addition, carotenoids are shown to possess antioxidant and anti-inflammatory properties, improving the immune system [51,52].

2.1.5. Vitamins

Microalgae are valuable sources of both water- and lipid-soluble vitamins that support the growth, immunity, and overall health of aquatic species. Several microalgal species, including Spirulina, Dunaliella, Haematococcus, Chlorella, and Aphanizomenon, contain a broad spectrum of vitamins, such as β-carotene, B-complex (B1, B2, B3, B5, B6, B7, B9, and B12), C, D, E, and K. These vitamins are essential in metabolic processes, including coenzyme activity, fatty acid synthesis, and DNA repair [53]. All these vitamins increase the nutritional value of microalgae and provide aquatic life with essential nutrients important for development, which they are unable to synthesise by themselves.

Species-specific examples include N. oceanica, which is rich in vitamin D, Tetraselmis suecica and Dunaliella tertiolecta for vitamin E, and Chlorella sp. and Dunaliella salina for vitamin C. The content and composition of these vitamins are influenced by cultivation conditions such as the nutrient levels, light intensity, and harvest stage [52].

2.2. Microalgae in Aquaculture-Current and Future Trends

The current landscape of microalgae-based aquafeeds is characterised by a focus on producing feeds with high nutritional value, improved digestibility, enhanced palatability, and higher yields, while simultaneously boosting the health and disease resistance of aquatic organisms. Additionally, the aquaculture technologies involved emphasise being cost-effective, environmentally friendly, and sustainable, with some systems also contributing to wastewater treatment and improving water quality [19,54,55].

Recent comprehensive reviews, such as Siddik et al. [56], have further highlighted that microalgae like Spirulina, Chlorella, Nannochloropsis, and Tetraselmis are increasingly utilised to replace or supplement traditional fishmeal in aquafeeds. These microalgae provide essential nutrients, including high-quality proteins, omega-3 fatty acids, pigments, and immunostimulants, offering both nutritional and functional benefits. Siddik and colleagues also noted that the inclusion of microalgae at appropriate levels (typically 2–10%) can enhance growth performance, immune responses, and survival rates in various aquatic species, supporting the sustainability agenda in global aquaculture [56].

Moreover, microalgae are being cultivated through sustainable systems such as integrated multi-trophic aquaculture (IMTA) and circular economy-based platforms, which recycle nutrients while producing biomass for feed. Technological advancements in photobioreactors, strain engineering, and precision harvesting have also enhanced the economic viability and scalability of microalgae for industrial aquafeed production [57,58].

Techniques like Green Water Aquaculture and Biofloc Technology (BFT) which was developed at the Waddell Mariculture Centre (United States) in the early 1990s are considered promising approaches for sustainable aquafarming [59,60]. ”Green water” and “pseudo-green water” techniques employ microalgae in larval rearing tanks, promoting higher survival and growth rates in marine fish larvae [59]. Nutrient-rich biomass is produced by fertilising ponds with agricultural or domestic waste, or chemical fertilisers, thereby supporting the growth of natural or inoculated algal populations and grazers [61]. The aquatic animals graze on this biomass, reducing the need for commercial feeds and fostering a healthier aquatic environment through managed fertilisation, grazing, and water circulation [62].

BFT involves the aggregation of microbial communities (algae, bacteria, and protozoa) into flocs, converting organic waste into microbial protein and improving water quality in intensive aquaculture systems [63,64]. Studies have demonstrated that bioflocs can protect shrimp against diseases such as acute hepatopancreatic necrosis disease without compromising growth performance or immune responses [65,66]. Jung et al. [67] reported enhanced immune responses in Nile tilapia (Oreochromis niloticus) when autotrophic BFT systems using microalgae like C. vulgaris and Scenedesmus obliquus were employed. Overall, BFT promotes nutrient recycling, optimises water quality, and improves aquatic growth, productivity, and survival rates [63,64].

However, despite these benefits, the use of live microalgae necessitates a comprehensive and systematic management system to maintain water quality, oxygen production, and nitrogen absorption, leading to higher maintenance costs [68]. As a result, there is an increasing trend toward the adoption of alternative delivery forms, such as whole-cell feeds (dried, paste, powder, cryopreserved, or flocculated microalgae) and formulated feeds (e.g., microencapsulated products), which offer similar bioactive benefits while being more cost-effective and easier to handle [69,70]. These formulations provide key nutrients, including proteins, polysaccharides, fatty acids, pigments, immunostimulants, and antimicrobial compounds that support aquatic animal health and production.

Microalgal pastes in dry or flocculated forms are increasingly used as protein-rich feeds for aquatic species, especially in small hatcheries, where they reduce the need for live algal cultures. Key harvesting methods include centrifugation and bio-flocculation, with strain selection enhancing cost-efficiency. Shelf-life extension technologies such as freezing, vacuum packaging, and lyophilization maintain the nutritional integrity of products like Nanno 3600 and LiveNanno, which can remain viable for months. Additionally, dry formulated aquafeeds, including pellet-based diets, are growing in popularity. While extrusion is the preferred method for large-scale production, cold pelleting better preserves bioactive compounds. Vacuum oil coating is applied for high-lipid formulations, particularly for species like salmon. Furthermore, emerging delivery systems such as microencapsulation and nanoencapsulation offer enhanced protection and controlled release of sensitive nutrients, including fatty acids, vitamins, and bioactive peptides, thereby improving feed efficiency, stability, and nutrient bioavailability in intensive aquaculture systems [71,72,73].

Recent advances in single-cell protein (SCP) technologies derived from microalgae are redefining the future of sustainable aquafeeds. Microalgae-based SCPs are increasingly recognised as a viable and eco-friendly alternative to fishmeal, offering high-quality proteins, complete amino acid profiles, and a wealth of functional metabolites such as pigments, antioxidants, and immunostimulants. Unlike traditional protein sources, SCPs from microalgae require significantly less arable land, freshwater, and production time, aligning with the goals of circular bioeconomy and low-carbon aquaculture. Li et al. [74] provided a comprehensive review of recent breakthroughs that are addressing previous bottlenecks in SCP production. Innovations include advanced bioprocess engineering for high-cell-density cultivation, continuous harvesting systems, and the use of cost-effective agro-industrial byproducts (e.g., molasses, glycerol, and lignocellulosic hydrolysates) as carbon sources, which significantly reduce production costs. Moreover, metabolic engineering and precision fermentation have enabled strain improvements to enhance protein yield, digestibility, and nutrient bioavailability, which are key parameters for aquafeed formulation [74].

In parallel, artificial intelligence (AI) technologies are being deployed to optimise microalgae cultivation and integration into aquafeeds. AI-driven aquaculture platforms facilitate real-time monitoring of growth parameters, nutrient composition, and environmental conditions, ensuring consistent biomass yield and quality. These platforms also enhance precision feeding strategies and predictive modelling of microalgal performance under variable aquaculture conditions, supporting sustainable feed development [75,76,77]. The convergence of AI, biotechnology, and circular aquaculture systems is thus transforming microalgae from a niche supplement to a cornerstone of future aquafeed solutions.

2.3. Advantages and Limitations of Microalgae Feed

There are several advantages of using microalgae as aquaculture feeds. Among them are that microalgae are much easier to cultivate, require minimal resources, and can grow in diverse environmental conditions, including wastewater, seawater, or closed-loop systems, produce more biomass in a short period, can accumulate beneficial metabolites depending on the treatment given, can be produced all-year-round, and do not require insecticide, fertile land, fertiliser, a large area, or an abundance of water for irrigation compared to terrestrial plants [78]. Additionally, the use of microalgae can reduce reliance on conventional feed (FM and FO), which have been decreasing in supplies but with soaring prices [79]. The use of microalgae as feed restores the taste of aquatic life as caught from the wild, giving the ‘natural river or marine taste’ [80]. High-quality microalgae produced through systematic and high-technology cultivation and harvesting techniques are exposed to lesser contaminations (bacteria and pathogens), thus preventing any epidemic outbreaks in the aquafarms, maintaining and producing good quality aquatic animals for human consumption [81]. Microalgae-based feed is known to be rich with various beneficial components, such as amino acids, polysaccharides, pigments, and fatty acids (Omega 3 with EPA and DHA) [82].This would be more likely to equip the aquatic animals with higher health benefits, thus increasing their value in the markets and helping improve the health status of the consumers.

However, some limitations or challenges need to be addressed when using microalgae as feed for aquaculture. The production of microalgae biomass is relatively expensive, with many steps involved, such as cultivating, harvesting, transforming into a feed, and long-term storage [26]. Furthermore, contamination may occur during mass cultivation, especially in open pond systems where the process is not controlled. Fluctuations in temperature and light intensities can also contribute to the unsuccessful cultivation of microalgae for aquafeed [83]. Variability in nutrient composition and the presence of indigestible cell walls also limit broad-scale adoption. Finding suitable and appropriate digestion techniques such as enzymatic pre-treatment, co-feeding strategies or identifying good strains with the best cell wall digestibility can be time and energy-consuming and increase cost [84]. Using aquaculture effluent as the medium for microalgae growth for aquafeed could face or create several technical problems, which include a lower growth rate due to the deficiency of nutrients in the effluent, producing an alkaline environment which is not suitable for many aquatic animals, higher energy consumption and operation cost needed if a temperature control system is included to maintain temperature during winter, the occurrence of bacterial bloom, which will affect the life of the aquatic animals, and high accumulation of heavy metals in microalgae if safety measures or precautions are not taken [85]. Additionally, species-specific responses to microalgae inclusion whereby multiple criteria including the fish age, feed inclusion rate, and environmental factors must be considered when formulating diets. For instance, while up to 25% fishmeal replacement improved growth in Senegalese sole, results may not directly translate to other species without optimisation [28].

Further research is warranted to determine optimal inclusion levels, improve biomass digestibility, and reduce cost through co-products and integrated cultivation systems. These advances will be essential to achieve industrial scalability without compromising performance or safety.

3. Green Technology Application for Feed Development

The application of green technologies in aquafeed processing encompasses the cultivation, harvesting, biomass preservation, and extraction of high-value compounds from microalgae. These approaches reduce energy inputs, minimise solvent use, and support eco-friendly feed production.

3.1. Biomass Cultivation, Harvesting and Dehydration

Microalgae are photosynthetic organisms that encompass almost 7000 species known to grow in numerous habitats. Freshwater, brackish water, or seawater are among the diverse environmental conditions that could serve as a habitat for microalgae [46]. In line with their ability to thrive in diverse environmental conditions, accordingly, they could be grown under various systems such as closed reactors, photobioreactors, open ponds, or marine environments. It is interesting to note that these systems could be established in a way that protects the environment by avoiding the use of herbicides or pesticides. Upon exposure to sunlight, microalgae convert carbon dioxide into oxygen and biomass [86,87,88]. The conventional approach of microalgae biomass production includes three main processes; namely, cultivation, harvesting, and biomass dehydration.

Microalgae cultivation relies on their metabolic ability to be photoautotrophic, heterotrophic, or mixotrophic. The characteristics of each ability are indicated in

Table 1. Characteristics of microalgae cultivation and metabolism ability.

Metabolic Ability	Microalgae Cultivation	Reference
Photoautotrophic	Depends on light for energy and inorganic components (CO2, salts) for metabolism	[89]
Heterotrophic	A combination of photoautotrophic and heterotrophic conditions that requires external organic substances or carbon sources (glucose) for growth
Mixotrophic	Subjected to a supply of both inorganic and some organic carbon sources (glucose and glycerol) for growth

. Three well-established cultivation systems are available: an open pond, closed photobioreactor, and hybrid production. Figure 2 shows the details and advantages of each system.

The conventional open pond systems are cost-effective but often challenging for aquafeed applications involving wastewater remediation due to the high contamination risk and inconsistent biomass quality. Generally, the most important characteristics for aquaculture cultivation are high photosynthesis rate, low cost, and high land utilisation efficiency. As such, two systems, called the raceway pond (closed system) and revolving algal biofilm (hybrid), are the preferred cultivation methods for the aquaculture industry [55].

Table 2 summarises two key microalgae cultivation systems: the raceway pond (RP) and revolving algal biofilm (RAB), highlighting their operational principles, advantages, and limitations in the context of aquafeed production and integrated aquaculture systems. The RP system, characterised by shallow open channels propelled by paddle wheels, is one of the most widely adopted low-cost methods for producing large volumes of microalgal biomass. However, it is constrained by several challenges, including susceptibility to contamination, exposure to environmental fluctuations, and energy-intensive harvesting procedures [55,90,91,92]. Recent developments in raceway pond technology have addressed some of these limitations through improved paddlewheel configurations and the introduction of alternative circulation mechanisms such as airlift and jet-type systems. Advances in fluid dynamics and computational modelling have further enhanced nutrient distribution, mixing efficiency, and system stability, thereby reducing energy consumption and supporting large-scale operations. These innovations contribute to positioning RP systems as viable, scalable, and environmentally responsible solutions for sustainable microalgae cultivation in aquafeed applications [20].

In contrast, the RAB system integrates cultivation and biomass harvesting through microalgal attachment to rotating biofilms in shallow ponds, often using aquaculture wastewater as a nutrient source. This closed-loop approach significantly enhances land use efficiency, simplifies biomass recovery without chemical additives, and supports circular bioeconomy practices [93]. Research by Wood et al. [94] demonstrated its effectiveness in cultivating high-value microalgal biomass and enhancing phycocyanin pigment production from cyanobacteria grown on oilfield- and natural gas-produced wastewater. Cyanobacterial strains cultured in RAB reactors under low-light conditions achieved a significantly higher phycocyanin yield (31.7 mg/g ash-free dry weight), although overall biomass productivity was lower compared to high-light conditions. Substrate evaluation revealed that cotton belt material supported healthier, photosynthetically active biofilms with higher phycocyanin yield (47.0 mg/g AFDW) and lower autotrophic index, compared to cotton rope. These findings highlight the RAB system’s dual potential for high-value pigment production and sustainable wastewater valorisation through optimised light conditions and substrate selection. The RAB system, while offering integrated harvesting and high-quality biomass, faces limitations such as microbial contamination due to open exposure and higher operational costs compared to simpler systems. Additionally, its effectiveness is influenced by substrate type, species compatibility, and sensitivity to light conditions, posing challenges for large-scale aquaculture applications [94].

The cultured biomass then undergoes the harvesting process to separate the microalgae from its culture medium. The choice of harvesting technique is interdependent on microalgae characteristics (e.g., density, size, and desired final product), and under certain circumstances, a combination of multiple techniques is also applied for enhanced effectiveness [84]. To date, four methods have been widely employed, known as biomass aggregation, flotation, centrifugation, and filtration. The flotation technique has been acknowledged as one of the most economical processes in microalgae harvesting. This method is an inverted sedimentation, with a small footprint, a low detention period, and a high flow rate [95]. In terms of its application for aquaculture, the microalgae biomass harvest as feed requires excessive safety control. Thus, in this modified flotation technique, it was suggested to use natural polymers (e.g., proteins or polysaccharides) instead of metal ions [55].

Following harvesting, dehydration is a critical post-harvest step to preserve biomass quality for further processing. Three main dehydration methods are commonly used: sun-drying, spray-drying, and freeze-drying. Sun-drying, the most economical option, relies solely on solar energy but is susceptible to weather variability, which can compromise final product quality [96]. Spray-drying produces a fine powder rapidly from a suspension of droplets, making it suitable for large-scale operations, though it entails high operational costs [96,97,98]. Freeze-drying applies the process of direct dehydration of frozen products and is usually applied at the laboratory scale [99,100]. Selecting appropriate dehydration methods is crucial to preserve proteins, pigments, fatty acids, and enzymes that contribute to aquafeed functionality.

Another promising technology is fungi-assisted harvesting, which involves adding filamentous fungi to microalgal cultures. These fungi form pellets that entrap the microalgal cells, allowing subsequent recovery through filtration [101]. However, the synthesis of fungal pellets may incur additional costs since it requires special attention to the equipment and fermentation conditions. Moreover, any fungal species used must be proven safe, without secreting toxic metabolites that could harm aquaculture systems [55].

In summary, suitable harvesting methods include three core criteria: Firstly, a minimal cost, in order to improve the effectiveness of microalgae feed over the traditional ones. Second, safety is deemed vital and, as such, the process is ensured to be free of toxic and harmful chemicals. Finally, the whole process should be time-saving and efficient. Both fungi-assisted harvesting and modified flotation represent advanced approaches that meet these criteria and show strong potential for aquaculture feed applications [55].

Table 2. The characteristics, advantages, and limitations of cultivation systems.

Cultivation System	Advantages and Limitations	Reference
Raceway pond (RP) A closed circulation channel (depth of 0.2–1.0 m) and one/two paddle wheels that drive the circulation of the water body	Advantages: Lower cost of investment with higher volume	[55,91,92,102]
	Limitations: High contamination risks of microalgae biomass by bacteria and other microbes Microalgae growth might be limited due to unfavourable conditions (temperature fluctuation, light deficiency) The system is highly influenced by the external environment Harvesting process is time-consuming and energy-intensive Shear stress and hydrodynamic damage
Revolving algal biofilm (RAB) A system consisting of microalgal biofilm, a drive unit, and an open pond with wastewater. Theoretically, the RAB system has higher land utilisation efficiency and biomass productivity than the RP system	Advantages: Integrates algae cultivation with biomass harvesting Cost-saving and eco-friendly to harvest biomass attached to film using a scraper Harvesting process is free of chemicals; the yield biomass is highly safe for aquaculture utilisation Promising technology for wastewater remediation and resource recycling in aquaculture based on nutrients recovery and biomass reuse perspectives	[55,90,93,103]
	Limitations: Exposure of the system to the atmosphere during operation causes simultaneous growth of bacteria/fungi with microalgae on the biofilm Higher cost than RP systems

Table 2. The characteristics, advantages, and limitations of cultivation systems.

Cultivation System	Advantages and Limitations	Reference
Raceway pond (RP) A closed circulation channel (depth of 0.2–1.0 m) and one/two paddle wheels that drive the circulation of the water body	Advantages: Lower cost of investment with higher volume	[55,91,92,102]
	Limitations: High contamination risks of microalgae biomass by bacteria and other microbes Microalgae growth might be limited due to unfavourable conditions (temperature fluctuation, light deficiency) The system is highly influenced by the external environment Harvesting process is time-consuming and energy-intensive Shear stress and hydrodynamic damage
Revolving algal biofilm (RAB) A system consisting of microalgal biofilm, a drive unit, and an open pond with wastewater. Theoretically, the RAB system has higher land utilisation efficiency and biomass productivity than the RP system	Advantages: Integrates algae cultivation with biomass harvesting Cost-saving and eco-friendly to harvest biomass attached to film using a scraper Harvesting process is free of chemicals; the yield biomass is highly safe for aquaculture utilisation Promising technology for wastewater remediation and resource recycling in aquaculture based on nutrients recovery and biomass reuse perspectives	[55,90,93,103]
	Limitations: Exposure of the system to the atmosphere during operation causes simultaneous growth of bacteria/fungi with microalgae on the biofilm Higher cost than RP systems

3.2. Extraction Process of Bioactive Compound Using Green Techniques

Microalgae biomass is well recognised as a rich source of natural compounds that are considered vital for almost all living organisms. These bioactive compounds are carotenoids, vitamins, pigments, fatty acids, proteins, and minerals, and their diversity and uniqueness are applied in numerous industries [86,104,105,106]. Despite the abundance of bioactive compounds, an efficient extraction process is the most essential factor in determining the quality of each extracted component.

Over the years, various studies have highlighted both conventional and non-conventional technologies. Conventional techniques commonly used include maceration, heat-assisted extraction, and Soxhlet extraction. In contrast, non-conventional approaches or green extraction technologies such as supercritical fluid extraction (SFE), pressurised liquid extraction (PLE), ultrasound-assisted extraction (UAE), microwave-assisted extraction (MAE), enzyme-assisted extraction (EAE), pulsed electric field (PEF), and ionic liquid (IL)-based extraction have emerged as sustainable alternatives to conventional solvent-based methods [107].

SFE utilises CO₂ under high pressure and low temperature to efficiently extract lipophilic compounds like PUFAs and carotenoids [108], while PLE employs eco-friendly solvents such as ethanol and water at elevated pressures for rapid and efficient recovery of high-value bioactives [109]. UAE enhances cell wall disruption and mass transfer, significantly reducing extraction time and solvent use [110], whereas MAE rapidly heats intracellular water to rupture microalgal cells, facilitating the release of polar compounds [110]. EAE, on the other hand, employs specific hydrolytic enzymes such as cellulase, protease, or lysozyme to degrade cell wall polymers under mild conditions, thereby improving the recovery of intracellular compounds like polysaccharides, proteins, and phenolics with minimal degradation [109]. These methods not only improve extraction yield and purity but also help preserve heat-sensitive bioactives such as astaxanthin, phycocyanin, and β-carotene [111,112,113]. PEF is a non-thermal technique that applies short, high-voltage pulses to microalgae cells, causing electroporation of the cell membranes. This enhances the release of intracellular compounds such as proteins, lipids, and pigments without degrading thermolabile bioactives, making it ideal for recovering high-value nutrients from wet microalgal biomass in aquafeed production [114]. IL extraction involves the use of tailor-made organic salts in liquid form at room temperature to disrupt microalgal cell walls and selectively extract bioactive compounds such as phycobiliproteins, carotenoids, and omega-3 fatty acids [115].

The selection of the extraction technique is related to several criteria that incorporate its intended application, biomass properties, and physical and chemical characteristics of the extracted molecules [116]. Conventional techniques are shown to be highly prone to several shortcomings, such as thermal degradation caused by high temperature or the presence of solvent residues that interfere with their end use [116]. Likewise, it is also necessary to address the need for a sample pre-treatment step before extracting the compounds that could facilitate mass transfer of intracellular compounds from microalgae chloroplasts [117,118,119,120,121]. The pre-treatment of microalgal cells is commonly addressed via three main techniques (chemical, enzymatic/biological, and mechanical/physical), where the selection relies on cell wall rigidity, extractable intracellular compounds, and physical and chemical properties [122]. Table 3 summarises the key extraction technologies, comparing conventional and green methods in terms of mechanisms, benefits, drawbacks, and suitability for aquafeed application.

Green technologies not only address these concerns but also improve extraction efficiency and reduce environmental impact. Among them, SFE has emerged as one of the most promising due to its many advantages. By operating above the critical temperature and pressure, SFE generates a supercritical fluid with low viscosity and high diffusivity, enhancing its transport properties. This allows for efficient recovery of bioactive compounds without volatility loss [123,124]. However, despite this technique being proposed as an eco-friendly technology with high yield and speed of extraction, it is still subject to the low polarity rate of supercritical carbon dioxide (CO₂) and increased investment cost [125].

Table 3. Comparison of microalgae extraction techniques and their suitability for aquafeed applications.

Extraction Method	Mechanism	Advantages	Limitations	Suitability for Aquafeed	References
Maceration	Solvent diffusion at room temperature	Simple, low-cost	Long extraction time, low efficiency	Limited due to solvent residue concerns	[126,127]
Heat-Assisted Extraction	Uses heat to enhance solubility	Faster than maceration	Thermal degradation of bioactives	Not ideal for heat-sensitive compounds	[128]
Soxhlet Extraction	Continuous solvent cycling with heating	Effective for stable compounds	Large solvent volumes, energy-intensive	Risk of solvent contamination in feed	[127]
Supercritical Fluid Extraction (SFE)	CO2 under high pressure and low temperature	High purity, preserves heat-sensitive compounds	Expensive equipment, low-polarity CO2	Highly suitable for lipophilic bioactives (e.g., EPA, DHA)	[129,130]
Pressurized Liquid Extraction (PLE)	Solvent under elevated pressure and temperature	Rapid extraction, eco-friendly solvents	Solvent selection critical, high pressure	Good for polar and semi-polar compounds	[109,131,132]
Ultrasound-Assisted Extraction (UAE)	Acoustic cavitation disrupts cells	Fast, low solvent use, scalable	Requires optimisation of parameters	Effective for a broad compound range	[132,133]
Microwave-Assisted Extraction (MAE)	Microwave heating of intracellular water	High efficiency, short time	Risk of thermal hotspots	Best for polar molecules (e.g., pigments, polyphenols)	[134,135]
Enzyme-Assisted Extraction (EAE)	Enzymes (e.g., cellulase or protease) degrade cell walls to release intracellular contents	Mild conditions, selective, eco-friendly	Enzyme cost, reaction time, and need for optimisation	Suitable for proteins, polysaccharides, and functional peptides	[109,125]
Pulsed Electric Field (PEF) Extraction	Applies short bursts of high-voltage electric pulses to create pores in cell membranes	Non-thermal, preserves bioactives, efficient for wet biomass	Limited by biomass conductivity and uneven field distribution	Suitable for lipid and protein recovery from wet microalgae	[114]
Ionic Liquid (IL) Extraction	Tailor-made ionic solvents disrupt cell walls and dissolve intracellular compounds	High efficiency, tunable selectivity, minimal volatility	Costly, potential toxicity, purification required for feed safety	Promising for high-value compounds, but detoxification essential for feed use	[115]

Table 3. Comparison of microalgae extraction techniques and their suitability for aquafeed applications.

Extraction Method	Mechanism	Advantages	Limitations	Suitability for Aquafeed	References
Maceration	Solvent diffusion at room temperature	Simple, low-cost	Long extraction time, low efficiency	Limited due to solvent residue concerns	[126,127]
Heat-Assisted Extraction	Uses heat to enhance solubility	Faster than maceration	Thermal degradation of bioactives	Not ideal for heat-sensitive compounds	[128]
Soxhlet Extraction	Continuous solvent cycling with heating	Effective for stable compounds	Large solvent volumes, energy-intensive	Risk of solvent contamination in feed	[127]
Supercritical Fluid Extraction (SFE)	CO2 under high pressure and low temperature	High purity, preserves heat-sensitive compounds	Expensive equipment, low-polarity CO2	Highly suitable for lipophilic bioactives (e.g., EPA, DHA)	[129,130]
Pressurized Liquid Extraction (PLE)	Solvent under elevated pressure and temperature	Rapid extraction, eco-friendly solvents	Solvent selection critical, high pressure	Good for polar and semi-polar compounds	[109,131,132]
Ultrasound-Assisted Extraction (UAE)	Acoustic cavitation disrupts cells	Fast, low solvent use, scalable	Requires optimisation of parameters	Effective for a broad compound range	[132,133]
Microwave-Assisted Extraction (MAE)	Microwave heating of intracellular water	High efficiency, short time	Risk of thermal hotspots	Best for polar molecules (e.g., pigments, polyphenols)	[134,135]
Enzyme-Assisted Extraction (EAE)	Enzymes (e.g., cellulase or protease) degrade cell walls to release intracellular contents	Mild conditions, selective, eco-friendly	Enzyme cost, reaction time, and need for optimisation	Suitable for proteins, polysaccharides, and functional peptides	[109,125]
Pulsed Electric Field (PEF) Extraction	Applies short bursts of high-voltage electric pulses to create pores in cell membranes	Non-thermal, preserves bioactives, efficient for wet biomass	Limited by biomass conductivity and uneven field distribution	Suitable for lipid and protein recovery from wet microalgae	[114]
Ionic Liquid (IL) Extraction	Tailor-made ionic solvents disrupt cell walls and dissolve intracellular compounds	High efficiency, tunable selectivity, minimal volatility	Costly, potential toxicity, purification required for feed safety	Promising for high-value compounds, but detoxification essential for feed use	[115]

Assisted extractions, which utilise enzymes, ultrasound, and microwave technology, have also gained attention for their uniqueness and superiority. EAE is an eco-friendly and low-cost approach that eliminates solvent use using food-grade enzymes (cellulase, α-amylase, and pepsin). Action of the enzymes facilitates the removal of unnecessary components and bioactive release; however, optimum temperature conditions and time should be carefully monitored to generate maximum extraction yield [125]. MAE, in contrast, is based on electromagnetic radiation frequencies that disrupt the hydrogen bonds and the migration of dissolved ions, causing the target compound to be extracted. MAE is considered helpful for its lower solvent usage and improved extraction yield and rate; however, it is limited for heat-sensitive compounds [136,137]. UAE utilises ultrasound waves and is reported as a simple and cost-efficient method, with minimal damage to heat-sensitive compounds. An additional benefit is that the equipment required is significantly less expensive compared to other green techniques. Nevertheless, wave attenuation in dispersed phase systems is addressed as a specific challenge of this technique [125,138]. PEF facilitates the release of intracellular compounds while preserving thermolabile bioactives. PEF is highly energy-efficient, compatible with wet biomass, and particularly suitable for extracting proteins and lipids [24,114,116]. However, treatment uniformity and dependence on the electrical conductivity of the biomass are considered limitations. IL extraction is highly selective and recyclable, making it attractive for green extraction. However, challenges include high cost, potential toxicity, and the need for downstream purification to ensure safety in aquafeed applications [115,129].

3.3. Benefits of Green Technology in Aquafeed Development

The selection of appropriate conditions for the extraction of bioactive compounds is highly reliant on their final intended applications. Each bioactive compound has been highlighted for various uses and continuously explored along with technological improvements. In a recent review documented by Molino and colleagues [122], commercialised products that have been marketed globally for aquaculture feed were mainly composed of carotenoids and vitamins (astaxanthin, β-carotene, canthaxanthin, and vitamin A). In addition, microalgae that are well-known as protein-rich sources (Chlorella vulgaris, Spirulina platensis, Scenedesmus obliquus, Dunaliella sp., Porphyridium sp., and Tetraselmis suecica) have also been utilised for aquaculture feed [139]. In the past, commercial applications of microalgae as aquaculture feed were shown to be limited by the high costs associated with upstream production, concentration, and storage, which eventually hinder their economic feasibility [140]. Hence, the practical approach to green technologies for sustainable aquafeed development is deemed extremely important.

The significant benefits of green technologies have been experimented and demonstrated in numerous studies. In a study by Sanzo and team [141], bioactive metabolites’ extraction from H. pluvialis used supercritical fluid extraction with CO₂ combined with ball-milling as a mechanical pre-treatment. H. pluvialis is well known for its ability to accumulate high levels of astaxanthin, lutein, and fatty acids. However, achieving high-purity extracts in an eco-friendly and cost-effective manner has remained a challenge. In this study, SFE-CO₂ demonstrated greater selectivity for fatty acids compared to astaxanthin and lutein. Notably, the method also enabled the recovery of astaxanthin and lutein with higher purity, even at lower recovery yields, highlighting its potential for efficient extraction of sensitive bioactives under mild and sustainable processing conditions [141].

In terms of protein extraction, cell disruption as an initial pre-treatment step is extremely important. A study in the year 2014 demonstrated the application of high-pressure and alkaline treatment on the cell disruption of several microalgae species that included P. cruentum, Arthrospira platensis, C. vulgaris, N. oculata, and H. pluvialis. The results concluded that mechanical pre-treatment is more effective, accounted for by its ability to disrupt cell walls and protein aggregates [142]. Similar observation was also reported in a past study that isolated proteins from D. salina using a PLE technique [143].

Overall, non-conventional extraction, also known as green extraction, is advantageous in several aspects. The utilisation of non-hazardous chemicals, replacement with safer auxiliary solvents or water, an energy efficient procedure, eco-friendly processing conditions, minimal derivative synthesis, usage of renewable feedstocks, overall cost ratio, enhanced efficacy, and elimination of degradation effects, as well as prevention of protection and deprotection steps, are the common and main advantages that have been portrayed and acknowledged with respect to these modern techniques, compared to traditional approaches [107].

Apart from lab-scale applications, green technology approaches in aquafeed development at an industrial scale are also equally important. A review in 2019 by Yarnold and colleagues [54] showcased several green technologies in aquafeed that were commercialised at an industrial scale, along with their sustainable benefits. Green water aquaculture is an efficient, low-maintenance and cost-effective technique used across Southeast Asia. This concept yields nutrient-rich biomass of natural and inoculated algae as well as the grazers in a fertilised constructed pond [144]. This significantly reduces reliance on commercial aquafeeds, as the aquaculture-farmed animals directly graze on the available biomass. This system portrays multiple benefits where grazing assists in maintaining a healthy aquatic environment along with an optimal carbon to nitrogen ratio and lower biological oxygen demand [144].

Furthermore, expansion of the green water farming concept introduces BFT as a rapidly emerging and sophisticated method of sustainable high-value ‘biofloc meal’ generation for use in commercial aquafeeds [145]. These flocs are typically grown in closed photobioreactors, where extended knowledge of the microbial ecosystem is mandatory to develop accurate methods for the synthesis of biofloc-based and fish-free marine microbe feeds. Microalgae utilisation in diverse feed and delivery systems signifies their essential roles in aquaculture. At the same time, discovery and continuous improvement with low-cost technologies will further enhance microalgae-based aquaculture feeds’ sustainability for future commercialisation and industrial applications [54].

3.4. Toward Scalable and Circular Biorefinery Approaches

The integration of circular economy principles into aquafeed production is gaining attraction, especially through biorefinery models that maximise resource efficiency and minimise waste. Microalgae-based biorefineries enable the sequential extraction of high-value bioactives such as pigments, fatty acids, and proteins, while allowing for downstream valorisation of residual biomass through bioenergy conversion or soil enhancers, ensuring complete biomass utilisation [146,147].

Recent developments have shown that scalable biorefineries can adopt decentralised or modular systems integrated into aquaculture operations, using waste streams as nutrient inputs for algal cultivation. Ahmad et al. [148] demonstrated the successful scale-up of marine microalgae Fistulifera peliculosa and N. oculata in low-footprint systems optimised for aquafeed applications, showing high productivity and lipid yields essential for sustainable FM alternatives.

Cell disruption methods such as mechanical pre-treatment coupled with green solvents are now widely used to extract valuable compounds with minimal environmental impact. Taj-Liad et al. [130] emphasised the role of deep eutectic solvents (DESs) and emerging aqueous biphasic systems in improving selectivity and sustainability of extraction processes, enabling circular bioprocessing with low toxicity and cost.

Moreover, technologies such as microbial electrolysis, anaerobic digestion, and photobioreactors coupled with aquaculture systems have been employed to upcycle waste into electricity, biomethane, or nutrient-rich digestate. For instance, Chatzimaliakas et al. [146] demonstrated an optimised dual-stage process where fresh Scenedesmus sp. biomass was converted into bioethanol via enzymatic saccharification and fermentation, followed by anaerobic digestion of the residual biomass to recover biomethane. This cascading strategy allowed for a total energy recovery of over 800 kWh/ton of algal biomass, with biomethane accounting for more than 85% of total energy output. Further, Santos et al. [147] reported on circular integration strategies, where aquaculture effluents serve as nutrient sources for microalgae, closing nutrient loops while producing feedstock for bio-based industries.

Despite promising advancements, economic feasibility remains constrained by energy-intensive harvesting and processing. However, coupling low-energy extraction technologies with integrated aquaculture infrastructure, as explored by Ahmad et al. [11], can significantly reduce operational costs and enhance scalability, contributing to a resilient and low-carbon aquafeed system.

As emphasised by Sarker and Kaparaju [149], aligning the microalgal bioeconomy with Sustainable Development Goals (SDGs) through circular biorefineries represents a paradigm shift in aquaculture nutrition, combining environmental sustainability with food security innovation.

4. Recent Innovation in Microalgae-Based Aquafeed Development

The rising demand for aquaculture products and the need for sustainable production systems have catalysed the innovation of microalgae-based aquafeeds. Recent advances address critical issues such as nutrient-rich effluent discharge, limited natural feedstocks, and environmental degradation. Through biotechnological innovation, system integration, and circular bioeconomy models, microalgae are increasingly recognised as a multifunctional resource, supporting feed production, bioremediation, and nutrient recovery. This section discusses key innovations, including waste valorisation, IMTA, genetic enhancement, advanced delivery systems, and biorefinery integration, with future outlooks toward AI-driven scale-up.

4.1. Waste Valorisation and Circular Economy Models

Microalgae can be cultivated on nutrient-rich effluents such as aquaculture wastewater, agro-industrial discharge, and brewery waste, turning environmental liabilities into bioresources. This dual-function approach achieves wastewater remediation while generating valuable biomass suitable for aquafeed applications, aligning with circular economy principles [11,147].

Tham et al. [150] emphasised that both marine and freshwater microalgae offer abundant lipids, proteins, carbohydrates, and high-value compounds essential for fish growth and immunity. Importantly, microalgae can be cultivated using brackish, freshwater, or marine systems and integrated into circular bioeconomy models that enable nutrient recycling, carbon mitigation, and wastewater remediation. Furthermore, microalgae cultivation can support zero-waste approaches via biorefinery frameworks, generating multiple co-products such as pigments, bioactive peptides, and polyunsaturated fatty acids (PUFAs) [151]. These contribute not only to fish health and pigmentation but also to the feed conversion efficiency and environmental performance of aquaculture systems. However, scalability and biomass consistency in open cultivation remain challenges that require further optimisation.

4.2. Mixed-Microalgae Culture for Biomass Production

Aside from monocultures, several studies have also assessed the potential of mixed-microalgae cultures in wastewater treatment systems for enhancing biomass and lipid production while maintaining more stable microalgae communities in the presence of pathogens and grazing [152,153,154]. Tossavainen and team [155] showed that the co-culturing of microalgae Euglena gracilis and Selesnastrum sp. in biowaste produced a higher yield of LC-PUFAs such as EPA, DHA, and arachidonic acid (ARA) as compared to Euglena gracilis monoculture and was more resistant to bacterial infections. Higher yield of tocopherol was also noted, which is an important component of animal feed normally added in animal feed to protect fatty acids from oxidation [154]. The potential of integrating this co-culturing method in a recirculating aquaculture system (RAS) was further investigated by the same team, where better nutrient uptake and a longer growth duration, as well as higher biomass and higher yields of LC-PUFAs and α-tocopherol, were observed in the mixed microalgae cultures grown in sludge-amended pikeperch wastewater compared to other cultures [155].

4.3. Microalgae as Aquafeed in Integrated Multi-Tropic Aquaculture (IMTA) Systems

Another innovative application of microalgae as feed in wastewater systems is in an IMTA system. IMTA systems combine complementary aquaculture models at different tropic levels in a single environment in order to optimise nutrient utilisation by conversion of the culture residues of the main species into food for another species [156]. Here, biofilters such as bivalves, sponges, bacteria, and microalgae can be used as aquafeed for aquacultures occupying a different trophic level, hence providing economic and environmental sustainability through co-cultivation [157]. Utilisation of microalgae in IMTA systems is explored by Li and team [158] by combining European sea bass grown in RAS systems with high-rate algal ponds (HRAPs) and separate oyster tanks. In this study, a natural marine microalgae assemblage consisting of diatoms Tetraselmis sp. and Phaeodactylum sp. was effective in removing nutrients from European sea bass aquaculture wastewater. At the same time, the total suspended solids and chlorophyll content increased significantly, indicating high microalgae biomass in the wastewater. Microalgae biomass was then circulated to the lower trophic oyster tanks as feed. These models enhance ecosystem services, create circular nutrient loops, and improve sustainability metrics, though site-specific optimisation is needed to balance trophic load and species compatibility [158].

4.4. Genetic Engineering and Strain Optimisation

Advancements in genetic engineering have significantly transformed the potential of microalgae for aquafeed development. Targeted genome editing, particularly through CRISPR-Cas systems, and synthetic biology tools have enabled precise metabolic rewiring of microalgae to improve their nutritional content, resilience, and growth efficiency.

Dhokane et al. [159] reviewed the potential of CRISPR-based bioengineering in microalgae for the production of industrially relevant biomolecules. The review highlights how microalgae serve as promising biofactories due to their rapid growth, high protein and lipid content, and ability to synthesise compounds valuable for food, feed, fuel, cosmetics, and pharmaceuticals.

Complementing this, Ahmad et al. [160] reviewed the potential of genetic engineering to enhance the production of bioactive compounds in microalgae, emphasising their application in aquafeed, nutraceuticals, and biofuels. Microalgae are naturally rich in valuable metabolites such as lipids, proteins, pigments, and carbohydrates, making them ideal for sustainable biorefineries. The review outlines key tools such as CRISPR/Cas9, TALENs, ZFNs, and transformation techniques including electroporation, particle bombardment, glass-bead agitation, and Agrobacterium-mediated transformation. With expanding access to genomic and omics datasets across species, the development of superior engineered strains is becoming increasingly feasible. The paper also highlights the importance of selecting appropriate expression vectors and promoters to achieve high-yield recombinant strains [160].

Further, a recent CRISPR/Cas9 study in C. vulgaris FSP-E showed promising lipid enhancement by knocking out CrPEPC1, a phosphoenolpyruvate carboxylase gene involved in carbon partitioning. This edit led to increased acetyl-CoA availability for fatty acid synthesis, boosting total lipid content by over 30% compared to wild-type strains [161]. Notably, the engineered strains maintained robust growth under photoautotrophic conditions, which is essential for scalable outdoor cultivation systems.

Despite these advancements, challenges persist; namely, regulatory hurdles for genetically modified (GM) algae, strain stability, and public acceptance. Future directions include AI-assisted genome editing and synthetic biology platforms to accelerate trait stacking and precision aquafeed design.

4.5. Challenges and AI-Driven Outlook

Despite promising innovations, several bottlenecks limit the widespread adoption of microalgae-based aquafeeds. These include high capital costs for photobioreactors, variable outdoor biomass yields, energy-intensive harvesting, and a lack of standardised regulatory frameworks for GM and waste-derived feed ingredients [162]. To address this, the adoption of modular bioreactors, strain co-cultivation, and hybrid systems (e.g., raceway–photobioreactor integration) are being explored [163,164]. AI-based approaches such as digital twins, predictive analytics, and machine learning offer real-time process control, forecasting of biomass yield, and automated nutrient balancing in RAS/IMTA systems. These technologies can enhance consistency, reduce production risks, and accelerate commercial readiness. Strategic public–private partnerships, investment in pilot-scale demonstrations, and harmonisation of feed safety regulations are critical to scale this sector sustainably.

5. Conclusions and Future Perspective

Microalgae represent a transformative solution for the future of aquafeed, offering a nutrient-dense, sustainable, and versatile alternative to traditional FM and FO. Their inherent richness in high-quality proteins, essential fatty acids, and bioactive compounds supports not only fish growth and health but also enhances the functional quality of aquafeeds. Advances in biotechnology, particularly in genetic and metabolic engineering, have further elevated the potential of microalgae by enhancing lipid accumulation, improving stress tolerance, and enabling the targeted manipulation of valuable metabolic pathways. Integrated production models such as BFT, RAS, and the incorporation of microalgae into circular bioeconomy frameworks support energy and nutrient recycling while mitigating environmental footprints. Additionally, innovations in encapsulation, feed delivery systems, and biorefinery approaches are bridging the gap between lab-scale efficacy and commercial-scale deployment. Looking forward, the future of aquafeed must align with the FAO’s Blue Transformation agenda, prioritising sustainable intensification, ecosystem resilience, and equitable nutrition. This necessitates scaling up cost-effective microalgae cultivation using non-arable land, wastewater or marine water systems, and renewable energy sources. Enhancing strain performance through omics-driven tools and genome editing technologies like CRISPR/Cas9 will be critical in improving biomass yield and metabolic productivity. To ensure long-term impact, regulatory frameworks must evolve to support the safe commercialisation of genetically engineered microalgae, while public–private partnerships can accelerate product development and market acceptance. Ultimately, microalgae-based aquafeed can redefine the aquaculture landscape by reducing pressure on marine resources, safeguarding environmental and human health, and contributing to a resilient global food system.