Exploring Regenerative Aquaculture Initiatives for Climate-Resilient Food Production: Harnessing Synergies Between Technology and Agroecology

Abstract

This review evaluates regenerative aquaculture (RA) technologies and practices as viable pathways to foster resilient, ecologically restorative aquaculture systems. The key RA technologies examined include modern periphyton technology (PPT), biofloc technology (BFT), integrated multitrophic aquaculture (IMTA), and alternative feed sources like microalgae and insect-based diets. PPT and BFT leverage microbial pathways to enhance water quality, nutrient cycling, and fish growth while reducing environmental pollutants and reliance on conventional feed. IMTA integrates species from various trophic levels, such as seaweeds and bivalves, to recycle waste and improve ecosystem health, contributing to nutrient balance and reducing environmental impact. Microalgae and insect-based feeds present sustainable alternatives to fishmeal, promoting circular resource use and alleviating pressure on wild fish stocks. Beyond these technologies, RA emphasizes sustainable practices to maintain fish health without antibiotics or hormones. Improved disease monitoring programs, avoidance of unprocessed animal by-products, and the use of generally recognized as safe (GRAS) substances, such as essential oils, are highlighted for their role in disease prevention and immune support. Probiotics are also discussed as beneficial microbial supplements that enhance fish health by promoting gut microbiota balance and inhibiting harmful pathogens. This review, therefore, marks an important and essential step in examining the interconnectedness between technology, agroecology, and sustainable aquaculture. This review was based on an extensive search of scientific databases to retrieve relevant literature.

1. Introduction

Regenerative aquaculture (RA) is a fish farming approach that aims to restore and improve the systems while ensuring sustainable food production [1]. Regenerative aquaculture adopts integrated and holistic management strategies that emulate natural processes and enhance ecosystem functions [2]. The goal is to establish a mutually beneficial relationship between aquaculture activities and the environment, prioritizing both production and ecosystem health. The key principles of RA include ecosystem restoration, resource efficiency, closed-loop systems, agroecological practices, and climate resilience [3]. These principles guide the implementation of RA techniques and highlight the focus on ecological restoration, efficient resource use, environmentally friendly systems, sustainable farming practices, and adaptability to climate change [4,5]. While regenerative agricultural methods, which focus on boosting productivity with little-to-no negative environmental impact and aim to restore ecosystems to their natural, pre-degradation conditions, have been thoroughly investigated, the concept of regenerative aquaculture remains relatively unexplored and poorly understood, particularly in developing regions [6].

Regenerative aquaculture has garnered significant attention and holds great promise for the future [7,8]. It not only has the potential to address the challenge of feeding a growing population, but also presents a unique opportunity to restore our planet and develop resilient food systems [6]. In the current era focused on sustainability, regenerative aquaculture emerges as a powerful solution that embraces the wisdom of nature to provide nourishment for both humans and the Earth.

With the global population projected to reach 10 billion by 2050, the rising demand for fish protein is set to overwhelm existing local production systems, necessitating strategic shifts in both production methods and efficiency [3]. Embracing sustainable and ethical fish farming practices, whether offshore or on land, is crucial [9]. To achieve regenerative, eco-friendly, and ethical fish production, there is an urgent need to address gaps in the following practices of farmers: (1) The employment of regenerative techniques that enhance fisheries and aquaculture beyond their original conditions, such as cultivating shellfish and seaweed, which contribute to water quality, nutrient bioremediation, carbon sequestration, and additional ecosystem services. Other promising regenerative practices include leveraging natural microbes to boost productivity, as seen in PPT and BFT, as well as IMTA. Notably, BFT has been shown to cut feed usage by up to 30% [10]. (2) The adoption of sustainable feed solutions that minimize or eliminate reliance on wild fish, opting instead for fish byproducts from sustainable fisheries and incorporating alternative sources such as algae, insects, and microbial proteins [11,12]. (3) The management of farms with approaches that prioritize fish health, minimize antibiotic use, avoid hormones, and ensure the well-being of both animals and humans. (4) Advocacy for the adoption of aqua-technologies and the promotion of decent work opportunities, ensuring fair wages and safe working conditions [13].

According to Panigrahi et al. [14], achieving these goals demands collaborative efforts from multiple stakeholders since adopting these regenerative aquaculture practices, such as IMTA, often involves high initial investment costs and technical complexities that may be unaffordable or inaccessible for small-scale farmers [15]. These costs add to other challenges like poor management practices and limited technical knowledge [16]. To address these limitations, financial incentives such as subsidies, low-interest loans, or grants could help lower the barrier to entry for small-scale farmers, making advanced technologies more affordable [17]. Additionally, technical training and capacity-building programs focused on regenerative aquaculture practices can improve management efficiency and increase farmers’ ability to adopt these systems. Collaborative research and development efforts could drive the innovation of low-cost, scalable versions of IMTA, BFT, and PPT, ensuring accessibility to a broader range of producers [18].

This review marks an important step in the examination of the interconnectedness between technology, agroecology, and sustainable aquaculture practices. Our findings underscore the significance of these initiatives in addressing the challenges of climate-induced impacts on aquaculture and global food security. This review also explored four focal areas: innovative technologies in RA, such as PPT, BFT, IMTA, and shellfish and seaweed cultivation; the development of sustainable fish feed alternatives; sustainable management practices prioritizing fish health and welfare; and aquaculture operations that uphold environmental stewardship and fair labor standards. Therefore, this review aimed to critically examine and synthesize current insights on how regenerative aquaculture (RA) can drive sustainable, environmentally friendly advancements in fish farming practices. This study provides an essential foundation for understanding how RA can enhance food security, socio-economic well-being, and policy development for sustainable aquaculture.

2. Materials and Methods

This scoping review was meticulously designed to explore and assess regenerative aquaculture practices that focus on ecosystem restoration, resource efficiency, closed-loop systems, and the minimization of external inputs such as antibiotics and hormones. By synthesizing the literature on regenerative approaches, this review sought to offer a comprehensive understanding of how these innovative practices can contribute to climate-resilient food systems. The methodology followed systematic and scoping review protocols to ensure transparency and rigor in the processes of literature searching, screening, and data synthesis.

2.1. Literature Search Strategy

A comprehensive and structured literature search was conducted across four major scientific databases—PubMed, Web of Science, Scopus, and Google Scholar. These databases were selected based on their extensive repositories of peer-reviewed articles, technical reports, and conference proceedings relevant to aquaculture, environmental sustainability, and agricultural sciences. In constructing the search strategy, careful attention was paid to avoid overly narrow terms that could limit the scope of this review. Both controlled vocabulary terms and free-text terms, were utilized to ensure a broad yet targeted search that would capture the diversity of regenerative aquaculture practices.

The search terms were selected to cover a range of regenerative aquaculture approaches, with Boolean operators used to combine terms and enhance search inclusivity. The search included the following terms and combinations: “regenerative aquaculture”, “ecosystem-based aquaculture”, “low-impact fish farming”, and “closed-loop aquaculture systems” as general terms on regenerative aquaculture. In exploring fish health and ecosystem resilience, search terms like “fish health” AND (“disease prevention” OR “disease management”) AND “regenerative aquaculture”, along with “antibiotic-free” OR “hormone-free” AND “aquaculture” OR “fish farming” were included. To capture the literature on alternative feed sources and sustainable inputs, terms such as “insect” AND “aquaculture” OR “fish feed”; “microalgae” AND (“regenerative fish feed” OR “aquaculture feed”); and “seaweed” AND “aquaculture” OR “regenerative aquaculture feed” were applied. Terms associated with regenerative technologies and ecosystem enhancement included “biofloc technology” (BFT); “modern periphyton technology” (PPT); “integrated multi-trophic aquaculture” (IMTA); “shellfish cultivation” AND “ecosystem services”; and “seaweed cultivation” AND “carbon sequestration.” Finally, practices minimizing external inputs were captured through terms like “probiotics” OR “natural immunostimulants” OR “Generally Recognized as Safe” (GRAS) substances AND “regenerative aquaculture.”

This approach ensured a broad coverage of relevant studies and avoided the narrow focus that could exclude pertinent literature. The search strategy was iteratively reviewed and refined, with adjustments made to ensure all the facets of regenerative aquaculture, including those on innovative systems like IMTA, PPT, and BFT, were adequately represented.

2.2. Inclusion and Exclusion Criteria

To ensure the selection of relevant, high-quality studies, stringent inclusion and exclusion criteria were applied. Studies were included if they were peer-reviewed articles, literature reviews, or case studies that addressed regenerative aquaculture approaches. Specifically, studies had to focus on aspects like ecosystem restoration, biodiversity enhancement, or closed-loop systems in aquaculture with a publication date between 2005 and 2023. Only articles published in English were considered in order to maintain language consistency due to limitations in translation resources. Furthermore, selected studies had to address the ecological, economic, or health-related benefits of regenerative aquaculture methods, especially those focusing on minimizing external chemical inputs and utilizing natural or biological processes to support fish health.

Exclusion criteria were set to omit studies that did not meet the regenerative focus of this review. Articles were excluded if they centered on conventional aquaculture practices or traditional sustainable approaches without highlighting regenerative or ecosystem-enhancing methods. Studies published before 2005 were omitted to focus on more recent advances in regenerative aquaculture, and non-English publications were excluded due to translation limitations. Paywalled articles without open-access versions were also excluded to prioritize accessibility. Duplicates were removed, and studies with abstracts that did not align with the regenerative scope were excluded after a preliminary screening.

2.3. Search and Screening Process

The initial search yielded over 100,000 articles. A preliminary relevance screening was then conducted, prioritizing high-impact, peer-reviewed journals on aquaculture, ecology, and environmental science to ensure quality. A second round of abstract screening refined the search to 300 articles that explicitly addressed regenerative aquaculture practices, technologies, and ecosystem benefits. Further refinement involved a detailed review of each article’s content to assess alignment with the objectives of regenerative aquaculture.

After this rigorous screening, 244 unique articles were selected for full evaluation (Figure 1). Each article was thoroughly reviewed based on methodological rigor, outcomes related to regenerative aquaculture, and relevance to the objectives of this review. The final selection included studies that provided a representative and diverse foundation for analyzing regenerative approaches and their impact on aquaculture ecosystems.

2.4. Data Extraction and Analysis

Data from each selected article were extracted using a structured framework to ensure consistency and comprehensiveness. For each study, detailed information was recorded on several critical areas. First, this study’s objectives and scope were noted, particularly the focus on regenerative aquaculture, such as methods to restore ecosystems, enhance biodiversity, or implement closed-loop systems. Methodological details were recorded, including the type of aquaculture system studied (e.g., IMTA, BFT, and PPT), the scale of the system, the species involved, and the specific regenerative practices implemented. Key findings and outcomes were noted, especially evidence of ecosystem benefits such as nitrogen cycling, carbon sequestration, reduction in external inputs, fish health improvements, and economic feasibility. Geographic and ecological context was also documented to capture the study’s location, environmental conditions, and applicability to various climatic and socio-economic contexts.

This data extraction was followed by a thematic synthesis in which studies were grouped based on regenerative aquaculture approaches, focusing on closed-loop and ecosystem-based practices. Each article was examined to assess the primary regenerative benefits, such as nutrient recycling, disease prevention without antibiotics, and the use of sustainable feed alternatives like insect meal or microalgae. Through this synthesis, patterns, challenges, and opportunities were identified, providing a nuanced understanding of how regenerative aquaculture can support sustainable food production and ecosystem resilience.

2.5. Limitations

Several limitations are acknowledged in this review. The exclusion of non-English articles may have introduced a language bias, potentially overlooking regional studies on regenerative aquaculture practices in areas where such methods are common. Additionally, some relevant studies published in 2023 were inaccessible due to open-access embargoes, although alternative sources were pursued when available. As a narrative review, this analysis may not fully capture the regional and methodological diversity within regenerative aquaculture, though it does provide valuable insights into general trends and practices.

3. Results and Discussion

3.1. Technologies of Regenerative Aquaculture

3.1.1. Modern Periphyton Technology (PPT)

The use of microbial products from technologies such as PPT has recently received a great deal of attention as a regenerative fish production technology. Periphyton is an amalgamation of bacteria, fungi, algae, and inorganic and organic detritus that attach and grow on submerged substrates using a mucopolysaccharide matrix [19]. The concept was deduced from traditional fishing methods in Africa and Asia used to promote fisheries in coastal lagoons [20]. Periphyton productivity ranges between 1–3 g/ m² substrate. Day [21] worked under the synergism of two main principles, i.e., the introduction of vertical substrates for the attachment of the biofilms and adjustment of the C/N ratio [22].

i. Comparison to traditional aquaculture

In conventional aquaculture systems, a significant portion of the feed provided to fish remains uneaten, leading to the accumulation of ammonia in the water [23]. Even the feed that is consumed is not entirely transformed into fish growth, with a substantial amount being excreted as waste [24]. The combination of unconsumed feed and excreted waste—accounting for nearly 75% of the total feed—causes elevated levels of total ammonia nitrogen (TAN) and nitrite, which pose a threat to fish health [24]. The PPT helps mitigate this issue by reducing TAN and nitrite through three key nitrogen conversion processes: first, heterotrophic bacteria convert ammonia into bacterial biomass; second, chemoautotrophic bacteria convert ammonia to nitrate; and third, algae engage in the photoautotrophic removal of nitrogen [25].

ii. The mechanism driving Periphyton Technology

Periphyton technology operates through various mechanisms to enhance water quality and provide supplementary nutrition for fish. One of the primary pathways is the heterotrophic pathway, which is stimulated by adding carbon sources such as molasses or by increasing the carbon content in feed [26,27]. This is essential because heterotrophic bacteria require a specific balance of organic carbon and inorganic nitrogen that matches their cellular composition [28]. When carbon is added, these bacteria create a demand for inorganic nitrogen, promoting their growth [28]. Maintaining a carbon-to-nitrogen (C/N) ratio of 15–20, as suggested by Ahmad et al. [3], supports the microbial pathway for controlling ammonia levels. Heterotrophic bacteria colonize the leftover feed and fecal matter, absorbing nitrogen from the water and producing bacterial biomass that adheres to substrates, which then serves as a food source for fish [29,30]. This process is rapid, reducing elevated total ammonia nitrogen (TAN) levels within 1–3 days if an adequate amount of organic carbon is provided. The resulting microbial biomass improves growth rates, doubles feed efficiency, and lowers feed costs, making this technology resource efficient [31]. Additionally, this system promotes the growth of other organisms, such as snails, chironomids, mayflies, and crustaceans, which fish consume, thus enhancing the system’s productivity without competing for resources with biofilm-forming microorganisms [25].

The presence of ammonia and nitrite naturally supports the growth of nitrifying bacteria [30]. This autotrophic process occurs in two stages. The first stage involves ammonia-oxidizing bacteria from genera such as Nitrosomonas, Nitrosococcus, Nitrosospira, and others, which convert the ammonia derived from waste sources into nitrite in the presence of oxygen [31]. The second stage involves nitrite-oxidizing bacteria like Nitrobacter, Nitrococcus, Nitrospira, and Nitrospina, which transform nitrite into nitrate [9,32]. Nitrate is then taken up by algae and phytoplankton, which use it to synthesize chlorophyll, subsequently serving as direct or indirect food for fish through secondary trophic levels like benthos, prawns, and zooplankton [33]. This cycle continues as the system also facilitates denitrification, which leads to the conversion of nitrogen compounds into harmless nitrogen gas [34] and photoautotrophic nitrogen uptake, depending on environmental conditions [26]. The heterotrophic bacteria dominate due to their faster growth rate and higher biomass yield compared to autotrophic bacteria, playing a crucial role in maintaining water quality and providing nutritional feed for fish [35].

The algae in this system also contribute by directly assimilating ammonia and nitrite, producing algal biomass through photosynthesis [30]. Organic matter from leftover feed, dead organisms, and waste is decomposed, releasing nutrients that algae rapidly absorb and store in their cells. This conversion process relies on solar energy, with algae and phytoplankton acting as primary producers and key sources of dissolved oxygen, which is essential for fish growth and production [36]. Algal photosynthesis can also raise pH levels, leading to calcium phosphate precipitation and the formation of carbonate–phosphate complexes [19]. Studies indicate that periphytic algae have a higher production rate per unit of water surface compared to phytoplankton. Filter feeding on algae provides essential micronutrients and energy for herbivorous fish, which may not be adequately provided by phytoplankton [37]. The diversity of periphyton species, mainly comprising algae, is influenced by local abiotic and biotic factors such as nutrient levels, light, grazing pressure, and substrate characteristics [38,39].

Periphyton systems enhance feed efficiency by improving feed quality and refining feeding strategies to effectively deliver and reuse nutrients within the culture system [40]. The microbial biomass produced in these systems contains suitable levels of protein, fat, and ash for the growth of cultured species [41], making PPT a viable substitute for traditional fishmeal. This technology improves water quality while providing in situ microbial protein as a feed source for aquaculture species [42]. Maintaining optimal water quality with minimal water exchange reduces the risk of introducing pathogenic bacteria and protects surrounding ecosystems by limiting nutrient discharge [43]. Reduced water exchange also stabilizes the temperature within culture units [44]. By maintaining water quality and lowering organic load in effluent waters, PPT demonstrates high efficiency in sustainable aquaculture.

iii. Benefits and limitations of Periphyton Technology

Periphyton technology offers several advantages in aquaculture by optimizing natural resource utilization, improving feed efficiency, and aiding in both disease and environmental management—key factors that often constrain aquaculture production [41]. This technology boosts productivity by enhancing seed quality through improved reproductive performance and strengthening larvae’ immunity and resilience [45]. As a low-cost and feasible approach, PPT holds promise for significant advancements in regenerative aquaculture methods. One notable benefit is its ability to delay sexual maturity in Nile tilapia by around two months, thereby preventing overcrowding in ponds, which often leads to stunted growth due to excessive reproduction [39]. According to Biswas et al. [46], the use of PPT can lead to a 26–41% improvement in feed conversion ratios and an overall feed reduction of up to 30%, making it more efficient than traditional aquaculture systems. However, maintaining the periphyton surface can be labor-intensive, requiring consistent monitoring and cleaning to keep the system effective.

This technology has been widely implemented in countries like Indonesia and other parts of Asia, particularly in polyculture systems. It is effective for cultivating species that feed at different trophic levels within the food chain. In Indonesia, for example, PPT has been used successfully to culture species such as Labeo rohita (rohu), Catla catla, L. calbasu (kalbaush), and L. gonius (gonia). A case study by Azim [22] demonstrated its potential for enhancing fish growth and survival, yielding impressive results. In monoculture systems, yields of rohu and kalbaush increased by an average of 80% compared to control setups without substrate. In periphyton-based polyculture systems, fish production showed a 70–180% increase over control systems. Through using 75 m² experimental ponds with substrate surface areas roughly equal to the water surface area and stocking at a rate of 6000 rohu, 4000 catla, and 1500 kalbaush per hectare (a total of 11,500 juveniles), fish production reached 2306 kg within a 90-day culture period.

While PPT presents numerous benefits, including reduced feed costs, improved feed conversion ratios (FCR), enhanced fish growth, and environmental sustainability, several challenges hinder its widespread adoption and scalability, particularly in commercial fish production. The labor-intensive nature of maintaining periphyton surfaces is a significant limitation as it requires frequent cleaning and monitoring to ensure the biofilm remains effective [47]. This can significantly increase labor costs, particularly for large-scale operations. Additionally, the initial setup for substrates and the ongoing need to optimize environmental conditions (e.g., light and nutrient levels) may pose technological barriers, especially for smallholder farmers with limited technical knowledge and resources [45]. Scalability also poses a challenge; while the technology has shown success in small experimental systems, replicating these results in large, commercial-scale operations may be more complex due to the need for precise environmental control and substrate management. Furthermore, economic viability in large-scale applications requires careful consideration, as the cost of scaling up PPT, including substrates and maintenance, might outweigh the benefits, particularly in regions where labor costs are high or technical expertise is limited [48]. Therefore, to make PPT more accessible and scalable, future research must focus on reducing labor requirements, lowering setup costs, and developing automated systems for monitoring and managing biofilm growth.

3.1.2. Biofloc Technology

Biofloc technology (BFT) is a cutting-edge, environmentally friendly approach that offers a sustainable solution to boost aquaculture productivity, addressing the rising global demand while supporting the livelihoods of small-scale fish farmers [10,14]. This technique leverages clusters of beneficial microorganisms such as bacteria, algae, and protozoa, which are bound together with organic matter [49]. These BFT aggregates not only serve as a nutrient-rich feed for fish, but also help in waste management, enhancing water quality, and inhibiting the growth of harmful bacteria in intensive aquaculture systems [50]. All these features make BFT a sustainable and restorative aquaculture technology that should be adopted by aqua-farmers. The technology has been popularized by aquaculture scientists for the last two decades because of its advantages over traditional farming systems.

i. Benefits of BFT over conventional fish culture systems

In traditional farming systems, the intensification of the culture system results in the enrichment of water with toxic nitrogenous wastes from the high-protein commercial diets used [31]. To manage such problems, frequent water exchange rates are used for the release of nutrient-rich waters into the natural ecosystems as they may lead to eutrophication. The high-water exchange rates may also result in the introduction of pathogenic bacteria and increased production costs due to the high expenses involved in pumping large amounts of water [31]. With all these challenges, BFT seems to be a viable technology that can be used to solve most of the production challenges faced by fish farmers.

Biofloc technology requires zero or minimal water exchange rates and has the ability to improve water quality, reducing production costs while enhancing profitability [13]. It works under the principle of cycling nutrients through complex bio-pathways to produce proteinaceous natural food that regenerates itself [10]. The process requires the addition of external carbon sources and constant aeration. The introduction of an external supplemented carbon source necessitates the heterotrophic bacteria communities to create a demand for nitrogen [40], thus colonizing and degrading the nitrogenous wastes resulting from uneaten fish feeds and feces, thereby controlling water quality [51] and assimilating the wastes into proteinaceous microbial fish feed [52]. The C/N ratio should be maintained at a ratio higher than 15 to promote dense heterotrophic microbial biomass proliferation and microbial biomass production, which is 10 times higher than nitrifying bacteria, thus keeping ammonia levels at a very low concentration [35]. This solves the problem of ammonium accumulation that can lead to fish kills under aquaculture systems. Instead of the nutrients being stored in the pond bottom, they are continuously recycled and reutilized as single-cell proteins [53], as depicted in Figure 2.

The presence of heterogeneous microbial communities in the BFT, including bacteria, plankton, microalgae, fungi, etc., which can be sustained with the addition of cheap carbon sources such as molasses, helps in reducing production costs and making BFT a more viable technology to fish farmers, especially in developing countries [26]. For example, a study by Rego et al. [54] revealed that although BFT’s total production costs were eight times higher than those of conventional systems, its investment indicators were highly favorable. BFT achieved an operating profit of USD 1871.54 per hectare per year and a profitability index of 30.22%, compared to USD 21,523.83 per hectare per year and 59.79% profitability for conventional systems. In terms of investment analysis, BFT showed a notable net present value (NPV) of USD 142,004.42, though the internal rate of return (IRR) remained higher for conventional systems (131.86%). These results indicate that BFT, when managed effectively, can be a profitable and sustainable alternative to conventional systems, especially in supporting the sustainable development of marine shrimp farming.

Further, the dense microbial population, microalgae, and phytoplankton provide unlimited nutritious fish feed, hence minimizing the use of costly commercial feeds and decreasing the feed conversion ratio of the aquaculture species [13]. The consumption of these microbial communities also results in improved survival, growth and health status of the cultured species [55]. The BFT has also been proven to improve reproduction by promoting the formation and development of gonads and ovaries in fish broodstock [10].

ii. BFT and fish health

Biofloc technology (BFT) serves as a natural biosecurity measure, significantly reducing the reliance on antibiotics, which can have harmful ecological consequences [56]. In traditional aquaculture systems, high water exchange rates are often used to manage water quality, but this frequent exchange can inadvertently introduce pathogenic organisms from external water sources into the culture system [57]. These pathogens, once introduced, increase the risk of disease outbreaks, prompting farmers to rely on antibiotics for disease management. However, improper use of antibiotics has rendered many of them ineffective against harmful bacteria [58,59]. In contrast, research indicates that aquaculture species thrive and achieve optimal growth in environments with abundant natural biota [60]. The diverse microbial community in BFT functions as an immunostimulant, enhancing the immune response against pathogens [61,62].

According to Xu & Pan [63], aquaculture species raised in BFT exhibit significantly higher total hemocyte counts and greater phagocytic activity compared to those in traditional systems. This is attributed to the bacterial biomass present in BFT. The manipulation of the carbon-to-nitrogen (C/N) ratio promotes the growth of mixed bacterial communities that produce poly-β-hydroxybutyrate, a compound that has been shown to help prevent infections caused by Vibrio species [64,65]. Additionally, the carbohydrates added to the system act as a source of prebiotics, which can positively influence the gut microbiome of the cultured species, improving their overall health [3].

iii. Trials of BFT with various species

Extensive research has explored the utilization of BFT by various commercially valuable aquaculture species, such as Labeo rohita, Oreochromis niloticus, Oreochromis aureus, Oreochromis mossambicus, and Clarias gariepinus [31,51]. These studies have consistently reported significant positive outcomes, highlighting BFT as an optimal choice for fish farmers, particularly in developing regions. For instance, a study conducted at the Central Institute of Brackishwater Aquaculture in India demonstrated that BFT had a notable impact on shrimp growth and production, achieving productivity levels between 1640 to 2796 kg/ha/crop at a stocking density of 8–12 shrimp per square meter. Moreover, the system showed a higher return on operational costs (92%) compared to conventional shrimp farming practices (54%).

Despite these promising results, there remain gaps in knowledge regarding the adaptation and scalability of BFT, particularly for smallholder farmers. This underscores the need for further research, especially in areas concerning environmental sustainability and fish health, to improve the technology’s adoption and effectiveness on a broader scale.

Figure 2. A diagram showing the biological processes in a BFT. Adapted from Pérez-Rostro et al. [66].

Figure 2. A diagram showing the biological processes in a BFT. Adapted from Pérez-Rostro et al. [66].

iv. Limitations of the Biofloc Technology

While BFT presents several advantages in improving water quality, nutrient recycling, and disease management, it also has its challenges and limitations. One major challenge is the requirement for constant aeration and monitoring to maintain optimal water conditions [67]. The high microbial load within the system consumes significant amounts of oxygen, necessitating continuous aeration to prevent oxygen depletion, which can lead to fish stress or mortality [67]. Additionally, the accumulation of organic matter can result in an excessive increase in suspended solids, which, if not properly managed, can negatively affect fish gill function and overall health [31]. The management of solid waste and microbial flocs, therefore, requires careful regulation of the system’s carbon-to-nitrogen (C/N) ratio and regular monitoring, which can be labor-intensive and technically demanding for small-scale farmers lacking adequate resources or training.

Another limitation of BFT is the potential for fluctuations in water quality parameters such as pH, ammonia, and nitrate levels. These fluctuations can be harmful if not properly controlled, as imbalances in nitrogen cycling can lead to the buildup of toxic compounds like ammonia or nitrite, which are detrimental to fish health [35]. Moreover, while BFT reduces water usage, the technology may not be suitable for all species, particularly those that are not tolerant of high turbidity or have specific feeding habits. The initial setup costs, particularly for aeration equipment and monitoring tools, can also be prohibitive for small-scale and resource-limited farmers [30]. Furthermore, the success of BFT systems requires a level of technical expertise that many farmers in developing regions may not have, presenting a significant barrier to widespread adoption.

3.1.3. Integrated Multitrophic Aquaculture (IMTA), Shellfish, and Seaweed

Integrated Multitrophic Aquaculture (IMTA) is an innovative approach that cultivates multiple aquatic species from different trophic levels within a single, interconnected system. This method promotes ecosystem services, reduces waste, and enhances overall efficiency [68]. Unlike traditional polyculture systems, where species co-exist with minimal interaction, IMTA enables one species to benefit directly from another by utilizing uneaten feed and waste as nutrients. This strategy not only minimizes resource use but also mitigates environmental impacts [69]. While traditional polycultures may operate with overlapping biological and chemical processes, IMTA intentionally integrates a variety of species that occupy distinct ecological niches, leading to synergistic effects within the ecosystem [68].

The primary focus of IMTA is environmental sustainability, and species selection is guided by the goal of imitating natural ecosystems [70]. This integration of species allows for more efficient nutrient cycling, increased economic resilience through improved production efficiency, and potential benefits such as price premiums and product diversification [71]. As a result, multiple species can be harvested, generating additional sources of revenue.

In an IMTA system, macroalgae, invertebrates, and vertebrates are cultivated together in a balanced and well-managed ecosystem. This approach involves integrating fish species with organic extractive species like shellfish and inorganic species such as seaweeds, while considering site-specific conditions, safety standards, and regulatory limits [68]. Most of the inorganic extractive species belong to the genera Saccharina, Ulva, Laminaria, and Glacilaria, and they capture and use the inorganic nutrients as source of nutrients [72]. The wastes from fish production are therefore considered as a valuable resource rather than a burden. This results in an eco-friendly, sustainable system that ensures the efficient use of resources with increased production [73].

Aquatic plant bio-filtration is assimilative, which means it increases the environment’s nutrient assimilation capability. Plants photosynthesize new biomass with the help of sunlight and surplus nutrients, especially C, N, and P. Plant autotrophy counteracts fish and microbial heterotrophy in the culture system, not just in terms of nutrients but also in terms of oxygen, pH, and CO₂. Plant bio-filters can thereby lower the overall environmental impact of fish farming while also stabilizing the culture environment in a single step. Furthermore, the cultivation of low-food-chain species that get their nutrition from water requires a minimal amount of input [72,74]. The different biotic components and their significance in IMTA are as further discussed below.

Sea Weeds

Seaweeds are autotrophic organisms that inhabit the lowest trophic level of an aquatic ecosystem and remove nutrients from the water during the photosynthetic energy process [75]. The type of seaweed to be used in IMTA is based on the intended application. The major driving forces for the seaweeds industry are the high demand for hydrocolloids, environmental problems as a result of intensive fish culture, declining capture fisheries, depletion of natural stocks, and increased food demand [75]. They are highly preferred for human consumption because they are cost-effective and produce more than other aquatic plants. Generally, they have adequate content of minerals, fatty acids, proteins, and vitamins. Some such seaweeds include Caulerpa spp., Undaria pinnatifida, and Porphyra species, which are solely grown in Southeast and East Asia for direct consumption by humans [68]. They also have a large human market as feed supplements, pharmaceuticals, nutraceuticals, and agrichemicals.

Tropical species such as Eucheuma spp., and Kappaphycus alvarezii which have emerged to be promising seaweeds for integrated aquaculture, are exclusively cultured along the Indian coast for their valuable extracts. Other species of economic importance such as Sargassum spp., Laminaria japonica, and Gracilaria spp. have a capability of generating a viable seaweed mariculture and integrated aquaculture and therefore being cultured in Korea, Indonesia, China and Philippines [72,76].

If the main focus in IMA is bioremediation, which is the focus of climate-smart aquaculture, then the seaweeds chosen should be based on the uptake of nutrients, storage, and growth. A nutrient-extractive seaweed must be able to grow well in high concentrations of nutrients [68]. The seaweed must therefore be able to accumulate content of total internal nitrogen. Ulva genus is the major seaweed candidate for bioremediation because of its ‘thin sheet’ morphology, which enables it to grow faster and has a high capability to accumulate a high content of nitrogen biomass [71]. However, if the principal focus is on the produced biomass, then the primary determinant will be based on the tissue quality and added value secondary compounds [72]. Ulva genus, despite being a good candidate for bioremediation, is not a fleshy seaweed and, therefore, has a limited market for the harvested biomass.

The seaweed species to be chosen may also be based on resistance to diseases and epiphytes, high growth rate and tissue nitrogen concentration, a match between the eco-physiological features and the growth environment, control of lifecycle, and ease of cultivation [68]. The farmer should also avoid using non-native seaweed species which may have negative ecological impacts.

Bivalves

Bivalves play a crucial role as organic extractive species within open-water IMTA systems [71,77]. They help reduce nutrient loads in aquaculture cages by filtering and absorbing fish waste and excess nutrients produced by macroalgae and phytoplankton [78]. Instead of releasing these nutrients into natural ecosystems, as is common in traditional monocultures, the waste is converted into bivalve biomass that can be harvested [68]. By increasing the amount of feed given to fish, the growth and production of bivalves can also be enhanced, improving the system’s overall efficiency while minimizing environmental impacts from waste nutrients [75]. Since different bivalve species vary in their preferences for the size and type of particles they filter, selecting the appropriate species based on waste particle size is essential for a successful IMTA [72].

A well-designed IMTA system requires careful selection and placement of species to effectively capture both particulate and dissolved nutrients. For example, seaweeds, following the water flow, are typically positioned further away from the fish cages to absorb inorganic nutrients like nitrogen and phosphorus. In contrast, bivalves are placed near fish cages to filter organic particles directly. Additionally, deposit feeders such as sea urchins and sea cucumbers consume larger organic particles, like uneaten feed and feces, that settle below the cages [68]. Filter-feeding bivalves like clams, oysters, and mussels clean the water by capturing suspended particles. Among these, clams are the most widely cultured, accounting for 38% of the total global bivalve yield due to their high protein content, rich minerals, and increasing market demand for healthy food products [75].

Oysters are another major component of bivalve aquaculture, valued for their nutritional benefits, delicious taste, and medicinal properties. Commonly farmed edible oyster species include Crassostrea iredalei, C. angulate, C. madrasensis, C. gryphoides, C. commercialis, C. cucullata, C. rivularis, C. gigas, Ostrea edulis, and Saccostrea cucullata. However, a significant challenge in oyster farming is the limited availability of seeds.

Mussels contribute 13% to the global bivalve aquaculture industry and have a long history of cultivation, dating back around 3000 years. Mussel farming is primarily practiced in coastal regions for nutrient recycling, with leading producers including China, Chile, Spain, The Netherlands, and France. The most commonly farmed species are the Mediterranean and blue mussels [75]. Currently, global aquaculture produces approximately 17.14 million metric tons of mollusks [75].

For an IMTA system to be successful, the chosen species must be economically viable and farmed at densities that optimize nutrient uptake and waste recycling throughout the production process [79]. IMTA offers several advantages, such as increased productivity through diversification, improved disease control, reduced economic risks, effluent bio-mitigation, and the potential for higher profits through premium products [68]. Additionally, this approach addresses public concerns about intensive aquaculture by promoting better management practices [69]. However, it remains essential to raise public awareness about the environmental benefits of IMTA and provide reliable information to consumers to increase the social acceptance of aquaculture products [73].

3.2. Sustainable Fish Feeds That Reduce or Eliminate the Use of Wild Fish to Feed Farmed Fish

3.2.1. Microalgae as a Sustainable Fish Feed Ingredient

Microalgae have emerged as a promising alternative ingredient for sustainable fish feed [80].

Table 1. Overview of microalgae as a sustainable fish feed alternative in regenerative aquaculture.

Aspect	Subtopic	Details	Citations
Current Fish Feed Issues	Environmental Impact	Fishmeal usage is linked to unsustainable harvesting of forage fish, affecting ocean ecosystems. Terrestrial plant-based feeds increase freshwater usage and lead to deforestation.	[81,82]
	Nutritional Challenges	Plant-based feeds have high phosphorus levels, low Omega-3, and anti-nutritional factors that can slow fish growth and maturity.	[82,83]
Microalgae as Fish Feed	Growth and Cultivation	Microalgae thrive in aerated liquid cultures with nutrients, light, and CO₂. Global production is ~5 million kg annually, with 20% used in aquaculture. The market value is around USD 330/kg with growing demand.	[80,81,84]
	Nutritional Content	Rich in triglycerides, vitamins, pigments, amino acids; popular strains include Phaeodactylum, Skeletonema, Tetraselmis, Pavlova, and others. Ideal strains are digestible and nutrient-dense.	[85,86,87]
Industrial Usage	Aquaculture Application	Microalgae, such as Pavlova sp. and Isochrysis spp., are used for live feed production for fish larvae. They provide higher net biomass productivity than animal or plant sources, supporting fish at all stages.	[88]
Environmental Advantages	Reduced Land and Water Use	Can be cultivated without fertile land, using waste or seawater, thus minimizing freshwater needs and agricultural land use.	[89,90]
Biorefinery Applications	Pigment Production	Microalgae processing yields valuable metabolites. For example, Haematococcus pluvialis is a primary source of astaxanthin, enhancing fish color and market appeal.	[90,91]
Feed Composition	Digestibility	Microalgae are more digestible than plant-based feeds, lacking anti-nutritional factors like lignin and containing lower levels of hemicellulose.	[87,92,93]
	Protein and Fatty Acid Content	During growth, microalgae contain 30–40% protein and essential polyunsaturated fatty acids like arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid.	[94,95]
	Starch Content	Starch levels range from 7% to 45% across different species; Chlorella vulgaris, Chlamydomonas reinhardtii, and Tetraselmis subcordiformis have a higher starch content (30–49%).	[96,97]
Zooplankton Enhancement	Nutritional Pigments for Zooplankton	Algal pigments improve zooplankton’s nutritional profile, with copepods (e.g., Temora sp.) containing astaxanthin, lutein, and artemia rich in canthaxanthin.	[98]
Aquaculture Pond Benefits	Water Quality and Health Boost	Microalgae improve water quality, stabilize pH, regulate bacterial communities, enhance immunity, and exhibit probiotic effects, supporting the growth and survival of fish.	[99,100]

outlines the environmental, nutritional, and industrial advantages of using microalgae in aquaculture. It compares current fish feed issues with the benefits of microalgae, including aspects such as cultivation, nutrient content, biorefinery applications, and ecosystem impacts in aquaculture pond environments.

3.2.2. Insects

Insect farming offers a promising and sustainable alternative to traditional fish feed sources, enhancing both food and feed security [101,102].

Table 2. Key aspects of insects as sustainable fish feed alternatives in regenerative aquaculture.

Aspect	Details	Citations
Sustainability	Insects efficiently convert feed into protein without needing energy for body temperature regulation, making them a sustainable feed alternative.	[103,104,105]
Nutritional Composition	Nutrient profiles vary by insect species, life stage, and diet. Insects contain vital nutrients like hydroxyproline and taurine, promoting fish health and reducing antibiotic and hormone needs in aquaculture.	[106,107,108]
Resource Utilization	Insects can consume organic and inorganic waste, including agro-industrial byproducts, helping reduce competition for land and food resources.	[109,110]
Species Diversity	An estimated 5–10 million insect species exist globally, with only about 1 million identified, offering the potential for discovering diverse insect-based feeds.	[111,112]
Circular Economy Benefits	Insect farming aligns with circular economy principles by upcycling organic waste into high-quality protein, supporting “reuse” and “upcycle” values in food systems.	[103,113]
Consumer Acceptance	High consumer acceptance; in a survey, 90% of fish consumers in northern Italy favored fish fed on insect-based feeds.	[114]
Environmental Efficiency	Insects require minimal land, water, and energy. They can recover up to 50% of nitrogen and 70% of phosphorus from waste, creating nutrient-rich feed with 30% lipids and 40% crude protein.	[115,116,117,118,119,120]
Examples of Aquaculture Use	- Tenebrio molitor larvae is used as feed for Nile tilapia, European sea bass, and goldfish. - Musca domestica (house fly) and Bematistes macaria (butterfly) larvae used in African catfish diets. - Black soldier fly (BSF) larvae used in trout diets, replacing up to 25% fishmeal and 38% fish oil without impacting feed efficiency.	[121,122,123,124]
Performance Benefits	Insect-based feeds improve feed conversion ratios, weight gain, and growth. For example, cockroach meal (Nauphoeta cinerea) performs better than fish meal in tilapia culture. BSF larvae help reduce pathogens like Salmonella.	[125,126,127,128]
Challenges in Scaling	Challenges in commercializing insect meals include inconsistent organic waste supply and variations in nutritional content due to differing rearing conditions. Standardized waste input is necessary for reliable large-scale production.	[101,106]

outlines the sustainability, nutritional value, resource efficiency, and challenges of using insect-based feeds in aquaculture, emphasizing their potential to advance regenerative and circular practices in fish farming.

3.3. Sustainable Practices That Keep Fish Healthy Without Antibiotics and Hormones

i. Improved monitoring programs

The prevention of aquaculture animals from indigenous bacterial diseases can only be done through good monitoring programmes and management practices. The aquaculture animals should be tested periodically and be certified to ensure that the population are free of pathogens. The disease monitoring program is aimed at getting information concerning the health status of the farmed animal and the conditions and suitability under which the animals are maintained at a production installation. A well-planned and designed monitoring program should be so scheduled that specimens are examined every week or month of the year—depending on the species lifecycle, culture conditions, and risk involved—to ensure that the fish will be monitored under all ages and production conditions [129]. The monitoring program can be done by examining preserved or live specimens, media inoculated from specific organs or specific tissue slides. The examinations can be conducted by prior arrangement with selected laboratories, or by on-site evaluations by trained hatchery personnel. When the examinations are to be conducted away from the farm area, they should be preserved in wet ice, but not frozen.

Other preventive measures include reducing stress to avoid diseases, use of quality fish feeds, stoking healthy fish, and maintaining a suitable aquatic environment [130]. Feeding fish with good quality feeds is crucial for the growth and prevention of diseases as well as for overall wellbeing overall well-being [131].

Effective management of the environment, which may involve facility design, efficient waste removal, water source, optimal site selection, transport system, and fish handling, is essential for successful aquaculture and prevention of diseases [132].

ii. Avoiding the use of certain animal by-products

Farmers should avoid using animal by-products, such as raw manure, blood meal, and bone meal, to feed fish, as these materials can harbor pathogenic organisms that contribute to disease outbreaks in aquaculture systems [132]. For instance, raw manure from livestock, including cattle and poultry, is a known carrier of enteric bacteria such as E. coli and Salmonella, which can contaminate the water and pose serious health risks to both fish and humans [133]. Additionally, the use of improperly processed blood meal and bone meal from slaughterhouse waste can introduce pathogens like Clostridium and Listeria, further increasing the risk of disease outbreaks [134]. To mitigate these risks, any animal by-products applied in aquaculture should be thoroughly processed through methods such as heat treatment or composting to eliminate harmful pathogens and ensure the safety of the fish and the surrounding environment [132].

iii. Use of generally recognized as safe (GRAS) substances

Natural compounds derived from plants, such as essential oils classified as Generally Recognized as Safe (GRAS) substances, serve as promising prophylactic and therapeutic alternatives in fish farming. Essential oils are volatile liquids containing the aromatic compounds responsible for the characteristic scents of various plant parts, including buds, bark, roots, leaves, and fruits [135]. These oils are rich in phenolic compounds, which form the core of their antimicrobial properties [136]. Notable examples of these compounds include anethole from anise, cinnamaldehyde from cinnamon, carvacrol from oregano, thymol from thyme, and eugenol from clove [137,138].

Cinnamaldehyde has been shown to interfere with the quorum-sensing mechanism in Vibrio species by reducing the DNA-binding capability of the LuxR protein, leading to noticeable reductions in virulence. Essential oils have also been studied for their in vivo antibacterial properties, demonstrating effectiveness in controlling bacterial infections in fish [139]. For instance, immersing carp fillets in a solution containing carvacrol and thymol resulted in extended shelf life due to a decrease in bacterial growth [140]. Similarly, treating trout fillets with oregano extended their shelf life by 7 to 8 days [141]. Although research on the in vivo application of essential oils remains limited, the findings are promising.

Moreover, Yeh et al. [142] reported the antibacterial activity of essential oils against various pathogenic bacteria. In their study, shrimp (Litopenaeus vannamei) treated with hot-water extracts from Cinnamomum kanehirae twigs exhibited reduced sensitivity to Vibrio alginolyticus. In addition to essential oils, phage therapy has garnered attention as an effective method for preventing and controlling pathogenic infections in aquaculture [143].

iv. Probiotics

Probiotics have emerged as a promising alternative to antibiotics for promoting the healthy development of farmed fish [144]. Probiotics are live microorganisms that, when administered, offer benefits to the host by influencing the microbial community associated with the host or its surroundings. They can enhance disease resistance, improve nutrient absorption, boost feed efficiency, or optimize the quality of the surrounding environment [145]. This means that probiotics can aid in digestion, improve water conditions, stimulate immune responses, and inhibit the proliferation of harmful bacteria in both the gut and the external environment.

Various microbial strains have been tested and documented as probiotics in aquaculture, with lactic acid bacteria being the most thoroughly studied. These include genera like Lactococcus, Lactobacillus, Enterococcus, Streptococcus, Carnobacterium, Weissella, and Micrococcus [146,147,148,149]. Other strains such as Bacillus [150], Aeromonas [151], Vibrio [152], and Pseudomonas [153] have also been explored for their probiotic properties. Additionally, yeasts like Debaryomyces and Saccharomyces, as well as actinobacteria, are gaining attention for their high metabolic potential [154].

Probiotics have been effectively used across various aquatic species, including shrimp [155], prawns [156], and teleost fish [157], showing success in improving growth, digestion, and disease resistance. They are particularly beneficial during the early developmental stages, such as larval stages when aquatic organisms are most vulnerable to pathogenic bacteria. Probiotics inhibit the growth of harmful bacteria through several mechanisms, including releasing inhibitory substances, enhancing disease resistance, modulating the immune system, and competing for nutrients and adhesion sites [144,145]. Probiotics that consist of multiple bacterial strains with various modes of action are particularly effective in preventing pathogen proliferation [158]. This multi-strain approach allows the probiotics to adapt and dominate in a constantly changing environment [144].

4. Conclusions

This review underscores the transformative potential of regenerative aquaculture (RA) in advancing climate-resilient and sustainable food production systems. By harnessing innovative practices such as periphyton technology (PPT), biofloc technology (BFT), and integrated multitrophic aquaculture (IMTA), alongside sustainable feed alternatives like microalgae and insect-based feeds, RA can significantly reduce ecological impacts while enhancing food security. These findings emphasize the critical role of technology and agroecology in meeting the rising global demand for fish protein without compromising environmental integrity. Moving forward, further research and development should focus on scaling these regenerative techniques, particularly for smallholder and resource-limited fish farmers, to make them accessible and economically viable across diverse contexts. This work provides a foundation for RA as a blueprint for sustainable aquaculture, with implications for policy development and the broader transition toward eco-friendly, resilient food systems.