Integrated Application of Biofloc Technology in Aquaculture: A Review

Abstract

Although biofloc technology (BFT) currently offers advantages such as improving aquaculture water quality, providing natural bait for cultured animals, and reducing pests and diseases, single BFT systems face technical bottlenecks, including the complex regulation of the carbon–nitrogen ratio, accumulation of suspended substances, and acidification of the bottom sludge. Therefore, constructing a composite system with complementary functions through technology integration, such as with aquaponics, biofilm technology, integrated multi-trophic aquaculture systems (IMTAs), and recirculating aquaculture systems (RASs), has become the key path to breaking through industrialization barriers. This paper systematically reviews the action mechanisms, synergistic effects, and challenges of the four mainstream integration models incorporating BFT, providing theoretical support for the environmental–economic balance of intensive aquaculture.

1. Introduction

In 2024, China’s total aquatic product output reached 73.66 million tons, firmly ranking first globally [1]. Aquaculture plays a crucial role in global food security and the supply of high-quality protein, and its significance has become increasingly prominent with the growth of consumers’ demand for high-quality protein [2]. Driven by escalating health consciousness and policy support, the demand for high-quality aquatic products is continuously increasing [3]. Intensification in aquaculture, characterized by high-density farming and high feed input, has become widespread. However, while this intensification has boosted production efficiency, it has also introduced significant environmental and ecological challenges. Since farmed animals typically assimilate only 20–30% of dietary nutrients, the remaining nutrients are excreted into water bodies [4]. Uneaten feed, fish feces, and other factors can increase the concentrations of three forms of nitrogen in aquaculture water bodies. These tri-state nitrogen compounds are key factors contributing to water eutrophication, water quality deterioration, and the occurrence of diseases in cultured organisms [5,6,7]. Under high stocking density, this leads to accelerated accumulation of uneaten feed and fecal matter, triggering elevated ammonia–nitrogen release. Consequences include severe water eutrophication, heightened susceptibility to infectious diseases, and imbalanced nutrient profiles. Compromised water quality further facilitates bioaccumulation of toxic substances in cultured species, posing direct health risks to consumers [8].

To mitigate water quality issues in extensive aquaculture, improving feeding uniformity and accuracy has been proposed [9]. However, it cannot fully resolve water pollution issues in aquaculture. Traditional solutions for aquaculture wastewater treatment rely primarily on physical and biological methods. Physical methods include sedimentation, screening, flotation, aeration, and filtration [10]. These methods offer operational intuitiveness and cost control but exhibit limited efficacy in removing nitrogen–phosphorus nutrients and complex organic matter. Biological methods include microbial treatment, biological filtration, phytoremediation, etc. They have the advantages of sustainability, environmental friendliness, and nutrient recycling, and they can degrade toxic substances, suppress pathogenic bacteria, and optimize ecosystems [11]. However, limitations exist, such as longer treatment cycles, significant influence by environmental factors, and the need for ecological niche establishment time in some systems. Besides advances in water quality treatment technologies, the automatic cruise water quality monitoring system studied by Zhu et al. [12] and the aquaculture monitoring system researched by Shi et al. [13] can provide a more suitable growth environment for farmed animals.

Biofloc technology (BFT) is an innovative approach derived from zero-water-exchange aquaculture technology and activated sludge water treatment principles. Bioflocs are flocculent aggregates formed by bacteria, algae, protozoa, and other organisms through biological flocculation [14]. They play multiple roles in optimizing water quality, providing natural feed for cultured animals, and reducing disease incidence. BFT plays multiple roles in optimizing water quality, providing natural feed for farm animals and reducing disease incidence. Additionally, it exhibits significant advantages in reducing the feed conversion ratio, improving the survival rate of farmed animals, and protecting the water environment [15]. Widely applied in farming tilapia and Litopenaeus vannamei [16], BFT transforms nitrogen waste into nutrient-rich bioflocs through microbial communities to optimize water quality, provide natural feed, and enhance the growth performance and survival rate of tilapia and other aquaculture organisms [17]. This technology can also promote the proliferation of beneficial bacteria in shrimp aquaculture by maintaining the C/N ratio, enhancing biosecurity, reducing feed costs, and promoting the sustainable development of aquaculture [18]. BFT has become a key research focus due to its superiority over traditional aquaculture models.

Compared with other aquaculture methods, integrated multi-trophic aquaculture (IMTA), recirculating aquaculture systems (RASs), and biofilm aquaculture systems, the core advantage of BFT lies in its unique “functional integration” and “self-cycling ability”: it synchronizes water purification and natural feed production through microbial activities. This distinguishes it from aquaponics, which relies on plant nitrogen absorption [19]; IMTA, which depends on multi-species ecological niche coordination [20]; RAS, which relies on complex filtration equipment [21]; and biofilm systems, which focus solely on water purification [22]. Additionally, BFT’s microbial community exhibits stronger self-regulation capabilities than these other technologies—which are more dependent on external conditions—allowing it to serve as the “nutrient core” of integrated systems, providing stable water quality and resource support for other technologies [23], which makes it an irreplaceable cornerstone in aquaculture taking efficiency and sustainability into consideration.

However, practical applications of BFT face multiple technical challenges. The formation of bioflocs relies on microbial aggregation, which inherently leads to accumulation of fecal waste, uneaten feed, and aged flocs in water bodies [24]. This inevitably increases water turbidity and poses a risk of gill blockage to farmed animals [25]. A key challenge in BFT lies in the precise regulation of the carbon–nitrogen (C/N) ratio, which is critical for biofloc formation [26]. In practice, dynamic factors like feed input, water temperature, and farming density often disrupt the optimal C/N balance [27]. Environmental parameters such as pH swings, dissolved oxygen variations, and ionic strength changes further compromise floc efficiency [28]. Economically, BFT practice faces hurdles from high initial infrastructure costs and ongoing operational expenses, particularly for organic carbon sources like molasses and starch required to maintain the C/N ratio [29]. Additionally, in BFT systems, which typically use a zero-water-exchange mode, uneaten feed, feces, and aged flocs gradually accumulate in the sediment. This buildup fosters pathogenic growth and causes sediment acidification, threatening cultured animals’ health. The merits and shortcomings of BFT are shown in Figure 1.

In response to the technical bottlenecks of difficult C/N ratio regulation and suspended solid accumulation in standalone biofloc systems, as well as the economic challenge of high carbon source costs, the integration of BFT with complementary technologies has become a key path for breakthrough. This review systematically synthesizes the action mechanisms, synergistic effects, and operational challenges of multiple BFT-integrated models, providing theoretical support for balancing environmental sustainability and production efficiency in intensive aquaculture. By analyzing the functional complementarity between BFT and integrated technologies—including nutrient cycling enhancement, microbial community optimization, and water quality stabilization—this work identifies key knowledge gaps in system parameter optimization and long-term microbial dynamics, while highlighting the transformative potential of hybrid systems for addressing global aquaculture sustainability challenges.

2. Main Integrated Models of BFT in Aquaculture

2.1. BFT–Aquaponics Integration

Aquaponics is an aquaculture and hydroponic cultivation model that achieves efficient, environmentally friendly, and safe agricultural production through ecological design and technological integration, offering comprehensive economic, ecological, and social benefits. As an innovative agricultural model combining aquaculture and hydroponic planting, aquaponics demonstrates remarkable characteristics of resource circular utilization and technological integration advantages [30].

However, traditional aquaponics systems suffer from the drawback of low nitrogen utilization efficiency. The integration of microbial floc technology with aquaponics, known as “FLOCponics”, has emerged as an innovative integrated agricultural and aquacultural production model garnering widespread attention in recent years. This system combines the efficient water quality regulation of BFT with the nutrient cycling advantages of aquaponics. Through the treatment of nitrogen in aquaculture wastewater by microbial flocs and the absorption of nutrients by plants, FLOCponics forms a closed-loop resource utilization system, providing a new pathway for sustainable food production [31].

The core of the FLOCponics system lies in leveraging heterotrophic and nitrifying microbial communities in BFT to degrade aquaculture waste. This process converts toxic substances such as ammonia nitrogen into plant-absorbable nitrate nitrogen, during which efficient nutrient recycling is achieved [32]. Studies have shown that compared to single BFT systems, FLOCponics increases water and nitrogen utilization efficiency by 10% and 27%, respectively, and reduces solid waste emissions by 10% [33]. This synergistic effect not only reduces chemical fertilizer inputs but also mitigates the environmental pollution risks posed by aquaculture wastewater. By integrating biofloc aquaculture with hydroponic systems, FLOCponics demonstrates significant advantages in resource cycling, environmental sustainability, production diversity, and efficiency. Although its current environmental load is comparable to those of independent systems, its resource utilization efficiency and composite output capacity position it as a highly promising sustainable food production model. Especially with technological optimization and scale expansion, it is expected to further enhance sustainability and economic benefits [34]. Additionally, the protein-rich microbial flocs in BFT can serve as supplementary feed for cultured organisms, reducing feed costs and forming a “fish-microbe-plant” mutualistic symbiotic relationship [35].

Current research on FLOCponics focuses on system design, water quality regulation, and production performance evaluation (Table 1). Experimental designs encompass two main layouts: directly connected coupled systems with integrated water circulation and independent decoupled systems with staged regulation via filtration devices. In the aspect of plant production, leafy vegetables such as lettuce and Salicornia, as well as economic crops like tomatoes and peppers, exhibit varied growth performances. Some studies showed that plant yields in FLOCponics are comparable to or slightly higher than those in traditional hydroponics [36,37,38]. Pinho et al. [39] suggested that FLOCponics could be technically viable if specific fertilization management or mechanisms are developed to address key issues such as system nutrient imbalance and solid accumulation in plant roots to enhance yields. However, other research indicated that solid suspended matter accumulation may inhibit root development [40,41]. With regard to farmed animals, FLOCponics significantly improves the growth performance of farmed animals through the integration of biofloc and hydroponic systems. In a biofloc system for farming Litopenaeus vannamei and New Zealand spinach, The Litopenaeus vannamei’s weight increased by 1.36 g per week, and the system ensured the Litopenaeus vannamei’s growth performance while desalinating concentrate [42]. In the research of Nadia et al. [43], the effects of gut probiotics, water probiotics, and biofloc input on the growth of tilapia and tomatoes in aquaculture systems were compared. The results showed that tilapia exhibited superior growth performance in the biofloc integrated system, achieving the highest final weight, specific growth rate, and yield; the lowest feed conversion ratio; a higher survival rate; increased muscle crude protein content; and significantly improved overall health. Studies have shown that tilapia raised in FLOCponics grow faster with lower stress responses, while Pacific white shrimp and mullet exhibit higher survival rates and increased yields [44,45], all demonstrating efficient feed conversion and strong stress resistance. The growth performance indicators of farmed animals in FLOCponics, such as specific growth rate and feed conversion ratio, are similar to or superior to those in single BFT systems or in single aquaponics systems [46]. However, fine-tuned regulation of dissolved oxygen management and microbial community balance is still required under high-density culture conditions. From a sustainable development perspective, FLOCponics aligns with global demands for efficient resource utilization and low-carbon agriculture [47]. Its closed-loop nutrient cycling reduces reliance on external inputs, making it particularly suitable for regions with water scarcity or limited land [48]. In urban agriculture scenarios, the system can utilize vertical space for localized “aquaponic” production, shortening supply chains and reducing transportation-related emissions [49]. With advancements in microbiomics and modeling technologies, FLOCponics is poised to become a core technology linking aquaculture and crop cultivation, offering innovative solutions to address food security and environmental challenges.

Although FLOCponics demonstrates significant potential, it faces multiple challenges in achieving technological maturity. First, effective control of total suspended solids (TSS) is critical. Elevated TSS can clog hydroponic pipelines and hinder plant nutrient absorption, while excessive filtration may reduce floc volume in aquaculture water, compromising water quality and diminishing natural feed for farmed animals. Second, standardization of system parameters remains unachieved, as different species have varying requirements for C/N ratios, pH, and dissolved oxygen, making it difficult to develop universal optimization strategies. In terms of economic viability, high initial equipment investment and professional operation costs limit small-scale promotion [50]. Future research should focus on decoupled system design, enhancing stability through modular filtration and precise nutrient regulation [51], deciphering the interaction mechanisms between microbial communities and plant roots to develop targeted probiotic agents for promoting nutrient conversion, and integrating life cycle assessment (LCA) with energy efficiency analysis to construct an environmentally and economically sustainable production model.

Overall, the integration of BFT with aquaponics represents a cutting-edge direction in integrated agriculture–aquaculture systems. Its success hinges on interdisciplinary collaboration, requiring a balance among technical optimization, cost control, and ecological balance to lay the foundation for future sustainable food production systems.

2.2. BFT–Biofilm Technology Coupling

A biofilm is a three-dimensional aggregate formed by bacteria, fungi, algae, etc., adhering to a solid surface and encapsulated by extracellular polymeric substances (EPSs), featuring a highly organized structure and metabolic functions [52]. Biofilm technology enables microorganisms to form functional stratified structures on the surface of carriers and utilizes their diverse metabolic pathways to specifically treat high-nitrogen–phosphorus compounds, organic matter, and antibiotic residues in aquaculture wastewater [53]. It is one of the core technologies for the sustainable treatment of aquaculture wastewater. The integration of microbial floc technology and biofilm reactors has become a research hotspot for enhancing water quality regulation efficiency. Through functional complementarity and synergy, these two technologies demonstrate significant advantages in nitrogen and phosphorus removal, system stability, the improvement of farmed animal growth performance, and the optimization of microbial communities [54], providing a new pathway for the sustainable development of intensive aquaculture.

The moving bed biofilm reactor (MBBR) is a major type of biofilm technology, playing an important role in wastewater treatment and other fields. BFT removes ammonia nitrogen through the efficient assimilation and heterotrophic activity of suspended microbial flocs, while MBBRs rely on autotrophic nitrifying bacteria on the biofilm surface to convert ammonia nitrogen into nitrate. The combination of the two can form a biphasic treatment system consisting of suspended flocs and attached biofilms. In a study by Ramiro et al. [55], the addition of artificial substrates promoted biofilm formation, enhanced the nitrification capacity of the biofloc system, and optimized water quality, providing a sustainable solution for high-density shrimp farming. A study has shown that inoculating microbial flocs recovered from BFT into an MBBR can significantly accelerate the nitrification process, and the fluorescence gray scale ratio of viable cells in the biofilm significantly increased, indicating stronger biofilm activity [56]. This synergistic effect originates from the abundant ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the flocs, which accelerate biofilm colonization and functional differentiation, leading to rapid enrichment of dominant microbial communities [57].

Additionally, the combination of BFT and biofilm technology can effectively reduce aquaculture costs and feed usage (Table 1). In a pioneering study by Lara et al. [58], the quantitative effect of biofilms on feed savings was validated in a high-density biofloc system for the first time. The results showed that in the farming of Litopenaeus vannamei, the combination of biofilm and BFT achieved a production rate of 1.87 kg/m³ with a 35% reduction in artificial feed input, which was not significantly different from the high-feeding rate group’s production rate of 2.09 kg/m³. At the same time, the survival rate exceeded 97%. This provides data support for cost optimization and environmental sustainability in intensive shrimp farming. As a natural food supplement, biofilms can reduce the input of artificial feed, minimize feed waste and environmental pollution, and improve the sustainability of the system.

Biofilms can adsorb suspended solids, reduce turbidity and settleable solids, and minimize physiological damage to farmed animals caused by excessive suspended matter, thereby indirectly improving survival rates. Additionally, they provide surfaces for microbial attachment, promoting synergistic interactions between bioflocs and biofilms to optimize nitrogen cycling. Lara et al. [59] demonstrated that in the biofloc system, the addition of NaNO₂ at the time of seedling release has been shown to directly promote the metabolic activity of NOB through the provision of substrates. Biofilm has also been demonstrated to enhance the colonization and reproduction of NOB through the provision of attachment surfaces and the optimization of the microenvironment. The combination of the two has been shown to significantly accelerate the conversion of nitrite to nitrate, enhance the nitrification efficiency of the system, and ultimately improve the growth performance of shrimp. This synergistic effect provides an effective strategy for nitrogen pollution control in high-density aquaculture.

Aquaculture performance data further validate the advantages of this coupled system. In a culture system integrating bioflocs and biofilms, Ferreira et al. [60] showed that the treatment group with artificial substrate addition exhibited significantly lower solid sedimentation than the control group culturing Litopenaeus vannamei. The final body weight and specific growth rate of shrimp were significantly improved, the feed conversion ratio was reduced, and key water quality indicators remained at appropriate levels. In the culture of Anguilla marmorata, Jiang et al. [61] combined biofilm-cleaned gratings with exogenous carbon sources, reducing the daily water exchange rate by leading to a 69.2% and 74.4% reduction in the daily water exchange rate compared with the control group, respectively. Nitrogen and phosphorus pollutants such as total ammonia nitrogen and nitrite nitrogen, as well as vibrio density, significantly decreased, while the growth rates of the cultured species increased by 37.8% and 14.9%. By providing additional food sources, regulating suspended solids, and improving water quality, the combination of microbial flocs and biofilms effectively enhances the growth performance of different cultured species, reduces feed consumption and water exchange requirements, and demonstrates significant synergistic effects.

Despite the significant advantages shown in existing studies, large-scale application still faces challenges. For example, the material of biofilm carriers may be affected by microbial erosion, impacting long-term stability, while the accumulation of suspended solids in BFT may cause short-term blockages in the MBBR. Future research could focus on carrier optimization and the development of anti-pollution materials [62,63], precise carbon source regulation strategies based on microbial community dynamics [53], and energy efficiency improvement of coupled systems [64]. Additionally, integrating metabolomics with model simulation to analyze mass transfer and metabolic flux distribution at the interface between flocs and biofilms will provide more accurate theoretical support for process optimization.

In summary, the integration of microbial floc technology and biofilm reactors constructs an efficient and flexible water quality regulation system for aquaculture through functional synergy and microbial community complementarity. This approach provides an innovative paradigm for addressing nitrogen–phosphorus pollution and system stability issues in intensive aquaculture, holding broad application prospects and research value.

2.3. BFT–Integrated Multi-Trophic Aquaculture (IMTA) Coupling

IMTA is a sustainable aquaculture model that forms an ecological cycle of producers, consumers, and decomposers by integrating species from different trophic levels [65]. By simulating the nutrient cycling of natural ecosystems, IMTA converts aquaculture waste into resources, achieving the triple goals of production, purification, and added value. Its core principle lies in the functional complementarity and material cycling among species, which not only enhances economic benefits but also reduces environmental pressure [66].

The core advantage of integrating BFT with IMTA lies in the synergistic effect of cross-trophic species to efficiently regulate water quality and reduce pollutant accumulation (Table 1). For example, in a shrimp–tilapia integrated system, Nile tilapia (Oreochromis niloticus), as an organic consumer, reduced TSS concentration by feeding on microbial flocs, minimizing the need for physical clarification [14]. Studies showed that compared with monoculture shrimp systems, the introduction of tilapia significantly shortens system clarification time while maintaining TSS within suitable ranges. Macroalgae, as inorganic nutrient consumers, also play a critical role in IMTA. When red algae (Agarophyton tenuistipitatum) are co-cultured with shrimp, parameters including ammonia, nitrite, nitrate, phosphate, and chemical oxygen demand (COD) all declined markedly, thereby providing a more stable growth environment for shrimp [67]. Similarly, macroalgae enhance nitrogen and phosphorus recovery rates by absorbing inorganic nutrients, reduce turbidity, and optimize light conditions to promote symbiosis between microorganisms and plants.

The introduction of multi-trophic species also significantly improves the growth and survival of target organisms. In a shrimp–tilapia system, although tilapia density had no significant effect on the final body weight of shrimp, the overall system productivity was increased by 15–20%. Poli et al. [68] found that the growth performance of Litopenaeus vannamei and Oreochromis niloticus was not negatively affected in the BFT-coupled-with-IMTA system, but the total system yield was increased by 21.5% compared to the single BFT, and the level of wastes in the water was reduced. Additionally, the feed conversion ratio of tilapia indicates their ability to effectively utilize flocs as supplementary feed, reducing dependence on artificial feeding [69]. In another study, the addition of Gasar oysters (Crassostrea gasar) did not significantly reduce TSS, but their selective feeding on flagellated microorganisms highlighted potential roles in regulating floc microbial composition, providing new insights for the combination of filter-feeding organisms and BFT [70]. In another seaweed–shrimp integrated system, the shrimp specific growth rate and survival rate were significantly higher than those in single BFT systems, which was attributed to improved water quality and prebiotic effects released by seaweeds. Furthermore, separated culture of tilapia and shrimp dramatically enhanced shrimp survival compared to co-culture in the same pond, indicating that reasonable spatial configuration can reduce interspecific competition and optimize resource allocation [71]. It is worth noting that the selective feeding of different species on flocs affects their nutritional composition. The introduction of multi-trophic species significantly enhances the productivity of aquaculture systems and the survival rate of target organisms by optimizing resource allocation, improving water quality, and leveraging synergistic effects among organisms.

The combination of microbial flocculation technology and IMTA achieves the triple goals of reducing nutrient discharges, increasing aquaculture production, and improving fish quality through cross-species mate–industry recycling and energy conversion. Combinations of filter-feeding shellfish, omnivorous fish, and photosynthetic algae not only efficiently regulate water quality but also enhance feed utilization and aquaculture performance, providing sustainable solutions to address environmental and economic challenges in aquaculture. Future research should center on multi-species synergy mechanisms, system optimization, and large-scale application to promote the transformation of this technology from experimental research to industrial implementation.

2.4. BFT–Recirculating Aquaculture System (RAS) Hybrid System

The RAS is a mode of high-density aquaculture of aquatic organisms in a controlled environment through water quality filtration and recycling [72]. Compared with traditional pond aquaculture, RAS significantly excel in protein stability, antioxidant capacity, aquacultural efficiency, and meat quality. Notably, RAS demonstrates outstanding advantages in freezing storage adaptability and sustainability [73], making it particularly suitable for high-density and intensive aquaculture scenarios. Despite challenges in sensor maintenance and costs, with technological maturity and large-scale promotion, the RAS is expected to become the mainstream model for future aquaculture, helping to address the dual needs of global food security and ecological protection [74,75].

Enhanced nutrient cycling and feed efficiency represent core advantages of the combined system of BFT and RAS (Table 1). Bioflocs, rich in proteins, amino acids, and essential fatty acids, serve as natural feed for cultured organisms, reducing dependence on artificial feed. The closed environment of the RAS provides stable growth conditions for flocs, lowering the feed conversion ratio to 1.4–1.6, a 20–30% reduction compared to traditional ponds. In Litopenaeus vannamei culture systems, flocs supplement 30% of the nitrogen demand, with the protein efficiency ratio increasing by 15%. Additionally, probiotics in flocs secrete digestive enzymes that enhance intestinal digestion: the intestinal protease activity of Nile tilapia is significantly higher in the coupled system than in a single RAS [76].

In terms of culture performance, the use of BFT in RASs can significantly improve the growth performance and survival rate of Penaeus indicus, and this mode of combination can also reduce the concentration of ammonia nitrogen and nitrite in the water body and improve the activity of polyphenol oxidase (PPO), total serum proteins, and other immune indicators of shrimp, so as to realize the synergistic effect of optimizing the quality of the water and strengthening the immune system [77]. In terms of environmental and economic benefits, such a coupled system achieves a water saving rate of over 90% and reduces nitrogen and phosphorus emissions by 40–50%, which are significantly lower than those of traditional open systems [78]. Although the initial equipment investment exceeds that of traditional ponds, feed costs decrease dramatically, thereby boosting overall profitability.

Nonetheless, technical bottlenecks remain to be addressed. Under high-density conditions, fluctuations in dissolved oxygen and accumulation of nitrite are prone to occur, requiring dynamic regulation of carbon source addition through online sensors and machine learning. Microbial balance between nitrifying bacteria and heterotrophic bacteria is sensitive to C/N ratios and temperature, necessitating the screening of functional microbial groups tolerant to high temperatures and ammonia nitrogen, as well as the optimization of the community structure through artificial inoculation. In terms of energy consumption, aeration and water circulation equipment account for 40–50% of operating costs. Critical solutions include developing low-power technologies (e.g., efficient air pumps and solar-powered systems) and implementing wastewater resource recovery strategies.

3. Comparison Among Various Integrated Models

Table 1 presents the application cases and advantages of BFT-integrated models with aquaponics, biofilm technology, IMTA, and RASs, as detailed in the subsequent subsections. Among them, the combination of BFT and aquaponics realizes efficient nutrient cycling through the closed loop of “fish-microbe-plant”, which can improve water and nitrogen utilization and increase diversified outputs, but the difficulty in controlling TSS, the lack of standardization of system parameters, and the high initial investment limit the promotion of the model. BFT coupled with biofilm technology strengthens nitrogen cycling and water quality stabilization through a dual-microbial system, which can reduce feed inputs, but faces the problems that biofilm carriers are susceptible to erosion by microorganisms and short-term clogging risks. The hybrid system of BFT and RAS is suitable for high-density aquaculture with high water conservation and precise pollutant control, but high capital intensity and energy consumption are the main bottlenecks.

Table 1. Applications and advantages of BFT-integrated technologies in aquaculture.

Cultured Species	Combined Technology	Key Merits	Reference
Tilapia shrimp, Chinese carps, Crayfish, Crabs	Aquaponics	Nutrient cycle upgrade Expansion of economic benefits Enhancement of environmental sustainability	Martinez-Cordova, et al. [31]
Nile tilapia	Aquaponics	Nutrient cycling and water quality optimization Synergistic yield increase Comprehensive benefits breakthrough	Martins, et al. [32]
Oreochromis niloticus	Aquaponics	Resource utilization efficiency improvement Dual-output model breakthrough Water purification mechanism enhancement Synergistic benefit integration	Pinho, et al. [33]
Oreochromis niloticus	Aquaponics	Cross-trophic resource cycling Composite function upgrading System efficiency improvement New paradigm for sustainable agriculture	Pinho, et al. [34]
Oreochromis spp., Litopenaeus vannamei	Aquaponics	Cross-trophic closed-loop nutrient cycling Aquaculture-plant cultivation functional diversification Resource self-sufficiency and pollution reduction Urban sustainable agriculture adaptability	Yu, et al. [35]
Oreochromis niloticus	Aquaponics	Cross-trophic synergistic circulation mechanism Dual benefits of aquaculture and cultivation Water quality management optimization and systemic challenges	Pinho, et al. [39]
Oreochromis spp., Litopenaeus vannamei	Aquaponics	Cross-trophic water quality regulation mechanism Aquaculture-cultivation functional diversification Resource circulation and pollution reduction Urban sustainable agriculture adaptability and optimization needs	Pinho, et al. [41]
Litopenaeus vannamei, Mugil liza	Aquaponics	Cross-trophic water quality synergistic regulation Aquaculture performance maintenance Biomass enhancement and functional diversification Resource circulation and environmental benefit enhancement	Legarda, et al. [44]
GIFT Tilapia, Oreochromis niloticus	Aquaponics	Cross-trophic closed-loop nutrient cycling Tilapia-bell pepper dual-function production mode Water quality management and resource circulation efficiency improvement Root system regulation and aquatic animal welfare enhancement	Saseendran, et al. [45]
Oreochromis niloticus	Aquaponics	Cross-trophic closed-loop nutrient cycling and water quality optimization Maintenance of juvenile tilapia culture performance and dual benefits of vegetable production Resource circulation efficiency improvement and pollution reduction Economic viability’s market dependence and challenges	Pinho, et al. [50]
Litopenaeus vannamei	Biofilm technology	Microbial attachment and nitrogen cycle enhancement Water quality toxic substance control and stability improvement Litopenaeus vannamei growth and system productivity leap Dual microbial system synergistic purification mechanism Sustainable water quality solution for high-density aquaculture	de Lara, et al. [54]
Penaeus vannamei	Biofilm technology	Synergistic construction of dual microbial systems Enhancement of nitrogen cycle efficiency and microbial diversity Precision control of water quality toxic substances Leap in aquaculture performance of Penaeus vannamei Substrate management-driven system resilience strengthening Adaptability breakthrough for ultra-high density aquaculture	Ramiro, et al. [55]
Oreochromis niloticus	Biofilm technology	Dual microbial system synergistic startup mechanism Nitrogen pollutant removal efficiency leap Short-process adaptability and system resilience Dual application values for recirculating aquaculture systems	Zheng, et al. [56]
Litopenaeus vannamei	Biofilm technology	Construction of dual microbial attachment systems Precision removal of nitrogen pollutants and nitrification enhancement Comprehensive water quality improvement effects Adaptability to high-density Litopenaeus vannamei aquaculture	Xu, et al. [57]
Litopenaeus vannamei	Biofilm technology	Dual microbial carrier synergistic enhancement mechanism Feed input optimization and conversion efficiency improvement Microbial community-driven water quality stabilization Economical and environmentally friendly solution for high-density aquaculture	Lara, et al. [58]
Litopenaeus vannamei	Biofilm technology	Construction of dual microbial carrier synergistic system Water clarity improvement and stress mitigation effects Dynamic optimization of nitrogen cycling and long-term stability Feed conversion and growth performance enhancement Precision regulation strategy for stocking stage	Lara, et al. [59]
Anguilla marmorata	Biofilm technology	Construction of dual microbial carrier synergistic system Enhancement of heterotrophic bacteria-nitrifying bacteria symbiotic efficiency Pathogenic bacteria inhibition and water quality safety enhancement Efficient water resource utilization and pollution reduction Aquaculture performance and sustainability improvement of Anguilla marmorata	Jiang, et al. [61]
Salmo salar, Dicentrarchus labrax, Sparus aurata, Sciaenops ocellatus	IMTA	Cross-trophic synergistic system construction Multilevel removal of pollutants and nutrient cycling enhancement Metabolic pressure dispersion and water quality stability improvement Reduction in manual intervention and chemical inputs Dual-function integration of water purification and biological production Ecological solution for high-density aquaculture	Khanjani, et al. [14]
Litopenaeus vannamei	IMTA	Cross-trophic synergistic system construction Multilevel purification and cycling enhancement of nitrogen and phosphorus pollutants Dual-function enablement of red algae Improvement of system self-sustaining capacity-performance leap in Litopenaeus vannamei aquaculture Ecological dual-benefit model for high-density aquaculture	Sarkar, et al. [67]
Litopenaeus vannamei, Oreochromis niloticus	IMTA	Cross-trophic two-species synergistic system construction Targeted purification function of Nile tilapia Growth safeguard of white shrimp and dual-species production Double improvement of resource utilization efficiency and economic benefits Double reduction of environmental load in sustainable aquaculture	Holanda, et al. [69]
Litopenaeus vannamei, Crassostrea gasar	IMTA	Cross-trophic filter-feeding species synergistic system construction Microbial regulation mechanism of oyster selective feeding Particle distribution reshaping and water quality parameter stability Exploration of system compound production potential Ecological adaptability of low-density species introduction Exploration of sustainable aquaculture paradigm with multi-species functional complementarity	Costa, et al. [70]
Litopenaeus vannamei, Arthrospira platensis	IMTA	Cross-trophic phototrophic microalgae synergistic system construction Efficient biological uptake of nitrogen and phosphorus pollutants Photosynthesis-driven ecological regulation of water quality Resource utilization of pollutants and high-value biomass production Wastewater treatment paradigm for closed aquaculture systems	Holanda, et al. [71]
Oreochromis niloticus	RAS	Synergistic construction of biofloc- RAS Precision removal of pollutants and stabilization of physicochemical parameters Mechanism of physiological function enhancement in Nile tilapia Stress mitigation effects in high-density aquaculture Breaking through the application bottlenecks of single systems	Pai, et al. [76]
Oreochromis niloticus	RAS	Construction of biofloc-RAS synergistic purification system Precision control of nitrogen metabolites and reduction of pollution load Dynamic stabilization of water physicochemical parameters Enhancement of digestive and metabolic functions in Nile tilapia Stress mitigation and disease resistance improvement in high-density aquaculture “Water quality-growth-economy” three-dimensional synergistic benefits Breaking through the high-density aquaculture bottlenecks of single systems	Pai, et al. [78]

Table 1. Applications and advantages of BFT-integrated technologies in aquaculture.

Cultured Species	Combined Technology	Key Merits	Reference
Tilapia shrimp, Chinese carps, Crayfish, Crabs	Aquaponics	Nutrient cycle upgrade Expansion of economic benefits Enhancement of environmental sustainability	Martinez-Cordova, et al. [31]
Nile tilapia	Aquaponics	Nutrient cycling and water quality optimization Synergistic yield increase Comprehensive benefits breakthrough	Martins, et al. [32]
Oreochromis niloticus	Aquaponics	Resource utilization efficiency improvement Dual-output model breakthrough Water purification mechanism enhancement Synergistic benefit integration	Pinho, et al. [33]
Oreochromis niloticus	Aquaponics	Cross-trophic resource cycling Composite function upgrading System efficiency improvement New paradigm for sustainable agriculture	Pinho, et al. [34]
Oreochromis spp., Litopenaeus vannamei	Aquaponics	Cross-trophic closed-loop nutrient cycling Aquaculture-plant cultivation functional diversification Resource self-sufficiency and pollution reduction Urban sustainable agriculture adaptability	Yu, et al. [35]
Oreochromis niloticus	Aquaponics	Cross-trophic synergistic circulation mechanism Dual benefits of aquaculture and cultivation Water quality management optimization and systemic challenges	Pinho, et al. [39]
Oreochromis spp., Litopenaeus vannamei	Aquaponics	Cross-trophic water quality regulation mechanism Aquaculture-cultivation functional diversification Resource circulation and pollution reduction Urban sustainable agriculture adaptability and optimization needs	Pinho, et al. [41]
Litopenaeus vannamei, Mugil liza	Aquaponics	Cross-trophic water quality synergistic regulation Aquaculture performance maintenance Biomass enhancement and functional diversification Resource circulation and environmental benefit enhancement	Legarda, et al. [44]
GIFT Tilapia, Oreochromis niloticus	Aquaponics	Cross-trophic closed-loop nutrient cycling Tilapia-bell pepper dual-function production mode Water quality management and resource circulation efficiency improvement Root system regulation and aquatic animal welfare enhancement	Saseendran, et al. [45]
Oreochromis niloticus	Aquaponics	Cross-trophic closed-loop nutrient cycling and water quality optimization Maintenance of juvenile tilapia culture performance and dual benefits of vegetable production Resource circulation efficiency improvement and pollution reduction Economic viability’s market dependence and challenges	Pinho, et al. [50]
Litopenaeus vannamei	Biofilm technology	Microbial attachment and nitrogen cycle enhancement Water quality toxic substance control and stability improvement Litopenaeus vannamei growth and system productivity leap Dual microbial system synergistic purification mechanism Sustainable water quality solution for high-density aquaculture	de Lara, et al. [54]
Penaeus vannamei	Biofilm technology	Synergistic construction of dual microbial systems Enhancement of nitrogen cycle efficiency and microbial diversity Precision control of water quality toxic substances Leap in aquaculture performance of Penaeus vannamei Substrate management-driven system resilience strengthening Adaptability breakthrough for ultra-high density aquaculture	Ramiro, et al. [55]
Oreochromis niloticus	Biofilm technology	Dual microbial system synergistic startup mechanism Nitrogen pollutant removal efficiency leap Short-process adaptability and system resilience Dual application values for recirculating aquaculture systems	Zheng, et al. [56]
Litopenaeus vannamei	Biofilm technology	Construction of dual microbial attachment systems Precision removal of nitrogen pollutants and nitrification enhancement Comprehensive water quality improvement effects Adaptability to high-density Litopenaeus vannamei aquaculture	Xu, et al. [57]
Litopenaeus vannamei	Biofilm technology	Dual microbial carrier synergistic enhancement mechanism Feed input optimization and conversion efficiency improvement Microbial community-driven water quality stabilization Economical and environmentally friendly solution for high-density aquaculture	Lara, et al. [58]
Litopenaeus vannamei	Biofilm technology	Construction of dual microbial carrier synergistic system Water clarity improvement and stress mitigation effects Dynamic optimization of nitrogen cycling and long-term stability Feed conversion and growth performance enhancement Precision regulation strategy for stocking stage	Lara, et al. [59]
Anguilla marmorata	Biofilm technology	Construction of dual microbial carrier synergistic system Enhancement of heterotrophic bacteria-nitrifying bacteria symbiotic efficiency Pathogenic bacteria inhibition and water quality safety enhancement Efficient water resource utilization and pollution reduction Aquaculture performance and sustainability improvement of Anguilla marmorata	Jiang, et al. [61]
Salmo salar, Dicentrarchus labrax, Sparus aurata, Sciaenops ocellatus	IMTA	Cross-trophic synergistic system construction Multilevel removal of pollutants and nutrient cycling enhancement Metabolic pressure dispersion and water quality stability improvement Reduction in manual intervention and chemical inputs Dual-function integration of water purification and biological production Ecological solution for high-density aquaculture	Khanjani, et al. [14]
Litopenaeus vannamei	IMTA	Cross-trophic synergistic system construction Multilevel purification and cycling enhancement of nitrogen and phosphorus pollutants Dual-function enablement of red algae Improvement of system self-sustaining capacity-performance leap in Litopenaeus vannamei aquaculture Ecological dual-benefit model for high-density aquaculture	Sarkar, et al. [67]
Litopenaeus vannamei, Oreochromis niloticus	IMTA	Cross-trophic two-species synergistic system construction Targeted purification function of Nile tilapia Growth safeguard of white shrimp and dual-species production Double improvement of resource utilization efficiency and economic benefits Double reduction of environmental load in sustainable aquaculture	Holanda, et al. [69]
Litopenaeus vannamei, Crassostrea gasar	IMTA	Cross-trophic filter-feeding species synergistic system construction Microbial regulation mechanism of oyster selective feeding Particle distribution reshaping and water quality parameter stability Exploration of system compound production potential Ecological adaptability of low-density species introduction Exploration of sustainable aquaculture paradigm with multi-species functional complementarity	Costa, et al. [70]
Litopenaeus vannamei, Arthrospira platensis	IMTA	Cross-trophic phototrophic microalgae synergistic system construction Efficient biological uptake of nitrogen and phosphorus pollutants Photosynthesis-driven ecological regulation of water quality Resource utilization of pollutants and high-value biomass production Wastewater treatment paradigm for closed aquaculture systems	Holanda, et al. [71]
Oreochromis niloticus	RAS	Synergistic construction of biofloc- RAS Precision removal of pollutants and stabilization of physicochemical parameters Mechanism of physiological function enhancement in Nile tilapia Stress mitigation effects in high-density aquaculture Breaking through the application bottlenecks of single systems	Pai, et al. [76]
Oreochromis niloticus	RAS	Construction of biofloc-RAS synergistic purification system Precision control of nitrogen metabolites and reduction of pollution load Dynamic stabilization of water physicochemical parameters Enhancement of digestive and metabolic functions in Nile tilapia Stress mitigation and disease resistance improvement in high-density aquaculture “Water quality-growth-economy” three-dimensional synergistic benefits Breaking through the high-density aquaculture bottlenecks of single systems	Pai, et al. [78]

In terms of selection strategy, FLOCponics is preferred for resource recycling and multiple outputs. biofilm coupling is more suitable for efficient nitrogen removal and system stability, IMTA integration is more advantageous in the pursuit of ecological synergies and multi-species outputs, and the BFT-RAS hybrid system is the best choice for high-density farming, water conservation, and controlled environmental requirements. In the future, it will be necessary to optimize the technology for the pain points of each model and balance the ecological benefits and economic feasibility.

Understanding these integration strategies is crucial to the development of cost-effective and sustainable aquaculture, as single BFT faces bottlenecks such as the complex regulation of C/N balance, accumulation of suspended solids, and substrate acidification in high-density aquaculture, while the integration model builds up a synergistic system through technological complementation and realizes closed-loop resource utilization by means of a composite ecological chain, which consists of “microorganisms-biocarriers-aquaculture organisms”. The integration model builds a functional synergistic system through technological complementation, realizes closed-loop resource utilization through the “microorganisms-bio-carriers-aquaculture organisms” composite ecological chain, transforms underutilized nutrients in traditional aquaculture into recyclable resources, reduces the cost of artificial feeds and carbon inputs, and improves the efficiency of pollutant removal through a multi-stage purification mechanism to solve the problem of the deterioration of water quality under the mode of zero or low water exchange. This kind of integration strategy starts from “environment-economy” two-way optimization, reduces infrastructure and operation and maintenance costs through the closed loop of resources, and enhances the system’s resilience through the complementary functions of multi-technology units, so as to provide universal solutions for high-density aquaculture in water-scarce areas, vertical production in urban agriculture, and a synergistic increase in the production of multiple species in developing countries, whose core value lies in the construction of “input-reducing” and “carbon source-reducing” systems. The core value lies in the construction of a production system of “input reduction, output diversification, and pollution minimization”, which is of key practical significance in solving the resource constraints and ecological crisis faced by global aquaculture.

4. Current Challenges and Further Research Dimensions

In recent years, growing attention has been gradually paid to the growth environment of aquaculture animals and safety concerns regarding whether the aquaculture water quality meets the standards. Some studies even focus on monitoring the residual viruses in the bodies of farmed animals [79]. Therefore, it is of vital importance to provide suitable growth environments for aquaculture animals. Although the combined use of BFT with an MBBR, IMTA, and other technologies has demonstrated potential to enhance water purification and nutrient cycling, substantial technical challenges persist at the integration level. For example, in combined systems, the synergistic regulation of the C/N ratio, dissolved oxygen, and microbial community structure is crucial yet inherently difficult to achieve with precision in hybrid systems. The combination of BFT and biofilm technology in aquaculture still faces challenges such as microbial community coordination, water quality stability, and operational costs. In the future, it is necessary to further optimize substrate design, microbial inoculation strategies, and system operation parameters to enhance the synergistic effect between the two, so as to achieve efficient and sustainable aquaculture. Additionally, in BFT-IMTA systems, selective feeding on microbial flocs by filter-feeding organisms such as oysters and tilapia may alter the community composition of microbial flocs, thereby influencing nitrogen and phosphorus cycling pathways. This highlights the complexity of coupled regulation between multispecies ecological interactions and water quality parameters, placing high demands on operators’ systemic understanding and real-time regulation capabilities.

Additionally, the initial investment and continuous operating costs of integrated technologies represent significant barriers to widespread adoption. The continuous addition of carbon sources such as sucrose and glucose, adoption of high-efficiency biocarriers like artificial substrates and probiotic preparations, and installation of monitoring equipment such as water quality sensors and microbial detection platforms substantially increase upfront investment, which is difficult for small-scale aquaculture farmers to afford. Take the BFT-MBBR system as an example. The cost of biocarriers and the amount of carbon source addition need to be dynamically adjusted according to aquaculture density and pollutant load, requiring economic feasibility assessments to incorporate material consumption and maintenance costs during long-term operation. Furthermore, while introducing filter-feeding organisms can reduce TSS, daily aquaculture management—including density optimization and disease control—undoubtedly increases additional human and technical inputs and further exacerbates cost pressures.

In terms of long-term stability, the dynamic succession of microbial communities and insufficient tolerance to environmental stress are core issues. In BFT, the dominance of heterotrophic and autotrophic bacteria shifts with fluctuations in carbon source supply and dissolved oxygen. For example, halting carbon source addition can cause the system to transition from heterotrophic-dominated to nitrification-driven, potentially leading to nitrate accumulation and alkalinity imbalance. When integrated with IMTA, the disturbance of floc structure by fish feeding behavior and the release of metabolic waste may reduce community functional redundancy and increase the risk of system collapse.

Future research needs to focus on deciphering the synergistic mechanisms of cross-technology coupling and developing smart regulation strategies based on microbiomics. For example, high-throughput sequencing can detect the bacterial composition of the water body [80], which indirectly reflects the C/N ratio and dissolved oxygen status: a high proportion of heterotrophic bacteria decompose carbon sources faster than they utilize nitrogen sources, which may correspond to a lower C/N ratio; an elevated proportion of actinomycetes may suggest carbon accumulation and a possible increase in the C/N ratio. While the dominance of aerobic bacteria suggests sufficient dissolved oxygen, an increase in the proportion of anaerobic bacteria suggests very low dissolved oxygen and possibly an anaerobic environment [81]. Consequently, integrating high-throughput sequencing to construct dynamic community prediction models can achieve adaptive regulation of the C/N ratio and dissolved oxygen levels. In addition, screening low-cost carbon sources such as agricultural byproducts [82] and industrial organic wastewater [83], it is also a hot research topic at present. However, it is important to note the differences in effectiveness due to compositional variability when using agricultural byproducts as a carbon source for microbial flocculating systems and the species-specific effects of different carbon sources on fish nutrient composition. The selection of efficient functional microbiota [84] can reduce operational costs. Exploring multi-level synergistic nutrient retention and conversion pathways involving “bioflocs + biofilms + filter-feeding organisms” can enhance the system’s disturbance resistance. Additionally, there is a need to strengthen economic feasibility analyses, develop modular and easy-to-operate combined technology kits, and promote the implementation of these technologies in small-to-medium-scale farms. Meanwhile, attention should be paid to environmental effects during long-term operation, or relevant life cycle assessment frameworks to quantify greenhouse gas emissions and the spread of antibiotic resistance over time should be refined [85], to provide theoretical and technical support for sustainable intensive aquaculture.

5. Conclusions

Stand-alone BFT face a number of limitations, including the accumulation of suspended matter, complex regulation of C/N ratios, acidification of bottom sludge, and high operating costs. This review systematically demonstrates that the combination of BFT with complementary technologies—aquaponics, biofilm technology, IMTA, and RAS—effectively addresses these bottlenecks through different mechanisms of action and synergistic effects. Specifically, the integration of BFT with aquaponics creates a closed-loop nutrient cycle by combining microbial floc-driven nitrogen transformation with plant uptake to improve water and nitrogen use efficiency while reducing solid waste discharge, and the coupling of BFT with biofilm technology builds a dual microbial system of suspended flocs + attached biofilm to improve nitrification and nitrification efficiency through synergistic nitrogen removal and natural feed supplementation. BFT coupled with biofilm technology creates a dual microbial system of suspended flocs + attached biofilm that improves nitrification efficiency and reduces feed inputs through synergistic nitrogen removal and natural feed supplementation. At the same time, the BFT-RAS hybrid system optimizes nutrient cycling and feed efficiency, reduces feed conversion, and achieves over 90% water savings. Ecologically, these hybrid models improved water quality, enhanced microbial diversity, and reduced nitrogen and phosphorus discharges. Economically, they reduced feed costs, increased productivity, and struck a balance between environmental sustainability and productivity, providing theoretical support for the environmental–economic balance of intensive aquaculture.

Despite these advancements, key challenges remain, including imprecise regulation of the C/N ratio, unpredictable changes in microbial communities, high initial infrastructure costs, and long-term stability issues for microbial communities. Future research should focus on the following three dimensions: (1) utilizing microbiomics and high-throughput sequencing to decipher synergistic mechanisms, thereby constructing dynamic models for C/N ratio and dissolved oxygen adaptive regulation; (2) developing intelligent management strategies through machine learning and screening for low-cost carbon sources and functional microbial strains to reduce operational costs; (3) strengthening economic feasibility analysis and modular system design to promote adoption by small and medium-sized farms, while assessing long-term environmental impacts to ensure sustainability. By addressing these issues, the BFT integrated system can be optimized to fully realize its potential as a globally sustainable and efficient solution for aquaculture.