Multifunctional Applications of Biofloc Technology (BFT) in Sustainable Aquaculture: A Review

Abstract

Biofloc technology (BFT), traditionally centered on feed supplementation and water purification in aquaculture, harbors untapped multifunctional potential as a sustainable resource management platform. This review systematically explores beyond conventional applications. BFT leverages microbial consortia to drive resource recovery, yielding bioactive compounds with antibacterial/antioxidant properties, microbial proteins for efficient feed production, and algae biomass for nutrient recycling and bioenergy. In environmental remediation, its porous microbial aggregates remove microplastics and heavy metals through integrated physical, chemical, and biological mechanisms, addressing critical aquatic pollution challenges. Agri-aquatic integration systems create symbiotic loops where nutrient-rich aquaculture effluents fertilize plant cultures, while plants act as natural filters to stabilize water quality, reducing freshwater dependence and enhancing resource efficiency. Emerging applications, including pigment extraction for ornamental fish and the anaerobic fermentation of biofloc waste into organic amendments, further demonstrate its alignment with circular economy principles. While technical advancements highlight its capacity to balance productivity and ecological stewardship, challenges in large-scale optimization, long-term system stability, and economic viability necessitate interdisciplinary research. By shifting focus to its underexplored functionalities, this review positions BFT as a transformative technology capable of addressing interconnected global challenges in food security, pollution mitigation, and sustainable resource use, offering a scalable framework for the future of aquaculture and beyond.

1. Introduction

Over the past three decades, global aquaculture has experienced exponential proliferation, evolving into an indispensable pillar of global food security that now accounts for over 50% of total fish consumption [1,2,3]. This sector’s rapid expansion—driven by escalating demand for high-quality protein, demographic growth, and technological advancements—has underscored its pivotal role in sustaining livelihoods and fostering economic development [4]. Concurrently, however, intensive production paradigms have precipitated a critical juncture, wherein the imperatives of maximizing output clash with the imperatives of ecological stewardship, economic viability, and biosecurity resilience [5,6,7].

Conventional flow-through aquaculture systems, characterized by unidirectional water exchange and reliance on exogenous feed inputs, exemplify the unsustainability of linear resource-consumption models [8]. These systems generate effluents rich in nitrogenous and phosphorous compounds, which induce eutrophication in receiving water bodies, disrupting trophic dynamics and ecosystem services [9]. Moreover, the dependency on fishmeal-based feeds has exacerbated the overexploitation of wild forage fish, with 30% of global fishmeal now allocated to aquaculture, straining marine food webs and threatening the sustainability of fisheries [10]. Such practices are increasingly incompatible with international mandates for sustainable resource use, necessitating a fundamental shift toward closed-loop systems that decouple production from environmental degradation.

Biofloc technology (BFT) has emerged as a transformative solution, harnessing self-organizing microbial consortia to establish nutrient-recycling ecosystems that enhance productivity while minimizing external inputs. Central to BFT are microbial aggregates (300–500 μm in diameter), comprising heterotrophic bacteria (Bacillus, Pseudomonas), autotrophic microalgae, and extracellular polymeric substances (EPS), which immobilize particulate organic matter and mediate nitrogen transformations through coupled biochemical pathways [11]. This technology operates via two interdependent processes: (1) heterotrophic assimilation, whereby ammonia (maintained below 0.5 mg/L) is converted into microbial biomass with high nutritional value (crude protein 18.4–58%, lipid 0.1–5.4%); and (2) chemolithotrophic nitrification, in which nitrite is oxidized to nitrate by autotrophic bacteria, mitigating toxic nitrogen species [12]. This microbial symbiosis yields multifold benefits: feed conversion ratios are reduced by 15–20%, water exchange requirements are minimized by 90% (to <10% daily turnover), and water quality parameters—including dissolved oxygen (≥5 mg/L) and pH (7.5–8.5)—are stabilized through buffering by microbial metabolites [13,14]. Mechanistically, these improvements are underpinned by enhanced nutrient retention, reduced reliance on freshwater resources, and improved biosecurity: BFT systems exhibit a 40% lower viral load compared to conventional ponds, attributed to the competitive exclusion of pathogens by dominant microbiota and the production of bioactive compounds (e.g., short-chain fatty acids) that modulate host immune responses [13]. Multiple merits of the BFT system are summarized in Figure 1.

Quantitative analyses demonstrate that BFT investments outperform traditional systems in key financial metrics, with internal rate of return (IRR) and SWOT analysis indices indicating significant superiority [15]. This system showed a positive net margin and profitability per production cycle in most scenarios, with 87.29% of simulations resulting in a positive profit [16]. Depending on the species, feed management, biofloc consumption, and carbon/water supplement costs, BFT might reduce production costs by 10% for tilapia and 33% for shrimp (Penaeus semisulcatus) [17,18]. When benchmarked against RAS, BFT exhibits comparable bioremediation efficacy but confers lower capital expenditure [19]. Additionally, BFT’s ability to cut the feed conversion ratio (FCR) leads to an over 40% reduction in feed costs for tilapia farming [20]. Yet, BFT still faces bottlenecks during operation, including high energy consumption, excessive sludge production, and an elevated risk of pathogen proliferation (e.g., cyanobacteria and Vibrio spp.) [21,22].

Importantly, existing research has extensively evaluated the BFT’s core functions in feed supplementation and water purification [23,24,25]. However, its potential as a multifunctional bioprocessing platform with applications spanning resource recovery, environmental remediation, and agri-aquatic integration, remains largely unexplored. In this regard, the current review synthesizes recent advancements in the multifaced role of BFT, excluding its established functions in feed supplementation and water purification. By integrating microbial ecology with resource management, BFT addresses interconnected challenges in food security, environmental remediation, and circular economy. As a nexus technology, it reconciles productive efficiency with ecological responsibility, offering a scalable paradigm for sustainable aquaculture and beyond.

2. Multifunctional Roles of Bioflocs

2.1. Resource Recovery and Value-Added Production

2.1.1. Extraction of Bioactive Substances and Microbial Protein

Bioflocs harbor a diverse array of bioactive substances—including vitamins, phytosterols, carotenes, polysaccharides, and polyphenols—that exhibit antioxidant properties. BFT enables the biosynthesis of polyhydroxyalkanoates (PHAs), natural polyesters categorized as biodegradable polymeric materials (BPMs) produced by microbial consortia [26]. Notably, PHAs synthesized by biofloc bacteria exert antibacterial effects in the gastrointestinal tracts of farmed animals, which partially elucidates the capacity of bioflocs to mitigate inflammatory responses and oxidative stress in aquatic species under diverse stressors, such as bacterial/viral infections, high stocking density, and heavy metal exposure [27].

While PHAs are traditionally integrated into BFT systems as supplementary nutrients for farmed animals, their utility extends beyond aquaculture to industrial and commercial applications. Given their intracellular synthesis and storage by biofloc microbes, harnessing PHAs for external use requires optimized separation protocols to isolate and purify these compounds at scale. This dual functionality positions PHAs as both a nutritional resource within BFT and a valuable bioproduct for downstream industrial processing [26].

Specially, poly-β-hydroxybutyrate (PHB) is one of the most prevalent forms of PHAs reported [28]. PHB is a short-chain fatty acid polymer, constituting 15–20% of the biofloc biomass [29]. Upon ingestion by aquatic organisms, PHB is enzymatically degraded in the intestinal tract into β-hydroxybutyric acid (β-HB), a metabolite that facilitates energy metabolism and signaling in both epithelial cells and intestinal microbiota. Functional studies have evidenced that supplementing diets with optimal levels of PHB significantly enhances immune competence, growth performance, gut microbial homeostasis, and antioxidant capacity, while simultaneously augmenting disease resistance. For instance, an 8-week feeding trial demonstrated that dietary supplementation with 4% PHB significantly mitigated lipopolysaccharide (LPS)-induced oxidative stress, inflammation, and cell apoptosis in common carp (Cyprinus carpio) [30]. The mechanism involved regulation of genes associated with the antioxidant pathway and inhibition of NLRP3 inflammasome activation, thereby enhancing immune competence.

Importantly, a study [31] first confirmed that PHB constituted 7.2% of the suspended solids (SS) from a traditional BFT system, and they introduced an ecological approach to convert aquatic SS waste into PHB by optimizing fermentation conditions (C/N = 12) using wheat bran and microbial formulations, doubling PHB production. Their findings showed that PHB-enriched SS improved growth performance and immunity in tilapia (Oreochromis niloticus). In a comprehensive review, PHB co-production strategies based on biofloc technology (BFT) were systematically explored, highlighting commercial potential for reducing aquaculture waste pollution [26]. However, the review noted a critical limitation of the lack of empirical data to support its practical applications.

In addition to PHA, polyphenol can also be extracted from biofloc waste. Recent studies have focused on the valorization of aquacultural biofloc waste, optimizing the green synthesis process of silver nanoparticles (AgNPs) via polyphenol extraction and verifying their antibacterial properties. Specifically, one study [32] used Response Surface Methodology (RSM) to optimize polyphenol extraction conditions (temperature, time, ethanol concentration, solvent–solute ratio), synthesizing AgNPs with an average particle size of 25.3 nm. These AgNPs exhibited significant minimum inhibitory concentrations (MIC: 19.4–38.8 μg/mL) against Gram-negative bacteria and biofilm-destructive capabilities. However, limitations included the absence of Gram-positive bacteria testing and the lack of an exploration of practical application feasibility. Subsequently, another study [33] further introduced alkaline hydrolysis (2 M KOH combined with ultrasonication) for polyphenol extraction, synthesizing smaller AgNPs (22.4 nm) after optimization. Antibacterial testing was expanded to cover both Gram-positive and negative bacteria, demonstrating broad-spectrum bactericidal ability. Notably, neither study systematically evaluated the long-term stability of synthesized nanoparticles or costs associated with large-scale production, representing potential directions for future research to address.

Moreover, microbial protein recovery has emerged as a critical frontier for sustainable BFT production. A pioneering study [34] first integrated a biofloc–worm reactor with a recirculating aquaculture system (BW_RAS) to convert microbial protein into Tubificidae (Oligochaeta) biomass, serving as direct feed for fish culture. The results demonstrated that BW_RAS improved water quality, nitrogen use efficiency (NUE), and fish production by 17.1%, elevating output to a commercially viable level. Another study [35] compared the in situ biofloc-based aquaculture system (IBAS) with a separating assimilation reactor-based recirculating aquaculture system (SRAS). The results revealed that periodic microbial protein recovery can enhance nitrogen recovery efficiency to 44–57% by promoting the abundance of bacterium Herpetosiphon and suppressing anaerobic denitrifiers. Additionally, microbial co-occurrence network analysis unveiled that the synergistic and competitive interactions among organic matter-degrading bacteria, filamentous bacteria, nitrifiers, and denitrifiers governed microbial protein yield dynamics. These studies underscore the dual potential of microbial protein recovery to enhance resource efficiency in aquaculture while providing mechanistic insights into microbial community regulation in BFT systems.

2.1.2. Algae Cultivation and Nutrient Remediation

Algae play a multifaced role in BFT by assimilating nitrogenous compounds to synthesize proteins and carbohydrates while generating oxygen under light conditions [36]. These organisms serve as a food source for zooplankton, facilitating nutrient transfer to higher trophic levels, and provide high-quality nutrients for aquatic organisms [37]. Moreover, diatoms have been shown to improve growth performance, feed conversion ratio (FCR), and fatty acid content in Litopenaeus vannamei postlarvae [38]. Another study revealed that diatom species can inhibit pathogens (e.g., Vibrio) through the production of antibacterial metabolites [39].

BFT can be applied to algae cultivation and harvest, mainly including two categories: microalgae and macroalgae. Some researchers [40] studied the feasibility of using biofloc wastewater (BWW) to replace Bold Basal Medium (BBM) for cultivating Chlorella ellipsoidea. The results showed that BWW could significantly reduce cultivation costs and achieve water nutrient remediation, but the study did not explore the economic conversion pathways of subsequent algal products. Similarly, a microalgae–bacteria composite flocculation system was constructed in a previous study [41], which found that untreated seafood wastewater could promote the cultivation and bioflocculation of Chlorella vulgaris, with the flocculating activity of 92.0 ± 6.0%, nutrient removal of 88.0 ± 2.2%, and total suspended solids removal of 93.0 ± 5.5%, which was more economical and environmentally friendly than chemical flocculation. Another review [42] explored the potential of biocoagulants/bioflocculants in microalgae cultivating and harvesting, emphasizing their advantage of producing non-toxic by-products. The study systematically compared the differences in degradability, efficiency, and medium reuse potential between chemical and biocoagulants/bioflocculants, but pointed out that the problem of microbial stability in large-scale production still needs to be solved.

In addition, research on integrated systems of algae and BFT has gradually emerged. Taking the symbiosis of Ulva lactuca and Litopenaeus vannamei as a model, one study [43] revealed that a 75% biofloc inoculation percentage could balance nutrient removal (55% nitrate, 31% phosphate) and algal quality (high protein, chlorophyll-a, and low ash content). Yet, this study did not deeply analyze the ecological risks of long-term system operation. Some researchers [44] attempted to cultivate Arthrospira platensis with marine shrimp effluents treated by BFT. They confirmed the growth feasibility, but failed to quantify the specific impact of wastewater pretreatment on the yield of A. platensis. These studies collectively indicate the resource utilization potential of BFT aquaculture waste, but further optimization of technical economy and ecological safety is still required for large-scale application.

While algae offer nutritional and bioremediation benefits, their integration introduces trade-offs. Microalgae populations are highly sensitive to light, temperature, and pH fluctuations, which can disrupt microbial community balance. For example, excessive algal blooms in BFT systems have been shown to cause diurnal pH swings, temperature fluctuation, and oxygen supersaturation, inhibiting bacterial nitrification [36]. Inadequate shading management exacerbates this issue by promoting algal overgrowth, while certain algal species may produce toxins during blooms, posing risks to aquatic organisms [45]. Strategies such as light intensity control and periodic floc harvesting have shown promise in mitigating these issues [42], but long-term economic viability remains unproven in large-scale applications, highlighting a critical research gap in balancing productivity and system resilience.

2.2. Environmental Remediation and Pollutant Mitigation

2.2.1. Microplastic Removal

Microplastics (MPs), defined as microscopic plastic particles typically ≤5 mm in size, are ubiquitously distributed across global environments owing to their resistance to photodegradation and fine particle dimensions. Notably, elevated MP concentrations have been detected in aquaculture waters, including BFT systems [46]. The predominant MP types of concern in BFT include polyethylene (PE), polystyrene (PS), and polypropylene (PP), which persist due to their chemical stability and widespread industrial use.

MPs exert profound and multifaced effects on farmed animals, microbial communities, and floc structure (Figure 2). Upon MPs ingestion, farmed aquaculture animals exhibit behavioral, morphological, and physiological responses. A previous study [47] investigated the MP bioaccumulation in Litopenaeus vannamei within indoor super-intensive culture (ISCO) systems, revealing an alarming high MP intake rate of 647 MPs individual⁻¹ year⁻¹—markedly surpassing levels documented in wild shrimp populations. The primary driver was identified as the degradation of plastic infrastructure (e.g., pipelines, nets) in closed-loop systems, which releases MPs into water column and feed matrices. In another study, crabs Carcinus maenas that ingested food containing microfibers (0.3–1.0% plastic by weight) showed reduced daily food consumption from 0.33 to 0.03 g d⁻¹ and a critical decline in energy available for growth, plummeting from 0.59 to −0.31 kJ crab d⁻¹ in crabs fed with 1% plastic [48]. In contrast, some scholars [49] observed that MPs had no significant effect on the growth of tilapia farmed in the BFT system, but reduced the crude protein and lipid content of tilapia.

Regarding the effects on microbial community, a series of studies [50,51] showed that while nanoplastics (NPs, 80 nm) and MPs (8 μm) did not alter microbial diversity, they disrupted nitrogen cycling. In particular, NPs caused stronger toxicity, evident in elevated ammonia and nitrite levels, likely due to their higher surface-area-to-volume ratio enhancing microbial adsorption. Similarly, another study [52] also reported that MPs inhibited biofloc formation and altered microbial community composition and nitrogen transformation function.

As for the MPs removal, bioflocs, with their porous structure and charged surfaces, efficiently adsorb MPs through multiple mechanisms (Figure 2). First, physical entrapment occurs as MPs are captured within the sticky, porous matrix of extracellular polymeric substances (EPSs) secreted by microorganisms. This EPS matrix acts as a three-dimensional filter, leveraging its sticky consistency and structural porosity to physically retain particles. Second, chemical bonding occurs when EPS functional groups (e.g., carboxyl, amino) form hydrogen bonds or electrostatic links with MP surfaces [53], especially for charged MPs. Third, biodegradation by microbes—such as Bacillus spp.—facilitate the breakdown of plastics through the secretion of extracellular polymeric enzymes. Together, these integrated pathways establish bioflocs as natural filters for MP removal, impacting both aquatic ecosystems and potential water purification applications.

A growing body of research highlights bacterial taxa with dual functionalities in biofloc formation and MP degradation. Such characterized genera include Bacillus, Enterobacter, Staphylococcus, Pseudomonas, Klebsiella, Rhodococcus, Falvobacterium, and Nocardia [46], underscoring the ecological versatility of these microorganisms in mediating both flocculation and plastic polymer breakdown. For instance, one study [54] isolated the bioflocculant-producing bacteria Bacillus enclensis from a BFT system, demonstrating its capacity to degrade PE and PS while achieving a biofloc adsorption efficiency exceeding 70%. Similarly, another study [55] validated the efficacy of floc-forming bacteria Bacillus cereus SHBF2—isolated from a commercial mud crab BFT farm—in reducing the PE, PP, and PS particles. Interestingly, Flavobacterium lacus and Flavobacterium chungnamens were observed to form biofilm on PP surfaces, indicating the potential for PP biodegradation [56]. Collectively, these findings underscore the potential of biofloc technology as a dual-purpose strategy in aquaculture: not only sustaining productive microbial ecosystems but also mitigating MP contamination to safeguard aquatic and human health.

Notably, bioflocs can augment their microplastic removal capabilities through the inherent surface characteristics of microbial communities or engineered structural modifications. For instance, surface-functionalized fungi via targeted structural optimization exhibit markedly enhanced capture efficiency toward aqueous MPs, achieving a removal capacity 1.5- to 12.5-fold greater than previously reported MP adsorbents [53]. Concurrently, a recent study [57] employed synthetic biology and gene-editing techniques to integrate microorganisms into plastic matrixes, enabling these embedded microbial systems to activate self-degradation pathways under predefined environmental conditions.

2.2.2. Heavy Metal Removal

Interestingly, as a bioremediation strategy relying on self-assembled microbial communities, BFT exhibits unique potential for application in heavy metal removal. Microorganisms (e.g., heterotrophic bacteria, nitrifying bacteria) and algae within biofloc undergo coordination reactions with heavy metal ions through functional groups (e.g., carboxyl, amino, and phosphate) on biological macromolecules such as cell-wall polysaccharides and proteins [58].

Empirical studies demonstrate its multifaceted applicability. One study [59] investigated the detoxification effect of a flood and drain aquaponic system based on BFT on heavy metals. The researchers confirmed that among Cu, Fe, and Zn, only the Cu level did not exceed the quality standard, while tilapia and Samhong mustard exhibited robust growth with high survival rate (>95%). The abundance of Fe and Zn was hypothesized to have originated from fishmeal constituents. However, the study lacks an assessment of biofloc stability and economic feasibility during prolonged operation. Another study [60] compared the impacts of heavy metals (Cd, Cr, Pb, and Cu) on tilapia reared in BFT versus traditional earthen ponds. The results showed higher heavy metal accumulation in the muscles, gills, and liver of pond-reared tilapia compared to BFT, directly confirming that BFT effectively restricts the transfer of heavy metals along the food chain and enhances the safety of aquaculture products for human consumption. Another researcher [61] evaluated sugarcane bagasse and rice-bran as low-cost carbon sources in BFT for removing heavy metals (Pb, Cu, Ni, etc.) from marine aquaculture wastewater. This study found that bacterial growth boosted carbon breakdown and metal adsorption, with removal orders differing by carbon source (e.g., Pb > Cu > Ni for bagasse; Pb > Ni > Cu for rice-bran). PCA revealed 97.2% variability in microbial and metal profiles, indicating strong interactions. These results highlight the critical role of carbon-source and bacterial communities in regulating heavy metal levels, offering a sustainable paradigm for recirculating polluted aquaculture water.

Despite its notable advantages of low cost and ecological sustainability for heavy metal remediation [62], BFT faces critical challenges primarily related to environmental sensitivity, heavy metal toxicity thresholds, and resource recovery bottlenecks. For instance, the post-treatment disposal of heavy metal-laden bioflocs might require advanced strategies like functional mesoporous material adsorption [63] or magnetic separation to achieve metal recovery [64].

Nevertheless, emerging strategies are driving technological advancements of metal removal by bioflocs towards industrial scalability. For instance, the development of transgenic lines and genetically modified organisms are effective tools in reducing heavy metal burden [65]. AI-optimized machine learning models further predict dynamic carbon source–microbe–heavy metal interactions for real-time process optimization [66].

Notably, current research is constrained by limited data on long-term system stability, full-scale economic viability, and ecological risks. Future breakthroughs in stress-resistant strain domestication, intelligent process automation, and closed-loop metal recycling will be indispensable for transitioning BFT from lab-scale proof-of-concept to industrially scalable solutions, positioning it as a cornerstone technology for sustainable heavy metal pollution remediation.

2.3. Agri-Aquatic Integration

The integration of BFT with plant production systems (e.g., hydroponics, aeroponics) has recently emerged as a pivotal frontier for sustainable aquaculture. In such an aquaculture–agriculture integrated system, bioflocs serve as fertigation-fertilizing plants, and plants act as biological filters, efficiently scavenging excess nitrogen (NO₃⁻-N, TN) and phosphorus (PO₄³⁻-P) from aquaculture water, thereby stabilizing water quality parameters and mitigating eutrophication risks [67]. This closed-loop nutrient recycling framework can be further optimized by introducing fish-edible plant species, enabling the direct assimilation of plant biomass by farmed fish and enhancing trophic energy transfer efficiency. Comprehensive investigations have indicated that such an integrated system significantly improves water quality regulation, resource recycling efficiency, and system productivity [68,69].

Regarding the integration system design, Pinho et al. [70] first named it FLOCponics (biofloc + hydroponic), and they observed that FLOCponics offered satisfactory results for fish growth. Unfortunately, it provided worse visual and growth results of butter lettuce than traditional aquaponics. Moreover, they also developed the FLOCponics mathematical model, simulating a 10% improvement in water use efficiency, 27% nitrogen use efficiency, and 10% reduction in suspended solid discharge, providing theoretical validation for resource-efficient coupling. One study [69] investigated the integration of duckweed into a BFT system for Megalobrama amblycephala culture. The results showed that duckweed filtration reduced water nitrate (16.19 mg/L), total nitrogen (26.90 mg/L), and total phosphorus (1.45 mg/L) to near-optimum levels for fish growth. Mechanistic analyses revealed that duckweed-mediated microbiota modulation increased intestinal Cetobacterium abundance by 23.83%, upregulating digestive enzyme genes (e.g., trypsin, lipase) and antioxidant enzymes (SOD, CAT). Some scholars [71] integrated sea lettuce with Pacific white shrimp and mullet cultivated in biofloc, and found that sea lettuce can enhance the total yield, as well as the nitrogen and phosphorus recovery in the system. Another study [72] investigated the potential of adopting biofloc sludge as organic fertilization alternatives to chemical fertilization of Terminalia arjuna. The authors confirmed that biofloc sludge was an effective organic fertilizer for ornamental medicinal tree production and is comparable to or superior to commonly used synthetic fertilizers, indicating an environmentally friendly method of organic waste management through nutrient recycling.

Some researchers further focused on optimizing plant functional traits and spatial configurations within the integration system. A previous study [68] established an integrated multitrophic aquaculture (IMTA) system (shrimp, tilapia, and seaweed), and demonstrated that 2 g/L seaweed density enhanced nitrogen and phosphorus recycling efficiencies by 13.1% and 34%, respectively, through synergistic biofloc–plant uptake. One study [73] compared pine bark and perlite in cucumber aeroponics fertigated with biofloc aquaculture effluent, finding that pine bark increased single-plant yield by 11% under monoculture but induced micronutrient disorders (manganese toxicity: 120 mg/kg; boron deficiency: 15 mg/kg) due to low substrate pH (4.2 ± 0.1). Another study [74] established an optimal BFT–nutrient film technique (NFT) configuration, i.e., 150 tilapia/m³ stocked with 12 bell pepper no./m², achieving a significantly higher plant–fish revenue ratio (PFRR) than traditional NFT systems. Notably, Rodrigues et al. [75] pioneered the use of reverse osmosis concentrate for co-culturing Litopenaeus vannamei and New Zealand spinach in an aquaponic system with biofloc, implying possibilities of valorization of desalination concentrate and reducing impacts on the deposition of concentrate in natural environments.

Overall, analysis of biofloc-based fertigation studies reveals that farmed animal species in BFT are predominantly shrimp (Penaeus vannamei) and tilapia (Oreochromis niloticus). In contrast, plant species exhibit significant diversity, including but not limited to duckweed, seaweed, and lettuce (

Table 1. Performance of bioflocs serving as fertigation for plants.

Plant Species	Farmed Species	Key Results	Reference
Duckweed (Lemna minor)	Megalobrama amblycephala	Nutrient utilization (N, P, C) and animal welfare were improved	[69]
Seaweed (Ulva ohnoi)	Shrimp (Penaeus vannamei) and tilapia (Oreochromis niloticus)	Seaweed benefited the performance of all species by recycling N, P and increasing overall productivity	[68]
Bell pepper (Capsicum annum)	Oreochromis niloticus	Fish stocking density of 150/m3 and plant density of 12 no./m2 is optimum	[74]
New Zealand spinach	Litopenaeus vannamei	Shrimp survival was 18% due to high nitrite level using reverse osmosis concentrate	[75]
Sea lettuce (Ulva fasciata)	Shrimp (Litopenaeus vannamei) and mullet (Mugil liza)	Enhanced total yield and N, P recovery	[71]
Terminalia arjuna	Nile tilapia (Oreochromis niloticus)	Biofloc sludge served as an effective organic fertilizer for ornamental medicinal tree production	[72]
Lettuce (Lactuca sativa)	Nile tilapia (Oreochromis niloticus) juvenile	Integration did not improve the plants’ growth and nutrient uptake	[76]
Lettuce (Lactuca sativa)	Nile tilapia (Oreochromis niloticus) juvenile	Integration improved water and nutrient use efficiencies, and reduced solids disposal	[70]
Beit Alpha cucumber (Cucumis sativus)	Nile tilapia (Oreochromis niloticus)	Substrate evaluation of pine bark and perlite in cucumber aeroponics fertigated with biofloc aquaculture effluent	[73]

). Notably, a common limitation across studies is the scarcity of long-term operational data; only one study by Pinho et al. [70] has demonstrated the sustainability of FLOCponics through a five-year simulation. Also, they propose that expanding the planting area represents a potential strategy to enhance FLOCponics efficiency. Additionally, the operational synergy of such an integrated system remains uncertain in some contexts, particularly with regard to plant growth profiles [76]. Thus, FLOCponics may be technically viable if targeted fertilization management protocols or mechanistic interventions are developed to address critical system challenges—such as nutrient imbalances and root-zone solid accumulation—thereby optimizing plant productivity.

2.4. Emerging Applications and Byproduct Utilization

Beyond the studies discussed, few reports detail other alternative functions of bioflocs. One study isolated pigment-producing bacteria from biofloc systems, ranking their carotenoid biosynthesis capacity as Staphylococcus pasteuri > Staphylococcus arlettae > Exiguobacterium profundum > Chryseobacterium joostei [77]. Extracts from S. pasteuri boosted carotenoid accumulation, growth, and survival in swordtail fish (Xiphophorus helleri). This application of biofloc-derived pigments for ornamental fish color enhancement highlights their potential as sustainable plant-pigment substitutes in aquaculture. These bacterial pigments offer an ideal, natural solution for improving fish aesthetics, reducing reliance on traditional plant-based colorants.

One previous study [78] evaluated short-term anaerobic fermentation as a potential technology for biofloc waste valorization. The process modified raw bioflocs’ physicochemical properties and enabled waste to meet maturity criteria, establishing it as a viable agricultural resource. Notably, sole use of these fermented products significantly boosted Chinese cabbage (Brassica rapa L. chinensis) yield, highlighting their potential as sustainable organic amendments in horticulture. This approach tackles waste management while converting byproducts into value-added agricultural inputs, aligning with circular economy principles.

Another study [79] characterized the sludge generated by treating biofloc water with a plant tannin-based coagulant, revealing its suitable bromatological properties for inclusion in aquatic animal diets. However, this sludge exhibited inhibitory effects on plant growth. From environmental and economic perspectives, utilizing aquaculture byproducts—such as this coagulant-treated sludge—as supplementary feed for farmed animals presents a promising strategy.

3. Current Challenges and Future Direction

Despite its multifunctional promise, BFT faces critical bottlenecks requiring targeted solutions to unlock its industrial potential. Technically, resource recovery struggles with low-yield biosynthesis and energy-intensive separation of high-value compounds (e.g., PHAs), while microbial community instability under fluctuating conditions (e.g., pH shifts, pathogen pressure) undermines consistent nutrient recycling and pollution control. Ecologically, the environmental impact of engineered microbes (e.g., plastic-degrading strains, transgenics) and heavy metal accumulation in biofloc residues remains unaddressed, posing risks to open-system ecosystems. Economically, expensive infrastructure for large-scale processing (e.g., algae harvesting, sludge treatment) and the lack of standardized byproduct use (e.g., fermented waste as fertilizer) hinder adoption, especially in resource-constrained settings. Mechanistically, poorly understood microbe–plant–animal interactions in agri-aquatic systems (e.g., FLOCponics) lead to suboptimal nutrient management and operational inefficiencies.

Future progress demands integrated technological and policy solutions. For technical challenges, metabolic engineering and bioinformatics can boost microbial production reliability and predict community dynamics. Ecological safety requires risk-assessment frameworks for engineered strains and self-sustaining microbial consortia to reduce external inputs. Economically, circular bioeconomy models—co-producing feed, biofertilizers, and bioplastics from byproducts—can offset costs, while machine learning optimizes energy use in algae and water systems. Agri-aquatic integration needs omics-driven insights and precision tools (e.g., sensor-based nutrient delivery) to enhance symbiotic efficiency. Policy initiatives, such as international sustainability standards and public–private partnerships for pilot projects, will accelerate technology scaling. By addressing these through a multidisciplinary approach, BFT can transition from a niche technology to a scalable solution for global sustainable food and environmental systems.

4. Conclusions

BFT transcends conventional feed and water management roles in aquaculture, emerging as a transformative platform for sustainable resource management by integrating microbial consortia to enable resource recovery, environmental remediation, and agri-aquatic integration. While demonstrating dual capacity to enhance productivity and mitigate pollution, BFT faces challenges in large-scale optimization, long-term stability, and economic viability, necessitating interdisciplinary research on stress-resistant strains, intelligent controls, and life-cycle assessments. By addressing interconnected challenges in food security, pollution, and circular economy, BFT positions itself as a foundational technology for sustainable aquaculture, advocating its integration into broader strategies to achieve global resource and environmental goals through its multifunctional, closed-loop framework.