Microalgae as a Synergistic Enhancer for In Situ and Ex Situ Treatment Technologies in Sustainable Shrimp Aquaculture: A Critical Review

Abstract

The intensification of shrimp aquaculture is crucial for global food security, but poses significant environmental challenges. This review critically assesses the strengths and bottlenecks of two main treatment paradigms: in situ systems, chiefly biofloc technology (BFT), and advanced ex situ systems, such as recirculating aquaculture systems (RASs), constructed wetlands (CWs), and membrane bioreactors (MBRs). Although BFT enables nutrient recycling, it suffers from nitrate accumulation and a high energy demand. Likewise, ex situ technologies can achieve a high treatment efficiency, but contend with high costs, large footprints, or membrane fouling. In this review, we propose the strategic integration of microalgae, representing a universal and synergistic solution for overcoming these disparate bottlenecks. We dissect how a microalgal co-culture can simultaneously remove nitrate and reduce the aeration costs in BFT systems. Furthermore, we explore how microalgae-based units can serve as efficient polishing steps for RASs, enhance the performance of CWs, and mitigate fouling in MBRs. This review delves into the fundamental mechanisms of the microalgal–bacterial symbiosis that underpins these enhancements. Finally, we highlight the valorization of the resulting algal biomass as a high-value aquafeed ingredient, which can transform waste management into a value-creation opportunity. This review aims to provide a comprehensive roadmap for developing next-generation, microalgae-enhanced aquaculture systems.

1. Introduction

The escalating global demand for aquatic protein has propelled the shrimp aquaculture industry into an era of unprecedented intensification, solidifying its role as a cornerstone of global food security [1,2]. These paradigm shifts towards high-density production, however, have created a profound environmental conundrum [3,4]. Intensive and super-intensive farming practices, designed to maximize the yield per unit area, have inherently led to a substantial increase in waste generation [5]. The primary sources of this waste are uneaten feed and the metabolic byproducts of the cultured organisms. For instance, it is estimated that only 20–25% of the nitrogen and phosphorus from commercial shrimp feed is assimilated by the target species, with the vast majority being released into the culture environment [5,6]. Consequently, aquaculture effluents are heavily laden with high concentrations of organic matter, suspended solids, and—most critically—dissolved inorganic nutrients, such as total ammonia nitrogen (TAN), nitrite (NO₂⁻-N), and nitrate (NO₃⁻-N). This leads to severe water quality degradation within the culture system and the significant pollution of the receiving water bodies upon discharge [1,7]. The research by Ahmad et al. highlighted that the TAN concentrations in effluent can range from 0.5 to 2.0 mg/L; such levels are known to exert sub-lethal stress on most aquatic species. Additionally, the nitrate concentrations can exceed 40 mg/L [1]. Beyond nutrient loading, the industry’s reliance on a battery of chemicals, including antibiotics, hormones, and pesticides, has given rise to the proliferation of contaminants of emerging concern (CECs) in aquatic ecosystems, posing long-term risks to biodiversity and human health through food chain bioaccumulation [8]. The immense pressure to reconcile burgeoning production demands with environmental stewardship has therefore catalyzed an urgent search for technologically advanced, economically viable, and sustainable water management strategies [9,10].

In response to the environmental challenges posed by intensive aquaculture, water treatment technologies have largely evolved along two distinct strategic pathways: in situ treatments and ex situ treatments [7,11]. The in situ, or “within-system”, approach is best exemplified by biofloc technology (BFT), an innovative method that seeks to transform the culture vessel itself into a bioreactor [12,13]. The fundamental principle of BFT involves manipulating the carbon-to-nitrogen (C/N) ratio of the water to stimulate the proliferation of a heterotrophic microbial community. This community assimilates toxic nitrogenous wastes directly, converting them into a protein-rich microbial biomass—the biofloc—which simultaneously purifies the water and serves as a supplemental nutritional source for the cultured shrimp, thereby creating an internal loop of nutrient recycling [14,15]. In stark contrast, the ex situ, or “end-of-pipe”, paradigm involves extracting water from the culture tank and treating it in dedicated, external engineering units before it is either discharged or returned. This category encompasses a diverse array of advanced technologies, including highly engineered recirculating aquaculture systems (RASs), which employ sophisticated mechanical and biological filters to achieve water reuse rates of over 99% [4,10]; nature-based solutions such as constructed wetlands (CWs), which utilize the substrate, plants, and their associated microbiota to purify water through complex biogeochemical processes [16,17]; and barrier-driven technologies such as membrane bioreactors (MBRs), which combine biological treatment with membrane filtration to produce an exceptionally high-quality effluent [18]. Each of these paradigms offers a unique set of advantages and is tailored to different operational scales and sustainability objectives.

Despite their sophistication, both the in situ and ex situ treatment paradigms are beset by inherent, system-specific bottlenecks that curtail their widespread adoption and long-term sustainability. BFT, lauded for its resource efficiency, faces two critical operational hurdles. The first is the inevitable accumulation of nitrate (NO₃⁻-N) in mature, low-exchange systems [19,20]. As the system evolves, nitrification processes often begin to dominate, but a corresponding denitrification pathway is absent in a well-aerated BFT environment, leading to nitrate buildup that can eventually become limiting or toxic [7,21]. The second major drawback is its prohibitively high energy consumption, driven by the continuous, vigorous aeration required to keep the bioflocs in suspension and meet the high respiratory demand of the dense microbial community [9,14]. On the other hand, advanced ex situ technologies, while powerful, come with their own set of significant limitations. RASs are notoriously complex and characterized by high capital expenditures (CAPEXs) and operational expenditures (OPEXs), making them economically challenging for many producers, and they too can suffer from nitrate accumulation if a dedicated denitrification unit is not included [10,18,22]. CWs, while ecologically sound and low-energy, demand a very large land footprint, rendering them unsuitable for land-scarce regions, and their treatment efficiency can be comparatively lower, especially for high-strength wastewater [16,23]. Finally, membrane-based systems such as MBRs, which provide the ultimate barrier against pollutants, are plagued by the persistent and costly problem of membrane fouling, which necessitates frequent chemical cleaning, increases energy costs, and shortens the membrane lifespan [18,24,25]. This landscape of trade-offs reveals that no single existing technology offers a perfect, universally applicable solution.

This review advances the central thesis that the strategic integration of microalgae represents a powerful, unifying, and synergistic solution capable of overcoming the disparate bottlenecks that hamstring both in situ and ex situ shrimp aquaculture water treatment technologies. Rather than being viewed as yet another standalone alternative, microalgae should be conceptualized as a versatile “enhancement module” that can be harmoniously coupled with existing systems. The foundation of this synergy lies in the intricate and mutually beneficial relationship within microalgal–bacterial consortia [26,27,28]. For BFT, the introduction of microalgae to form autotrophic or mixotrophic systems (A-BFT) directly addresses its core weaknesses: microalgae avidly assimilate nitrate as a primary nutrient, thus closing the nitrogen loop, while their photosynthetic activity generates oxygen, thereby offsetting a portion of the mechanical aeration demand [29,30]. For ex situ systems, microalgae offer tailored enhancements. They can serve as a highly effective and value-adding “polishing” unit for nitrate-rich RAS effluent, converting a waste product into valuable biomass [31]. When integrated with CWs, they can boost the overall nutrient removal rates and system productivity [32]. For MBRs, the development of algal MBRs (A-MBRs) shows promise in not only enhancing nutrient removal, but also potentially mitigating membrane fouling [33]. A crucial part of this paradigm shift is the concept of valorization: the cultivated algal biomass, which is rich in proteins, lipids, and bioactive compounds, is not a waste, but a high-value co-product that can be looped back into the production cycle as a superior aquafeed ingredient [34,35,36]. This transforms the linear “treat-and-discard” model into a circular bioeconomy [9,37]. Accordingly, this review critically dissects the weaknesses of the current mainstream technologies, mechanistically details how microalgae can address these specific failings, analyzes the underlying symbiotic interactions, and discusses the pathways for biomass valorization, ultimately providing a comprehensive framework for designing the next generation of sustainable, microalgae-enhanced shrimp aquaculture systems.

2. In Situ Treatment: The Promises and Pitfalls of Biofloc Technology

Biofloc technology (BFT) has emerged as a revolutionary in situ water treatment paradigm, fundamentally reshaping the landscape of intensive aquaculture by internalizing nutrient cycling processes within the culture unit itself [14]. This approach stands in direct opposition to conventional flow-through or high-exchange systems, aspiring instead to create a self-sustaining microbial ecosystem that obviates the need for external water treatment and extensive water exchange [9,13]. The technology’s efficacy and appeal stem from a triad of interdependent benefits: robust water quality maintenance, the provision of a continuous endogenous feed source, and enhanced system biosecurity [38,39].

2.1. Principles and Acclaimed Advantages of BFT

The operational cornerstone of BFT is the deliberate manipulation of the aquatic environment’s carbon-to-nitrogen (C/N) ratio. By introducing an external, inexpensive carbohydrate source (e.g., molasses, tapioca), the C/N ratio is elevated to a level (typically >15:1) that selectively favors the proliferation of heterotrophic bacteria over autotrophic nitrifying bacteria [15,19,40]. These heterotrophic bacteria rapidly assimilate dissolved inorganic nitrogen, particularly toxic ammonia, directly into microbial protein. This process is markedly more efficient than conventional nitrification, as heterotrophic bacterial growth rates can be an order of magnitude higher than those of autotrophic nitrifiers, allowing for a swifter response to nitrogen spikes [15]. The resulting aggregation of bacteria, microalgae, protozoans, and organic detritus forms the biofloc—a dynamic, biologically active matrix that perpetually scrubs the water column of nitrogenous wastes [41,42].

Beyond its primary function as a water purification engine, the biofloc itself represents a significant economic and nutritional asset. These microbial aggregates are rich in protein, lipids, vitamins, and minerals, constituting a high-quality supplemental feed that is continuously available to the cultured shrimp [39]. Research has consistently demonstrated that the ingestion of biofloc can significantly improve feed conversion ratios (FCRs), enhance growth rates, and reduce the dependency on expensive formulated feeds, with some studies suggesting that biofloc can satisfy up to 30% of the shrimp’s nutritional requirements [38,43]. The work of Panigrahi et al., for instance, showed a dramatic improvement in the FCR from 2.32 in the control to 0.81 in an optimized BFT system [40]. Furthermore, the microbial constituents of biofloc, particularly beneficial strains such as Bacillus spp., exert a probiotic effect, improving the host’s gut health and stimulating its innate immune system [44,45,46,47]. This dual role of waste assimilation and nutritional supplementation positions BFT as a prime example of circularity within aquaculture, transforming a metabolic liability into a productive asset [13,14].

2.2. Critical Bottleneck 1: The Nitrate (NO₃⁻-N) Dead End

Despite the elegant efficiency of heterotrophic nitrogen assimilation, a persistent and well-documented challenge in mature BFT systems is the progressive and often substantial accumulation of nitrate (NO₃⁻-N) [20]. While the initial system management aims to promote the heterotrophic pathway, the stable, substrate-rich surfaces of the biofloc aggregates and the long solids retention time inherent to minimal-exchange systems provide an ideal niche for the colonization and proliferation of slow-growing autotrophic nitrifying bacteria [15,20]. Consequently, over time, a robust nitrification process often establishes itself, converting ammonia first to nitrite and subsequently to nitrate. However, conventional denitrification, the process that converts nitrate to inert nitrogen gas, requires anoxic conditions that are fundamentally incompatible with the highly aerated environment necessary to maintain floc suspension and support the cultured shrimp [9].

This functional gap in the nitrogen cycle leads to nitrate becoming a terminal product within the system. Studies have reported nitrate concentrations reaching levels as high as 150–300 mg/L in shrimp BFT systems, even under high C/N ratios intended to suppress nitrification [20]. For example, Ferreira et al. observed the nitrate levels steadily climbing throughout their trial in both heterotrophic and chemoautotrophic BFT setups [21], and Pimentel et al. noted significant nitrate accumulation as a characteristic of their BFT and synbiotic systems [7]. While nitrate is considerably less toxic to shrimp than ammonia or nitrite, high concentrations can still induce physiological stress, negatively impact growth and survival, and ultimately necessitate periodic water exchange to prevent toxicity, thereby undermining the “zero-exchange” promise of the technology [19,48]. This “nitrate dead end” represents a fundamental biogeochemical limitation of the conventional BFT model.

2.3. Critical Bottleneck 2: Prohibitive Energy Consumption

A second, and arguably more economically prohibitive, bottleneck of BFT is its substantial energy demand. The technology’s success is contingent upon maintaining the microbial flocs in a constant state of suspension throughout the water column to maximize their contact with nutrients and prevent the formation of anaerobic zones and sludge buildup. This necessitates continuous, vigorous mechanical aeration and mixing [9,14]. The high density of both the cultured animals and the microbial biomass (with the total suspended solids reaching several hundred mg/L) creates an enormous collective respiratory demand for dissolved oxygen, which must be met entirely through artificial means [43,49].

The energy required for this intensive aeration represents a major component of the operational expenditure. As systematically reviewed by Lovejan et al., energy costs can account for 30–40% of the total operating costs of a BFT farm [9]. Ogello et al. similarly emphasized that the high energy requirement of aeration is a primary impediment to the adoption of technology, particularly in developing regions where the electricity supply may be unreliable or prohibitively expensive [13]. This high energy footprint not only challenges the economic feasibility of BFT, but also raises questions about its overall environmental sustainability, especially if the electricity is sourced from fossil fuels, thereby contributing to a significant carbon footprint [22]. This reliance on a continuous energy input represents a critical vulnerability and a major barrier to the widespread, cost-effective implementation of BFT.

2.4. Other Operational Challenges

Beyond the primary bottlenecks of nitrate accumulation and a high energy demand, the practical implementation of BFT is further complicated by a set of operational challenges that demand a high level of technical expertise from the farm manager. The management of the floc volume, measured as the total suspended solids (TSS), is a delicate balancing act; an insufficient floc concentration results in poor water quality control, whereas excessive levels can clog shrimp gills, reduce visibility for feeding, and contribute to the already high oxygen demand [41,43]. Maintaining system stability is another concern, as improper C/N ratio management or sudden environmental shifts can lead to microbial community crashes and rapid water quality deterioration [9]. Furthermore, the performance of BFT systems can be species-specific. While it is highly effective for detritivorous or omnivorous species such as shrimp and tilapia that can readily consume the flocs, its applicability to carnivorous species is less established and may be limited [41,43,49]. These factors collectively contribute to a steeper learning curve and a higher operational risk compared to more traditional aquaculture methods.

3. Ex Situ Advanced Treatment: High Efficiency at a High Cost

In parallel to the development of in situ treatment methods such as BFT, a suite of sophisticated ex situ technologies have been engineered, all predicated on the principle of removing water from the culture tank for external treatment. These systems represent a more conventional engineering approach, employing dedicated physical, chemical, and biological unit processes to purify the effluent. While they often achieve exceptional levels of pollutant removal and system control, this high performance is consistently counterbalanced by significant economic and operational burdens, creating a distinct set of bottlenecks that differ from, but are no less challenging than, those faced by BFT.

3.1. Recirculating Aquaculture Systems (RASs): The High-Tech Approach

Recirculating aquaculture systems (RASs), characterized by their capacity for near-total water reclamation, represent the pinnacle of intensive, controlled-environment aquaculture [1,10]. By continuously cycling water through a series of treatment units—typically including mechanical filtration for solids removal, a biological filter for nitrification, and disinfection stages (e.g., UV or ozonation)—RASs can achieve water reuse rates exceeding 99% [4,18]. This operational model yields profound advantages, most notably a drastic reduction in water consumption and effluent discharge, which insulates the farm from external environmental variability and minimizes its pollution footprint [10]. Furthermore, the enclosed nature of RASs provides an unparalleled level of biosecurity, effectively shielding the cultured stock from pathogens prevalent in natural water bodies, a benefit highlighted by Moss et al. as a crucial component of disease prevention [50]. The controlled conditions also allow for production in non-traditional locations, independent of the climate or proximity to large water sources.

However, the strengths of RASs are mirrored by considerable weaknesses, primarily revolving around economic and biogeochemical constraints. The complexity and sophistication of the required equipment translate into exceptionally high capital and operational expenditures (CAPEXs/OPEXs), which often render the technology economically nonviable for many producers, particularly in developing regions [9,10]. A significant portion of the operational cost is driven by the high energy consumption of pumping and life support systems [22]. Moreover, the biological heart of a typical RAS—the nitrification biofilter—shares a fundamental limitation with mature BFT systems: it effectively converts highly toxic ammonia into less toxic nitrate, but does not remove it from the system [51,52]. As a result, nitrate inexorably accumulates in the recycled water, eventually reaching concentrations that necessitate a partial water exchange or the integration of an additional, and often complex, denitrification unit to prevent adverse effects on the shrimp [4,7,52]. Thus, while RASs offer superior control and water conservation, their high cost and the persistent nitrate issue remain significant barriers to their broader application.

3.2. Constructed Wetlands (CWs): The Ecological Engineering Approach

Representing a starkly different philosophy, constructed wetlands (CWs) are ex situ treatment systems that leverage natural ecological processes to purify water [23]. These engineered ecosystems, consisting of a substrate (e.g., gravel, sand), aquatic plants (macrophytes), and a diverse microbial community, remove pollutants through a combination of physical filtration, chemical precipitation and adsorption, and extensive biological transformations [16,23,53]. The primary allure of CWs lies in their low energy consumption, minimal operational complexity, and the potential to create valuable ecological habitats [16,54]. Studies have consistently demonstrated their effectiveness in treating aquaculture effluents, with vertical flow (VF) wetlands being particularly proficient at nitrification due to better oxygen transfer compared to horizontal flow (HF) systems, as shown by Konnerup et al. [16]. Wang et al. utilized a CW-RAS for a shrimp culture and confirmed the central role of the CW unit in removing the TAN, nitrite, and COD [53].

The ecological elegance of CWs, however, is offset by significant practical limitations. Their most prominent weakness is the substantial land area they require to achieve effective treatment, a constraint that makes them impractical for intensive farms in regions where land is scarce or expensive [11,23]. The treatment efficiency of CWs is also inherently lower and more variable than highly engineered systems such as RASs or MBRs. Their performance can be significantly influenced by climatic conditions such as temperature and rainfall, and they are less suited to treating the high-strength, concentrated wastewater generated by super-intensive culture operations [16,54]. Furthermore, Konnerup et al. observed that, while CWs can be effective at nitrogen and organic matter removal, their capacity for phosphorus removal is often limited, leading to the gradual accumulation of phosphate in the system over time [16]. These factors tend to relegate CWs to the role of a polishing step for lower-intensity systems or as a component of larger, hybrid treatment trains rather than as a standalone solution for intensive shrimp farming.

3.3. Membrane-Based Systems: The Absolute Barrier Approach

At the apex of physical–biological ex situ treatment are membrane-based systems, which integrate biological reactors with microfiltration or ultrafiltration membranes to achieve exceptional solid–liquid separation. Membrane bioreactors (MBRs), the most widely adopted configuration, produce a high-quality effluent largely free of suspended solids and pathogens, making them suitable for water reuse in intensive aquaculture [18,55,56,57]. This outstanding performance, however, comes at a very high price, centered on the universal and persistent problem of membrane fouling [24]. Fouling—the deposition and accumulation of materials such as microbial cells, extracellular polymeric substances (EPSs), and inorganic precipitates onto the membrane surface and within its pores—leads to a progressive decline in permeability [58,59,60]. This fouling escalates the operational costs through increased energy consumption, frequent chemical cleaning, and premature membrane replacement [61,62]. While MBRs offer an unparalleled effluent quality, the challenge of managing membrane fouling remains their defining operational and economic bottleneck.

Recent research has focused on advanced fouling mitigation technologies tailored to aquaculture wastewater. Membrane photobioreactors (MPBRs) leverage a microalgal–bacterial symbiosis to reduce fouling: microalgae supply photosynthetic oxygen, decreasing external aeration and limiting extracellular polymeric substance (EPS) secretion, while also acting as a bio-scouring agent that physically disrupts fouling layers. Quorum-quenching approaches further inhibit biofilm formation by disrupting bacterial communication [55]. Low-energy alternatives such as self-forming dynamic membranes (SFDMs) and gravity-driven membrane (GDM) filters utilize in situ-developed bioactive layers that function as integrated filtration and bioreaction zones, maintaining a stable flux with minimal energy input [56]. Mechanical strategies, including oscillatory and vibratory membrane systems, introduce shear forces to limit cake-layer formation without compromising biofilm activity. For saline aquaculture streams, membrane distillation and forward osmosis offer fouling-resistant routes towards near-zero liquid discharge [60]. These innovations highlight a shift from conventional fouling management towards integrated, process-inherent control strategies, enhancing the viability of membrane systems in sustainable aquaculture water treatment.

4. Microalgae Integration: A Unifying Strategy to Overcome System-Specific Bottlenecks

The distinct challenges inherent to both in situ and ex situ treatment paradigms necessitate a shift away from seeking a single “perfect” technology and towards developing synergistic, integrated solutions. Within this context, microalgae—the foundational primary producers of aquatic ecosystems—emerge not merely as another treatment option, but as a uniquely versatile and powerful enhancement agent capable of rectifying the core weaknesses of existing systems. Their fundamental photosynthetic metabolism allows them to simultaneously assimilate inorganic nutrients, capture carbon dioxide, and generate oxygen, making them natural biogeochemical engineers [63,64]. When purposefully integrated into aquaculture treatment schemes, this metabolic toolkit provides targeted solutions to the specific bottlenecks of BFT, RASs, CWs, and MBRs, creating systems that are more robust, efficient, and aligned with the principles of a circular bioeconomy (shown in Figure 1).

4.1. The Foundational Role of Microalgae in Bioremediation

Microalgae are exceptionally proficient at scavenging dissolved nutrients from water, a capability that has been extensively reviewed and validated for wastewater treatment (shown in

Table 1. Microalgae and their functions in both in situ and ex situ aquaculture treatments.

Technology Paradigm	Microalgae Phylum	Microalgae Species	Main Functions	References
In Situ	Chlorophyta	Chlorella vulgaris, Chlorella sp., Tetraselmis sp., Nannochloropsis sp., Dunaliella sp., Scenedesmus sp., Chlamydomonas sp.	Using microalgae to assimilate N/P, stabilize water quality, and provide live feed for larvae. Algal–bacterial consortia that convert ammonia into microbial protein for consumption by culture animals. Disease Control: Utilizing the antibacterial activity of microalgae to inhibit pathogens such as Vibrio.	[12,13,14,31,32,35,43]
	Bacillariophyta	Chaetoceros sp., Skeletonema sp., Thalassiosira sp., Phaeodactylum tricornutum, Nitzschia sp., Navicula sp., Amphora sp.
	Cyanobacteria	Spirulina/Arthrospira sp.
	Others	Isochrysis sp.
Ex Situ	Chlorophyta	Chlorella vulgaris, Chlorella sorokiniana, Chlorella pyrenoidosa, Chlorella minutissima, Scenedesmus obliquus, Scenedesmus quadricauda, Scenedesmus dimorphus, Tetraselmis suecica, Dunaliella salina, Dunaliella tertiolecta, Botryococcus braunii, Haematococcus pluvialis, Chlamydomonas reinhardtii, Platymonas subcordiformis, Selenastrum sp., Auxenochlorella protothecoides	Wastewater Remediation: Removal of ammonia, nitrate, phosphate, and COD. Effluent Treatment: Treating concentrated tail water from recirculating aquaculture systems. Resource Recovery: Producing biodiesel, bioplastics, feed proteins, and high-value compounds (e.g., astaxanthin, EPA, DHA). Carbon Mitigation: CO2 sequestration coupled with wastewater treatment.	[28,30,31,33,34,35,37,38]
	Cyanobacteria	Spirulina platensis, Oscillatoria sp., Phormidium sp. Leptolyngbya sp., Limnothrix sp. Plectonema terebrans, Trichocoleus desertorum, Synechocystis sp.
	Others	Nannochloropsis oculate, Nannochloropsis oceanica, Nannochloropsis gaditana, Euglena gracilis, Ochromonas sp., Porphyridium purpureum

) [12,65,66]. Their cellular machinery is primed to uptake inorganic nitrogen (in the forms of ammonium, nitrite, and nitrate) and phosphorus (as orthophosphate), incorporating these elements directly into their biomass as proteins, nucleic acids, and phospholipids [29,67]. The efficiency of this process can be remarkable; studies have consistently reported nutrient removal efficiencies exceeding 90% for both nitrogen and phosphorus under optimized conditions [26,64,65]. As phototrophs, microalgae utilize light energy to fix inorganic carbon, producing organic matter and, critically, releasing molecular oxygen as a byproduct. This photosynthetic activity creates a powerful symbiotic potential with the heterotrophic and chemoautotrophic bacteria that dominate many biological treatment systems, establishing a foundation for mutualistic enhancement [27,28,32]. It is this innate capacity for nutrient uptake and oxygen production that positions microalgae as a master key to unlock the latent potential of established aquaculture technologies.

4.2. Scenario 1: Enhancing BFT with Microalgae

The integration of microalgae into a conventional heterotrophic BFT system, thereby creating an autotrophic or mixotrophic biofloc environment (often termed A-BFT or green-water BFT), offers a direct and elegant solution to the technology’s two principal failings: nitrate accumulation and high energy costs.

First, the “nitrate dead end” is effectively resolved through direct algal assimilation. Unlike the bacteria in the system, which may require specific anoxic conditions for denitrification, microalgae readily consume nitrate as a primary nitrogen source, directly incorporating it into their cellular structure [29]. This introduces a vital nitrate sink that was previously absent, preventing nitrate accumulation and the associated risks of toxicity and the need for water exchange [30,49]. Second, the high aeration cost is mitigated by photosynthetic oxygenation. The photosynthetic oxygen produced by microalgae elevates the dissolved oxygen levels, supplementing mechanical aeration and supporting the respiratory demands of shrimp and microbiota [27,68]. This in situ oxygen generation reduces the operational load on mechanical aerators, leading to significant energy savings and a lower carbon footprint [69,70]. Beyond solving these core problems, the presence of microalgae enriches the nutritional profile of the biofloc, boosting its content of essential polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), pigments (e.g., chlorophylls, carotenoids), and vitamins. These nutrients are often limited in purely heterotrophic flocs; therefore, microalgae enhance the value of the biofloc as a supplemental feed [30,34].

4.3. Scenario 2: Enhancing RASs with Algal-Based Polishing Units

For recirculating aquaculture systems, whose primary weakness is the accumulation of nitrate in the final effluent, microalgae provide an ideal ex situ “polishing” or tertiary treatment solution. The nitrate-rich discharge from an RAS, which represents a disposal challenge and a loss of valuable nutrients, can be repurposed as a nutrient-dense feedstock for a dedicated algal cultivation unit [10,31]. Technologies such as high-rate algal ponds (HRAPs) and algal turf scrubbers (ATSs) are exceptionally well-suited for this purpose [69,71,72]. An HRAP is a shallow, raceway-style pond that optimizes light exposure for suspended microalgal growth, while an ATS cultivates a dense mat of attached filamentous algae on a screen over which the effluent flows. Both systems have been proven to efficiently strip the nitrate and residual phosphate from RAS effluent [31,72]. As demonstrated by Arbour et al., such integration can reduce the eutrophication potential of the entire system by over 15–44% [31]. This strategy accomplishes two critical goals: it brings the RAS closer to a true zero-discharge model by treating its final waste stream, and it enacts the principle of valorization by converting dissolved nitrogenous waste into a tangible, harvestable asset—algal biomass—which can then be processed into high-value aquafeed ingredients [34,73].

4.4. Scenario 3: Enhancing CWs by Fostering Algal–Bacterial Synergy

The primary limitations of constructed wetlands—their large land requirement and comparatively lower volumetric treatment efficiency—can be addressed by actively leveraging microalgal activity to intensify the treatment process. While algae are naturally present in CWs, their role is often passive. A strategy focused on enhancing the symbiotic relationship between algae and bacteria within the wetland’s biofilm matrix holds significant potential. The biofilms coating the substrate and plant roots in CWs provide an ideal habitat for a co-located community of algae and bacteria [16,23,53]. Promoting robust algal growth within this biofilm (e.g., through optimized light exposure or a hydraulic design) would lead to localized hyper-oxygenation, directly stimulating the aerobic bacterial degradation of organic matter and nitrification within the biofilm, thus boosting the overall pollutant removal rates per unit area [32]. This intensification could allow for the design of more compact, efficient wetlands capable of handling higher organic and nutrient loads, making them a more viable option for space-constrained aquaculture operations. The work by Gao et al., which physically separated but symbiotically linked, algal and bacterial compartments, demonstrates the power of such engineered consortia. This is a principle that could be applied to redesign CWs into more potent bioreactors [32].

4.5. Scenario 4: Enhancing Membrane Systems via Algal Membrane Bioreactors

Even for the most advanced MBR systems, microalgae offer a pathway for achieving enhanced performance and mitigating the key bottleneck of MBR systems: membrane fouling. The development of algal membrane bioreactors (A-MBRs), often in configurations such as a membrane-coupled high-rate algal pond (MHRAP), represents this innovative frontier [33]. The introduction of a healthy algal population into mixed liquor can fundamentally alter the physicochemical environment and the characteristics of the biomass, which in turn influences the fouling propensity. Photosynthetic oxygenation can reduce the energy required for diffused aeration, a major operational cost in conventional MBRs. More importantly, the extracellular polymeric substances (EPSs) produced by microalgae differ in composition from those produced by bacteria under the stressful, oxygen-limited conditions often found in a sludge layer [33,74]. Some research suggests that the nature of algal–bacterial bioflocculation can lead to larger, more porous, and less compressible flocs, which are less likely to cause severe pore blocking and cake layer compaction on the membrane surface [27,75]. For example, Tran et al. found that integrating an ATS module with an MHRAP significantly reduced fouling by lowering key foulant precursors, such as bound EPSs [72]. Although the mechanisms are complex and still under investigation, the potential for microalgae to co-exist with and favorably modify the fouling behavior of activated sludge in a membrane environment presents a compelling strategy for improving the sustainability and economic feasibility of MBRs in aquaculture. A summary of these integrated approaches is presented in

Table 2. Comparative analysis of conventional shrimp aquaculture water treatment technologies and their enhancement through microalgal integration.

Technology Paradigm	Treatment Technology	Critical Bottlenecks	Microalgal Enhancement Strategy	Underlying Mechanisms	References
In Situ	Biofloc Technology	Nitrate accumulation High energy demand	Integration of microalgae to create an autotrophic/ mixotrophic BFT	Direct assimilation of nitrate by microalgae Photosynthetic oxygenation reduces mechanical aeration	[7,9,20,27,29,30]
Ex Situ	Recirculating Aquaculture System	High CAPEX/OPEX Nitrate accumulation in effluent	Use of an external algal unit (e.g., HRAP, ATS)	Removal of nitrate in effluent Valorization of waste stream into valuable microalgal biomass	[10,18,22,31,69,72]
Ex Situ	Constructed Wetland	Large land footprint Lower volumetric treatment efficiency	Actively fostering algal–bacterial synergy within the wetland’s biofilm matrix	Intensification of nutrient removal via localized photosynthetic oxygenation Enhanced biofilm activity	[16,23,32,53,54]
Ex Situ	Membrane Bioreactor	Severe membrane fouling High energy costs for scouring and pumping	Development of algal membrane bioreactors	Alteration of foulant characteristics Formation of larger, more porous flocs Partial oxygen supply via photosynthesis	[18,24,25,33,72,74]

CAPEX/OPEX: capital expenditure and operational expenditure; HRAP: high-rate algal pond; ATS: algal turf scrubber.

.

5. The Underlying Mechanism: Unraveling Microalgae–Bacteria–Floc Interactions

The successful integration of microalgae into diverse aquaculture treatment systems is not a matter of simple co-existence, but is predicated on a web of intricate and dynamic interactions between the algal and bacterial communities. These interspecies relationships, refined over evolutionary timescales, form a complex symbiotic engine that drives the observed enhancements in nutrient removal, system stability, and biomass production. Understanding these underlying mechanisms at the metabolic, community, and physical levels is paramount for designing and optimizing next-generation, bio-integrated aquaculture technologies. This section dissects the three principal pillars of this interaction: the symbiotic exchange of essential metabolites, the active shaping of the microbial community, and the pivotal role of extracellular polymeric substances (EPSs) in mediating physical aggregation.

5.1. The Symbiotic Nexus: Nutrient Cycling, Gas Exchange, and Metabolite Exchange

At the most fundamental level, the microalgal–bacterial consortium operates on a powerful symbiotic exchange of gases and nutrients [26,27,28]. The classic depiction of this relationship involves the direct coupling of photosynthesis and respiration: microalgae utilize light energy to fix CO₂, produced by bacterial respiration, and in turn, they release O₂, which is consumed by aerobic bacteria for the degradation of organic matter [27]. This elegant loop simultaneously removes a bacterial waste product (CO₂) and supplies a crucial bacterial substrate (O₂), thereby reducing the need for external aeration and enhancing the efficiency of organic matter removal [70,76]. Beyond this gas exchange, a critical nutrient-cycling synergy exists. Heterotrophic bacteria play the role of “remineralizers,” breaking down complex organic compounds in the wastewater into simpler, inorganic forms of nitrogen (e.g., ammonium) and phosphorus (e.g., orthophosphate) that are readily bioavailable for algal uptake [32,77,78]. Research by Gao et al. using a novel bacterial–algal coupling reactor elegantly demonstrated this, showing how fermentative bacteria could produce volatile fatty acids that served as a carbon and nutrient source for microalgae, creating a stable, high-performance system [32]. This relationship can extend to more subtle, yet vital, exchanges. Certain bacteria are known to produce B-group vitamins, such as B12 (cobalamin), which many microalgal species are incapable of synthesizing themselves, but require as essential cofactors for growth, highlighting a profound metabolic interdependence [27,28].

5.2. Shaping the Microbiome: Promoting Beneficial Bacteria and Consortium Communication

The influence of microalgae extends beyond simple metabolic exchange to actively sculpting the composition and function of the associated bacterial community. The oxygen-rich phycosphere environment created by photosynthetically active algae selectively promotes the growth of specific aerobic and facultative bacterial taxa while potentially outcompeting obligate anaerobes and microaerophiles [33,79]. Of particular importance is the potential for microalgae to foster a robust community of bacteria capable of heterotrophic nitrification and aerobic denitrification (HNAD). These remarkable microorganisms, such as strains of Pseudomonas, Bacillus, and Zobellella, can perform both nitrification and denitrification simultaneously under aerobic conditions, providing a complete nitrogen removal pathway within a single reactor environment and bypassing the limitations of conventional systems [80,81,82,83,84]. The work of Xiang et al. showed that bio-augmenting a moving bed biofilm reactor (MBBR) with a novel halophilic HNAD strain significantly enhanced nitrogen removal from mariculture wastewater, a process that could be further stabilized by the localized oxygen supply from co-cultured microalgae [81,84,85].

Communication between these kingdoms is mediated by a complex chemical language, most notably through quorum sensing (QS). Bacteria release signaling molecules such as N-acyl-homoserine lactones (AHLs) to coordinate group behaviors, and evidence suggests that microalgae can perceive and respond to these signals [86,87]. This microalgal–bacterial signaling can influence processes such as bio-aggregation and the formation of protective biofilms, which are crucial for system stability and performance [26,86]. By modulating the microbial environment and participating in this chemical crosstalk, microalgae act as ecological engineers, curating a microbial community that is not only more effective at nutrient cycling, but also potentially more resilient to environmental perturbations.

5.3. The Role of Extracellular Polymeric Substances (EPSs) and Bio-Aggregation

A defining feature of microalgal–bacterial consortia is their tendency to self-aggregate into flocs or biofilms, a process fundamentally mediated by the secretion of extracellular polymeric substances (EPSs) [27,77]. EPSs comprise a complex, hydrated matrix composed primarily of polysaccharides, proteins, humic-like substances, and extracellular DNA (e-DNA) that acts as a “biological glue,” binding cells to each other and to surfaces [59,88,89]. The production and composition of EPSs are influenced by environmental conditions and the specific microbial species present [90,91]. This aggregation is critical for the success of integrated systems. In suspended growth systems such as A-BFT, EPS-driven bioflocculation creates larger, denser particles that are more easily harvestable through simple gravity settling, thus addressing a major hurdle in microalgal biotechnology [77,92]. As observed by Wei et al., prokaryotic communities vary significantly with floc size, with larger flocs hosting more complex and functionally specialized communities capable of enhanced nutrient cycling [42]. The physical structure of the floc, as described by Tansel, provides a scaffold that facilitates the close proximity required for the efficient symbiotic exchanges discussed previously [91].

However, the role of EPSs is a “double-edged sword,” particularly in the context of membrane-based systems. While EPSs are essential for forming the beneficial biofilm on carriers in an AGMBR [74] or the flocs in the bulk liquid, they are also widely recognized as the principal agents of membrane fouling in MBRs [24,25]. The soluble fraction of EPSs, known as soluble microbial products (SMPs), along with the loosely bound EPS fraction, can adsorb onto the membrane surface and block pores, leading to a rapid increase in filtration resistance and operational costs [59,60,88]. Therefore, managing the dynamics of EPS production and composition is a key challenge. The goal in microalgae-enhanced systems is to leverage the aggregative properties of EPSs for biomass retention and symbiotic efficiency while simultaneously controlling their expression to minimize their detrimental impact on membrane surfaces [75,93].

6. Valorization of Harvested Biomass: Towards a Circular Bioeconomy in Aquaculture

The integration of microalgae into aquaculture water treatment systems initiates a profound paradigm shift, transforming the operational philosophy from one of linear “waste management” to one of cyclical “resource creation” (shown in Figure 2). The biomass generated through the assimilation of effluent nutrients is not a terminal sludge to be disposed of, but rather a valuable raw material, a feedstock for a new, circular bioeconomy within the aquaculture sector itself. This process of valorization—the conversion of low-value waste streams into higher-value products—is the economic linchpin that makes microalgae-enhanced systems not only environmentally sustainable, but also potentially more profitable.

6.1. From Waste Management to Resource Creation: The Circular Bioeconomy Concept

The circular bioeconomy model is a direct response to the unsustainable linear trajectory of traditional industries, which follows a “take–make–dispose” pattern [9,94]. In aquaculture, this is manifested by the input of finite resources (water, feed) and the output of nutrient-rich waste. A circular approach, as explored by researchers such as Fraga-Corral et al. and Javourez et al., seeks to close these loops, designing waste out of the system and recapturing material and energy flows [9,95]. Microalgae-enhanced treatment systems are a quintessential example of this principle in action. They intercept the flow of nitrogen and phosphorus that would otherwise be lost as pollutants and convert them into a concentrated, solid-phase resource: microbial and algal biomass [37,73]. This act of recovery and upgrading fundamentally alters the economic equation of aquaculture, creating new revenue streams or cost-saving opportunities that can offset the investment in advanced water treatment infrastructure.

6.2. Algal and Microbial Biomass as a Sustainable Aquafeed Ingredient

The most immediate and synergistic application of the harvested biomass is its reintroduction into the production cycle as a high-quality aquafeed ingredient [34]. The global aquaculture industry’s heavy reliance on fishmeal and fish oil is a well-documented point of unsustainability, driving the over-exploitation of forage fish stocks and creating price volatility [6,96,97]. The biomass produced in microalgae-enhanced systems, often referred to as single-cell protein (SCP) when of microbial origin, presents a powerful alternative [98,99].

This biomass is nutritionally dense, with a protein content that can range from 30% to over 70% of the dry weight, and it often possesses an amino acid profile comparable or complementary to fishmeal [98,99,100]. Several studies have demonstrated that microalgal or microbial meals can successfully replace significant portions of fishmeal in shrimp diets without compromising the growth performance, and in some cases, even improving it [101,102]. As reviewed by Yarnold et al., biofloc-derived supplements have been shown to boost shrimp growth rates by nearly 50% compared to standard diets [34]. Biomass is also a rich source of other essential nutrients that are often lacking in plant-based protein alternatives, including long-chain PUFAs such as EPA and DHA, pigments such as astaxanthin and other carotenoids, sterols, and vitamins [34,39]. Furthermore, the presence of bioactive compounds and probiotic bacteria within the biomass can confer additional health benefits, improve disease resistance, and reduce the need for antibiotics [103,104]. By producing this valuable feed component on-site from waste nutrients, aquaculture operations can significantly reduce their dependence on external feed inputs, lower their FCR, cut operational costs, and enhance the sustainability credentials of their final product [98,105].

6.3. Co-Products and Diversified Applications: Biofuels, Bioplastics, and Nutraceuticals

Beyond its application as aquafeed, the harvested biomass opens the door to a full-fledged biorefinery concept, where multiple products are extracted to maximize value [37,63]. The lipid fraction of certain microalgal species can be readily converted into third-generation biodiesel, offering a renewable energy source to potentially power farm operations, though economic feasibility remains a challenge [67,106]. A more promising avenue for valorization lies in the production of high-value biopolymers. Certain bacteria cultivated in these systems can be induced to produce polyhydroxyalkanoates (PHAs), a family of biodegradable bioplastics that can serve as a sustainable alternative to petroleum-based plastics [107].

Furthermore, the biomass is a treasure trove of high-value compounds for the nutraceutical, pharmaceutical, and cosmetic industries. Microalgae are natural sources of potent antioxidants such as astaxanthin and beta-carotene, anti-inflammatory compounds, and natural colorants [63,67]. By selecting appropriate algal species and optimizing the cultivation conditions, an aquaculture facility could diversify its output, producing not only shrimp, but also a portfolio of valuable co-products. This diversification creates multiple revenue streams, enhancing the economic resilience of the farm and further cementing the financial case for investing in sustainable, circular production models.

6.4. The Harvesting Hurdle: Technological and Economic Challenges in Biomass Recovery

Despite the immense potential of biomass valorization, a significant technological and economic barrier remains: the efficient and cost-effective harvesting of the microbial and algal cells from the water column [106]. Microalgal cells are typically microscopic (5–50 µm), have a density very close to that of water, and carry a negative surface charge, which causes them to remain in a stable colloidal suspension [66,92]. Traditional harvesting methods such as centrifugation are highly effective, but prohibitively energy-intensive for all but the highest-value products [106]. Filtration methods, while less energy-intensive, are susceptible to the same fouling issues that plague MBRs [108,109].

Consequently, flocculation followed by sedimentation or flotation is widely regarded as the most promising approach for large-scale harvesting [66,92]. While chemical flocculants (e.g., alum, ferric chloride) are effective, they can contaminate the biomass, limiting its use in feed or food applications, and they can interfere with the recycling of the culture medium [66,110]. This has spurred intensive research into bio-based flocculants, such as chitosan (derived from shrimp shell waste, creating another circular opportunity), plant-based coagulants such as Moringa seed extract, and microbial bioflocculants [92,110]. The self-aggregating nature of A-BFT systems, driven by EPS production, represents a form of in situ bioflocculation that can significantly simplify harvesting [77]. Nevertheless, developing a harvesting technology that achieves a high recovery efficiency at a low cost, without compromising the biomass quality or water recyclability, remains the critical final step in closing the loop of the circular bioeconomy for aquaculture.

The emerging biorefinery approach represents a pivotal strategy for enhancing the economic viability and sustainability of microalgal biomass processing. By implementing integrated and sequential extraction techniques, it is possible to simultaneously recover multiple high-value compounds—including pigments such as fucoxanthin and astaxanthin, lipids for biofuels or omega-3 fatty acids, and proteins for nutritional applications—from a single batch of biomass [111,112,113]. For instance, studies have demonstrated the feasibility of co-extracting fucoxanthin along with EPA and chrysolaminarin from Phaeodactylum tricornutum through a multi-step process using green solvents such as ethanol and hexane [114]. This multi-product valorization not only maximizes resource utilization and minimizes waste, but also helps distribute and offset the costs associated with harvesting and downstream processing, thereby improving the overall economic balance. Moreover, the residual biomass after extraction can be further valorized for bioenergy, animal feed, or fertilizer applications, contributing to a circular bioeconomy [115]. By consolidating the recovery of diverse valuable products within a unified framework, the biorefinery model significantly enhances the commercial feasibility and sustainability of marine microalgae-based industries.

7. Future Perspectives and Research Gaps

The preceding sections have meticulously elucidated the principles, applications, and comparative efficiencies of biofloc technology alongside other advanced ex situ wastewater treatment systems utilized in shrimp aquaculture. While substantial progress has been achieved in enhancing productivity and mitigating environmental impacts, the journey towards fully sustainable and optimally robust aquaculture systems is ongoing. This necessitates a forward-looking perspective, identifying critical research gaps and proposing future directions that can further unlock the potential of these technologies (shown in

Table 3. Key research and development priorities for microalgae-enhanced aquaculture.

Priority Area	Key Challenge	Proposed Research Direction
Optimization of microalgal–bacterial consortia	Limited deep understanding and strategic manipulation of microbial communities for stability and performance.	Characterize microbial diversity via sequencing; engineer consortia using probiotics/prebiotics; explore quorum sensing.
Value-added products from bio-based flocculants	Excess sludge/bioflocs are often discarded as low-value waste, missing resource recovery opportunities.	Valorize biomass into high-value products (feed, bioplastics, biofuels); improve harvesting and processing.
Long-term ecological and economic sustainability assessments	Lack of comprehensive long-term studies on environmental impacts and economic viability.	Conduct life cycle assessments; perform economic modeling covering costs, markets, and socio-economic impacts.
Developing protocols and optimizing parameters for BFT	High variability in system designs and operations leads to inconsistent results and challenges in technology transfer.	Standardize BFT protocols; develop decision-support tools; use IoT and AI for real-time optimization and efficient aeration.
Addressing disease management and biosecurity in BFT	Insufficient understanding of pathogen dynamics within BFT’s unique microbial environment.	Study biofloc–pathogen interactions; develop tailored disease strategies; enhance immunity and breed resistant strains.

).

7.1. Optimization of Microalgal–Bacterial Consortia

The stability and performance of microalgal–bacterial consortia across systems are intimately linked to the structure, function, and dynamics of their resident microbial community [43,116,117]. While conventional approaches have focused on managing bulk water quality, a deeper understanding and the strategic manipulation of microbial consortia present a significant avenue for improvement. Future research should employ high-throughput sequencing technologies, such as metagenomics, metatranscriptomics, and metaproteomics, to comprehensively characterize the microbial diversity of these systems and identify the key functional groups responsible for nutrient cycling and probiotic effects [118].

This advanced understanding could pave the way for microbial community engineering, where specific beneficial bacterial strains, probiotics, prebiotics, or even bacteriophages could be introduced to enhance system resilience, improve nutrient utilization, and actively suppress pathogens [47]. For instance, targeted interventions could be developed to increase the efficiency of specific nitrification or denitrification pathways, or to enhance the production of enzymes beneficial for digestibility in shrimp. The potential for manipulating quorum-sensing mechanisms within the biofloc community also holds promise for disease prevention and enhancing beneficial microbial interactions [87].

7.2. Value-Added Products from Bio-Based Flocculants

The continuous accumulation of bio-based flocculants, while beneficial as a feed supplement, also presents a challenge in terms of sludge management. Currently, excess activated sludge and bioflocs are often discarded or used as low-value fertilizer, representing a missed opportunity for resource recovery [38,78]. A significant research gap exists in developing economically viable and environmentally sound strategies for valorizing this nutrient-rich biomass into higher-value products.

Future research should explore the potential of activated sludge, bioflocs, and microalgae biomass as a feedstock for various biotechnological applications. This could include its conversion into novel feed ingredients for other aquaculture species or terrestrial livestock, owing to its high protein and lipid content [41]. Other possibilities include its use as a source material for bioplastics, biofuels, or specific biochemicals [107]. Developing efficient and cost-effective methods for harvesting, dewatering, and processing biofloc sludge is critical to unlocking these potential value streams, thereby transforming a waste product into a valuable resource and reinforcing the circularity of the aquaculture system [92].

7.3. Long-Term Ecological and Economic Sustainability Assessments

While numerous studies have highlighted the short-term benefits of these advanced systems, comprehensive long-term assessments of their ecological and economic sustainability are still limited. There is a critical need for rigorous life cycle assessment (LCA) studies that compare the cradle-to-gate or even cradle-to-grave environmental impacts of different aquaculture wastewater treatment technologies [94]. A previous review provided a critical technological foundation for the long-term ecological and economic sustainability of RASs by systematically evaluating the efficiency and trade-offs of various treatment processes for key pollutants. This comparative analysis of removal technologies directly informs such assessments, highlighting the need to integrate performance data, environmental impacts, and operational costs to select solutions that ensure both ecological balance and economic viability over the long term [16]. These assessments should consider a broader range of impacts, including greenhouse gas emissions, freshwater consumption, land use, and potential ecotoxicity, not just for the production phase, but also to produce inputs (e.g., carbon sources, feeds, energy for aeration).

Furthermore, robust economic modeling, accounting for long-term operational costs, market fluctuations, consumer preferences, and evolving regulatory landscapes, is essential for guiding investment decisions and policy development [94]. Such evaluations should also consider the socio-economic impacts on local communities, including the labor skill requirements and job creation. Understanding the cumulative ecological footprint and economic viability over extended periods will provide a more holistic understanding of each technology’s true sustainability potential.

7.4. Developing Protocols and Optimizing Parameters for BFT

The inherent variability in BFT system designs, operational parameters, and management approaches across different farms and research groups often leads to inconsistent results and makes technology transfer challenging [13]. To facilitate a wider adoption and ensure a predictable performance, there is a pressing need for the development of robust, standardized, and easily replicable protocols for BFT implementation. This would involve establishing clear guidelines for initial system setup, biofloc inoculation, C/N ratio management under various conditions, optimal solids management strategies, and effective monitoring programs. Comprehensive training programs for aquaculture professionals and farmers are also vital to imparting the necessary technical knowledge and skills for successful BFT operation [19,45]. Furthermore, developing user-friendly decision-support tools and accessible diagnostic kits for water quality and microbial health monitoring would significantly lower the entry barrier for new adopters, fostering the responsible and widespread implementation of BFT.

Despite extensive research, the precise optimization of the BFT operating parameters for different life stages and environmental conditions remains an area ripe for further investigation. The current operational guidelines for parameters such as the C/N ratio, alkalinity, DO levels, and TSS are often generalized or empirically derived [42]. Future research should focus on developing dynamic and site-specific optimization models that can adjust parameters in real time. This includes leveraging advanced monitoring technologies, such as Internet of Things (IoT) sensors, to collect comprehensive data sets on water quality, microbial activity, and shrimp behavior [119]. The integration of artificial intelligence (AI) and machine learning algorithms can then enable predictive modeling and automated control systems, leading to more stable and efficient BFT operations and minimizing human error and resource waste [104]. Furthermore, energy-efficient aeration and mixing techniques, potentially incorporating novel designs or renewable energy sources, are crucial for reducing the substantial operational costs associated with BFT, making it economically viable in a wider range of geographical contexts [85].

7.5. Addressing Disease Management and Biosecurity in BFT

While BFT is recognized for its potential to enhance shrimp immunity and biosecurity, specific research addressing the dynamics of prevalent shrimp diseases within BFT environments is still evolving. Future studies need to specifically investigate how the unique microbial community of BFT systems interacts with common shrimp pathogens (e.g., Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease, AHPND) [47]. This includes understanding the role of bioflocs in pathogen transmission, persistence, and potential suppression.

Research should aim to develop targeted disease management strategies tailored for BFT, which might involve incorporating specific immune-enhancing feed additives, utilizing novel biological control agents, or integrating advanced early warning systems for pathogen detection [103]. The interplay between BFT-induced immune responses and host genetics also warrants further exploration, potentially leading to the development of disease-resistant shrimp strains compatible with BFT systems [52].

8. Conclusions

The global intensification of shrimp aquaculture is an essential trajectory to meet rising food demands, yet it is unsustainable under current technological paradigms. This review critically examined the inherent bottlenecks of both in situ and ex situ systems, revealing persistent trade-offs between efficiency, cost, and environmental impact. A key synthesis emerges: the strategic integration of microalgae offers a unifying enhancement pathway, transcending these traditional limitations.

8.1. Synthesis: A Universal Enhancement Strategy

Microalgae function not as a replacement, but as a keystone module for existing technologies. In biofloc systems, they rectify core biogeochemical imbalances by assimilating accumulated nitrate and providing photosynthetic oxygenation. For advanced recirculating systems, microalgae transform a terminal waste stream into valuable biomass, closing a critical resource loop. Even in nature-based constructed wetlands, fostering algal-bacterial synergy intensifies nutrient processing, reducing land footprint. This universal applicability underscores their role as a versatile, cross-cutting solution for sustainable intensification.

8.2. A Shift in Paradigm: From Treating Waste to Cultivating Resources

Integrating microalgae signifies a fundamental shift from a linear waste-treatment model to a circular resource-cultivation framework. Aquaculture effluent is no longer merely a pollutant but a nutrient resource for cultivating valuable algal biomass. This reimagines the treatment unit as a secondary production biorefinery, aligning economic incentives with environmental performance and creating more resilient, diversified production systems.

For this paradigm to achieve commercial maturity, targeted research must address key challenges in strain selection, system engineering, and biomass valorization. By doing so, the industry can fully harness microalgae to enable intensive shrimp production that is both productive and holistically sustainable.