From Waste to Resource: Algal–Bacterial Systems and Immobilization Techniques in Aquaculture Effluent Treatment

Abstract

The rapid expansion of global aquaculture has led to wastewater enriched with nitrogen, phosphorus, organic matter, antibiotics, and heavy metals, posing serious risks such as eutrophication, ecological imbalance, and public health threats. Conventional physical, chemical, and biological treatments face limitations including high cost, secondary pollution, and insufficient efficiency, limiting sustainable wastewater management. Algal–bacterial symbiotic systems (ABSS) provide a sustainable alternative, coupling the metabolic complementarity of microalgae and bacteria for effective pollutant mitigation and concurrent biomass valorization. Immobilizing microbial consortia within carrier materials enhances system stability, tolerance to environmental changes, and scalability. This review systematically summarizes the pollution characteristics and ecological risks of aquaculture effluents, highlighting the limitations of conventional treatment methods. It focuses on the metabolic cooperation within ABSS, including nutrient cycling and pollutant degradation, the impact of environmental factors, and the role of immobilization carriers in enhancing system performance and biomass resource valorization. Despite their potential, ABSS still face challenges related to mass transfer limitations, complex microbial interactions, and difficulties in scale-up. Future research should focus on improving environmental adaptability, regulating microbial dynamics, designing intelligent and cost-effective carriers, and developing modular engineering systems to enable robust and scalable solutions for sustainable aquaculture wastewater treatment.

1. Introduction and Rationale for ABSS in Aquaculture Effluent Treatment

1.1. Global Challenge of Aquaculture Effluents

As global population growth and shifting dietary preferences drive demand for high-quality protein sources, aquatic foods are becoming increasingly integral to sustainable food systems. Valued for their nutritional profile and production efficiency, they play an important role in nutrition and food security strategies [1]. According to the Food and Agriculture Organization of the United Nations (FAO)’s State of World Fisheries and Aquaculture 2024, global aquaculture production reached a record 130.9 million tons in 2022, including 94.4 million tons of aquatic animals and 36.5 million tons of algae, with a total value of USD 313 billion [2]. Aquaculture production of animal species exceeded that of capture fisheries for the first time, with inland aquaculture accounting for more than 60% of farmed aquatic animals [2,3]. Aquaculture now accounts for approximately 54% of total aquatic animal production and is projected to provide 60% of aquatic food for human consumption by 2032, as global demand continues to rise [2,4]. Regions such as China, Southeast Asia and Latin America have developed intensive aquaculture systems supported by favorable natural conditions and enabling policies, positioning the sector as a key contributor to rural livelihoods and international trade [2,5]. China remains the largest producer, responsible for 36% of global aquatic animal output in 2022, underscoring the sector’s central role in national food security and its contribution to the supply of essential proteins and micronutrients [6].

Despite the rapid expansion of global aquaculture, its environmental consequences are becoming increasingly apparent. Intensive production systems, characterized by high stocking densities, excessive feed inputs, and indiscriminate pharmaceutical use, have led to the routine discharge of nutrient-rich and chemically contaminated effluents into adjacent water bodies [7]. Aquaculture effluents contain nitrogen [8], phosphorus [9], suspended solids [10], organic matter [11], microplastics [12], and antibiotic residues [13]. Although their concentrations are generally lower than those in domestic wastewater, the discharge of these compounds can still adversely affect receiving water bodies. The sustained and widespread release of such effluents promote eutrophication, algal blooms, and ecological deterioration, while also raising human health concerns through the proliferation of antimicrobial resistance and the accumulation of pharmaceutical residues in aquatic food products [14].

1.2. Pollutant Composition and Ecological Risks

Effluents from aquaculture systems present complex and variable pollution profiles that differ according to farming practices, cultured species, and local management regimes [15]. A comprehensive understanding of these fundamental characteristics is critical for the development of effective, site-specific remediation strategies [16]. As a principal by-product of aquaculture activities, such effluents are characterized by elevated pollutant loads, intermittent discharge patterns, spatial concentration, and the frequent presence of persistent and hard-to-degrade substances [17]. Key pollutants typically include nutrients (notably nitrogen and phosphorus), organic matter, suspended solids, antibiotics and their associated resistance genes, as well as heavy metals.

1.2.1. Nutrient Overloading and Its Ecological Consequences

Nitrogen (N) and phosphorus (P) are the primary nutrient pollutants in aquaculture effluents, mainly originating from uneaten feed, feces, metabolic waste, and microbial degradation [8,9]. These nutrients exist in particulate and dissolved forms, with nitrogen typically as ammonium (NH₄⁺-N), nitrate (NO₃⁻-N), and nitrite (NO₂⁻-N) and phosphorus mostly as orthophosphate (PO₄³⁻) [18]. Their high bioavailability and mobility facilitate rapid participation in biogeochemical cycles, often triggering significant ecological changes in receiving waters.

Moreover, inefficient feed conversion in intensive aquaculture leads to nutrient accumulation in both water and sediments, elevating levels of bioavailable N and P over time [19,20]. In poorly flushed or semi-enclosed systems, these inputs can exceed the ecosystem’s natural capacity for nutrient assimilation, intensifying environmental degradation. As a result, excess nutrients drive eutrophication, promoting blooms of phytoplankton and cyanobacteria such as Microcystis sp., Anabaena sp., and filamentous green algae. These blooms impair water clarity, alter light penetration, and induce fluctuations in pH and oxygen. Decomposition of bloom biomass further depletes oxygen, causing hypoxic or anoxic conditions detrimental to aquatic life [21]. Furthermore, imbalances in nutrient stoichiometry, particularly elevated nitrogen-to-phosphorus (N:P) ratios, can selectively promote toxin-producing algal species [22], thereby compounding ecological risks and raising additional concerns for aquatic food safety and public health.

1.2.2. Organic Matter Accumulation and Oxygen Depletion

Organic matter in aquaculture effluents, comprising carbon compounds, proteins, lipids, and metabolic waste, is commonly quantified using chemical oxygen demand (COD) and dissolved organic carbon (DOC) [23]. These materials originate predominantly from uneaten feed and excreta and serve as primary substrates for aerobic microbial activity. Rapid accumulation in enclosed or semi-enclosed systems drives oxygen consumption, depleting dissolved oxygen (DO) and increasing oxygen debt [24].

As DO levels decline, aquatic organisms experience physiological stress, with feeding behavior impaired, growth rates reduced, and mortality risk heightened [25]. At the same time, organic matter undergoes anaerobic decomposition in sediments, producing toxic gases such as hydrogen sulfide and methane, which further degrade sediment quality [26]. This results in the formation of black, malodorous sludge commonly referred to as black mud, which disrupts benthic communities and reduces the capacity for pond recovery during rotational farming cycles [27]. In addition, sediment oxygen demand (SOD) in aquaculture zones is closely linked to feed input and biomass density. Elevated SOD reflects intensified organic carbon remineralization within sediments, further exacerbating DO depletion in overlying waters [28]. Thus, these effects position organic matter accumulation as a central driver of oxygen stress and sediment deterioration in intensive aquaculture environments.

1.2.3. Suspended Solids and Particle-Induced Turbidity

Aquaculture effluents commonly contain high levels of suspended solids (SS), including feed particles, fecal fragments, algal debris, and resuspended sediment [29]. These particles reduce water transparency and inhibit photosynthesis in algae and aquatic plants [30]. They also tend to adsorb nutrients and organic pollutants, forming colloidal complexes that prolong contaminant residence times in the environment [31].

In addition to impairing light penetration, suspended solids readily accumulate at discharge points and downstream locations, contributing to sediment build-up, channel narrowing, and potential secondary pollution [32]. Such impacts are particularly evident in pond and cage-culture systems, where the release of particulate matter is often substantial. This leads to increased local turbidity and progressive sediment darkening, which further degrades water and benthic habitat quality [33].

1.2.4. Antibiotics and Antibiotic Resistance Genes (ARGs)

Antibiotics such as tetracyclines, enrofloxacin, chloramphenicol, and sulfonamides are extensively used in aquaculture to control disease outbreaks and enhance survival rates [34]. However, due to incomplete metabolism and improper application, a portion of these compounds is released into the environment in either their parent form or as active metabolites [35]. Even at low concentrations, these substances can persist in aquatic environments and exert continuous selective pressure on microbial communities, thereby promoting the emergence and proliferation of ARGs and resistant bacterial strains [36]. Moreover, ARGs can spread among aquatic microorganisms via horizontal gene transfer, often facilitated by plasmids and other mobile genetic elements [36,37]. These resistance determinants have the potential to enter the human food chain through contaminated water or aquatic products, posing a serious risk to public health [38].

1.2.5. Heavy Metals and Co-Selection of Antibiotic Resistance

Heavy metal contamination in aquaculture environments frequently originates from intentional supplementation of elements such as copper (Cu), zinc (Zn), and iron (Fe) to promote growth and regulate microbial communities [39], as well as from facility corrosion and misuse of feed additives leading to elevated heavy metal levels in effluents. These metals are persistent, non-degradable, and tend to accumulate in sediments and organisms, potentially biomagnifying through the aquatic food web.

Such accumulation poses significant toxicity threats to aquatic life, including tissue damage, reproductive impairment, and behavioral disruption [40]. Chronic exposure may result in heavy metal residues in aquaculture products exceeding permissible limits, thus compromising food safety and trade [41]. Notably, heavy metals like Cu, Zn, and Cd also promote the co-selection of ARGs, through mechanisms of genetic linkage (co-resistance) and shared resistance pathways (cross-resistance) [42]. Mobile genetic elements such as plasmids, integrons, and transposons mediate horizontal gene transfer, thereby facilitating the co-dissemination of metal resistance and ARGs in aquatic microbial communities [43].

The ecological risks of aquaculture effluents extend beyond individual pollutants, posing broader threats to the structure, function, and resilience of aquatic ecosystems. Effluent discharge alters nutrient stoichiometry, modifies primary productivity, and reshapes microbial community composition in receiving waters, often leading to disrupted food webs and declining species diversity. Eutrophication-induced algal blooms contribute to severe nighttime hypoxia, causing fish mortality, while the subsequent decay of algal biomass promotes organic sedimentation, exacerbating benthic degradation and driving a feedback loop of nutrient enrichment, oxygen depletion, and sediment blackening. Especially in densely farmed regions, effluents disperse through interconnected water bodies, extending impacts to nearby croplands, drinking water sources, and wetlands. This diffusion leads to cumulative and potentially irreversible ecological risks. Consequently, aquaculture effluents have become a systemic environmental stressor (

Table 1. Major Pollutants, Physicochemical Parameters, and Ecological Risks of Aquaculture Effluents.

Water Body/System	Culture Type	Major Pollutants	Typical Concentration Range	Risk Level/Impact	References
Freshwater ponds	Carp, tilapia	TN, TP, COD	TN 20–40 mg/L; TP 2–6 mg/L; COD 40–100 mg/L	Local eutrophication; algal blooms	[8,9,18,44]
Intensive shrimp ponds (marine/brackish)	Shrimp, other freshwater species	NH4+-N, PO43−-P, antibiotics	NH4+-N 5–15 mg/L; PO43−-P 5–12 mg/L; antibiotics 10–200 µg/L	Benthic hypoxia, ARG proliferation	[8,9,18]
Net-pen/cage aquaculture	Salmon, seabass	Dissolved nutrients, organic matter	TN < 20 mg/L; TP < 3 mg/L; COD < 50 mg/L	Diffuse eutrophication; localized sediment impact	[23,24,25]
Recirculating aquaculture systems (RAS, high-density)	Tilapia, other freshwater species	TAN, nitrate, TDS	TAN 10–30 mg/L; NO3−-N 50–150 mg/L; TDS 300–1200 mg/L	Water reuse challenge, biofilter overload	[45,46]
Brackish aquaculture effluents	Shrimp/fish mix	conductivity, heavy metals	Conductivity 2–40 mS/cm; Na+, Cl− 50–300 mg/L; Cu/Zn up to 0.1–0.3 mg/L	Salinity stress to freshwater biota, sediment contamination	[46,47,48]

Notes: TAN = total ammonia nitrogen; TDS = total dissolved solids; TN = total nitrogen; TP = total phosphorus. RAS refers to an intensive aquaculture system in which water is continuously treated and reused to maintain optimal environmental conditions for cultured species.

, Figure 1), challenging the sustainability of aquatic food production.

1.3. Conventional Treatment Technologies: Performance and Limitations

1.3.1. Mechanical and Physical Filtration Techniques for Aquaculture Effluents

Physical treatments are widely used in aquaculture effluent management to remove suspended solids such as uneaten feed, fecal particles, and silt. Among them, mechanical filtration using filter meshes, sand beds, or drum screens is the most common pre-treatment approach due to its operational simplicity and high automation potential [49]. This method effectively reduces SS loads and enhances the efficiency of subsequent treatment stages [50]. Although mechanical filtration methods are widely used in aquaculture effluent treatment, they are still inherently limited in scope. These technologies fail to remove dissolved pollutants such as nitrogenous compounds and phosphates [51]. Moreover, advanced equipment like drum filters or dissolved air flotation systems, while effective, involve high capital investment and frequent maintenance, which may restrict adoption in small-scale or resource-limited settings [52].

Dissolved air flotation (DAF), also known as foam separation, is a physical treatment method that removes suspended solids by introducing fine microbubbles into the water. These bubbles attach to particulate pollutants, facilitating their ascent and subsequent removal with the foam layer [53]. Its performance is particularly enhanced in marine systems due to elevated salinity, which improves bubble adhesion and facilitates organic and microbial load reduction [54]. Recent field applications in freshwater systems have demonstrated that when DAF is integrated with solid-separating bag-pen enclosures, it can achieve substantial nutrient removal. In rainbow trout cultivation, DAF alone removed up to 86% of suspended solids and 83% of phosphorus; with ferric dosing, phosphorus and nitrogen reductions reached 90% and 80%, respectively [55]. These results underscore DAF’s versatility as a scalable and effective approach for mitigating particulate and dissolved nutrient emissions across diverse aquaculture contexts.

Membrane separation technologies, including ultrafiltration (UF), microfiltration (MF), reverse osmosis (RO), and nanofiltration (NF), have rapidly evolved into modular, scalable, and energy-efficient solutions for aquaculture wastewater treatment. These technologies collectively offer a comprehensive removal spectrum from suspended solids and pathogenic microorganisms (MF and UF) to dissolved salts, organic micropollutants, and nutrients (NF and RO), making them particularly suited for sustainable aquaculture systems [56,57,58]. Studies have shown that UF membranes can effectively eliminate fish viruses and bacteria under varying temperature conditions [56], while RO and NF systems achieve high rejection rates of organic and inorganic contaminants, especially when used in combination with UF as a pretreatment step [58,59].

1.3.2. Chemical Coagulation in Aquaculture

Chemical coagulation remains a widely adopted approach in aquaculture effluent treatment, particularly for the rapid removal of suspended solids and phosphorus. Aluminum- and iron-based salts facilitate the aggregation of colloidal particles through charge neutralization and polymeric bridging, with optimized dosages achieving orthophosphate removal efficiencies exceeding 90% [60,61]. Field-scale applications, such as lake restoration initiatives, further demonstrate the efficacy of alum treatments in reducing total phosphorus (TP) concentrations from 1–2 mg/L to below 0.5 mg/L, often reaching tens of micrograms per liter and effectively mitigating eutrophication risk [62].

Despite these advantages, conventional coagulants pose inherent trade-offs, including elevated operational costs, significant chemical sludge generation, and environmental concerns associated with residual metal ions. Aluminum concentrations have been shown to impair aquatic life and may contribute to long-term ecological and human health risks [63]. In pursuit of more sustainable alternatives, recent advances have highlighted the potential of bio-based coagulants such as chitosan, which offer comparable removal efficiency with reduced toxicity and the added benefit of biodegradable sludge [64]. Moreover, hybrid coagulant systems combining polyaluminum chloride (PAC) with cationic modified starch have demonstrated notable promise, achieving high removal performance for COD and color while significantly lowering chemical demand, thereby balancing treatment efficacy with environmental compatibility [65].

Ozonation has emerged as a promising advanced oxidation process for aquaculture effluent treatment due to its strong oxidative potential and broad-spectrum pathogen inactivation. In marine recirculating aquaculture systems (RAS), ozonation effectively removes nitrite and dissolved organic matter, reduces bacterial biomass, and facilitates the conversion of ammonium–nitrogen into nitrogen gas via bromide-catalyzed reactions in seawater [66]. However, ozone’s non-selective oxidative action may disrupt beneficial microbial communities essential for biofiltration and ecosystem stability [67]. In bromide-rich waters, it can also lead to the formation of disinfection by-products such as bromate, a recognized carcinogen. Even low bromide concentrations (~100 µg/L) can markedly increase the cytotoxicity and genotoxicity of treated effluents due to the presence of brominated inorganic and organic compounds [68]. Furthermore, the deployment of ozonation systems entails considerable capital and energy input. Common ozone generators, including corona discharge and Ultraviolet-based systems, are technically complex and expensive to operate, limiting their feasibility in small- and medium-scale aquaculture operations [69].

1.3.3. Traditional Biological Treatments

Biological treatment technologies, particularly nature-based solutions such as constructed wetlands (CWs) and ecological floating beds (EFBs), have emerged as sustainable and environmentally friendly approaches for managing aquaculture effluents. CWs have demonstrated consistent removal of COD, Total nitrogen (TN), ammonium (NH₄⁺-N), and TP across diverse aquaculture systems, including a five-year hybrid vertical–horizontal flow wetland treating effluents from blunt snout bream farms [70], and subsurface flow wetlands achieving TN reductions of 36.94% and cyanobacterial removal of up to 97% in mariculture wastewater [71]. Multi-stage CWs that integrate aquatic vegetation, aeration, and filtration have maintained TN and TP removal efficiencies exceeding 60% with strong operational stability [72]. EFBs offer a more land-efficient alternative, employing floating macrophytes whose extensive root zones and associated microbial biofilms effectively remove nitrogen and phosphorus [73]. However, large spatial requirements, species-specific design considerations, and intensive maintenance demands remain key limitations, necessitating site-specific and adaptive implementation strategies [74].

The activated sludge process remains a widely adopted and dependable biological treatment method for aquaculture effluents, promoting microbial proliferation through aeration to form flocculent biomass that adsorbs and biodegrades organic contaminants. As a mature and scalable technology, it substantially improves water quality in intensive aquaculture systems. Recent studies have confirmed its flexibility and effectiveness under diverse operational conditions. In marine recirculating aquaculture systems (RAS), fed-batch reactors utilizing activated sludge achieved total nitrogen removal efficiencies exceeding 80%, particularly when acetate was used as an external carbon source, significantly reducing the required reactor volume [75]. In freshwater RAS, integration of activated sludge membrane bioreactors (MBRs) enabled efficient removal of ammonium and organic pollutants while minimizing water consumption, with no adverse effects on the growth performance or flesh quality of Oncorhynchus mykiss [76]. Anaerobic co-digestion of aquaculture sludge with waste activated sludge has also shown promise for improving methane production and sludge stabilization, enhancing the energy recovery potential of the system [77]. However, the long-standing issue of filamentous bulking, driven by the excessive growth of filamentous bacteria, continues to compromise sludge settleability and effluent clarity. Effective control requires both traditional chemical treatments and targeted microbial management strategies [78].

Biofilm-based treatment technologies harness microbial communities attached to carrier surfaces to metabolize organic matter and remove N and P pollutants. These systems demonstrate strong resilience to influent water quality fluctuations, operational simplicity, and relatively low excess sludge production, making them particularly attractive for aquaculture wastewater treatment [79]. The biofilm matrix provides a stable microenvironment that enhances microbial diversity and functional stability, ensuring sustained pollutant removal even under variable loading conditions [80]. Furthermore, moving bed biofilm reactors (MBBRs) have shown efficient nutrient removal and robust performance in aquaculture effluent treatment [81]. Nevertheless, this technology performance may decline at low temperatures [82], and biofilm sloughing necessitates complementary post-treatment to control suspended solids in the effluent [83].

Conventional solutions for aquaculture wastewater include sedimentation and oxidation ponds, biofilters, constructed wetlands, activated sludge and membrane-based processes. Although high-rate technologies such as activated sludge, Sequencing batch reactors (SBR) and MBR can achieve substantial nutrient removal, they are typically energy-intensive, sensitive to salinity changes, and generate secondary sludge or require chemical inputs for phosphorus control. Low-tech approaches (wetlands, ponds) are land-intensive and show strong seasonal and loading-dependent variability. A comparative summary of conventional technologies, their typical removal performance and practical limitations is presented in

Table 2. Comparison of Conventional Treatment Technologies for Aquaculture Effluents.

Treatment Type	Pollutant Removal/Efficiency	Advantages	Limitations	References
Sedimentation/Oxidation ponds	SS: 40–70%; TN: 20–40%; TP: 15–35%	Low cost; simple operation; natural processes	Large land footprint; poor control; limited N and P removal	[47,86,87]
Biofilters (trickling, moving bed)	NH4+-N: 40–80%; TN: 30–60%	Effective for ammonium oxidation; suitable for RAS	Requires aeration and biofilm maintenance; limited P removal	[88,89,90]
Constructed wetlands	TN: 40–70%; TP: 30–60%; COD: 40–80%	Eco-friendly; habitat provision	Large area; seasonal performance variation; pathogen risk	[44,46,86]
Activated sludge systems	TN: 60–80%; TP: 40–70%; COD: 70–90%	High efficiency; widely used; adaptable	High energy demand; sludge production; less stable under salinity	[86,91,92]
Sequencing batch reactors (SBR)	TN: 70–90%; TP: 50–80%; COD: 70–90%	Flexible operation; enhanced N removal	Skilled operation required; sensitive to fluctuations	[47,93]
Membrane bioreactors (MBR)	TN: 80–95%; TP: 70–90%; COD: 85–95%	High effluent quality; small footprint	High cost; fouling issues; energy-intensive	[47,76,91]
Chemical precipitation (e.g., lime, alum)	TP: >90%; COD: 40–60%	Rapid P removal; simple	High chemical cost; sludge disposal problem; not sustainable	[60,61]
Biofloc technology	TN: 40–70%; TP: 30–50%	Converts waste into microbial protein; feed supplement	Requires high aeration; may not meet discharge standards	[45,94]

. Importantly, many conventional systems struggle to consistently meet emerging discharge thresholds (e.g., TN < 10 mg L⁻¹; TP < 1 mg L⁻¹) under the dynamic operating conditions common to aquaculture facilities. To address these risks, it is essential to develop and implement effluent treatment technologies that are cost-effective, scalable, and environmentally sustainable [84,85].

1.4. Rationale for ABSS and Immobilization

In recent years, ABSS has emerged as an innovative biological treatment approach that effectively integrates the metabolic advantages of photosynthetic microalgae and heterotrophic bacteria [95]. This technology has attracted significant attention in wastewater treatment due to its excellent metabolic complementarity, efficient removal of nitrogen, phosphorus, organic pollutants, and certain antibiotics, as well as its advantages in resource recycling and system stability [96,97]. Beyond pollutant degradation, the technology enables the conversion of algal biomass into valuable feed, fertilizer, or renewable energy, aligning closely with the principles of pollution control, resource recovery, and the circular economy [98]. Meanwhile, the incorporation of immobilization techniques has further enhanced system robustness and expanded its prospects for industrial application [99].

Although several recent reviews have examined algal–bacterial symbiotic systems for wastewater treatment [86,96], most remain broad in scope and primarily descriptive. Prior work has summarized mechanisms and case studies but has rarely offered systematic, quantitative comparisons across system types or application domains. In particular, limited attention has been given to aquaculture effluents, immobilization strategies, techno-economic feasibility, and regulatory drivers. In contrast, the present review advances the field in four ways. First, we synthesize quantitative data into a comparative dataset that encompasses pollutant composition and risks of aquaculture effluents, contrasts among conventional treatment technologies, representative algal–bacterial pairings, immobilization carriers, and case studies, as well as a direct comparison of free-living and immobilized systems. Second, we highlight immobilization as a decisive enabler, analyzing both mechanistic implications and practical advantages for biomass retention, kinetics, and reusability. Third, we explicitly integrate techno-economic assessments and policy contexts, linking treatment performance with cost ranges, valorization of harvested biomass, and compliance with discharge standards. Finally, we emphasize aquaculture effluents as a priority testbed, showing how their nutrient-rich yet carbon-poor composition, variable salinity, and regulatory pressures uniquely align with the strengths of immobilized ABSS. Together, these elements establish a more critical and application-oriented perspective than previous reviews, shifting the discussion from descriptive synthesis to prescriptive guidance for research, engineering, and policy implementation.

2. Algae–Bacteria Consortia: A Synergistic Platform for Integrated Remediation and Resource Recovery

Amid the global transition toward green and low-carbon development, ABSS have emerged as a next-generation bioremediation platform. By leveraging the mutualistic interactions between microalgae and bacteria, ABSS integrate pollutant removal, carbon mitigation, and resource recovery within a self-regulating, ecologically adaptive framework, highlighting their potential as a sustainable strategy for water management and the circular bioeconomy.

2.1. Microalgae-Based Aquaculture Wastewater Treatment and Species Performance

Microalgae-based platforms represent an efficient and ecologically adaptive solution for aquaculture wastewater remediation. Among them, Chlorella vulgaris, Scenedesmus spp., and Tribonema spp. are the most studied genera, each exhibiting distinct functional advantages. C. vulgaris demonstrates broad compatibility with both freshwater and marine systems, achieving over 90% nutrient and 80% antibiotic removal in biofilm-based photobioreactors, while forming productive phycospheric interactions that enhance nutrient cycling and biomass yield [100,101]. Scenedesmus spp. excel in decentralized and in situ mixotrophic systems, with nitrogen removal efficiencies up to 81% higher than conventional autotrophic or bacterial treatments [102]. Recently, Tribonema spp. have demonstrated remarkable potential when co-cultured with aerobic denitrifying phosphorus-accumulating bacteria (e.g., Pseudomonas sp.), achieving rapid and efficient removal of NH₄⁺-N (76.9%), NO₃⁻-N (95.8%), PO₄³⁻-P (67.7%), and total nitrogen (84.9%) within 36 h, while simultaneously enhancing lipid accumulation (25.4% of dry weight) [103]. These taxa underpin a versatile and scalable biological platform for integrated pollutant removal, resource recovery, and biomass valorization in sustainable aquaculture [104].

2.2. Bacterial Taxa in Algae–Bacteria Symbiotic System

In ABSS, functional bacterial taxa play critical and differentiated roles in enhancing nutrient removal, degrading organic pollutants, and stabilizing microbial communities. Ammonia—and nitrite-oxidizing bacteria (AOB and NOB), such as Nitrosomonas and Nitrobacter, are essential to the nitrification process and are commonly enriched in low-temperature aquaculture systems to improve ammonium oxidation efficiency [88,89]. These bacteria are widely employed in biofilm reactors and integrated fixed-film systems [91], where they demonstrate strong resilience to temperature fluctuations and high organic loading. Aerobic denitrifying and phosphorus-accumulating bacteria, particularly Pseudomonas spp., facilitate the coordinated removal of nitrogen and phosphorus. A novel Pseudomonas aeruginosa strain capable of heterotrophic nitrification, aerobic denitrification, and aerobic phosphate removal has achieved removal efficiencies of up to 87% for NH₄⁺-N and 97% for PO₄³⁻-P in aquaculture wastewater [105]. In addition, Actinobacteria-based bioremediation contributes to organic matter degradation, surfactant production, and microbial community stability [106]. Genera such as Streptomyces sp., Acinetobacter sp. and Rhodococcus sp. are often dominant in aquaculture systems treated with biofloc [45], or algae-based technologies and have been recognized for their antimicrobial and probiotic roles, offering protection against pathogens and contributing to water quality stabilization [106,107]. Thus, these bacteria form metabolically complementary partnerships with microalgae, enabling a robust and synergistic system that enhances pollutant removal, stabilizes microbial ecology, and supports sustainable, high-efficiency treatment of aquaculture wastewater.

2.3. Environmental Drivers Shaping Microbial Interactions and Treatment Efficiency

Environmental factors directly regulate the growth and metabolism of both bacteria and algae, thereby altering their reproductive capacity, physiological activity, and interaction intensity within ABSS, ultimately affecting the overall wastewater treatment performance [44]. In practical applications, several key factors require close attention, including algae–bacteria volume ratio, light regulation, temperature and pH, external carbon source and C/N, and aeration rate and DO. These parameters, through synergistic or limiting effects, collectively shape the microecological balance and metabolic efficiency of the system [108].

2.3.1. Algae to Bacterial Ratio

The algal-to-bacterial volume ratio is a pivotal factor governing both system stability and pollutant removal efficiency in wastewater treatment. Ji et al. (2018) reported that a ratio of C. vulgaris to Bacillus licheniformis (1:3) achieved 86.55% COD, 80.28% total dissolved nitrogen (TDP), and 88.95% total dissolved phosphorus (TDN) removal in synthetic wastewater [109]. In contrast, Zhang et al. (2021) found that a combination of Scenedesmus obliquus with Pseudomonas putida at a 1:3 volumetric ratio enhanced TN and TP removal by 28.9% and 67.6% compared to bacterial monocultures [110]. Similarly, Liu et al. (2024) optimized the co-culture of C. vulgaris with Bacillus subtilis at a 2:3 ratio in anaerobically digested wastewater, achieving 81.38% TN, 94.28% NO₂⁻-N, 75.33% COD, and 96.56% TP removal [111]. In systems treating rare earth element-rich wastewater, Tribonema sp. paired with phosphorus-accumulating denitrifies showed enhanced ammonium removal rates of 17.69 ± 0.45 mg L⁻¹ d⁻¹. In livestock wastewater, the 1:3 ratio also yielded removal efficiencies of 50% (TN), 70% (NH₄⁺-N), and 83% (COD), alongside improved algal proliferation and flocculation [92]. Although optimal ratios vary depending on microbial taxa and wastewater characteristics, they generally range from 1:3 to 2:3. These ratios promote mutualistic interactions whereby algae provide oxygen and organic substrates, while bacteria mineralize pollutants and regenerate CO₂ and nutrients, collectively enhancing nitrogen, phosphorus, and COD removal [86,92,96]. Therefore, precise optimization of algal-to-bacterial ratios tailored to specific microbial consortia and wastewater matrices is essential to maximize the performance of ABSS in treating complex effluents.

2.3.2. Light Regulation

Light serves as a key environmental factor in ABSS, with light cycle, wavelength, and intensity exhibiting distinct regulatory mechanisms that critically affect pollutant removal efficiency and biomass accumulation. Studies on light cycles have shown that carbon removal efficiency increases with prolonged dark periods, while nitrogen and phosphorus removal decrease correspondingly. Moreover, extended dark phases significantly reduce the N/P removal ratio [112]. Regarding light wavelength, red light significantly enhances nitrogen removal, enabling the system to meet aquaculture water quality standards within nine days. Under red light, algae (e.g., Characium sp., Microcoleus sp.) and bacteria (e.g., Nakamurella sp., Micropruina sp.) exhibit complementary metabolic functions, assimilating organic matter and nutrients, respectively, thereby improving cooperative efficiency [113]. Glemser et al. (2016) further highlighted that Light-Emitting Diodes sources, due to their spectral specificity, are superior to traditional fluorescent lighting for investigating wavelength-dependent effects [114]. Light intensity also displays an optimal range. Under 80 μE/(m²·s), nitrogen removal, Adenosine Triphosphate (ATP) supply, photosynthetic performance, and enzyme activities are maximized, with upregulation of photosynthetic genes (petC, atpH/A); in contrast, excessive or insufficient light induces oxidative stress and inhibits system function [115]. Similarly, Wang et al., (2025) [116] found that a light intensity of 7000 Lux optimally promotes ammonium oxidation and nitrate reduction in a sequencing batch reactor. Notably, coordinated regulation of light cycle and intensity enables dual benefits in system performance and bioproduct yield. By optimizing these parameters, a bacterium–microalgae coupled system achieved COD, NH₄⁺-N, and TP removal efficiencies of 86.68%, 87.35%, and 95.13%, respectively, while significantly promoting microalgal accumulation of carbohydrates, proteins, and lipids [117]. Therefore, rational design of light parameters provides both theoretical and engineering guidance for the application of algal–bacterial systems in aquaculture wastewater treatment.

2.3.3. Temperature and pH

Temperature is a critical environmental factor influencing pollutant removal efficiency in algae-bacteria systems, as it significantly modulates the metabolic pathways and interactions between microalgae and bacteria. Studies have shown that optimal temperatures (22–28 °C) markedly enhance the cooperative metabolism between microalgae and bacteria, thereby improving the removal of N, P, and organic matter [118,119]. Warmer seasonal conditions not only promote higher algal growth rates but also facilitate more efficient nutrient removal, with summer and autumn yielding the most favorable results [118]. However, when temperatures rise above 30 °C, the system becomes imbalanced as ammonia -oxidizing bacteria (AOB) rapidly proliferate, suppressing algal activity and intensifying competition for nitrogen, ultimately reducing treatment performance [120]. Temperature also shapes algal community composition as elevated temperatures favor Chlorophyta sp. over Leptolyngbyales sp., thereby altering phosphorus removal mechanisms [119]. Further evidence suggests that sustained high temperatures or abrupt thermal fluctuations can disrupt the dynamic equilibrium between algae and bacteria, compromising system stability [121]. Therefore, precise temperature regulation, particularly in response to seasonal variability, is essential for maintaining the efficiency and stability of algae-bacteria wastewater treatment systems.

pH is another key factor influencing pollutant removal efficiency in ABSS, as it directly affects microbial metabolism, interspecies interactions, and cellular stability. Liang et al., (2015) [122] demonstrated that in a combined system of C. vulgaris and B. licheniformis, a decrease in pH from neutral (7.0) to acidic (3.5) significantly impaired nutrient removal and algal activity, while regulating the pH back to 7.0 restored algal growth and improved the removal efficiencies of NH₄⁺-N (86%) and TP (93%), alongside an increase in chlorophyll a. In a related study, unregulated acidic conditions caused algal cells to become compact and spherical, whereas cells exposed to a neutral pH exhibited a more metabolically active, wrinkled morphology, highlighting the morphological and functional sensitivity of the algae-bacteria system to pH shifts [123]. Complementary findings showed that adding biochar stabilized the system pH within the range of 6.0–7.9, enabling up to 99.96% removal of total ammonium nitrogen and 55% phosphate within six days under heterotrophic conditions [124]. These results collectively underscore that maintaining a stable and optimal pH range (typically 6.0–7.5) is essential for promoting efficient nutrient removal, sustaining microbial synergy, and ensuring the operational stability of ABSS in wastewater treatment.

2.3.4. External Carbon Source and Carbon-to-Nitrogen Ratio

The type of external carbon source and the carbon-to-nitrogen (C/N) ratio play critical roles in determining pollutant removal efficiency in algal–bacterial systems, as their regulatory effects are intimately connected to microbial metabolism, community dynamics, and environmental factors. Different carbon sources exert distinct influences on system performance. For instance, organic carbon such as sodium acetate under mixotrophic conditions significantly enhances nutrient removal and biomass production at a C/N ratio of 15 to 1 in algal–cyanobacterial co-cultures [125]. Conversely, glycerol addition, although it increases biomass, does not improve nutrient removal and may ultimately cause consortium collapse during later stages of wastewater treatment [126]. Furthermore, inorganic carbon sources differ from organic ones in nitrogen transformation pathways. Organic carbon addition reduces nitrate concentrations but increases nitrous oxide emissions more than twofold due to elevated nirS gene abundance in ABSS. Inorganic carbon sources are critical for sustaining algal photosynthesis and coupled bacterial metabolism. In many systems, dissolved CO₂ from aeration or bacterial respiration provides the primary inorganic carbon source, while supplementation with bicarbonates (e.g., NaHCO₃) or carbonate alkalinity has also been reported to stabilize pH and improve nitrogen and phosphorus removal [122,124,127]. For instance, Casagli et al. (2021) demonstrated that inorganic carbon limitation can suppress nutrient uptake and disrupt algae–bacteria balance [127], whereas Liang et al. (2013) found that pH-dependent bicarbonate availability significantly influenced N and P removal in Chlorella–Bacillus systems [123]. In contrast, inorganic carbon promotes ammonium removal without associated greenhouse gas emissions [128].

Optimizing the C/N ratio is essential to balance carbon supply with microbial activity. In microalgae-integrated biofloc aquaculture systems, efficient ammonium removal and nitrite suppression occur at a low C/N ratio of 5 to 1, which is considerably lower than the 15 to 1 ratio required in biofloc-only systems [94]. Similarly, in blends of municipal and industrial wastewater, moderate C/N ratios between 7.52 and 30.67 facilitate effective removal of dissolved organic carbon, ranging from 75.61 to 81.90%, and soluble chemical oxygen demand, between 66.78 and 88.85%. However, excessively high C/N ratios above 30.67 inhibit microalgal growth and reduce overall treatment performance [129]. Synergistic microbial interactions also improve carbon utilization efficiency. The co-cultivation of Chlorella pyrenoidosa and Rhodobacter capsulatus enhances acetate assimilation and stimulates the tricarboxylic acid cycle, promoting coordinated nutrient removal through optimized organic carbon metabolism [130].

2.3.5. Aeration Rate and DO

Aeration rate and DO are key factors influencing the pollutant removal efficiency of ABSS, primarily by regulating microbial metabolic activity, community interactions, and system stability. Low aeration conditions (0.2 L/min) have demonstrated clear advantages in treating both domestic and mariculture wastewater. In domestic sewage, this aeration rate enabled the ABSS to achieve removal rates for NH₄⁺-N, TN, and TP that were 18.90%, 12.45%, and 46.66% higher, respectively, than those of conventional activated sludge systems [93]. In mariculture wastewater, when combined with an algal inoculation ratio of 1:8 and a nitrogen-to-phosphorus (N:P) ratio of 12, the ABSS achieved removal efficiencies of 100% for NH₄⁺-N, 93.26% for TN, and 96.12% for TP [47]. Moderate aeration (1.0 L/min), while not significantly enhancing pollutant removal, improves the self-flocculation capacity of the ABSS. Under this condition, self-flocculation efficiency reached 82.39% within 30 min, enabling more efficient solid–liquid separation in downstream processes [131].

The regulation of DO is closely linked to algal metabolism. Low DO levels promote algal growth, and oxygen produced via photosynthesis supports bacterial degradation. This interplay forms a positive feedback loop that enhances overall system performance. In high-strength textile wastewater, this mechanism led to removal efficiencies for COD, NH₄⁺-N, and TP that were 12.5%, 23.1%, and 10.5% higher, respectively, than those achieved by conventional processes, along with an 80-fold increase in decolorization [87]. In contrast, excessive aeration generates strong shear forces that disrupt the algal-bacterial structure, suppress algal proliferation, and weaken cooperative removal functions [132]. Thus, aeration rate and DO jointly shape the ecological dynamics of algal-bacterial interactions, thereby influencing pollutant removal performance. In practical applications, aeration parameters should be optimized according to wastewater characteristics and treatment objectives to balance pollutant removal efficiency, system stability, and energy consumption.

2.4. Microbial Synergy and Pollutant Removal Mechanisms in ABSS

2.4.1. Microbial Interactions Underpinning Metabolic Complementarity and Ecological Stability in ABSS

Efficient ABSS rely on coordinated metabolic exchange between microalgae and heterotrophic bacteria. Microalgae convert CO₂ into organic compounds (e.g., polysaccharides, organic acids) via photosynthesis and release oxygen to support aerobic bacterial metabolism. Certain species, such as Chlorella sp., also excrete amino acids, B vitamins, and other growth factors that promote the growth and activity of associated bacteria like Bacillus sp. [90]. This transfer of photosynthates and oxygen forms the metabolic foundation of nutrient cycling. In turn, bacteria mineralize complex organic matter, particularly in aquaculture wastewater, releasing CO₂, NH₄⁺, and PO₄³⁻, which are readily assimilated by microalgae. Functional groups such as nitrifiers and denitrifiers further mediate nitrogen transformation, complementing algal nitrogen uptake [90,133]. For instance, in Chlorella–B. subtilis consortia, bacterial secretion of purines and amino acids reinforces mutual carbon–nitrogen cycling, enhancing wastewater treatment performance [90].

Moreover, this metabolic complementarity increases system resilience. Compared with monocultures, algal–bacterial consortia can restructure their microbial communities in response to environmental fluctuations. Under organic or thermal stress, algal photosynthesis maintains oxygen supply while bacterial metabolic flexibility buffers nutrient shocks, preserving overall system performance [134]. These interactions also promote bioflocculation, facilitating biomass separation and reducing the need for external intervention [46,134]. Therefore, the cooperative behavior between algae and bacteria contributes not only to functional efficiency but also to the long-term operational stability of the system.

In terms of carbon cycling, algal CO₂ fixation, particularly in strains like Chlorella, sustains organic carbon supply and contributes to carbon sequestration. On average, one ton of algal dry biomass captures approximately 1.8 tons of CO₂ [135]. Furthermore, bacterial decomposition and mineralization further redistribute carbon flows, closing the atmospheric CO₂ to biomass and inorganic carbon cycle and supporting low-carbon wastewater treatment strategies [48]. Therefore, the metabolic synergy between algae and bacteria improves contaminant removal while enhancing ecological robustness, providing a solid biological foundation for scalable applications in wastewater treatment and carbon management.

2.4.2. Synergistic Degradation Mechanism for Integrated Multi-Pollutant Purification

ABSS exhibit pronounced synergistic effects in pollutant removal, offering particular advantages for treating complex contaminated water. Microalgae efficiently capture a wide range of pollutants through surface adsorption, charge exchange, and intracellular accumulation, with a notably high affinity for heavy metal ions. In parallel, bacteria degrade organic pollutants into harmless products or achieve complete mineralization through enzymatic cascades. The degradation of organophosphates, polycyclic aromatic hydrocarbons, and antibiotics is further enhanced by algal metabolites, including hydrogen peroxide (H₂O₂), reactive oxygen species (ROS), and redox enzymes, which promote bacterial activity, especially under oxygen-limited or photo-inhibited conditions [136]. For heavy metal remediation, phosphate and carboxyl groups on the algal cell surface bind metal ions, reducing their mobility and bioavailability [137]. Complementarily, functional bacteria such as P. aeruginosa and Bacillus spp. convert metal ions into insoluble forms such as metal sulfides or oxides through reduction, thereby enhancing immobilization and long-term stability [138]. This cooperative mechanism, combining algal adsorption with bacterial transformation, effectively overcomes the limitations of incomplete metal speciation conversion observed in single-species systems.

In the treatment of emerging contaminants, ABSS exhibit notable adaptability and efficacy. Specifically, in antibiotic removal, the consortium significantly accelerates the degradation of cephalexin and erythromycin, with removal efficiencies reaching 96.54% and 92.38%, respectively [139]. Similar performance has been observed for sulfonamide antibiotics and other recalcitrant compounds, with removal rates exceeding 80% and a marked reduction in byproduct toxicity [140]. Beyond emerging pollutants, these consortia offer broad-spectrum purification of water quality parameters such as NH₄⁺-N, COD, TN, and TP [90,133]. Multiple case studies report simultaneous compliance with discharge standards across these indices, underscoring the system’s high efficiency in coordinated multi-pollutant remediation [86,96,141].

2.4.3. Molecular Mechanisms Underlying Efficient Nitrogen and Phosphorus Removal

The ABSS is a sustainable wastewater treatment platform that leverages the complementary metabolic capabilities of microalgae and heterotrophic bacteria. At the molecular level, ABSS integrates metabolic complementarity, gene-mediated catalysis, and microecological regulation to achieve precise, multi-scale transformation and removal of N and P pollutants from aquaculture effluents.

Nitrogen metabolism in ABSS is a tightly regulated process involving gene-driven oxidation, assimilation, and reduction pathways. Under aerobic conditions, ammonia monooxygenase (amoA) and hydroxylamine oxidoreductase mediate the stepwise oxidation of NH₄⁺ to NO₂⁻, while comammox bacteria such as Nitrospira sp. complete the entire nitrification process by encoding both amoA and NxrAB, directly converting NH₄⁺ to NO₃⁻ within a single organism, enhancing efficiency and continuity [142]. Nitrogen assimilation adapts to ammonium levels: the Glutamine Synthetase-Glutamate Synthase (GS-GOGAT) pathway dominates under low NH₄⁺, while the Glutamate Dehydrogenase (GDH) pathway is induced under high NH₄⁺, ensuring metabolic flexibility [143]. In anoxic microenvironments, denitrifiers express narG, nirS, norB, and nosZ sequentially to reduce NO₃⁻ to N₂, with community coordination and environmental cues such as nutrient load and redox potential minimizing intermediate accumulation and preventing secondary pollution [144,145].

Phosphorus removal is governed by gene-regulated transport and physicochemical stabilization. PO₄³⁻ is taken up via phosphate-specific transporters (PPTs), including the high-affinity PhoP-regulated PstSCAB system and the low-affinity PitH transporter. Intracellularly, phosphate is polymerized by polyphosphate kinases into polyphosphates, serving as precursors for ATP and membrane phospholipids [146,147]. Extracellularly, PO₄³⁻ is immobilized through non-covalent binding with secreted polysaccharides or precipitated via complexation with Fe³⁺, Ca²⁺, and other metal ions [148]. In aquaculture wastewater, organic phosphorus is first hydrolyzed by bacterial phosphatases and nucleotidases into PO₄³⁻ for assimilation [146], while a portion is retained via interactions with hydroxyl and carboxyl groups in exopolysaccharides (EPS) produced by algal–bacterial consortia. Polysaccharides such as polygalacturonic acid enhance this retention by reinforcing EPS–phosphorus binding [147,148,149]. Central to this process are polyphosphate-accumulating organisms (e.g., Accumulibacter sp.), which achieve efficient phosphorus uptake under alternating anaerobic–aerobic conditions, modulated by operational strategies [147,150].

The ABSS establishes a dynamic microecological interface via metabolic synergy, enabling efficient pollutant removal and system stability. Algal photosynthesis elevates pH by shifting the CO₂–HCO₃⁻–CO₃²⁻ balance [151], promoting HN-AD for nitrogen removal and facilitating phosphate precipitation as Ca₃(PO₄)₂ and Ca₅(PO₄)₃OH. Combined with phosphorus assimilation by polyphosphate-accumulating algae such as Craticula molestiformis and Chlamydomonas pulvinata [152], this forms a dual phosphorus recovery pathway. Alkalinity buffering is essential to prevent carbon limitation and suppress N₂O emissions [126,153]. Diurnal variations in algal photosynthesis drive DO and Oxidation-Reduction Potential (ORP) fluctuations, which regulate microbial gene expression and alternate nitrification and denitrification [151]. In Microalgal-Bacterial Sequencing Batch Reactors (MB-SBRs), this synchronization achieves up to 68% nitrogen removal, while ORP-guided aeration reduces energy use by 30% [153,154]. Algal EPS supports bacterial growth [154], and niche competition by phosphorus-rich algae enhances phosphate uptake [152]. Thus, the ABSS achieve coordinated pollutant removal and resource recovery by coupling carbon, oxygen, nitrogen, and phosphorus cycling, where algae regulate pH and DO, bacteria respond to environmental signals, and microbial substrates and community structure adaptively stabilize the microenvironment (Figure 2).

3. Application of Algal–Bacterial Immobilization Technology

3.1. Principles of Immobilization Technology

Immobilization technology is a biological treatment technique that confines free microbial cells within a defined space or onto the surface of a carrier through physical, chemical, or biological means, allowing them to retain high activity, stability, and repeated functionality. Its core principle involves the use of natural polymers such as sodium alginate and agar, or synthetic polymers including polyvinyl alcohol and polyacrylamide, as carriers. Immobilization is achieved through adsorption, whereby microorganisms adhere to carrier surfaces via electrostatic interactions and van der Waals forces; covalent binding, in which chemical reagents facilitate the formation of stable covalent linkages between microbial cells and the carrier; entrapment, where cells are enclosed within porous matrices that permit the diffusion of substrates and metabolic products while preventing microbial loss; or encapsulation, which involves the formation of microcapsules enveloped by semi-permeable membranes to enhance protection. These approaches construct a microenvironment conducive to microbial metabolism [155]. This spatial confinement improves microbial resistance to environmental stressors, including toxic heavy metals and temperature fluctuations [156], while also enhancing biocatalytic efficiency by reducing the physical distance between microorganisms and substrates and accelerating the exchange of metabolites. In wastewater treatment applications, immobilization can elevate nutrient removal efficiencies to above 60% and is particularly effective in targeting refractory organic compounds, heavy metals, nitrogen, and phosphorus, with previous work highlighting the beneficial role of sodium alginate in enhancing microbial interactions and treatment performance [155,157].

When applied in conjunction with ABSS, the advantages of immobilization technology are further amplified. Co-immobilization of bacteria and microalgae on a common carrier such as composite gel beads enables the formation of a tightly integrated metabolic network. Microalgae release oxygen via photosynthesis to support aerobic bacterial processes such as nitrification, while bacteria respire and generate carbon dioxide to sustain algal photosynthesis, concurrently degrading organic pollutants and supplying nutrients that promote algal growth [95,158]. The spatial organization enforced by the immobilization matrix enhances material exchange and molecular signaling between bacteria and algae, including the transfer of quorum-sensing signals, promotes niche complementarity, mitigates biomass loss and separation challenges inherent to free-living microbial systems, and increases nitrogen and phosphorus removal as well as overall pollutant degradation by facilitating more efficient electron transfer [158]. In practical applications such as aquaculture wastewater treatment, immobilized algal–bacterial systems have achieved ammonium nitrogen removal rates exceeding 93%, while simultaneously reducing pathogenic microbial populations and antibiotic resistance genes [159]. Thus, the immobilization strategy in ABSS provides a dual advantage by enabling high-efficiency purification while ensuring ecological safety.

3.2. Carrier Types and Approaches for Algal-Bacterial Immobilization Technologies

3.2.1. Inorganic Carrier

Inorganic carrier materials are integral to ABSS, offering attachment sites, enhancing mass transfer, and improving hydraulic performance and stability. Their high surface area and pore density support microbial colonization, promote stable biofilm formation, and minimize biomass loss, forming the microscopic basis of their attachment function [138]. Natural minerals such as zeolite and diatomite are widely employed in practice due to their low cost and excellent mechanical properties. Zeolites, characterized by regular pore structures and ion exchange capabilities, provide stable anchoring sites for algae and bacteria through ionic interactions. Their capacity to adsorb nitrogen and phosphorus complements microbial metabolism, achieving up to 75% total nitrogen removal and promoting metabolic synergy when combined with marine algae [160,161]. Diatomite, with its high porosity and surface area, promotes micro-particle formation and enhances microbial attachment, facilitating material exchange and metabolism among microbes such as denitrifying polyphosphate-accumulating organisms, and supports phosphate removal efficiencies reaching 80% [96,162]. Other carriers, including activated carbon, quartz sand, and vermiculite, function through mechanisms such as high adsorption capacity, chemical stability, and ion exchange ability. Among them, activated carbon not only provides extensive adsorption surfaces for micropollutants and organic matter but also improves sludge floc structure, enhances settling performance, and promotes biodegradation efficiency [163]. These carriers enrich pollutants, optimize hydraulic conditions, and modulate microenvironments, respectively. All operate in accordance with the natural interaction mechanisms between microbes and minerals [138], collectively enhancing microbial attachment, interspecies exchange, and system stability, and thereby improving the overall performance of algal-bacterial symbioses in wastewater treatment and environmental remediation.

3.2.2. Organic Carriers

Organic carriers exhibit excellent biocompatibility and have shown considerable promise in immobilizing microorganisms such as algae and bacteria. By reducing biomass loss and providing a favorable microenvironment for microbial metabolism, they effectively address the limitations of free-living microorganisms in environmental remediation, particularly low stability and efficiency [164]. Among these, natural polymers such as sodium alginate (SA) and chitosan are especially prominent due to their abundance and environmental friendliness.

SA, a widely used natural carrier, offers excellent biocompatibility, hydrophilicity, and reversible swelling [165]. Its carboxyl groups crosslink with multivalent cations (e.g., Ca²⁺) to form porous hydrogel beads, which support microbial attachment and growth while enabling efficient diffusion of nutrients and metabolites. This structure ensures both system stability and mass transfer. Performance can be enhanced by algal strain selection; for example, Scenedesmus abundans, with high phosphate uptake, reduces phosphate-induced degradation of the calcium–alginate matrix, extending carrier durability and enabling stable operation for up to 42 days [166]. Incorporating inorganic materials or functional polymers, such as peptide-modified matrices [167], further improves alginate’s adsorption capacity and structural integrity. Chitosan, another natural polymer, combines biocompatibility, biodegradability, and film-forming ability. Its amino groups electrostatically bind to negatively charged microbial surfaces, enhancing immobilization. To address individual material limitations, chitosan is often combined with alginate to form hybrid carriers, improving mechanical strength and acid resistance [168]. These composites perform well in pollutant removal, with Pb²⁺ adsorption up to 180 mg/g. In marine aquaculture wastewater, chitosan-based aerogels co-immobilized with degrading bacteria and Caulerpa lentillifera achieved COD and TN removal rates of 68.61% and 59.03%, respectively [169].

In addition to natural polymers, synthetic materials such as polyvinyl alcohol (PVA) and polyacrylamide (PAM) have been widely used for microbial immobilization. More recently, macroporous cryogels have emerged as promising alternatives [164]. Produced via cryogelation under sub-zero conditions, these materials possess high porosity, elasticity, and mechanical strength. Their structure minimizes microbial detachment and promotes mass transfer, enhancing both microbial activity and pollutant removal. While PVA gels form stable networks via freeze–thaw cycles, their biocompatibility is relatively limited and often requires surface modification to improve microbial affinity. In contrast, cryogels allow for structural design that balances mechanical performance with biological compatibility.

3.3. Immobilized ABSS: Advances and Justifications

Immobilization has emerged as a pivotal strategy to overcome the inherent limitations of free-living algae–bacteria consortia in aquaculture wastewater treatment. Free-living cultures, whether algae-only, bacteria-only, or co-cultivated, often suffer from biomass washout, fluctuating nutrient removal efficiencies, and sensitivity to environmental perturbations such as diurnal pH shifts and seasonal temperature variations [44,86]. In contrast, immobilized systems, where cells are entrapped or attached to carriers such as alginate, zeolite, or activated carbon, demonstrate enhanced biomass retention, higher and more stable removal efficiencies, and the capacity for repeated reuse [155,158,160,166].

Quantitative comparisons across system types highlight these advantages (

Table 3. Comparative Performance of Algae-only, Bacteria-only, Free-living ABSS, and Immobilized ABSS in Aquaculture Effluent Treatment.

Feature	Algae-Only	Bacteria-Only	Free-Living ABSS	Immobilized ABSS	Advantages/Disadvantages	References
Nutrient Removal Efficiency	NH4+-N: 30–70%; TP: 20–50%	NH4+-N: 60–85%; COD: 50–90%	NH4+-N: 70–90%; TP: 60–80%	NH4+-N: 85–95%; TP: 75–90%	Immobilized systems achieve higher and more stable removal; algae-only limited by light; bacteria-only poor in P removal	[44,100,101,102,104,109,111,155,158,159]
Kinetic Parameters	Vmax: low (0.2–0.5 mg N/L·h); t1/2: >48 h	Vmax: 0.6–1.0 mg N/L·h; t1/2: 24–36 h	Vmax: 0.8–1.2 mg N/L·h; t1/2: 20–30 h	Vmax: 1.2–1.8 mg N/L·h; t1/2: 12–24 h	Immobilization improves volumetric rates and shortens half-life	[101,158,159]
Biomass Retention	Low (washout prone)	Low–moderate	Moderate, but unstable	High; cells firmly attached	Immobilization ensures stable biomass over long operation	[155,156,157,158,160,168]
Reusability/Operational Lifetime	Limited, mostly batch	Limited	Moderate, prone to collapse	High; reusable carriers, >10 cycles reported	Improves process economics	[158,159,160,162]
Environmental Stability	Sensitive to pH/light/temp	Sensitive to organic shock loads	Moderate	High tolerance to fluctuations	Key advantage for aquaculture effluents	[155,156,157,158,160]
Operational Complexity & Cost	Low-cost, simple	Low-cost	Moderate	Higher setup cost, carrier preparation required	Trade-off: stability vs. cost	[155,156,157,158,160]
Limitations	Light dependency, limited P uptake	Insufficient P removal, poor resilience	Biomass washout, unstable long-term	Mass transfer limits, carrier fouling, higher capital cost	Choice depends on effluent type & scale	[155,156,157,158,160]

). Algae-only systems typically achieve moderate nutrient removal (NH₄⁺-N: 30–70%; TP: 20–50%) but are constrained by light dependence and low resilience under nutrient-rich conditions. Bacteria-only systems excel in rapid ammonium and COD removal (NH₄⁺-N: 60–85%; COD: 50–90%), yet often fail to meet phosphorus discharge standards. Free-living ABSS achieve synergistic removal of N and P (NH₄⁺-N: 70–90%; TP: 60–80%) but remain limited by biomass washout and operational instability. Immobilized ABSS, by contrast, consistently report NH₄⁺-N removal >90% and TP removal >80%, alongside improved kinetic parameters such as higher volumetric reaction rates (Vmax 1.2–1.8× higher than free-living systems) and reduced half-lives for nutrient depletion (t₁/₂ shortened by 20–40%) [100,101,158,159].

Beyond performance, immobilization also addresses operational and economic concerns. The reusability of carriers over multiple treatment cycles reduces biomass loss and lowers operational costs. Immobilized systems are also more robust to salinity, temperature, and pH fluctuations, making them particularly suited for aquaculture effluents, which are characterized by nutrient heterogeneity and environmental variability [102,160]. Finally, immobilized biomass can be valorized into aquafeeds, fertilizers, and bioenergy products, providing additional economic incentives and aligning with circular economy policies [170,171,172,173,174].

Immobilization is not merely a technical refinement but a necessary step for advancing ABSS from laboratory trials to field-scale applications. Despite the growing interest in algae–bacteria consortia, field-scale applications for aquaculture effluents remain scarce, largely constrained by scale-up challenges and environmental variability. Nevertheless, several pilot- and semi-pilot trials provide important evidence of feasibility. For instance, Peng et al. (2020) demonstrated the operation of a biofilm membrane photobioreactor (BF-MPBR) integrating C. vulgaris for simultaneous nutrient and sulfonamide removal from marine aquaculture wastewater, achieving TN removal above 90% and antibiotic removal around 70–85% [100]. Mubashar et al. (2022) tested a floating permeable nutrient uptake system (FPNUS) under mixotrophic algal cultivation, reporting efficient nitrogen removal (75–85%) under outdoor aquaculture pond conditions [102]. More recently, Sun et al. (2025) employed immobilized algal–bacterial systems with alginate-based carriers to specifically target Vibrio pathogens and antibiotic resistance genes in aquaculture wastewater, achieving >90% ammonium removal alongside significant reductions in microbial risks [159]. These examples, while limited, demonstrate the translational potential of immobilized ABSS in real or semi-real aquaculture environments. They also highlight the added value of immobilization strategies in enhancing biomass stability, facilitating pathogen control, and enabling system reusability. To consolidate these findings, representative pilot and field-scale case studies have been summarized in

Table 4. Case Studies of Immobilized Algal–Bacterial Consortia in Aquaculture Wastewater.

Algal Partner	Bacterial Partner(s)	Carrier/System Type	Scale	Pollutant Removal Efficiency	Additional Outcomes	References
C. vulgaris	Indigenous bacteria	BF-MPBR	Semi-pilot (outdoor)	TN > 90%; sulfonamides 70–85%	Simultaneous removal of nutrients and antibiotics	[100]
Microalgae (mixed)	Indigenous bacterial community	FPNUS	Pilot (aquaculture pond)	TN 75–85%; TP 60–70%	Operated under outdoor mixotrophic conditions	[102]
C. vulgaris	Mixed bacterial community	Alginate–chitosan beads	Lab/pilot	NH4+-N > 90%; TP 75–85%	Reduction in Vibrio spp. and ARGs	[160]
C. vulgaris	Indigenous bacteria	Alginate beads	Lab (batch)	NH4+-N 85–90%; TP 70–80%	Reusability across ≥ 4 cycles	[156,159]
Scenedesmus sp.	Indigenous bacteria	Alginate beads	Lab (continuous)	TP > 80%	Stable operation for 42 days without carrier degradation	[167]
Mixed algal culture (Chlorella sp., Scenedesmus sp.)	Nitrifiers, denitrifiers	Zeolite granules	Lab	NH4+-N > 90%; TP ~80%	Improved pH buffering; salinity tolerance	[161]
C. vulgaris	Indigenous bacteria	BF-MPBR	Semi-pilot (outdoor)	TN > 90%; sulfonamides 70–85%	Simultaneous removal of nutrients and antibiotics	[100]

, which captures the diversity of algal–bacterial pairings, carrier types, and treatment efficiencies across aquaculture contexts. Such evidence underscores that although large-scale deployments remain rare, the foundation for practical implementation is already emerging.

3.4. ABSS Enhanced by Immobilization: A Promising Strategy for Biomass Resource Valorization

ABSS, particularly co-culture systems of microalgae with fungi or bacteria, exhibit superior potential for biomass resource development compared to monocultures due to their unique ecological synergism [170]. Immobilization technology is a key advancement that enhances the stability and performance of these consortia by overcoming structural instability inherent in traditional co-cultures. By reinforcing the mechanical strength of particles while maintaining a porous, light-permeable microenvironment, immobilized algal-microbial granules sustained over 80% pollutant removal efficiency after nine days of continuous operation, significantly outperforming non-immobilized systems [171]. Furthermore, immobilization promotes the accumulation and stable extraction of high-value bioactive compounds; for example, astaxanthin yields increased by over 20%, ensuring continuous and controllable production [171,172]. This approach not only extends system lifespan and operational stability but also simplifies biomass harvesting, greatly reducing energy and chemical inputs.

The integration of algal-microbial co-cultivation with immobilization demonstrates remarkable application potential across multiple sectors. In energy, co-cultures significantly enhance lipid content, reaching up to 23% dry weight, providing a stable and efficient feedstock for biodiesel production; algal residues further serve as substrates for anaerobic digestion, increasing methane yields [173,174]. In agriculture, co-culture biomass can be converted into organic fertilizers rich in amino acids and vitamins, boosting crop yields by 15–20% while reducing disease incidence; as feed additives, they markedly improve animal growth and immunity [175,176]. In pharmaceuticals and nutraceuticals, co-cultivation systems efficiently produce natural pigments and polysaccharides with antioxidant and immunomodulatory properties, catering to high-value markets [86,175,177]. Additionally, biomass from co-cultures can be processed into biodegradable bioplastics and functional biochar, effectively supporting pollution remediation and circular economy initiatives [178,179]. In addition to carrier-based immobilization, several studies have reported the development of self-immobilized co-cultures, such as algal–bacterial granular sludge, which naturally aggregate both types of microorganisms without external carriers. These self-immobilized systems exhibit high structural stability and efficient nutrient removal comparable to carrier-based systems, while avoiding the cost and complexity of carrier materials [8,44]. However, challenges remain in controlling granule formation and maintaining long-term stability, which require further investigation [86].

Therefore, the ABSS combined with immobilization successfully achieves the triple goals of environmental remediation, resource recovery, and economic benefits, underscoring its broad application potential and irreplaceable strategic value in circular economy, carbon neutrality, sustainable agriculture, and the food industry (Figure 3).

3.5. Biomass Valorization and Circular Applications

Beyond wastewater remediation, one of the defining advantages of immobilized ABSS lie in the valorization of harvested biomass, which can offset treatment costs and support a circular bioeconomy (

Table 5. Biomass Composition and Valorization Pathways of Immobilized ABSS.

Valorization Pathway	Key Biomass Composition/Yield	Application/Benefit	References
Aquafeed	Protein 45–55% DW; essential amino acids; feed substitution up to 30%	Improves fish growth, immunity, and feed conversion ratios	[176]
Biofertilizer	N, P-rich biomass; residual organic matter	Enhances soil fertility, nutrient recycling, reduces chemical fertilizer demand	[170]
Biofuels	Lipid 20–40% DW (biodiesel); residual biomass for methane	Renewable energy generation, integration with circular aquaculture systems	[170,178]
Bioplastics	Polyhydroxyalkanoates (PHAs) and carbohydrate-rich fractions	Pilot-scale biopolymer production; biodegradable alternatives to plastics	[179]
Pigments & High-Value Products	Astaxanthin (>20% higher under immobilization), phycocyanin	High-value nutraceuticals, natural pigments, antioxidant supplements	[172,177]

). In the aquaculture sector, microalgal biomass such as Spirulina sp. and Chlorella sp. has long been recognized as a high-protein feed supplement. Recent feeding trials show that substitution of up to 30% of conventional feed with Spirulina platensis significantly improved growth, hematological indices, and immune parameters in Nile tilapia [176]. Protein levels in algal biomass typically reach 45–55% of dry weight (DW), while lipid fractions range between 20% and 40% DW, making them suitable as both nutritional supplements and energy feedstocks [170].

As biofertilizers, co-culture biomass provides nitrogen- and phosphorus-rich organic amendments that enhance soil fertility and crop yields while recycling nutrients recovered from aquaculture tailwater. This dual role of waste remediation and fertilizer production strengthens the economic viability of ABSS by reducing external input costs. In the bioenergy domain, immobilized algal biomass enriched in lipids can serve as feedstock for biodiesel, while residual fractions can be digested anaerobically to produce methane [170]. Emerging work has also highlighted the potential of microalgal bioplastics, with conversion efficiencies sufficient to support pilot-scale production of biodegradable polymers [178,179].

High-value bioproducts provide an additional dimension of economic return. For instance, immobilization has been shown to enhance the accumulation of astaxanthin in Haematococcus pluvialis by >20% compared to free cultures [172], while Spirulina-derived phycocyanin is already commercialized as a natural pigment with antioxidant and nutraceutical benefits [177]. These products command significantly higher market values than conventional biofuels, offering a pathway to economic sustainability. It should be emphasized that the bioproducts discussed here are derived from controlled cultivation systems rather than directly from wastewater or effluent treatment processes. Consequently, applications for human consumption are limited to biomass produced under controlled, safe cultivation conditions, avoiding potential safety and public perception concerns [180]. Thus, biomass valorization through feed, fertilizer, biofuels, bioplastics, and pigments transforms immobilized ABSS from cost centers into value-generating biorefineries, directly addressing both techno-economic feasibility and environmental sustainability.

4. Key Findings and Critical Discussion

4.1. Aquaculture Effluents: Distinct Composition and Ecological Implications

In general, aquaculture effluents are characterized by moderate-to-high nitrogen (NH₄⁺-N: 2–15 mg L⁻¹; TN: 10–60 mg L⁻¹) and phosphorus concentrations (TP: 2–15 mg L⁻¹), but relatively low organic carbon compared to municipal wastewater where COD often exceeds 200–500 mg L⁻¹ [44,47,86]. This imbalance in the C: N: P ratio makes conventional heterotrophic treatments less effective. In contrast, industrial effluents (e.g., food processing) often have much higher COD and organic loads but lower N:P ratios, highlighting the uniqueness of aquaculture wastewater composition.

Across countries, nutrient profiles vary with farming intensity and culture type. Semi-intensive freshwater ponds in Asia and Africa typically generate effluents with TN 20–40 mg L⁻¹ and TP 2–6 mg L⁻¹, while intensive marine shrimp systems in Latin America and Southeast Asia can reach TN 50–80 mg L⁻¹ and TP 10–15 mg L⁻¹ [47,90,94]. Cage aquaculture in Europe often releases lower concentrations (TN < 20 mg L⁻¹, TP < 3 mg L⁻¹) but over larger volumes, contributing to diffuse eutrophication. Nutrient heterogeneity is further influenced by production practices. For instance, protein-rich formulated feeds increase ammonium and phosphate loads, whereas integrated multi-trophic aquaculture and biofloc systems tend to reduce soluble nutrients while increasing particulate organic matter [45,94]. Management factors such as water exchange rate, aeration, and feed conversion ratio also affect effluent composition. Consequently, aquaculture effluents display higher variability than municipal wastewater, which is relatively stable across countries. This heterogeneity underscores the need for flexible treatment strategies such as immobilized ABSS, which can adapt to variable nutrient regimes while maintaining stable performance.

4.2. Principles for Designing Effective ABSS

Designing robust ABSS is central to their translation from laboratory studies to field applications. Species selection is the first principle: microalgae such as C. vulgaris, Scenedesmus spp., and Tribonema sp. provide high nutrient uptake and tolerance to salinity and pH fluctuations, while bacterial partners include nitrifiers (Nitrosomonas, Nitrobacter), heterotrophic nitrifier–aerobic denitrifiers (e.g., Pseudomonas spp.), and phosphorus-accumulating organisms (PAOs). Tailored pairings enable high rates of ammonium, nitrate, and phosphate removal; for example, a Tribonema–PAO consortium removed 76.9% NH₄⁺-N and 95.8% NO₃⁻-N within 36 h [103].

Functional complementarity underpins the ecological synergy: algae release oxygen and exudates such as carbohydrates, amino acids, and vitamins that support bacterial growth [90,101], while bacteria mineralize organics, regenerate CO₂, and produce metabolites that enhance algal growth and detoxify contaminants [106,107,133]. Optimizing inoculation ratios is equally critical. Ji et al. reported that a C. vulgaris–B. licheniformis ratio of 1:3 achieved 86.6% COD, 80.3% TDP, and 88.9% TDN removal [109], while Liu et al. found that a 2:3 ratio optimized TN (81.4%) and TP (96.6%) removal [111]. Ratios between 1:3 and 2:3 consistently outperform monocultures [92,111]. Environmental compatibility is decisive: Scenedesmus sp. withstands wide pH fluctuations, Chlorella sp. adapts to brackish water [102,122,123], nitrifiers remain active at low temperatures [88,89], and aerobic denitrifiers perform under nutrient fluctuations [105]. Engineering constraints such as growth rate mismatch, nutrient competition, and hydrodynamic stress must also be considered, as they can destabilize community dynamics [93,125,126].

4.3. Why Immobilization? Mechanistic and Kinetic Advantages

Free-living ABSS can achieve high nutrient removal, but their application is constrained by biomass washout, instability, and sensitivity to environmental perturbations. Immobilization mitigates these issues by anchoring algal and bacterial cells onto carriers such as alginate, chitosan, zeolite, or diatomite. Immobilization concentrates cells, reduces intercellular distances, and strengthens metabolic coupling, resulting in higher volumetric reaction rates and shorter pollutant half-lives. For example, immobilized consortia achieve NH₄⁺ removal Vmax of 0.30–0.45 mg N L⁻¹ h⁻¹ compared to 0.15–0.28 mg N L⁻¹ h⁻¹ in free-living systems [155,158]. Biomass retention is enhanced, and reuse across 5–10 cycles has been reported without major performance decline [159,160]. However, immobilization also introduces mass transfer limitations and carrier degradation risks, requiring careful selection of carrier porosity and durability.

4.4. Techno-Economic and Regulatory Dimensions

From an economic perspective, immobilized ABSS offer potential cost advantages compared with conventional treatment technologies. Reported treatment costs range between 0.3 and 0.8 USD m⁻³ for immobilized systems, depending on carrier type and operational scale [155,158], which is competitive with activated sludge and membrane bioreactors that often exceed 1.0 USD m⁻³ [91]. Importantly, the reusability of immobilized biomass over multiple operational cycles can reduce sludge management and reinoculation costs by 20–40% [159,160].

With respect to discharge parameters, immobilized ABSS consistently achieve nutrient levels below regulatory thresholds in many regions: TN < 10 mg L⁻¹, TP < 1 mg L⁻¹, and NH₄⁺-N often reduced to <2 mg L⁻¹ [47,177]. These performances not only satisfy typical discharge standards in Europe and East Asia, but also provide an additional buffer against seasonal fluctuations that often lead to compliance failure in free-living systems.

Beyond pollution removal, the harvested biomass represents a valuable resource. Immobilized ABSS produce biomass with 20–40% lipids and 40–55% protein (dry weight), which can be processed into aquafeed supplements improving fish growth and immunity [176], biofertilizers that recycle N and P into agriculture, and bioenergy feedstocks for biodiesel and biogas production [170,173,178]. High-value compounds such as astaxanthin and phycocyanin can also be extracted, contributing to nutraceutical and food industries [172,177]. This valorization potential offsets treatment costs and supports integration into a circular bioeconomy. Thus, these techno-economic and application perspectives underscore that immobilized ABSS are not only environmentally effective but also economically viable, particularly in aquaculture where nutrient-rich effluents can be directly converted into value-added biomass streams.

4.5. Critical Insights

Our synthesis of comparative data (Table 1, Table 2, Table 3, Table 4 and Table 5) yields four critical insights. First, ABSS consistently outperform algae- or bacteria-only systems, with immobilized consortia showing superior nutrient removal (70–95% for nitrogen, 60–90% for phosphorus), faster kinetics, and greater stability. Second, immobilization enhances reusability, allowing multiple treatment cycles with reduced reinoculation and sludge handling. Third, valorization of biomass improves the techno-economic case by generating co-products that offset treatment costs. Fourth, aquaculture effluents represent a high-priority application domain due to their nutrient-rich but carbon-poor profile, strong regulatory drivers, and potential for on-site biomass reuse.

5. Overcoming Limitations and Future Directions

Immobilized ABSS have demonstrated superior nutrient removal, biomass retention, and reusability compared to free-living systems. However, their deployment beyond laboratory settings is constrained by several critical challenges that must be addressed for practical aquaculture wastewater treatment.

5.1. Scale-Up and Reactor Design

Most laboratory studies rely on alginate beads or simple biofilm carriers, which do not replicate the light and mass transfer dynamics of ponds or raceways. At larger scales, uneven illumination and hydrodynamics reduce performance by up to 30–40% in tubular photobioreactors [181,182]. Hydraulic shocks can further detach immobilized cells, decreasing stability [183]. Recent innovations, including modular photobioreactors and fluidized-bed carriers, enhance mixing and nutrient accessibility while reducing washout [155,162]. 3D-printed porous carriers offer tunable geometries that increase surface area-to-volume ratios and cell density. Hybrid systems that combine immobilized biomass for stability with free-living populations for flexibility have also demonstrated robust outcomes under variable loading [44,92].

5.2. Environmental Fluctuations

Aquaculture effluents are subject to diurnal and seasonal changes in light, temperature, and pH. Free-living systems often collapse under such stresses, while immobilization buffers against short-term perturbations. This buffering can be enhanced through biochar- and zeolite-based carriers, which stabilize pH and adsorb excess ammonium [124,160]. Nonetheless, immobilized consortia remain vulnerable to extreme conditions: nitrification efficiency declines by up to 82% at 10 °C [184], and heat stress reduces algal viability by 35–40% [185]. AI-assisted control of aeration, light, and carbon dosing has been proposed to balance photosynthetic and bacterial processes in real time [93,134], while rotational deployment of carrier modules across seasons can mitigate performance variability [118,120].

5.3. Carrier Durability and Fouling

Natural polymers such as alginate exhibit excellent biocompatibility but degrade within 40–60 days in high-ionic-strength environments, causing biomass leakage [158,186]. Synthetic carriers, such as latex-based polymers, provide structural durability but restrict gas permeability and light penetration, impairing algal–bacterial interactions [186,187]. Composite carriers (alginate–chitosan blends, PVA cryogels, organic–inorganic hybrids) improve mechanical strength and resist fouling [166,168]. Inorganic carriers such as diatomite, zeolite, and activated carbon offer longer lifespans and recyclability [160,162,166], and environmental safety. Future efforts should focus on biodegradable yet robust composite carriers [179,186].

5.4. Mass Transfer Limitations and Metabolic Imbalance

Within thick or densely packed carriers, nutrient and gas diffusion is restricted, leading to concentration gradients. Oxygen generated by algae may fail to reach inner bacterial zones, impairing nitrification, while CO₂ produced by bacteria may not reach algal cells efficiently [186,188]. Such imbalances create inactive core zones in columnar reactors, lowering overall treatment efficiency [187]. Impaired metabolite exchange has been linked to nitrogen removal efficiency losses of 20–50% [133,183]. Engineering carrier porosity and incorporating responsive materials are emerging strategies to alleviate these bottlenecks [186,188].

5.5. Biomass Recovery and Risk of Secondary Pollution

Downstream processing of immobilized systems remains difficult. Strong adhesion between biomass and carriers complicates harvesting, sometimes requiring harsh chemical treatments that degrade lipids and proteins [189]. Disposal of non-biodegradable carriers, such as latex-derived polymers, contributes to microplastic pollution and secondary contamination [186]. Furthermore, carriers can adsorb heavy metals, creating persistent pollutant complexes with long-term ecological risks [179]. Developing recyclable and biodegradable carriers, coupled with integrated biomass recovery technologies, will be essential for sustainable deployment.

5.6. Economic and Policy Considerations

Immobilized systems entail higher capital and operational expenditures than free-living cultures, primarily due to carrier production and replacement. However, valorization of biomass into aquafeeds, fertilizers, pigments, bioplastics, and biofuels offer substantial cost recovery [170,171,172,173,174,177,178,179]. Life-cycle assessments suggest that when reuse and valorization are factored in, immobilized ABSS can be economically viable for intensive aquaculture [157,158]. Integration with carbon credits, nutrient trading, and circular economy incentives may further improve competitiveness [48,141]. However, policy frameworks currently emphasize discharge compliance without promoting resource recovery. Forward-looking governance should include certification schemes for algal biomass-derived products, subsidies for bio-based carriers, and harmonized nutrient recovery standards to enable international adoption [141,177].

5.7. Integrated Future Directions

Immobilization is thus more than a laboratory method: it is a strategic enabler for scaling ABSS. To overcome limitations, future research (Figure 4) should focus on (i) modular reactor designs and scalable architectures to ensure effective light and nutrient delivery [181,182,183]; (ii) next-generation composite carriers with high porosity, durability, and biodegradability [167,169,186]; (iii) systems biology and machine learning to decode and regulate algal–bacterial interactions [93,134]; (iv) techno-economic and life-cycle assessments to validate viability under operational conditions [157,158]; and (v) policy frameworks that incentivize nutrient recovery and biomass valorization [141,177,186]. Through coordinated advances in engineering, biology, materials science, and governance, immobilized ABSS can transition from experimental prototypes to robust technologies for sustainable aquaculture effluent management.

6. Conclusions

Aquaculture effluents are characterized by nutrient-rich yet carbon-poor and highly variable compositions, which limit the effectiveness of conventional treatment strategies. ABSS directly address these imbalances through synergistic exchanges, with algae providing oxygenation and nutrient uptake while bacteria drive mineralization, detoxification, and carbon recycling. Immobilization enhances these interactions by improving biomass retention, accelerating nutrient turnover, and enabling repeated use, resulting in consistently higher efficiencies than free-living cultures.

Our synthesis highlights that immobilized ABSS achieve 70–95% nitrogen and 60–90% phosphorus removal, faster kinetics, and enhanced resilience, while also generating valorized products such as feed, fertilizer, pigments, and bioenergy. These advantages make immobilized systems not only technically effective but also economically and environmentally competitive when carrier reuse and resource recovery are realized.

Nonetheless, challenges remain. Carrier degradation, biofouling, scale-up constraints, and environmental fluctuations continue to limit widespread application. Addressing these limitations will require composite and 3D-printed carriers with tailored porosity, modular photobioreactor designs, adaptive operational control, and systems biology-guided consortium engineering. Equally important, techno-economic validation and supportive policy frameworks are needed to enable large-scale deployment.

Taken together, immobilized ABSS represent a transformative opportunity for aquaculture wastewater treatment, turning effluents from an ecological burden into a renewable resource within a circular bioeconomy. Looking forward, the integration of immobilized ABSS into aquaculture aligns with global efforts to safeguard food security, reduce nutrient pollution, and advance carbon neutrality, positioning this technology as a cornerstone for sustainable water–energy–food systems.