Ensuring high production and quality in aquaculture requires effective water quality management. Degraded water quality negatively affects fish growth and disease resistance (Sallenave, 2019; Deswati et al., 2022). Suboptimal water quality parameters can lead to physiological stress, and retarded growth, as well as disease susceptibility leading to a massive production loss (MacIntyre et al., 2008). Aquaculture wastewater contains various pollutants, including solid waste (e.g. faeces and uneaten feed) and excess nutrients (e.g. nitrogen and phosphorus), which, if not probably managed, can cause production loss. These pollutants originate from overfeeding, faeces, and metabolic waste including ammonia molecules (Maillard et al., 2005; Sharrer et al., 2007). Improper water management may result in oxygen deprivation, eutrophication, and proliferation of harmful microorganisms, alongside nitrite and ammonia toxicities (Hoang et al., 2020; Cao et al., 2016; Wu et al., 2020; Yang et al., 2015; Gobler et al., 2012; Sin and Lee, 2020; Liu et al., 2020). To ensure a sustainable growth for the aquaculture industry, efficient water management strategies are essential (Lin et al., 2010). Several conventional water quality control means including water exchange, aeration, filtration, and chemical treatments, have been employed. However, these approaches often come with high costs and environmental drawback (Posadas and LaSalle, 1997; Tom et al., 2021).
Bioremediation methods have recently gained popularity for the treatment of wastewater, due to their efficiency and environmentally benefits. Naturally abundant and cost effective bioremediation methods are sustainable applications beneficial for the aquaculture sustainability (Rangabhashiyam and Balasubramanian, 2019; Shahid et al., 2020). This review provides an overview of the latest technological advancement in sustainable aquaculture wastewater treatment such as bacteria, microalge, bacteria-algae symbiosis based methods, including wetlands, ecological floating beds, recirculating aquaculture system (RAS), biofloc system, aquaponics system, and integrated multitrophic aquaculture (IMTA); also this review reveals possible integrations among those production systems.
Bacteria are the dominant microorganisms in aquatic ecosystems representing more than 90% of the microbial population (Hahn, 2006). In water body, the predominant types of bacteria includes Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes phyla, while the sediment includes Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes phyla (Zhang et al., 2016) (Table 1).
The predominant bacteria in different aquaculture waters
| Bacteria population | Water type | References |
|---|---|---|
| Proteobacteria, Bacteroidetes and Verrucomicrobia | Marine water, cucumber (Apostichopus japonicas) | Zhou et al., 2022 |
| Proteobacteria, Cyanobacteria, Actinomycetes and Bacteroides | Water and sediment of fish ponds | Liu et al., 2020 |
| Proteobacteria, Fusobacteriota, Actinobacteriotam Myxococcota, Desulfobacterota and Proteobacteria | Water and sediment of striped catfish (Pangasianodon hypophthalmus) ponds | Truong et al., 2022 |
| Proteobacteria and Bacteroidetes | Fresh water farm | Clols-Fuentes et al., 2024 |
| ß-Proteobacteria, α-Proteobacteria, and Actinobacteria | Saline-alkali water carp culture | Huang et al., 2014 |
| Bacteroidetes | Fresh water shrimp pond | Tang et al., 2015 |
| Bacteroidetes, α-Proteobacteria, and γ-Proteobacteria | Circulating culture system of flounder | Matos et al., 2011 |
| Proteobacteria, Bacteroidetes, and Actinobacteria | Grass carp (Ctenopharyngodon idellus) farming ponds | Zhang et al., 2016; Zhou et al., 2013 |
Main bacteria in nitrification and denitrification process in aquatic water
| No. | Process | Organism involved | References |
|---|---|---|---|
| 1. Nitrification | 1.1. Bacterial autotrophic ammonia oxidation | Nitrosomonas europaea, N. eutropha, Nitrosospira multiformis, Nitrosococcus oceanus, N. halophilus, Nitrosolobus sp., Nitrosovibrio sp. | Yin et al., 2018; Preena et al., 2021 |
| 1.2. Bacterial heterotrophic ammonia oxidation | Alcaligenes faecalis, Pseudomonas putida, Paracoccus denitrificans, Thermus, Azoarcus, Bacillus licheniformis | Yusoff et al., 2011 | |
| 1.3. Archaeal ammonia oxidation | Nitrosopumilus maritimus, N. adriaticus, N. piranensis, N. koreensis, Nitrosotalea devanterra | Yin et al., 2018 | |
| 1.4. Nitrite oxidation | Nitrobacter winogradskyi, Nitrospira, Nitrococcus mobilus, Nitrospina gracilis | Su et al., 2023 | |
| 1.5. Complete ammonia oxidation to nitrate (Comammox) | Nitrospira sp. | ||
| 1.6. Anaerobic ammonia oxidation (Anammox) | Planctomyces, Gemmata, Isosphaera, Candidatus brocadia, Candidatus kuenenia, and Candidatus anammoxoglobus | Strous et al., 2006 | |
| 2. Denitrification | 2.1.1. Nitrite reduction | Alcaligenes faecalis, Paracoccus denitrificans, sp. halodenitrificans, Pseudomonas aeruginosa, sp. stutzeri, Thiobacillus denitrifcans, Azospirillum brasilense | Schreier et al., 2010; Song et al., 2011 |
| 2.1. Bacterial heterotrophic denitrification | |||
| 2.1.2. Nitric oxide reduction | Alcaligenes faecalis, Pseudomonas stutzeri, Paracoccus halodenitrificans and Paracoccus denitrificans | Schreier et al., 2010; Song et al., 2011 | |
| 2.1.3. Nitrous oxide reduction | Alcaligenes sp., Azospirillum sp., Bacillus sp., Pseudomonas sp., Thiobacillus versutus, Thiosphaera pantotropha | Low et al., 2012; Preena et al., 2021 | |
| 2.2 Bacterial autotrophic denitrification | – | Rhodobacter sp., Thiomicrospira sp., Hydrogenophaga sp., Thiothrix sp., Thiobacillus denitrificans and Sulfurimonas denitrificans | Chen et al., 2018; Shao et al., 2010; Preena et al., 2021 |
| 3. Fungal denitrification | – | Aspergillus niger | Sankaran et al., 2010; Preena et al., 2021 |
| 4. Archaeal denitrification | – | Halobacterium denitrificans, Pyrobaculum aerophilum and Haloferax denitrificans | Li et al., 2018; Preena et al., 2021 |
| 5. Dissimilatory nitrate reduction to ammonia | – | Firmicutes and Proteobacteria | Wang et al., 2024; Preena et al., 2021 |
Bacterial functions on water quality and host health represent major elements in aquaculture systems (Hahn, 2006). The main challenges against aquaculture sustainability are nitrogen, phosphorus levels, and disease outbreak (Wang et al., 2018). Nitrogenous compounds mainly originate from aquatic organism metabolism and releases to water through gills or faeces, in addition to the bacterial action on uneaten feed in aquaculture system (Crab et al., 2007). According to carbon: nitrogen ratio there are two major groups of bacteria in aquatic water: the first is autotrophic bacteria, while the second is heterotrophic bacteria. Autotrophic bacteria are dominant with a low C/N ratio, while heterotrophic bacteria are dominant with a high C/N ratio (Liu et al., 2021; Zhu et al., 2018). Autotrophic bacteria oxidize ammonia molecules to nitrite by ammonia oxidizing bacteria, and the nitrite could be oxidized to nitrate by nitrite oxidizing bacteria or nitrite oxidizing archaea (Wang et al., 2018). This nitrate could turn to a nitrogen gas by denitrifying bacteria. Heterotrophic bacteria could directly metabolize the ammonia molecules as nitrogen source in presence of organic carbon source and produce bacterial proteins in form of flocs (El-Husseiny et al., 2018).
Nitrifying and denitrifying bacteria have an effective role in nitrogen transformation in aquatic water through nitrification and denitrification process (Xia et al., 2019). In nitrification process bacteria convert ammonia to nitrite then nitrate, while denitrification process transforms the nitrate form to nitrite then gaseous nitrogen, subsequently the nitrogen stock is reduced in fish ponds. The processes of nitrification and denitrification, which are predominant in various aquaculture systems, will be discussed in this review’s subsequent sections. Several studies have been reported on validation of nitrifying and denitrifying bacteria in ammonia and nitrite removal from aquatic water (Liu et al., 2019; Jia et al., 2021). According to Preena et al. (2021) there are many species of microorganisms contributing to nitrification and denitrification process in aquaculture (Table 2).
Bacillus species are another type of bacteria that play an effective role in treating nitrogenous and phosphorus compounds, also maintaining the microbial balance in aquaculture (Soltani et al., 2019). Same authors reported that Bacillus are mostly used in removing the organic matter load in aquaculture, thereby recycling nutrients in the water column and reducing sludge accumulation.
In catfish ponds using Bacillus velezensis AP193 reduced phosphate ions to an acceptable level (Thurlow et al., 2019). Using of aerobic denitrifier bacteria Bacillus megaterium S379 achieved high removal rate of nitrite in intensive aquaculture ponds (Gao et al., 2018). Both Bacillus cereus PB8 and Bacillus amyloliquefaciens DT eliminated NO2-N from wastewater, respectively, according to Hui et al. (2019) and Barman et al. (2018). According to Koops and Pommerening-Roser (2001), Bacillus successfully transforms organic matter into CO2 which is then used as a carbon source by β- and γ-proteobacteria, whereas other bacteria mostly convert organic matter into slime or bacterial biomass (Mohapatra et al., 2013; Zorriehzahra et al., 2016). Bacillus probiotic has a positive impact on water quality in aquaculture including decomposition of organic debris, decreased phosphate and nitrogen concentrations, greater dissolved oxygen, management of nitrite, hydrogen sulphide, and ammonia, and decreased disease occurrence (Boyd and Gross, 1998; Cha et al., 2013; Ramzan et al., 2025). Bacillus strains can control the eutrophication phenomena in aquatic water by consuming phosphate in metabolic activity (Rao, 2002). This was observed when concentration of orthophosphate was reduced in water treated by Bacillus probiotic (Sunitha and Padmavathi, 2013).
Specific role of Bacillus bacteria in wastewater treatments
| Bacteria strain | Condition | Specific role of bacteria | Reference |
|---|---|---|---|
| Bacillus megaterium | Water quality for major carps | Modulation of DO | Hura et al., 2018 |
| mixture of Bacillus | Water quality for tilapia | Hainfellner et al., 2018 | |
| mixture of Bacillus | During transport of fish | Gomes et al., 2008; Zink et al., 2011 | |
| mixture of Bacillus | Tilapia ponds | Removal of TDS | Elsabagh et al., 2018 |
| B. megaterium | Fish pond | Hura et al., 2018 | |
| B. cereus PB88 | Shrimp culture | Barman et al., 2018 | |
| B. subtilis HS1 | European seabass larvae culture | Md et al., 2015 | |
| B. megaterium | Carp culture | Modulation of alkalinity and pH | Hura et al., 2018 |
| Bacillus | Tilapia ponds | Elsabagh et al., 2018 | |
| mixture of Bacillus | – | Phosphate reduction | Reddy et al., 2018 |
| mixture of Bacillus | – | Lalloo et al., 2007 | |
| Commercial probiotic | Shrimp ponds | Wang et al., 2005 | |
| B. velezensis | Catfish ponds | Thurlow et al., 2019 |
Bacillus species have an effective role in modulating different water quality parameters such as dissolved oxygen (DO), total dissolved solids (TDS), alkalinity and pH, as summarized in Table 3.
On the other side, using mixture strains of Bacillus increased the efficiency of nutrients removal rate (John et al., 2020). Bacillus subtilis, Bacillus licheniformis, Bacillus coagulans, and Bacillus lateralis are the well-known bacteria that can work in mixture to remove nitrogenous and phosphorus compounds in aquaculture ponds (Elsabagh et al., 2018; Kuebutornye et al., 2019). Using the mixture of Bacillus megaterium and Bacillus subtilis in carp ponds significantly decreased the concentration of NH4+-N, NO2-N, NO3-N and total phosphorus (TP) by 46.3%, 76.3%, 35.6%, and 80.3%, respectively (Li et al., 2021). Aquatic water treated with a mixture of different strains of bacillus has a lower concentration of phosphate ions, for example using a mixture of B. subtilis, Bacillus mojavensis, and B. cereus (Reddy et al., 2018), a mixture of B. subtilis, B. cereus, and B. licheniformis (Lalloo et al., 2010), Bacillus (commercial probiotic) in shrimp ponds (Wang et al., 2005) and B. velezensis in catfish ponds (Thurlow et al., 2019).
Anaerobic ammonium oxidation (anammox) is a sustainable biological treatment for nitrogen removal in the presence of autotrophic bacteria (anammox bacteria), which have the ability to convert ammonium to dinitrogen gas (N2), nitrogen occurring in the diatomic form (its most stable form) by direct oxidation (Fan et al., 2020; Jo et al., 2020; Tang et al., 2017). Nitrate, a clearly poisonous, and highly energetic hydrazine is a byproduct of biological activity (Cho et al., 2020; Ma et al., 2016). Anammox bacteria can produce energy by using different sources, such as inorganic compounds (ammonia and nitrite), organic acids, and amines (Weralupitiya et al., 2021). Other species of anammox bacteria can use organic substances such as acetate and propionate as energy sources (Jetten et al., 2009), while other species use inorganic metals such as Mn (IV) and Fe (III) (Shaw et al., 2020). The anammox treatment method is a successful and popular wastewater treatment method in comparison with other wastewater treatment methods due to the following advantages: low cost, where it does not require aeration or an external carbon source, no CO2 release (Yu et al., 2016; Jiang et al., 2018; Tomaszewski et al., 2017), and reducing the carbon footprint (Cho et al., 2020; Laureni et al., 2016; Tang et al., 2017), saving energy and reducing sludge (Blackburne et al., 2008.) Additionally, the increased tolerance for ammonium and nitrogen (Fan et al., 2020; Tomar and Gupta, 2016), organic waste, temperature, and other pollutants like fluorine and phenol (Li et al., 2019). Anammox bacteria play an important role in ammonia treatment in aquaculture, which have a super-efficient removal rate of ammonia compared to microalgae (Liu et al., 2019; Weralupitiya et al., 2021). Production of nitrate as a byproduct of anammox process is a big problem, while the combinations between anammox bacteria and the denitrification process resolve the drawbacks of anammox process and exhibited a higher nitrogen removal efficiency more than 90% (Zhang et al., 2020).
Photosynthetic bacteria are the starter of photosynthesis process. They have a variety of metabolic pathways that help them quickly metabolize organic substrates (C, N, P, S), nitrate, ammonia, and sulfide under light or oxygen conditions (Lu et al., 2011). They can also use light as an energy source and organics to realize autotrophic and heterotrophic growth, respectively (Chen et al., 2019 b; Meng et al., 2018; Yang et al., 2019). Photosynthetic bacteria are an effective method for nitrogen removal in wastewater treatment. It was successful in removing nitrate from lake or aquarium water that was tainted with nitrogen (Nagadomi et al., 1999). As well, PSB has higher ammonia removal efficiency (83–99%) from wastewater (Zhou et al., 2015; Yang et al., 2017). Furthermore, Yang et al., (2019) found NO3-N, NO2-N, and NH4+-N can all be effectively used by PSB. When the conditions were present, nitrogen removal efficiencies of over 90% were attained. Beside the effective role of PSB in wastewater treatment it can produce protein, coenzyme Q10, 5-ALA, carotenoids, bacteriochlorin, and polyhydroxyalkanoates (Cao et al., 2020).
The term “phycoremediation” refers to the process of using microalgae to remove contaminants from wastewaters or effluents before they are released or used again (Emparan et al., 2019). Algae represent an important phylum in plant kingdom which also use sunlight as an energy source and carbon dioxide as a carbon source for their photosynthesis process. Algae absorb phosphorus as an important nutrient for their biological processes (Leng et al., 2018; Wang et al., 2015).
Algal metabolism is the fundamental mechanism underlying this process, however the amount of pollution removed will vary depending on the type of microalgae utilized and the properties of the effluents (Pacheco et al., 2020). Microalgae have been shown to be an effective method for wastewater remediation because they can efficiently absorb nutrients in eutrophic water bodies (Leng et al., 2018; Wang et al., 2015). Also they offer a number of benefits, including the chance to sequester carbon and create novel bio-products with are used across a variety of industries (Pacheco et al., 2020). In aquaculture, high-oxygen-generating microalgae could function as a bio-pump for aeration and regulate the microbial community in a body of water (Lu et al., 2019). As a result, it would be possible to effectively manage the water quality in aquaculture operations to prevent algal bloom or oxygen depletion. The utilization of microalgae for aquaculture wastewater remediation has lately come into the spotlight as a result of the advantages outlined above (Han et al., 2019). The idea of utilizing microalgae in aquaculture has just been put out, and a lot of work is being done to encourage the commercialization of aquaculture using microalgae (Sirakov et al., 2015). In general, integrating microalgae with fish rearing has many advantages, such as maintaining a recommended level of dissolved oxygen in the fish pond without the use of an aeration device, avoiding the presence of undesirable algae, enhancing the immunity of aquatic animals without the use of antibiotics, and offering a low-cost method of treating aquaculture effluent (Sirakov et al., 2015). In order to maximize benefit of using microalgae for aquaculture wastewater remediation it is necessary to apply costly cultivation method of microalgae biomass, choose microalgae strain for achieving both wastewater remediation and aquaculture feed production, using simple and economic harvesting method and comprehend the mechanisms underlying how microalgae affect aquatic animal growth (Raza et al., 2024 a; Sirakov et al., 2015). Microalgae production on a lab scale has an effective role of nutrient recovery from wastewater produced by the food, fermentation, and aquaculture industries (Chen et al., 2020; Deng et al., 2021; Lu et al., 2016). Addition of microalgae improves the health status of aquatic animals by increasing the desirable microorganisms in the water (Yang et al., 2019). Beside the effective role of microalgae in removing eutrophication pollutants from wastewater, microalgal biomass can produce a variety of value-added components, such as proteins, lipids, and carbohydrates, as well as some high-value compounds, such as astaxanthin, phycocyanin, polyunsaturated fatty acids (PUFAs), and other advantageous high-value compounds for aquatic animals (Chen et al., 2021).
Microalgae assimilates nitrogen compounds in water by active transportation, that ammonium is used for amino acids synthesis, and nitrite and nitrate are converted to ammonium by nitrate and nitrite reductases (Christenson and Sims, 2011; Sanz-Luque et al., 2015). The algal amino acid metabolism is processed within two pathways, the glutamine synthetase-glutamine oxoglutarate aminotransferase (GS-GOGAT) pathway and the glutamate dehydrogenase (GDH) pathway (Lu et al., 2018). These two pathways include an intermediary metabolite called α-ketoglutarate which is a main intermediate in carbon metabolism in Krebs cycle (Lu et al., 2018). Microalgae can assimilate the inorganic source of carbon (CO2 and HCO3−) by photosynthesis (Lu et al., 2016). On the other side, organic carbon sources are more difficult to assimilate by microalgae, especially insoluble solids (Lu et al., 2015).
Microalgae play a vital role in aquaculture water quality control either in ectopic or in-situ treatments (Raza et al., 2024 c, 2025); regarding in-situ treatment the addition of fresh microalgae in aquaculture system directly has the advantages of in-situ nutrient removal, oxygen production, and the production of aquatic feed (Lu et al., 2019). Integrated culture between microalgae (Chlorella sp.) and fish in the absence of traditional feed is an effective method for reducing the eutrophication of culture water. The addition of microalgae to culture water after 6 days significantly decreased the COD by 51, 70, 56, 122, and 233 mg/L at 2, 4, 6, 8, and 10 fish gradient densities per unit volume of water, respectively. Also, total ammonia nitrogen was at safe levels of 15.5 mg/L compared to a semi-lethal concentration (Chen et al., 2020). Microalgae increase the values of pH in culture water because of the consumption of bicarbonate by microalgae photosynthesis (Li et al., 2019). Using inactive microalgae, Scenedesmus sp. and Chlorella sp., by sodium alginate form in the RAS system to treat the waste-water has an effective role in removing the TAN and total phosphorus (TP) at a rate of 43% and 45%, respectively (Sarkheil et al., 2022). As well, microalgae have a positive effect on reducing the ammonia toxicity in fish farms by converting the harmful form of nitrogen (TAN) to safe form (NO3) (Mohamed Ramli et al., 2017). High recovery rates of N (86%) and P (83%) were achieved when microalgae were used in forms of membrane photobioreactors (MBPR) to mitigate aquaculture wastewater (Gao et al., 2016). On the other side, microalgae have a positive effect on removing the antibiotic from wastewater by biosorption, bioaccumulation, and biodegradation (Hena et al., 2021; Leng et al., 2020).
Algae-bacteria interactions include nutrient exchange between the two microorganisms’ groups (Raza et al., 2025). Heterotrophic bacteria generate carbon dioxide which could be used by algae as carbon source, while algae generate some carbohydrates and extracellular polymers such as glycolic acid that not only protects their cells but also provides bacteria with an efficient supply of organic carbon for metabolism, in addition to oxygen molecules which also could be used by heterotrophic bacteria (Lau and Armbrust, 2006; Mishra et al., 2011; Cho et al., 2015). In addition, autotrophic bacteria generate nitrate molecules which could be used by algae as nitrogen source. Algae release simple and complex polysaccharides or even the dead algae themselves as organic matter metabolized by heterotrophic bacteria (Lau and Armbrust, 2006; Mishra et al., 2011). Algae produce glycolic acid molecules as inhibitors of phosphoenolpyruvate carboxylase activity which could affect bacterial glucose metabolism activity.
Bacteria affect algal metabolic activity by producing some antagonistic growth molecules including anatoxin, saponin, hemagglutinin, and microcystin (Saravanan et al., 2021; Zhang et al., 2020). At enzymatic level, algal and bacterial enzymes show effects on both microorganism’s metabolic activities. Moreover, bacteria support microalgae growth by secretion of beneficial components such as siderophores which simulate the algae-bacteria synergy (Amin et al., 2009).
Furthermore, there is a good relationship between microalgae and bacteria in wastewater treatments in aquaculture through the gas exchange (i.e., CO2 and O2) in the presence of C, N, P, and other nutrients as a substance (Cho et al., 2015). In this context, microalgae play an effective role to the growth of aerobic bacteria by offering O2 and fixed CO2 during photosynthesis under light condition. The release of O2 by microalgae boosts the growth of good bacteria like Bacillus subtilis, nitrifying bacteria, and even yeasts, while preventing the spread of some toxic anaerobic bacteria, which is essential for the proper development of aquatic animals (Liu et al., 2017; Wang et al., 2015).
Bacteria can break down wastewater’s macromolecules or other difficult-to-degrade suspended particles into soluble and low-molecular-weight organic materials, which microalgae can use to its advantage. Bacteria and microalgae can work effectively together in phosphorus cycle in aquatic water. Phosphorus is typically used by microalgae to fuel growth. A portion of the phosphorus (P) in a phosphorus-rich water environment may be dissolved in the water by microalgae as dissolved organophosphorus. To be recycled by microalgal cells, some bacteria can convert dissolved organophosphorus into phosphate (Brembu et al., 2017).
The use of symbiosis between algae and bacteria in wastewater treatment in aquaculture is a promising trend and more effective than individual, where it can perform significantly better at recovering nutrients (Hernandez et al., 2013; Liu et al., 2017). It has been thought that biological treatment using bacteria and/or microalgae is an affordable and effective way to convert and remove nitrogen (Nie et al., 2020). Either microalgae or bacteria secrete some substances contributing to the formation of a synergistic relationship, such as vitamins produced by bacteria (Croft et al., 2005). Algae-bacteria symbiosis has higher efficiency to alleviate ammonia toxicity and prevent the accumulation of pollutants in aquatic water (Yang et al., 2019). Algae-bacteria symbiosis plays a vital role in carbon assimilation in aquaculture wastewater, where algae absorb the carbon dioxide that bacteria produce while bacteria use the oxygen that is released by algal photosynthesis (Su et al., 2012; Hernández et al., 2013). In this context, bacteria secrete extracellular enzymes; these enzymes contribute to the transformation of complicated carbon forms into simple forms such as volatile fatty acids, amino acids, and glucose, which are suitable for assimilation by microalgae (Hernández et al., 2013). Application of algae-bacteria symbiotic for waste-water treatment in raceway pond system (12 m3 raceway pond) had a higher removal efficiency of 28% COD, 53% BOD5, 31% TN, and 64% TP (Van Den Hende et al., 2014). Total nitrogen (TN), total ammonia-N (TAN), and nitrite-N concentrations in RAS system supplied with bacteria-microalgae with biofilm carriers were all lower than they were in the treatment with conventional ponds by 29.15%, 51.28%, and 33.48%, respectively (Wang et al., 2022).
Recently, constructed wetland (CW) has drawn interest for application in effluent purification in aquaculture due to its low operating costs, high efficiency, simple design and practical operation (Li et al., 2021). Constructed wetlands are populations of water, plants, animals, and microorganisms, these components work together to improve water quality (Kurzbaum et al., 2015). Wetlands preserve water quality by capturing sediments, holding onto extra nutrients, and retaining other pollutants like heavy metals. Because wetlands have slow-moving water, sediments can build at the bottom, where they are held in place by wetlands plants (Kurzbaum et al., 2015). By using a variety of processes such sedimentation, filtration, assimilation, plant absorption, biological, and microbiological activities, CW efficiently remove organic matter, suspended matter, and nutrients. This reduces the need for water exchange and intensive aeration (Pham et al., 2021).
Efficiency of constructed wetlands in improving water quality depends on offering more surface area by increasing stem and leaves of plants in the water column, which is a good substrate for attaching a desirable microbial population as well as the effective role of plants in gas exchange from the atmosphere, especially oxygen, which is necessary for plant growth (Kurzbaum et al., 2015). As a result, aquatic animals can graze on the nutrients and energy, benefiting microorganisms and macrophytes in wetlands.
Several studies have examined the effective role of CW and its ability to purify, including its use in aquaculture with vertical and horizontal flows. In this context, constructed wetlands have an effective role in improving water quality for fish culture. Water quality parameters such as dissolved oxygen, pH, ammonia, nitrite, and nitrate were improved and kept in optimal range, when cat-fish was cultured in different sizes of constructed wetlands and different seasons of the year (Kurzbaum et al., 2015). As well, concentration of phosphorus, total suspended solids, and chlorophyll a were decreased in catfish ponds with constructed wetlands compared to control (without wetlands) (Kurzbaum et al., 2015). In order to improve the water quality of fish ponds, constructed wetlands can successfully lower the loads of nutrients, phytoplankton, metals, and microbiological pollutants in the effluents of fish ponds. Thus, an advantageous approach to achieving environmental sustainability may be the use of CW in intensive fish farming systems (Li et al., 2021). Major pollutants, such as suspended particles, organic matter, and inorganic nitrogen in water and effluent from aquaculture ponds, can be effectively and reliably removed by constructed wetlands (Lin et al., 2002; Sindilariu et al., 2009). In this context, CW has higher removal efficiency rate of NH4–N, NO2–N, NO3–N, total inorganic nitrogen (TIN), COD, suspended solids, and chlorophyll a at ratio 86%–98%, >99%, 82%–99%, 95%–98%, 25%–55%, 47%–86%, and 76%–95% respectively through the hydraulic loading rate (1.8–13.5 cm day−1) as well as, the removal rate of phosphorus decreased from 71.2% to 31.9%, when the hydraulic loading rate increased from 2.3 to 13.5 cm day−1 (Lin et al., 2002). Application of CW in shrimp ponds reared in recirculating aquaculture system significantly improved the water quality parameters (Lin et al., 2010). As well, CW plays a significant role in managing the concentration of total nitrogen and total phosphorus, when it is used in intensive trout farms as an effluent purification system (Sindilariu et al., 2008). Constructed wetlands (0.97 m2) offer a tremendous potential for treating aquaculture effluent, which helped with wastewater recycling (Omotade et al., 2019). Water quality parameters such as chemical oxygen demand (COD), total aerobic bacteria, and nitrate were all significantly reduced over the course of 50 days in a study in a laboratory-based horizontal subsurface flow CW (125 cm × 20 cm × 50 cm), which also enhanced the water quality for the shrimp culture (Pham et al., 2021). Meanwhile Gorito et al., (2018) found that in freshwater aquaculture effluents, organic micro contaminants can be successfully removed over the course of 4 weeks by using CW microcosms (40 cm × 30 cm × 30 cm) with vertical subsurface flow.
Ecological floating beds are also known as ecological floating islands and artificial floating islands, which used the technical principle of soilless culture with carriers like bamboo and high macromolecular materials (Deng and Ni, 2013). A bio-floating bed typically consists of a structure for a floating island made of natural materials such as bamboo and batten, a floating plant bed, an anchoring mechanism, and aquatic plants. Hydrophytes and light molecular materials are typically used to create floating bodies (Liu et al., 2018). They adopted the technology of implanting plants on the surface without soil and did so using modern agronomy and ecological engineering methods. Using ecological floating bed not only reduced the amount of nitrogen, phosphorus and other contaminants in water, but it also had economic benefits comparable to or even greater than those of land agriculture (Hu et al., 2010). Aquatic plants are the backbone of bio-floating bed, where it has a significant ability to fix nitrogen and phosphorus by the adsorption process through their roots (Xu and Lu, 2011). Water spinach (Ipomoea aquatic) and Canna are famous aquatic plants cultured in floating bed and had an effective role for enhancing the water quality parameters, especially total nitrogen and total phosphorus by absorption effect. Also there are other aquatic plants like Phragmites communis, Typha orientalis Presl, Nelumbo sp., Charophyceae, Potamogeton pectinatus, and Ceratophyllum demersum which had higher efficiency for removing total nitrogen, total phosphorus, and ammonia NH3-N in water (Bai et al., 2013; Maringo and Torretta, 2013).
In recent years, bio-floating beds have proven to be an effective technology for solving the water eutrophication problem in aquaculture. It has low-cost, eco-friendly, and energy-provision technology that is based on solar energy (Nduvamana et al., 2007; Nakai et al., 2008; Stewart et al., 2008; Li et al., 2010; Zhang et al., 2019). Also, the application of bio-floating bed technology in aquaculture plays a vital role in enhancing the aquatic culture environment and fish quality (Zhang et al., 2019). Floating beds cultured with water spinach (Ipomoea aquatica Forsskal) plant caused a significant improvement in aquaculture water quality, where it removed TN, NH4+-N, NO2-N, and TP at rates of 11.2%, 60.0%, 60.2%, and 27.3%, respectively (Zhang et al., 2014). The presence of ecological floating beds in swan lakes played an effective role for solving eutrophication phenomena and enhanced the water quality, where it removed total nitrogen (TN), ammonia (NH3-N), total phosphorus (TP), and chemical oxygen demand (COD) from water with efficiencies of 31.5%, 33%, 30.5%, and 53%, respectively. Moreover, fish and vegetation flourished, producing some economic gain (Zheng and Wang, 2017). Live submerged macrophytes (Elodea nuttallii) can be used in aquaculture to not only bioremediate the water in place without creating aquaculture wastewater but also to enhance the nutritional value and flavour of cultured largemouth bass (Micropterus salmoides). As a result, this ecological aquaculture model is valuable and beneficial to the environment, making it deserving of widespread use and exposure (Zheng et al., 2022). In intensive aquaculture ponds for 100 days, the usage of water spinach floating beds had the highest direct absorption rates of TN and TP, which were 52.35 and 5.39 kg hm−2, respectively (Chen et al., 2010). Application of a bio-floating bed in polyculture fish (grass carp and silver carp) by using particles of natural mineral or industrial waste (ceramsite) as a substrate for macrophytes, which has high biological, chemical stability and readily allows microbes to grow (Bao et al., 2016), plays an effective role in improving water quality parameters like ammonia, total nitrogen, and total phosphorus compared to conventional floating beds (Li et al., 2018). Also in the same study, ceramsite floating beds had a higher variety of phytoplankton species, bacterial population, metabolic activity, microbial diversity and fish growth compared to conventional floating beds.
Recirculating aquaculture system (RAS) is a technology for wastewater treatment in aquaculture. It treats the wastewater by eliminating toxic pollutants and recycling the treated water (Tom et al., 2021). RAS has an effective role for maintaining water usage in aquaculture, while producing large quantities of fish. RAS contains two types of filters: mechanical filter and biological filter. Mechanical filter removes the solids waste, while biological filter transforms ammonia to nitrite and nitrates through nitrification process (Hamlin et al., 2008). Nitrification and denitrification process plays a vital role for nitrogen removal in RAS. There are many microorganisms contributing in the last two processes such as heterotrophic aerobic denitrifies, anaerobic ammonia oxidizers, and chemolithotrophic autotrophic nitrifiers (Preena et al., 2021).
Biological filters in RAS mainly depend on microorganisms which have positive effect in nitrogen transformation. The end product of nitrification process in bio-filter is nitrate and lower pH in culture water, so it is necessary to exchange 10–20% from water daily for reducing nitrates level and maintaining good water quality for fish (Piedrahita, 2003; Martins et al., 2010). Denitrification process is another way for reducing nitrates level through reducing inorganic nitrogen compounds such as nitrite and nitrate to elemental nitrogen, subsequently increasing the efficiency of RAS (Martins et al., 2010; Gichana et al., 2018). Also denitrification process mainly depends on microorganisms such as heterotrophic bacteria in the presence of carbon source and limits oxygen condition; for example, using Pseudomonas stutzeri in biological denitrification reduced nitrate level form 50.79 mg l−1 to 0.57 mg l−1 (Singh et al., 2006). Furthermore, NH4+ and NO2- are directly transformed into N2 gas by the microbial process known as anaerobic ammonia oxidation (anammox) (Kuenen, 2008). Bioelectrochemical systems (BES) such as microbial fuel cells (MFC) or microbial electrolysis cells (MEC) is another technique for energy-efficient wastewater treatment for nitrates removal in RAS (Zhang and Ngelidaki, 2013; Zou and He, 2018). This technique depends on exoelectrogens (electrochemically active microorganisms transferring electrons to electrode) as anodic bio-catalysts to anaerobically oxidize organics in wastewater (Logan, 2009). Both direct electrochemical autotrophic denitrification in the cathode (Cecconet et al., 2018) and diffusion/migration through an anion exchange membrane (AEM) from the BES cathode into the anode, where subsequent heterotrophic denitrification occurs, are options for nitrate removal in a BES technique (Mook et al., 2012). In this context Zou et al. (2018) found higher removal rate of nitrate and ammonium, from RAS water by using exoelectrogendenitrifier (MFC equipped with AEM), where the overall specific nitrogen removal rate was 0.051 ± 0.004 kg Nm−3 NCC d−1 with nitrate (15.85±2.24 mg L−1 NO3−-N) as the major form of nitrogen compound in the cathode effluent. Operating RAS with symbiotic between simultaneous partial nitrification, anammox and denitrification (SNAD) achieved high-efficient removal of nitrogen and COD in spontaneous environment (Lu et al., 2020).
Biofloc system is a good bioremediation technique for improving the culturing water quality in aquaculture (Raza et al., 2024 a). It is known as the new “water revolution” in the field of aquaculture. The structure of this system mainly depends on microorganisms, especially bacteria and algae (Avnimelech, 2006; Ahmad et al., 2017). Beside bacteria and algae biofloc contains other microorganisms like protozoans, diatoms, fungi, nematode, rotifer and particulate organic materials, such as faeces and uneaten feed. Each floc is held together in a loose matrix of mucus that is secreted by bacteria, held by electrostatic attraction (Raza et al., 2024 b; Hargreaves, 2006). There are synergetic effects between bacteria and algae, where some strains of bacteria support the growth of microalgae, furthermore both bacteria and algae have a positive effect on water treatment; this is mentioned in the bacteria and algae section in this review. In biofloc system algae are the first microorganism to grow during biofloc formation period, then the growth of heterotrophic bacteria increases gradually until becoming dominant in the system (Khanjani et al., 2020). To achieve the best growth of heterotrophic bacteria in biofloc system it is necessary to maintain carbon: nitrogen ratios above 10 by addition of external carbon source such as molasses, wheat flour, starch or using low protein diet (Crab et al., 2012; Khanjani et al., 2017, 2019). Efficiency of heterotrophic bacteria for ammonia immobilization is higher than that of denitrifying bacteria, because of the higher uptake rate of inorganic nitrogen compound by heterotrophic bacteria; subsequently heterotrophic bacteria have 10 times higher microbial biomass per unit compared to denitrifying bacteria (Hargreaves, 2006). Heterotrophic bacteria can live in a wide variety of conditions and are frequently found in soil, freshwater, and saltwater. One of the most crucial functions in the food webs is played by aquatic habitats, which recycle large volumes of dissolved and particulate organic materials (Avnimelech, 2007). There are three pathways occurring in biofloc system for removing ammonia nitrogen; the first is photoautotrophic removal by algae, the second is autotrophic bacterial conversion from ammonia to nitrate, and the third is heterotrophic bacterial conversion of ammonia nitrogen directly to microbial biomass (Ebeling et al., 2006). Autotrophic bacterial conversion is the most efficient process in the long term (Hagopian and Riley, 1998). For controlling TSS in biofloc system Soaudy et al. (2023) recommended that by adjusting the heterotrophic and nitrifying bacterial activity, new management techniques can control the TSS level.
Biofloc system plays an effective role for improving water quality in aquaculture, where it can help with the removal of total ammonia nitrogen (TAN) and nitrite, as well as with the reduction of water use and waste production, Vibrio abundance, feed utilisation efficiency, and body bound crude protein (Brito et al., 2016; Bossier and Ekasari, 2017). Biofloc system contributes to enhance the water quality by minimizing the level of NH4+, NO2 in shrimp ponds (Wang et al., 2016). Similar positive effect on water quality parameter (ammonia, nitrite and nitrate) was noticed using different carbon source molasses, starch, and wheat flour in shrimp biofloc tanks (Khanjani et al., 2016). Water quality parameters were enhanced in tilapia tanks under biofloc system by carbon supplementation compared with RAS system (Luo et al., 2014). In a research utilizing stable isotopes, Burford et al. (2004) estimated a daily nitrogen retention of 18–29% into the prawns acquired from biofloc biota, whereas Avnimelech and Kochba (2009) reported that tilapia, using the same method, assimilate about 25% of the nitrogen consumed.
Aquaponics is a technique that uses phyto- and bioremediation processes to treat water through a fixed nitrogen cycle assessment (Bandi et al., 2020). Large quantities of different microorganisms are also present in aquaponic systems, which aid in both fish growth and plant nutrient uptake, subsequently enhancing the water quality (Ngien et al., 2022). Microorganisms in these system play an effective role in converting waste from fish into soluble nutrients for plants, while the plants function as a kind of biofilter, enhancing the water’s quality before it is pumped back to fish tank, then the cycle is repeated (Silva et al., 2015; Huang et al., 2021; Ngien et al., 2022). In aquaponics system total suspended solids are removed by mechanical filter, while in biofilter ammonia oxidizes to nitrates by microorganisms through nitrification process. If the system is appropriately balanced, this process enables the bacteria, plants, and fish to coexist harmoniously and to create an environment that is conducive to healthy growth (Oommen et al., 2019). Water lettuce (Pistia sp.), water hyacinth (Eichhoria crassipes) and water fern (Azolla sp.) are common floating plants cultivated in aquaponics system, these plants can be used as commercial food for herbivorous fish such as tilapia and carp and also control the growth of phytoplankton in water. Furthermore, floating plants in aquaponics such as water hyacinth (Eichhoria crassipes) can remove more than one gram of nitrogen per square meter per day (Jusoh et al., 2020). Aquaponics system offered suitable condition for fish by maintaining water quality at recommended level for tilapia (pH 7.4–7.6, dissolved oxygen 8–10 mg/l, NH4 0.05–05 mg/l, NO2 0.1–3.2 mg/l, NO3 0–80 mg/l, 0.02–0.3 mg, PO4 0.02–0.3 mg/l) also offered nutrients for plants (Filep et al., 2016).
Different species used in IMTA and their efficiency of wastewater treatment
| Species in IMTA system | Efficiency of wastewater treatment | References |
|---|---|---|
| Bivalves | Bio controllers for fish farm effluents (POM and eutrophication) | MacDonald et al., 2011; Handa et al., 2012; Lander et al., 2013; Granada et al., 2016 |
| Can extract up to 23% OM, and 88% suspended solid waste which was up to 33% organic N; it reduced the chlorophyll a up to 96% and 88% bacteria in the system | Nederlof et al., 2022 | |
| Reduce the suspended solids load and nitrogenous and phosphorous Reserved 58% of TAN-N and 41% of PO4– | MacDonald et al., 2011 | |
| P excreted by the fish (only with an assimilation efficiency of 87%) | Fang et al., 2017; Nederlof et al., 2022 | |
| Sea cucumbers | Consume up to 70% of the deposited organic matter | Granada et al., 2016 |
| Reduced the accumulation of both organic carbon and phytopigments | Slater and Carton, 2009 | |
| Assimilation efficiencies of sea cucumbers in integrated systems are highly inconstant (14 to 88%) | Nederlof et al., 2022 | |
| Have higher removal rate of OM 0.1–20%, 3–10% organic C, 7–16% organic N, and 21–25% organic P (from the aquaculture waste fed directly or from sediments enriched with aquaculture waste) | Yokoyama, 2013; Nederlof et al., 2022 | |
| Polychaetes | Annelids can perform biofiltration, aerate the sediment, positively impact biogeochemical reactions, and contribute to waste control | Brown et al., 2011; Granada et al., 2016; Galasso et al., 2020; Nederlof et al., 2020 |
| The ability to filter, accumulate, and remove from bacterial waste groups, including human potential pathogens and vibrios | Stabili et al., 2010 | |
| Receiving wastewater from a sea bream recirculation system by the addition in settling tank | Bischoff et al., 2009 | |
| Seaweeds | Absorb the nutrients entering the water column and, thus, reduce eutrophication and contribute in bioremediation | Chopin, 2006; Barrington et al., 2009; Nederlof et al., 2022; Samocha et al., 2015 |
| Significantly affected the microbial community’s structure and make-up, releasing algal growth and morphogenesis-promoting factors | Ghaderiardakani et al., 2019 | |
| Concentration of PO4 –P was reduced by 93.5%, NH4 –N by 34%, and NO3 –N by 100% | Marinho-Soriano et al., 2009 | |
| Sponges | Filtering organic matter | Muller et al., 2009; Granada et al., 2016; Gokalp et al., 2019, 2021; Varamogianni-Mamatsi et al., 2022 |
| Produce interesting bio-commercial products | ||
| Introduce biomedical agents, biosilica, biosintering, and collagen | ||
| Removing DOM | ||
| Remediate organic pollution from aquaculture cages | Ledda et al., 2014; Gokalp et al., 2019 | |
| High efficiency of removing bacteria (12.3 × 104 cells ml−1 with a maximum retention efficiency of 61%) when used in marine environmental bioremediation | Stabili et al., 2006 | |
| Remove pathogenic bacteria, achieving removal of 60.0–90.2% of faecal coliform bacteria, 37.6–81.6% of pathogenic Vibrio spp., and 45.1–83.9% of the total bacteria in a 1.5-m3 turbot (Scophthalmus maximus) aquaculture system | Zhang et al., 2010 | |
| Accumulate, remediate, and metabolize halophilic Vibrio spp., heterotrophic bacteria, total culturable bacteria, faecal coliforms, and faecal Streptococci | Longo et al., 2010 |
On the other side symbiosis between RAS and aquaponics system increased the efficiency of water quality by removed ammonia, nitrite, nitrate, total suspended solids and BOD by 83%, 87%, 70%, 60%, 88% and 63%, respectively (Lam et al., 2014).
Integrated multitrophic aquaculture (IMTA) is a promising system in wastewater treatment in aquaculture. This system is symbiotic between different economic species and is different in feeding habitats such as macro algae, mussels, oysters or extractive species (e.g. autotrophs, filter and deposit feeder); these species can encourage a nitrogen cycle by extracting nutrients in particulate and diluted phases in aquaculture effluent (Chopin, 2013; Nederlof et al., 2022). The main idea in IMTA system is reducing nutrient losses in aquatic water by recycling it by different species in the system. Efficiency of IMTA for nutrients removal varies between 2 and 100% by extractive species (Troell et al., 2003; Schneider et al., 2005). Each extractive species has specific role in IMTA system, where seaweeds (e.g. Ulva and Gracilaria) have higher efficiency in organic nitrogen removal (Chow et al., 2001; Jones et al., 2002). Bivalve has higher efficiency of POM removal from the water column (i.e. suspended solids, fish faeces and feed fines). Sea cucumbers or polychaetes have higher efficiency from 14% to 88% for decreasing organic matter (OM) (Yuan et al., 2006; Zamora and Jeffs, 2011). Integration between shrimp (Penaeus chinensis), crab (Portunus trituberculatus), bivalve (Sinonovacula constricta), and fish (Cynoglossus semilaevis) in IMTA system has improved water quality through boosting the number of cyanobacteria, which through photosynthesis release dissolved oxygen into the water below, improve nitrification (mostly ammonia oxidation), and increase the system’s ability to remove ammonia from water. While this is happening, bivalves in this system can boost bacterial diversity and abundance by controlling dissolved oxygen (Kong et al., 2023). Table 4 summarized different species in IMTA and their efficiency of wastewater treatments. Beside the species mentioned in the table there are other fish used in IMTA such as common carp (Cyprinus carpio), tilapia and mullet (Mugil liza). Mullet fish has an effective role for consuming the vegetable matter and recycle energy from waste products of aquaculture systems into animal biomass (Shpigel et al., 2016; Holanda et al., 2020).
Integration between IMTA and biofloc system significantly increases the efficiency of waste produce in the system and resolves some drawbacks of the system like accumulation of TSS (Poli et al., 2019, 2021). In this context Soaudy et al. (2023) mentioned that IMTA is an effective strategy for remediating the accumulation of TSS in biofloc system. Selected filter feeder species such as tilapia and M. liza in IMTA with biofloc system increase the efficiency of TSS removable (Khanjani et al., 2022).
This review provides an overview of the latest technological options for sustainable aquaculture wastewater treatment such as bacteria, microalgae, bacteria-algae symbiosis beside the bioremediation system such as constructed wetlands, ecological floating beds, RAS system, biofloc system, aquaponics system, and integrated multitrophic aquaculture (IMTA). Also this review aims for possible integrations among water quality treatments. Further studies can elucidate the possible applications of bioremediation in aquaculture sector to achieve best water quality and higher biosecurity by using eco-friendly and environmental techniques.