3.1. Water Scarcity and Effluent Discharges

There is no doubt that water is essential to the production of energy, food, economic development, and ecosystems. Despite this, 40% of the world’s population suffers from water scarcity, and 80% of sewage reaches the ecosystem without being treated or reused [76]. Aquaculture professionals are striving to reduce the amount of water consumed in the process of aquaculture. Approximately 70% of the world’s population will experience water scarcity by 2050 [9] and the aquaculture industry must embrace such issue. Some aquaculture systems (such as conventional system) need >20,000 L of water to produce 1 k of fish or shrimp; however, others such as RAS, aquaponics, and BFT can rely on less than 200 L/kg produced [77–80]. Timmons and Losordo [81] described several aquaculture operations and found water utilization values of 21, 64.7, 210, and 20 m³ of water per kilogram produced of tilapia (pond systems, Taiwan), catfish (pond systems, USA), trout (raceways, USA), and shrimp (pond, Americas), respectively.

Aquaculture systems are typically polluted and deteriorated by their food supply. About 30% of the nutrients provided are converted to a product, whereas the rest must be removed and disposed of as effluents. The types of waste produced by aquaculture farms are basically similar, although there are differences in their composition and quantity, which depend on the system and the cultured species [82, 83]. The main types of discharge in laboratories and farms are (a) feces and metabolites, (b) food remains, and (c) residues of disinfectants, antibiotics, and biocides [84]. Furthermore, when discharges from some farms are drained near the water intakes of others, cross-contamination effects are created as nutrients, particulate matter, and microorganisms can move from one farm to another [18, 85].

The environment is negatively affected by waste containing N, P, and dissolved organic carbon compounds [86]. The major source of these particles is unconsumed food, fish waste, and the residual part where unassimilated forms accumulate the most nutrients. Minerals require additional treatment to be utilized effectively [87]. There is evidence that up to 70% of the feed supplied to aquaculture production systems ends up as particulate matter at a daily average of 0.4%–12.3% [84, 88]. Normally, this matter contains approximately 7%–32% nitrogen as well as 30%–84% phosphorous for the development of the cultured organisms. There are two types of particulate fractions in aquaculture; suspended solids and settleable solids [89]. In aquaculture systems, suspended solids are fine particles ranging from 30 to 100 micrometers (m), so they donnot settle and stay suspended in the water, making them hard to collect [90]. Meanwhile, settleable solids are bigger particles (100 >µm) and form sediment more quickly. They can be collected and removed from culture systems more easily than suspended solids [91].

3.2. Social Conflicts

Traditional aquaculture uses large amounts of natural resources. In the case of mariculture, the facilities are located in the coastal zone, while in freshwater, they are located near rivers, streams, and lakes. Traditional farms with extensive and semi-intensive systems are characterized by having large areas. These can modify the natural environment, and depending on the location, they can affect other activities and generate conflicts. Social impacts are usually related to competition in land and water use, landscape modification, and interference with other productive activities [92]. Therefore, aquaculture expansion strategies must be accompanied by sustainability studies and the preservation of natural resources [93–95]. In certain regions, aquaculture has negatively impacted marine and artisanal fisheries [96, 97]. These include the obstruction of access to the sea for local fishermen, placement of nets, and other daily activities [96]. In addition, the installation of farms in the coastal zone has generated conflicts with tourism. For several years, the installation of cages and other aquaculture facilities in coastal areas has been incorporated as a negative landscape element [98]. While aquaculture contributes more than 40% of aquatic products, tourism is an activity with significant expansion which has a substantial economic impact; therefore, adequate strategies must be established that allows a coexistence between the two industries [99].

The conversion and abandonment of agricultural land for aquaculture development is a phenomenon that has been registered in some countries such as China and Malaysia. Some farms have been established on land that was previously used to cultivate rice and other vegetables that are of great importance to meet the growing demand for food in the world [100]. In addition, the threat of climate change requires taking efficient mitigation and protection actions. Environments such as mangroves, coral reefs, beaches, and brackish marshes must be adequately conserved and protected due to the critical role they play in the biotic and abiotic processes of the coastal zone [101, 102], for which economic activities, including aquaculture, must be developed in a sustainable way considering the future scenario.

3.3. Presence of Diseases

Disease outbreaks pose a latent risk for aquaculture regardless of the cultivated species. Infectious diseases may lead to catastrophic losses in aquaculture, causing entire aquaculture parks to give up their operations and start over. Infectious diseases can be caused by bacteria, viruses, fungus, and parasites; however, diseases that might not typically affect wild species can become problematic in aquaculture [103]. Some important diseases caused by pathogenic bacteria are mycobacteriosis pathoge Mycobacterium fortuitum [104], streptococcosis pathoge Streptococcus agalactiae [105], vibriosis pathoge Vibrio harveyi [106], aeromoniasis pathoge Aeromonas hydrophila [107], edwardsiellosis pathoge Edwardsiella tarda [108], and pseudomonasis pathoge Pseudomonas anguilliseptica [109].

During the past decades, recommendations for preventing opportunistic diseases included suitable water source and quality, moderating stocking density, and using pesticides and antibiotics [103]. However, the current aquaculture requires to be intensified to cope with the food demand; simultaneously, antibiotics are restricted or banned in some countries due to antibiotic resistance to pathogens, and threats to human health [110]. Therefore, the current challenge is to produce aquatic protein in intensive but biosecured environment. One of the latent risks in fish farming is the appearance of diseases that are not detected until the infection process is in the advanced stages. For example, granulomatous diseases caused by bacteria can remain encapsulated by the same fish for weeks and eventually break into the body leading the host to a precarious health status [111, 112]. Under this scenario, the use of antibiotics becomes necessary; however, early detection methods, including molecular tests, can provide a wide margin of action; also, the establishment of prophylactic measures and the implementation of closed systems prevent the spread of pathogens. In this sense, modern aquaculture requires systems that do not necessarily need to be connected to bodies of water, while at the same time maximizing/reusing its use and avoiding the spread of pathogens to the environment and, finally, to other farms [113].

3.4. Antibiotic Use

Antibiotics are used worldwide, especially in salmon and shrimp aquaculture [114, 115]. There is a wide variety of bactericidal compounds, and their use depends on availability, price, and the type of infectious agent to be eradicated. The continuous use of antibiotics creates resistance and affects the composition of the natural bacterial flora [116, 117]. A change in the structure of the bacterial community in the sediments and the water affects the decomposition process of organic matter and interferes with the biogeochemical cycle of some nutrients [118]. In this sense, Chen et al. [119] suggested that, due to the risks involved in antibiotics, it is necessary to promote strict management measures and environmental monitoring in water bodies that receive aquaculture effluents. Tetracycline, amoxicillin, flumequine, oxytetracycline, sulfamerazine, thiamphenicol, and erythromycin are among the most commonly used antibiotics in aquaculture [120]. Antibiotic contaminants are new environmental pollutants that may change the balance of aquatic ecosystems [115]. The overuse of antibiotics can have negative effects like changing the population of environmental bacteria [121], changing the population of host digestive microflora [122], and changing fish responses to stress [123].

The persistence of antibiotics in fish and the consumption of fish by humans can cause bacterial infections in humans and weaken of immune system [115, 120, 124], problems related to allergy and poisoning of workers [125], changing the natural flora of the environment, plankton, microbiota [110, 126], and changing the ecological balance of the environment [127, 128].

3.5. Wild-Caught Fishmeal Replacement

In 2018, 88% (156 million tons) of world fishery production was used for direct human consumption, while the remaining 12% (22 million tons) for nonfood purposes, highlighting the production of fishmeal and fish oil, with 18 million tons [129]. Although this amount has remained stable since 2010, it is still high, and it is necessary to continue exploring the use of alternative sources to produce aquafeeds.

The substitution of fish protein for the elaboration of aquaculture feeds has had important advances. In its beginnings, the most critical challenges for replacement were related to the content of essential amino acids, digestibility, and the presence of antinutritional compounds in alternative sources [130]. However, recent studies indicate that different animal processing by-products (e.g., poultry waste meal) and insect meal have a suitable amino acid profile and digestibility, so they can be included in diets in satisfactory percentages without affecting the productive response of shrimp, tilapia, and some other species [131–133]. Additionally, there are promising sources such as biomass-derived from bioethanol fermentation, microbial protein, cereal flours, cereal glutens, legume meals, etc. [74, 134, 135].

5.1. BFT to Reduce Effluent, Land, and Water (R’s 1, 2, 3, and 4)

Biofloc does not generate significant aquaculture effluents since only a limited quantity of water is exchanged [135]. Conventional (semi-intensive) production of fish (e.g., tilapia) and shrimp (e.g., Litopenaeus vannamei) in earthen ponds normally reach ~10 and ~3 tons/ha in ~180 and ~120 days, respectively. Of course, these are just random examples and might change case by case. However, it is clear that production can significantly be improved and the land optimized in BFT systems. For the same hectare of production, values of 60 and 30 tons/ha can be found in tilapia and L. vannamei in BFT-based systems [29]. In these senses, there are clear advantages in terms of land optimization and opportunities for controlled large-scale production [157], as well as focused on premium products (e.g., fresh never frozen shrimp) in close-to-market areas [149]. However, BFT systems require higher aeration and present high-power consumption in comparison to conventional pond farming [20]. The high aeration/water turbulence promotes higher evaporation rates, and top-ups of 2%–4% of pond volume per day are often observed [9, 13]. On the other hand, this high demand is translated into an efficient and rapid reduction of ammonium concentrations [158–160], 30% more economical than conventional biofilters [161–163].

In terms of water use, BFT minimizes water consumption since there is limited water exchange during production [9]. Table 1 presents the water consumption in different aquaculture systems. For instance, freshwater consumption has been reported at 6.8 m³/kg of shrimp Macrobrachium rosenbergii and at 0.071 m³/kg of Nile tilapia Oreochromis niloticus [78, 79]. Comparatively, traditional freshwater aquaculture uses 16.9 m³ of water per kilogram of production. Consequently, it is essential to adopt farming techniques that use natural resources and increase production [173]. In addition, Krummenauer et al. [77] reported that the amount of saltwater needed to produce shrimp (L. vannamei) using BFT system varies from 98 to 169 L of water per kilogram of production. Otoshi et al. [21] calculated that 163 L of saltwater is required to produce 1 kg of L. vannamei using biofloc-based super-intensive systems. Krummenauer et al. [174] documented a similar low water use of 169 L/kg of shrimp produced in 35-m³ raceways. Further, Samocha et al. [175] reported that only 98 L of water was required to produce 1 kg of shrimp in an experimental zero-exchange super-intensive system.

Not only reduction, but also reusing this limited resource has been documented in BFT. Krummenauer et al. [77] observed advantages in terms of survival, growth, and feed conversion rates of L. vannamei cultured in reuse water. For tilapia, Malpartida Pasco et al. [176] established a biofloc culture using 50% biofloc-rich water as inoculum and found no adverse effects caused by the water source on survival and productivity. Other advantages such as comparable proximal composition, superior gonad maturity, and healthy status were found when water from BFT systems as recycled for tilapia cultivation [156, 177].

5.2. Biofloc as an In Situ Food Source and Ingredient in Aquafeeds (R’s 1, 2, and 3)

In BFT farming systems, bioflocs act as an in situ food source, available continuously providing complementary nutrients for aquatic species within the rearing media [178].

Some studies on biofloc’s use in cultured aquatic diets can be found in Table 2. Aquatic species with adequate morphological structure (e.g., shrimp, tilapia, and bivalves) have advantages enabling them to graze/filter/capture the microbial aggregates properly [188–190]. As a result, a decrease in FCR and improved growth rates have been reported for shrimp, freshwater prawns, and fish [79, 191, 192].

In L. vannamei, over 29% of shrimp’s diet can be replaced by bioflocs in open pond conditions [193]. Wasielesky et al. [192] demonstrated that by consuming flocs, the L. vannamei FCR can be reduced from 1.39 to 1.03, and the growth rate is increased from 0.39 to 1.25 g/week. By reducing FCR and increasing feed efficiency, biofloc can be used to replace approximately 30% of L. vannamei feed without affecting their growth [194]. Azim and Little [195] reported reduced FCR and improved growth in tilapia juveniles raised in BFT in comparison to clear-water conditions. Pérez-Fuentes et al. [79] found similar outcomes, but now for M. rosenbergii reared in ponds, in which BFT outperformed the traditional water-exchange method.

Biofloc systems can reduce the dietary protein requirement [196]; however, it is not always the case [192, 197]. Tilapia, crustaceans, and carp can use in situ microbial proteins instead of dietary feed-based protein reducing its content in formulations [26, 27, 196–201]. In some cases, for example tilapia, bioflocs may contribute about 50% of fish’s protein requirement [9]. Mansour and Esteban [198] demonstrated that tilapia fed with 20% crude protein (CP) diet in biofloc performed significantly better than those fed a 30% CP diet in clear-water conditions. Growth performance, humoral and cellular immune parameters, and superoxide dismutase and catalase activity were significantly improved in biofloc treatments. Besides the reduction of dietary CP, BFT system also allowed the inclusion of alternative feed ingredients [202]. Some examples in tilapia culture include (i) inclusion of insect meal-based diets [203] and (ii) food waste pizzeria by-product [204]; increasing the circularity and reducing the carbon footprint of the diets. Olier et al. [205] suggested that the addition of a vertical substrate enabled savings on dietary protein (reduction of 35% to 30% CP content) without losses on growth performance and chemical aspects in L. vannamei biofloc-based culture. Silva et al. [196] observed in biofloc-based tilapia juveniles culture (10–60 and 60–230 g) fish can be fed on diets with 28% of CP (26% of digestible protein) and 22% CP (20% of digestible protein), respectively, without compromising performance. Interestingly, Ekasari et al. [189] showed that biofloc consumption by shrimp, red tilapia, and mussels occurs irrespective of floc size but that floc size can play an important role in the quality of biofloc in terms of nutritional composition and nitrogen retention by the animals.

As ingredient in aquafeeds, BFT is emerging as a sustainable way to produce high-value “biofloc meal” used in commercial aquafeeds [134]. Nitrogen transformation/recycling process and low-cost agricultural by-products can be used as substrates for microbial growth in controlled environment [28]. Similarly, other microbial-derivate ingredients (e.g., Novacq) have shown positive results in L. vannamei, P. monodon, and tilapia, improving growth, feed efficiency, and resilience during pathogen challenges [74, 75, 206].

Ex situ biofloc is normally produced in especially designed units, for example, sequencing batch reactor (SBR), which works independently [28, 190, 207, 208]. Using a small diameter mesh (e.g., 10 µm), biofloc biomass can be collected, decanted or filtered, centrifuged, dried/freeze-dried, and converted into a fine powder or “meal” [209, 210]. This relatively “new ingredient” can be incorporated into formulated diets and replace premium feedstuff with comparable performance [134, 211, 212]. Shao et al. [212] found that the 15% replacement of fishmeal with biofloc meal did not make negative difference on growth performance and digestive enzymes of shrimps compared with control group. A 28-day study conducted by Bauer et al. [134] investigated the effect of replacing fish meal by soy protein concentrate and biofloc meal on the growth and food intake of L. vannamei juveniles and found no adverse effects when replacing it completely. Shyne Anand et al. [213] showed that the addition of 4%–8% biofloc to the diet of P. monodon led to immunomodulatory effects and improved physiological condition. In brief, this area of research offers great potential since the nutritional properties of the biofloc can potentially be manipulated. However, production costs (e.g., US$/kg of biofloc meal), especially considering the drying methods and the impact on costs and performance, need further improvement and investigation.

5.3. BFT: A Natural “Probiotic” Source and Elimination of Antibiotic Use (R’s 1, 2, 4, and 8)

The aquaculture industry faces a major problem with diseases outbreaks with increasing intensification and scrutiny regarding antibiotic usage. Despite vaccines being developed and marketed (e.g., fish farming), they cannot be used as a universal tool and cost-effective means of disease control in all farms and regions [214].

In response, new strategies for disease management in aquaculture have been developed. For instance, biofloc can be an effective in situ strategy for managing diseases [215]. There is a “natural probiotic” effect created by the presence of beneficial bacteria in the biofloc, competing with pathogens and improving immunity both internally and externally [20, 216–218]. A probiotic is a beneficial bacterium that plays a key role in maintaining a healthy microbiome and water environment. Studies show that biofloc probiotics tend to mitigate the invasion of pathogenic bacteria, improving fish and shrimp immunity. The biofloc system significantly improves nonspecific immunity of animals cultured with these beneficial bacteria [219, 220].

External microbial blends (known as probiotics) can be added to enhance the microbial function of BFT. The study on external probiotics applied in BFT systems is summarized in Table 3. Table 4 shows that bioflocs have probiotic properties that reduce the activity of pathogenic agents, enhance immunity in farmed aquatic animals, and increase their survival rates. The use antibiotics in biofloc-based farming likely can drastically impact the natural microbial biota, causing disfuction of water quality and health attributes.

5.4. BFT as a High-Yield System to Boost Productivity and Coproduction (R’s 1, 2, 3, 4, 8, 9, and 10)

One of the important goals of farmers is to reduce production costs, improve yields, and profitability. There are several strategies to achieve such goals (e.g., increase or reduce stock densities, single or multiple phases, etc.); however, market prices play a key role on the approach selected [138, 139]. Production costs are primarily determined by growth rate, survival, and FCR. Additional costs such as electricity and labor also play a critical role [175]. In this sense, new technologies must be implemented to achieve greater profits, consistency, and predictability. According to Ray et al. [243], L. vannamei production increased by 41% with the biofloc system. Wasielesky et al. [192] reported that bioflocs improve the digestion of shrimp, increase growth by as much as 15%, and reduce the FCR by as much as 40%. Higher growth rates impact on the cycle’s duration, translating in lower production costs. Compared to flow-through water-exchange systems, costs for pumping can be more economical in BFT due to reduced water exchange rates and less energy demand [9, 20]. However, aeration to supply proper levels of dissolved oxygen and provide water movement can significantly increase the production costs in BFT depending on the region. In some cases, higher profitability can be achieved using BFT [169], and the improved feed efficiency, yields, and water recycling can be determinant for positive economic outcomes and “green credentials.”

Using BFT, a kilogram of green tiger shrimp (P. semisulcatus) and tilapia can be produced with 33% and 10% cost reduction, respectively [244].

Compared to traditional clear-water systems, Nile tilapia in biofloc-based conditions increased production by 43% in small-scale tanks [195]. In Table 5, the values of the FCR and production in the BFT and the increased percentage compared to the clear water system are presented. High survival was found in tilapia cultured in greenhouse ponds with BFT, ranging from 80% to 97% [30]. In shrimp pond cultures using biofloc, productivity has been found to be 8%–43% higher than in conventional methods [28, 148, 169, 210]. However, the production management (e.g., water quality and microbial management), species, feed and feeding, carbohydrates source, and biofloc consumption may have a direct impact on those numbers [137, 251].

Combining BFT with other species can improve production, diversity, and profitability, as well as enhancing circularity, water quality, and feed efficiency [153, 160, 252]. Two successful examples at experimental scale are combining BFT with IMTA [40, 63, 252] and with plant production in aquaponics, nowadays called as FLOCponics [153, 253, 254]. Coupling fish (tilapia) production with shrimp (L. vannamei) in IMTA-biofloc based decreased the sludge production per kilogram of fish biomass produced, and the recovery of nitrogen and phosphorus increased 27.9% and 223.0%, respectively. Pinheiro et al. [254] evaluated the production of the halophyte Sarcocornia ambigua integrated with L. vannamei in FLOCponics and observed an increase in nitrogen assimilation efficiency by 25%. In the future, the adoption of BFT combined with other techniques, for example IMTA or aquaponics, certainly will have a massive impact in large-scale operations nutrient optimization and system efficiency.

5.5. The BFT Main Challenges

Despite BFT’s many advantages, several factors limit its expansion and further adoption. In the sections above, we discussed how BFT aligns with several environmental sustainability goals. However, there are several challenges to properly and effectively mitigate the negative impacts. Recently, a comprehensive review by Khanjani et al. [20] showcased several negative aspects of BFT farming, and potential ways to overcome those challenges. For instance, this technology is relatively complex and needs deep water quality and microbiology knowledge [9]. Same occurs with other technologies including RASs and IMTA. Skilled staff, and a proper engineering, water quality, and microbial management not only play a key on the success of BFT [9, 149] but also in RAS and IMTA. Similarly, other aspects that can be also associated include (i) high implementation costs (e.g., liner ponds, greenhouses, shade mesh, etc.) and electricity demand for aeration and water circulation, (ii) risks with rapid dissolved oxygen depletion due to higher (microbial, fish-shrimp) respiration, (iii) associate costs with water quality supplements and monitoring, (iv) excess of suspended solid and needs for proper sludge treatment; (v) poor water quality management and high N-toxic compounds may lead to poor performance, health and mortalities issues [29, 141]. In BFT, water consumption can be reduced if the same water were to be reused in multiple cultures [76]. However, it is crucial to examine the potential effects of reusing water on the productivity and nutritional quality of cultivating organisms. In this regard, diseases or parasites may spread or toxins may accumulate in the final product by using water from previous cultures [82]. In addition, salt content in BFT effluents is also considered a key issue, thus a proper management (e.g., dilution and/or concentration + suitable disposal) must be considered [23]. To help overcome some of these challenges, other examples include (i) controlling microbial populations and maintaining a balanced community is essential for the successful operation of BFT. Effective monitoring tools for BFT systems are also necessary to ensure stable and consistent production; (ii) scaling up BFT systems to commercial production levels is another challenge to reduce implementation and running costs. Optimizing system design, management practices, and developing economically viable production models are necessary for the BFT adoption at scale; and (iii) creation of tailored BFT waste management practices (e.g., control and disposal of sludge). From an animal welfare perspective, research has shown that at high stocking densities (e.g., 400 and 500 shrimp/m²), the activities of digestive enzymes are reduced in a biofloc-based shrimp culture, as well as the immune status, leading to mortalities when challenged with V. harveyi [255]. Further research to understand the impacts that high-density rearing has on shrimp is needed to develop rearing methodologies that foster improvements in immunological and health outcomes of the shrimp.