Aerobic biological treatment systems, including nitrification–denitrification plants, are commonly applied for the biotreatment of domestic wastewater and a range of agro-industrial wastewaters, due to their simplicity in operation, low cost of installation, high efficiency, and ability to biologically remove nitrogen through nitrification–denitrification. During the activated sludge process, organic matter is oxidized using air, mainly to carbon dioxide and water, and the microbial flocs formed are separated in a sedimentation tank [78]. Despite the fact that effluents of high organic content could be subjected to anaerobic digestion, the inability to biologically remove nitrogen in an efficient and simple manner and the high cost of installation often make the activated sludge process attractive for the biotreatment of certain agro-industrial effluents, especially those in which the COD concentration is low or moderate, or those that can be co-processed with municipal wastewater or washings. Even though the anaerobic treatment of agro-industrial wastewaters has the benefit of the production of biogas, this is balanced by the high HRT required, increasing the volume of the required digesters and resulting in specific space requirements, as well as the instability of the process, which provides no assurance of stable and satisfactory energy production [79]. Moreover, aerobic treatment enables the effective removal of nutrients, which is considered a strong benefit of the process, as high quality effluents are produced, capable of satisfying the stricter standards for disposal, which are not met in the case of anaerobic treatment systems [80].

Thus, there are several examples of using aerobic biological treatment systems for the depuration of agro-industrial effluents. For instance, activated sludge was immobilized on polyurethane particles in an aerobic bench-scale bioreactor for the treatment of winery wastewater under a maximum organic loading rate of 8.8 kg COD/m³·d and a hydraulic retention time of 0.8 d. Even at an OLR of 3 kg COD/m³·d, the ability of the aerobic immobilized cell bioreactor to remove COD was high, recording a COD removal efficiency of 87% [81]. Moreover, Roveroto et al. [82] treated brewery wastewater in a fixed-bed batch reactor, which operated under an intermittent aeration of 3 h aeration in 4 h cycle and a hydraulic retention time (HRT) of 0.83 d. The COD and BOD of the raw brewery wastewater ranged between 2 and 10 g/L and 1.2 to 3.6 g/L, respectively, while the total nitrogen reached up to 0.08 g/L. The highest removal efficiency, 92%, was recorded in the bioreactor when the influent COD was 2.7 g/L and the COD/N ratio was 107. Under these conditions, the nitrification efficiency was 88% and the total nitrogen (TN) removal was 85%.

Antiloro et al. [40] investigated the biotreatment of citrus processing wastewater with a high organic content and essential oils concentration, i.e., between 20 and 30 g/L and 0.6 to 1.0 g/L, respectively, in an aerated lagoon system, reporting COD removal efficiencies from 59 to 97% and the establishment of a microbial community capable of coping with the increased concentration of essential oils. In addition, two aerobic granular sludge bench-scale SBRs operating under a sludge retention time (SRT) of 10 d and organic loading rates (OLRs) ranging from 3 to 15 kg COD/m³·d were used for the biotreatment of a citrus processing effluent of 5.5 g/L COD. At a neutral pH, the biosystem could remove COD by 90% regardless of the organic loading rate applied, although the reactor’s efficiency under acidic conditions declined to 75% when the OLR exceeded 7 kg COD/m³·d. Furthermore, Zema et al. [83] treated citrus processing wastewater of 5.0g/L COD and an essential oils concentration of 0.5 g/L under aerobic conditions in a full-scale treatment plant, reporting reasonable COD and essential oils removal efficiencies.

Moore at al. [84] treated wastewater deriving from mixtures of fruits and vegetables in an aerobic pilot-scale ultrafiltration membrane bioreactor (MBR), for potential water reuse. Lettuce, beets, carrots, and cassava were processed to produce the first wastewater mixture, while potatoes, carrots, apples, onions, lettuce, beets, and bananas constituted the raw materials for the production of the second mixture of wastewater. The COD and total Kjeldahl nitrogen (TKN) content of the first mixture were 1.5 g/L and 0.01 g/L, respectively, whereas the respective concentrations in the second mixture were 7.1 g/L and 0.23 g/L. The HRT in the two experimental schemes examined varied from 24 to 52 h, whereas the OLR ranged from 0.82 to 2.7 kg COD/m³·d in the first and from 2.9 to 6.5 kg COD/m³·d in the second experimental setup. For both fruit- and vegetable-derived effluents treated in the MBR, high COD removal efficiencies of 97–98% were recorded, whereas the TKN removal efficiencies exceeded 91% for both wastewater mixtures. In this case, the activated sludge system, in combination with UV disinfection and the implementation of activated carbon for color removal, could produce an effluent of enhanced quality, which could be used in the agri-food sector.

More than 10.5 million tons of coffee were exported by its producing countries in 2020 [85], a process that leads to the production of significant amounts of wastewater, since up to 45 kg of wastewater is generated during the pulping and washing of 1 kg of green coffee. Villa-Montoya et al. [3] treated coffee processing wastewater of a high organic content (COD of 7 to 15 g/L) and a TN concentration between 0.03 and 0.04 g/L in a sequencing batch reactor (SBR) under an OLR of 9 g COD/L.d, reporting that the intermittently aerated biological system achieved a COD removal efficiency of 92%. Coffee processing wastewater of a high COD concentration (17 g/L) was also treated in a constructed wetland system by Rossmann et al. [86], in order to achieve the efficient removal of nutrients and phenolic content. At an HRT of 11.8 d, the biosystem could remove total nitrogen (TN), total phosphorus, and total phenolic compounds by 69.1, 72.1, and 72.2%, respectively.

Microorganisms are an important source of enzymes, as they grow rapidly in a short period of time. In addition, a wide variety of agro-industrial residues and wastes can be used as substrate, thus reducing overall production costs and the use of natural resources while value-added products are produced. Enzymes of microbial origin can find a variety of applications in industry, such as in the production of food and beverages, as well as in the manufacture of chemicals and pharmaceuticals. The properties and activities of an enzyme are considered to be directly dependent on the strain that is capable of inducing them, while their effectiveness in biotechnological applications is being constantly and increasingly evaluated. Therefore, there is a strong scientific interest and a wide scientific field in the search for new strains capable of producing high-activity enzymes at a reduced cost with potential uses in industry [87]. Moreover, aerobic bioreactor systems treating agro-industrial wastewater can be considered as microbial cell factories producing a wide range of industrial enzymes, such as cellullases, xylanases, glycosidases, lipases, and proteases.

For instance, Zerva et al. [4] assessed the hydrolytic potential of an immobilized cell bioreactor treating caper wastewater at an elevated salinity (3.12 to 101 g/L). The non-halotolerant microbiota of the immobilized cells at a salinity of up to 20 g/L were able to highly hydrolyse celluloses, hemicelluloses, starch, fats, and proteins. Increased endo-1,4-β-xylanase activity above 1785 U/g protein was recorded throughout the experimental period. Endo-1,4-β-D-glucanase activity of 250 U/g protein was also reported, even though it was highly affected by the elevated salinity. Regarding polygalacturonase, its activity exceeded 533 U/g protein and further increased to 959 U/g protein under the highest salinity. Furthermore, β-1,4-D-glucosidase activity was above 510 U/g protein, while the increase in the organic loading rate and low salinity resulted in the elevation of α-1,4-D-glucosidase activity up to 905 U/g protein. Initial lipase activity was above 352 U/g protein but was affected by a salinity concentration of 1% w/v and decreased to 130 U/g protein. Moreover, Zerva et al. [5] treated pepper processing wastewater in an aerobic immobilized cell bioreactor and monitored the hydrolytic potential of bacteria isolated from the immobilized biomass of the biosystem, reporting a high endo-1,4-β-xylanase activity of 107,000, 72,000 and 70,000 U/g protein for three bacterial isolates belonging to the genera Nocardia and Gordonia. Bacterial isolates related to Aquincola, Microbacterium, Planococcus, Sphigopyxis, and Xanthobacter were also found to exert endo-1,4-β-xylanase activity from 29,700 to 37,400 U/mg protein.

In addition, several white-rot fungi can be used for the biotreatment of various agro-industrial enzymes and produce ligninolytic enzymes. For instance, a Phanerochaete chrysosporium strain was immobilized by Sharari et al. [88] on polyurethane foam for the treatment of bagasse wastewater and the simultaneous production of ligninolytic enzymes, reporting peroxidase activity of 260 U/L and laccase activity of 131 U/L, whereas xylanase activity of 74 U/L was also detected.

Moreover, Mafakher et al. [89] isolated lipase-and citric acid-producing yeasts from agro-industrial wastewater treatment plants. Among the 300 yeast isolates examined, 6 exhibited a high lipase activity, which were identified as Yarrowia lypolitica isolates.

The recent development and application of high-throughput sequencing techniques have led to a better understanding of microbial communities’ structure and functions in bioengineering systems. In the last decade, the implementation of molecular methods, such as next generation sequencing techniques, has permitted the elucidation of the microbial ecology and biotechnological potential of certain aerobic bioreactor systems treating agro-industrial wastewaters.

In that direction, by implementing high-throughput sequencing techniques, Fang et al. [90] stated the dominance of Zoogloea in the activated sludge of an SBR treating rice winery wastewater under an OLR of 2.4 g COD/L.d. Apart from the presence of Zoogloea species, Rhodobacter and Rubrivax were also detected in high abundances. The dominance of Zoogloea spp. in the activated sludge of this aerobic bioreactor system can find a biotechnological application potential, since this genus is considered an important PHA accumulating microorganism [91]. Bacteria of the genus Amaricoccus, Zoogloea, and Azoarcus were also identified in winery wastewater using FISH, whereas Amaricoccus species dominated the constructed clone library [92].

Moreover, in meat processing wastewater treated in an SBR, the activated sludge microbial community was dominated by the class Alphaproteobacteria, which are frequently identified in similar samples [93], where Amaricoccus spp. covered 11% of the microbial diversity in the SBR. Furthermore, the biotreatment of dairy wastewater in a full-scale aerobic SBR under an OLR of 2.5 kg COD/m³·d revealed the predominance of the genera Proteiniphilum, Byssovorax, Acidobacterium, and Zoogloea, which covered 35.9, 14.5, 10.1, and 8.3% of the total relative abundance [94], despite the fact that Proteiniphilum and Byssovorax bacteria are rarely reported as microbial constituents of activated sludge. The same authors also reported that Thiothrix and Leptothrix spp. were the main filamentous bacteria of the activated sludge system, with the presence of Thauera being involved with the formation of granular structures and the cohesion of the activated sludge due to the release of extracellular polymeric substances (EPS).

Other major inhabitants of activated sludge systems treating agricultural wastewater are members of the genera Bacillus, Pseudomonas, Thauera, Xanthomonas, Spingobacterium, and Comamonas, such as in aerobic biosystems treating olive mill [95], winery [96], and dairy [97] wastewaters.

In addition, Pires et al. [98] isolated bacterial and fungal strains from a coffee processing wastewater treatment plant. The bacterial isolates were mainly members of the phyla Proteobacteria, e.g., Acetobacter, Serratia, and Enterobacter spp.; Actinobacteria, e.g., Corynebacterium and Arthrobacter; and Bacteroidetes, e.g., Chrysobacterium. Regarding the fungal community structure, the majority of isolates were identified as yeasts of the order Sacharomycetales, such as Wickerhamomyces, Torulaspora, Kazachstania, Saturnispora, Meyerozyma, Hanseniaspora, and Pichia spp., which have been often detected in municipal wastewater treatment plants and in other biosystems treating agro-industrial wastewater, e.g., palm oil effluent [99,100]. Pires et al. [98] also detected filamentous fungi, such as Alternaria alternata and Fusarium oxysporum. Petruccioli et al. [101] also isolated yeasts from the activated sludge of an aerobic jet loop reactor treating winery wastewater, identifying microbiota such as Saccharomyces, Candida, and Trichosporum, reporting a link between the presence of Saccharomyces and the formation of biofilm.