Microorganisms are responsible for the suitable performance of all biological technologies described previously. A high number of microorganisms are able to degrade polyphenols in aquatic environments, including bacteria, fungi, and protozoa. Efficient biodegradation could be carried out by a single species [119,120] or microbial consortia [24,77]. During the design of a bioprocess, the selection of microorganisms or microbial consortia according to the nature of the water and the target pollutants is essential. The ability to achieve high performance will depend on the contaminant nature and the metabolic possibilities of the biomass in the bioreactor [91]. However, some drawbacks are found in urban or industrial wastewater, given the complexity of the matrices. Therefore, the microbial consortia employed as inoculum are generally selected by the technology configuration and influent composition since some microorganisms have competitive advantages in consuming, digesting, or degrading compounds under different abiotic and biotic parameters.

Given that phenol is widespread, some microorganisms have developed metabolic pathways for using it as carbon and/or energy source in several environments [1]. Undoubtedly, some microbial groups are more resistant to phenolic compounds. The microorganisms that are able to degrade polyphenols have been recognized in both the Bacteria and Eukarya domains. Among the best-known microorganisms that can successfully carry out phenol biodegradation, there are bacteria such as Bacillus, Pseudomonas, Flavobacterium, and Alcaligenes, as well as fungal representatives, such as Trichosporon, Aspergillus, Trametes, and the yeast Candida tropicalis [24,121].

Aerobic bacteria transform phenol into nontoxic intermediate compounds that enter into the tricarboxylic acid cycle through ortho- or meta-pathways of degradation (Figure 3) [12]. In both pathways, phenol is firstly converted into catechol by the monohydroxylation of the C₆ ring at the ο-position, which is catalyzed by phenol hydroxylase [91]. Phenol hydroxylase catalyzes the attachment of a hydroxyl group at the ortho-position of the aromatic ring, and then phenol is converted into catechol. This reaction is carried out by NADP-dependent flavin mono-oxygenase enzyme [12]. All mono-oxygenases include one atom of molecular oxygen in the corresponding substrate, while the other oxygen atom is reduced to H₂O by a hydrogen donor, which is different for each enzyme. In addition to the hydroxylation of phenol, which is the preferred substrate of the phenol hydroxylase, this enzyme can catalyze the hydroxylation of hydroxyl-, amino-, halogen-, or methyl-substituted phenols [12]. Chlorophenol and (choloromethyl) phenol hydroxylases are employed to convert the substrates into chlorinated catechols or chloromethylcatechols, which play a key role in ortho- or meta-pathways. Phenol hydroxylase also catalyzes the conversion of alkylphenols into alkylcatechols. The aromatic ring of catechol is further opened by catechol 1,2-dioxygenase, leading to the formation of succinyl-CoA and acetyl CoA, or by catechol 2,3-dioxygenase, leading to the formation of pyruvate and acetaldehyde. Moreover, long-chain alkylphenols, nitrophenols, chloronitrophenols, and bisphenols require specific peripheral degradation pathways [91]. The bacterial degradation of nitrophenols can start with mono-oxygenation (a mono-oxygenase catalyzes the nitro groups elimination as a nitrite ion by adding an oxygen atom), the reduction of the nitro group (a nitroreductase catalyzes the nitrogen group reduction into amino groups or hydroxylamine), reductive dehalogenation from halonitrophenol compounds (a reductive dehalogenase removes the halogen atom, following the oxidative removal of the nitro group), and dioxygenation (insertion of two hydroxyl groups with the removal of the nitro group as nitrite ion) [122,123,124].

Some nitrophenol-degrading bacteria have been isolated by utilizing media enriched in mononitrophenols, halonitrophenols, or polynitrophenols. Among the isolated strains were Arthrobacter nitrophenolicus sp. [126], Burkholderia sp. RKJ [127], Pseudomonas sp. [122], Rhodotorula glutinis [128], Sphingomonas sp. [122], and Paraburkholderia [129].

In Mediterranean countries, OWW has been widely studied due to its recalcitrant nature that is related to high polyphenol content. For example, Maza-Marquez et al. [26] demonstrated that the phenolic pollutants found in an OWW storage basin could be treated using specific bacterial taxa, such as Firmicutes and Clostridiales. Muñoz-Palazon et al. [24] observed that the microbial communities in AGS reactors treating high polyphenol concentrations were dominated by Lampropedia, Acinetobacter, Arenimonas, Pseudomonas, and Corynebacterium.

Eukarya microorganisms are widespread in environmental and engineering niches and play an essential role in the bioremediation field. Many studies have focused on phenolic compound degradation by fungi due to their ability to use organic pollutants as substrates for their growth. Some Ascomycota members have been isolated in systems designed for the treatment of OMWW with polyphenols as the sole carbon source, including Aspergillus niger, Penicillium sp., Fusarium sp., and Alternaria sp. [59]. The Basidiomycota phylum is the major fungal group that has members able to degrade toxic compounds due to their rich production of tyrosinases, laccases, and peroxidases [130]. Tyrosinases oxidate both monophenols and 1,2-diphenols (catechols) to quinones; laccases of a low-molecular-weight use 1,4-diphenols as substrate, which acts as monophenols and polyphenols; peroxidases are oxidoreductases that catalyze peroxide reduction and the concomitant oxidation of various substrates, including phenols [131,132]. These fungal enzymes are widely employed in industrial processes due to their role in improving organoleptic properties. For this reason, some authors highlighted the need for improved knowledge about the employment of wild-type and bioengineered fungi to obtain these enzymes of industrial interest [130,133].

In addition to bacteria and fungi, microalgae have also been recognized for their high capability to resist toxic compounds due to their extraordinary ability to produce extracellular laccases that allow for the biodegrading and transforming of aromatic compounds [134,135]. Microalgae can biotransform, mineralize, and remove compounds under phototrophic or mixotrophic conditions. Some phylotypes, such as Chlorella sp., can remove polyphenols under light or dark conditions [136,137]; moreover, it has been reported that Scenedesmus quadricauda and Ankistrodesmus braunii biotransform polyphenols in simpler compounds [138].

The immense diversity of the metabolic pathways and resistance of prokaryotic and eukaryotic microorganisms allows for the development of various strategies for biotechnological tools in order to provide a high-quality water effluent. However, further combined efforts among chemical, engineering, and microbiological areas have to be made to obtain higher yields via the microorganisms dwelling in engineering systems.