There are several mechanisms of bioremediation described for filamentous fungi (Figure 1). The first one is adsorption of the toxic compounds into the cell wall. Bioadsorption is a physico-chemical process in which the concentration of toxic compounds is adsorbed on the bio-surface of fungi. Absorption takes place via specific aminopolysaccharides that are part of the composition of the cell wall, such as chitosan or chitin (Kumari et al., 2016). The functional groups of glucosamine in chitosan act as metal absorbent sites for heavy metal chelation or complexation facilitating the reduction and recovery of heavy metal from the polluted environment (Alsharari et al., 2018; Geetha et al., 2021). Absorption is the predominant mechanism of bioremediation of the heavy metals Copper (Cu) and Cobalt (Co.) described for Trichoderma, Penicillium, and Aspergillus (Dusengemungu et al., 2020). In filamentous fungi Phoma sp. biosorption into fungal mycelia has an important role for some pharmaceutical compounds removal, until this bioadsorption reaches equilibrium (Hofmann and Schlosser, 2016). Filamentous fungi Mucor shows considerable promise to be applied as a mycoremediation agent for the removal of cyanobacterial toxins from aquatic environments due to excellent toxin uptake into the fungal cell (Balsano et al., 2015). Removal of Fe³⁺ and Co²⁺ by fungi Aspergillus sp. AHM69 and Penicillium sp. AHM96 was shown via biosorption and bioaccumulation on the biomass surface (El-Bondkly and El-Gendy, 2022).

The other mechanism of bioremediation is associated with biosurfactants production by filamentous fungi. These biomolecules reduce the surface/interfacial tension between fluid phases (da Silva et al., 2021). Lipopeptides, molecules consisting of a short amino acid chain, covalently modified with lipids are well known class of biosurfactants, proved suitable for bioremediation of crude oil (Carolina et al., 2021). The biotechnological potential of Penicillium, Aspergillus and Fusarium for Lipopeptides production is described (Gautam et al., 2014; Qazi et al., 2014; Bills et al., 2016). The produced crude biosurfactant or fungal strain Mucor circinelloides could be directly used for the mycoremediation of crude oil contamination in oil fields (Hasanizadeh et al., 2017). However, microbial biosurfactant production is still quite restricted, since the production costs are currently higher than chemical surfactants. Besides most bioprocesses show low yield and productivity.

The other mechanism of filamentous fungi to counteract with a toxic compounds is biomineralization or bio-precipitation. Oxalate is a key metabolite that plays a significant role in many metal and mineral transformations mediated by fungi. Oxalic acid, (COOH)₂ is a relatively strong organic di-acid with the ability of the oxalate anion to complex metals including those of Co, Cd, Cu, Mn, Mg, Ni, Sr, Pb and Zn (Gadd, 1999). It is generally stated that metal oxalate formation may confer protection from the potentially toxic effects of such metals (Johansson et al., 2008; Gadd et al., 2014). Oxalic acid produced by a variety of filamentous fungi (Gadd et al., 2014).

It is well described that in Aspergillus niger, oxalic acid synthesized by conversion of oxaloacetate to oxalate and acetate by a cytoplasmic oxaloacetate acetylhydrolyase. Oxaloacetate in turn synthesized from pyruvate, coming from glycolysis, by the action of pyruvate carboxylase (Pedersen et al., 2000a; Pedersen et al., 2000b). This pathway may be widely distributed in fungi (Gadd et al., 2014). Oxalate is potentially toxic in high concentration and needs to efflux from cells. It was demonstrated copper oxalates formation by A. niger (Frank-Kamenetskaya et al., 2021) that can be used to develop of copper bioremediation from soil. A strain of Aspergillus nomius, isolated from a heavily-polluted soil from a zinc smelting region, was able to precipitate zinc oxalate (Sutjaritvorakul et al., 2016).

Lead is one of the most widely found toxic metal contaminants in the environment arising from industrial activities (Flora et al., 2012). Complete removal of Pb from solution and extensive precipitation of lead oxalate (PbC₂O₄) around the mycelium of A. niger and Paecilomyces javanicus was demonstrated (Liang et al., 2016). Other study also demonstrated reduction of Pb toxicity by Aspergillus niger and Penicillium oxalicum via formation of insoluble Pb minerals, primarily lead oxalate (Tian et al., 2019). Penicillium chrysogenum was effectively utilized for the biomineralization of chromate and lead from an aqueous solution and contaminated soil. It was shown efficient fungal-mediated calcite precipitation of heavy metals in the remediation (Qian et al., 2017).

The above mentioned mechanisms include non-enzymatic process. The other strategies include biotransformation and biodegradation mediated by enzymatic systems. Enzymatic fungal-mediated biotransformation in turn, can be carried out by means of extracellular and intracellular enzymes. Extracellular enzymes catalyze variety of reactions (e.g., oxidative coupling products, hydroxylation, CO₂ emission, ether cleavage, aromatic ring fission, quinoid products formation and other) resulting in biotransformation of toxic compounds facilitating bioremediation processes (Singh et al., 2021). The biodegradation is particularly committed for filamentous fungi since they can produce the extracellular non-specific lignin-modifying enzymes, laccases, manganese peroxidases, lignin peroxidase, dye decolorizing peroxidases, peroxygenases (El-Gendi et al., 2022).

Decolourization is a process in which filamentous fungi are particularly effective (Al-Ansari et al., 2022; Dhir, 2022). This process involves the removal of color from a solution, often by breaking down the colored compounds present in the solution. Filamentous fungi have been shown to accomplish this through the production of laccase and manganese peroxidase enzymes (Bilal et al., 2016a; Bilal et al., 2016b). Laccase is a type of enzyme that can break down a wide range of colored compounds through oxidation, acting on a variety of colored compounds such as azo dyes and natural pigments (Srinivasan and Sadasivam, 2018). Therefore, fungal laccases were widely applied for the bioremediation of complex synthetic dyes by altering the dye molecules into non-colored, safer, and ecofriendly structures (Sanghi et al., 2009; El-Fakharany et al., 2016). Manganese peroxidase (MnP) is another enzyme that can be involved in decolorization by filamentous fungi. MnP uses hydrogen peroxide as a cofactor to oxidize a wide range of compounds, particularly lignin-derived compounds which are found in industrial effluents and are responsible for the color of the solution (Bilal et al., 2016b). The use of filamentous fungi in bioremediation processes can take place in different types of reactors, including solid-state fermentation, submerged fermentation, or adsorption-biodegradation (Svobodová and Novotný, 2018; Zapana-Huarache et al., 2020; Usuldin et al., 2021). The process can be improved by optimizing the environmental conditions, such as pH, temperature, and oxygen availability, and by selecting the appropriate fungal strains. It is also important to note that decolorization alone may not remove other pollutants in the solution, thus the process should be combined with other remediation techniques, such as biodegradation, in order to achieve complete remediation of the contaminated site (Bilal et al., 2016a; Bilal et al., 2016b).

On the other hand, polycyclic aromatic hydrocarbons are abundant and widespread contaminants for the environment. Aspergillus oryzae and Mucor irregularis isolated from crude oil efficiently degraded hydrocarbons from oil by the action of secreted laccase, manganese peroxidase, and lignin peroxidase (Asemoloye et al., 2020). Plastic pollution poses serious environmental problems, in part due to the extremely stable and durable nature of this polymer. Fungal secreted hydrolases (lipases, carboxylesterases, cutinases and proteases) able to modify the plastic surface, increasing its hydrophilicity (Vertommen et al., 2005). These enzymes were successfully used to degrade polyethylene terephthalate and polyurethane hydrolyzing chemical bonds in the polymer structures (Cregut et al., 2013; Webb et al., 2013). Highly stable carbon–carbon bonds in plastic polymers require oxidation before the depolymerisation process (Restrepo-Florez et al., 2014). These reactions efficiently facilitate secreted oxidoreductases (laccases and peroxidases) which are involved in plastic degradation into smaller molecules such as oligomers, dimers and monomers (Alvarez-Barragan et al., 2016). Fungal laccases and peroxidases are very promising enzymes in degrading polyethylene and polyvinyl chloride (Temporiti et al., 2022). Secreted fungal laccases and peroxidases enzymes can be effectively used for detoxification of heavy metals and pharmaceuticals (Olicon-Hernandez et al., 2017; Mousavi et al., 2021).

Intracellular enzymes participating in bioremediation of toxic compounds can be divided in two groups. First–cytochromes and second–glutathione transferases. The cytochrome P450 system is a large family of enzymes, mainly monooxygenases catalyzing reactions of hydroxylation, oxygenation, dealkylation, epoxidation of C=C bonds, reduction, and dehalogenation (Díaz-Cruz et al., 2014). It was shown that P450 play an indirect but crucial role in the process of clearance of cadmium and lead in filamentous fungi Phanerochaete chrysosporium belonging to the Basidiomycota phylum (Zhang et al., 2015). CYP63A2 P450 monooxygenase from this fungus oxidized polycyclic aromatic hydrocarbons, alkylphenols, and alkanes from crude oil (Syed et al., 2013). Cytosolic and mitochondrial iso-forms of P450 from Fusarium oxysporum and other fungi are used in degradation of dioxins (Guengerich and Munro, 2013; Sakaki et al., 2013). F. oxysporum P450 monooxygenases are promising catalysts in production of omega hydroxy fatty acids when heterologously expressed in Saccharomyces cerevisiae (Durairaj et al., 2015). It was demonstrated that several Aspergillus species are capable of degrading a carcinogenic contaminant Benzo [a]pyrene by the action of the cytochrome P450 monooxygenase (Loss et al., 2019).

Fungal glutathione S-transferases (GST) are detoxification enzymes which can catalyze the conjugation of glutathione to non-polar compounds containing an electrophilic carbon, nitrogen, or sulfur atom. By this mechanism, glutathione S-transferases are able to metabolize drugs, pesticides, xenobiotics, heavy metals and other toxic compaunds (Pocsi et al., 2004). GST have been reported to contribute to the defense against heavy metal stress in different filamentous fungi including A. nidulans (Fraser et al., 2002). Glutathione transferases play an important role in the intracellular reduction of Cr (VI) in fungi (Garcia-Hernandez et al., 2017). It was shown that the detoxification of penicillin side-chain precursors might depend on microsomal GST in P. chrysogenum (Emri et al., 2003). Fungal cytochromes can catalase a lot of different reactions, which enables them to degrade xenobiotics and pollutants (Syed et al., 2013; Chen et al., 2019; Wang et al., 2019; Carstens et al., 2020; Hu et al., 2020). Fungal enzymes, isolated from Basidiomycetes and Ascomycetes, show high ability of plastic waste biodegradation. Fungal laccases and peroxidases, generally used by fungi to degrade lignin, polyethylene and polyvinyl chloride, while esterases such as cutinases and lipases were successfully used to degrade polyethylene terephthalate and polyurethane (Temporiti et al., 2022).

Physical wastewater treatment process refers to separating particle matter and solids in sanitary and industrial effluents (Pirzadeh, 2022). Depending on the sewage type, fabric fragments, sand, plastic bits, and tree foliage may be in the wastewater entering the treatment plants. These particles can cause damage to the equipment (including pipes, pumps, and fittings) used in wastewater treatment. Furthermore, failing to remove these things puts a lot of strain on the machinery in biological and chemical wastewater treatment, lowering the output quality.

In the physical wastewater treatment process, mechanical procedures based on physical rules are employed to remove pollutants (Woodard, 2001). Physical operations are typically simpler and more quantitatively effective than other wastewater treatment methods. Physical wastewater treatment techniques remove pollutants using naturally occurring forces, including electrostatic attraction, gravity, van der Waal forces, and physical barriers (Tripathi and Misra, 2019). In general, the techniques involved in physical treatment do not lead in changes in chemical composition of the target compounds. In some cases, the physical state is altered, as in vaporization, and scattered substances are often made to agglomerate, as in filtration (Crittenden et al., 2012). The first phase in every wastewater treatment system is filtration (Gerba and Pepper, 2019). This procedure requires the separation of non-biodegradable contaminants from a wastewater treatment plant. Sedimentation, skimming, adsorption, aeration, and flotation are physical methods of wastewater treatment (Saravanathamizhan and Perarasu, 2021), as are barriers such as deep bed filters, screens, bar racks, and membranes.

Chemical wastewater treatment is another process of wastewater treatment. It is considered a tertiary treatment process that incorporates chemical treatment (Ahmed et al., 2021). Chemicals are used in this process, which involves separating or converting pollutants because of their chemical reaction. Chemical precipitation, neutralization, disinfection (ozone, chlorine, UV light), ion exchange, and adsorption are the most commonly used chemical treatment processes (Samer, 2015).

Biological wastewater treatment involves the use of microorganisms in wastewater treatment, a poorly understood process that combines biology and biochemistry (Sahu et al., 2019). This process is used in removing organic, soluble, biodegradable, organic and nutrient-containing compounds, and colloids, present in wastewater. The wastewater is introduced into a specifically designed bioreactor, where organic matter is utilised by bacteria (anaerobically or aerobically), fungi and algae (aerobically) (Samer, 2015). The bioreactor provides suitable environmental conditions for microorganisms to grow and utilize dissolved organic materials as a source of energy. The biological oxidation of organic substances will continue as long as the microorganisms receive oxygen and food from collected wastewater. Bacteria, which form the fundamental trophic level of the food chain in the bioreactor, carry out the majority of the biological process.

The conversion of dissolved organic molecules into thick bacterial biomass via bioconversion has the potential to purify wastewater (Meena et al., 2021). Following that, sedimentation is used to segregate the microbial biomass from the treated wastewater. Microorganisms breakdown organic materials via two distinct biological processes: biosynthesis and biological oxidation (Samer, 2015). Biosynthesis converts colloidal and dissolved organic materials into dense biomass, which then can be recovered via sedimentation. In this case colloidal and dissolved organic molecules are converted into dense biomass, which can then be removed via sedimentation. Some biological oxidation by-products, such as minerals, remain in the solution and are eliminated with the effluent.

The excessive amount of pharmaceutical compounds released into environments poses a long-term risk to humans and wildlife, even under low concentration (Angeles et al., 2020; Akerman-Sanchez and Rojas-Jimenez, 2021). Large range of common pharmaceutical compounds were found in wastewater treatment plants and effluent waters, including analgesics, antidiabetics, anti-inflammatories, antibiotics, anti-hypertensives, beta-blockers, diuretics, and lipid regulators negativelly. These compounds negatively impact on environmental and aquatic ecosystems health (Olicon-Hernandez et al., 2019; Akerman-Sanchez and Rojas-Jimenez, 2021). Filamentous fungi belong to the microorganisms responsible for the degradation of most organic compounds polluting environment (Bulkan et al., 2020; Ferreira et al., 2020). Increasing studies indicate that filamentous fungi can transform many of pharmaceutical compounds, including antibiotics, anti-inflammatories, β-blockers, etc., (Bulkan et al., 2020; Alamo et al., 2021; Kasonga et al., 2022). Recent studies have shown prospects of biotechnology based on filamentous fungi for almost complete elimination of a wide range of pharmaceutical compounds that may have ecotoxic effects in the environment (Table 2). Reports (Dalecka et al., 2020a; Dhiman et al., 2022) have shown that filamentous fungi can efficiently remove pharmaceutical compounds at level of 78%–100% from a synthetic wastewater media. Research of past years mostly have shown a slow rate of degradation of pharmaceutical compounds with a treatment duration of more than 26 days (Li et al., 2015; Badia-Fabregat et al., 2016; Mir-Tutusaus et al., 2017). However, studies with the white-rot fungus Trametes versicolor (Shreve et al., 2016) and recent results with species of Aspergillus, Mucor, Penicillium, Rhizopus, Trametes and Trichoderma demonstrate (Mohapatra et al., 2022; Shourie and Vijayalakshmi, 2022) demonstrated significant degradation with high removal rates in 4 h–10 days (Olicon-Hernandez et al., 2019; Dalecka et al., 2020b; Alamo et al., 2021; Kasonga et al., 2022). Using adsorption to solid supports, specifically, polyurethane foam carriers for immobilized white rot fungus Trametes versicolor resulted in 99.9% diclofenac removal after even 4 h during batch experiments (Stenholm et al., 2019). The choice of carrier and the level of cell immobilization are importance in this process. Whereas, experiments that utilized polyethylene-carriers with negligible immobilization of T. versicolor, a 98% total diclofenac removal was achieved only after one week investigation. To optimize the elimination of pharmaceuticals, the type of bioreactor acts as another important factors. The fungal fixed-bed reactor could be more suitable than the stirred tank reactor to remove pharmaceutical compounds from wastewater, since it was able to remove PhACs to a great extent and simultaneously detoxify real wastewater. A trickle-bed bioreactor (TBB) using fungal biomass immobilized on rice husks, achieved an elimination of 88.6% and 89.8% in synthetic and real wastewater, respectively (Tormo-Budowski et al., 2021). Additionally, toxicological tests showed a decrease in the hospital wastewater’s toxicity after the treatment in the TBB. The exploring with focusing on optimizing the conditions inside the bioreactors reveals as meangfull for the effective mycoremediation process (Akhtar and Mannan, 2020). A novel idea with effective and fast treatment of actual pharmaceutical wastewater containing β-lactam antibiotics was presented in recent research (Ji et al., 2021). Aspergillus niger mycelial pellets were used as biological carriers for displaying β-lactamase on the cell surface of fungi. This A. niger-Bla system significantly improved the removal of antibiotics for > 60% and demonstrated complete degradation of amoxicillin and ampicillin within only 1 h, and cefamezin at 80.45%.

Degradation of individual pharmaceuticals was more efficient than their elimination from а mixture. For example, diclofenac (5 mg/L) was completely removed by Trametes versicolor to below its detection limit (1 mg/L) within 8 h in the individual experiment vs. after 24 h in a mixture with the other pharmaceuticals (Alharbi et al., 2019). A similar trend was visible with trimethoprim (TMP), carbamazepine (CBZ), and sulfamethoxazole (SMX), with 95% vs. 39%, 82% vs. 34%, and 56% vs. 49% removal after 48 h with 5 mg/L of TMP, CBZ, and SMX individually or as mixtures, respectively.

Thе ability of filamentous fungi to degrade a wide variety of pharmaceutical compounds and their easy handling make them excellent tool for the bioremediation of emerging contaminants of pharmaceutical origin. The study of different carriers, such as solid ones for fungal cells or biological ones for their enzymes, type of fungal reactor serves as important role that can accelerate mycoremediation time and removal effeciency of pharmaceutical compounds and bring closer the time of their large-scale application for wastewater treatment.

Filamentous fungi can be considered as an important factor in bioremediation and heavy metal treatment due to their ability of biosorption, bioacumulation and metal recovery. Filamentous fungi capable to tolerating high metal concentrations, can decontaminate the environment encumbered with heavy metal pollutants (Manguilimotan and Bitacura, 2018; Kapahi and Sachdeva, 2019; Dusengemungu et al., 2021). Filamentous fungy can be used in recovery of many essential metals from various metal sources, including solid mine wastes and polluted soils, mine tailings and electronic waste, spent catalysts and low-grade ores solubilizing metals through the secretion of organic acids (Ghosh et al., 2020; Dusengemungu et al., 2021) (Table 3).

One of the most studied in this regard is the genus Aspergillus which demonstrates high leaching and removal capacity, as well as multi-metal tolerant properties. The removal capacity of A. niger was reached at 100% from Cd and Pb polluted sewage in 6 days and only 65% was reached when using Rhizopus oligosporium (Ghyadh et al., 2019). Aspergillus species are known for their ability to tolerate different metals such as Al, Cd, Co, Cr, Cu, Fe, Mn, Mg, Ni, Pb, Zn, and U (Dusengemungu et al., 2021; Naveen Kumar and Prakash, 2021). A unique microbial biotechnology for simultaneous bioremediation and biomining of twelve ionic metals overcoming the obstacles of multimetal toxicity to microbes were described. Three new strains of Mucor hiemalis was demonsrated multimetal-resistance, hyper-accumulation and elicitation power, intracellular fixing and deposition of mercury as nanospheres in sporangiospores (Hoque and Fritscher, 2019). Microbiomes, germinated spores and dead insoluble cellwalls of these strains removed > 81%–99% of applied Al, Cd, Co, Cr, Cu, Hg, Ni, Pb, U, and Zn simultaneously and furthermore enriched precious Ag, Au and Ti from water all within 48 h (Hoque and Fritscher, 2019).

The eco-friendliness and cost-effectiveness of recent advances in metal biorecovery and bioremediation by fungi show that filamentous fungi have an exceptional impact for industrial-scale bioremediations in future operations. Problems of optimization of metal recovery technology, how to extract metals from the cells after bioaccumulation/biosorption, as well as exploration of optimal alternative sources of energy for fungal growth are challenges for the current research community, that will be necessary to overcome for commercialization fungal bioremediation.

The use of microorganisms for bioremediation and restoration of oil hydrocarbons contaminated soils and aquatic ecosystems have the challenge that a huge amount of petroleum hydrocarbons accumulated in environments that are of great toxicity (Varjani, 2017; Chicca et al., 2022). Bioremediation of crude oil polluted environments is often limited by the scarcity microorganisms with complementary substrate specificity required for degrading different hydrocarbons (Varjani, 2017; Anno et al., 2021; Chicca et al., 2022). Filamentous fungi are reported for their ability to degrade hydrocarbon pollutants, similar to many bacteria (Widdel and Rabus, 2001; Xu et al., 2018; Zahri et al., 2021), yeasts (Rusyn et al., 2003; Farag and Soliman, 2011; Al-Dhabaan, 2021) and algae (Al-Hussieny et al., 2020; Anno et al., 2021; Ghodrati et al., 2021). Depending on the strain of filamentous fungi characterized the rate of crude oil removal efficiencies ranged from 30.4% to 98.1% during 7–10 days (Table 4). Consortia of filamentous fungi and bacteria e.g. Aspergillus and Bacillus, was more effective in bioremediation and reached 99.0% in comparison with monocultures which utilized 98.0% and 20.0% in 7 days (Perera et al., 2021). The ability of Penicillium sp. to tolerate oil pollutants from 2.5% to 10% and degradate more than 50% suggest that it could be employed as an bioremediation agent for restoring the ecosystem when contaminated by oil (Vanishree et al., 2014; Dirisu et al., 2018). Among 84 filamentous fungal isolates belonging to eight different genera, Penicillium polonicum AMF16, P. chrysogenum AMF47 and two isolates affiliated to P. cyclopium, were determined as the most promising isolates for bioremediation of crude oil pollution (1%–5%) in the marine environment within the frame of bioaugmentation or biostimulation processes (Maamar et al., 2020). Degradation of petroleum hydrocarbons both by single filament strains and in synergism with bacteria allows progressive increases in bioremediation of contaminated sites.

Wastewaters containing pollutants such as pharmaceutically active compounds, heavy metals, aliphatic and polycyclic aromatic hydrocarbons, herbicides, pesticides, surfactants, dyes, personal care products and others can be purified by filamentous fungi (Ferreira et al., 2020; Morsi et al., 2020). Waste or side streams generated from the agricultural, forest, industrial, food and municipal sectors can be converted to value-added components by these organisms. Side streams are generally rich in carbohydrates (lignocellulose, starch, sugar), proteins, fat, minerals, etc., that can be converted to a range of value-added components such as fungal biomass, ethanol, hydrolytic enzymes, and organic acids.

Wastewaters, in contrast to side streams, contain minor amounts of carbohydrates and nitrogen sources commonly used by filamentous fungi. Thus, for removal of pollutants, additional nutrients should be spent to support growth of filamentous fungi. As a result, fungal biomass and enzymes are only obtained value-added products. The use of fungal biomass extracts as nutrients can be applied to enrich wastewaters or side streams where nutrient supplementation is required (Nair et al., 2017). It is necessary to classify side streams aimed for bioremediation, focused on removal of pollutants, and those aimed for valorization into products, for integration into anthropogenic activities. Some strategies were proposed for integration of valorization of side streams with removal of pollutants from wastewaters by filamentous fungi. For example, paper and pulp industries produce side streams that have been considered in both perspectives (Ferreira et al., 2020). However, there are no commercial processes presently known.

Filamentous fungal biomass is the main value-added component. It is generated independently of the intended valuable product to be produced. Fungal biomass grown in different side streams contains 40%–60% protein, as well as profiles of amino acids and polyunsaturated fatty acids similar to those in fishmeal and soybean meal, which are the main protein sources for animal feed. Several representatives of filamentous fungi, e.g., A. oryzae, Fusarium venenatum, Monascus purpureus, Neurospora intermedia, Rhizopus microsporas, Rhizopus oligosporus, and Rhizopus oryzae have been used for production of fermented foods, and are recognized as GRAS (Generally recognized as safe) microorganisms (Ferreira et al., 2020; Sar et al., 2022b). Their GRAS status is a necessary point for consideration of fungal biomass for feed applications. Filamentous fungi have been used for biomass production on a variety of food industry side-streams such as fish industry wastewaters, vinasse, olive oil mill wastewater, thin stillage, etc., (Ferreira et al., 2015; Karimi et al., 2019; Sar et al., 2020a; Sar et al., 2020b; Sar et al., 2021). It was described that fungal biomass production by Rhizopus delemar at an industrial scale contained 53% crude protein from edible potato protein liquor (Sar et al., 2022b). The R. delemar fungal biomass can be a promising raw material for feed and food production, since its protein and fatty acid profiles include 41% essential amino acids and 33% polyunsaturated fatty acids (Sar et al., 2022a).

Despite the fact that fungal biomass first of all is considered as a promising material for feed and food production, other potential applications of residual fungal biomass are proposed. The cell wall of fungal biomass contain chitosan, chitin, and β-glucans, with confirmed immune-stimulation activities when used in feed recipes (Karimi et al., 2018). Additionally, potential applications of chitin and chitosan in pharma, cosmetics, bioplastics, biopolymers, and agricultural sectors are well described (Isaza-Perez et al., 2020).

The filamentous fungus Mucor indicus provided promising results in heavy metal removal from wastewaters (Javanbakht et al., 2011). The biomass of this fungus has shown a great potential to be used as a rich nutritional source. Cells of Mucor indicus are great sources of chitosan and polyunsaturated fatty acids particularly γ-linolenic acid (Karimi and Zamani, 2013). Moreover, this fungus produced high ethanol production levels during fermentation of glucose and lignocellulosic hydrolysates, which is an important value-added product. Increase of ethanol yield from glucose was reached by supplementation with fungal biomass autolysates (Asachi et al., 2011).

Aspergillus oryzae and Neurospora intermedia were employed for the production of ethanol and high-protein biomass by cultivation on enzymatically liquefied bread-waste medium (Kawa-Rygielska et al., 2022). The cultivation of Neurospora intermedia in wheat-derived thin stillage resulted in extra ethanol production (Ferreira et al., 2015). Fusarium oxysporum is among the few filamentous fungi able to ethanol production directly from lignocellulose biomass. This fungus revealed the ability to produce ethanol from Ficus fruits employing a mild hydrothermal pretreatment without supplementing any extraneous enzymes using (Nongthombam et al., 2022). A cellulolytic thermophilic filamentous fungus Myceliophthora thermophila revealed huge potential for ethanol production from glucose and cellobiose. Recombinant strains expressing the cellodextrin transport system from N. crassa and alcohol dehydrogenase from Saccharomyces cerevisiae produced increased amounts of ethanol from cellobiose during fermentation at 48°C (Li et al., 2020).

Filamentous fungi play a significant role in the production of a wide range of lignocellulolytic enzymes, which are important value-added products (Ghosh, 2015; Ghosh et al., 2021). Such hydrolytic and oxidative enzymes are used for the production of important metabolites. Wild type strains have limited efficiency in enzyme production. Despite great progress in optimizing the cultivation conditions for enzyme production (Ferreira et al., 2016), molecular engineering methods were used for more pronounced improvement of the fungal production of lignocellulolytic enzymes. Constitutive production of pectinases (Alazi et al., 2019) and arabinolytic enzymes (Reijngoud et al., 2019) in Aspergillus niger were reached by point mutation in GaaR and AraR regulators, respectively. Deletion of the negative regulator CreA resulted in higher production of hemicellulase (Robl et al., 2018) in A. niger. Overexpression of mutated AraR in Penicillium oxalicum lead to constitutive production of α-L-arabinofuranosidase (Gao et al., 2019). Deletion of the regulatory gene Atf1 increased cellulase and xylanase production in P. oxalicum (Zhao et al., 2019). Deletion of repressors SxlR and Rce1 in Trichoderma reesei significantly stimulated xylanase (Liu et al., 2017) and cellulase (Cao et al., 2017) activities, respectively. Constitutive and increased production of xylanases and cellulases was also reached using the recombinant Trichoderma reesei overexpressing an artificial transcription activator Xyr1-Cre1b (Zhang et al., 2017).

Organic acids, predominantly citric, gluconic and itaconic acids, are value-added compounds produced by filamentous fungi (Ferreira et al., 2016). Citric acid production is the second largest fermentation product after ethanol production (Dhillon et al., 2013). Citric acid is mostly used in the food industry. Currently, A. niger is used for large scale production of this acid from sucrose or glucose containing substrates such as molasses or glucose syrup (Tsay and To, 1987; Show et al., 2015). To decrease citric acid production costs, other cost-effective substrates were investigated, e.g. apple pomace, orange processing waste, starch, rape seed oil (Behera, 2020). Huge efforts were made to optimize the fermentation process (Barrington et al., 2009). A significant increase of citric acid production was reached with metabolic engineering approaches of A. niger directed to carbon utilization and respiratory chain improvement, precursor biosynthesis enhancement, by-product removal and feedback inhibition reduction improvement (Tong et al., 2019).

Gluconic acid is an important biotechnological product used in food, feed, beverage, textile, pharmaceutical and construction industries. Gluconic acid produced with A. niger from glucose can be done at an industrial scale (Ramachandran et al., 2006; Yan et al., 2022). Other representatives of Aspergillus and Penicillium spp. have also been recognized as robust producers of this acid (Ma et al., 2022). Environmental and economical friendly processes of gluconic acid production trended to replace those using glucose and sucrose form waste products (e.g., hydrolysates of sugarcane, corn stover, corn cob, tea waste, starch, inulin, whey, figs, bananas, grapes, surpluses, wastepaper and lignocellulose) (Ferreira et al., 2016).

Itaconic acid is widely used in chemical synthesis industries (Wierckx et al., 2020). It was reported that itaconic acid suitable for the synthesis of antimicrobial biopolymers, drug carriers, intelligent food packaging, superabsorbent polymers, hydrogels in water treatment and analysis (Teleky and Vodnar, 2021). Itaconic acid production is carried out by fermentation more commonly using Aspergillus terreus from molasses or glucose (Huang et al., 2021). But currently several filamentous fungi are genetically engineered to produce this acid in high quantities and on different bio-wastes substrates (Sun L. et al., 2020b). Overall, filamentous fungi have great potential for further applications as robust producers of value-added products.

Furthermore, fungal biomass grown in heavy metal-rich media can be used as a source of nanocatalysts and nanoparticles (NPs) with potential application in chemical industries and micropollutant removal approaches (Huang et al., 2018; Kratosova et al., 2019). Mycosynthesis of metal-containing nanoparticles is alternative to conventional physico-chemical processes (Sebesta et al., 2022). This is a innovative biological approach to nanoparticle synthesis which leads its beginning from 2001 (Mukherjee et al., 2001). Then, formation of silver and gold nanoparticles using the fungus Verticillium was shown below the cell wall surface due to reduction of the metal ions by enzymes present in the cell wall membrane. NPs can be produced extracellular, outside the cell walls, which makes their separation from the biomass a simple process (Yadav et al., 2015; Priyadarshini et al., 2021). Some NPs synthesize intracellular, on the cell walls and even on the inner side of the cell walls (Mukherjee et al., 2001; Priyadarshini et al., 2021). Currently, nanoparticles of a wide range of different chemical compounds are known which are synthesised with the help of а filamentous fungi, such as metal Ag, Au, Cu, Pb, Pt, and bimetallic Ag-Au NPs, and also oxides, such as BaTiO3, Bi2O3, CoFe2O4, Co3O4, Fe2O3, Fe3O4, NiO, TiO2, ZnO, and ZrO2 (Mousa et al., 2021; Priyadarshini et al., 2021; Sebesta et al., 2022). Myconanoparticles can be used in various fields, i.e., in biomedicine, antimicrobial applications, catalysis, biosensing, mosquito control, and precision agriculture (Sebesta et al., 2022).