Beneficial Roles of Fungi: History
Please note this is an old version of this entry, which may differ significantly from the current revision.
Subjects: Mycology

Besides plants and animals, the Fungi kingdom describes several species characterized by various forms and applications. They can be found in all habitats and play an essential role in the excellent functioning of the ecosystem, for example, as decomposers of plant material for the cycling of carbon and nutrients or as symbionts of plants. Furthermore, fungi have been used in many sectors for centuries, from producing food, beverages, and medications. 

  • biodeterioration
  • filamentous fungi
  • fungal biotechnology
  • natural products
  • secondary metabolites

1. Introduction

Fungi are the kingdom of those organisms whose species can populate practically all ecosystems. They are found as free-living and symbiotic unicellular or multicellular organisms and exist under varied morphologies [19]. They exist in almost all environmental types, from soil to water, and are best known for their essential roles in ecology as decomposers and symbionts. Fungi have also been used for centuries in several practices in the food and medicine fields. Recently, fungi have emerged as a valuable resource in modern biotechnology, with numerous applications across different sectors and as a sustainable candidate.
Fungi appear in various sizes, starting with microfungi such as molds and yeasts and progressing to macromyctes such as mushrooms or truffles. The macro-sized fungi are most often used for human consumption as supplements or food; on the other hand, the micro-sized fungi, including species such as Aspergillus, Penicillium, and Saccharomyces, are used for synthesizing enzymes and metabolites. According to these described abilities, fungi are considered one of the cornerstones of modern biotechnology [20].
Fungi indubitably dominate the biotechnology sphere; therefore, it is expected that their utilization is going to grow exponentially hereafter. They play a crucial role in various industrial processes, including manufacturing enzymes, pigments, vitamins, and so on [21]. Moreover, they are used to manufacture different types of food pigments such as benzoquinone (Penicillium europium), anthraquinones (Paecilomyces farinosus), melanin (Aspergillus spp.), and β-carotene (Blackeslea trispora) [8,9].
Fungi could contribute to the aspiration to develop more sustainable manufacturing to protect the environment, being an optimal candidate to produce several products such as textiles and myco-leather, biofuels, building materials, wastewater treatment, and sustainable meat substitutes [4,22,23].
Before people identifed the different fungi species and understood the definition of fungi, they had been used to produce various food in different parts of the world, such as fermented food, bread, wine, and cheese [20]. Today, a significant part of worldwide cuisine is represented by products made with fungi, usually products that result after fermentation.

2. Medicine/Health

Natural products (NPs) produced by fungi are responsible for several effects, such as antimicrobial, immunosuppressive, anticancer, antidiabetic, immunomodulatory, and anti-inflammatory effects, many of which have been developed as treatments and have potential therapeutic applications for human diseases.
NPs such as non-ribosomal peptides (i.e., penicillin produced by Penicillium rubens; cephalosporin C by Acremonium chrysogenum, pneumocandins by Glarea lozoyensis and Pezicula (Cryptosporiopsis), or ribosomal peptides (amatoxins, piperazines), polyketides, lipopeptides, lipodepsipeptides and secondary metabolites produced by fungi mediate antimicrobial resistance and virulence and act in competition against other microorganisms [24].
Regarding antibiotic production by filamentous fungi, it has been proved that they initiated the golden era of natural antibiotics in the 20th century, as a consequence of extensive antibiotic use, especially in hospital settings, with the appearance of antimicrobial resistance phenomenon in the 21st century, especially to ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) [25].
Table 1 lists the NPs known as antimicrobial agents produced by different filamentous fungi strains or macromycetes.
Table 1. Antimicrobial agents produced by filamentous fungi.

3. Fungi in Agriculture

Fungi can also act as biological control agents against plant pathogens. Trichoderma, for instance, demonstrated antagonistic effects against a wide range of plant-pathogenic fungi [13,70,71,72,73]. Trichoderma species have been used intensively in different biotechnological fields. Even so, they represent an outstanding contribution to agriculture because they show an excellent potential to defend against disease crops and attenuate the unfavorable conditions that can affect plant growth and stimulate plant growth [74,75,76,77,78]. These fungi are involved in biocontrol applications, versus fungi that can be plant-pathogenic, oomycetes, or nematodes [79]. Several fungi are used to control insect pests; for instance, species such as Beauveria bassiana attacks corn borer, Verticillium lecanii is known to control whitefly and aphids, and Metarhizium anisopliae are used against scarab larvae [34,80,81]. The action of the fungi is to infect the body surface, which leads to the attachment of the fungus to the integuments of the affected insect, where it will develop and continue to proliferate until the fungus entirely covers the insect [82]. Plant-parasitic nematodes depict another threat to the wellness of plants. Using fungi can be a sustainable strategy to avoid the intensive use of chemical nematicides. The leading group of filamentous fungi that were studied for the biocontrol of nematode pests is known as Trichoderma. The mechanisms involved in damaging nematodes can be found in the antibiosis (production of secondary metabolites), enzymes, or space competition [83].
The presented applications have the potential to improve crop yield, reduce the use of synthetic fertilizers and pesticides, avoid the use of toxic compounds, and promote sustainable agriculture practices. Therefore, fungi have an essential contribution to the agriculture sector, and they must be exploited [84,85,86].

4. Industry

Fungi play an essential role in the food industry. They have been used since ancient times for various purposes, such as fermentation, production of enzymes, and as a source of food.
For centuries, humans learned to select and collect several macroscopic fungi known as mushrooms. They can be wild-harvested or commercially raised, and they are rich in protein; also, they can develop on inexpensive substrates, sometimes even agro-industrial wastes [87]. The most frequently farmed species worldwide are A. bisporus, P. ostreatus, Flammulina, and Lentinula edodes, used in salads, soups, and other recipes. Many additional mushrooms are collected from the wild for personal use or sale, amongst which are king boletes, milk mushrooms, morels, chanterelles, truffles, black trumpets, and porcini mushrooms. They frequently appear in upscale cuisine [88].
Filamentous fungi have long been used to produce fermented foods such as cheese, bread, and beer. Soy sauce, miso, tempeh, mold-cheeses, and alcoholic beverages, including beer, wine, and spirits, are all products of traditional fungi and yeast fermentation techniques. Using fungi in these industries has significantly improved the final products’ quality, taste, and shelf life. One example of the use of filamentous fungi is cheese production. The first evidence of various cheese types dates from 897 for Gorgonzola, 1070 for Roquefort, and 1791 for Camembert [89]. Mold-ripening is the central aspect for an increased quality of the cheese for a reason during this process, as the flavor and consistency are improved. P. roqueforti makes blue cheese (Roquefort, Gorgonzola, Danish blue, etc.). It produces blue-green veins and gives the cheese its distinctive flavor after inoculation and growth [90]. On the other hand, Penicillium camemberti is inoculated on the surface of the cheese, and it changes the consistency—a soft texture—more than the flavor. These types of cheese are Camembert and Brie [91].
Molds have been used to manufacture fermented sausages since the Greek and Roman empires, where fermented and air-dried sausage had widespread popularity among peasants due to its long-term stability at room temperature as a replacement for refrigerators nowadays. Various types of meat, including cow, goat, horse, lamb, pork, and chicken, are used to make salami [92]. Penicillium nalgiovense is most frequently used as a starting culture when curing fermented meat products; also, the species is recognized as safe to use [93].
The potential use of fungi is great because, currently, farming is conducted at higher rates. There is a need to find other alternatives to avoid soil erosion speeding up and environmental pollution; therefore, the alternative is microorganism cultivation aiming at the production of edible biomass [94]. Quorn™ is a company with fungi-based food products producing dried fungal biomass from Fusarium venenatum. The product is a mycoprotein, low-fat, low-calorie, cholesterol-free food that is highly popular in Anglo-Saxon nations [95]. Mycoprotein is known to help against body weight issues because it gives a feeling of satiety. Therefore, an investigation of the safety of F. venenatum mycelia for human eating was conducted between 1970 and 1980 following the isolation and subsequent suitability testing of F. venenatum (at that time, still known as F. graminearum). The potential for the fungus to create mycotoxins was a significant worry, as many Fusarium species are notorious for producing these toxins due to their role as phytopathogens [77,96].
For the production of Japanese traditional goods, such as seasonings or alcoholic drinks (soy sauce, miso, soju), Aspergillus oryzae is the predominant species used in fermentation processes. Starting in China between 3000 and 2000 years ago, koji became a popular item in Japan with the purpose of a starter for secondary fermentation [97]. Applying A. oryzae spores to heated rice produces koji. The resulting mixture is combined with soybeans or other steamed rice, water, and yeasts to ferment. Besides A. oryzae, other filamentous fungi are used to make koji, such as Aspergillus sojae, Aspergillus kawachii, and Aspergillus awamori [98].
Manufacturing alcoholic beverages such as wine and beer is another common usage of the fungal species in the food industry. For example, Botrytis cinerea, a plant-pathogenic fungi, is exploited in southern France and other locations to increase the sugar level in grapes before harvesting, producing “noble rot,” a sweet and premium wine [99]. For centuries, mankind has used Saccharomyces yeasts to make beer, bread, and wine. Since high quantities of ethanol harm most other bacteria, yeasts have historically been utilized as efficient methods to protect food and beverages’ nutritional value and security. The most well-known among all the beneficial yeasts is S. cerevisiae. It can be utilized to make wine, beer, and bread. Additionally, kefir is created by the symbiotic relationship between bacteria and Saccharomyces yeasts [100].
One of the numerous beneficial features of fungi is the synthesis of fungal enzymes and organic acids. Cellulase (Penicillium funiculosum, Trichoderma viride), α-amylases and invertase (A. niger, A. oryzae), proteinases (A. oryzae), and citric acid (A. niger) can be listed among them.
Several fungal species have been used regarding food processes since the beginning of agriculture. Fungal biodiversity is undoubtedly an important provider of resources for food as well as other higher value uses.
In the present, society confronts many manufactured challenges, among which high pollution levels or the lack of nutritional resources to support population growth occupy a central position [101,102]. The transition to a zero-carbon sustainable bioeconomy is the only direction that offers humankind the possibility to address these challenges, and it involves the transformation of a linear economy into a sustainable circular economy. Microorganisms are critical players in the circular economy since they harbor many intrinsic characteristics that recommend them for biobased industrial applications [23,102]. Among microbial strains with industrial potential and a high impact on the circular bio-economy, fungal strains have the unique metabolic ability to convert many organic materials (including wastes) into various by-products relevant to different industrial applications [23].

5. Fungi and the Environment

Currently, concerns about environmental safety are emerging since there are issues relating to pollution and toxic wastes. Therefore, there is a need to develop new strategies to sustain the environment’s health. Fungi are an integral part of the environment and play essential roles in many ecosystems. Besides the impact on nutrient cycling, decomposition, and soil health, fungi exhibit great potential for developing strategies that enhance environmental protection. For instance, in the fight against pollution, climate change, and various other issues, fungi are quickly surfacing as essential protagonists, involved in practices such as the bioremediation of pharmaceutical compounds, agricultural wastes, or degradation of various pollutants.
Mycoremediation is mediated by two mechanism types: enzymatic (fungal secreted enzymes) and non-enzymatic (adsorption of toxic compounds inside the cell wall, biosurfactants production) [253]. For example, filamentous fungi belonging to the Trichoderma, Penicillium, and Aspergillus genera are able, through absorption mechanisms, to absorb heavy metals such as copper and cobalt [254].
A study by Asemoloye et al. established that two fungal strains belonging to Mucor irregularis and A. oryzae, isolated from oil-contaminated places, could be used to clean up the soil after hydrocarbon contamination. Moreover, the two fungi displayed a remarkable capacity to degrade hydrocarbons [255].
Filamentous fungi are highly efficient in the process of decolorization. There is evidence that filamentous fungi produce the enzymes laccase and manganese peroxidase to achieve this. By converting complex synthetic dye molecules into non-colored, safer, and environmentally secure structures, fungal laccases were widely used for bioremediation [253]. It has been demonstrated that microorganisms exploit agricultural waste, specifically cellulose—the most renewable source of biomass in the biosphere—to produce valuable goods, such as sugars, cheap energy resources, and enzymes. Waste products from industry and agriculture are some of the things that pollute the environment [228]. Their transformation into beneficial products might lessen the issues they create. These wastes, including grains, leaves, corn cobs, and other materials, are underutilized.
As mentioned in the previous section, fungi can secrete cellulase, enzymes responsible for breaking down the cellulose in agricultural wastes into simple glucose molecules. Cellulolytic fungi, including Chaetomium, Fusarium, Myrothecium, and Trichoderma, produce celluloses through cellulolysis [256].
Another way to save the environment is using renewable energy from living organisms, known as biofuels. Biodiesel production was greatly enhanced by cultivating filamentous oleaginous fungi with lignocellulosic biomass, such as Mortierella isabellina and Aspergillus terreus [257]. A second way to produce biofuels is to develop bio-ethanol. Biomass of crops from grains and corn, rich in sugar and starch, is the base of bio-ethanol production. Filamentous fungi can convert sugars to ethanol. The pre-treatment of the biomass is realized with the aid of fungi and lignin-degrading enzymes (pectinases, xylanases, mannanases). Pre-treatment methods can improve enzyme cellulose availability during enzymatic hydrolysis, which converts sugars into fermented ethanol [258].
Utilizing biofuels is an excellent alternative to diminish the use of petroleum oil, which leads to reducing carbon dioxide emissions, air pollution, and a safe environment.
The additional use of fungi to enhance environmental wellness is described by a new strategy named mycofiltration. Mycofiltration, or the process of treating contaminated water by passing it through a network of fungal mycelium, is one way that fungi are used in mycoremediation [259]. For example, a preliminary study by Taylor and their team proved the use of basidiomycete Stropharia rugoso-annulata as an adjuvant to improve synthetic stormwater Escherichia coli removal through wood chips [260].

6. Research

In order to facilitate the study of particular biological phenomena, yeasts and filamentous fungi are used as research model organisms. Studies on these fungi provide relevant biological insights into other organisms, such as genetics, cell biology, meiosis, and pathogenesis. Yeasts and filamentous fungi are fascinating lower eukaryotes involved in understanding cellular processes. Their advantages are that they are easy to grow on inexpensive media and have easy access to molecular and classical genetics. The fact that fungi are more closely related to animals than plants underscores these organisms’ value as convenient models of human cells [261]. Fungi provide an excellent model for understanding the structure and function of chromatin in both actively transcribed regions (euchromatin) and transcriptionally silent regions (heterochromatin). Saccharomyces and Aspergillus are among the most prevalent fungi preferred by geneticists and molecular developmental biologists, but the first species used was Neurospora. Learning about epigenetic phenomena in other systems without the filamentous fungus N. crassa would have been challenging or impossible. S. cerevisiae, for instance, does not have the same characteristics in Neurospora, including DNA methylation and unique RNA interferences that act in mitotic and meiotic cells. Moreover, it contains an (RNAi)-based silencing system [262].
The initial usage of fungi for nanotechnology applications dates back to the early 2000s, making fungal nanotechnology a relatively new field of study. For example, palladium is a precious metal frequently used in catalysis, and in 2002, researchers at the University of California, Riverside, reported synthesizing palladium nanoparticles using a fungus called N. crassa. It has now been proven for the first time that fungi can operate as biological factories to create nanoparticles with distinct features. Since then, fungal nanotechnology has proliferated and has a wide range of potential uses, including the production of antibacterial agents, biosensors, and drug delivery systems. In addition, researchers are investigating methods to create various nanoparticles with varying shapes, sizes, and surface qualities utilizing several fungal species, including Aspergillus, Fusarium, and Trichoderma [263]. Apart from S. cerevisiae, many other yeast species, such as Kluyveromyces (K. marxianus and K. lactis); Pichia (Pichia pastoris renamed Komagataella phaffii, Pichia anomala renamed Wickerhamomyces anomalus); Hansenula polymorpha (renamed Ogataea polymorpha) and Yarrowia lipolytica were described as suitable research models, especially for biotechnological studies. Members of K. marxianus species are Crabtree-negative, can metabolize a broad spectrum of low-cost feedstocks such as whey and dairy industry wastes, and presents an exceptional ability to grow at elevated temperatures, thus being helpful in their use as a versatile host for a wide range of applications in the food, feed and pharmaceutical industries [264,265]. Y. lipolytica is considered a real industrial workhorse—the most extensively studied non-conventional yeast. Members of this species are strictly aerobic and are used to produce a variety of industrially important metabolites such as lipids, biosurfactants, and enzymes. Additionally, Y. lipolytica was used as a research model for dimorphism studies in yeasts and as a popular system for expressing heterologous proteins [266,267]. K. phaffii was recognized as an important host for the industrial production of heterologous proteins due to its possibility to run high-density fermentation associated with high secretory efficiency and its specific eukaryotic post-translational modifications [268].

7. Conclusions

Fungi have been used as a cell factory to produce enzymes and small molecule compounds for almost a century. Biomass produced during these production processes has generally been considered a waste stream. This inconvenience may change in the future since fungal biomass is now being explored as the basis of sustainable bio-materials. In agriculture, the presented applications have the potential to improve crop yield, reduce the use of synthetic fertilizers and pesticides, avoid the use of toxic com-pounds, and promote sustainable agriculture practices. Therefore, further attention must be paid to uncovering the biomolecules from fungi for agriculture and pharmaceutical applications through studying metagenomics, genomics, and proteomics.Humans are endowed by evolution with robust defenses against invasive fungal diseases, successfully treating many of them. However, we are still vulnerable to invasive fungal infections. People suffering from opportunistic and primary invasive fungal infections urgently need resources and research efforts to bring them new diagnostics and treatments regardless of commercial potential. Enormous work over the past three decades has opened vast new views in fungal biology; we can expand upon them to fulfill modern medical advances' promises.

This entry is adapted from the peer-reviewed paper 10.3390/microorganisms11061384

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