Industrial enzymes are normally produced in bioreactors that contain up to over 200,000 litres and are subsequently purified in the industrial downstream processes. Therefore, the fungi that can be used for such processes must be fast growing but not be pathogens or mycotoxin producers. The use of heterologous expression, recombinant DNA technology and gene cloning to improve the production yield of enzymes, as well as their activity, can circumvent the difficulties associated with the production of large quantities.

## 48. Preservatives

Aside from the antibiotics that are used in human and veterinary medicine, secondary metabolites of fungi that exert antimicrobial activities may also have great use in the food and cosmetics industries, e.g. as food or cosmetics ingredients. In these markets, natural compounds are interesting if they (1) show significant biological activities in relevant test systems; (2) are derived from edible species; (3) are devoid of significant toxicity and (4) can be made available at low costs of goods.

Attempts have been made to replace classical synthetic preservatives, such as benzoic and sorbic acids, by natural ingredients, predominantly by plant-derived extracts and compounds (Davidson et al. 2013; Ribes et al. 2017). In fact, fungal metabolites are ideal candidates for such natural preservatives, since they can be produced in large quantities by biotechnological processes.

A recent success story relating to the successful development of such a class of molecules is based on the glycolipids from the fan-shaped jelly fungus, *Dacryopinax spathularia* and other species of the basidiomycete class Dacrymycetales. These compounds are characterized by rather broad spectrum antimicrobial effects, which have precluded their development as classical antibiotics, because such compounds should at least have selective activities against either pathogenic fungi (eukaryotes) or bacteria (prokaryotes), but not both. Ideal candidates for antibiotics should also address a defined, specific molecular target that is only present in the pathogens (examples see entry on antibacterials, e.g. enzymes catalysing glucan synthesis for antimycotics or peptidoglucan synthesis for antibacterial antibiotics). In the classical search for antibiotics such non-selective compounds that have broad-spectrum would have been sorted out at an early stage because of lacking selectivity. However, as described in a patent application (Stadler et al. 2012), the glycolipids from *D. spathularia* (Fig. 52) had particularly strong activities against acidophilic yeasts and food and beverage spoilage bacteria such as *Lactobacillus plantarum*, when the serial dilution assays were carried out in “natural” matrices such as apple juice. The fungus *Dacryopinax spathularia* is regarded as edible (Ao et al. 2016; Boa 2004) in various countries of the world and its edible basidiomata contain glycolipids (M. Stadler et al. unpubl.). Moreover, the activity persisted for up to several weeks and even yeast strains such as *Zygosaccharomyces bailii* that

<figure><img src="image_75.png" /><figcaption>**Fig. 52** Chemical structure of one of the major glycolipids from *Dacryopinax spathularia* and an images of its basidiomes in the natural habitat</figcaption></figure>

<figure><img src="image_76.png" /></figure>
had become sensitive to the commonly used non-natural
preservatives, such as benzoic acid and sorbic acid (cf.
Kuanyshev et al. 2017), were found to be highly sensitive.
These data have only been reported in the patent applica-
tion by Stadler et al. (2012) and were not yet published in a
peer-reviewed scientific journal. The production process
for the glycolipids was further developed to attain them in
multi-gram and even kg scale, and at the same time, the
downstream processing procedure was simplified substan-
tially, leading to a drastic decrease of the cost of goods.
The material was then subjected to in vivo studies,
demonstrating favorable pharmacokinetics (Bitzer et al.
2017a) as well a lack of toxicity (Bitzer et al.
2017b, c, 2018). Recently, the large German chemical
company Lanxess has licensed the project and the glycol-
ipids are now being produced at industrial scale as natural
preservative agents. Curiously, the glycolipids of *Dacry-
opinax* species can be produced by a wide variety of genera
in the Dacrymycetales, and the patent application by Sta-
dler et al. (2012) even included a claim based on homology
of 28S rDNA sequences to define the potential producer
organisms. The production of these compounds seems to be
a valid chemotaxonomic feature that has been “preserved”
in the producer organisms in the course of their evolution,
probably as the fungi have a selective advantage over their
competitors.

A recent review by Günther et al. (2017) has also out-
lined the potential of glycolipids, which can be produced at
industrial scale by yeast-like Basidiomycota such as *Usti-
lago* and *Pseudozyma* species (Ustilagomycetes), for other
industrial applications. These compounds are biosurfac-
tants and can be used as natural emulsifiers for various
applications. They have potential to replace the currently
used petrochemical products in cosmetics, as well as
pharmaceutical or biomedical applications and may even
be useful for bioremediation technologies, such as solu-
bilisation and removal of oils from contaminated soil.
However, for many of these applications, the costs of
goods are presently still prohibitive, and the existing
biotechnological production processes remain to be opti-
mized further.

49. Organic acids

Organic acids are low molecular weight compounds which contain functional groups with acidic properties such as carboxyl, sulfonic, thiol and alcohol groups (Yin et al. 2015). Organic acids have a vast array of applications in different fields including food and beverages, pharmaceuticals, cosmetics and agriculture. Before the advancement of industrial biotechnology, most of the building block chemicals such as organic acids involved in industrial scale chemical production were derived from petroleum sources

(Sauer et al. 2008). Nowadays, many organic acids are being produced at industrial scale using different fungal species, relying on sustainable biotechnological processes that can easily compete with organic synthesis (Table 25). Natural metabolic pathways or genetically modified natural product biosynthetic pathways of these fungi are favored in low cost production of organic chemicals with certain functional groups that require costly oxidative processes in industrial scale chemical production (Sauer et al. 2008). Fungi produce a diverse range of organic acids in vitro as well as in the natural environment and many species can tolerate very low pH values. These capabilities may constitute a competitive advantage, since they can “acidify” the environment to inhibit the growth of other microorganisms and to solubilize soil metals for easy absorbance. In this entry, we focus mainly on organic acids containing carboxyl functional groups with industrial scale applications.

Applications and production:

Citric acid

Citric acid is a tri-carboxylic acid which is extensively
used in the food and beverage industry as an acidulate, pH
adjuster, flavoring agent, emulsifier in ice-cream (He et al.
2019) and processed cheese production, and antimicrobial
agent. Furthermore, citric acid is employed in food as an
acidulant and antioxidant additive, in therapeutic apheresis
as an anticoagulant (Lee and Arepally 2012), in cosmetics
and toiletries as a buffering agent with metal ion chelating
abilities, and in industrial scale applications such as metal
cleaning for metal oxide removal from metal surfaces
(Soccol et al. 2006).

Before the discovery of industrial scale citric acid biosynthesis with *Aspergillus niger* using submerged fermentation techniques (Currie 1917; Show et al. 2015), it was commercially produced in England beginning around 1826 by direct extraction from Italian lemons (Papagianni 2007; Show et al. 2015). Other species of *Aspergillus*, such as *A. awamori*, *A. fonsecaeus*, *A. nidulans*, *A. phoenicis*, *A. saitoi* and *A. wentii*, have also been reported to accumulate citric acid in considerable quantities (Soccol et al. 2006; Papagianni 2007). The organic substrates for citric acid biosynthesis by fermentation of starch hydrolysates include sugarcane broth, cane molasses and beet molasses (Soccol et al. 2006). A recombinant strain of the yeast, *Yarrowia lipolytica*, has also been successfully utilized in citric acid production using sucrose as the starting material (Fig. 53) (Förster et al. 2007).

Fumaric acid

Fumaric acid was first isolated from the plant *Fumaria officinalis* and the acid is a building block component in polymerization and esterification reactions. High purity
<table><caption>**Table 25** Organic acids produced by fungi and diversity of their applications</caption><thead><tr><th>Organic acids</th><th>Organisms</th><th>Applications</th><th>Chemical formula</th><th>Molecular structure</th></tr></thead><tbody><tr><td rowspan="8">Citric acid</td><td>Aspergillus awamori</td><td>Cosmetics</td><td rowspan="8">C<sub>6</sub>H<sub>8</sub>O<sub>7</sub></td><td rowspan="8">[Chemical structure of Aspergillus awamori]</td></tr><tr><td>Aspergillus flavus</td><td>Food and beverages</td></tr><tr><td>Aspergillus fonsecaeus</td><td>Metal cleaning</td></tr><tr><td>Aspergillus nidulans</td><td>Pharmaceuticals</td></tr><tr><td>Aspergillus niger</td><td>Toiletries</td></tr><tr><td>Aspergillus phoenicis</td><td></td></tr><tr><td>Aspergillus saitoi</td><td></td></tr><tr><td>Aspergillus wentii</td><td></td></tr><tr><td>Yarrowia lipolytica</td><td></td><td></td><td></td><td></td></tr><tr><td rowspan="4">Fumaric acid</td><td>Rhizopus arrhizus</td><td>Bio-polymers</td><td rowspan="4">C<sub>4</sub>H<sub>4</sub>O<sub>4</sub></td><td rowspan="4">[Chemical structure of Fumaric acid]</td></tr><tr><td>Rhizopus formosa</td><td>Cattle feed</td></tr><tr><td>Rhizopus nigricans</td><td>Food and beverages</td></tr><tr><td>Rhizopus oryzae</td><td>Pharmaceuticals</td></tr><tr><td rowspan="2">Gluconic acid</td><td rowspan="2">Aspergillus niger</td><td>Derivatization reactions</td><td rowspan="2">C<sub>6</sub>H<sub>12</sub>O<sub>7</sub></td><td rowspan="2">[Chemical structure of Gluconic acid]</td></tr><tr><td>Food and beverages</td></tr><tr><td rowspan="5">Itaconic acid</td><td>Aspergillus terreus</td><td>Coatings</td><td rowspan="5">C<sub>5</sub>H<sub>6</sub>O<sub>4</sub></td><td rowspan="5">[Chemical structure of Itaconic acid]</td></tr><tr><td>Saccharomyces cerevisiae</td><td>Detergents</td></tr><tr><td rowspan="3">Ustilago maydis</td><td>Polymers (poly-MMA)</td></tr><tr><td>Rubber industry</td></tr><tr><td>Super-absorbents</td></tr><tr><td rowspan="5">Lactic acid</td><td rowspan="5">Recombinant yeast strains<br/>Rhizopus oryzae</td><td>Biodegradable polymers</td><td rowspan="5">C<sub>3</sub>H<sub>6</sub>O<sub>3</sub></td><td rowspan="5">[Chemical structure of Lactic acid]</td></tr><tr><td>Cosmetics</td></tr><tr><td>Food industry</td></tr><tr><td>Oral hygiene products</td></tr><tr><td>Bio-polymers</td></tr><tr><td rowspan="2">Succinic acid</td><td rowspan="2">Rhizopus sp.</td><td>Derivatization reactions</td><td rowspan="2">C<sub>4</sub>H<sub>6</sub>O<sub>4</sub></td><td rowspan="2">[Chemical structure of Succinic acid]</td></tr><tr><td></td></tr></tbody></table>

<figure><img src="image_77.png" /></figure>

<figure><img src="image_78.png" /></figure>

<figure><img src="image_79.png" /></figure>

<figure><img src="image_80.png" /></figure>

<figure><img src="image_81.png" /></figure>

<figure><img src="image_82.png" /></figure>

grade fumaric acid is administered in the management of psoriasis in humans (Balak 2015) and has shown to significantly reduce methane emission by cattle, when added

as a supplement in cattle feed (Roa Engel et al. 2008). It also has applications in food and beverage industry as an acidulant and flavor enhancing agent. Fumaric acid can

<figure><img src="image_83.png" /></figure>
<figure><img src="image_84.png" /><figcaption>**Fig. 53** Schematic representation of general organic acid production procedure using fungi</figcaption></figure>

undergo derivatization reactions to produce malic acid and L-aspartic acid (Goldberg et al. 2006; Roa Engel et al. 2008). Bio-based fumaric acid is produced by the fermentation of different substrates such as glucose by *Rhizopus arrhizus*, *R. nigricans*, and *R. oryzae*, molasses by *R. arrhizus* and cassava bagasse by *R. formosa* (Table 25) (Roa Engel et al. 2008; Xu et al. 2012).

## Gluconic acid

Since the chemical structure of gluconic acid combines both, carboxylic and alcohol functional groups, it can undergo various derivatization reactions including intra molecular esterification. Gluconic acid has applications in the food and beverage industry as a sensory property enhancer, acidity regulator and preservative for pickled food and processed meat products (Canete-Rodriguez et al. 2016). Gluconic acid is produced by surface or submerged fermentation procedures with various types of input materials such as starch, lignocellulosic biomass, sugarcane molasses, whey, waste paper, figs, banana must and grape must as carbon source using *Aspergillus niger* strains (Table 25) (Canete-Rodriguez et al. 2016). During the fermentation process, glucose in the medium is converted extracellularly by the enzymatic reaction of glucose oxidase by *A. niger* (Magnuson and Lasure 2004).

## Itaconic acid

Itaconic acid has applications in detergents, coatings and in the rubber industry. Poly(acrylamide-co-itaconic acid) a super absorbent polymer which is used to absorb aqueous solutions is also derived from itaconic acid (Choi et al. 2015). The most on demand industrial scale application is the conversion of itaconic acid to methyl methacrylate

(MMA) and the production of poly MMA, commonly known as Plexiglass (Becker et al. 2015; Choi et al. 2015). The acid is generally produced via fermentation of glucose using *Aspergillus terreus*. Furthermore, *Ustilago maydis* and *Saccharomyces cerevisiae* are also capable of producing itaconic acid by glucose fermentation (Table 25) (Becker et al. 2015).

## Lactic acid

Lactic acid is widely used in food industry in yoghurt and cheese production, cosmetic industry in skin care products, and oral hygiene products (Martinez et al. 2013). One of the most important uses of lactic acid is the manufacturing of polylactic acid which has applications in the textile industry and food packaging utensils (Sauer et al. 2008; Bozell and Petersen 2010; Martinez et al. 2013).

Lactic acid is mostly produced by fermentation with lactic acid bacteria (Sauer et al. 2008); however, the exploitation of *Rhizopus oryzae* has shown promising outcomes by producing higher titers of lactic acid of 280 g/L as anhydrous calcium lactate with 0.92 g/g productivity of glucose input under fed-batch cultures (Yamane and Tanaka 2013). Xylose, a pentose sugar derived from lignocellulosic biomass hydrolysis, can also be utilized as an input carbon source for lactic acid biosynthesis. Xylose fermentation is carried out by employing recombinant yeast strains (Sauer et al. 2010) and *R. oryzae*, grown in mineral medium (Magnuson and Lasure 2004; Maas et al. 2006) (Table 25). The extracellular release of amylases by fungi is an added advantage of the fermentation process in hydrolyzing starch from various input sources, especially by the species of *Rhizopus* (Martinez et al. 2013).
## Succinic acid

Succinic acid acts as a building block component for the synthesis of valuable chemicals, such as 1,4-butanediol, tetrahydrofuran, γ-butyrolactone, N-methylpyrrolidone, and even in the synthesis of bio-based polymers such as polybutylene succinate and polyester polyols, which may eventually replace conventional petrol-derived polymers in the future (Choi et al. 2015). An improved fermentation process for *Rhizopus* species was patented by DuPont to increase the TCA cycle based carboxylic acid production by limiting the dissolved oxygen levels in fermenters between 30 and 80%. During this fermentation process fumaric acid, succinic acid and L-malic acid are produced (Ling and Ng 1989). In a recent study 209.7 g/L succinic acid titre was obtained under fed batch fermentation conditions using *Yarrowia lipolytica* fed with crude glycerol as the carbon source (Li et al. 2018).

Commercial scale production of organic acids is highly dependent on strain performance. Since most of the wild type strains do not produce commercially acceptable yields, fermentation conditions need to be modified according to the requirement and strain (Xu et al. 2012). To meet industrial scale requirements, the wild type strains are being genetically modified or subjected to classical mutagenesis with the goal to increase production. Recently, it was reported that the deletion of the mitochondrial fumarase gene and introduction of succinate/fumarate transporter increased fumaric acid production in *Saccharomyces cerevisiae* (Yin et al. 2015). A high yielding fumaric acid producing *Rhizopus oryzae* RUR709 strain was developed by UV and γ-ray mutagenesis and finally produced 32.1 g/L fumaric acid—a concentration 1.9-fold higher than the wild type strain (Huang et al. 2010). Glucose oxidase deficient mutants of *Aspergillus carbonarius* have shown increased citric acid production by reducing by-product (gluconic acid) formation through an increase of the carbon flux towards the reductive tricarboxylic acid pathway (Yang et al. 2014b).

These metabolic engineering techniques have led to the industrial scale production of natural products by modifying natural biosynthetic pathways to increase productivity or synthesize novel derivatives to meet the global demand for organic acids.

## 50. Textile dyes

Fungi are important as natural dye producers in textile industries (Mapari et al. 2010; Chadni et al. 2017). The textile industry is the largest consumer of organic pigments and synthetic dyes (Mapari et al. 2010). Tons of dyes are lost as effluents and can result in environmental pollution and serious human health problems, especially if their

release is not properly treated. Colour fastness to washing and cropping are essential qualities for any dye/ fabric combination. Fungal species that are used in textile dyeing are listed in Table 26.

Hernández et al. (2018a) reported that wood rotting fungi can be used in textile dyeing. Suciatmih (2002) studied the effect of colouring pH and mordant on fungal dyes quality using woolen yarn (Fig. 54). In their study, three isolates of *Aspergillus*, three isolates of *Penicillium*, two isolates of *Paecilomyces*, one isolate of *Monascus purpureus* and one isolate of *Trichoderma harzianum* were used with two different mordants (alum and FeSO₄) by three different dying pH (3, 6, and 9). The results indicated that low pH value exhibited a strong colour as well as the mordant FeSO₄ produced almost darker colour.

When used in manufactured products, concerns related to the presence of toxic metabolites in pigments and dyes produced by fungi are commonly raised. In this regard, the correct identification of fungal strains and the implementation of toxicity tests are key factors to ensure a safe environment for workers and harmless products for end users (Hernández et al. 2018a). Regarding the broad spectrum of the fungal pigments, fungi including edible and non-edible mushrooms are a resource of natural dyes.

## The future

### Functional genomics and the search for novel anti-infectives

Functional genomics is the approach used to study functions and interactions of genes and their products in a specific context (Liu et al. 2010a; Buza and McCarthy 2013). This requires sequencing of the entire genome. Sequencing techniques have come a long way, since the release of the first whole fungal genome of *Saccharomyces cerevisiae* (Goffeau et al. 1996). Today the combining of newly arising techniques like PacBio with Illumina to provide fully closed genomes has led to numerous fungal genome databases, such as the fungal genome initiative (Haas et al. 2011), comprising over 100 fungal genomes, or FungiDB (Stajich et al. 2012) and Ensembl Fungi (Kersey et al. 2010) with over 1000 fungal genomes. Out of many examples that target various product categories, we will here only give some examples on what is feasible now for the secondary metabolite biosynthesis due to the employment of—OMICS and bioinformatics tools and synthetic biotechnology.

The genomes of the Fungi contain many genes and gene clusters that encode for potentially beneficial products, including industrially important enzymes as well as secondary metabolites. Also the bioinformatics tools for the
<table><caption>**Table 26** Examples of pigments produced by fungi</caption><thead><tr><th>Fungal producer</th><th>Pigment name/colour</th><th>Application</th><th>References</th></tr></thead><tbody><tr><td>Acrostalagmus sp.</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Agaricus xanthodermus</td><td>Yellow</td><td></td><td>Hanson (2008)</td></tr><tr><td rowspan="2">Alternaria alternata</td><td></td><td>Dyeing of wool and silk</td><td>Sharma et al. (2012)</td></tr><tr><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Amanita muscaria</td><td>Betains(Orange-red</td><td></td><td>Li and Oberlies (2005)</td></tr><tr><td>Aspergillus niger</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Aspergillus sp.</td><td>Yellow</td><td>Dyeing of cotton, silk and silk cotton</td><td>Anchana devi (2014), Kumar et al. (2017), Sarkar et al. (2017)</td></tr><tr><td>Boletales (Gomphidiaceae and Suillaceae)</td><td>Yellow pulvinic acid derivatives</td><td></td><td>Knight and Pattenden (1976)</td></tr><tr><td>Bisporomyces sp.</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Chlorociboria aeruginosa</td><td>Xylindein/Green</td><td>Colourfast dyeing of cotton, polyamide, polyester and wool</td><td>Weber et al. (2014), Hinsch and Robinson (2016)</td></tr><tr><td>Cortinarius cinnabarinus (European toadstool)</td><td>Fallacinol/ Dark orange</td><td></td><td>Gill (1994)</td></tr><tr><td>Cortinarius violaceus</td><td>Striking deep violet colour</td><td></td><td>Von Nussbaum et al. (1998)</td></tr><tr><td>Cortinarius sp.</td><td>Dimeric anthraquinone derivative/ Bright yellow</td><td></td><td>Velišek and Cejpek (2011)</td></tr><tr><td>Cunninghamella sp.</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Curvularia lunata</td><td></td><td>Dyeing of wool and silk</td><td>Sharma et al. (2012)</td></tr><tr><td>Dermocybe sanguinea</td><td>Anthraquinone compounds as aglycones</td><td></td><td>Hynninen et al. (2000), Räisänen et al. (2000)</td></tr><tr><td>Dermocybe sp.</td><td>Dimeric anthraquinone derivative/ Bright yellow</td><td></td><td>Velišek and Cejpek (2011)</td></tr><tr><td>Fusarium oxysporum</td><td>Anthraquinone/Purple</td><td>Dyeing of wool</td><td>Nagia and El-Mohamedy (2007), Hernández et al. (2018a)</td></tr><tr><td>Gymnopilus sp.</td><td>Yellow-brown styrylpyrone pigments bis-noryangonin and hispidin</td><td></td><td>Gill (1994)</td></tr><tr><td>Hymenochaetaceae (Inonotus, Onnia and Phellinus)</td><td>Yellow pigment hispolon</td><td></td><td>Lee and Yun (2006)</td></tr><tr><td>Hypholoma sp.</td><td>Yellow-brown styrylpyrone pigments bis-noryangonin and hispidin</td><td></td><td>Gill (1994)</td></tr><tr><td>Hygrocybe sp. (witch's hat)</td><td>Muscaflavin/yellow</td><td></td><td>Li and Oberlies (2005)</td></tr><tr><td>Penicillium chrysogenum</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Penicillium italicum</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Penicillium minioluteum</td><td></td><td>Dyeing of web blue goat nappa skin</td><td>Gupta and Aggarwal (2016)</td></tr><tr><td>Penicillium murcianum</td><td>Yellow</td><td>Dyeing of wool</td><td>Hernández et al. (2018a, b)</td></tr><tr><td>Penicillium oxalicum</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Penicillium regulosum</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011)</td></tr><tr><td>Penicillium sp.</td><td></td><td>Dyeing of cotton and silk</td><td>Sarkar et al. (2017)</td></tr><tr><td>Pholiota sp.</td><td>Yellow-brown styrylpyrone pigments bis-noryangonin and hispidin</td><td></td><td>Gill (1994)</td></tr><tr><td>Phymatotrichum sp.</td><td>Brown and reddish brown</td><td></td><td>Atalla et al. (2011) tested</td></tr><tr><td rowspan="2">Scytalidium cuboideum</td><td rowspan="2">Draconin red</td><td>Colourfast dyeing of cotton, polyamide, polyester and wool</td><td>Weber et al. (2014), Hinsch and Robinson (2016)</td></tr><tr><td>Colourfasten</td><td></td></tr><tr><td>Scytalidium ganodermophthorum</td><td>Yellow</td><td>Colourfast dyeing of cotton, polyamide, polyester and wool</td><td>Weber et al. (2014), Hinsch and Robinson (2016)</td></tr></tbody></table>
<table><caption>**Table 26** continued</caption><thead><tr><th>Fungal producer</th><th>Pigment name/colour</th><th>Application</th><th>References</th></tr></thead><tbody><tr><td><i>Suillus grevillei</i></td><td>Contains at least 11 yellow, orange and red pigments</td><td></td><td>Besl and Bresinsky (1997)</td></tr><tr><td><i>Talaromyces australis</i></td><td>Red</td><td>Dyeing of wool</td><td>Hernández et al. (2018a, b)</td></tr><tr><td><i>Talaromyces sp.</i></td><td>Orange</td><td></td><td>Morales-Oyervides et al. (2017), Hernández et al. (2018a)</td></tr><tr><td><i>Talaromyces verruculosus</i></td><td>Red</td><td>Adequate colour tone for cotton fabric without any cytotoxic effect</td><td>Chadni et al. (2017)</td></tr><tr><td><i>Thermomyces sp.</i></td><td>Yellow</td><td>Dyeing of silk</td><td>(Poorniammal et al. 2013)</td></tr><tr><td><i>Trichoderma spirale</i></td><td>Yellow</td><td></td><td>Hernández et al. (2018a)</td></tr><tr><td><i>Trichoderma virens</i></td><td></td><td>Dyeing of wool and silk and have antifungal properties</td><td>Sharma et al. (2012)</td></tr><tr><td><i>Trichoderma sp.</i></td><td></td><td>Dyeing of cotton, silk and silk cotton</td><td>Anchana devi (2014)</td></tr><tr><td><i>Tricholoma sp.</i></td><td>Dimeric anthraquinone derivative/ Bright yellow</td><td></td><td>Velišek and Cejpek (2011)</td></tr><tr><td><i>Xylaria polymorpha</i></td><td>Blackish brown</td><td></td><td>Kumar et al. (2017)</td></tr></tbody></table>

<figure><img src="image_85.png" /><figcaption>**Fig. 54** a Colour variation on woolen yarn dyed with *Purpureocillium lilacinum* dye with different mordants and dyeing pH. b Colour variation on woolen yarn dyed with *Penicillium* sp. dye with different</figcaption></figure>

mordants and dyeing pH (Fe = $FeSO_4·7H_2O$, A = alum and K = pH control) (courtesy of Suciatmih)

annotation of genomes have significantly improved and today, next to the long established antiSMASH (Blin et al. 2017), fungi-specific algorithms for identifying biosynthetic gene clusters, like the FunGeneClusterS (Vesth et al. 2016) exist. These tools have enabled researchers to heterologously express such gene clusters in well-known hosts, such as *Aspergillus niger* (Boecker et al. 2018). This strategy can be used not only to facilitate an easier production of a known metabolite at industrial scale, but also

to express previously silent gene clusters, which were found while analysing the genome—a technique often referred to as ‘genome mining’, offering a whole new source for the discovery of novel anti-infectives. Heterologous expression of specific gene clusters in a different host now also allows for the elucidation of biosyntheses of known antibiotics/natural products. One of the first fungal biosynthesis studied in such manner, was this of the mycotoxin trichothecene (Tokai et al. 2007). Over the
<figure><img src="image_86.png" /><figcaption>**Fig. 55** Stages of the production and isolation of a biologically active metabolite from the cultures of a basidiomycete (*Omphalotus nidiformis*). a Submerged cultivation in shake flasks. b Stirred tank fermentation in a parallel 1.5 L Bioreactor systems. C. Bench-Scale 10 L stirred tank. D. Column chromatography for fractionation and</figcaption></figure>

compound recovery using the polymeric adsorbent XAD. E. Eluted fractions from compound purification. F. Crystals of pure compound. Images by Teresa Briem and Lillibeth Chaverra-Muñoz, HZI, Braunschweig, Germany

years, many other studies on Ascomycota have followed, but as of recently even the Basidiomycota have been targeted for elucidation of the biosynthesis of their secondary metabolites (Lin et al. 2019). Most recently, the biosynthesis of the antifungal strobilurins (see entry on antimycotics and fungicides), has been elucidated, through expression in *Aspergillus oryzae* (Nofiani et al. 2018). In the future, modifying the biosynthesis of a fungal metabolite in order to enhance its production at commercial scale or to achieve adjusted, better bioavailable drugs, may well become the norm. Studies on the regulation of secondary metabolite biosynthesis (Brakhage and Schroeckh 2010) have also been developed in model organisms and are now available for broad applications across the fungal kingdom. This may soon lead to the discovery of totally novel classes of metabolites, using genome mining, which was already demonstrated for enzymes (e.g. Dilokpimol et al. 2018). Figure 55 illustrates the production and isolation procedure for a bioactive metabolite from a basidiomycete culture, which was obtained in very high yields in a relatively short time, owing to the fact that modern bio-process technology and methods of systems biology were employed.

**Acknowledgements** This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences, Grant No. XDB31000000. Naritsada Thongklang would like to thank Thailand research fund grants “Study of saprobic Agaricales in Thailand to find new industrial mushroom products” (Grant No. DBG6180015) and Mae Fah Luang University grant “Optimal

conditions for domestication and biological activities of selected species of *Ganoderrma*" (Grant No. 621C1535). K.D. Hyde and Naritsada Thongklang would like to thank to Thailand research fund grants “Domestication and bioactive evaluation of Thai *Hymenopelis*, *Oudemansiella*, *Xerula* and *Volvariella* species (basidiomycetes)” (Grant No. DBG6180033). K.D. Hyde thanks the financial support from the Visiting Professor grant at Chiang Mai University, Thailand and KIB. The authors acknowledge the contribution of M.M. Vasanthakumari, K.M. Manasa and P. Rajani, in various stages of preparation of the manuscript. Samantha C. Karunarathna thanks CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (Number 2018PC0006), and the National Science Foundation. Associate Professor R Jeewon thanks University of Mauritius for support. Binu C. Samarakoon offers her sincere gratitude to the “National Research Council of Thailand” (NRCT Grant No. 256108A3070006) for the financial support. Peter E Mortimer would like to thank the National Science Foundation of China and the Chinese Academy of Sciences for financial support under the following Grants: 41761144055, 41771063, Y4ZK111B01. M. Doilom would like to thank Chiang Mai University, the 5th batch of Post-doctoral Orientation Training Personnel in Yunnan Province and the 64th batch of China Postdoctoral Science Foundation. T.S. Suryanarayanan thanks the United States-India Educational Foundation (USIEF), New Delhi and the Fulbright Scholar Program (USA) for the award of a Fulbright-Nehru Senior Researcher grant to conduct research in the Department of Chemistry and Biochemistry, The Ohio State University, USA. Thanks to Research and Researchers for Industries Grant (PHD5710015) for financial support to Boontiya Chuankid. Birthe Sandargo is grateful to the Deutsche Forschungsgemeinschaft (DFG) for a PhD grant. Clara Chepkirui is indebted to a PhD stipend from the German Academic Exchange Service (DAAD) and the Kenya National Council for Science and Technology (NACOSTI). Kevin D Hyde would also like to thank the National Research Council of Thailand grants Thailands’ Fungal Diversity, Solving Problems and Creating Biotechnological Products (Grant No. 61201321016). This work is partly supported by the Department of
Biotechnology, Government of India, New Delhi (Chemical Ecology of the North East Region (NER) of India: A collaborative programme Linking NER and Bangalore Researchers; DBT-NER/Agri/24/2013) and Indian Council of Agricultural Research (ICAR-CAAST-Project F.No./NAHEP/CAAST/2018-19), Government of India, New Delhi.

**Open Access** This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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