Fungal photobiology: visible light as a signal for stress, space and time

Fungi: Pioneers of chemical creativity - Techniques and strategies to uncover fungal chemistry

Natural product discovery from fungi for drug development and description of novel chemistry has been a tremendous success. This success is expected to accelerate even further, owing to the advent of sophisticated technical advances of technical advances that recently led to the discovery of an unparalleled biodiversity in the fungal kingdom. This review aims to give an overview on i) important secondary metabolite-derived drugs or drug leads, ii) discuss the analytical and strategic framework of how natural product discovery and drug lead identification transformed from earlier days to the present, iii) how knowledge of fungal biology and biodiversity facilitates the discovery of new compounds, and iv) point out endeavors in understanding fungal secondary metabolite chemistry in order to systematically explore fungal genomes by utilizing synthetic biology. An outlook is given, underlining the necessity for a collaborative and cooperative scenario to harness the full potential of the fungal secondary metabolome.

Characterization of Blue Light Receptors LreA and LreB in Aspergillus flavus

Light is a key external signal factor that regulates asexual development, stress resistance, and secondary metabolism in fungi. In the presence of light, photoreceptors sense several light receptors and affect fungal life. In this study, we characterized the function of the blue light receptors LreA and LreB in Aspergillus flavus, a potent pathogenic and toxigenic fungus. lreA or lreB deletion increased the growth rate but decreased conidial production in the presence or absence of light. The ΔlreA-mutant strain and the ΔlreB-mutant strain produced abnormal conidiophores, suggesting that lreA and lreB were essential for proper conidiation in A. flavus. The absence of lreA or lreB slightly decreased the stress response tolerance against thermal and oxidative stresses. In kernel infection, the ΔlreA mutant strain and the ΔlreB mutant strain produced conidia and aflatoxin B1 that were less than those produced by the control strains. Therefore, LreA and LreB play key roles in the growth, asexual development, and pathogenicity of A. flavus.

Characterization of putative antimicrobial compounds produced by endolichenic Fusarium solani exposed to light treatments

The endolichenic Fusarium solani (EF5), known to show induced metabolite production when exposed to red and green lights, was selected for characterization of their putative light-regulated bioactive compounds. To achieve this, fractionation was first performed for crude extracts from cultures of F. solani (EF5) incubated in green, red, white-fluorescent light and dark conditions. The extract yielded 12 (dark condition) to 15 (exposed to green, red, and white-fluorescent lights) fractions, and each of the fractions was tested for antimicrobial activities. The fraction (fraction 5) that showed the most promising antimicrobial activity was then subjected to high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) to identify the bioactive compounds. Results revealed detection of two new metabolites from endolichenic F. solani, putatively identified as 8-deoxyjavanicin and fusolanone A, which are known to have antimicrobial properties. This study revealed that red and green lights trigger the production of 8-deoxyjavanicin and fusolanone A, which likely contributed to the antimicrobial properties demonstrated by endolichenic F. solani.

Yield increment and transcriptome response caused by blue light treatment in Hericium coralloides

BACKGROUND

Hericium coralloides is a traditional edible and medicinal mushroom. Light is a key factor in forming fruiting bodies of fungi; however, the effects of different light on the yield and morphogenesis of H. coralloides are still unknown. Therefore, the morphology, yield, and transcriptome of H. coralloides under blue, red, and white light conditions were investigated.

RESULT

Fruiting bodies under blue light exhibited superior morphological traits, such as milky white color, larger size, elongated stalks, and higher spine count, leading to higher yields. Different light treatments led to dramatic transcriptome changes ranging from 10,827 differentially expressed genes (DEGs) induced by blue light in Blue-4d to 11,375 DEGs induced by red light in Red-4d and accounted for 64.56% to 67.81% of all expressed genes. This massive amount of light-responsive genes has never been reported in fungi. Gene Ontology analysis showed that light affected nearly all aspects of life in H. coralloides; suggesting that the influence of light on fungi may have been underestimated. Blue light-induced yield increment may be achieved by specifically upregulating the growth-related processes such as DNA replication, chromosomes, and cell division.

CONCLUSIONS

This study offers preliminary insights into the potential role of blue light in modulating gene expression and yield stimulation in H. coralloides, potentially improving cultivation practice.

Effects of Blue Light on Fruiting Body Production and Ergothioneine Content During Sawdust Cultivation of Shiitake (Lentinula edodes)

The cultivation period of shiitake (Lentinula edodes) is approximately 120-150 d, which is longer than that of other edible mushrooms. The development of fruiting bodies in shiitake is affected by light exposure. In this study, we investigated the effects of blue light on the production and ergothioneine contents of shiitake mushrooms. Fruiting body production (yield) on the medium irradiated with blue light increased in both cultivars (L808, 555 ± 60 g/3 kg medium; Sanbackhyang, 1090 ± 106 g/3 kg medium). Additionally, blue light increased the ergothioneine contents and antioxidative activities, and the ergothioneine content of L808 (about 2.8 mg/g) was higher than that of Sanbackhyang (about 1.2 mg/g). These results suggest that blue light is effective in shortening the cultivation period and increasing ergothioneine contents during shiitake cultivation.

Characterization of Bipolaris bicolor germination: effects of a physical factor on fungal adaptability

Studies on physiological responses to stimuli from physical factors are essential for understanding the dynamics of the microorganisms and higly important for the management of plant diseases. Besides, the development of an epidemiological model for pathogen populations requires studying their physiological responses to physical stimuli. The objective of this study was to evaluate the germination dynamics of spores from six isolates of Bipolaris bicolor under effects of light at 25 °C. Suspensions of 1.6 × 105 conidia mL- 1 from the B. bicolor isolates were inoculated onto Petri dishes containing agar-water culture medium and incubated in a BOD chamber under two physical conditions: (a) constant darkness and (b) constant light for five hours. The study was conducted in a completely randomized design, with a 6 × 2 factorial arrangement (six B. bicolor isolates and two physical conditions) and five replications. The length of the germ tube was measured hourly. The constant darkness resulted in higher mean germ tube growth for the pathogen; however, differences in the final germination percentage were found among the isolates. The isolate F-24-02 exhibited the highest germination adaptability to constant darkness, presenting the longest germ tube length.

Effects of light quality on agronomic traits, antioxidant capacity and nutritional composition of Sarcomyxa Edulis

Sarcomyxa edulis, a notable edible and medicinal mushroom indigenous to northeast China, is celebrated for its high nutritional value and delightful taste. In this study, white light as a control and examined the effects of red, green, and blue light on the agronomic traits, antioxidant capabilities, and nutritional composition of S. edulis. The results showed that different monochromatic light qualities affected the color of S. edulis pileus, with blue light demonstrating particular efficacy. Furthermore, blue light also regulated pileus length, whereas red light was instrumental in significantly increasing stalk length. Regarding antioxidant capacity, compared with red and green light, the activities of POD, SOD, and CAT were significantly improved by blue light irradiation, decreased MDA levels, and improved free radical scavenging potential. Additionally, blue light exposure led to an increase in the contents of 15 amino acids. Green light treatment reduced the crude fat content. For the first time, we found that light quality is a key factor in controlling the color of S. edulis. Blue light is an effective way to regulate the color and pileus size of S. edulis, and improve the antioxidant properties. The photobiological characteristics and the response of nutritional quality to light environment of S. edulis were clarified.

Influence of coloured lights on growth and enzyme production of beneficial endophytic fungi

The influence of light regulation on fungal growth and enzyme production was tested on endophytic isolates of Fusarium proliferatum (CCH), Colletotrichum boninense (PL1, PL9, OL2), Colletotrichum gloeosporiodes (OL3) and Colletotrichum siamense (PL3). The isolates were treated with blue, red, green, and yellow light, while white fluorescent light (12 h light/12 h dark photoperiod) and 24 h dark conditions were applied as control. Results revealed that coloured light treatments induced formation of circadian rings, while exposure to white light and dark conditions showed less pronounced circadian rings. Growth and sporulation of endophytes were not significantly influenced by light. By contrast, enzyme production was affected by coloured light treatments, notably with red (amylase), blue (cellulase) and yellow (cellulase, xylanase, L-asparaginase) light, resulting in lower enzyme levels for certain isolates. Under control conditions, enzyme production was relatively higher for amylase, cellulase, xylanase (for cultures incubated in the dark), and for L-asparaginase (for cultures incubated in white fluorescent light). Among the endophytic isolates, F. proliferatum (CCH) showed better response to coloured light treatment as higher sporulation and enzyme production was detected, although growth was significantly suppressed. On the contrary, C. gloeosporiodes (OL3) showed better growth but significantly lower enzyme production and sporulation when treated with the various coloured light. This study revealed that coloured light may have the potential to manipulate growth, sporulation and enzyme production in certain fungal species as strategies for fungal control or for harnessing of valuable enzymes.

Light reception of Phycomyces revisited: several white collar proteins confer blue- and red-light sensitivity and control dynamic range and adaptation

The giant-fruiting body, sporangiophore, of the fungus Phycomyces blakesleeanus grows toward near-UV/blue-light (phototropism). The blue-light photoreceptor, MadA, should contain FAD bound to the LOV domain, and forms a complex with MadB. Both proteins are homologs of white collar proteins WC-1 and WC-2 from the fungus Neurospora crassa and should be localized in nuclei, where they function as a light-sensitive transcription factor complex. The photoreceptor properties of two further Wc proteins, WcoA and WcoB, remain unclear because of lack of mutants. We propose that WcoA and/or WcoB play essential roles in photoreception by enlarging the dynamic range that help explain complex stimulus-response relationships. Even though red light does not elicit photo-movement or -differentiation in Phycomyces, it affects the effectiveness of blue light which indicates an underlying photochromic receptor. Protein sequence searches show that other fungal red-light receptors are absent in Phycomyces. The solution to the red-light riddle is thus sought in the ability of Wc complexes to generate after blue-light irradiation a neutral flavosemiquinone radical that absorbs red light and functions as primary photochemical signal. Phototropism requires Ras-GAP (MadC) as part of the signal transduction cascade and, we propose, to allocate photoreceptors in the plasmalemma of the growing zone, which allows for receptor dichroism, range adjustment and contrast recognition for spatial orientation. Phototropic signal chains must entail transduction networks between Wc receptors and small G-proteins and their associated Ras-GAP and Ras-GEF proteins. The interactions among these proteins should occur in trans-Golgi vesicles and the plasmalemma of the growing zone.

The GATA transcription factor BcWCL2 regulates citric acid secretion to maintain redox homeostasis and full virulence in Botrytis cinerea

Botrytis cinerea is a typical necrotrophic plant pathogenic fungus which can deliberately acidify host tissues and trigger oxidative bursts therein to facilitate its virulence. The white collar complex (WCC), consisting of BcWCL1 and BcWCL2, is recognized as the primary light receptor in B. cinerea. Nevertheless, the specific mechanisms through which the WCC components, particularly BcWCL2 as a GATA transcription factor, control virulence are not yet fully understood. This study demonstrates that deletion of BcWCL2 results in the loss of light-sensitive phenotypic characteristics. Additionally, the Δbcwcl2 strain exhibits reduced secretion of citrate, delayed infection cushion development, weaker hyphal penetration, and decreased virulence. The application of exogenous citric acid was found to restore infection cushion formation, hyphal penetration, and virulence of the Δbcwcl2 strain. Transcriptome analysis at 48 h post-inoculation revealed that two citrate synthases, putative citrate transporters, hydrolytic enzymes, and reactive oxygen species scavenging-related genes were down-regulated in Δbcwcl2, whereas exogenous citric acid application restored the expression of the above genes involved in the early infection process of Δbcwcl2. Moreover, the expression of Bcvel1, a known regulator of citrate secretion, tissue acidification, and secondary metabolism, was down-regulated in Δbcwcl2 but not in Δbcwcl1. ChIP-qPCR and electrophoretic mobility shift assays revealed that BcWCL2 can bind to the promoter sequences of Bcvel1. Overexpressing Bcvel1 in Δbcwcl2 was found to rescue the mutant defects. Collectively, our findings indicate that BcWCL2 regulates the expression of the global regulator Bcvel1 to influence citrate secretion, tissue acidification, redox homeostasis, and virulence of B. cinerea.IMPORTANCEThis study illustrated the significance of the fungal blue light receptor component BcWCL2 protein in regulating citrate secretion in Botrytis cinerea. Unlike BcWCL1, BcWCL2 may contribute to redox homeostasis maintenance during infection cushion formation, ultimately proving to be essential for full virulence. It is also demonstrated that BcWCL2 can regulate the expression of Bcvel1 to influence host tissue acidification, citrate secretion, infection cushion development, and virulence. While the role of organic acids secreted by plant pathogenic fungi in fungus-host interactions has been recognized, this paper revealed the importance, regulatory mechanisms, and key transcription factors that control organic acid secretion. These understanding of the pathogenetic mechanism of plant pathogens can provide valuable insights for developing effective prevention and treatment strategies against fungal diseases.

Effects of Light on the Fruiting Body Color and Differentially Expressed Genes in Flammulina velutipes

Light plays vital roles in fungal growth, development, reproduction, and pigmentation. In Flammulina velutipes, the color of the fruiting body exhibits distinct changes in response to light; however, the underlying molecular mechanisms remain unknown. Therefore, in this study, we aimed to analyze the F. velutipes transcriptome under red, green, and blue light-emitting diode (LED) lights to identify the key genes affecting the light response and fruiting body color in this fungus. Additionally, we conducted protein-protein interaction (PPI) network analysis of the previously reported fruiting body color-related gene, Fvpal1, to identify the hub genes. Phenotypic analysis revealed that fruiting bodies exposed to green and blue lights were darker than those untreated or exposed to red light, with the color intensifying more after 48 h of exposure to blue light compared to that after 24 h of exposure. Differentially expressed gene (DEG) analyses of all light treatments for 24 h revealed that the numbers of DEGs were 17, 74, and 257 under red, green, and blue lights, respectively. Subsequently, functional enrichment analysis was conducted of the DEGs identified under green and blue lights, which influenced the color of F. velutipes. In total, 103 of 168 downregulated DEGs under blue and green lights were included in the enrichment analysis. Among the DEGs enriched under both green and blue light treatments, four genes were related to monooxygenases, with three genes annotated as cytochrome P450s that are crucial for various metabolic processes in fungi. PPI network analysis of Fvpal1 revealed associations with 11 genes, among which the expression of one gene, pyridoxal-dependent decarboxylase, was upregulated in F. velutipes exposed to blue light. These findings contribute to our understanding of the molecular mechanisms involved in the fruiting body color changes in response to light and offer potential molecular markers for further exploration of light-mediated regulatory pathways.

Transcriptome Analysis Reveals Candidate Genes for Light Regulation of Elsinochrome Biosynthesis in Elsinoë arachidis

Light regulation is critical in fungal growth, development, morphogenesis, secondary metabolism, and the biological clock. The fungus Elsinoë arachidis is known to produce the mycotoxin Elsinochrome (ESC), a key factor contributing to its pathogenicity, under light conditions. Although previous studies have predominantly focused on the light-induced production of ESC and its biosynthetic pathways, the detailed mechanisms underlying this process remain largely unexplored. This study explores the influence of light on ESC production and gene expression in E. arachidis. Under white light exposure for 28 days, the ESC yield was observed to reach 33.22 nmol/plug. Through transcriptome analysis, 5925 genes were identified as differentially expressed between dark and white light conditions, highlighting the significant impact of light on gene expression. Bioinformatics identified specific light-regulated genes, including eight photoreceptor genes, five global regulatory factors, and a cluster of 12 genes directly involved in the ESC biosynthesis, with expression trends confirmed by RT-qPCR. In conclusion, the study reveals the substantial alteration in gene expression associated with ESC biosynthesis under white light and identifies potential candidates for in-depth functional analysis. These findings advance understanding of ESC biosynthesis regulation and suggest new strategies for fungal pathogenicity control.

Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Light as a source of information regulates morphological and physiological processes of fungi, including development, primary and secondary metabolism, or the circadian rhythm. Light signaling in fungi depends on photoreceptors and downstream components that amplify the signal to govern the expression of an array of genes. Here, we investigated the effects of red and far-red light in the mycoparasite Trichoderma guizhouense on its mycoparasitic potential. We show that the invasion strategy of T. guizhouense depends on the attacked species and that red and far-red light increased aerial hyphal growth and led to faster overgrowth or invasion of the colonies. Molecular experiments and transcriptome analyses revealed that red and far-red light are sensed by phytochrome FPH1 and further transmitted by the downstream MAPK HOG pathway and the bZIP transcription factor ATF1. Overexpression of the red- and far-red light-induced fluffy gene fluG in the dark resulted in abundant aerial hyphae formation and thereby improvement of its antagonistic ability against phytopathogenic fungi. Hence, light-induced fluG expression is important for the mycoparasitic interaction. The increased aggressiveness of fluG-overexpressing strains was phenocopied by four random mutants obtained after UV mutagenesis. Therefore, aerial hyphae formation appears to be a trait for the antagonistic potential of T. guizhouense.

Integrated transcriptome and metabolome analysis provides insights into blue light response of Flammulina filiformis

Blue light promotes primordium differentiation and fruiting body formation of mushroom. However, the blue light response mechanism of mushroom remains unclear. In this study, mycelium of Flammulina filiformis was exposed to blue light, red light and dark conditions, and then the comparative metabolome and transcriptome analysis was applied to explore metabolic regulation mechanism of F. filiformis under blue light and red light conditions. The yield of the fruiting body of F. filiformis under blue light condition was much higher than that under dark and red light conditions. Metabolome analysis showed that blue light treatment reduced the concentrations of many low molecular weight carbohydrates in the pilei, but it promoted the accumulation of some low molecular weight carbohydrates in the stipes. Blue light also decreased the accumulation of organic acids in the stipes. Blue light treatment reduced the levels of tyrosine and tryptophan in the stipes, but it largely promoted the accumulation of lysine in this organ. In the stipes of F. filiformis, blue light shifted metabolite flow to synthesis of lysine and carbohydrates through inhibiting the accumulation of aromatic amino acids and organic acids, thereby enhancing its nutritional and medicinal values. The transcriptome analysis displayed that blue light enhanced accumulation of lysine in fruiting body of F. filiformis through downregulation of lysine methyltransferase gene and L-lysine 6-monooxygenase gene. Additionally, in the stipes, blue light upregulated many hydrolase genes to improve the ability of the stipe to biodegrade the medium and elevated the growth rate of the fruiting body.

Growth, morphology, and formation of cinnabarin in Pycnoporus cinnabarinus in relation to different irradiation spectra

BACKGROUND

The demand for natural pigments in general, and for fungi-derived pigments in particular, is constantly rising. Wood-decomposing fungi represent a promising source for natural pigments and they are usually easy to cultivate in pure culture. One of them, i.e., Pycnoporus cinnabarinus, offers a highly interesting spectrum of bioactivity, partly due to the formation of the orange-red pigment cinnabarin. However, apart from a few studies addressing its diverse potential biotechnological applications, there is still a large gap of knowledge concerning the influence of light on the formation of cinnabarin. The aim of this work was to investigate the effect of different irradiations on the cinnabarin content, the growth, and the morphology of three different P. cinnabarinus strains. We used highly standardized irradiation conditions and cultivation techniques in combination with newly developed methods for the extraction and direct quantification of cinnabarin.

RESULTS

Red, green, blue, and UV-A irradiation (mean irradiance Ee = 1.5 ± 0.18 W m-2) had considerable effects on the growth and colony appearance of all three P. cinnabarinus strains tested. The cinnabarin content determined was, thus, dependent on the irradiation wavelength applied, allowing strain-specific thresholds to be defined. Irradiation with wavelengths below this strain-specific threshold corresponded to a lower cinnabarin content, at least at the intensity applied. The orange-red pigment appeared by light microscopy as incrusted extracellular plaques present on the hyphal walls. Highly efficient vegetative propagation occurred by arthroconidia, and we observed the tendency that this asexual reproduction was (i) most frequent in the dark but (ii) never occurred under UV-A exposure.

CONCLUSION

 This study highlights a differential photo-dependence of growth, morphology, and cinnabarin formation in P. cinnabarinus. This confirms that it is advisable to consider the wavelength of the light used in future biotechnological productions of natural pigments.

Integration of Metabolomes and Transcriptomes Provides Insights into Morphogenesis and Maturation in Morchella sextelata

True morels (Morchella, Pezizales) are a popular edible and medicinal fungus with great nutritional and economic value. The dynamics and regulatory mechanisms during the morphogenesis and maturation of morels are poorly understood. In this study, the metabolomes and transcriptomes of the mycelium (MY), primordium differentiation (PR), young fruiting body (YFB), and mature fruiting body (MFB) were comprehensively analyzed to reveal the mechanism of the morphogenesis and maturation of Morchella sextelata. A total of 748 differentially expressed metabolites (DEMs) and 5342 differentially expressed genes (DEGs) were detected, mainly enriched in the carbohydrate, amino acid, and lipid metabolism pathways, with the transition from the mycelium to the primordium being the most drastic stage at both the metabolic and transcriptional levels. The integrated metabolomics and transcriptomics highlighted significant correlations between the DEMs and DEGs, and specific amino acid and nucleotide metabolic pathways were significantly co-enriched, which may play key roles in morphological development and ascocarp maturation. A conceptual model of transcriptional and metabolic regulation was proposed during morphogenesis and maturation in M. sextelata for the first time, in which environmental factors activate the regulation of transcription factors, which then promote metabolic and transcriptional regulation from vegetative to reproductive growth. These results provide insights into the metabolic dynamics and transcriptional regulation during the morphogenesis and maturation of morels and valuable resources for future breeding enhancement and sustainable artificial cultivation.

Influence of light regulation on growth and enzyme production in rare endolichenic fungi

The influence of light regulation on the growth and enzyme production of three endolichenic fungal isolates, i.e. Pseudopestalotiopsis theae (EF13), Fusarium solani (EF5), and Xylaria venustula (PH22), was determined. The isolates were exposed to blue, red, green, yellow, white fluorescent light (12 h light-12 h dark photoperiod) (test), and 24 h dark (control) conditions. Results revealed that the alternating light-dark conditions resulted in the formation of dark rings in most fungal isolates but was absent in PH22. Red light induced sporulation while yellow light elicited higher biomass in all isolates (0.19 ± 0.01 g, 0.07 ± 0.00 g, and 0.11 ± 0.00 g, for EF13, PH22, and EF5, respectively) as compared to incubation in the dark. Results also showed that blue light induced higher amylase activity in PH22 (15.31 ± 0.45 U/mL) and L-asparaginase activity in all isolates (0.45 ± 0.01 U/mL, 0.55 ± 0.39 U/mL, and 0.38 ± 0.01 U/mL, for EF13, PH22, and EF5, respectively) compared to both control conditions. Green light enhanced the production of xylanase (6.57 ± 0.42 U/mL, 10.64 ± 0.12 U/mL, and 7.55 ± 0.56 U/mL for EF13, PH22, and EF5, respectively) and cellulase (6.49 ± 0.48 U/mL, 9.57 ± 0.25 U/mL, and 7.28 ± 0.63 U/mL, for EF13, PH22, and EF5, respectively). In contrast, red light was the least effective light treatment as production of enzymes was the least, with lower levels of amylase, cellulase, xylanase, and L-asparaginase detected. To conclude, all three endolichenic fungi are light-responsive, with fungal growth regulated with the use of red light and yellow light, and manipulation of enzyme production via blue and green light.

Light-Induced Changes in Secondary Metabolite Production of Trichoderma atroviride

Many studies aim at maximizing fungal secondary metabolite production but the influence of light during cultivation has often been neglected. Here, we combined an untargeted isotope-assisted liquid chromatography-high-resolution mass spectrometry-based metabolomics approach with standardized cultivation of Trichoderma atroviride under three defined light regimes (darkness (PD), reduced light (RL) exposure, and 12/12 h light/dark cycle (LD)) to systematically determine the effect of light on secondary metabolite production. Comparative analyses revealed a similar metabolite profile upon cultivation in PD and RL, whereas LD treatment had an inhibiting effect on both the number and abundance of metabolites. Additionally, the spatial distribution of the detected metabolites for PD and RL was analyzed. From the more than 500 detected metabolites, only 25 were exclusively produced upon fungal growth in darkness and 85 were significantly more abundant in darkness. The majority were detected under both cultivation conditions and annotation revealed a cluster of substances whose production followed the pattern observed for the well-known T. atroviride metabolite 6-pentyl-alpha-pyrone. We conclude that cultivation of T. atroviride under RL can be used to maximize secondary metabolite production.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Photoenzymatic Decarboxylation to Produce Hydrocarbon Fuels: A Critical Review

Photoenzymatic decarboxylation shows great promise as a pathway for the generation of hydrocarbon fuels. CvFAP, which is derived from Chlorella variabilis NC64A, is a photodecarboxylase capable of converting fatty acids into hydrocarbons. CvFAP is an example of coupling biocatalysis and photocatalysis to produce alkanes. The catalytic process is mild, and it does not yield toxic substances or excess by-products. However, the activity of CvFAP can be readily inhibited by several factors, and further enhancement is required to improve the enzyme yield and stability. In this article, we will examine the latest advancements in CvFAP research, with a particular focus on the enzyme's structural and catalytic mechanism, summarized some limitations in the application of CvFAP, and laboratory-level methods for enhancing enzyme activity and stability. This review can serve as a reference for future large-scale industrial production of hydrocarbon fuels.

White Collar 1 Modulates Oxidative Sensitivity and Virulence by Regulating the HOG1 Pathway in Fusarium asiaticum

Fusarium asiaticum is an epidemiologically important pathogen of cereal crops in east Asia, accounting for both yield losses and mycotoxin contamination problems in food and feed products. FaWC1, a component of the blue-light receptor White Collar complex (WCC), relies on its transcriptional regulatory zinc finger domain rather than the light-oxygen-voltage domain to regulate pathogenicity of F. asiaticum, although the downstream mechanisms remain obscure. In this study, the pathogenicity factors regulated by FaWC1 were analyzed. It was found that loss of FaWC1 resulted in higher sensitivity to reactive oxygen species (ROS) than in the wild type, while exogenous application of the ROS quencher ascorbic acid restored the pathogenicity of the ΔFawc1 strain to the level of the wild type, indicating that the reduced pathogenicity of the ΔFawc1 strain is due to a defect in ROS tolerance. Moreover, the expression levels of the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway genes and their downstream genes encoding ROS scavenging enzymes were downregulated in the ΔFawc1 mutant. Upon ROS stimulation, the FaHOG1-green fluorescent protein (GFP)-expressing signal driven by the native promoter was inducible in the wild type but negligible in the ΔFawc1 strain. Overexpressing Fahog1 in the ΔFawc1 strain could recover the ROS tolerance and pathogenicity of the ΔFawc1 mutant, but it remained defective in light responsiveness. In summary, this study dissected the roles of the blue-light receptor component FaWC1 in regulating expression levels of the intracellular HOG-MAPK signaling pathway to affect ROS sensitivity and pathogenicity in F. asiaticum. IMPORTANCE The well-conserved fungal blue-light receptor White Collar complex (WCC) is known to regulate virulence of several pathogenic species for either plant or human hosts, but how WCC determines fungal pathogenicity remains largely unknown. The WCC component FaWC1 in the cereal pathogen Fusarium asiaticum was previously found to be required for full virulence. The present study dissected the roles of FaWC1 in regulating the intracellular HOG MAPK signaling pathway to affect ROS sensitivity and pathogenicity in F. asiaticum. This work thus extends knowledge of the association between fungal light receptors and the intracellular stress signaling pathway to regulate oxidative stress tolerance and pathogenicity in an epidemiologically important fungal pathogen of cereal crops.

Light in the box-photobiological examination chamber with light trap ventilation system for studying fungal surface cultures illustrated with Metarhizium brunneum and Beauveria brongniartii

Due to their versatile way of life as saprophytes, endophytes, and entomopathogens, fungi of the genera Metarhizium and Beauveria are exposed to varying illumination conditions in their natural habitats, which makes a thorough adaptation to light very likely. While the few available studies for these genera support this assumption, research in this field is still in its infancy and the data material restricted to only a few fungal species. Thus, the aim of this work was to explore how light influences growth, conidial production and secondary metabolite formation of two industrial relevant strains of M. brunneum (MA 43, formerly M. anisopliae var. anisopliae BIPESCO 5/F52) and B. brongniartii (BIPESCO 2). To achieve this, we constructed an easily adjustable illumination device for highly standardized photophysiological studies of fungi on Petri dishes, the so-called LIGHT BOX. With the aid of this device, M. brunneum and B. brongniartii were grown on S4G or S2G agar at 25 °C for 14 days either in complete darkness or under constant illumination with red light (λpeak = 635 nm), green light (λpeak = 519 nm) or blue light (λpeak = 452 nm). In addition, for each wavelength the effect of different illumination intensities was tested, i.e., intensities of red light ranging from 22.1 ± 0.1 to 136.5 ± 0.3 µW cm-2, green light from 16.5 ± 0.1 to 96.2 ± 0.1 µW cm-2, and blue light from 56.1 ± 0.2 to 188.9 ± 0.6 µW cm-2. Both fungi strongly responded in terms of growth, conidial production, pigmentation and morphology to changes in the wavelength and irradiation intensity. The wavelength-dependent production of the well-known secondary metabolite oosporein which is secreted by the genus Beauveria in particular, was also increased under green and blue light exposure. The established LIGHT BOX system allows not only to optimize conidial production yields with these biotechnologically relevant fungi, but also allows the photobiological exploration of other fungi.

An Anatomy of Fungal Eye: Fungal Photoreceptors and Signalling Mechanisms

Organisms have developed different features to capture or sense sunlight. Vertebrates have evolved specialized organs (eyes) which contain a variety of photosensor cells that help them to see the light to aid orientation. Opsins are major photoreceptors found in the vertebrate eye. Fungi, with more than five million estimated members, represent an important clade of living organisms which have important functions for the sustainability of life on our planet. Light signalling regulates a range of developmental and metabolic processes including asexual sporulation, sexual fruit body formation, pigment and carotenoid production and even production of secondary metabolites. Fungi have adopted three groups of photoreceptors: (I) blue light receptors, White Collars, vivid, cryptochromes, blue F proteins and DNA photolyases, (II) red light sensors, phytochromes and (III) green light sensors and microbial rhodopsins. Most mechanistic data were elucidated on the roles of the White Collar Complex (WCC) and the phytochromes in the fungal kingdom. The WCC acts as both photoreceptor and transcription factor by binding to target genes, whereas the phytochrome initiates a cascade of signalling by using mitogen-activated protein kinases to elicit its cellular responses. Although the mechanism of photoreception has been studied in great detail, fungal photoreception has not been compared with vertebrate vision. Therefore, this review will mainly focus on mechanistic findings derived from two model organisms, namely Aspergillus nidulans and Neurospora crassa and comparison of some mechanisms with vertebrate vision. Our focus will be on the way light signalling is translated into changes in gene expression, which influences morphogenesis and metabolism in fungi.

Light Stress in Yeasts: Signaling and Responses in Creatures of the Night

Living organisms on the surface biosphere are periodically yet consistently exposed to light. The adaptive or protective evolution caused by this source of energy has led to the biological systems present in a large variety of organisms, including fungi. Among fungi, yeasts have developed essential protective responses against the deleterious effects of light. Stress generated by light exposure is propagated through the synthesis of hydrogen peroxide and mediated by regulatory factors that are also involved in the response to other stressors. These have included Msn2/4, Crz1, Yap1, and Mga2, thus suggesting that light stress is a common factor in the yeast environmental response.

Effects of UV Stress in Promoting Antioxidant Activities in Fungal Species Тrametes versicolor (L.) Lloyd and Flammulina velutipes (Curtis) Singer

Trametes versicolor and Flammulina velutipes, after submerged cultivation, with intermittent exposure to ultraviolet light (UV), were studied for Total Phenolic content (TP) and Total Proteins (TPR) contents and antioxidant properties against free radicals. The TP and TPR were determined by a spectrophotometric method and Lowry's assay, respectively. Liquid chromatography with mass spectrometry (LC-MS/MS) was used to quantify polyphenols. Different in vitro assays determined the antioxidant activities of the extracts. Mycelia extract from F. velutipes after 14 days and filtrate from T. versicolor after 21 days of incubation gave the highest TP 59.60 ± 0.14 and 50.03 ± 0.66 mg GAE/g d.w., respectively. Mycelia extract from T. versicolor after 28 days of incubation had the highest TPR (183.53 ± 2.84 mg BSAE/g d.w.). The LC-MS/MS analysis indicated that p-hydroxybenzoic and protocatechuic acids are the most abundant. Trametes versicolor filtrate after 14 days and F. velutipes filtrate after 21 days (71.29 ± 0.54% and 73.5 ± 1.81, respectively) had the highest scavenging activity in SOA. Correlation analysis indicated that all extracts' antioxidant (AO) potential strongly correlated with TP (R² = 0.83-1.0). The data confirmed that stress factors such as UV exposure could stimulate the production of secondary metabolites and natural AOs, especially phenolic acids in test fungi.

Fungal Contamination in Microalgal Cultivation: Biological and Biotechnological Aspects of Fungi-Microalgae Interaction

In the last few decades, the increasing interest in microalgae as sources of new biomolecules and environmental remediators stimulated scientists’ investigations and industrial applications. Nowadays, microalgae are exploited in different fields such as cosmeceuticals, nutraceuticals and as human and animal food supplements. Microalgae can be grown using various cultivation systems depending on their final application. One of the main problems in microalgae cultivations is the possible presence of biological contaminants. Fungi, among the main contaminants in microalgal cultures, are able to influence the production and quality of biomass significantly. Here, we describe fungal contamination considering both shortcomings and benefits of fungi-microalgae interactions, highlighting the biological aspects of this interaction and the possible biotechnological applications.

Media optimization of antimicrobial activity production and beta-glucan content of endophytic fungi Xylaria sp. BCC 1067

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Xylaria is an untapped resource for natural product discovery.

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Xylaria mycelial extract contains antimicrobials and immunomodulator beta-glucan.

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Achieved high mycelial biomass and antifungal activity using media-type selection.

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Media replacement approach lowers cultivation time and enhances bioactivity.

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Additive effect of mycelial extract and salicylic or citric acid against P. acne.

Fungi is a notable asset for drug discovery and production of pharmaceuticals; however, slow growth and poor product yields have hindered industrial utilization. Here, the mycelial biomass of Xylaria sp. BCC 1067 was examined in parallel with the assessment of antimicrobial properties by using media-type selection. To enhance both mycelial content and antifungal activity, the media replacement approach was successfully applied to stimulate fungal growth and successively switched to poorer malt-peptone extract media for metabolite production. This simple optimization reduced fungal cultivation time by 7 days and yielded 4-fold increased mycelial mass (32.59 g/L), with approximately 3-fold increased antifungal activity against the model yeast Saccharomyces cerevisiae strain. A high level of β-glucan (115.84 mg/g of cell dry weight) and additive antibacterial effect against Propionibacterium acnes were also reported. This simple strategy of culture media optimization allows for investigation of novel and rich source of health-promoting substances for effective microbial utilization.

The effect of indoor daylight spectrum and intensity on viability of indoor pathogens on different surface materials

Built environments play a key role in the transmission of infectious diseases. Ventilation rates, air temperature, and humidity affect airborne transmission while cleaning protocols, material properties and light exposure can influence viability of pathogens on surfaces. We investigated how indoor daylight intensity and spectrum through electrochromic (EC) windows can impact the growth rate and viability of indoor pathogens on different surface materials (polyvinyl chloride [PVC] fabric, polystyrene, and glass) compared to traditional blinds. Results showed that tinted EC windows let in higher energy, shorter wavelength daylight than those with clear window and blind. The growth rates of pathogenic bacteria and fungi were significantly lower in spaces with EC windows compared to blinds: nearly 100% growth rate reduction was observed when EC windows were in their clear state followed by 41%-100% reduction in bacterial growth rate and 26%-42% reduction in fungal growth rate when EC windows were in their darkest tint. Moreover, bacterial viabilities were significantly lower on PVC fabric when they were exposed to indoor light at EC-tinted window. These findings are deemed fundamental to the design of healthy modern buildings, especially those that encompass sick and vulnerable individuals.

The Zymoseptoria tritici white collar-1 gene, ZtWco-1, is required for development and virulence on wheat

The fungus Zymoseptoria tritici causes Septoria Tritici Blotch (STB), which is one of the most devastating diseases of wheat in Europe. There are currently no fully durable methods of control against Z. tritici, so novel strategies are urgently required. One of the ways in which fungi are able to respond to their surrounding environment is through the use of photoreceptor proteins which detect light signals. Although previous evidence suggests that Z. tritici can detect light, no photoreceptor genes have been characterised in this pathogen. This study characterises ZtWco-1, a predicted photoreceptor gene in Z. tritici. The ZtWco-1 gene is a putative homolog to the blue light photoreceptor from Neurospora crassa, wc-1. Z. tritici mutants with deletions in ZtWco-1 have defects in hyphal branching, melanisation and virulence on wheat. In addition, we identify the putative circadian clock gene ZtFrq in Z. tritici. This study provides evidence for the genetic regulation of light detection in Z. tritici and it open avenues for future research into whether this pathogen has a circadian clock.

UV-B-induced DNA damage and repair pathways in polar Pseudogymnoascus sp. from the Arctic and Antarctic regions and their effects on growth, pigmentation, and coniodiogenesis

Solar radiation regulates most biological activities on Earth. Prolonged exposure to solar UV radiation can cause deleterious effects by inducing two major types of DNA damage, namely cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs). These lesions may be repaired by the photoreactivation (Phr) and nucleotide excision repair (NER) pathways; however, the principal UV-induced DNA repair pathway is not known in the fungal genus Pseudogymnoascus. In this study, we demonstrated that an unweighted UV-B dosage of 1.6 kJ m^-2 d^-1 significantly reduced fungal growth rates (by between 22 and 35%) and inhibited conidia production in a 10 d exposure. The comparison of two DNA repair conditions, light or dark, which respectively induced photoreactivation (Phr) and nucleotide excision repair (NER), showed that the UV-B induced CPDs were repaired significantly more rapidly in light than in dark conditions. The expression levels of two DNA repair genes, RAD2 and PHR1 (encoding a protein in NER and Phr, respectively) demonstrated that NER rather than Phr was primarily activated for repairing UV-B-induced DNA damage in these Pseudogymnoascus strains. In contrast, Phr was inhibited after exposure to UV-B radiation, suggesting that PHR1 may have other functional roles. This article is protected by copyright. All rights reserved.

Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi

Abstract

While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light.

Key points

• Fungal biological processes alter upon illumination, also under the microscope

• Red shifted fluorescent protein toolboxes decrease interference by illumination

• Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity

Involvement of VIVID in white light-responsive pigmentation, sexual development and sterigmatocystin biosynthesis in the filamentous fungus Podospora anserina

Light serves as a source of information and regulates diverse physiological processes in living organisms. Fungi perceive and respond to light through a complex photosensory system. Fungi have evolved the desensitization mechanism to adapt to the changing light signal in a natural environment. White light exerts multiple essential impacts on the model filamentous fungus P. anserina. However, the light sensing and response in this species has not been investigated. In this study, we demonstrated that the loss of function of the light desensitization protein VIVID (VVD) in P. anserina triggered exacerbated light responses, and therefore led to drastic morphological and physiological changes. The white light-sensitive mutant Δvvd showed growth reduction, spermatia overproduction, enhanced hyphae pigmentation and reduced oxidative stress tolerance. We observed the decreased expression level of sterigmatocystin gene cluster by transcriptome analysis, and finally detected the reduced production of sterigmatocystin in Δvvd in response to white light. Our data indicate that VVD acts as a repressor of white collar complex. This study exhibits a vital role of VVD in governing white light-responsive gene expression and secondary metabolite production, and contributes to a better understanding of the photoreceptor VVD in P. anserina. This article is protected by copyright. All rights reserved.

The Photoreaction of the Proton-Pumping Rhodopsin 1 From the Maize Pathogenic Basidiomycete Ustilago maydis

Microbial rhodopsins have recently been discovered in pathogenic fungi and have been postulated to be involved in signaling during the course of an infection. Here, we report on the spectroscopic characterization of a light-driven proton pump rhodopsin (UmRh1) from the smut pathogen Ustilago maydis, the causative agent of tumors in maize plants. Electrophysiology, time-resolved UV/Vis and vibrational spectroscopy indicate a pH-dependent photocycle. We also characterized the impact of the auxin hormone indole-3-acetic acid that was shown to influence the pump activity of UmRh1 on individual photocycle intermediates. A facile pumping activity test was established of UmRh1 expressed in Pichia pastoris cells, for probing proton pumping out of the living yeast cells during illumination. We show similarities and distinct differences to the well-known bacteriorhodopsin from archaea and discuss the putative role of UmRh1 in pathogenesis.

A Simple and Low-Cost Strategy to Improve Conidial Yield and Stress Resistance of Trichoderma guizhouense through Optimizing Illumination Conditions

Light is perceived by photoreceptors in fungi and further integrated into the stress-activated MAPK HOG pathway, and thereby potentially activates the expression of genes for stress responses. This indicates that the precise control of light conditions can likely improve the conidial yield and stress resistance to guarantee the low cost and long shelf life of Trichoderma-based biocontrol agents and biofertilizers. In this study, effects of wavelengths and intensities of light on conidial yield and stress tolerance to osmotic, oxidative and pH stresses in Trichoderma guizhouense were investigated. We found that 2 μmol photons/(m² × s) of blue light increased the conidial yield more than 1000 folds as compared to dark condition and simultaneously enhanced conidial stress resistance. The enhanced conidial stress resistance is probably due to the upregulated stress-related genes in blue light, which is under the control of the blue light receptor BLR1 and the MAP kinase HOG1.

Photobiology of the keystone genus Metarhizium

Metarhizium fungi are soil-inhabiting ascomycetes which are saprotrophs, symbionts of plants, pathogens of insects, and participate in other trophic/ecological interactions, thereby performing multiple essential ecosystem services. Metarhizium species are used to control insect pests of crop plants and insects that act as vectors of human and animal diseases. To fulfil their functions in the environment and as biocontrol agents, these fungi must endure cellular stresses imposed by the environment, one of the most potent of which is solar ultraviolet (UV) radiation. Here, we examine the cellular stress biology of Metarhizium species in context of their photobiology, showing how photobiology facilitates key aspects of their ecology as keystone microbes and as mycoinsectides. The biophysical basis of UV-induced damage to Metarhizium, and mechanistic basis of molecular and cellular responses to effect damage repair, are discussed and interpreted in relation to the solar radiation received on Earth. We analyse the interplay between UV and visible light and how the latter increases cellular tolerance to the former via expression of a photolyase gene. By integrating current knowledge, we propose the mechanism through which Metarhizium species use the visible fraction of (low-UV) early-morning light to mitigate potentially lethal damage from intense UV radiation later in the day. We also show how this mechanism could increase Metarhizium environmental persistence and improve its bioinsecticide performance. We discuss the finding that visible light modulates stress biology in the context of further work needed on Metarhizium ecology in natural and agricultural ecosystems, and as keystone microbes that provide essential services within Earth's biosphere.

Transcriptome sequencing and global analysis of blue light-responsive genes provide clues for high carotenoid yields in Blakeslea trispora

Blakeslea trispora has great potential uses in industrial production because of the excellent capability of producing a large quantity of carotenoids. However, the mechanisms of light-induced carotenoid biosynthesis even the structural and regulatory genes in pathways remain unclear. In this paper, we reported the first transcriptome study in B. trispora in which we have carried out global survey of expression changes of genes participated in blue light response. We verified that the yield of β-carotene increased 3-fold when transferred from darkness to blue light for 24 h and the enhancement of transcription levels of carRA and carB presented a positive correlation with the increase in carotenoid production. RNA-seq analysis revealed that 1124 genes were upregulated and 740 genes were downregulated respectively after blue light exposure. Annotation through GO, KEGG, Swissprot, and COG databases showed 11119 unigenes compared well with known gene sequences, 5514 unigenes were classified into Gene Ontology, and 4675 unigenes were involved in distinct pathways. Among the blue light-responsive genes, 4 genes (carG1, carG3, carRA and carB) identified to function in carotenoid metabolic pathways were dominantly upregulated. We also discovered that 142 TF genes belonging to 45 different superfamilies showed significant differential expression (p≤ 0.05), 62 of which were obviously repressed by blue light. The detailed profile of transcription data will not only allow us to conduct further functional genomics study in B. trispora, but also enhance our understanding of potential metabolic pathway and regulatory network involved in light-regulated carotenoid synthesis.

Light Intensity Alters the Behavior of Monilinia spp. in vitro and the Disease Development on Stone Fruit-Pathogen Interaction

The development of brown rot caused by the necrotrophic fungi Monilinia spp. in stone fruit under field and postharvest conditions depends, among others, on environmental factors. The effect of temperature and humidity are well studied but there is little information on the role of light in disease development. Herein, we studied the effect of two lighting treatments and a control condition (darkness) on: (i) several growth parameters of two Monilinia spp. (M. laxa and M. fructicola) grown in vitro and (ii) the light effect in their capacity to rot the fruit (nectarines) when exposed to the different lighting treatments. We also assessed the effect of such abiotic factors in the development of the disease on inoculated nectarines during postharvest storage. Evaluations also included testing the effect of fruit bagging on disease development as well as on ethylene production. Under in vitro conditions, lighting treatments altered colony morphology and conidiation of M. laxa but this effect was less acute in M. fructicola. Such light-induced changes under in vitro development also altered the capacity of M. laxa and M. fructicola to infect nectarines, with M. laxa becoming less virulent. The performance of Monilinia spp. exposed to treatments was also determined in vivo by inoculating four bagged or unbagged nectarine cultivars, indicating an impaired disease progression. Incidence and lesion diameter of fruit exposed to the different lighting treatments during postharvest showed that the effect of the light was intrinsic to the nectarine cultivar but also Monilinia spp. dependent. While lighting treatments reduced M. laxa incidence, they enhanced M. fructicola development. Preharvest conditions such as fruit bagging also impaired the ethylene production of inoculated fruit, which was mainly altered by M. laxa and M. fructicola, while the bag and light effects were meaningless. Thus, we provide several indications of how lighting treatments significantly alter Monilinia spp. behavior both in vitro and during the interaction with stone fruit. This study highlights the importance of modulating the lighting environment as a potential strategy to minimize brown rot development on stone fruit and to extent the shelf-life period of fruit in postharvest, market, and consumer's house.

Inhibition of Aspergillus oryzae Mycelium Growth and Conidium Production by Irradiation with Light at Different Wavelengths and Intensities

Aspergillus oryzae is a safe filamentous fungus widely used in the food, medicine, and feed industries, but there is currently not enough research on the light response of A. oryzae. In this study, 12 different light conditions were set and A. oryzae GDMCC 3.31 was continuously irradiated for 72 h to investigate the effect of light on mycelial growth and conidium production. Specifically, each light condition was the combination of one light wavelength (475, 520, or 630 nm) and one light intensity (20, 40, 60, or 80 μmol photon m-2 s-1). The results show that mycelium growth was inhibited significantly by green light (wavelength of 520 nm and intensities of 20 and 60 μmol photon m-2 s-1) and blue light (wavelength of 475 nm and intensity of 80 μmol photon m-2 s-1). The production of conidia was suppressed only by blue light (wavelength of 475 nm and intensities of 40, 60, and 80 μmol photon m-2 s-1), and those levels of inhibition increased when the intensity of blue light increased. When the strain was irradiated by blue light (80 μmol photon m-2 s-1), the number of conidia was 57.4% less than that of the darkness group. However, within our set range of light intensities, A. oryzae GDMCC 3.31 was insensitive to red light (wavelength of 630 nm) in terms of mycelium growth and conidium production. Moreover, interaction effects between light wavelength and intensity were found to exist in terms of colony diameter and the number of conidia. This research investigated the light response of A. oryzae, which may provide a new method to regulate mixed strains in fermented foods by light. IMPORTANCE Studies on the monochromatic light response of Aspergillus nidulans and Neurospora crassa have gone deep into the molecular mechanism. However, research methods for the light response of A. oryzae remain in the use of white light sources. In this study, we first demonstrated that A. oryzae GDMCC 3.31 was sensitive to light wavelength and intensity. We have observed that blue light inhibited its growth and sporulation and the inhibitory effect increased with intensity. This research not only adds new content to the study of the photoreaction of Aspergillus but also brings new possibilities for the use of light to regulate mixed strains and ultimately improve the flavor quality of fermented foods.

Asexual reproduction and vegetative growth of Bionectria ochroleuca in response to temperature and photoperiod

Growth and reproduction are two essential life-history traits for fungi. Understanding life-history strategies provides insight into the environmental adaption of species. Here, we investigated the colonial morphology, vegetative growth, and asexual reproduction of the ascomycete fungus Bionectria ochroleuca in response to a variety of environmental conditions. We demonstrated that the increased temperature from 15 to 25°C induced mycelial growth and conidiation in B. ochroleuca. We also found that the optimal temperatures for mycelial growth and conidial formation in this fungus species were 25 and 30°C, respectively. However, as the temperature increased from 25 to 30°C, mycelial growth was suppressed, but the total number of conidia was significantly increased. The shift in light-dark cycles dramatically changed the morphological features of the colonies and affected both vegetative growth and asexual reproduction. Under incubation environments of alternating light and dark (16:8 and 8:16 light:dark cycles), conidiophores and conidia in the colonies formed dense-sparse rings and displayed synchronous wave structures. When the light duration was prolonged in the sequence of 0, 8, 16, and 24 hr per day, mycelial growth was suppressed, but conidiation was promoted. Together, our results indicate that temperature and light period may trigger a trade-off between vegetative growth and asexual reproduction in B. ochroleuca.

Transcription factor control of virulence in phytopathogenic fungi

Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.

Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis

Ustilago maydis encodes ten predicted light-sensing proteins. The biological functions of only a few of them are elucidated. Among the characterized ones are two DNA-photolyases and two rhodopsins that act as DNA-repair enzymes or green light-driven proton pumps, respectively. Here we report on the role of two other photoreceptors in U. maydis, namely White collar 1 (Wco1) and Phytochrome 1 (Phy1). We show that they bind flavins or biliverdin as chromophores, respectively. Both photoreceptors undergo a photocycle in vitro. Wco1 is the dominant blue light receptor in the saprophytic phase, controlling all of the 324 differentially expressed genes in blue light. U. maydis also responds to red and far-red light. However, the number of red or far-red light-controlled genes is less compared to blue light-regulated ones. Moreover, most of the red and far-red light-controlled genes not only depend on Phy1 but also on Wco1, indicating partial coregulation of gene expression by both photoreceptors. GFP-fused Wco1 is preferentially located in the nucleus, Phy1 in the cytosol, thus providing no hint that these photoreceptors directly interact or operate within the same complex. This is the first report on a functional characterization and coaction of White collar 1 and phytochrome orthologs in basidiomycetes.

Light Signaling Regulates Aspergillus niger Biofilm Formation by Affecting Melanin and Extracellular Polysaccharide Biosynthesis

Light is an important signal source in nature, which regulates the physiological cycle, morphogenetic pathways, and secondary metabolites of fungi. As an external pressure on Aspergillus niger, light signaling transmits stress signals into the cell via the mitogen-activated protein kinase (MAPK) signaling pathway. Studying the effect of light on the biofilm of A. niger will provide a theoretical basis for light in the cultivation of filamentous fungi and industrial applications. Here, the characterization of A. niger biofilm under different light intensities confirmed the effects of light signaling. Our results indicated that A. niger intensely accumulated protective mycelial melanin under light illumination. We also discovered that the RlmA transcription factor in the MAPK signaling pathway is activated by light signaling to promote the synthesis of melanin, chitin, and other exopolysaccharides. However, the importance of melanin to A. niger biofilm is rarely reported; therefore, we knocked out key genes of the melanin biosynthetic pathway—Abr1 and Ayg1. Changes in hydrophobicity and electrostatic forces resulted in the decrease of biofilm caused by the decrease of melanin in mutants.

Identification and characterization of Aspergillus species of fruit rot fungi using microscopy, FT-IR, Raman and UV-Vis spectroscopy

During the investigation of fungal isolation from fruit, the major genera were Aspergillus, Penicillium, cladosporium, Alternaria, fusarium, Colletotrichum were found. Among them Aspergillus (15 species) was found major dominant on different fruits. Fifteen different Aspergillus species viz. Aspergillus brasiliensis, Aspergillus phoenicis, Aspergillus carbonarius, four Aspergillus flavus, Aspergillus acidus, two Aspergillus awamori, Aspergillus aculeatus, Aspergillus eucalypticola, Aspergillus oryzae and two Aspergillus Spp. have been differentiate and identify using morphology (microscopic technique), Fourier Transforms Infrared spectroscopy (FTIR), Raman Spectroscopy (RS) and UV-visible spectrophotometry (UV-vis). The fungal mass in powder form was used in present study. In FTIR the finger print region is important for the characterization of Aspergillus because this region is unique and contains peaks indicating the presence of DNA. From the results were found Fourier transform infrared (FTIR) technique and Raman spectroscopy a useful tool, sensitive, fast, economical, accurate, not require sample preparation and successfully used to identify fungi.

Impact of the White Collar Photoreceptor WcoA on the Fusarium fujikuroi Transcriptome

The proteins of the White Collar 1 family (WC) constitute a major class of flavin photoreceptors, widely distributed in fungi, that work in cooperation with a WC 2 protein forming a regulatory complex. The WC complex was investigated in great detail in Neurospora crassa, a model fungus in photobiology studies, where it controls all its major photoresponses. The fungus Fusarium fujikuroi, a model system in the production of secondary metabolites, contains a single WC-1 gene called wcoA. The best-known light response in this fungus is the photoinduction of the synthesis of carotenoids, terpenoid pigments with antioxidant properties. Loss of WcoA in F. fujikuroi results in a drastic reduction in the mRNA levels of the carotenoid genes, and a diversity of morphological and metabolic changes, including alterations in the synthesis of several secondary metabolites, suggesting a complex regulatory role. To investigate the function of WcoA, the transcriptome of F. fujikuroi was analyzed in the dark and after 15-, 60- or 240-min illumination in a wild strain and in a formerly investigated wcoA insertional mutant. Using a threshold of four-fold change in transcript levels, 298 genes were activated and 160 were repressed in the wild strain under at least one of the light exposures. Different response patterns were observed among them, with genes exhibiting either fast, intermediate, and slow photoinduction, or intermediate or slow repression. All the fast and intermediate photoresponses, and most of the slow ones, were lost in the wcoA mutant. However, the wcoA mutation altered the expression of a much larger number of genes irrespective of illumination, reaching at least 16% of the annotated genes in this fungus. Such genes include many related to secondary metabolism, as well as others related to photobiology and other cellular functions, including the production of hydrophobins. As judged by the massive transcriptomic changes exhibited by the wcoA mutant in the dark, the results point to WcoA as a master regulatory protein in F. fujikuroi, in addition to a central function as the photoreceptor responsible for most of the transcriptional responses to light in this fungus.

Light-Photoreceptors and Proteins Related to Monilinia laxa Photoresponses

Light represents a ubiquitous source of information for organisms to evaluate their environment. The influence of light on colony growth and conidiation was determined for three Monilinia laxa isolates. The highest mycelial growth rate was observed under red light for the three M. laxa isolates, followed by green light, daylight or darkness. However, reduced sporulation levels were observed in darkness and red light, but conidiation enhancement was found under daylight, black and green light with more hours of exposure to light. Putative photoreceptors for blue (white-collar and cryptochromes), green (opsins), and red light (phytochromes) were identified, and the photoresponse-related regulatory family of velvet proteins. A unique ortholog for each photoreceptor was found, and their respective domain architecture was highly conserved. Transcriptional analyses of uncovered sets of genes were performed under daylight or specific color light, and both in time course illumination, finding light-dependent triggered gene expression of MlVEL2, MlPHY2, MlOPS2, and MlCRY2, and color light as a positive inductor of MlVEL3, MlVEL4, MlPHY1, and MlCRY1 expression. M. laxa has a highly conserved set of photoreceptors with other light-responsive fungi. Our phenotypic analyses and the existence of this light-sensing machinery suggest transcriptional regulatory systems dedicated to modulating the development and dispersion of this pathogen.

Ultraviolet Radiation From a Plant Perspective: The Plant-Microorganism Context

Ultraviolet (UV) radiation directly affects plants and microorganisms, but also alters the species-specific interactions between them. The distinct bands of UV radiation, UV-A, UV-B, and UV-C have different effects on plants and their associated microorganisms. While UV-A and UV-B mainly affect morphogenesis and phototropism, UV-B and UV-C strongly trigger secondary metabolite production. Short wave (<350 nm) UV radiation negatively affects plant pathogens in direct and indirect ways. Direct effects can be ascribed to DNA damage, protein polymerization, enzyme inactivation and increased cell membrane permeability. UV-C is the most energetic radiation and is thus more effective at lower doses to kill microorganisms, but by consequence also often causes plant damage. Indirect effects can be ascribed to UV-B specific pathways such as the UVR8-dependent upregulated defense responses in plants, UV-B and UV-C upregulated ROS accumulation, and secondary metabolite production such as phenolic compounds. In this review, we summarize the physiological and molecular effects of UV radiation on plants, microorganisms and their interactions. Considerations for the use of UV radiation to control microorganisms, pathogenic as well as non-pathogenic, are listed. Effects can be indirect by increasing specialized metabolites with plant pre-treatment, or by directly affecting microorganisms.

Influence of Different Light Regimes on the Mycoparasitic Activity and 6-Pentyl-α-pyrone Biosynthesis in Two Strains of Trichoderma atroviride

The ascomycete Trichoderma atroviride is well known for its mycoparasitic lifestyle. Similar to other organisms, light is an important cue for T. atroviride. However, besides triggering of conidiation, little is known on the physiological responses of T. atroviride to light. In this study, we analyzed how cultivation under different light wavelengths and regimes impacted the behavior of two T. atroviride wild-type strains: IMI206040 and P1. While colony extension of both strains was slightly affected by light, massive differences in their photoconidation responses became evident. T. atroviride P1 colonies conidiated under all conditions tested including growth in complete darkness, while IMI206040 required white, blue or green light to trigger asexual reproduction. Interestingly, deletion of the stress-activated MAP kinase-encoding gene tmk3 abolished the ability of strain P1 to conidiate in red and yellow light as well as in darkness. Furthermore, light-dependent differences in the mycoparasitic activity and in the biosynthesis of the secondary metabolite 6-pentyl-α-pyrone (6-PP) became evident. 6-PP production was highest upon dark incubation, while light, especially exposure to white light as light/dark cycles, had an inhibitory effect on its biosynthesis. We conclude that the response of T. atroviride to light is strain-dependent and impacts differentiation, mycoparasitism, and 6-PP production; hence, this should be considered in experiments testing the mycoparasitic activity of these fungi.

Fungal evolution: cellular, genomic and metabolic complexity

The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.