Journal of Fungi

Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. Breeding programs that take advantage of this characteristic are widely used for selecting starters for wine industry, especially in the recent years when winemakers need to adapt their production to climate change. The aim of this work was to evaluate a marker assisted selection (MAS) program to improve malic acid consumption capacity of Saccharomyces cerevisiae in grape juice. Optimal individuals of two unrelated F1-hybrids were crossed to get a new genetic background carrying many “malic consumer” loci. Then, eleven quantitative trait loci (QTLs) already identified were used for implementing the MAS breeding program. By this method, extreme individuals able to consume more than 70% of malic acid in grape juice were selected. These individuals were tested in different enological matrixes and compared to their original parental strains. They greatly reduced the malic acid content at the end of alcoholic fermentation, they appeared to be robust to the environment, and they accelerated the ongoing of malolactic fermentations by Oenococcus oeni. This study illustrates how MAS can be efficiently used for selecting industrial Saccharomyces cerevisiae strains with outlier properties for winemaking. Full article

Population growth and food necessity envisaged the dire need for supplementation to a larger community balance in food production. With the advent of the green revolution, agriculture witnessed the insurrection of horticultural fruit crops and field crops in enormous modes. Nevertheless, chemical fertilizer usage foresees soil pollution and fertility loss. Utilization of biocontrol agents and plant growth promotion by microbial colonization enrooted significant restoration benefits. Constant reliability for healthy foods has been emancipated across the globe stressing high nutritive contents among indigenous field crops like tomato (Solanum lycopersicum). However, stress tolerance mechanisms and efficient abatement require deeper insights. The applicability of arbuscular mycorrhizal fungi (AMF) poses as an ultimate strategy to minimize the deleterious consequences of abiotic stress such as salt, drought, temperature and heavy metal stress sustainably. The rational modality employing the application of AMF is one of significant efforts to lessen cell damages under abiotic stress. The novelty of the compilation can be redressed to cohesive literature for combating stress. The literature review will provide agricultural scientists worldwide in providing a rational approach that can have possible implications in not only tomato but also other vegetable crops. Full article

Horizontal gene transfer, a process through which an organism acquires genes from other organisms, is a rare evolutionary event in yeasts. Artificial random gene transfer can emerge as a valuable tool in yeast bioengineering to investigate the background of complex phenotypes, such as heat tolerance. In this study, a cDNA library was constructed from the mRNA of a methylotrophic yeast, Ogataea polymorpha, and then introduced into Saccharomyces cerevisiae. Ogataea polymorpha was selected because it is one of the most heat-tolerant species among yeasts. Screening of S. cerevisiae populations expressing O. polymorpha genes at high temperatures identified 59 O. polymorpha genes that contribute to heat tolerance. Gene enrichment analysis indicated that certain S. cerevisiae functions, including protein synthesis, were highly temperature-sensitive. Additionally, the results confirmed that heat tolerance in yeast is a complex phenotype dependent on multiple quantitative loci. Random gene transfer would be a useful tool for future bioengineering studies on yeasts. Full article

Calamus castaneus is a common rattan palm species in the tropical forests of Peninsular Malaysia and is noticeable by the yellow-based spines that cover the stems. This study aimed to determine the prevalence of fungal endophytes within C. castaneus spines and whether they inhibit the growth of fungal pathogens. Twenty-one genera with 40 species of fungal endophytes were isolated and identified from rattan palm spines. Based on molecular identification, the most common isolates recovered from the spines were Colletotrichum (n = 19) and Diaporthe spp. (n = 18), followed by Phyllosticta spp., Xylaria sp., Trichoderma spp., Helminthosporium spp., Penicillium spp., Fusarium spp., Neopestalotiopsis spp., Arthrinium sp., Cyphellophora sp., Cladosporium spp., Curvularia sp., Bionectria sp., and Acremonium spp. Non-sporulating fungi were also identified, namely Nemania primolutea, Pidoplitchkoviella terricola, Muyocopron laterale, Acrocalymma fici, Acrocalymma medicaginis, and Endomelanconiopsis endophytica. The isolation of these endophytes showed that the spines harbor endophytic fungi. Most of the fungal endophytes inhibited the growth of several plant pathogenic fungi, with 68% of the interactions resulting in mutual inhibition, producing a clear inhibition zone of <2 mm. Our findings demonstrate the potential of the fungal endophytes from C. castaneus spines as biocontrol agents. Full article

Calcium controls important processes in fungal metabolism, such as hyphae growth, cell wall synthesis, and stress tolerance. Recently, it was reported that calcium affects polyphosphate and lipid accumulation in fungi. The purpose of this study was to assess the effect of calcium on the accumulation of lipids and polyphosphate for six oleaginous Mucoromycota fungi grown under different phosphorus/pH conditions. A Duetz microtiter plate system (Duetz MTPS) was used for the cultivation. The compositional profile of the microbial biomass was recorded using Fourier-transform infrared spectroscopy, the high throughput screening extension (FTIR-HTS). Lipid content and fatty acid profiles were determined using gas chromatography (GC). Cellular phosphorus was determined using assay-based UV-Vis spectroscopy, and accumulated phosphates were characterized using solid-state ³¹P nuclear magnetic resonance spectroscopy. Glucose consumption was estimated by FTIR-attenuated total reflection (FTIR-ATR). Overall, the data indicated that calcium availability enhances polyphosphate accumulation in Mucoromycota fungi, while calcium deficiency increases lipid production, especially under acidic conditions (pH 2–3) caused by the phosphorus limitation. In addition, it was observed that under acidic conditions, calcium deficiency leads to increase in carotenoid production. It can be concluded that calcium availability can be used as an optimization parameter in fungal fermentation processes to enhance the production of lipids or polyphosphates. Full article

Hybridization between more divergent organisms is likely to generate progeny with more novel genetic interactions and genetic variations. However, the relationship between parental genetic divergence and progeny phenotypic variation remains largely unknown. Here, using strains of the human pathogenic Cryptococcus, we investigated the patterns of such a relationship. Twenty-two strains with up to 15% sequence divergence were mated. Progeny were genotyped at 16 loci. Parental strains and their progeny were phenotyped for growth ability at two temperatures, melanin production at seven conditions, and susceptibility to the antifungal drug fluconazole. We observed three patterns of relationships between parents and progeny for each phenotypic trait, including (i) similar to one of the parents, (ii) intermediate between the parents, and (iii) outside the parental phenotypic range. We found that as genetic distance increases between parental strains, progeny showed increased fluconazole resistance and growth at 37 °C but decreased melanin production under various oxidative and nitrosative stresses. Our findings demonstrate that, depending on the traits, both evolutionarily more similar strains and more divergent strains may be better parents to generate progeny with hybrid vigor. Together, the results indicate the enormous potential of Cryptococcus hybrids in their evolution and adaptation to diverse conditions. Full article

Mucormycosis (MCR) has been increasingly described in patients with coronavirus disease 2019 (COVID-19) but the epidemiological factors, presentation, diagnostic certainty, and outcome of such patients are not well described. We review the published COVID-19-associated mucormycosis (CAMCR) cases (total 41) to identify risk factors, clinical features, and outcomes. CAMCR was typically seen in patients with diabetes mellitus (DM) (94%) especially the ones with poorly controlled DM (67%) and severe or critical COVID-19 (95%). Its presentation was typical of MCR seen in diabetic patients (mostly rhino-orbital and rhino-orbital-cerebral presentation). In sharp contrast to reported COVID-associated aspergillosis (CAPA) cases, nearly all CAMCR infections were proven (93%). Treating physicians should have a high suspicion for CAMCR in patients with uncontrolled diabetes mellitus and severe COVID-19 presenting with rhino-orbital or rhino-cerebral syndromes. CAMR is the convergence of two storms, one of DM and the other of COVID-19. Full article

Banana, the main export fruit for Colombia, is threatened by Fusarium wilt (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), tropical race 4 (TR4). Pathogen containment through disinfecting tools, machinery, shoes, and any means that may carry contaminated soil particles with proper disinfectants is at the forefront of disease management. In this study, the biocide efficacy of 10 commercial quaternary ammonium compounds (QACs) products and one based on glutaraldehyde (GA) were evaluated on both reproductive structures (microconidia and macroconidia) and survival spores (chlamydospores) of Foc TR4 (strain 140038) isolated from La Guajira, Colombia. QACs were evaluated at 1200 ppm and two exposure times: <1 and 15 min in the absence or presence of soil. For GA disinfectant, four different concentrations (500, 800, 1200, and 2000 ppm) were evaluated at both contact times in the presence of soil. In the absence of soil, all QACs showed 100% biocidal efficiency against microconidia, macroconidia, and chlamydospores at both <1 and 15 min. The presence of soil decreased the efficacy of disinfectants, but some of them, such as QAC3_1st, QAC7_4th, and QAC5_4th, showed 98%, 98%, and 100% efficacy against Foc TR4 chlamydospores, respectively, after <1 min of contact time. For instance, the GA-based disinfectant was able to eliminate all Foc TR4 propagules after 15 min for all concentrations tested. Full article

Acid rain (AR) is an increasingly serious environmental problem that frequently occurs in Southern China with sulfuric acid rain (SAR) as the main type. SAR can negatively affect the growth and physiological properties of trees, but mycorrhizal associations may mitigate such detrimental effects. However, the mechanisms by which arbuscular mycorrhizal fungi control SAR-induced impacts on Torreya grandis plants remain unclear. A pot experiment was conducted on T. grandis seedlings, an economically important tree species in Southern China, in which inoculated and non-inoculated T. grandis seedlings were subjected to three simulated SAR regimes (pH of 5.6, 4.0, and 2.5, respectively) to examine the effects on the growth, osmotic regulation, and nutrient absorption of these seedlings. The results show that, although SAR had no effect on the accumulation of biomass, it significantly decreased the concentrations of proline and soluble protein, shoot Zn²⁺, P, K⁺, and Ca²⁺ concentrations, and the Fe²⁺ and Mn²⁺ concentrations of shoots and roots. Mycorrhizal inoculation, especially with Rhizophagus irregularis, significantly increased total biomass, proline concentration, and the Zn²⁺, P, and K⁺ concentrations in the shoots of T. grandis under lower pH conditions. Moreover, our findings suggest that the combination of root colonization, acid tolerance, and the concentrations of shoot-P, shoot-Zn²⁺, and root-Fe²⁺ of T. grandis jointly conferred mycorrhizal benefits on the plants under SAR conditions. Given the enhancement of the nutritional quality of T. grandis owing to mycorrhizal associations, inoculation with R. irregularis may be preferable for the culturing and management of these plants under acidic conditions. Full article

The resistance of the notorious rice pest Nilaparvata lugens to many insecticides has caused significant concerns. Our previous study demonstrated that the fungus Metarhizium anisopliae CQMa421 shows great potential for the control of this pest, but the interactions between them are still unclear. Thus, we further investigated fungal infection-related microRNAs (miRNAs) in N. lugens during M. anisopliae CQMa421 challenge using Illumina sequencing. In this study, we constructed twenty-four small RNA libraries over different time courses (i.e., 4 h, 8 h, 16 h, and 24 h). A total of 478.62 M clean reads were collected, with each sample producing more than 13.37 M reads, after the removal of low-quality reads. We identified 2324 miRNAs and their 11,076 target genes within the twenty-four libraries by bioinformatics analysis. Differentially expressed miRNAs (DEmiRNAs), including 58 (32 upregulated vs. 26 downregulated), 62 (30 upregulated vs. 32 downregulated), 126 (71 upregulated vs. 55 downregulated), and 109 (40 upregulated vs. 69 downregulated) DEmiRNAs were identified at 4 h, 8 h, 16 h, and 24 h post-infection, respectively. We further conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to predict the functions of all target genes of DEmiRNAs. These DEmiRNAs targets identified during 24 h of infection were primarily involved in energy metabolism, lysine degradation, the FoxO signaling pathway, ubiquitin-mediated proteolysis, the mRNA surveillance pathway, and the MAPK signaling pathway. Taken together, our results provide essential information for further study of the interactions between the entomopathogenic fungus M. anisopliae and N. lugens at the posttranscriptional level. Full article

Neofusicoccum parvum, in the family Botryosphaeriaceae, was identified as the causal agent of bot gummosis of lemon (Citrus × limon) trees, in the two major lemon-producing regions in Italy. Gummy cankers on trunk and scaffold branches of mature trees were the most typical disease symptoms. Neofusicoccum parvum was the sole fungus constantly and consistently isolated from the canker bark of symptomatic lemon trees. It was identified on the basis of morphological characters and the phylogenetic analysis of three loci, i.e., the internal transcribed spacer of nuclear ribosomal DNA (ITS) as well as the translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2) genes. The pathogenicity of N. parvum was demonstrated by wound inoculating two lemon cultivars, ‘Femminello 2kr’ and ‘Monachello’, as well as citrange (C. sinensis × Poncirus trifoliata) ‘Carrizo’ rootstock. In artificial inoculations, the fungus was very aggressive on lemons and weakly virulent on citrange, consistently with symptoms observed in the field as a consequence of natural infections. This is the first report of N. parvum, both in a wide and in a strict taxonomic sense, as a pathogen of lemon in Italy. Full article

Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under the ground. Truffles in northern Thailand have been recorded in association with Betulaalnoides and Carpinus poilanei. In this study, we investigated the soil mycobiota diversity of soil samples from both of these truffle host plants in native forests using environmental DNA metabarcoding to target the internal transcribed spacer 1 (ITS1) region of the rDNA gene for the purposes of investigation of truffle diversity and locating truffles during the non-fruiting phase. In this study, a total of 38 soil samples were collected from different locations. Of these, truffles had been found at three of these locations. Subsequently, a total of 1341 putative taxonomic units (OTUs) were obtained. The overall fungal community was dominated by phylum-level sequences assigned to Ascomycota (57.63%), Basidiomycota (37.26%), Blastocladiomycota (0.007%), Chytridiomycota (0.21%), Glomeromycota (0.01%), Kickxellomycota (0.01%), Mortierellomycota (2.08%), Mucoromycota (0.24%), Rozellomycota (0.01%), Zoopagomycota (0.003%), and unidentified (2.54%). The results revealed that six OTUs were determined to be representative and belonged to the genus Tuber. OTU162, OTU187, OTU447, and OTU530 belonged to T. thailandicum, T. lannaense, T. bomiense, and T. magnatum, whereas OTU105 and OTU720 were acknowledged as unrecognized Tuber species. From 38 locations, OTUs of truffles were found in 33 locations (including three previously known truffle locations). Thus, 30 collection sites were considered new locations for T. thailandicum, T. bomiense, and other unrecognized Tuber species. Interestingly, at 16 new locations, mature ascocarps of truffles that were undergoing the fruiting phase were located underground. All 16 truffle samples were identified as T. thailandicum based on morphological characteristics and molecular phylogenetic analysis. However, ascocarps of other truffle species were not found at the new OTUs representative locations. The knowledge gained from this study can be used to lead researchers to a better understanding of the occurrence of truffles using soil mycobiota diversity investigation. The outcomes of this study will be particularly beneficial with respect to the search and hunt for truffles without the need for trained animals. In addition, the findings of this study will be useful for the management and conservation of truffle habitats in northern Thailand. Full article

Triazole-resistance has been reported increasingly in Aspergillus fumigatus. An international expert team proposed to avoid triazole monotherapy for the initial treatment of invasive aspergillosis in regions with >10% environmental-resistance, but this prevalence is largely unknown for most American and African countries. Here, we screened 584 environmental samples (soil) from urban and rural locations in Mexico, Paraguay, and Peru in Latin America and Benin and Nigeria in Africa for triazole-resistant A. fumigatus. Samples were screened using triazole-containing agars and confirmed as triazole-resistant by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth dilution reference method. Isolates were further characterized by cyp51A sequencing and short-tandem repeat typing. Fungicide presence in samples was likewise determined. Among A. fumigatus positive samples, triazole-resistance was detected in 6.9% (7/102) of samples in Mexico, 8.3% (3/36) in Paraguay, 9.8% (6/61) in Peru, 2.2% (1/46) in Nigeria, and none in Benin. Cyp51A gene mutations were present in most of the triazole-resistant isolates (88%; 15/17). The environmentally-associated mutations TR₃₄/L98H and TR₄₆/Y121F/T289A were prevalent in Mexico and Peru, and isolates harboring these mutations were closely related. For the first time, triazole-resistant A. fumigatus was found in environmental samples in Mexico, Paraguay, Peru, and Nigeria with a prevalence of 7–10% in the Latin American countries. Our findings emphasize the need to establish triazole-resistance surveillance programs in these countries. Full article

Green synthesis of nanoparticles (NPs) is a safe, eco-friendly, and relatively inexpensive alternative to conventional routes of NPs production. These methods require natural resources such as cyanobacteria, algae, plants, fungi, lichens, and naturally extracted biomolecules such as pigments, vitamins, polysaccharides, proteins, and enzymes to reduce bulk materials (the target metal salts) into a nanoscale product. Synthesis of nanomaterials (NMs) using lichen extracts is a promising eco-friendly, simple, low-cost biological synthesis process. Lichens are groups of organisms including multiple types of fungi and algae that live in symbiosis. Until now, the fabrication of NPs using lichens has remained largely unexplored, although the role of lichens as natural factories for synthesizing NPs has been reported. Lichens have a potential reducible activity to fabricate different types of NMs, including metal and metal oxide NPs and bimetallic alloys and nanocomposites. These NPs exhibit promising catalytic and antidiabetic, antioxidant, and antimicrobial activities. To the best of our knowledge, this review provides, for the first time, an overview of the main published studies concerning the use of lichen for nanofabrication and the applications of these NMs in different sectors. Moreover, the possible mechanisms of biosynthesis are discussed, together with the various optimization factors influencing the biological synthesis and toxicity of NPs. Full article

Oral mucositis is an acute side effect of radiation therapy that is especially common with head and neck cancer treatment. In recent years, several studies have revealed the predisposing factors for mucositis, leading to the pre-treatment of patients to deter the development of opportunistic oral fungal infections. Although many clinical protocols already advise the use of probiotics to counteract inflammation and fungal colonization, preclinical studies are needed to better delineate the mechanisms by which a host may acquire benefits via co-evolution with oral microbiota, probiotics, and fungal commensals, such as Candida albicans, especially during acute inflammation. Here, we review the current understanding of radiation therapy-dependent oral mucositis in terms of pathology, prevention, treatment, and related opportunistic infections, with a final focus on the oral microbiome and how it may be important for future therapy. Full article

This study reports the draft genome of Amorphotheca resinae KUC30009, a fungal isolate with promising industrial-scale melanin production potential. The mechanisms for melanin or melanin-related pigment formation of this strain were examined through bioinformatic and biochemical strategies. The 30.11 Mb genome of A. resinae contains 9638 predicted genes. Genomic-based discovery analyses identified 14 biosynthetic gene clusters (BGCs) associated with secondary metabolite production. Moreover, genes encoding a specific type 1 polyketide synthase and 4-hydroxynaphthalene reductase were identified and predicted to produce intermediate metabolites of dihydroxy naphthalene (DHN)-melanin biosynthesis pathway, but not to DHN-melanin. These findings were further supported by the detection of increased flaviolin concentrations in mycelia and almost unchanged morphologies of the culture grown with tricyclazole. Apart from this, the formation of melanin in the culture filtrate appeared to depend on the laccase-like activity of multi-copper oxidases. Simultaneously, concentrations of nitrogen-containing sources decreased when the melanin formed in the media. Interestingly, melanin formation in the culture fluid was proportional to laccase-like activity. Based on these findings, we proposed novel strategies for the enhancement of melanin production in culture filtrates. Therefore, our study established a theoretical and methodological basis for synthesizing pigments from fungal isolates using genomic- and biochemical-based approaches. Full article

Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management. Full article

Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains. Full article

Agricultural wastes are lignocellulosic biomasses that contain high mineral and nutrient contents. This waste can be used as a raw material in industrial enzyme production by microbial fermentation. Phytase is an important enzyme used in animal feed to enhance the amount of phosphorus available for the growth and overall health improvement of monogastric animals. Fungi offer high potential as an effective source in the production of various extracellular enzymes. In this study, the production of lignocellulolytic enzymes (endoglucanase and xylanase) and phytase by a thermophilic fungus, namely Thermoascus aurantiacus strain SL16W, was evaluated using sixteen different Thai agricultural forms of waste under conditions of high temperature (45 °C). Semi-solid state fermentation was used in the production experiments. The results of this study reveal that the highest phytase activity (58.6 U/g substrate) was found in rice bran, whereas the highest degrees of activity of endoglucanase and xylanase were observed in wheat bran and red tea leaves at 19 and 162 U/g substrate, respectively. Consequently, the optimal conditions for phytase production of this fungus using rice bran were investigated. The results indicate that the highest phytase yield (58.6 to 84.1 U/g substrate) was observed in rice bran containing 0.5% ammonium sulfate as a nitrogen source with 10 discs of inoculum size at a cultivation period of 9 days at 45 °C and moisture content of 95%. Notably, the phytase yield increased by 1.71-fold, while endoglucanase and xylanase were also increased by 1.69- and 1.12-fold, respectively. Furthermore, the crude enzyme obtained from the optimal condition was extracted. The crude enzyme extract was then separately added to red tea leaves, rice straw, corncobs, palm residue, and peanut husks. Subsequently, total reducing sugar and phosphorus contents were determined. The results indicate that the highest level of reducing sugar (122.6 mg/L) and phosphorus content (452.6 mg/L) (p < 0.05) were obtained in palm residue at 36 and 48 h, respectively, after the addition of the crude enzyme extract. This study has provided valuable information on a potentially eco-friendly way to valorize agricultural waste into value-added products as industrial enzymes. Full article