Journal of Fungi

11 pages, 1832 KiB

Open AccessArticle

Engineered Saccharomyces cerevisiae for the De Novo Biosynthesis of (−)-Menthol

by Xueqin Lv, Xuan Zhou, Jun Ma, Mengrui Tao, Yanfeng Liu, Jianghua Li, Guocheng Du and Long Liu

J. Fungi 2022, 8(9), 982; https://doi.org/10.3390/jof8090982 - 19 Sep 2022

Cited by 6 | Viewed by 2298

Abstract

Menthol, a high-value commodity monoterpenoid chemical, holds an important market share commercially because of its distinct functions. The menthol on the market mainly originates from plant extraction, which is facing challenges such as the seasonal fluctuations and long growth cycle of plants. Therefore, [...] Read more.

Menthol, a high-value commodity monoterpenoid chemical, holds an important market share commercially because of its distinct functions. The menthol on the market mainly originates from plant extraction, which is facing challenges such as the seasonal fluctuations and long growth cycle of plants. Therefore, this study attempted to realize the de novo synthesis of menthol through microbial fermentation. First, through heterologous expression and subcellular localization observation, a synthetic route from glucose to (−)-menthol was successfully designed and constructed in Saccharomyces cerevisiae. Then, the mevalonate (MVA) pathway was enhanced, and the expression of farnesyl diphosphate synthase (ERG20) was dynamically regulated to improve the synthesis of D-limonene, a key precursor of (−)-menthol. Shake flask fermentation results showed that the D-limonene titer of the recombinant strain reached 459.59 mg/L. Next, the synthesis pathway from D-limonene to (−)-menthol was strengthened, and the fermentation medium was optimized. The (−)-menthol titer of 6.28 mg/L was obtained, implying that the de novo synthesis of menthol was successfully realized for the first time. This study provides a good foundation for the synthesis of menthol through microbial fermentation. Full article

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16 pages, 4165 KiB

Open AccessArticle

50 Years of Cumulative Open-Source Data Confirm Stable and Robust Biodiversity Distribution Patterns for Macrofungi

by Haili Yu, Tiejun Wang, Andrew Skidmore, Marco Heurich and Claus Bässler

J. Fungi 2022, 8(9), 981; https://doi.org/10.3390/jof8090981 - 19 Sep 2022

Cited by 1 | Viewed by 1959

Abstract

Fungi are a hyper-diverse kingdom that contributes significantly to the regulation of the global carbon and nutrient cycle. However, our understanding of the distribution of fungal diversity is often hindered by a lack of data, especially on a large spatial scale. Open biodiversity [...] Read more.

Fungi are a hyper-diverse kingdom that contributes significantly to the regulation of the global carbon and nutrient cycle. However, our understanding of the distribution of fungal diversity is often hindered by a lack of data, especially on a large spatial scale. Open biodiversity data may provide a solution, but concerns about the potential spatial and temporal bias in species occurrence data arising from different observers and sampling protocols challenge their utility. The theory of species accumulation curves predicts that the cumulative number of species reaches an asymptote when the sampling effort is sufficiently large. Thus, we hypothesize that open biodiversity data could be used to reveal large-scale macrofungal diversity patterns if these datasets are accumulated long enough. Here, we tested our hypothesis with 50 years of macrofungal occurrence records in Norway and Sweden that were downloaded from the Global Biodiversity Information Facility (GBIF). We first grouped the data into five temporal subsamples with different cumulative sampling efforts (i.e., accumulation of data for 10, 20, 30, 40 and 50 years). We then predicted the macrofungal diversity and distribution at each subsample using the maximum entropy (MaxEnt) species distribution model. The results revealed that the cumulative number of macrofungal species stabilized into distinct distribution patterns with localized hotspots of predicted macrofungal diversity with sampling efforts greater than approximately 30 years. Our research demonstrates the utility and importance of the long-term accumulated open biodiversity data in studying macrofungal diversity and distribution at the national level. Full article

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23 pages, 1648 KiB

Open AccessArticle

Comparison of Primers for the Detection of Phytophthora (and Other Oomycetes) from Environmental Samples

by Treena I. Burgess, Diane White and Sarah J. Sapsford

J. Fungi 2022, 8(9), 980; https://doi.org/10.3390/jof8090980 - 19 Sep 2022

Cited by 9 | Viewed by 2418

Abstract

Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 [...] Read more.

Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 primer combinations have been designed to amplify oomycetes, or more specifically, Phytophthora species, from environmental samples. We used the Illumina sequencing platform to compare 13 primer combinations on mock communities and environmental samples. The primer combinations tested varied significantly in their ability to amplify Phytophthora species in a mock community and from environmental samples; this was due to either low sensitivity (unable to detect species present in low concentrations) or a lack of specificity (an inability to amplify some species even if they were present in high concentrations). Primers designed for oomycetes underestimated the Phytophthora community compared to Phytophthora-specific primers. We recommend using technical replicates, primer combinations, internal controls, and a phylogenetic approach for assigning a species identity to OTUs or ASVs. Particular care must be taken if sampling substrates where hybrid species could be expected. Overall, the choice of primers should depend upon the hypothesis being tested. Full article

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23 pages, 5571 KiB

Open AccessArticle

Biodiversity and Bioprospecting of Fungal Endophytes from the Antarctic Plant Colobanthus quitensis

by Laura Bertini, Michele Perazzolli, Silvia Proietti, Gloria Capaldi, Daniel V. Savatin, Valentina Bigini, Claudia Maria Oliveira Longa, Marina Basaglia, Lorenzo Favaro, Sergio Casella, Benedetta Fongaro, Patrizia Polverino de Laureto and Carla Caruso

J. Fungi 2022, 8(9), 979; https://doi.org/10.3390/jof8090979 - 19 Sep 2022

Cited by 9 | Viewed by 2854

Abstract

Microorganisms from extreme environments are considered as a new and valuable reservoir of bioactive molecules of biotechnological interest and are also utilized as tools for enhancing tolerance to (a)biotic stresses in crops. In this study, the fungal endophytic community associated with the leaves [...] Read more.

Microorganisms from extreme environments are considered as a new and valuable reservoir of bioactive molecules of biotechnological interest and are also utilized as tools for enhancing tolerance to (a)biotic stresses in crops. In this study, the fungal endophytic community associated with the leaves of the Antarctic angiosperm Colobanthus quitensis was investigated as a new source of bioactive molecules. We isolated 132 fungal strains and taxonomically annotated 26 representative isolates, which mainly belonged to the Basidiomycota division. Selected isolates of Trametes sp., Lenzites sp., Sistotrema sp., and Peniophora sp. displayed broad extracellular enzymatic profiles; fungal extracts from some of them showed dose-dependent antitumor activity and inhibited the formation of amyloid fibrils of α-synuclein and its pathological mutant E46K. Selected fungal isolates were also able to promote secondary root development and fresh weight increase in Arabidopsis and tomato and antagonize the growth of pathogenic fungi harmful to crops. This study emphasizes the ecological and biotechnological relevance of fungi from the Antarctic ecosystem and provides clues to the bioprospecting of Antarctic Basidiomycetes fungi for industrial, agricultural, and medical applications. Full article

(This article belongs to the Special Issue Biological Activity of Fungi: Interaction with the Environment)

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13 pages, 3363 KiB

Open AccessArticle

Fungi Classification in Various Growth Stages Using Shortwave Infrared (SWIR) Spectroscopy and Machine Learning

by Zhuo Liu and Yanjie Li

J. Fungi 2022, 8(9), 978; https://doi.org/10.3390/jof8090978 - 19 Sep 2022

Cited by 2 | Viewed by 1403

Abstract

Dark septate endophytes (DSEs) fungi are beneficial to host plants with regard to abiotic stress. Here, we examined the capability of SWIR spectroscopy to classify fungus types and detected the growth stages of DSEs fungi in a timely, non-destructive and time-saving manner. The [...] Read more.

Dark septate endophytes (DSEs) fungi are beneficial to host plants with regard to abiotic stress. Here, we examined the capability of SWIR spectroscopy to classify fungus types and detected the growth stages of DSEs fungi in a timely, non-destructive and time-saving manner. The SWIR spectral data of five DSEs fungi in six growth stages were collected, and three pre-processing methods and sensitivity analysis (SA) variable selection methods were performed using a machine learning model. The results showed that the De-trending + first Derivative (DET_FST) processing spectra combined with the support vector machine (SVM) model yielded the best classification accuracy for fungi classification at different growth stages and growth stage detection on different fungus types. The mean accuracy of generic model for fungi classification and growth stage detection are 0.92 and 0.99 on the calibration set, respectively. Seven important bands, 1164, 1456, 2081, 2272, 2278, 2448 and 2481 nm, were found to be related to the SVM fungi classification. This study provides a rapid and efficient method for the classification of fungi in different growth stages and the detection of fungi growth stage of various types of fungi and could serve as a tool for fungi study. Full article

(This article belongs to the Section Fungi in Agriculture and Biotechnology)

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15 pages, 2932 KiB

Open AccessArticle

The Colletotrichum siamense Hydrophobin CsHydr1 Interacts with the Lipid Droplet-Coating Protein CsCap20 and Regulates Lipid Metabolism and Virulence

by Na Wang, Jiyuan Wang, Jingwen Lu, Yu Liu, Yitao Xi, Miao Song, Xiaoling Guan, Zhigang Li, Xiao Li, Yu Zhang, Chunhua Lin and Weiguo Miao

J. Fungi 2022, 8(9), 977; https://doi.org/10.3390/jof8090977 - 19 Sep 2022

Cited by 3 | Viewed by 1570

Abstract

Previous studies of the lipid droplet-coating protein Cap20 in Colletotrichum show that it plays a key role in appressorium development and virulence. In this study, the hydrophobin CsHydr1, which contains a signal peptide of 19 amino acids and a hydrophobic domain (HYDRO), was [...] Read more.

Previous studies of the lipid droplet-coating protein Cap20 in Colletotrichum show that it plays a key role in appressorium development and virulence. In this study, the hydrophobin CsHydr1, which contains a signal peptide of 19 amino acids and a hydrophobic domain (HYDRO), was shown to interact with CsCap20 in Colletotrichum siamense. The CsHydr1 deletion mutant showed slightly enhanced mycelial growth, small conidia, slow spore germination and appressoria formation, cell wall integrity and virulence. Like CsCAP20, CsHydr1 is also localized on the lipid droplet surface of C. siamense. However, when CsCap20 was absent, some CsHydr1 was observed in other parts. Quantitative lipid determination showed that the absence of either CsHydr1 or CsCap20 reduced the content of lipids in mycelia and conidia, while the effect of CsCap20 was more obvious; these results suggest that an interaction protein CsHydr1 of CsCap20 is localized on the lipid droplet surface and involved in lipid metabolism, which affects appressorium formation and virulence in C. siamense. Full article

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15 pages, 1194 KiB

Open AccessReview

Zearalenone and Its Masked Forms in Cereals and Cereal-Derived Products: A Review of the Characteristics, Incidence, and Fate in Food Processing

by Huilin Yu, Junhui Zhang, Yixuan Chen and Jiajin Zhu

J. Fungi 2022, 8(9), 976; https://doi.org/10.3390/jof8090976 - 18 Sep 2022

Cited by 9 | Viewed by 2764

Abstract

Zearalenone (ZEA) is known as a Fusarium-produced mycotoxin, representing a risk to cereal food safety with repercussions for economies and worldwide trade. Recent studies have reported the co-occurrence of ZEA and masked ZEA in a variety of cereals and cereal-based products, which may [...] Read more.

Zearalenone (ZEA) is known as a Fusarium-produced mycotoxin, representing a risk to cereal food safety with repercussions for economies and worldwide trade. Recent studies have reported the co-occurrence of ZEA and masked ZEA in a variety of cereals and cereal-based products, which may exert adverse effects on public health due to additive/synergistic interactions. However, the co-contamination of ZEA and masked ZEA has received little attention. In order to minimize the threats of co-contamination by ZEA and masked ZEA, it is necessary to recognize the occurrence and formation of ZEA and masked ZEA. This review focuses on the characteristics, incidence, and detection of ZEA and its masked forms. Additionally, the fate of ZEA and masked ZEA during the processing of bread, cake, biscuits, pasta, and beer, as well as the ZEA limit, are discussed. The incidence of masked ZEA is lower than that of ZEA, and the mean level of masked ZEA varies greatly between cereal samples. Published data showed a considerable degree of heterogeneity in the destiny of ZEA during cereal-based food processing, mostly as a result of the varying contamination levels and complicated food processing methods. Knowledge of the fate of ZEA and masked ZEA throughout cereal-based food processing may reduce the likelihood of severe detrimental market and trade ramifications. The revision of legislative limits of masked ZEA may become a challenge in the future. Full article

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15 pages, 3709 KiB

Open AccessArticle

Amine-Regulated pri-SMTP Oxidation in SMTP Biosynthesis in Stachybotrys: Possible Implication in Nitrogen Acquisition

by Ryota Iwama, Yu Sasano, Taichi Hiramatsu, Shinya Otake, Eriko Suzuki and Keiji Hasumi

J. Fungi 2022, 8(9), 975; https://doi.org/10.3390/jof8090975 - 18 Sep 2022

Cited by 2 | Viewed by 1582

Abstract

SMTP (the name SMTP is derived from Stachybotrys microspora triprenyl phenol) is a family of triprenyl phenol secondary metabolites from a black mold, Stachybotrys microspora. Some SMTP congeners exhibit anti-inflammatory and profibrinolytic activities that, in combination, contribute to the treatment of ischemic [...] Read more.

SMTP (the name SMTP is derived from Stachybotrys microspora triprenyl phenol) is a family of triprenyl phenol secondary metabolites from a black mold, Stachybotrys microspora. Some SMTP congeners exhibit anti-inflammatory and profibrinolytic activities that, in combination, contribute to the treatment of ischemic stroke. The final step in the SMTP biosynthesis is a non-enzymatic amine conjugation with an o-phthalaldehyde moiety of the precursor pre-SMTP, which can form adducts with proteins and nucleic acids. Thus, pre-SMTP formation should be a precisely regulated, rate-limiting step in the SMTP biosynthesis. To address the mechanism backing this regulation, we purified a metabolite that rapidly disappeared following amine feeding, identifying a novel compound, pri-SMTP. Furthermore, an enzyme, designated as pri-SMTP oxidase, responsible for pri-SMTP conversion to pre-SMTP, was purified. The formation of pri-SMTP, which is regulated by nitrogen and carbon nutrients, occurred in particular septate mycelia. Although pri-SMTP oxidase was expressed constitutively, the consumption of pri-SMTP was accelerated only when a primary amine was fed. Thus, SMTP biosynthesis is regulated by at least three mechanisms: (i) pri-SMTP formation affected by nutrients, (ii) the compartmentalization of pri-SMTP formation/storage, and (iii) amine-regulated pri-SMTP oxidation. Amine-regulated SMTP formation (i.e., amine-capturing with pre-SMTP) may play a role in the nitrogen acquisition/assimilation strategy in S. microspora, since pri-SMTP synthesis occurs on non-preferred nitrogen. Full article

(This article belongs to the Section Fungal Cell Biology, Metabolism and Physiology)

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13 pages, 3394 KiB

Open AccessArticle

The CfSnt2-Dependent Deacetylation of Histone H3 Mediates Autophagy and Pathogenicity of Colletotrichum fructicola

by Yuan Guo, Zhenhong Chen, He Li and Shengpei Zhang

J. Fungi 2022, 8(9), 974; https://doi.org/10.3390/jof8090974 - 18 Sep 2022

Cited by 2 | Viewed by 1465

Abstract

Camellia oleifera is one of the most valuable woody edible-oil crops, and anthracnose seriously afflicts its yield and quality. We recently showed that the CfSnt2 regulates the pathogenicity of Colletotrichum fructicola, the dominant causal agent of anthracnose on C. oleifera. However, [...] Read more.

Camellia oleifera is one of the most valuable woody edible-oil crops, and anthracnose seriously afflicts its yield and quality. We recently showed that the CfSnt2 regulates the pathogenicity of Colletotrichum fructicola, the dominant causal agent of anthracnose on C. oleifera. However, the molecular mechanisms of CfSnt2-mediated pathogenesis remain largely unknown. Here, we found that CfSnt2 is localized to the nucleus to regulate the deacetylation of histone H3. The further transcriptomic analysis revealed that CfSnt2 mediates the expression of global genes, including most autophagy-related genes. Furthermore, we provided evidence showing that CfSnt2 negatively regulates autophagy and is involved in the responses to host-derived ROS and ER stresses. These combined functions contribute to the pivotal roles of CfSnt2 on pathogenicity. Taken together, our studies not only illustrate how CfSnt2 functions in the nucleus, but also link its roles on the autophagy and responses to host-derived stresses with pathogenicity in C. fructicola. Full article

(This article belongs to the Section Fungal Pathogenesis and Disease Control)

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16 pages, 3381 KiB

Open AccessArticle

Phytophthora × cambivora as a Major Factor Inciting the Decline of European Beech in a Stand within the Southernmost Limit of Its Natural Range in Europe

by Mario Riolo, Francesco Aloi, Sebastiano Conti Taguali, Antonella Pane, Massimo Franco and Santa Olga Cacciola

J. Fungi 2022, 8(9), 973; https://doi.org/10.3390/jof8090973 - 18 Sep 2022

Cited by 3 | Viewed by 2036

Abstract

The objective of this study was to investigate the role of the oomycete Phytophthora× cambivora in the decline affecting European beech (Fagus sylvatica) in the Nebrodi Regional Park (Sicily, southern Italy). In a survey of a beech forest stand in [...] Read more.

The objective of this study was to investigate the role of the oomycete Phytophthora× cambivora in the decline affecting European beech (Fagus sylvatica) in the Nebrodi Regional Park (Sicily, southern Italy). In a survey of a beech forest stand in the heart of the park, Phytophthora× cambivora was the sole Phytophthora species recovered from the rhizosphere soil and fine roots of trees. Both A1 and A2 mating type isolates were found. Direct isolation from the stem bark of trees showing severe decline symptoms and bleeding stem cankers yielded exclusively P. gonapodyides, usually considered as an opportunistic pathogen. The mean inoculum density of P.× cambivora in the rhizosphere soil, as determined using the soil dilution plating method and expressed in terms of colony forming units (cfus) per gm of soil, the isolation frequency using leaf baiting, and the percentage of infected fibrous roots from 20 randomly selected beech trees with severe decline symptoms (50 to 100 foliage transparency classes) were 31.7 cfus, 80%, and 48.6%, respectively. These were significantly higher than the corresponding mean values of 20 asymptomatic or slightly declining trees, suggesting P.× cambivora is a major factor responsible for the decline in the surveyed stand. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance 2.0)

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9 pages, 409 KiB

Open AccessArticle

Performance of Multiplex PCR and β-1,3-D-Glucan Testing for the Diagnosis of Candidemia

by Özlem Koc, Harald H. Kessler, Martin Hoenigl, Johannes Wagener, Sebastian Suerbaum, Sören Schubert and Karl Dichtl

J. Fungi 2022, 8(9), 972; https://doi.org/10.3390/jof8090972 - 17 Sep 2022

Cited by 4 | Viewed by 2020

Abstract

Bloodstream infections caused by Candida yeasts (candidemia) are associated with high morbidity and mortality. Diagnosis remains challenging, with the current gold standard—isolation from blood culture (BC)—being limited by low sensitivity and long turnaround time. This study evaluated the performance of two nonculture methods: [...] Read more.

Bloodstream infections caused by Candida yeasts (candidemia) are associated with high morbidity and mortality. Diagnosis remains challenging, with the current gold standard—isolation from blood culture (BC)—being limited by low sensitivity and long turnaround time. This study evaluated the performance of two nonculture methods: PCR and β-1,3-D-glucan (BDG) testing. The sera of 103 patients with BC-proven candidemia and of 46 controls were analyzed with the Fungiplex Candida Real-Time PCR and the Wako β-Glucan Test. The BDG assay demonstrated higher sensitivity than the multiplex PCR (58% vs. 33%). This was particularly evident in ICU patients (60% vs. 28%) and in C. albicans candidemia (57% vs. 37%). The earlier prior to BC sampling the sera were obtained, the more the PCR sensitivity decreased (46% to 18% in the periods of 0–2 and 3–5 days before BC, respectively), while BDG testing was independent of the sampling date. No positive PCR results were obtained in sera sampled more than five days before BC. Specificities were 89% for BDG and 93% for PCR testing. In conclusion, BDG testing demonstrated several advantages over PCR testing for the diagnosis of candidemia, including higher sensitivity and earlier diagnosis. However, BC remains essential, as BDG does not allow for species differentiation. Full article

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26 pages, 2193 KiB

Open AccessArticle

Unveiling the Secretome of the Fungal Plant Pathogen Neofusicoccum parvum Induced by In Vitro Host Mimicry

by Forough Nazar Pour, Bruna Pedrosa, Micaela Oliveira, Cátia Fidalgo, Bart Devreese, Gonzalez Van Driessche, Carina Félix, Nuno Rosa, Artur Alves, Ana Sofia Duarte and Ana Cristina Esteves

J. Fungi 2022, 8(9), 971; https://doi.org/10.3390/jof8090971 - 17 Sep 2022

Cited by 12 | Viewed by 2782

Abstract

Neofusicoccum parvum is a fungal plant pathogen of a wide range of hosts but knowledge about the virulence factors of N. parvum and host–pathogen interactions is rather limited. The molecules involved in the interaction between N. parvum and Eucalyptus are mostly unknown, so [...] Read more.

Neofusicoccum parvum is a fungal plant pathogen of a wide range of hosts but knowledge about the virulence factors of N. parvum and host–pathogen interactions is rather limited. The molecules involved in the interaction between N. parvum and Eucalyptus are mostly unknown, so we used a multi-omics approach to understand pathogen–host interactions. We present the first comprehensive characterization of the in vitro secretome of N. parvum and a prediction of protein–protein interactions using a dry-lab non-targeted interactomics strategy. We used LC-MS to identify N. parvum protein profiles, resulting in the identification of over 400 proteins, from which 117 had a different abundance in the presence of the Eucalyptus stem. Most of the more abundant proteins under host mimicry are involved in plant cell wall degradation (targeting pectin and hemicellulose) consistent with pathogen growth on a plant host. Other proteins identified are involved in adhesion to host tissues, penetration, pathogenesis, or reactive oxygen species generation, involving ribonuclease/ribotoxin domains, putative ricin B lectins, and necrosis elicitors. The overexpression of chitosan synthesis proteins during interaction with the Eucalyptus stem reinforces the hypothesis of an infection strategy involving pathogen masking to avoid host defenses. Neofusicoccum parvum has the molecular apparatus to colonize the host but also actively feed on its living cells and induce necrosis suggesting that this species has a hemibiotrophic lifestyle. Full article

(This article belongs to the Special Issue Fungi: What Have We Learned from Omics?)

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17 pages, 4218 KiB

Open AccessArticle

Alternative CUG Codon Usage in the Halotolerant Yeast Debaryomyces hansenii: Gene Expression Profiles Provide New Insights into Ambiguous Translation

by Daniel Ochoa-Gutiérrez, Anya M. Reyes-Torres, Ileana de la Fuente-Colmenares, Viviana Escobar-Sánchez, James González, Rosario Ortiz-Hernández, Nayeli Torres-Ramírez and Claudia Segal-Kischinevzky

J. Fungi 2022, 8(9), 970; https://doi.org/10.3390/jof8090970 - 16 Sep 2022

Viewed by 2300

Abstract

The halotolerant yeast Debaryomyces hansenii belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the [...] Read more.

The halotolerant yeast Debaryomyces hansenii belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine–serine ambiguity in cellular adaptations to extreme environments. Here, we examine sequences and structures of tRNA_CAG from the CTG-Ser1 clade yeasts, finding that D. hansenii conserves the elements to translate ambiguously. Then, we show that D. hansenii has tolerance to conditions of salinity, acidity, alkalinity, and oxidative stress associated with phenotypic and ultrastructural changes. In these conditions, we found differential expression in both the logarithmic and stationary growth phases of tRNA^Ser, tRNA^Leu, tRNA_CAG, LeuRS, and SerRS genes that could be involved in the adaptive process of this yeast. Finally, we compare the proteomic isoelectric points and hydropathy profiles, detecting that the most important variations among the physicochemical characteristics of D. hansenii proteins are in their hydrophobic and hydrophilic interactions with the medium. We propose that the ambiguous translation, i.e., leucylation or serynation, on translation of the CUG-encoded residues, could be linked to adaptation processes in extreme environments. Full article

(This article belongs to the Special Issue Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii)

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18 pages, 2517 KiB

Open AccessEditor’s ChoiceArticle

Root Colonization by Fungal Entomopathogen Systemically Primes Belowground Plant Defense against Cabbage Root Fly

by Catalina Posada-Vergara, Katharina Lohaus, Mohammad Alhussein, Stefan Vidal and Michael Rostás

J. Fungi 2022, 8(9), 969; https://doi.org/10.3390/jof8090969 - 16 Sep 2022

Cited by 4 | Viewed by 2331

Abstract

Entomopathogenic fungi infect insects via spores but also live inside plant tissues as endophytes. Frequently, colonization by entomopathogens provides plants with increased resistance against insects, but the mechanisms are little understood. This study investigated direct, local, and systemic root-mediated interactions between isolates of [...] Read more.

Entomopathogenic fungi infect insects via spores but also live inside plant tissues as endophytes. Frequently, colonization by entomopathogens provides plants with increased resistance against insects, but the mechanisms are little understood. This study investigated direct, local, and systemic root-mediated interactions between isolates of the fungus Metarhizium brunneum and larvae of the cabbage root fly (CRF) Delia radicum attacking Brassica napus plants. All fungal isolates infected CRF when conidia were present in the soil, leading to 43–93% mortality. Locally, root-associated M. brunneum isolates reduced herbivore damage by 10–20% and in three out of five isolates caused significant insect mortality due to plant-mediated and/or direct effects. A split-root experiment with isolate Gd12 also demonstrated systemic plant resistance with significantly reduced root collar damage by CRF. LC-MS analyses showed that fungal root colonization did not induce changes in phytohormones, while herbivory increased jasmonic acid (JA) and glucosinolate concentrations. Proteinase inhibitor gene expression was also increased. Fungal colonization, however, primed herbivore-induced JA and the expression of the JA-responsive plant defensin 1.2 (PDF1.2) gene. We conclude that root-associated M. brunneum benefits plant health through multiple mechanisms, such as the direct infection of insects, as well as the local and systemic priming of the JA pathway. Full article

(This article belongs to the Special Issue Entomopathogenic Fungi in Biological Plant Protection: The Machinery of Multicomponent System Interactions)

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15 pages, 1489 KiB

Open AccessArticle

Insights on KP4 Killer Toxin-like Proteins of Fusarium Species in Interspecific Interactions

by Isabel Vicente, Giuseppe Quaratiello, Riccardo Baroncelli, Giovanni Vannacci and Sabrina Sarrocco

J. Fungi 2022, 8(9), 968; https://doi.org/10.3390/jof8090968 - 16 Sep 2022

Cited by 3 | Viewed by 2039

Abstract

KP4 killer toxins are secreted proteins that inhibit cell growth and induce cell death in target organisms. In Fusarium graminearum, KP4-like (KP4L) proteins contribute to fungal virulence in wheat seedling rot and are expressed during Fusarium head blight development. However, fungal KP4L [...] Read more.

KP4 killer toxins are secreted proteins that inhibit cell growth and induce cell death in target organisms. In Fusarium graminearum, KP4-like (KP4L) proteins contribute to fungal virulence in wheat seedling rot and are expressed during Fusarium head blight development. However, fungal KP4L proteins are also hypothesized to support fungal antagonism by permeabilizing cell walls of competing fungi to enable penetration of toxic compounds. Here, we report the differential expression patterns of F. graminearum KP4L genes (Fgkp4l-1, -2, -3 and -4) in a competitive interaction, using Trichoderma gamsii as the antagonist. The results from dual cultures indicate that Fgkp4l-3 and Fgkp4l-4 could participate in the recognition at the distance of the antagonist, while all Fgkp4l genes were highly activated in the pathogen during the physical interaction of both fungi. Only Fgkp4l-4 was up-regulated during the interaction with T. gamsii in wheat spikes. This suggests the KP4L proteins could participate in supporting F. graminearum interspecific interactions, even in living plant tissues. The distribution of KP4L orthologous within the genus Fusarium revealed they are more represented in species with broad host-plant range than in host-specific species. Phylogeny inferred provides evidence that KP4L genes evolved through gene duplications, gene loss and sequence diversification in the genus Fusarium. Full article

(This article belongs to the Special Issue Plant-Pathogenic Fusarium Species)

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11 pages, 799 KiB

Open AccessArticle

Multicenter Collaborative Study of the Interaction of Antifungal Combinations against Candida Spp. by Loewe Additivity and Bliss Independence-Based Response Surface Analysis

by Joseph Meletiadis, David R. Andes, Shawn R. Lockhart, Mahmoud A. Ghannoum, Cindy C. Knapp, Luis Ostrosky-Zeichner, Michael A. Pfaller, Vishnu Chaturvedi and Thomas J. Walsh

J. Fungi 2022, 8(9), 967; https://doi.org/10.3390/jof8090967 - 16 Sep 2022

Cited by 3 | Viewed by 2125

Abstract

Combination antifungal therapy is widely used but not well understood. We analyzed the spectrophotometric readings from a multicenter study conducted by the New York State Department of Health to further characterize the in vitro interactions of the major classes of antifungal agents against [...] Read more.

Combination antifungal therapy is widely used but not well understood. We analyzed the spectrophotometric readings from a multicenter study conducted by the New York State Department of Health to further characterize the in vitro interactions of the major classes of antifungal agents against Candida spp. Loewe additivity-based fractional inhibitory concentration index (FICi) analysis and Bliss independence-based response surface (BIRS) analysis were used to analyze two-drug inter- and intraclass combinations of triazoles (AZO) (voriconazole, posaconazole), echinocandins (ECH) (caspofungin, micafungin, anidulafungin), and a polyene (amphotericin B) against Candida albicans, C. parapsilosis, and C. glabrata. Although mean FIC indices did not differ statistically significantly from the additivity range of 0.5–4, indicating no significant pharmacodynamic interactions for all of the strain–combinations tested, BIRS analysis showed that significant pharmacodynamic interactions with the sum of percentages of interactions determined with this analysis were strongly associated with the FIC indices (Χ² 646, p < 0.0001). Using a narrower additivity range of 1–2 FIC index analysis, statistically significant pharmacodynamic interactions were also found with FICi and were in agreement with those found with BIRS analysis. All ECH+AB combinations were found to be synergistic against all Candida strains except C. glabrata. For the AZO+AB combinations, synergy was found mostly with the POS+AB combination. All AZO+ECH combinations except POS+CAS were synergistic against all Candida strains although with variable magnitude; significant antagonism was found for the POS+MIF combination against C. albicans. The AZO+AZO combination was additive for all strains except for a C. parapsilosis strain for which antagonism was also observed. The ECH+ECH combinations were synergistic for all Candida strains except C. glabrata for which they were additive; no antagonism was found. Full article

(This article belongs to the Special Issue Pharmacodynamics of Antifungal Drugs)

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22 pages, 3923 KiB

Open AccessArticle

Taxonomic and Phylogenetic Reassessment of Pyrgidium (Mycocaliciales) and Investigation of Ascospore Morphology

by Vinodhini Thiyagaraja, Damien Ertz, Robert Lücking, Dhanushka N. Wanasinghe, André Aptroot, Marcela Eugenia da Silva Cáceres, Kevin D. Hyde, Wanaporn Tapingkae and Ratchadawan Cheewangkoon

J. Fungi 2022, 8(9), 966; https://doi.org/10.3390/jof8090966 - 15 Sep 2022

Cited by 3 | Viewed by 2072

Abstract

Mycocaliciales comprise non-lichenized either saprotrophic or lichenicolous fungi which occur in temperate and tropical regions. The mazaediate, saprotrophic and monospecific genus, Pyrgidium, is currently assigned to this order, yet the phylogenetic placement of the genus has remained uncertain due to the absence [...] Read more.

Mycocaliciales comprise non-lichenized either saprotrophic or lichenicolous fungi which occur in temperate and tropical regions. The mazaediate, saprotrophic and monospecific genus, Pyrgidium, is currently assigned to this order, yet the phylogenetic placement of the genus has remained uncertain due to the absence of molecular data. In order to investigate the systematic position of Pyrgidium, two specimens collected in Brazil and Thailand, respectively, were used to generate mtSSU, SSU, LSU and ITS sequences. However, given that most other representatives of this order only have LSU and ITS sequences available, the phylogenetic reconstruction was limited to these two markers. The phylogenetic analyses confirmed placement of the genus within Mycocaliciales, the genus possessing a sister group relationship with the lichenicolous genus Sphinctrina. Detailed morphological descriptions and illustrations are provided, including those for type specimens of the various synonyms subsumed under the hitherto only accepted species, Pyrgidium montellicum (Beltr.) Tibell. The ascospore morphology was investigated using compound and scanning electronic microscopy (SEM). Principal component analysis (PCA) was performed for the ascospore size using PC-ORD 7. The molecular data and re-examination of the type specimens support the monospecific nature of this genus. Full article

(This article belongs to the Special Issue Ascomycota: Diversity, Taxonomy and Phylogeny)

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18 pages, 3246 KiB

Open AccessArticle

Biotransformation of the Fluoroquinolone, Levofloxacin, by the White-Rot Fungus Coriolopsis gallica

by Amal Ben Ayed, Imen Akrout, Quentin Albert, Stéphane Greff, Charlotte Simmler, Jean Armengaud, Mélodie Kielbasa, Annick Turbé-Doan, Delphine Chaduli, David Navarro, Emmanuel Bertrand, Craig B. Faulds, Mohamed Chamkha, Amina Maalej, Héla Zouari-Mechichi, Giuliano Sciara, Tahar Mechichi and Eric Record

J. Fungi 2022, 8(9), 965; https://doi.org/10.3390/jof8090965 - 15 Sep 2022

Cited by 10 | Viewed by 2386

Abstract

The wastewater from hospitals, pharmaceutical industries and more generally human and animal dejections leads to environmental releases of antibiotics that cause severe problems for all living organisms. The aim of this study was to investigate the capacity of three fungal strains to biotransform [...] Read more.

The wastewater from hospitals, pharmaceutical industries and more generally human and animal dejections leads to environmental releases of antibiotics that cause severe problems for all living organisms. The aim of this study was to investigate the capacity of three fungal strains to biotransform the fluoroquinolone levofloxacin. The degradation processes were analyzed in solid and liquid media. Among the three fungal strains tested, Coriolopsis gallica strain CLBE55 (BRFM 3473) showed the highest removal efficiency, with a 15% decrease in antibiogram zone of inhibition for Escherichia coli cultured in solid medium and 25% degradation of the antibiotic in liquid medium based on high-performance liquid chromatography (HPLC). Proteomic analysis suggested that laccases and dye-decolorizing peroxidases such as extracellular enzymes could be involved in levofloxacin degradation, with a putative major role for laccases. Degradation products were proposed based on mass spectrometry analysis, and annotation suggested that the main product of biotransformation of levofloxacin by Coriolopsis gallica is an N-oxidized derivative. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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27 pages, 2742 KiB

Open AccessReview

Research Progress on Elements of Wild Edible Mushrooms

by Shuai Liu, Honggao Liu, Jieqing Li and Yuanzhong Wang

J. Fungi 2022, 8(9), 964; https://doi.org/10.3390/jof8090964 - 15 Sep 2022

Cited by 13 | Viewed by 3344

Abstract

Wild edible mushrooms are distributed all over the world and are delicious seasonal foods, rich in polysaccharides, amino acids, vitamins, and other components. At the same time, they contain many essential trace elements and are highly enriched in heavy metals (compared to green [...] Read more.

Wild edible mushrooms are distributed all over the world and are delicious seasonal foods, rich in polysaccharides, amino acids, vitamins, and other components. At the same time, they contain many essential trace elements and are highly enriched in heavy metals (compared to green plants and cultivated edible mushrooms). Consumers may be exposed to health risks due to excessive heavy metals in the process of consumption. This is also one of the important factors affecting the import and export of edible mushrooms, which is of great concern to consumers and entry and exit inspection and quarantine departments. In this paper, the contents of four essential trace elements of iron, manganese, zinc, and copper and four harmful heavy metals of cadmium, lead, mercury, and arsenic in nearly 400 species of wild edible mushrooms from 10 countries are reviewed. It was found that the factors affecting the elemental content of edible mushrooms are mainly divided into internal and external factors. Internal is mainly the difference in species element-enrichment ability, and external is mainly environmental pollution and geochemical factors. The aim is to provide a reference for the risk assessment of edible mushrooms and their elemental distribution characteristics. Full article

(This article belongs to the Special Issue Edible and Medicinal Macrofungi)

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18 pages, 14618 KiB

Open AccessArticle

Biofilm Formation by Chromoblastomycosis Fungi Fonsecaea pedrosoi and Phialophora verrucosa: Involvement with Antifungal Resistance

by Ingrid S. Sousa, Thaís P. Mello, Elaine P. Pereira, Marcela Q. Granato, Celuta S. Alviano, André L. S. Santos and Lucimar F. Kneipp

J. Fungi 2022, 8(9), 963; https://doi.org/10.3390/jof8090963 - 15 Sep 2022

Cited by 4 | Viewed by 1909

Abstract

Patients with chromoblastomycosis (CBM) suffer chronic tissue lesions that are hard to treat. Considering that biofilm is the main growth lifestyle of several pathogens and it is involved with both virulence and resistance to antimicrobial drugs, we have investigated the ability of CBM [...] Read more.

Patients with chromoblastomycosis (CBM) suffer chronic tissue lesions that are hard to treat. Considering that biofilm is the main growth lifestyle of several pathogens and it is involved with both virulence and resistance to antimicrobial drugs, we have investigated the ability of CBM fungi to produce this complex, organized and multicellular structure. Fonsecaea pedrosoi and Phialophora verrucosa conidial cells were able to adhere on a polystyrene abiotic substrate, differentiate into hyphae and produce a robust viable biomass containing extracellular matrix. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) showed the tridimensional architecture of the mature biofilms, revealing a dense network of interconnected hyphae, inner channels and amorphous extracellular polymeric material. Interestingly, the co-culture of each fungus with THP-1 macrophage cells, used as a biotic substrate, induced the formation of a mycelial trap covering and damaging the macrophages. In addition, the biofilm-forming cells of F. pedrosoi and P. verrucosa were more resistant to the conventional antifungal drugs than the planktonic-growing conidial cells. The efflux pump activities of P. verrucosa and F. pedrosoi biofilms were significantly higher than those measured in conidia. Taken together, the data pointed out the biofilm formation by CBM fungi and brought up a discussion of the relevance of studies about their antifungal resistance mechanisms. Full article

(This article belongs to the Special Issue Fungal Biofilms- New Perspectives and Practices)

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11 pages, 533 KiB

Open AccessArticle

Fungal Keratitis: Clinical Features, Risk Factors, Treatment, and Outcomes

by Sarah Atta, Chandrashan Perera, Regis P. Kowalski and Vishal Jhanji

J. Fungi 2022, 8(9), 962; https://doi.org/10.3390/jof8090962 - 15 Sep 2022

Cited by 4 | Viewed by 2592

Abstract

Fungal keratitis (FK) can be challenging to diagnose and treat. In this retrospective case series, FK cases presenting at the University of Pittsburgh Medical Center, Pennsylvania, USA, from 2015 to 2021 were reviewed for ocular risk factors, clinical presentation, management, and outcomes. Twenty-eight [...] Read more.

Fungal keratitis (FK) can be challenging to diagnose and treat. In this retrospective case series, FK cases presenting at the University of Pittsburgh Medical Center, Pennsylvania, USA, from 2015 to 2021 were reviewed for ocular risk factors, clinical presentation, management, and outcomes. Twenty-eight cases of FK were included. The median presenting age was 58.5 (18.5) years, and the median symptom duration prior to presentation was 10 (35.8) days. Predisposing ocular risk factors included contact lens use (67.9%), recent ocular trauma/abrasion (42.9%), and history of ocular surgery (42.9%). The median presenting visual acuity (VA) was 1.35 (1.72) LogMAR. About half presented with a central ulcer (42.9%), large infiltrate (6.7 (6.3) mm²), corneal thinning (50.0%), and hypopyon (32.1%). The majority of isolated fungal species were filamentous (75.0%). Most common antifungal medications included topical voriconazole (71.4%) and natamycin (53.6%) drops and oral voriconazole (64.3%). Surgical management was necessary in 32.1% of cases and enucleation in one case. Defect resolution occurred in 42.5 (47.0) days, and median final VA was 0.5 (1.84) LogMAR. Features associated with poor final visual outcomes included poor initial VA (p < 0.001) and larger defect size (p = 0.002). In conclusion, unlike prior studies in the northeast region of the USA, FK was commonly caused by filamentous fungi, and antifungal management most often consisted of topical and oral voriconazole. Full article

(This article belongs to the Special Issue Fungal Eye Infections)

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10 pages, 1059 KiB

Open AccessArticle

Penicillium digitatum, First Clinical Report in Chile: Fungal Co-Infection in COVID-19 Patient

by Isabel Iturrieta-González, Annesi Giacaman, Patricio Godoy-Martínez, Fernando Vega, Marcela Sepúlveda, Cledir Santos, Valentina Toledo, Gonzalo Rivera, Leandro Ortega, Andrés San Martín, Vitalia Bahamondes, Felipe Collao, Raúl Sánchez and Flery Fonseca-Salamanca

J. Fungi 2022, 8(9), 961; https://doi.org/10.3390/jof8090961 - 14 Sep 2022

Cited by 4 | Viewed by 3772

Abstract

Penicillium digitatum is one of the most important phytopathogens. It causes deterioration and rotting of citrus fruits, generating significant economic losses worldwide. As a human pathogen, it is extremely rare. We present a case of pulmonary co-infection in a patient diagnosed with pneumonia [...] Read more.

Penicillium digitatum is one of the most important phytopathogens. It causes deterioration and rotting of citrus fruits, generating significant economic losses worldwide. As a human pathogen, it is extremely rare. We present a case of pulmonary co-infection in a patient diagnosed with pneumonia due to SARS-CoV-2. A 20-year-old female patient, primigravid, 36 weeks of gestation, without comorbidities, and diagnosed with severe pneumonia due to the SARS-CoV-2, showed rapid lung deterioration for which their pregnancy was interrupted by surgery. The patient was hospitalized in the Intensive Care Unit (ICU), connected to mechanical ventilation and receiving corticosteroids and antibiotics. The diagnosis of pulmonary fungal infection was made through bronchoalveolar lavage (BAL) culture, and the species identification was performed by sequencing of β-tubulin. Phylogenetic analysis with related species was performed for the confirmation of species identification. Antifungal susceptibility tests were performed for itraconazole (4 µg/mL), voriconazole (2 µg/mL), and amphotericin B (2 µg/mL). The patient was successfully treated with itraconazole. This is the second worldwide report of pulmonary infection by P. digitatum and the first in Chile. Although it is a fungus that rarely infects humans, it could represent an emerging opportunistic fungal pathogen, with associated risk factors that should be considered in the differential diagnosis of Penicillium species isolated from infections in humans. Full article

(This article belongs to the Special Issue Fungal Infections in COVID-19 Patients)

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16 pages, 4918 KiB

Open AccessArticle

A Novel Monoclonal Antibody 1D2 That Broadly Inhibits Clinically Important Aspergillus Species

by Xihua Lian, Amy Scott-Thomas, John G. Lewis, Madhav Bhatia and Stephen T. Chambers

J. Fungi 2022, 8(9), 960; https://doi.org/10.3390/jof8090960 - 14 Sep 2022

Cited by 1 | Viewed by 1321

Abstract

Aspergillus fumigatus is a ubiquitous airborne fungus, is the predominant cause (>90%) of invasive aspergillosis (IA) in immunosuppressed patients and has a high mortality. New approaches to prevention and treatment are needed because of the poor efficacy, toxicity and side effects of the [...] Read more.

Aspergillus fumigatus is a ubiquitous airborne fungus, is the predominant cause (>90%) of invasive aspergillosis (IA) in immunosuppressed patients and has a high mortality. New approaches to prevention and treatment are needed because of the poor efficacy, toxicity and side effects of the current anti-Aspergillus drugs on patients. Thus, we aim to explore a new avenue to combat Aspergillus infection by using a novel monoclonal antibody (mAb) 1D2 against a glycoprotein on the cell wall of Aspergillus. The ability of this mAb to inhibit attachment, germination, and growth of Aspergillus conidia and hyphae in vitro were examined. A dose-dependent growth inhibition of Aspergillus conidia in the presence of mAb 1D2 was found. The mAb 1D2 inhibited attachment of Aspergillus conidia to an untreated slide surface and fibronectin-treated surface compared to an unrelated mAb 6B10. When conidia were exposed to 1D2 concomitantly with inoculation into culture media, the mAb prevented the swelling and germination of conidia. This inhibitory ability of 1D2 was less apparent if it was added two hours after inoculation. Damage to hyphae was also observed when 1D2 was added to Aspergillus hyphae that had been incubated in media overnight. These in vitro results indicate that mAb 1D2 broadly inhibits clinically important Aspergillus species and has a promising therapeutic effect both as prophylaxis to inhibit an Aspergillus infection as well as a treatment. Full article

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10 pages, 288 KiB

Open AccessArticle

In Vitro Assessment of Azole and Amphotericin B Susceptibilities of Malassezia spp. Isolated from Healthy and Lesioned Skin

by Wissal Chebil, Najoua Haouas, Elja Eskes, Paul Vandecruys, Sameh Belgacem, Hichem Belhadj Ali, Hamouda Babba and Patrick Van Dijck

J. Fungi 2022, 8(9), 959; https://doi.org/10.3390/jof8090959 - 13 Sep 2022

Cited by 3 | Viewed by 1679

Abstract

Malassezia yeasts have recently gained medical importance as emerging pathogens associated with a wide range of dermatological and systemic infections. Since standardized methods for in vitro antifungal susceptibility testing have not yet been established for Malassezia spp., related diseases are always treated empirically. [...] Read more.

Malassezia yeasts have recently gained medical importance as emerging pathogens associated with a wide range of dermatological and systemic infections. Since standardized methods for in vitro antifungal susceptibility testing have not yet been established for Malassezia spp., related diseases are always treated empirically. As a result, a high rate of recurrence and decreased antifungal susceptibility have appeared. Thus, the aims of the study were to assess and analyze the in vitro susceptibility of Malassezia isolated from pityriasis versicolor (PV) lesions and healthy controls. A total of 58 Malassezia strains isolated from PV patients and healthy controls were tested. In vitro antifungal susceptibility testing was conducted using the CLSI broth microdilution with some modifications. Candida spp. criteria established in accordance with CLSI guidelines were used for data interpretation. Ketoconazole and posaconazole seemed to be the most effective molecules against Malassezia species. However, considerable percentages of itraconazole, fluconazole, and amphotericin B ‘‘resistant’’ strains (27.6%, 29.3%, and 43.1%, respectively) were revealed in this study. Malassezia furfur, M. sympodialis, and M. globosa showed different susceptibility profiles to the drugs tested. These results emphasize the importance of accurately identifying and evaluating the antifungal susceptibility of Malassezia species in order to guide a specific and effective treatment regimen. Full article

(This article belongs to the Special Issue New Perspectives for Superficial Fungal Infections)

19 pages, 2892 KiB

Open AccessArticle

Identification of Candidate Ice Nucleation Activity (INA) Genes in Fusarium avenaceum by Combining Phenotypic Characterization with Comparative Genomics and Transcriptomics

by Shu Yang, Mariah Rojas, Jeffrey J. Coleman and Boris A. Vinatzer

J. Fungi 2022, 8(9), 958; https://doi.org/10.3390/jof8090958 - 13 Sep 2022

Cited by 3 | Viewed by 2002

Abstract

Ice nucleation activity (INA) is the capacity of certain particles to catalyze ice formation at temperatures higher than the temperature at which pure water freezes. INA impacts the ratio of liquid to frozen cloud droplets and, therefore, the formation of precipitation and Earth’s [...] Read more.

Ice nucleation activity (INA) is the capacity of certain particles to catalyze ice formation at temperatures higher than the temperature at which pure water freezes. INA impacts the ratio of liquid to frozen cloud droplets and, therefore, the formation of precipitation and Earth’s radiative balance. Some Fusarium strains secrete ice-nucleating particles (INPs); they travel through the atmosphere and may thus contribute to these atmospheric processes. Fusarium INPs were previously found to consist of proteinaceous aggregates. Here, we determined that in F. avenaceum, the proteins forming these aggregates are smaller than 5 nm and INA is higher after growth at low temperatures and varies among strains. Leveraging these findings, we used comparative genomics and transcriptomics to identify candidate INA genes. Ten candidate INA genes that were predicted to encode secreted proteins were present only in the strains that produced the highest number of INPs. In total, 203 candidate INA genes coding for secreted proteins were induced at low temperatures. Among them, two genes predicted to encode hydrophobins stood out because hydrophobins are small, secreted proteins that form aggregates with amphipathic properties. We discuss the potential of the candidate genes to encode INA proteins and the next steps necessary to identify the molecular basis of INA in F. avenaceum. Full article

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17 pages, 2905 KiB

Open AccessArticle

Identification of Genes Promoting Growth of Ustilago maydis on Biomolecules Released from Cells Killed by Oxidation

by Jelena Malesevic, Milorad Kojic, Stefan Stanovcic, Natalija Azanjac and Mira Milisavljevic

J. Fungi 2022, 8(9), 957; https://doi.org/10.3390/jof8090957 - 13 Sep 2022

Viewed by 1510

Abstract

Much headway has been made in understanding the numerous strategies that enable microorganisms to counteract various types of environmental stress, but little is known about how microbial populations recover after a massive death caused by exposure to extreme conditions. Using the yeast-like fungus [...] Read more.

Much headway has been made in understanding the numerous strategies that enable microorganisms to counteract various types of environmental stress, but little is known about how microbial populations recover after a massive death caused by exposure to extreme conditions. Using the yeast-like fungus Ustilago maydis as a model, our recent post-stress regrowth under starvation (RUS) studies have demonstrated that this organism reconstitutes devastated populations with remarkable efficiency. Subsequently, we have identified four RUS-gene products. Two of these, Did4 and Tbp1, play parallel roles in protecting the genome. To identify additional molecular components, we took a molecular-genetic and a transcriptomic approach. By employing a simple and novel screening method, we identified five RUS-deficient mutants (snf8, slm1, vrg4, snf5, hsf1), three of which (snf8, slm1, and hsf1) displayed sensitivity to different genotoxic agents, indicating that the corresponding gene products have roles in genome protection. The global transcriptomic changes of cells grown in supernatants derived from peroxide-treated cell suspensions revealed sets of uniquely expressed genes. Importantly, among the genes induced by the substrates was Chk1, which encodes a protein kinase required for checkpoint-mediated cell cycle arrest in response to DNA damage. Mutants of U. maydis deleted of Chk1 are severely incapacitated in RUS. Full article

(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)

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15 pages, 2832 KiB

Open AccessArticle

Penicillium digitatum as a Model Fungus for Detecting Antifungal Activity of Botanicals: An Evaluation on Vietnamese Medicinal Plant Extracts

by Hanh My Tran, Diep Hong Le, Van-Anh Thi Nguyen, Tao Xuan Vu, Nguyen Thi Kim Thanh, Do Hoang Giang, Nguyen Tien Dat, Hai The Pham, Marc Muller, Huy Quang Nguyen and Van-Tuan Tran

J. Fungi 2022, 8(9), 956; https://doi.org/10.3390/jof8090956 - 13 Sep 2022

Cited by 4 | Viewed by 2910

Abstract

Medicinal plants play important roles in traditional medicine, and numerous compounds among them have been recognized for their antimicrobial activity. However, little is known about the potential of Vietnamese medicinal plants for antifungal activity. In this study, we examined the antagonistic activity of [...] Read more.

Medicinal plants play important roles in traditional medicine, and numerous compounds among them have been recognized for their antimicrobial activity. However, little is known about the potential of Vietnamese medicinal plants for antifungal activity. In this study, we examined the antagonistic activity of twelve medicinal plant species collected in Northern Vietnam against Penicillium digitatum, Aspergillus flavus, Aspergillus fumigatus, and Candida albicans. The results showed that the antifungal activities of the crude extracts from Mahonia bealei, Ficus semicordata, and Gnetum montanum were clearly detected with the citrus postharvest pathogen P. digitatum. These extracts could fully inhibit the growth of P. digitatum on the agar medium, and on the infected citrus fruits at concentrations of 300–1000 µg/mL. Meanwhile, the other tested fungi were less sensitive to the antagonistic activity of the plant extracts. In particular, we found that the ethanolic extract of M. bealei displayed a broad-spectrum antifungal activity against all four pathogenic fungi. Analysis of this crude extract by enrichment coupled with high-performance liquid chromatography revealed that berberine and palmatine are major metabolites. Additional inspections indicated berberine as the key compound responsible for the antifungal activity of the M. bealei ethanolic extract. Our study provides a better understanding of the potential of Vietnamese medicinal plant resources for combating fungal pathogens. This work also highlights that the citrus pathogen P. digitatum can be employed as a model fungus for screening the antifungal activity of botanicals. Full article

(This article belongs to the Section Fungal Pathogenesis and Disease Control)

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12 pages, 537 KiB

Open AccessArticle

Diagnosis of Fungal Keratitis in Low-Income Countries: Evaluation of Smear Microscopy, Culture, and In Vivo Confocal Microscopy in Nepal

by Jeremy J. Hoffman, Reena Yadav, Sandip Das Sanyam, Pankaj Chaudhary, Abhishek Roshan, Sanjay Kumar Singh, Simon Arunga, Victor H. Hu, David Macleod, Astrid Leck and Matthew J. Burton

J. Fungi 2022, 8(9), 955; https://doi.org/10.3390/jof8090955 - 13 Sep 2022

Cited by 5 | Viewed by 2088

Abstract

Clinically diagnosing fungal keratitis (FK) is challenging; diagnosis can be assisted by investigations including in vivo confocal microscopy (IVCM), smear microscopy, and culture. The aim of this study was to estimate the sensitivity in detecting fungal keratitis (FK) using IVCM, smear microscopy, and [...] Read more.

Clinically diagnosing fungal keratitis (FK) is challenging; diagnosis can be assisted by investigations including in vivo confocal microscopy (IVCM), smear microscopy, and culture. The aim of this study was to estimate the sensitivity in detecting fungal keratitis (FK) using IVCM, smear microscopy, and culture in a setting with a high prevalence of FK. In this cross-sectional study nested within a prospective cohort study, consecutive microbial keratitis (MK) patients attending a tertiary-referral eye hospital in south-eastern Nepal between June 2019 and November 2020 were recruited. IVCM and corneal scrapes for smear microscopy and culture were performed using a standardised protocol. Smear microscopy was performed using potassium hydroxide (KOH), Gram stain, and calcofluor white. The primary outcomes were sensitivities with 95% confidence intervals [95% CI] for IVCM, smear microscopy and culture, and for each different microscopy stain independently, to detect FK compared to a composite referent. We enrolled 642 patients with MK; 468/642 (72.9%) were filamentous FK, 32/642 (5.0%) were bacterial keratitis and 64/642 (10.0%) were mixed bacterial-filamentous FK, with one yeast infection (0.16%). No organism was identified in 77/642 (12.0%). Smear microscopy had the highest sensitivity (90.7% [87.9–93.1%]), followed by IVCM (89.8% [86.9–92.3%]) and culture (75.7% [71.8–79.3%]). Of the three smear microscopy stains, KOH had the highest sensitivity (85.3% [81.9–88.4%]), followed by Gram stain (83.2% [79.7–86.4%]) and calcofluor white (79.1% [75.4–82.5%]). Smear microscopy and IVCM were the most sensitive tools for identifying FK in our cohort. In low-resource settings we recommend clinicians perform corneal scrapes for microscopy using KOH and Gram staining. Culture remains an important tool to diagnose bacterial infection, identify causative fungi and enable antimicrobial susceptibility testing. Full article

(This article belongs to the Special Issue Fungal Eye Infections)

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21 pages, 7174 KiB

Open AccessArticle

The Adaptor Protein UvSte50 Governs Fungal Pathogenicity of Ustilaginoidea virens via the MAPK Signaling Pathway

by Huijuan Cao, Hao Gong, Tianqiao Song, Mina Yu, Xiayan Pan, Junjie Yu, Zhongqiang Qi, Yan Du and Yongfeng Liu

J. Fungi 2022, 8(9), 954; https://doi.org/10.3390/jof8090954 - 11 Sep 2022

Cited by 5 | Viewed by 1519

Abstract

The mitogen-activated protein kinase (MAPK) signaling pathways regulate diverse cellular processes and have been partially characterized in the rice false smut fungus Ustilaginoidea virens. UvSte50 has been identified as a homolog to Saccharomyces cerevisiae Ste50, which is known to be an adaptor [...] Read more.

The mitogen-activated protein kinase (MAPK) signaling pathways regulate diverse cellular processes and have been partially characterized in the rice false smut fungus Ustilaginoidea virens. UvSte50 has been identified as a homolog to Saccharomyces cerevisiae Ste50, which is known to be an adaptor protein for MAPK cascades. ΔUvste50 was found to be defective in conidiation, sensitive to hyperosmotic and oxidative stresses, and non-pathogenic. The mycelial expansion of ΔUvste50 inside spikelets of rice terminated at stamen filaments, eventually resulting in a lack of formation of false smut balls on spikelets. We determined that UvSte50 directly interacts with both UvSte7 (MAPK kinase; MEK) and UvSte11 (MAPK kinase kinase; MEKK), where the Ras-association (RA) domain of UvSte50 is indispensable for its interaction with UvSte7. UvSte50 also interacts with UvHog1, a MAP kinase of the Hog1-MAPK pathway, which is known to have important roles in hyphal growth and stress responses in U. virens. In addition, affinity capture–mass spectrometry analysis and yeast two-hybrid assay were conducted, through which we identified the interactions of UvSte50 with UvRas2, UvAc1 (adenylate cyclase), and UvCap1 (cyclase-associated protein), key components of the Ras/cAMP signaling pathway in U. virens. Together, UvSte50 functions as an adaptor protein interacting with multiple components of the MAPK and Ras/cAMP signaling pathways, thus playing critical role in plant infection by U. virens. Full article

(This article belongs to the Section Fungal Pathogenesis and Disease Control)

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13 pages, 1261 KiB

Open AccessArticle

Odor Profile of Four Cultivated and Freeze-Dried Edible Mushrooms by Using Sensory Panel, Electronic Nose and GC-MS

by Inmaculada Gómez, Rebeca Lavega González, Eva Tejedor-Calvo, Margarita Pérez Clavijo and Jaime Carrasco

J. Fungi 2022, 8(9), 953; https://doi.org/10.3390/jof8090953 - 11 Sep 2022

Cited by 10 | Viewed by 2168

Abstract

Cultivated mushrooms are well-known nutrient inputs for an equilibrated diet. Some species are broadly appreciated due to their medicinal properties. Lately, a number of novel foods and nutraceuticals based on dehydrated and freeze-dried powder obtained from cultivated mushrooms has been reaching the market. [...] Read more.

Cultivated mushrooms are well-known nutrient inputs for an equilibrated diet. Some species are broadly appreciated due to their medicinal properties. Lately, a number of novel foods and nutraceuticals based on dehydrated and freeze-dried powder obtained from cultivated mushrooms has been reaching the market. The food industry requires fast and reliable tools to prevent fraud. In this, work we have cultivated Agaricus bisporus sp. bisporus (AB) (white button mushroom), Agaricus bisporus sp. brunnescens (ABP) (portobello), Lentinula edodes (LE) (shiitake) and Grifola frondosa (GF) (maitake) using tailor-made substrates for the different species and standardized cropping conditions, which were individually freeze-dried to obtain the samples under evaluation. The aim of this article was to validate the use of two different methodologies, namely, electronic nose and sensory panel, to discriminate the olfactory profile of nutritional products based on freeze-dried mushrooms from the different cultivated species. Additionally, GC-MS was used to detect and quantify the most abundant volatile organic compounds (VOCs) in the samples. The multivariate analysis performed proved the utility of electronic nose as an analytical tool, which was similar to the classical sensory panel but faster in distinguishing among the different species, with one limitation it being unable to differentiate between the same species. GC-MS analysis showed the chemical volatile formulation of the samples, also showing significant differences between different samples but high similarities between varieties of the same cultivated species. The techniques employed can be used to prevent fraud and have the potential to evaluate further medicinal mushroom species and build solid and trustful connections between these novel food products and potential consumers. Full article

(This article belongs to the Special Issue Edible Mushrooms 2.0)

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J. Fungi, Volume 8, Issue 9 (September 2022) – 94 articles

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