Pub Date : 2022-08-23eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.957577
Mariana Handelman, Nir Osherov
The leading fungal pathogens causing systemic infections in humans are Candida spp., Aspergillus fumigatus, and Cryptococcus neoformans. The major class of antifungals used to treat such infections are the triazoles, which target the cytochrome P450 lanosterol 14-α-demethylase, encoded by the ERG11 (yeasts)/cyp51A (molds) genes, catalyzing a key step in the ergosterol biosynthetic pathway. Triazole resistance in clinical fungi is a rising concern worldwide, causing increasing mortality in immunocompromised patients. This review describes the use of serial clinical isolates and in-vitro evolution toward understanding the mechanisms of triazole resistance. We outline, compare, and discuss how these approaches have helped identify the evolutionary pathways taken by pathogenic fungi to acquire triazole resistance. While they all share a core mechanism (mutation and overexpression of ERG11/cyp51A and efflux transporters), their timing and mechanism differs: Candida and Cryptococcus spp. exhibit resistance-conferring aneuploidies and copy number variants not seen in A. fumigatus. Candida spp. have a proclivity to develop resistance by undergoing mutations in transcription factors (TAC1, MRR1, PDR5) that increase the expression of efflux transporters. A. fumigatus is especially prone to accumulate resistance mutations in cyp51A early during the evolution of resistance. Recently, examination of serial clinical isolates and experimental lab-evolved triazole-resistant strains using modern omics and gene editing tools has begun to realize the full potential of these approaches. As a result, triazole-resistance mechanisms can now be analyzed at increasingly finer resolutions. This newfound knowledge will be instrumental in formulating new molecular approaches to fight the rapidly emerging epidemic of antifungal resistant fungi.
{"title":"Experimental and in-host evolution of triazole resistance in human pathogenic fungi.","authors":"Mariana Handelman, Nir Osherov","doi":"10.3389/ffunb.2022.957577","DOIUrl":"10.3389/ffunb.2022.957577","url":null,"abstract":"<p><p>The leading fungal pathogens causing systemic infections in humans are <i>Candida</i> spp., <i>Aspergillus fumigatus</i>, and <i>Cryptococcus neoformans</i>. The major class of antifungals used to treat such infections are the triazoles, which target the cytochrome P450 lanosterol 14-α-demethylase, encoded by the <i>ERG11</i> (yeasts)/<i>cyp51A</i> (molds) genes, catalyzing a key step in the ergosterol biosynthetic pathway. Triazole resistance in clinical fungi is a rising concern worldwide, causing increasing mortality in immunocompromised patients. This review describes the use of serial clinical isolates and <i>in-vitro</i> evolution toward understanding the mechanisms of triazole resistance. We outline, compare, and discuss how these approaches have helped identify the evolutionary pathways taken by pathogenic fungi to acquire triazole resistance. While they all share a core mechanism (mutation and overexpression of <i>ERG11/cyp51A</i> and efflux transporters), their timing and mechanism differs: <i>Candida and Cryptococcus</i> spp. exhibit resistance-conferring aneuploidies and copy number variants not seen in <i>A. fumigatus</i>. <i>Candida</i> spp. have a proclivity to develop resistance by undergoing mutations in transcription factors (<i>TAC1, MRR1, PDR5</i>) that increase the expression of efflux transporters. <i>A. fumigatus</i> is especially prone to accumulate resistance mutations in <i>cyp51A</i> early during the evolution of resistance. Recently, examination of serial clinical isolates and experimental lab-evolved triazole-resistant strains using modern omics and gene editing tools has begun to realize the full potential of these approaches. As a result, triazole-resistance mechanisms can now be analyzed at increasingly finer resolutions. This newfound knowledge will be instrumental in formulating new molecular approaches to fight the rapidly emerging epidemic of antifungal resistant fungi.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-19eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.956837
Tracey V Steinrucken, Joseph S Vitelli, David G Holdom, Yu Pei Tan
There are five closely related Sporobolus species, collectively known as weedy Sporobolus grasses (WSG) or the rat's tail grasses. They are fast growing, highly competitive, unpalatable weeds of pastures, roadsides and woodlands. An effective biological control agent would be a welcomed alternative to successive herbicide application and manual removal methods. This study describes the initial exploratory phase of isolating and identifying native Australian microfungi associated with WSG, prior to evaluating their efficacy as inundative biological control agents. Accurate species-level identification of plant-pathogenic microfungi associated with WSG is an essential first step in the evaluation and prioritisation of pathogenicity bioassays. Starting with more than 79 unique fungal morphotypes isolated from diseased Sporobolus grasses in Queensland, Australia, we employed multi-locus phylogenetic analyses to classify these isolates into 54 fungal taxa. These taxa belong to 22 Ascomycete families (12 orders), of which the majority fall within the Pleosporales (>24 taxa in 7 families). In the next phase of the study, the putative species identities of these taxa will allow us to prioritise those which are likely to be pathogenic based on existing literature and their known ecological roles. This study represents the first step in a systematic, high-throughput approach to finding potential plant pathogenic biological control agents.
{"title":"The diversity of microfungi associated with grasses in the <i>Sporobolus indicus</i> complex in Queensland, Australia.","authors":"Tracey V Steinrucken, Joseph S Vitelli, David G Holdom, Yu Pei Tan","doi":"10.3389/ffunb.2022.956837","DOIUrl":"10.3389/ffunb.2022.956837","url":null,"abstract":"<p><p>There are five closely related <i>Sporobolus</i> species, collectively known as weedy <i>Sporobolus</i> grasses (WSG) or the rat's tail grasses. They are fast growing, highly competitive, unpalatable weeds of pastures, roadsides and woodlands. An effective biological control agent would be a welcomed alternative to successive herbicide application and manual removal methods. This study describes the initial exploratory phase of isolating and identifying native Australian microfungi associated with WSG, prior to evaluating their efficacy as inundative biological control agents. Accurate species-level identification of plant-pathogenic microfungi associated with WSG is an essential first step in the evaluation and prioritisation of pathogenicity bioassays. Starting with more than 79 unique fungal morphotypes isolated from diseased <i>Sporobolus</i> grasses in Queensland, Australia, we employed multi-locus phylogenetic analyses to classify these isolates into 54 fungal taxa. These taxa belong to 22 Ascomycete families (12 orders), of which the majority fall within the Pleosporales (>24 taxa in 7 families). In the next phase of the study, the putative species identities of these taxa will allow us to prioritise those which are likely to be pathogenic based on existing literature and their known ecological roles. This study represents the first step in a systematic, high-throughput approach to finding potential plant pathogenic biological control agents.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41170988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-15eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.957021
Ricardo Lima, Felipe C Ribeiro, Arnaldo L Colombo, Joăo N de Almeida
Antifungal resistance in humans, animals, and the environment is an emerging problem. Among the different fungal species that can develop resistance, Candida tropicalis is ubiquitous and causes infections in animals and humans. In Asia and some Latin American countries, C. tropicalis is among the most common species related to candidemia, and mortality rates are usually above 40%. Fluconazole resistance is especially reported in Asian countries and clonal spread in humans and the environment has been investigated in some studies. In Brazil, high rates of azole resistance have been found in animals and the environment. Multidrug resistance is still rare, but recent reports of clinical multidrug-resistant isolates are worrisome. The molecular apparatus of antifungal resistance has been majorly investigated in clinical C. tropicalis isolates, revealing that this species can develop resistance through the conjunction of different adaptative mechanisms. In this review article, we summarize the main findings regarding antifungal resistance and Candida tropicalis through an "One Health" approach.
{"title":"The emerging threat antifungal-resistant <i>Candida tropicalis</i> in humans, animals, and environment.","authors":"Ricardo Lima, Felipe C Ribeiro, Arnaldo L Colombo, Joăo N de Almeida","doi":"10.3389/ffunb.2022.957021","DOIUrl":"https://doi.org/10.3389/ffunb.2022.957021","url":null,"abstract":"<p><p>Antifungal resistance in humans, animals, and the environment is an emerging problem. Among the different fungal species that can develop resistance, <i>Candida tropicalis</i> is ubiquitous and causes infections in animals and humans. In Asia and some Latin American countries, <i>C. tropicalis</i> is among the most common species related to candidemia, and mortality rates are usually above 40%. Fluconazole resistance is especially reported in Asian countries and clonal spread in humans and the environment has been investigated in some studies. In Brazil, high rates of azole resistance have been found in animals and the environment. Multidrug resistance is still rare, but recent reports of clinical multidrug-resistant isolates are worrisome. The molecular apparatus of antifungal resistance has been majorly investigated in clinical <i>C. tropicalis</i> isolates, revealing that this species can develop resistance through the conjunction of different adaptative mechanisms. In this review article, we summarize the main findings regarding antifungal resistance and <i>Candida tropicalis</i> through an \"One Health\" approach.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-10eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.944234
Taryn A Miller, Debbie A Hudson, Richard D Johnson, Jaspreet S Singh, Wade J Mace, Natasha T Forester, Paul H Maclean, Christine R Voisey, Linda J Johnson
Epichloë festucae var. lolii and Epichloë sp. LpTG-3 are filamentous fungal endophytes of perennial ryegrass (Lolium perenne) that have a substantial impact on New Zealand's agricultural economy by conferring biotic advantages to the host grass. Overall, Epichloë endophytes contribute NZ$200 million to the economy annually, with strain AR37 estimated to contribute NZ$3.6 billion to the New Zealand economy over a 20-year period. This strain produces secondary metabolites, including epoxyjanthitrems, which are a class of indole diterpenes, associated with the observed effects of AR37 on livestock and insect pests. Until very recently, AR37 was intractable to genetic modification but this has changed with the application of CRISPR-Cas9 based gene editing techniques. In this paper, gene inactivation by CRISPR-Cas9 was used to deconvolute the genetic basis for epoxyjanthitrem biosynthesis, including creating an AR37 strain that has been edited to remove the biosynthesis of all indole diterpenes. We show that gene editing of Epichloë can be achieved without off-target events or introduction of foreign DNA (footprint-less) through an AMA1-based plasmid that simultaneously expresses the CRISPR-Cas9 system and selectable marker. Genetic modification events in these transformants were investigated through genome sequencing and in planta chemistry.
{"title":"Dissection of the epoxyjanthitrem pathway in <i>Epichloë</i> sp. <i>Lp</i>TG-3 strain AR37 by CRISPR gene editing.","authors":"Taryn A Miller, Debbie A Hudson, Richard D Johnson, Jaspreet S Singh, Wade J Mace, Natasha T Forester, Paul H Maclean, Christine R Voisey, Linda J Johnson","doi":"10.3389/ffunb.2022.944234","DOIUrl":"https://doi.org/10.3389/ffunb.2022.944234","url":null,"abstract":"<p><p><i>Epichloë festucae</i> var. <i>lolii</i> and <i>Epichloë</i> sp. <i>Lp</i>TG-3 are filamentous fungal endophytes of perennial ryegrass (<i>Lolium perenne</i>) that have a substantial impact on New Zealand's agricultural economy by conferring biotic advantages to the host grass. Overall, <i>Epichloë</i> endophytes contribute NZ$200 million to the economy annually, with strain AR37 estimated to contribute NZ$3.6 billion to the New Zealand economy over a 20-year period. This strain produces secondary metabolites, including epoxyjanthitrems, which are a class of indole diterpenes, associated with the observed effects of AR37 on livestock and insect pests. Until very recently, AR37 was intractable to genetic modification but this has changed with the application of CRISPR-Cas9 based gene editing techniques. In this paper, gene inactivation by CRISPR-Cas9 was used to deconvolute the genetic basis for epoxyjanthitrem biosynthesis, including creating an AR37 strain that has been edited to remove the biosynthesis of all indole diterpenes. We show that gene editing of <i>Epichloë</i> can be achieved without off-target events or introduction of foreign DNA (footprint-less) through an AMA1-based plasmid that simultaneously expresses the CRISPR-Cas9 system and selectable marker. Genetic modification events in these transformants were investigated through genome sequencing and <i>in planta</i> chemistry.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-04eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.958798
Rei Yoshimoto, Fumiko Ishida, Miyuki Yamaguchi, Shigeyuki Tanaka
The biogenesis of small non-coding RNAs is a molecular event that contributes to cellular functions. The basidiomycete fungus Ustilago maydis is a biotrophic pathogen parasitizing maize. A hallmark of its genome structure is an absence of RNAi machinery including Dicer and Argonaute proteins, which are responsible for the production of small RNAs in other organisms. However, it remains unclear whether U. maydis produces small RNAs during fungal growth. Here we found that U. maydis cells accumulate approximately 20-30 nucleotides of small RNA fragments during growth in the axenic culture condition. The RNA-seq analysis of these fragments identified that these small RNAs are originated from tRNAs and 5.8S ribosomal RNA. Interestingly, majority of their sequences are generated from tRNAs responsible for asparagine, glutamine and glycine, suggesting a bias of origin. The cleavage of tRNAs mainly occurs at the position near anticodon-stem-loop. We generated the deletion mutants of two genes nuc1 and nuc2 encoding RNase T2, which is a candidate enzyme that cleaves tRNAs. The deletion mutants of two genes largely fail to accumulate tRNA-derived RNA fragments. Nuc1 and tRNA are co-localized at the tip of budding cells and tRNA fragment could be detected in culture supernatant. Our results suggest that specific tRNAs would be cleaved during secretory processes and tRNA fragments might have extracellular functions.
{"title":"The production and secretion of tRNA-derived RNA fragments in the corn smut fungus <i>Ustilago maydis</i>.","authors":"Rei Yoshimoto, Fumiko Ishida, Miyuki Yamaguchi, Shigeyuki Tanaka","doi":"10.3389/ffunb.2022.958798","DOIUrl":"https://doi.org/10.3389/ffunb.2022.958798","url":null,"abstract":"<p><p>The biogenesis of small non-coding RNAs is a molecular event that contributes to cellular functions. The basidiomycete fungus <i>Ustilago maydis</i> is a biotrophic pathogen parasitizing maize. A hallmark of its genome structure is an absence of RNAi machinery including Dicer and Argonaute proteins, which are responsible for the production of small RNAs in other organisms. However, it remains unclear whether <i>U. maydis</i> produces small RNAs during fungal growth. Here we found that <i>U. maydis</i> cells accumulate approximately 20-30 nucleotides of small RNA fragments during growth in the axenic culture condition. The RNA-seq analysis of these fragments identified that these small RNAs are originated from tRNAs and 5.8S ribosomal RNA. Interestingly, majority of their sequences are generated from tRNAs responsible for asparagine, glutamine and glycine, suggesting a bias of origin. The cleavage of tRNAs mainly occurs at the position near anticodon-stem-loop. We generated the deletion mutants of two genes <i>nuc1</i> and <i>nuc2</i> encoding RNase T2, which is a candidate enzyme that cleaves tRNAs. The deletion mutants of two genes largely fail to accumulate tRNA-derived RNA fragments. Nuc1 and tRNA are co-localized at the tip of budding cells and tRNA fragment could be detected in culture supernatant. Our results suggest that specific tRNAs would be cleaved during secretory processes and tRNA fragments might have extracellular functions.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41177616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-02eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.918052
Guillermo A M Flores, Rocio P Lopez, Carolina S Cerrudo, V Fabiana Consolo, Corina M Berón
Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the "core bacteriome" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of Culex quinquefasciatus reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota Penicillium polonicum and Cladosporium sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.
{"title":"<i>Culex quinquefasciatus</i> Holobiont: A Fungal Metagenomic Approach.","authors":"Guillermo A M Flores, Rocio P Lopez, Carolina S Cerrudo, V Fabiana Consolo, Corina M Berón","doi":"10.3389/ffunb.2022.918052","DOIUrl":"10.3389/ffunb.2022.918052","url":null,"abstract":"<p><p>Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the \"core bacteriome\" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of <i>Culex quinquefasciatus</i> reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota <i>Penicillium polonicum</i> and <i>Cladosporium</i> sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41124677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-28eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.939007
Kathrin Blumenstein, Johanna Bußkamp, Gitta Jutta Langer, Eeva Terhonen
Increased drought combined with emerging pathogens poses an increased threat to forest health. This is attributable to the unpredictable behaviour of forest pathosystems, which can favour fungal pathogens over the host under persistent drought stress conditions. Diplodia sapinea (≡ Sphaeropsis sapinea) is one of the most severe pathogens in Scots pine (Pinus sylvestris) causing Diplodia tip blight (conifer blight) under certain environmental conditions. Recently, the fungus has also been isolated from non-conifer hosts, indicating that it has a broader host range than previously known. In this study we compared the impact of different levels of water availability on necrosis length caused by D. sapinea strains isolated as endophytes (eight strains isolated from asymptomatic Scots pine) and pathogens (five strains isolated from symptomatic Scots pine) and five strains isolated from symptomatic non-pine hosts. For all strains the decreased water availability increased the necrosis length in Scots pine shoots. The isolates from non-pine hosts caused the most severe reactions under all water availabilities. The results of the study indicate the likelihood that effects of climatic changes such as drought will drive D. sapinea damage in Scots pine-dominated forests and increase mortality rates in affected trees. Further, the higher necrosis in the Scots pines caused by strains that had performed a host switch are concerning with regard to future scenarios thus increasing infection pressure on Scots pine from unknown sources.
{"title":"Diplodia tip blight pathogen's virulence empowered through host switch.","authors":"Kathrin Blumenstein, Johanna Bußkamp, Gitta Jutta Langer, Eeva Terhonen","doi":"10.3389/ffunb.2022.939007","DOIUrl":"https://doi.org/10.3389/ffunb.2022.939007","url":null,"abstract":"Increased drought combined with emerging pathogens poses an increased threat to forest health. This is attributable to the unpredictable behaviour of forest pathosystems, which can favour fungal pathogens over the host under persistent drought stress conditions. Diplodia sapinea (≡ Sphaeropsis sapinea) is one of the most severe pathogens in Scots pine (Pinus sylvestris) causing Diplodia tip blight (conifer blight) under certain environmental conditions. Recently, the fungus has also been isolated from non-conifer hosts, indicating that it has a broader host range than previously known. In this study we compared the impact of different levels of water availability on necrosis length caused by D. sapinea strains isolated as endophytes (eight strains isolated from asymptomatic Scots pine) and pathogens (five strains isolated from symptomatic Scots pine) and five strains isolated from symptomatic non-pine hosts. For all strains the decreased water availability increased the necrosis length in Scots pine shoots. The isolates from non-pine hosts caused the most severe reactions under all water availabilities. The results of the study indicate the likelihood that effects of climatic changes such as drought will drive D. sapinea damage in Scots pine-dominated forests and increase mortality rates in affected trees. Further, the higher necrosis in the Scots pines caused by strains that had performed a host switch are concerning with regard to future scenarios thus increasing infection pressure on Scots pine from unknown sources.","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41169012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-28eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.894590
Timothy R Satterlee, Felicia N Williams, Marina Nadal, Anthony E Glenn, Lily W Lofton, Mary V Duke, Brian E Scheffler, Scott E Gold
Fusarium verticillioides is a mycotoxigenic fungus that is a threat to food and feed safety due to its common infection of maize, a global staple crop. A proposed strategy to combat this threat is the use of biological control bacteria that can inhibit the fungus and reduce mycotoxin contamination. In this study, the effect of multiple environmental isolates of Streptomyces on F. verticillioides was examined via transcriptome analysis. The Streptomyces strains ranged from inducing no visible response to dramatic growth inhibition. Transcriptionally, F. verticillioides responded proportionally to strain inhibition with either little to no transcript changes to thousands of genes being differentially expressed. Expression changes in multiple F. verticillioides putative secondary metabolite gene clusters was observed. Interestingly, genes involved in the fusaric acid gene cluster were suppressed by inhibitory strains of Streptomyces. A F. verticillioides beta-lactamase encoding gene (FVEG_13172) was found to be highly induced by specific inhibitory Streptomyces strains and its deletion increased visible response to those strains. This study demonstrates that F. verticillioides does not have an all or nothing response to bacteria it encounters but rather a measured response that is strain specific and proportional to the strength of inhibition.
{"title":"Transcriptomic Response of <i>Fusarium verticillioides</i> to Variably Inhibitory Environmental Isolates of <i>Streptomyces</i>.","authors":"Timothy R Satterlee, Felicia N Williams, Marina Nadal, Anthony E Glenn, Lily W Lofton, Mary V Duke, Brian E Scheffler, Scott E Gold","doi":"10.3389/ffunb.2022.894590","DOIUrl":"https://doi.org/10.3389/ffunb.2022.894590","url":null,"abstract":"<p><p><i>Fusarium verticillioides</i> is a mycotoxigenic fungus that is a threat to food and feed safety due to its common infection of maize, a global staple crop. A proposed strategy to combat this threat is the use of biological control bacteria that can inhibit the fungus and reduce mycotoxin contamination. In this study, the effect of multiple environmental isolates of <i>Streptomyces</i> on <i>F. verticillioides</i> was examined <i>via</i> transcriptome analysis. The <i>Streptomyces</i> strains ranged from inducing no visible response to dramatic growth inhibition. Transcriptionally, <i>F. verticillioides</i> responded proportionally to strain inhibition with either little to no transcript changes to thousands of genes being differentially expressed. Expression changes in multiple <i>F. verticillioides</i> putative secondary metabolite gene clusters was observed. Interestingly, genes involved in the fusaric acid gene cluster were suppressed by inhibitory strains of <i>Streptomyces.</i> A <i>F. verticillioides</i> beta-lactamase encoding gene (FVEG_13172) was found to be highly induced by specific inhibitory <i>Streptomyces</i> strains and its deletion increased visible response to those strains. This study demonstrates that <i>F. verticillioides</i> does not have an all or nothing response to bacteria it encounters but rather a measured response that is strain specific and proportional to the strength of inhibition.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41159431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-28eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.906681
Farnaz Daneshnia, Süleyha Hilmioğlu Polat, Macit Ilkit, Erika Shor, João Nobrega de Almeida Júnior, Larissa M Favarello, Arnaldo Lopes Colombo, Amir Arastehfar, David S Perlin
Fluconazole-resistant Candida parapsilosis (FLZR-CP) outbreaks are a growing public health concern and have been reported in numerous countries. Patients infected with FLZR-CP isolates show fluconazole therapeutic failure and have a significantly increased mortality rate. Because fluconazole is the most widely used antifungal agent in most regions with outbreaks, it is paramount to restore its antifungal activity. Milbemycin oxim (MOX), a well-known canine endectocide, is a potent efflux pump inhibitor that significantly potentiates the activity of fluconazole against FLZR C. glabrata and C. albicans. However, the FLZ-MOX combination has not been tested against FLZR-CP isolates, nor is it known whether MOX may also potentiate the activity of echinocandins, a different class of antifungal drugs. Furthermore, the extent of involvement of efflux pumps CDR1 and MDR1 and ergosterol biosynthesis enzyme ERG11 and their link with gain-of-function (GOF) mutations in their transcription regulators (TAC1, MRR1, and UPC2) are poorly characterized among FLZR-CP isolates. We analyzed 25 C. parapsilosis isolates collected from outbreaks in Turkey and Brazil by determining the expression levels of CDR1, MDR1, and ERG11, examining the presence of potential GOF mutations in their transcriptional regulators, and assessing the antifungal activity of FLZ-MOX and micafungin-MOX against FLZR and multidrug-resistant (MDR) C. parapsilosis isolates. ERG11 was found to be universally induced by fluconazole in all isolates, while expression of MDR1 was unchanged. Whereas mutations in MRR1 and UPC2 were not detected, CDR1 was overexpressed in three Brazilian FLZR-CP isolates, which also carried a novel TAC1L518F mutation. Of these three isolates, one showed increased basal expression of CDR1, while the other two overexpressed CDR1 only in the presence of fluconazole. Interestingly, MOX showed promising antifungal activity against FLZR isolates, reducing the FLZ MIC 8- to 32-fold. However, the MOX and micafungin combination did not exert activity against an MDR C. parapsilosis isolate. Collectively, our study documents that the mechanisms underpinning FLZR are region specific, where ERG11 mutations were the sole mechanism of FLZR in Turkish FLZR-CP isolates, while simultaneous overexpression of CDR1 was observed in some Brazilian counterparts. Moreover, MOX and fluconazole showed potent synergistic activity, while the MOX-micafungin combination showed no synergy.
{"title":"Determinants of fluconazole resistance and the efficacy of fluconazole and milbemycin oxim combination against <i>Candida parapsilosis</i> clinical isolates from Brazil and Turkey.","authors":"Farnaz Daneshnia, Süleyha Hilmioğlu Polat, Macit Ilkit, Erika Shor, João Nobrega de Almeida Júnior, Larissa M Favarello, Arnaldo Lopes Colombo, Amir Arastehfar, David S Perlin","doi":"10.3389/ffunb.2022.906681","DOIUrl":"https://doi.org/10.3389/ffunb.2022.906681","url":null,"abstract":"<p><p>Fluconazole-resistant <i>Candida parapsilosis</i> (FLZR-CP) outbreaks are a growing public health concern and have been reported in numerous countries. Patients infected with FLZR-CP isolates show fluconazole therapeutic failure and have a significantly increased mortality rate. Because fluconazole is the most widely used antifungal agent in most regions with outbreaks, it is paramount to restore its antifungal activity. Milbemycin oxim (MOX), a well-known canine endectocide, is a potent efflux pump inhibitor that significantly potentiates the activity of fluconazole against FLZR <i>C</i>. <i>glabrata</i> and <i>C</i>. <i>albicans.</i> However, the FLZ-MOX combination has not been tested against FLZR-CP isolates, nor is it known whether MOX may also potentiate the activity of echinocandins, a different class of antifungal drugs. Furthermore, the extent of involvement of efflux pumps <i>CDR1</i> and <i>MDR1</i> and ergosterol biosynthesis enzyme <i>ERG11</i> and their link with gain-of-function (GOF) mutations in their transcription regulators (<i>TAC1</i>, <i>MRR1</i>, and <i>UPC2</i>) are poorly characterized among FLZR-CP isolates. We analyzed 25 C. <i>parapsilosis</i> isolates collected from outbreaks in Turkey and Brazil by determining the expression levels of <i>CDR1</i>, <i>MDR1</i>, and <i>ERG11</i>, examining the presence of potential GOF mutations in their transcriptional regulators, and assessing the antifungal activity of FLZ-MOX and micafungin-MOX against FLZR and multidrug-resistant (MDR) <i>C</i>. <i>parapsilosis</i> isolates. <i>ERG11</i> was found to be universally induced by fluconazole in all isolates, while expression of <i>MDR1</i> was unchanged. Whereas mutations in <i>MRR1</i> and <i>UPC2</i> were not detected, <i>CDR1</i> was overexpressed in three Brazilian FLZR-CP isolates, which also carried a novel <i>TAC1<sup>L518F</sup></i> mutation. Of these three isolates, one showed increased basal expression of <i>CDR1</i>, while the other two overexpressed <i>CDR1</i> only in the presence of fluconazole. Interestingly, MOX showed promising antifungal activity against FLZR isolates, reducing the FLZ MIC 8- to 32-fold. However, the MOX and micafungin combination did not exert activity against an MDR <i>C</i>. <i>parapsilosis</i> isolate. Collectively, our study documents that the mechanisms underpinning FLZR are region specific, where <i>ERG11</i> mutations were the sole mechanism of FLZR in Turkish FLZR-CP isolates, while simultaneous overexpression of <i>CDR1</i> was observed in some Brazilian counterparts. Moreover, MOX and fluconazole showed potent synergistic activity, while the MOX-micafungin combination showed no synergy.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41170339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-26eCollection Date: 2022-01-01DOI: 10.3389/ffunb.2022.928622
Shiyu Cai, Abigail B Snyder
Black yeasts have been isolated from acidic, low water activity, and thermally processed foods as well as from surfaces in food manufacturing plants. The genomic basis for their relative tolerance to food-relevant environmental stresses has not been well defined. In this study, we performed whole genome sequencing (WGS) on seven black yeast strains including Aureobasidium (n=5) and Exophiala (n=2) which were isolated from food or food production environments. These strains were previously characterized for their tolerance to heat, hyperosmotic pressure, high pressure processing, hypochlorite sanitizers, and ultraviolet light. Based on the WGS data, three of the strains previously identified as A. pullulans were reassigned as A. melanogenum. Both haploid and diploid A. melanogenum strains were identified in this collection. Single-locus phylogenies based on beta tubulin, RNA polymerase II, or translation elongation factor protein sequences were compared to the phylogeny produced through SNP analysis, revealing that duplication of the fungal genome in diploid strains complicates the use of single-locus phylogenetics. There was not a strong association between phylogeny and either environmental source or stress tolerance phenotype, nor were trends in the copy numbers of stress-related genes associated with extremotolerance within this collection. While there were obvious differences between the genera, the heterogenous distribution of stress tolerance phenotypes and genotypes suggests that food-relevant black yeasts may be ubiquitous rather than specialists associated with particular ecological niches. However, further evaluation of additional strains and the potential impact of gene sequence modification is necessary to confirm these findings.
{"title":"Genomic characterization of polyextremotolerant black yeasts isolated from food and food production environments.","authors":"Shiyu Cai, Abigail B Snyder","doi":"10.3389/ffunb.2022.928622","DOIUrl":"https://doi.org/10.3389/ffunb.2022.928622","url":null,"abstract":"<p><p>Black yeasts have been isolated from acidic, low water activity, and thermally processed foods as well as from surfaces in food manufacturing plants. The genomic basis for their relative tolerance to food-relevant environmental stresses has not been well defined. In this study, we performed whole genome sequencing (WGS) on seven black yeast strains including <i>Aureobasidium</i> (n=5) and <i>Exophiala</i> (n=2) which were isolated from food or food production environments. These strains were previously characterized for their tolerance to heat, hyperosmotic pressure, high pressure processing, hypochlorite sanitizers, and ultraviolet light. Based on the WGS data, three of the strains previously identified as <i>A. pullulans</i> were reassigned as <i>A. melanogenum</i>. Both haploid and diploid <i>A. melanogenum</i> strains were identified in this collection. Single-locus phylogenies based on beta tubulin, RNA polymerase II, or translation elongation factor protein sequences were compared to the phylogeny produced through SNP analysis, revealing that duplication of the fungal genome in diploid strains complicates the use of single-locus phylogenetics. There was not a strong association between phylogeny and either environmental source or stress tolerance phenotype, nor were trends in the copy numbers of stress-related genes associated with extremotolerance within this collection. While there were obvious differences between the genera, the heterogenous distribution of stress tolerance phenotypes and genotypes suggests that food-relevant black yeasts may be ubiquitous rather than specialists associated with particular ecological niches. However, further evaluation of additional strains and the potential impact of gene sequence modification is necessary to confirm these findings.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41156420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}