| 1. |
- Karlsson, Magnus, et al.
(author)
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Insights on the Evolution of Mycoparasitism from the Genome of Clonostachys rosea
- 2015
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 7:2, s. 465-480
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Journal article (peer-reviewed)abstract
- Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here, we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mb, and contains 14,268 predicted genes. A phylogenomic analysis shows that C. Tosco clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Tfichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. Clonostachys rosea contains significantly more ATP-binding cassette (ABC) transporters, polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases, and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), whereas an increase in subgroup C (multidrug resistance-associated proteins) is evident in Tfichoderma virens. In contrast with mycoparasitic Tfichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes was induced in C. rosea during exposure to the Fusafium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chiororaphis. The data suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea.
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| 2. |
- Kosawang, Chatchai, et al.
(author)
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Zearalenone detoxification by zearalenone hydrolase is important for the antagonistic ability of Clonostachys rosea against mycotoxigenic Fusarium graminearum
- 2014
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In: Fungal Biology. - : Elsevier BV. - 1878-6146 .- 1878-6162. ; 118:4, s. 364-373
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Journal article (peer-reviewed)abstract
- The fungus Clonostachys rosea is antagonistic against plant pathogens, including Fusarium grarninearum, which produces the oestrogenic mycotoxin zearalenone (ZEA). ZEA inhibits other fungi, and C. rosea can detoxify ZEA through the enzyme zearalenone lactonohydrolase (ZHD101). As the relevance of ZEA detoxification for biocontrol is unknown, we studied regulation and function of ZHD101 in C. rosea. Quantitative reverse-transcription PCR revealed zhd101 gene expression in all conditions studied and demonstrated dose-dependent induction by ZEA. Known inducers of the Polyketide Synthase pathway did not induce zhd101 expression, suggesting specificity of the enzyme towards ZEA. To assess the role of ZHD101 during biocontrol interactions, we generated two Delta zhd101 mutants incapable of ZEA-detoxification and confirmed their defect in degrading ZEA by HPLC. The Delta zhd101 mutants displayed a lower in vitro ability to inhibit growth of the ZEA-producing F. graminearum (strain 1104-14) compared to the wild type. In contrast, all three C. rosea strains equally inhibited growth of the F. graminearum mutant (Delta PKS4), which is impaired in ZEA-production. Furthermore, the Delta zhd101 mutants failed to protect wheat seedlings against foot rot caused by the ZEA-producing F. graminearum. These data show that ZEA detoxification by ZHD101 is important for the biocontrol ability of C. rosea against F. graminearum.
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| 3. |
- Petrucci, Arianna, et al.
(author)
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Understanding the mechanisms underlying biological control of Fusarium diseases in cereals
- 2023
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In: European Journal of Plant Pathology. - 0929-1873 .- 1573-8469. ; 167:4, s. 453-476
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Research review (peer-reviewed)abstract
- Many Fusarium species cause serious diseases for cereal cultivation. These include Fusarium head blight and crown rot on wheat and bakanae disease on rice. These represent a major concern both in terms of food security and food safety. The latter is connected with the risk of mycotoxin contamination of grains. Biological control has proven its potential for controlling head blight and crown rot diseases of cereals caused by Fusarium species in a number of studies, and indeed several commercial products are under development. We review current knowledge of the mechanisms underlying biological control with a focus on fungal biocontrol agents, and also include challenges related to co-occurrence of Fusarium species. Several of the established biological control mechanisms (antibiosis, competition, hyperparasitism and induced resistance) can act simultaneously, thus resulting in disease control and, consequently, reduction of mycotoxin contamination. We also review the biological roles of some of the many mycotoxins produced by Fusarium species, and the mechanisms by which they are detoxified by cereal enzymes or by other fungi and how biological control agents (BCAs) can stimulate their degradation. Finally, the effect of biocontrol agents on the resident microbiota, as well as the effect of the resident microbiota on the performances of BCAs, are discussed. New perspectives on the use of biocontrol agents for the management of Fusarium diseases on cereals.
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| 6. |
- Broberg, Martin, et al.
(author)
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Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales)
- 2021
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In: Evolutionary applications. - : Wiley. - 1752-4571. ; 14, s. 476-497
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Journal article (peer-reviewed)abstract
- Various strains of the mycoparasitic fungal speciesClonostachys roseaare used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy ofC. roseain biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction betweenC. roseaand plant pathogenic fungi. Here, we determined the genome sequences of 11Clonostachysstrains, representing five species inClonostachyssubgenusBionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p <= .05) in theBionectriasubgenus lineage. This was accompanied with gene copy number increases (p <= .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. MostClonostachysspecies were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of theC. roseagenome included expansions (p <= .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter geneabcG6inC. roseawas induced (p <= .009) by exposure to the antifungalFusariummycotoxin zearalenone (1121-fold) and various fungicides. Deletion ofabcG6resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites inClonostachyssubgenusBionectria.
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| 7. |
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| 8. |
- Broberg, Martin, et al.
(author)
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Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping
- 2018
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 9
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Journal article (peer-reviewed)abstract
- There is an increasing importance for using biocontrol agents in combating plant diseases sustainably and in the long term. As large scale genomic sequencing becomes economically viable, the impact of single nucleotide polymorphisms (SNPs) on biocontrol-associated phenotypes can be easily studied across entire genomes of fungal populations. Here, we improved a previously reported genome assembly of the biocontrol fungus Clonostachys rosea strain IK726 using the PacBio sequencing platform, which resulted in a total genome size of 70.7 Mbp and 21,246 predicted genes. We further performed whole-genome re-sequencing of 52 additional C. rosea strains isolated globally using Illumina sequencing technology, in order to perform genome-wide association studies in conditions relevant for biocontrol activity. One such condition is the ability to grow at lower temperatures commonly encountered in cryic or frigid soils in temperate regions, as these will be prevalent for protecting growing crops in temperate climates. Growth rates at 10 degrees C on potato dextrose agar of the 53 sequenced strains of C. rosea were measured and ranged between 0.066 and 0.413 mm/day. Performing a genome wide association study, a total of 1,478 SNP markers were significantly associated with the trait and located in 227 scaffolds, within or close to (<1000 bp distance) 265 different genes. The predicted gene products included several chaperone proteins, membrane transporters, lipases, and proteins involved in chitin metabolism with possible roles in cold tolerance. The data reported in this study provides a foundation for future investigations into the genetic basis for cold tolerance in fungi, with important implications for biocontrol.
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| 9. |
- Dubey, Mukesh, et al.
(author)
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An ATP-Binding Cassette Pleiotropic Drug Transporter Protein Is Required for Xenobiotic Tolerance and Antagonism in the Fungal Biocontrol Agent Clonostachys rosea
- 2014
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In: Molecular plant-microbe interactions. - 0894-0282 .- 1943-7706. ; 27, s. 725-732
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Journal article (peer-reviewed)abstract
- ATP-binding cassette (ABC) transporters mediate active efflux of natural and synthetic toxicants and are considered to be important for drug tolerance in microorganisms. In biological control agents (BCA), ABC transporters can play important roles in antagonism by providing protection against toxins derived from the fungal prey and by mediating the secretion of endogenous toxins. In the present study, we generated deletion and complementation strains of the ABC transporter abcG5 in the fungal BCA Clonostachys rosea to study its role in xenobiotic tolerance and antagonism. Gene expression analysis shows induced expression of abcG5 in the presence of the Fusarium mycotoxin zearalenone (ZEA), secreted metabolites of F. graminearum, and different classes of fungicides. Phenotypic analysis of abcG5 deletion and complementation strains showed that the deletion strains were more sensitive towards F. graminearum culture filtrates, ZEA, and iprodione-and mefenoxam-based fungicides, thus suggesting the involvement of abcG5 in cell protection. The Delta abcG5 strains displayed reduced antagonism towards F. graminearum in a plate confrontation assay. Furthermore, the Delta abcG5 strains failed to protect barley seedlings from F. graminearium foot rot disease. These data show that the abcG5 ABC transporter is important for xenobiotic tolerance and biocontrol traits in C. rosea.
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| 10. |
- Dubey, Mukesh, et al.
(author)
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Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil
- 2022
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In: Fungal Biology. - : Elsevier BV. - 1878-6146. ; 126, s. 356-365
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Journal article (peer-reviewed)abstract
- Successful application of microbial biofertilizers, such as phosphorus (P) solubilizing fungi to agroecosystems, is constrained from the lack of knowledge about their ecology; for example in terms of how they respond to an external input of carbon (C) to get established in the soil. In two soil incubation experiments we examined the performance of the P solubilizing fungus Penicillium aculeatum in non sterile and semi-sterile (gamma-irradiated) soil with different C and P sources. Results from the first experiment with C sources showed that starch and cellulose generally improved P solubilization by P. aculeatum measured as water extractable P (P-wep), though only significantly in non-sterile soil. This coincided with an increased population density of P. aculeatum measured with a hygromycin B resistant strain of this fungus. Soil respiration used to measure soil microbial activity was overall much higher in treatments with C compounds than without C in both non-sterile and semi-sterile soil. However, soil respiration was highest with cellulose in semi-sterile soil, especially in combination with P. aculeatum. Hence, for the second experiment with P sources (tricalcium phosphate (TCP) and sewage sludge ash) cellulose was used as a C source for P. aculeatum growth in all treatments. Main results showed that P. aculeatum in combination with cellulose soil amendment increased soil P-wep independent of soil sterilization and P source treatments. Soil resin P (P-res) and microbial P (P-mic), which represents stocks of potentially plant available P, were also affected from P. aculeatum inoculation. Increased soil Pres from TCP and sewage sludge ash was observed with P. aculeatum independent of soil type. On the other hand soil P-mic was higher after P. aculeatum inoculation only in semi-sterile soil. Population density of P. aculeatum measured with qPCR was maintained or increased in non-sterile and semi-sterile soil, respectively, compared to the original inoculum load of P. aculeatum. In conclusion, our results underline the importance of C source addition for P. aculeatum if used as a biofertilizer. For this, cellulose seems to be a promising option promoting P. aculeatum growth and P solubilization also in non-sterilized soil. (C)& nbsp;2022 Published by Elsevier Ltd on behalf of British Mycological Society.
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