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Adan IH, Asudi GO, Niassy S, Jalloh AA, Mutua JM, Chidawanyika F, Khamis F, Khan Z, Subramanian S, Dubois T, Mutyambai DM. Comparative microbiome diversity in root-nodules of three Desmodium species used in push-pull cropping system. Front Microbiol 2024; 15:1395811. [PMID: 38966391 PMCID: PMC11222577 DOI: 10.3389/fmicb.2024.1395811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/28/2024] [Indexed: 07/06/2024] Open
Abstract
Background Desmodium species used as intercrops in push-pull cropping systems are known to repel insect-pests, suppress Striga species weeds, and shift soil microbiome. However, the mechanisms through which Desmodium species impact the soil microbiome, either through its root exudates, changes in soil nutrition, or shading microbes from its nodules into the rhizosphere, are less understood. Here, we investigated the diversity of root-nodule microbial communities of three Desmodium species- Desmodium uncinatum (SLD), Desmodium intortum (GLD), and Desmodium incanum (AID) which are currently used in smallholder maize push-pull technology (PPT). Methods Desmodium species root-nodule samples were collected from selected smallholder farms in western Kenya, and genomic DNA was extracted from the root-nodules. The amplicons underwent paired-end Illumina sequencing to assess bacterial and fungal populations. Results We found no significant differences in composition and relative abundance of bacterial and fungal species within the root-nodules of the three Desmodium species. While a more pronounced shift was observed for fungal community compositions compared to bacteria, no significant differences were observed in the general diversity (evenness and richness) of fungal and bacterial populations among the three Desmodium species. Similarly, beta diversity was not significantly different among the three Desmodium species. The root-nodule microbiome of the three Desmodium species was dominated by Bradyrhizobium and Fusarium species. Nevertheless, there were significant differences in the proportion of marker gene sequences responsible for energy and amino acid biosynthesis among the three Desmodium species, with higher sequence proportions observed in SLD. Conclusion There is no significant difference in the microbial community of the three Desmodium species used in PPT. However, root-nodule microbiome of SLD had significantly higher marker gene sequences responsible for energy and amino acid biosynthesis. Therefore, it is likely that the root-nodules of the three Desmodium species host similar microbiomes and influence soil health, consequently impacting plant growth and agroecosystem functioning.
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Affiliation(s)
- Isack H. Adan
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- Department of Biochemistry, Microbiology, and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - George Ochieng Asudi
- Department of Biochemistry, Microbiology, and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Saliou Niassy
- Inter-African Phytosanitary Council of the African Union, Yaoundé, Cameroon
| | - Abdul A. Jalloh
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | | | - Frank Chidawanyika
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- Department of Zoology and Entomology, University of Free State, Bloemfontein, South Africa
| | - Fathiya Khamis
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Zeyaur Khan
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | | | - Thomas Dubois
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Daniel Munyao Mutyambai
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- Department of Life Science, South Eastern Kenya University, Kitui, Kenya
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Enriquez-Felix EE, Pérez-Salazar C, Rico-Ruiz JG, Calheiros de Carvalho A, Cruz-Morales P, Villalobos-Escobedo JM, Herrera-Estrella A. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiol Spectr 2024; 12:e0316523. [PMID: 38441469 PMCID: PMC10986496 DOI: 10.1128/spectrum.03165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 04/06/2024] Open
Abstract
Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host's cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride-RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2, and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma-host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition (het) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established.IMPORTANCEThere is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride.
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Affiliation(s)
- Eli Efrain Enriquez-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - Camilo Pérez-Salazar
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - José Guillermo Rico-Ruiz
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | | | - Pablo Cruz-Morales
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
- Plant and Microbial Biology Department, University of California, Berkeley, Carlifornia, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, Carlifornia, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
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Sun ZB, Yu SF, Sun MH, Li SD, Hu YF, Song HJ. Transcriptomic Response of Clonostachys rosea Mycoparasitizing Rhizoctonia solani. J Fungi (Basel) 2023; 9:818. [PMID: 37623589 PMCID: PMC10455738 DOI: 10.3390/jof9080818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Clonostachys rosea is an important mycoparasitism biocontrol agent that exhibits excellent control efficacy against numerous fungal plant pathogens. Transcriptomic sequencing may be used to preliminarily screen mycoparasitism-related genes of C. rosea against fungal pathogens. The present study sequenced and analyzed the transcriptome of C. rosea mycoparasitizing a Basidiomycota (phylum) fungal pathogen, Rhizoctonia solani, under three touch stages: the pre-touch stage, touch stage and after-touch stage. The results showed that a number of genes were differentially expressed during C. rosea mycoparasitization of R. solani. At the pre-touch stage, 154 and 315 genes were up- and down-regulated, respectively. At the touch stage, the numbers of up- and down-regulated differentially expressed genes (DEGs) were 163 and 188, respectively. The after-touch stage obtained the highest number of DEGs, with 412 and 326 DEGs being up- and down-regulated, respectively. Among these DEGs, ABC transporter-, glucanase- and chitinase-encoding genes were selected as potential mycoparasitic genes according to a phylogenetic analysis. A comparative transcriptomic analysis between C. rosea mycoparasitizing R. solani and Sclerotinia sclerotiorum showed that several DEGs, including the tartrate transporter, SDR family oxidoreductase, metallophosphoesterase, gluconate 5-dehydrogenase and pyruvate carboxylase, were uniquely expressed in C. rosea mycoparasitizing R. solani. These results significantly expand our knowledge of mycoparasitism-related genes in C. rosea and elucidate the mycoparasitism mechanism of C. rosea.
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Affiliation(s)
- Zhan-Bin Sun
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Shu-Fan Yu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Man-Hong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ya-Feng Hu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Han-Jian Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
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Maciag T, Kozieł E, Rusin P, Otulak-Kozieł K, Jafra S, Czajkowski R. Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts. Int J Mol Sci 2023; 24:12227. [PMID: 37569603 PMCID: PMC10418420 DOI: 10.3390/ijms241512227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements.
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Affiliation(s)
- Tomasz Maciag
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Piotr Rusin
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Sylwia Jafra
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland
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Giehl A, dos Santos AA, Cadamuro RD, Tadioto V, Guterres IZ, Prá Zuchi ID, Minussi GDA, Fongaro G, Silva IT, Alves SL. Biochemical and Biotechnological Insights into Fungus-Plant Interactions for Enhanced Sustainable Agricultural and Industrial Processes. PLANTS (BASEL, SWITZERLAND) 2023; 12:2688. [PMID: 37514302 PMCID: PMC10385130 DOI: 10.3390/plants12142688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The literature is full of studies reporting environmental and health issues related to using traditional pesticides in food production and storage. Fortunately, alternatives have arisen in the last few decades, showing that organic agriculture is possible and economically feasible. And in this scenario, fungi may be helpful. In the natural environment, when associated with plants, these microorganisms offer plant-growth-promoting molecules, facilitate plant nutrient uptake, and antagonize phytopathogens. It is true that fungi can also be phytopathogenic, but even they can benefit agriculture in some way-since pathogenicity is species-specific, these fungi are shown to be useful against weeds (as bioherbicides). Finally, plant-associated yeasts and molds are natural biofactories, and the metabolites they produce while dwelling in leaves, flowers, roots, or the rhizosphere have the potential to be employed in different industrial activities. By addressing all these subjects, this manuscript comprehensively reviews the biotechnological uses of plant-associated fungi and, in addition, aims to sensitize academics, researchers, and investors to new alternatives for healthier and more environmentally friendly production processes.
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Affiliation(s)
- Anderson Giehl
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Angela Alves dos Santos
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
| | - Rafael Dorighello Cadamuro
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Viviani Tadioto
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Iara Zanella Guterres
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Isabella Dai Prá Zuchi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Gabriel do Amaral Minussi
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Environment and Sustainable Technologies, Federal University of Fronteira Sul, Cerro Largo 97900-000, RS, Brazil
| | - Gislaine Fongaro
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Izabella Thais Silva
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Sergio Luiz Alves
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Environment and Sustainable Technologies, Federal University of Fronteira Sul, Cerro Largo 97900-000, RS, Brazil
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Bahadoor A, Robinson KA, Loewen MC, Demissie ZA. Clonostachys rosea 'omics profiling: identification of putative metabolite-gene associations mediating its in vitro antagonism against Fusarium graminearum. BMC Genomics 2023; 24:352. [PMID: 37365507 DOI: 10.1186/s12864-023-09463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Clonostachys rosea is an established biocontrol agent. Selected strains have either mycoparasitic activity against known pathogens (e.g. Fusarium species) and/or plant growth promoting activity on various crops. Here we report outcomes from a comparative 'omics analysis leveraging a temporal variation in the in vitro antagonistic activities of C. rosea strains ACM941 and 88-710, toward understanding the molecular mechanisms underpinning mycoparasitism. RESULTS Transcriptomic data highlighted specialized metabolism and membrane transport related genes as being significantly upregulated in ACM941 compared to 88-710 at a time point when the ACM941 strain had higher in vitro antagonistic activity than 88-710. In addition, high molecular weight specialized metabolites were differentially secreted by ACM941, with accumulation patterns of some metabolites matching the growth inhibition differences displayed by the exometabolites of the two strains. In an attempt to identify statistically relevant relationships between upregulated genes and differentially secreted metabolites, transcript and metabolomic abundance data were associated using IntLIM (Integration through Linear Modeling). Of several testable candidate associations, a putative C. rosea epidithiodiketopiperazine (ETP) gene cluster was identified as a prime candidate based on both co-regulation analysis and transcriptomic-metabolomic data association. CONCLUSIONS Although remaining to be validated functionally, these results suggest that a data integration approach may be useful for identification of potential biomarkers underlying functional divergence in C. rosea strains.
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Affiliation(s)
- Adilah Bahadoor
- Metrology Research Center, National Research Council Canada, 1200 Montreal Rd, Ottawa, ON, K1A 0R6, Canada
| | - Kelly A Robinson
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada
| | - Michele C Loewen
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada.
| | - Zerihun A Demissie
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, ON, Canada.
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Liu Q, Dong C. Dual Transcriptomics Reveals Interspecific Interactions between the Mycoparasite Calcarisporium cordycipiticola and Its Host Cordyceps militaris. Microbiol Spectr 2023; 11:e0480022. [PMID: 36946736 PMCID: PMC10100745 DOI: 10.1128/spectrum.04800-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Calcarisporium cordycipiticola is a mycoparasite of the edible fungus Cordyceps militaris, and mycoparasitism causes devastating diseases of mushrooms. In this study, dual-transcriptomic analysis was performed to reveal interspecific interactions between the mycoparasite C. cordycipiticola and its host C. militaris. At 4 and 8 days postinfection (dpi), 2,959 and 2,077 differentially expressed genes (DEGs) of C. cordycipiticola and 914 and 1,548 DEGs of C. militaris were identified compared with the mycelial stage, respectively, indicating that C. cordycipiticola responded more quickly than C. militaris. Lectins of the pathogen may play a role in the recognition of fungal prey. Both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that primary metabolism was vigorous for the pathogen to colonize the host and that the pathogen's attack substantially altered C. militaris' primary metabolism. C. cordycipiticola upregulated some carbohydrate-active enzyme (CAZyme) genes, including CBM18, GH18, GH16, and GH76, for degrading the host cell wall and defending against host immunity. C. militaris produced excessive reactive oxygen species (ROS) to respond to the infection. The GO term "heme binding" was the only shared term enriched at both stages at 4 and 8 dpi, indicating that iron was important for both the pathogen and the host. The uptake of iron by pathogens through multiple pathways promoted colonization and removed high ROS levels produced by the host. The transcription levels of Cmhsp78, Cmhsp70, and Cmhyd1 in C. militaris responded quickly, and these genes have potential as candidates for the breeding of resistant varieties. This study provides clues for understanding the interactions between a mycoparasite and its mushroom host and will be helpful for the breeding of resistant varieties and disease prevention and control for this edible fungus. IMPORTANCE White mildew disease caused by Calcarisporium cordycipiticola is devastating for the fruiting body cultivation of Cordyceps militaris, a popular and highly valued edible fungus. Here, the pathogenic mechanisms of C. cordycipiticola, the responses of C. militaris to the infection, and the interaction of these two phylogenetically close species were revealed by time course dual-transcriptome profiles. In general, the host C. militaris responds more slowly than the pathogen C. cordycipiticola. For the first time, we found that iron was important for both the mycoparasite and the host. C. cordycipiticola takes up iron by multiple pathways to promote colonization and remove high ROS levels produced by the host. The rapidly responding genes Cmhsp70, Cmhsp78, and Cmhyd1 in C. militaris may have the potential as candidate genes for the breeding of resistant varieties. This study expands our understanding of the mycoparasitic interactions of two species from sister families and will be helpful for the breeding of and disease prevention and control in mushrooms.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Assessing the Biocontrol Potential of Clonostachys Species Isolated as Endophytes from Coffea Species and as Mycoparasites of Hemileia Rusts of Coffee in Africa. J Fungi (Basel) 2023; 9:jof9020248. [PMID: 36836362 PMCID: PMC9962503 DOI: 10.3390/jof9020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
During surveys conducted in South America and Africa to identify natural fungal enemies of coffee leaf rust (CLR), Hemileia vastatrix, over 1500 strains were isolated, either as endophytes from healthy tissues of Coffea species or as mycoparasites growing on rust pustules. Based on morphological data, eight isolates-three isolated from wild or semiwild coffee and five from Hemileia species on coffee, all from Africa-were provisionally assigned to the genus Clonostachys. A polyphasic study of their morphological, cultural and molecular characteristics-including the Tef1 (translation elongation factor 1 alpha), RPB1 (largest subunit of RNA polymerase II), TUB (β-tubulin) and ACL1 (ATP citrate lyase) regions-confirmed these isolates as belonging to three species of the genus Clonostachys: namely C. byssicola, C. rhizophaga and C. rosea f. rosea. Preliminary assays were also conducted to test the potential of the Clonostachys isolates to reduce CLR severity on coffee under greenhouse conditions. Foliar and soil applications indicated that seven of the isolates had a significant effect (p < 0.05) in reducing CLR severity. In parallel, in vitro tests that involved conidia suspensions of each of the isolates together with urediniospores of H. vastatrix resulted in high levels of inhibition of urediniospore germination. All eight isolates showed their ability to establish as endophytes in C. arabica during this study, and some proved to be mycoparasites of H. vastatrix. In addition to reporting the first records of Clonostachys associated with healthy coffee tissues and with Hemileia rusts of coffee, this work provides the first evidence that Clonostachys isolates have potential as biological control agents against CLR.
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Khairullina A, Micic N, Jørgensen HJL, Bjarnholt N, Bülow L, Collinge DB, Jensen B. Biocontrol Effect of Clonostachys rosea on Fusarium graminearum Infection and Mycotoxin Detoxification in Oat ( Avena sativa). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030500. [PMID: 36771583 PMCID: PMC9918947 DOI: 10.3390/plants12030500] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 06/01/2023]
Abstract
Oat (Avena sativa) is susceptible to Fusarium head blight (FHB). The quality of oat grain is threatened by the accumulation of mycotoxins, particularly the trichothecene deoxynivalenol (DON), which also acts as a virulence factor for the main pathogen Fusarium graminearum. The plant can defend itself, e.g., by DON detoxification by UGT-glycosyltransferases (UTGs) and accumulation of PR-proteins, even though these mechanisms do not deliver effective levels of resistance. We studied the ability of the fungal biocontrol agent (BCA) Clonostachys rosea to reduce FHB and mycotoxin accumulation. Greenhouse trials showed that C. rosea-inoculation of oat spikelets at anthesis 3 days prior to F. graminearum inoculation reduced both the amount of Fusarium DNA (79%) and DON level (80%) in mature oat kernels substantially. DON applied to C. rosea-treated spikelets resulted in higher conversion of DON to DON-3-Glc than in mock treated plants. Moreover, there was a significant enhancement of expression of two oat UGT-glycosyltransferase genes in C. rosea-treated oat. In addition, C. rosea treatment activated expression of genes encoding four PR-proteins and a WRKY23-like transcription factor, suggesting that C. rosea may induce resistance in oat. Thus, C. rosea IK726 has strong potential to be used as a BCA against FHB in oat as it inhibits F. graminearum infection effectively, whilst detoxifying DON mycotoxin rapidly.
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Affiliation(s)
- Alfia Khairullina
- Division of Pure and Applied Biochemistry, Lund University, 221 00 Lund, Sweden
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Nikola Micic
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Hans J. Lyngs Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Nanna Bjarnholt
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Leif Bülow
- Division of Pure and Applied Biochemistry, Lund University, 221 00 Lund, Sweden
| | - David B. Collinge
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Birgit Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, DK-1871 Frederiksberg, Denmark
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10
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Piombo E, Guaschino M, Jensen DF, Karlsson M, Dubey M. Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes. Front Microbiol 2023; 14:1112673. [PMID: 36876087 PMCID: PMC9978495 DOI: 10.3389/fmicb.2023.1112673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction The fungal secretome comprise diverse proteins that are involved in various aspects of fungal lifestyles, including adaptation to ecological niches and environmental interactions. The aim of this study was to investigate the composition and activity of fungal secretomes in mycoparasitic and beneficial fungal-plant interactions. Methods We used six Clonostachys spp. that exhibit saprotrophic, mycotrophic and plant endophytic lifestyles. Genome-wide analyses was performed to investigate the composition, diversity, evolution and gene expression of Clonostachys secretomes in relation to their potential role in mycoparasitic and endophytic lifestyles. Results and discussion Our analyses showed that the predicted secretomes of the analyzed species comprised between 7 and 8% of the respective proteomes. Mining of transcriptome data collected during previous studies showed that 18% of the genes encoding predicted secreted proteins were upregulated during the interactions with the mycohosts Fusarium graminearum and Helminthosporium solani. Functional annotation of the predicted secretomes revealed that the most represented protease family was subclass S8A (11-14% of the total), which include members that are shown to be involved in the response to nematodes and mycohosts. Conversely, the most numerous lipases and carbohydrate-active enzyme (CAZyme) groups appeared to be potentially involved in eliciting defense responses in the plants. For example, analysis of gene family evolution identified nine CAZyme orthogroups evolving for gene gains (p ≤ 0.05), predicted to be involved in hemicellulose degradation, potentially producing plant defense-inducing oligomers. Moreover, 8-10% of the secretomes was composed of cysteine-enriched proteins, including hydrophobins, important for root colonization. Effectors were more numerous, comprising 35-37% of the secretomes, where certain members belonged to seven orthogroups evolving for gene gains and were induced during the C. rosea response to F. graminearum or H. solani. Furthermore, the considered Clonostachys spp. possessed high numbers of proteins containing Common in Fungal Extracellular Membranes (CFEM) modules, known for their role in fungal virulence. Overall, this study improves our understanding of Clonostachys spp. adaptation to diverse ecological niches and establishes a basis for future investigation aiming at sustainable biocontrol of plant diseases.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Micol Guaschino
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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11
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Pimentel MF, Arnao E, Warner AJ, Rocha LF, Subedi A, Elsharif N, Chilvers MI, Matthiesen R, Robertson AE, Bradley CA, Neves DL, Pedersen DK, Reuter-Carlson U, Lacey JV, Bond JP, Fakhoury AM. Reduction of Pythium Damping-Off in Soybean by Biocontrol Seed Treatment. PLANT DISEASE 2022; 106:2403-2414. [PMID: 35171634 DOI: 10.1094/pdis-06-21-1313-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pythium spp. is one of the major groups of pathogens that cause seedling diseases on soybean, leading to both preemergence and postemergence damping-off and root rot. More than 100 species have been identified within this genus, with Pythium irregulare, P. sylvaticum, P. ultimum var ultimum, and P. torulosum being particularly important for soybean production given their aggressiveness, prevalence, and abundance in production fields. This study investigated the antagonistic activity of potential biological control agents (BCAs) native to the U.S. Midwest against Pythium spp. First, in vitro screening identified BCAs that inhibit P. ultimum var. ultimum growth. Scanning electron microscopy demonstrated evidence of mycoparasitism of all potential biocontrol isolates against P. ultimum var. ultimum and P. torulosum, with the formation of appressorium-like structures, short hyphal branches around host hyphae, hook-shaped structures, coiling, and parallel growth of the mycoparasite along the host hyphae. Based on these promising results, selected BCAs were tested under field conditions against six different Pythium spp. Trichoderma afroharzianum 26 used alone and a mix of T. hamatum 16 + T. afroharzianum 19 used as seed treatments protected soybean seedlings from Pythium spp. infection, as BCA-treated plots had on average 15 to 20% greater plant stand and vigor than control plots. Our results also indicate that some of these potential BCAs could be added with a fungicide seed treatment with minimum inhibition occurring, depending on the fungicide active ingredient. This research highlights the need to develop tools incorporating biological control as a facet of soybean seedling disease management programs. The harnessing of native BCAs could be integrated with other management strategies to provide efficient control of seedling diseases.
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Affiliation(s)
- Mirian F Pimentel
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901
| | - Erika Arnao
- College of Public Health, University of Iowa, Iowa City, IA 52242
| | | | - Leonardo F Rocha
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901
| | - Arjun Subedi
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901
| | - Nariman Elsharif
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Rashelle Matthiesen
- Department of Plant Pathology and Microbiology, Iowa State University, IA 50010
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, IA 50010
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445
| | - Danilo L Neves
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445
| | - Dianne K Pedersen
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801
| | | | - Jonathan V Lacey
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445
| | - Jason P Bond
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901
| | - Ahmad M Fakhoury
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901
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12
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ATP-Binding Cassette (ABC) Transporters in Fusarium Specific Mycoparasite Sphaerodes mycoparasitica during Biotrophic Mycoparasitism. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent transcriptomic profiling has revealed importance membrane transporters such as ATP-binding cassette (ABC) transporters in fungal necrotrophic mycoparasites. In this study, RNA-Seq allowed rapid detection of ABC transcripts involved in biotrophic mycoparasitism of Sphaerodes mycoparasitica against the phytopathogenic and mycotoxigenic Fusarium graminearum host, the causal agent of Fusarium head blight (FHB). Transcriptomic analyses of highly expressed S. mycoparasitica genes, and their phylogenetic relationships with other eukaryotic fungi, portrayed the ABC transporters’ evolutionary paths towards biotrophic mycoparasitism. Prior to the in silico phylogenetic analyses, transmission electron microscopy (TEM) was used to confirm the formation of appressorium/haustorium infection structures in S. mycoparasitica during early (1.5 d and 3.5 d) stages of mycoparasitism. Transcripts encoding biotrophy-associated secreted proteins did uncover the enrolment of ABC transporter genes in this specific biocontrol mode of action, while tandem ABC and BUB2 (non-ABC) transcripts seemed to be proper for appressorium development. The next-generation HiSeq transcriptomic profiling of the mycoparasitic hypha samples, revealed 81 transcripts annotated to ABC transporters consisting of a variety of ABC-B (14%), ABC-C (22%), and ABC-G (23%), and to ABC-A, ABC-F, aliphatic sulfonates importer (TC 3.A.1.17.2), BtuF, ribose importer (TC 3.A.1.2.1), and unknown families. The most abundant transcripts belonged to the multidrug resistance exporter (TC 3.A.1.201) subfamily of the ABC-B family, the conjugate transporter (TC 3.A.1.208) subfamily of the ABC-C family, and the pleiotropic drug resistance (PDR) (TC 3.A.1.205) subfamily of the ABC-G family. These findings highlight the significance of ABC transporter genes that control cellular detoxification against toxic substances (e.g., chemical pesticides and mycotoxins) in sustaining a virulence of S. mycoparasitica for effective biotrophic mycoparasitism on the F. graminearum host. The findings of this study provide clues to better understand the biotrophic mycoparasitism of S. mycoparasitica interacting with the Fusarium host, which implies that the ABC transporter group of key proteins is involved in the mycoparasite’s virulence and multidrug resistance to toxic substances including cellular detoxification.
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13
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Murtaza B, Li X, Dong L, Javed MT, Xu L, Saleemi MK, Li G, Jin B, Cui H, Ali A, Wang L, Xu Y. Microbial and enzymatic battle with food contaminant zearalenone (ZEN). Appl Microbiol Biotechnol 2022; 106:4353-4365. [PMID: 35705747 DOI: 10.1007/s00253-022-12009-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
Abstract
Zearalenone (ZEN) contamination of various foods and feeds is an important global problem. In some animals and humans, ZEN causes significant health issues in addition to massive economic losses, annually. Therefore, removal or degradation of the ZEN in foods and feeds is required to be done. The conventional physical and chemical methods have some serious issues including poor efficiency, decrease in nutritional value, palatability of feed, and use of costly equipment. Research examined microbes from diverse media for their ability to degrade zearalenone and other toxins, and the findings of several investigations revealed that enzymes produced from microbes play a significant role in the degradation of mycotoxins. In established bacterial hosts, genetically engineered technique was used to enhance heterologously produced degrading enzymes. Then, the bio-degradation of ZEN by the use of micro-organisms or their enzymes is much more advantageous and is close to nature and ecofriendly. Furthermore, an effort is made to put forward the work done by different scientists on the biodegradation of ZEN by the use of fungi, yeast, bacteria, and/or their enzymes to degrade the ZEN to non-toxic products. KEY POINTS: •Evolved microbial strains degraded ZEA more quickly •Different degrading properties were studied.
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Affiliation(s)
- Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China.,Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian, 116600, China
| | - Liming Dong
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, 100048, China
| | | | - Le Xu
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
| | | | - Gen Li
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
| | - Huijing Cui
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China
| | - Ashiq Ali
- Department of Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China.,Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian, 116600, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, China. .,Center for Food Safety of Animal Origin, Ministry of Education, Dalian University of Technology, Dalian, 116600, China.
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14
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Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea. Appl Environ Microbiol 2022; 88:e0064322. [PMID: 35695572 PMCID: PMC9275246 DOI: 10.1128/aem.00643-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact, and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small RNAs (sRNAs) are vital components of posttranscriptional gene regulation, although their role in gene expression regulation during mycoparasitisms remain understudied. Here, we investigated the role of sRNA-mediated gene regulation in mycoparasitism by performing sRNA and degradome tag sequencing of the mycoparasitic fungus Clonostachys rosea interacting with the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum at two time points. The majority of differentially expressed sRNAs were downregulated during the interactions with the mycohosts compared to a C. rosea self-interaction control, thus allowing desuppression (upregulation) of mycohost-responsive genes. Degradome analysis showed a positive correlation between high degradome counts and antisense sRNA mapping and led to the identification of 201 sRNA-mediated potential gene targets for 282 differentially expressed sRNAs. Analysis of sRNA potential gene targets revealed that the regulation of genes coding for membrane proteins was a common response against both mycohosts. The regulation of genes involved in oxidative stress tolerance and cellular metabolic and biosynthetic processes was exclusive against F. graminearum, highlighting common and mycohost-specific gene regulation of C. rosea. By combining these results with transcriptome data collected during a previous study, we expand the understanding of the role of sRNA in regulating interspecific fungal interactions and mycoparasitism. IMPORTANCE Small RNAs (sRNAs) are emerging as key players in pathogenic and mutualistic fungus-plant interactions; however, their role in fungus-fungus interactions remains elusive. In this study, we employed the necrotrophic mycoparasite Clonostachys rosea and the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum and investigated the sRNA-mediated gene regulation in mycoparasitic interactions. The combined approach of sRNA and degradome tag sequencing identified 201 sRNA-mediated putative gene targets for 282 differentially expressed sRNAs, highlighting the role of sRNA-mediated regulation of mycoparasitism in C. rosea. We also identified 36 known and 13 novel microRNAs (miRNAs) and their potential gene targets at the endogenous level and at a cross-species level in B. cinerea and F. graminearum, indicating a role of cross-species RNA interference (RNAi) in mycoparasitism, representing a novel mechanism in biocontrol interactions. Furthermore, we showed that C. rosea adapts its transcriptional response, and thereby its interaction mechanisms, based on the interaction stages and identity of the mycohost.
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15
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Abdellatif L, Fernandez MR, Lokuruge P. Mode of action of potential biocontrol agents against Fusarium species and Cochliobolus sativus. Mycologia 2022; 114:476-486. [PMID: 35583987 DOI: 10.1080/00275514.2022.2051986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The antagonistic activities of three potential biocontrol agents (BCAs), Clonostachys miodochialis, C. rosea, and Minimedusa polyspora, were tested in vitro against the target fungi Fusarium acuminatum, F. avenaceum, F. equiseti, F. graminearum, and Cochliobolus sativus. In vitro dual-culture assay revealed that the BCAs were able to inhibit the mycelial growth of most of the target fungi, with the most common mode of action being mycoparasitism. After 5 d of incubation, depending on the host-parasite interface, biotrophic mycoparasitism was observed via attachment structures on F. avenaceum, F. equiseti, and C. sativus. Haustoria and appressoria were formed by C. miodochialis and M. polyspora on F. avenaceum and C. sativus, respectively. Clamp-like structures were also produced by both BCAs, depending on the host fungus. Clonostachys rosea formed only contact points on its hosts. Coiling structure was observed with C. rosea and M. polyspora occasionally in pure culture but more abundantly in the dual-culture assay. After an additional 3 to 5 d of incubation, the BCAs started damaging their host cells. Asexual fruiting bodies of the BCAs spread necrotrophically on F. acuminatum and F. graminearum and began destroying their mycelia after the initial 5 d of incubation. Furthermore, mycelial dissolution of F. acuminatum by an excreted substance was observed at a distance before direct contact with C. miodochialis. The diffuse metabolite assay revealed that the highest inhibition of the three BCAs was on C. sativus and their least effectiveness was observed on F. graminearum. Overall, these results provide evidence that C. miodochialis, C. rosea, and M. polyspora are potential candidates for biological control of the tested target fungi. This constitutes the first report that these three BCAs are able to establish an initial biotrophic relationship followed by a necrotrophic lifestyle. In addition, C. miodochialis has not previously been reported as a BCA.
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Affiliation(s)
- Lobna Abdellatif
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Box 1030, Swift Current, Saskatchewan S9H 3X2, Canada
| | - Myriam R Fernandez
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Box 1030, Swift Current, Saskatchewan S9H 3X2, Canada
| | - Prabhath Lokuruge
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Box 1030, Swift Current, Saskatchewan S9H 3X2, Canada
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16
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Osborn RK, Ordóñez ME, Cognato AI. Ecuadorian Coptoborus beetles harbor Fusarium and Graphium fungi previously associated with Euwallacea ambrosia beetles. Mycologia 2022; 114:487-500. [PMID: 35608329 DOI: 10.1080/00275514.2022.2065441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Ambrosia beetles from the scolytine tribe Xyleborini (Curculionidae) are important to the decomposition of woody plant material on every continent except Antarctica. These insects farm fungi on the walls of tunnels they build inside recently dead trees and rely on the fungi for nutrition during all stages of their lives. Such ambrosia fungi rely on the beetles to provide appropriate substrates and environmental conditions for growth. A small minority of xyleborine ambrosia beetle-fungal partnerships cause significant damage to healthy trees. The xyleborine beetle Coptoborus ochromactonus vectors a Fusarium (Hypocreales) fungus that is lethal to balsa (Ochroma pyramidale (Malvaceae)) trees in Ecuador. Although this pathogenic fungus and its associated beetle are not known to be established in the United States, several other non-native ambrosia beetle species are vectors of destructive plant diseases in this country. This fact and the acceleration of trade between South America and the United States demonstrate the importance of understanding fungal plant pathogens before they escape their native ranges. Here we identify the fungi accompanying Coptoborus ambrosia beetles collected in Ecuador. Classification based ribosomal internal transcribed spacer 1 (ITS) sequences revealed the most prevalent fungi associated with Coptoborus are Fusarium sp. and Graphium sp. (Microascales: Microascaceae), which have been confirmed as ambrosia fungi for xyleborine ambrosia beetles, and Clonostsachys sp. (Hypocreales), which is a diverse genus found abundantly in soils and associated with plants. Phylogenetic analyses of the Fusarium strains based on ITS, translation elongation factor (EF1-α), and two subunits of the DNA-directed RNA polymerase II (RPB1 and RPB2) identified them as Fusarium sp. AF-9 in the Ambrosia Fusarium Clade (AFC). This Fusarium species was previously associated with a few xyleborine ambrosia beetles, most notably the species complex Euwallacea fornicatus (Eichhoff 1868) (Curculionidae: Scolytinae: Xyleborini). Examination of ITS and EF1-α sequences showed a close affinity between the Graphium isolated from Coptoborus spp. and other xyleborine-associated Graphium as well as the soil fungus Graphium basitruncatum. This characterization of ambrosia fungi through DNA sequencing confirms the identity of a putative plant pathogen spread by Coptoborus beetles and expands the documented range of Fusarium and Graphium ambrosia fungi.
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Affiliation(s)
- Rachel K Osborn
- Department of Entomology, Michigan State University, East Lansing, Michigan 48823, USA
| | - Maria Eugenia Ordóñez
- Escuela de Ciencias Biológicas, Pontifica Universidad Católica del Ecuador, Quito, Ecuador, 17-01-2184
| | - Anthony I Cognato
- Department of Entomology, Michigan State University, East Lansing, Michigan 48823, USA
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17
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Rafiei V, Ruffino A, Persson Hodén K, Tornkvist A, Mozuraitis R, Dubey M, Tzelepis G. A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene. MOLECULAR PLANT PATHOLOGY 2022; 23:291-303. [PMID: 34825755 PMCID: PMC8743018 DOI: 10.1111/mpp.13162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/19/2021] [Accepted: 11/01/2021] [Indexed: 05/05/2023]
Abstract
Terpenes constitute a major part of secondary metabolites secreted by plants in the rhizosphere. However, their specific functions in fungal-plant interactions have not been investigated thoroughly. In this study we investigated the role of monoterpenes in interactions between oilseed rape (Brassica napus) and the soilborne pathogen Verticillium longisporum. We identified seven monoterpenes produced by B. napus, and production of α-pinene, β-pinene, 3-carene, and camphene was significantly increased upon fungal infection. Among them, β-pinene was chosen for further analysis. Transcriptome analysis of V. longisporum on exposure to β-pinene resulted in identification of two highly expressed pleotropic drug transporters paralog genes named VlAbcG1a and VlAbcG1b. Overexpression of VlAbcG1a in Saccharomyces cerevisiae increased tolerance to β-pinene, while deletion of the VlAbcG1a homologous gene in Verticillium dahliae resulted in mutants with increased sensitivity to certain monoterpenes. Furthermore, the VlAbcG1a overexpression strain displayed an increased tolerance to β-pinene and increased virulence in tomato plants. Data from this study give new insights into the roles of terpenes in plant-fungal pathogen interactions and the mechanisms fungi deploy to cope with the toxicity of these secondary metabolites.
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Affiliation(s)
- Vahideh Rafiei
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Alessandra Ruffino
- Department of Plant BiologyUppsala BiocenterSwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | - Kristian Persson Hodén
- Department of Plant BiologyUppsala BiocenterSwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | - Anna Tornkvist
- Department of Plant BiologyUppsala BiocenterSwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | | | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Georgios Tzelepis
- Department of Forest Mycology and Plant PathologyUppsala BiocenterSwedish University of Agricultural SciencesUppsalaSweden
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18
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Kim SH, Vujanovic V. Early transcriptomic response of the mycoparasite Sphaerodes mycoparasitica to the mycotoxigenic Fusarium graminearum 3-ADON, the cause of Fusarium head blight. BIORESOUR BIOPROCESS 2022; 8:127. [PMID: 34993050 PMCID: PMC8683091 DOI: 10.1186/s40643-021-00479-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
Mycoparasites are an assemblage of biotrophic and necrotrophic fungi that occur on plant pathogenic fungal hosts. Biotrophic mycoparasites are often overlooked in transcriptomic-based biocontrol studies. Sphaerodes mycoparasitica (S.m.) is a specific biotrophic mycoparasite of plant pathogenic Fusarium graminearum (F.g.), a devastating Fusarium head blight (FHB) disease in small-grain cereals. To understand the biotrophic mycoparasitism comprehensively, we performed Illumina RNA-Seq transcriptomic study on the fungus–fungus interaction in vitro. The aim is to identify the transcript-level mechanism related to the biotrophic S.m. mycoparasitism, particularly its ability to effectively control the F.g. 3-ADON chemotype. A shift in the transcriptomic profile of the mycoparasite was triggered in response to its interaction with F.g. during recognition (1.5 days) and colonization (3.5 days) steps. RNA-Seq analysis revealed ~ 30% of annotated transcripts with "function unknown". Further, 14 differentially expressed genes functionally linked to the biotrophic mycoparasitism were validated by quantitative real-time PCR (qPCR). The gene expression patterns of the filamentous haemagglutinin/adhesin/attachment factor as well as cell wall-degrading glucanases and chitinases were upregulated by host interaction. Besides, mycoparasitism-associated antioxidant resistance genes encoding ATP-binding cassette (ABC) transporter(s) and glutathione synthetase(s) were upregulated. However, the thioredoxin reductase was downregulated which infers that this antioxidant gene can be used as a resistance marker to assess S.m. antifungal and antimycotoxigenic activities. The interactive transcriptome of S. mycoparasitica provides new insights into specific mycoparasitism and will contribute to future research in controlling FHB.
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Affiliation(s)
- Seon Hwa Kim
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Vladimir Vujanovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
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19
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Piombo E, Dubey M. Computational Analysis of HTS Data and Its Application in Plant Pathology. Methods Mol Biol 2022; 2536:275-307. [PMID: 35819611 DOI: 10.1007/978-1-0716-2517-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to handle data coming from a variety of sequencing experiments, focusing on the analysis of Illumina reads. We describe how to perform genome assembly and annotation with DNA reads, correctly analyze RNA-seq data to discover differentially expressed genes, handle amplicon sequencing data from microbial communities, and utilize small RNA sequencing data to predict miRNA sequences and their putative targets.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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20
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Dou K, Pang G, Cai F, Chenthamara K, Zhang J, Liu H, Druzhinina IS, Chen J. Functional Genetics of Trichoderma Mycoparasitism. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Zehra A, Swapnil P. Role of Microbial Bioagents as Elicitors in Plant Defense Regulation. TRANSCRIPTION FACTORS FOR BIOTIC STRESS TOLERANCE IN PLANTS 2022:103-128. [DOI: 10.1007/978-3-031-12990-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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22
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Asghar W, Kataoka R. Green manure incorporation accelerates enzyme activity, plant growth, and changes in the fungal community of soil. Arch Microbiol 2021; 204:7. [PMID: 34870760 DOI: 10.1007/s00203-021-02614-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/29/2022]
Abstract
Green manure can sustain agricultural production, preserve biodiversity, and mitigate soil degradation caused by long-term application of chemical fertilizers. Moreover, the application of green manure can improve soil health through increased soil biological activities. Nevertheless, little attention has been paid to the effects of leguminous and non-leguminous plants on phosphorus- and carbon-related enzyme activities and fungal community composition in soil. In this study, a pot experiment was carried out to elucidate the effects of two green manures on plant growth promoting potential, phosphorus- and carbon-related enzyme activities, and soil fungal community composition. Two green manure treatments (Brassica juncea and hairy vetch), poultry compost and control (no amendment) were applied and soil samples were collected after incorporation of green manure and after plant harvest. The results revealed that plant growth with hairy vetch was significantly higher than that with B. juncea and poultry compost, and soil enzyme activities were markedly higher with hairy vetch than with B. juncea. Both green manure amendments altered the soil fungal community composition. It is possible that the incorporation of green manure into soil and their mineralization and decomposition were controlled by the carbon: nitrogen ratio of the manures and that these manures were easily degradable by soil fungi. In particular, the incorporation of leguminous (hairy vetch) green manure with a low carbon: nitrogen ratio resulted in better plant growth through fast mineralization. Our findings suggest that green manure incorporation is an effective practice and provides substantial benefits to the soil-plant system.
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Affiliation(s)
- Waleed Asghar
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Japan
| | - Ryota Kataoka
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Japan.
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Piombo E, Vetukuri RR, Broberg A, Kalyandurg PB, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M. Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions. Microbiol Spectr 2021; 9:e0109921. [PMID: 34549988 PMCID: PMC8557909 DOI: 10.1128/spectrum.01099-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Dicer-like proteins (DCLs) play a vital role in RNA interference (RNAi), by cleaving RNA filament into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in mycoparasitic interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and characterize the functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced secondary metabolite production, antagonism toward the plant-pathogenic fungus Botrytis cinerea, and reduced ability to control Fusarium foot rot disease on wheat, caused by Fusarium graminearum. Transcriptome sequencing of the in vitro interaction between the C. rosea Δdcl2 strain and B. cinerea or F. graminearum identified the downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes, and secondary metabolites biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild-type interaction. A total of 61 putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea, and 11 were downregulated in the Δdcl2 mutant. In addition to putative endogenous gene targets, these milRNAs were predicted to target B. cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the Δdcl2 mutant incapable of producing the targeting milRNAs. In summary, this study constitutes the first step in elucidating the role of RNAi in mycoparasitic interactions, with important implications for biological control of plant diseases, and poses the base for future studies focusing on the role of cross-species RNAi regulating mycoparasitic interactions. IMPORTANCE Small RNAs mediated RNA interference (RNAi) known to regulate several biological processes. Dicer-like endoribonucleases (DCLs) play a vital role in the RNAi pathway by generating sRNAs. In this study, we investigated a role of DCL-mediated RNAi in interference interactions between mycoparasitic fungus Clonostachys rosea and the two fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohosts). We found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea. We also found C. rosea sRNAs putatively targeting known virulence factors in the mycohosts, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and poses a base for future works studying the role of DCL-based cross-species RNAi in fungal interactions.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pruthvi B. Kalyandurg
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Sandeep Kushwaha
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. mSystems 2021; 6:e0054421. [PMID: 34636668 PMCID: PMC8510539 DOI: 10.1128/msystems.00544-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum, supporting the hypothesis that this species is parasitizing Armillaria. Most notably, we identified differentially upregulated E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most differentially upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases—enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species; however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome was reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction. IMPORTANCE By studying fungi that parasitize other fungi, we can understand the basic biology of these unique interactions. Studies focused on the genetic mechanisms regulating mycoparasitism between host and parasite have thus far concentrated on a single fungal lineage within the Ascomycota. The work presented here expands our understanding of mycoparasitic relationships to the Basidiomycota and represents the first transcriptomic study to our knowledge that examines fungal-fungal relationships in their natural setting. The results presented here suggest that even distantly related mycoparasites utilize similar mechanisms to parasitize their host. Given that species of the mushroom-forming pathogen Armillaria cause plant root-rot diseases in many agroecosystems, an enhanced understanding of this interaction may contribute to better control of these diseases through biocontrol applications.
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Ntsobi N, Fanadzo M, Le Roes-Hill M, Nchu F. Effects of Clonostachys rosea f. catenula Inoculum on the Composting of Cabbage Wastes and the Endophytic Activities of the Composted Material on Tomatoes and Red Spider Mite Infestation. Microorganisms 2021; 9:microorganisms9061184. [PMID: 34072654 PMCID: PMC8228010 DOI: 10.3390/microorganisms9061184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 11/16/2022] Open
Abstract
Globally, fungal inocula are being explored as agents for the optimization of composting processes. This research primarily evaluates the effects of inoculating organic vegetable heaps with the entomopathogenic fungus Clonostachys rosea f. catenula (Hypocreales) on the biophysicochemical properties of the end-product of composting. Six heaps of fresh cabbage (Brassica oleracea var. capitata) waste were inoculated with C. rosea f. catenula conidia and another six were not exposed to the fungus. The composted materials from the fungus- and control-treated heaps were subsequently used as a medium to cultivate tomatoes (Solanum lycopersicum). The biophysicochemical characteristics of the composted materials were also assessed after composting. In addition, the protective effect of the fungal inoculum against red spider mite (Tetranychus urticae) infestations in the tomatoes was evaluated through the determination of conidial colonization of the plant tissue and the number of plants infested by the insect. Furthermore, phytotoxicity tests were carried out post experiment. There were few significant variations (p < 0.05) in heap temperature or moisture level between treatments based on the weekly data. We found no significant differences in the levels of compost macronutrient and micronutrient constituents. Remarkably, the composted materials, when incorporated into a growth medium from fungus-treated heaps, induced a 100% endophytic tissue colonization in cultivated tomato plants. While fewer red spider mite infestations were observed in tomato plants grown in composted materials from fungus-treated heaps, the difference was not significant (χ2 = 0.96 and p = 0.32). The fungal treatment yielded composted materials that significantly (p < 0.05) enhanced tomato seed germination, and based on the phytotoxicity test, the composted samples from the heaps exposed to the C. rosea f. catenula inoculum were not toxic to tomato seeds and seedlings. In conclusion, this study showed that C. rosea f. catenula improved the quality of composted materials in terms of fungal endophytism and seed germination.
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Affiliation(s)
- Nomfusi Ntsobi
- Department of Agriculture, Wellington Campus, Cape Peninsula University of Technology, Jan Van Riebeeck Street, Private Bag X8, Wellington 7654, South Africa; (N.N.); (M.F.)
- Department of Horticultural Sciences, Bellville Campus, Cape Peninsula University of Technology, Symphony Way, P.O. Box 1906, Bellville 7535, South Africa
| | - Morris Fanadzo
- Department of Agriculture, Wellington Campus, Cape Peninsula University of Technology, Jan Van Riebeeck Street, Private Bag X8, Wellington 7654, South Africa; (N.N.); (M.F.)
| | - Marilize Le Roes-Hill
- Applied Microbial and Health Biotechnology Institute, Bellville Campus, Cape Peninsula University of Technology, Symphony Way, P.O. Box 1906, Bellville 7535, South Africa;
| | - Felix Nchu
- Department of Horticultural Sciences, Bellville Campus, Cape Peninsula University of Technology, Symphony Way, P.O. Box 1906, Bellville 7535, South Africa
- Correspondence:
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Bika R, Baysal-Gurel F, Jennings C. Botrytis cinereamanagement in ornamental production: a continuous battle. CANADIAN JOURNAL OF PLANT PATHOLOGY 2021; 43:345-365. [PMID: 0 DOI: 10.1080/07060661.2020.1807409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/04/2020] [Indexed: 05/26/2023]
Affiliation(s)
- Ravi Bika
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN 37110, USA
| | - Fulya Baysal-Gurel
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN 37110, USA
| | - Christina Jennings
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN 37110, USA
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Salcedo-Sarmiento S, Aucique-Pérez CE, Silveira PR, Colmán AA, Silva AL, Corrêa Mansur PS, Rodrigues FÁ, Evans HC, Barreto RW. Elucidating the interactions between the rust Hemileia vastatrix and a Calonectria mycoparasite and the coffee plant. iScience 2021; 24:102352. [PMID: 33870142 PMCID: PMC8044427 DOI: 10.1016/j.isci.2021.102352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Calonectria hemileiae, a fungus associated with pustules of the coffee leaf rust (CLR, Hemileia vastatrix) in Brazil, was tested in vitro and in planta to assess its biocontrol potential. The fungus inhibited the germination of rust spores by over 80%. CLR severity was reduced by 93% when Calonectria was applied to coffee leaf discs inoculated with H. vastatrix, whilst a reduction of 70-90% was obtained for in planta experiments. Mycoparasitism was demonstrated through the fulfillment of Koch's postulates. Elucidation of the biochemical interaction between Calonectria and Hemileia on coffee plants indicated that the mycoparasite was able to increase plant resistance to rust infection. Coffee plants sprayed with Calonectria alone showed greater levels of chitinase, β-1,3-glucanase, ascorbate peroxidase and peroxidase. Although effective in controlling the rust, fungicide applications damaged coffee photosynthesis, whereas no harm was caused by Calonectria. We conclude that C. hemileiae shows promise as a biocontrol agent of CLR.
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Affiliation(s)
| | | | - Patrícia R. Silveira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Adans A. Colmán
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - André L. Silva
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | | | | | - Harry C. Evans
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
- CAB International, UK Centre, Egham, Surrey, UK
| | - Robert W. Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
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Efficacy of bioagents against Pythium deliense Meurs associated with yellowing of black pepper. Arch Microbiol 2021; 203:2597-2604. [PMID: 33693985 DOI: 10.1007/s00203-021-02252-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 10/21/2022]
Abstract
Yellowing and wilting of black pepper vines is a serious concern in many black pepper growing tracts where Pythium deliense was recently emerged as a pathogen from the rhizosphere of affected vines, which is proved to be pathogenic by Koch's postulates. As a measure to manage the symptoms, bioagents were evaluated against infection by P. deliense. Among the seven bioagents tested, Trichoderma harzianum and Streptomyces albulus showed 100% inhibition in vitro followed by one Streptomyces sp. and S. rimosus (75.33%). The potential ones were further evaluated under the hydroponic system in vivo by challenge inoculation. No root infection was noticed with T. harzianum and S. albulus inoculation, instead, the inoculated plants showed root regeneration. This suggests the efficiency of these bioagents on plant growth promotion as well as on disease suppression. Biochemical analysis of the hydroponic medium showed an increase in membrane conductivity in all the treatments except in T. harzianum. The release of phenolic compounds into the medium was lowest with T. harzianum indicating the prevention of pathogen invasion. In planta evaluation under greenhouse condition and field evaluation also showed the protective effect of T. harzianum and S. albulus with a reduction in the intensity of yellowing to an extent of 73.1% and 71.2%, respectively. The study revealed that T. harzianum and the actinomycete S. albulus had the potential to prevent the root rot caused by P. deliense.
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Kim SH, Lahlali R, Karunakaran C, Vujanovic V. Specific Mycoparasite- Fusarium Graminearum Molecular Signatures in Germinating Seeds Disabled Fusarium Head Blight Pathogen's Infection. Int J Mol Sci 2021; 22:ijms22052461. [PMID: 33671098 PMCID: PMC7957488 DOI: 10.3390/ijms22052461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 01/04/2023] Open
Abstract
Advances in Infrared (IR) spectroscopies have entered a new era of research with applications in phytobiome, plant microbiome and health. Fusarium graminearum 3-ADON is the most aggressive mycotoxigenic chemotype causing Fusarium head blight (FHB) in cereals; while Sphaerodes mycoparasitica is the specific Fusarium mycoparasite with biotrophic lifestyle discovered in cereal seeds and roots. Fourier transform infrared (FTIR) spectroscopy analyses depicted shifts in the spectral peaks related to mycoparasitism mainly within the region of proteins, lipids, also indicating a link between carbohydrates and protein regions, involving potential phenolic compounds. Especially, S. mycoparasitica contributes to significant changes in lipid region 3050–2800 cm−1, while in the protein region, an increasing trend was observed for the peaks 1655–1638 cm−1 (amide I) and 1549–1548 cm−1 (amide II) with changes in indicative protein secondary structures. Besides, the peak extending on the region 1520–1500 cm−1 insinuates a presence of aromatic compounds in presence of mycoparasite on the F. graminearum root sample. Monitoring shift in improved seed germination, fungus-fungus interface through scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM), and FTIR molecular signatures combined with principal component analysis (PCA) proved useful tools to detect an early mycoparasitism as a vital asset of the preventive biocontrol strategy against plant pathogens.
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Affiliation(s)
- Seon Hwa Kim
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada;
| | - Rachid Lahlali
- Canadian Light Source, 44 Innovation Blvd, Saskatoon, SK S7N 2V3, Canada; (R.L.); (C.K.)
- Department of Plant Protection, Phytopathology Unit, Ecole Nationale d’Agriculture de Meknès, BP/S 40, Meknès 50001, Morocco
| | - Chithra Karunakaran
- Canadian Light Source, 44 Innovation Blvd, Saskatoon, SK S7N 2V3, Canada; (R.L.); (C.K.)
| | - Vladimir Vujanovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada;
- Correspondence:
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Gimeno A, Stanley CE, Ngamenie Z, Hsung MH, Walder F, Schmieder SS, Bindschedler S, Junier P, Keller B, Vogelgsang S. A versatile microfluidic platform measures hyphal interactions between Fusarium graminearum and Clonostachys rosea in real-time. Commun Biol 2021; 4:262. [PMID: 33637874 PMCID: PMC7910300 DOI: 10.1038/s42003-021-01767-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Routinely, fungal-fungal interactions (FFI) are studied on agar surfaces. However, this format restricts high-resolution dynamic imaging. To gain experimental access to FFI at the hyphal level in real-time, we developed a microfluidic platform, a FFI device. This device utilises microchannel geometry to enhance the visibility of hyphal growth and provides control channels to allow comparisons between localised and systemic effects. We demonstrate its function by investigating the FFI between the biological control agent (BCA) Clonostachys rosea and the plant pathogen Fusarium graminearum. Microscope image analyses confirm the inhibitory effect of the necrotrophic BCA and we show that a loss of fluorescence in parasitised hyphae of GFP-tagged F. graminearum coincides with the detection of GFP in mycelium of C. rosea. The versatility of our device to operate under both water-saturated and nutrient-rich as well as dry and nutrient-deficient conditions, coupled with its spatio-temporal output, opens new opportunities to study relationships between fungi.
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Affiliation(s)
- Alejandro Gimeno
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
- Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Claire E Stanley
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland.
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Zurich, Switzerland.
- Department of Bioengineering, Imperial College London, London, UK.
| | - Zacharie Ngamenie
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
| | - Ming-Hui Hsung
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Zurich, Switzerland
| | - Florian Walder
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Zurich, Switzerland
| | - Stefanie S Schmieder
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Beat Keller
- Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Susanne Vogelgsang
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland.
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Broberg M, Dubey M, Iqbal M, Gudmundssson M, Ihrmark K, Schroers H, Funck Jensen D, Brandström Durling M, Karlsson M. Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales). Evol Appl 2021; 14:476-497. [PMID: 33664789 PMCID: PMC7896725 DOI: 10.1111/eva.13134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/09/2020] [Accepted: 09/02/2020] [Indexed: 12/16/2022] Open
Abstract
Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, 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 the Bionectria subgenus 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. Most Clonostachys species 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 the C. rosea genome 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 gene abcG6 in C. rosea was induced (p ≤ .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121-fold) and various fungicides. Deletion of abcG6 resulted 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 in Clonostachys subgenus Bionectria.
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Affiliation(s)
- Martin Broberg
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mudassir Iqbal
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Gudmundssson
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Dan Funck Jensen
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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Ding M, Chen W, Ma X, Lv B, Jiang S, Yu Y, Rahimi M, Gao R, Zhao Z, Cai F, Druzhinina I. Emerging salt marshes as a source of Trichoderma arenarium sp. nov. and other fungal bioeffectors for biosaline agriculture. J Appl Microbiol 2021; 130:179-195. [PMID: 32590882 PMCID: PMC7818382 DOI: 10.1111/jam.14751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023]
Abstract
AIMS Sustainable agriculture requires effective and safe biofertilizers and biofungicides with low environmental impact. Natural ecosystems that closely resemble the conditions of biosaline agriculture may present a reservoir for fungal strains that can be used as novel bioeffectors. METHODS AND RESULTS We isolated a library of fungi from the rhizosphere of three natural halotolerant plants grown in the emerging tidal salt marshes on the south-east coast of China. DNA barcoding of 116 isolates based on the rRNA ITS1 and 2 and other markers (tef1 or rpb2) revealed 38 fungal species, including plant pathogenic (41%), saprotrophic (24%) and mycoparasitic (28%) taxa. The mycoparasitic fungi were mainly species from the hypocrealean genus Trichoderma, including at least four novel phylotypes. Two of them, representing the taxa Trichoderma arenarium sp. nov. (described here) and T. asperelloides, showed antagonistic activity against five phytopathogenic fungi, and significant growth promotion on tomato seedlings under the conditions of saline agriculture. CONCLUSIONS Trichoderma spp. of salt marshes play the role of natural biological control in young soil ecosystems with a putatively premature microbiome. SIGNIFICANCE AND IMPACT OF THE STUDY The saline soil microbiome is a rich source of halotolerant bioeffectors that can be used in biosaline agriculture.
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Affiliation(s)
- M.‐Y. Ding
- Fungal Genomics Laboratory (FungiG)Nanjing Agricultural UniversityNanjingP.R. China
| | - W. Chen
- Jiangsu Provincial Key Lab of Solid Organic Waste UtilizationJiangsu Collaborative Innovation Center of Solid Organic WastesEducational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingP.R. China
| | - X.‐C. Ma
- Jiangsu Provincial Key Lab of Solid Organic Waste UtilizationJiangsu Collaborative Innovation Center of Solid Organic WastesEducational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingP.R. China
| | - B.‐W. Lv
- Jiangsu Provincial Key Lab of Solid Organic Waste UtilizationJiangsu Collaborative Innovation Center of Solid Organic WastesEducational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingP.R. China
| | - S.‐Q. Jiang
- Fungal Genomics Laboratory (FungiG)Nanjing Agricultural UniversityNanjingP.R. China
| | - Y.‐N. Yu
- Jiangsu Provincial Key Lab of Solid Organic Waste UtilizationJiangsu Collaborative Innovation Center of Solid Organic WastesEducational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingP.R. China
| | - M.J. Rahimi
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE)TU WienViennaAustria
| | - R.‐W. Gao
- Fungal Genomics Laboratory (FungiG)Nanjing Agricultural UniversityNanjingP.R. China
| | - Z. Zhao
- Fungal Genomics Laboratory (FungiG)Nanjing Agricultural UniversityNanjingP.R. China
| | - F. Cai
- Fungal Genomics Laboratory (FungiG)Nanjing Agricultural UniversityNanjingP.R. China
- Jiangsu Provincial Key Lab of Solid Organic Waste UtilizationJiangsu Collaborative Innovation Center of Solid Organic WastesEducational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingP.R. China
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE)TU WienViennaAustria
| | - I.S. Druzhinina
- Fungal Genomics Laboratory (FungiG)Nanjing Agricultural UniversityNanjingP.R. China
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE)TU WienViennaAustria
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Extremophilic Fungi and Their Role in Control of Pathogenic Microbes. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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The Influence of Trichoderma harzianum Rifai T-22 and Other Biostimulants on Rhizosphere Beneficial Microorganisms of Carrot. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10111637] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The principles of good agricultural and horticultural practice, which consider both giving environmental protection and high yielding of plants, require modern cultivation methods. Modern cultivation of horticultural plants uses, for example, cover crops, living mulches, plant growth-promoting microorganisms (PGPMs), plant growth regulators (PGRs) and other biostimulants protecting the soil against degradation and plants against phytopathogens and stress. The purpose of field and laboratory studies was to determine the effect of Trianum P (containing Trichoderma harzianum Rifai T-22 spores), Beta-Chikol (a.s.—chitosan), Timorex Gold 24 EC (based on tea tree oil) and fungicide Zaprawa Nasienna T 75 DS/WS (a.s.—tiuram 75%) on the health of carrot (Daucus carota L.) plants and the microorganism population in the rhizosphere of this plant. Moreover, the antagonistic effect of rhizosphere fungi on selected carrot fungal pathogens was determined. Laboratory mycological analysis allowed one to determine the qualitative and quantitative composition of fungi colonizing the underground parts of carrot plants. In addition, the total population of fungi and bacteria was determined (including Bacillus sp. and Pseudomonas sp.) based on the microbiological analysis of the rhizosphere soil. The application of the plant growth-promoting fungus (Trichoderma harzianum T-22), chitosan and tea tree oil positively influenced the growth, development and health status of carrot plants. T. harzianum T-22, chitosan and fungicide most effectively protected carrots against infection by soil-borne fungi from the genus Alternaria, Fusarium, Haematonectria, Sclerotinia and Rhizoctonia. The rhizosphere population of Bacillus sp. and Pseudomonas sp. in the treatments with Trianum P or Zaprawa Nasienna T 75 DS/WS was bigger than in the other experimental treatments. A reverse relationship was observed in the population of rhizosphere fungi. T. harzianum T-22, chitosan and tea tree oil promoted the growth of antagonistic fungi (Albifimbria sp., Clonostachys sp., Penicillium sp., Talaromyces sp. and Trichoderma sp.) in the carrot rhizosphere. Antagonistic activity of these fungi towards Alternaria dauci, Alternaria radicina, Sclerotiniasclerotiorum and Rhizoctonia solani was higher after the application of the preparations compared to control. Consequently, Trianum P, Beta-Chikol and Timorex Gold 24 EC can be recommended as plant biostimulants in ecological agricultural production, including Daucus carota cultivation.
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Iqbal M, Broberg M, Haarith D, Broberg A, Bushley KE, Brandström Durling M, Viketoft M, Funck Jensen D, Dubey M, Karlsson M. Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping. Evol Appl 2020; 13:2264-2283. [PMID: 33005223 PMCID: PMC7513725 DOI: 10.1111/eva.13001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/09/2020] [Accepted: 05/13/2020] [Indexed: 01/28/2023] Open
Abstract
Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤ .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10-10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Martin Broberg
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Deepak Haarith
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Anders Broberg
- Department of Molecular Sciences Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Kathryn E Bushley
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Maria Viketoft
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
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Karlsson Green K, Stenberg JA, Lankinen Å. Making sense of Integrated Pest Management (IPM) in the light of evolution. Evol Appl 2020; 13:1791-1805. [PMID: 32908586 PMCID: PMC7463341 DOI: 10.1111/eva.13067] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Integrated Pest Management (IPM) is a holistic approach to combat pests (including herbivores, pathogens, and weeds) using a combination of preventive and curative actions, and only applying synthetic pesticides when there is an urgent need. Just as the recent recognition that an evolutionary perspective is useful in medicine to understand and predict interactions between hosts, diseases, and medical treatments, we argue that it is crucial to integrate an evolutionary framework in IPM to develop efficient and reliable crop protection strategies that do not lead to resistance development in herbivores, pathogens, and weeds. Such a framework would not only delay resistance evolution in pests, but also optimize each element of the management and increase the synergies between them. Here, we outline key areas within IPM that would especially benefit from a thorough evolutionary understanding. In addition, we discuss the difficulties and advantages of enhancing communication among research communities rooted in different biological disciplines and between researchers and society. Furthermore, we present suggestions that could advance implementation of evolutionary principles in IPM and thus contribute to the development of sustainable agriculture that is resilient to current and emerging pests.
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Affiliation(s)
- Kristina Karlsson Green
- Department of Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Johan A. Stenberg
- Department of Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Åsa Lankinen
- Department of Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
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Lv B, Jiang N, Hasan R, Chen Y, Sun M, Li S. Cell Wall Biogenesis Protein Phosphatase CrSsd1 Is Required for Conidiation, Cell Wall Integrity, and Mycoparasitism in Clonostachys rosea. Front Microbiol 2020; 11:1640. [PMID: 32760382 PMCID: PMC7373758 DOI: 10.3389/fmicb.2020.01640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/24/2020] [Indexed: 12/29/2022] Open
Abstract
Cell wall biogenesis protein phosphatases play important roles in various cellular processes in fungi. However, their functions in the widely distributed mycoparasitic fungus Clonostachys rosea remain unclear, as do their potential for controlling plant fungal diseases. Herein, the function of cell wall biogenesis protein phosphatase CrSsd1 in C. rosea 67-1 was investigated using gene disruption and complementation approaches. The gene-deficient mutant ΔCrSsd1 exhibited much lower conidiation, hyphal growth, mycoparasitic ability, and biocontrol efficacy than the wild-type (WT) strain, and it was more sensitive to sorbitol and Congo red. The results indicate that CrSsd1 is involved in fungal conidiation, osmotic stress adaptation, cell wall integrity, and mycoparasitism in C. rosea.
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Affiliation(s)
- Binna Lv
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Na Jiang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rakibul Hasan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Chen
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manhong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shidong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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38
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Sun ZB, Wang Q, Sun MH, Li SD. The Mitogen-Activated Protein Kinase Gene Crmapk Is Involved in Clonostachys chloroleuca Mycoparasitism. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:902-910. [PMID: 32282260 DOI: 10.1094/mpmi-03-20-0062-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Clonostachys chloroleuca is a mycoparasite used for biocontrol of numerous fungal plant pathogens. Sequencing of the transcriptome of C. chloroleuca following mycoparasitization of the sclerotia of Sclerotinia sclerotiorum revealed significant upregulation of a mitogen-activated protein kinase (MAPK)-encoding gene, crmapk. Although MAPKs are known to regulate fungal growth and development, the function of crmapk in C. chloroleuca mycoparasitism is unclear. In this study, we investigated the role of crmapk in C. chloroleuca mycoparasitism through gene knockout and complementation. Deletion of crmapk had no influence on the C. chloroleuca morphological characteristics but could significantly reduce the mycoparasitic ability to sclerotia and biocontrol capacity to soybean Sclerotinia stem rot; crmapk complementation restored these abilities. Transcriptome analysis between Δcrmapk and the wild-type strain revealed numerous genes were significantly down-regulated after crmapk deletion, including cytochrome P450, transporters, and cell wall-degrading enzymes (CWDEs). Our findings indicate that crmapk influences C. chloroleuca mycoparasitism by regulation of genes controlling the activity of CWDEs or antibiotic production. This study provides a basis for further studies of the molecular mechanism of C. chloroleuca mycoparasitism.
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Affiliation(s)
- Zhan-Bin Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Qi Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Man-Hong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Demissie ZA, Witte T, Robinson KA, Sproule A, Foote SJ, Johnston A, Harris LJ, Overy DP, Loewen MC. Transcriptomic and Exometabolomic Profiling Reveals Antagonistic and Defensive Modes of Clonostachys rosea Action Against Fusarium graminearum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:842-858. [PMID: 32116115 DOI: 10.1094/mpmi-11-19-0310-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mycoparasite Clonostachys rosea ACM941 is under development as a biocontrol organism against Fusarium graminearum, the causative agent of Fusarium head blight in cereals. To identify molecular factors associated with this interaction, the transcriptomic and exometabolomic profiles of C. rosea and F. graminearum GZ3639 were compared during coculture. Prior to physical contact, the antagonistic activity of C. rosea correlated with a response heavily dominated by upregulation of polyketide synthase gene clusters, consistent with the detected accumulation of corresponding secondary metabolite products. Similarly, prior to contact, trichothecene gene clusters were upregulated in F. graminearum, while those responsible for fusarielin and fusarin biosynthesis were downregulated, correlating with an accumulation of trichothecene products in the interaction zone over time. A concomitant increase in 15-acetyl deoxynivalenol-3-glucoside in the interaction zone was also detected, with C. rosea established as the source of this detoxified mycotoxin. After hyphal contact, C. rosea was found to predominantly transcribe genes encoding cell wall-degradation enzymes, major facilitator superfamily sugar transporters, anion:cation symporters, as well as alternative carbon source utilization pathways, together indicative of a transition to necrotropism at this stage. F. graminearum notably activated the transcription of phosphate starvation pathway signature genes at this time. Overall, a number of signature molecular mechanisms likely contributing to antagonistic activity by C. rosea against F. graminearum, as well as its mycotoxin tolerance, are identified in this report, yielding several new testable hypotheses toward understanding the basis of C. rosea as a biocontrol agent for continued agronomic development and application.
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Affiliation(s)
- Zerihun A Demissie
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Thomas Witte
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kelly A Robinson
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Simon J Foote
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Anne Johnston
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - David P Overy
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Michele C Loewen
- Aquatic and Crop Resource Development, National Research Council of Canada, Ottawa, Ontario, Canada
- Department of Biomedical and Molecular Sciences, Queens University, Kingston, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
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40
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Gimeno A, Kägi A, Drakopoulos D, Bänziger I, Lehmann E, Forrer HR, Keller B, Vogelgsang S. From laboratory to the field: biological control of Fusarium graminearum on infected maize crop residues. J Appl Microbiol 2020; 129:680-694. [PMID: 32176428 PMCID: PMC7496986 DOI: 10.1111/jam.14634] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 11/29/2022]
Abstract
Aim To evaluate biological control agents (BCAs) against Fusarium graminearum on infected maize stalks as a means to reduce Fusarium head blight (FHB) in subsequently grown wheat. Methods and Results In the laboratory, BCAs were applied against F. graminearum on maize stalk pieces. Clonostachys rosea inhibited the perithecia development and ascospore discharge when applied before, simultaneously with and after the pathogen. In the field, we simulated a system with high disease pressure, that is, a maize‐wheat rotation under no‐tillage, by preparing maize stalks inoculated with F. graminearum. The infected stalks were treated with formulations of C. rosea selected in vitro or the commercial BCA strain Trichoderma atrobrunneum ITEM908 and exposed to field conditions over winter and spring between winter wheat rows. Monitoring with spore traps and of FHB symptoms, as well as quantification of F. graminearum incidence and DNA in harvested grain revealed significant reductions by C. rosea by up to 85, 91, 69 and 95% compared with an inoculated but untreated positive control, respectively. Deoxynivalenol (DON) and zearalenone (ZEN) contents were reduced by up to 93 and 98%, respectively. Treatments with T. atrobrunneum were inconsistent, with significant reductions of DON and ZEN under warm and wet climatic conditions only. Conclusions The findings support the application of C. rosea against F. graminearum on residues of maize to suppress the primary inoculum of FHB. Significance and Impact of the Study As sustainable agriculture requires solutions to control FHB, hence, the application of C. rosea during the mulching of maize crop residues should be evaluated in on‐farm experiments.
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Affiliation(s)
- A Gimeno
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland.,Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - A Kägi
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
| | - D Drakopoulos
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland.,Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich D-USYS, Zurich, Switzerland
| | - I Bänziger
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
| | - E Lehmann
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
| | - H-R Forrer
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
| | - B Keller
- Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - S Vogelgsang
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
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41
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Sun ZB, Li SD, Ren Q, Xu JL, Lu X, Sun MH. Biology and applications of Clonostachys rosea. J Appl Microbiol 2020; 129:486-495. [PMID: 32115828 DOI: 10.1111/jam.14625] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 01/07/2023]
Abstract
Clonostachys rosea is a promising saprophytic filamentous fungus that belongs to phylum Ascomycota. Clonostachys rosea is widespread around the world and exists in many kinds of habitats, with the highest frequency in soil. As an excellent mycoparasite, C. rosea exhibits strong biological control ability against numerous fungal plant pathogens, nematodes and insects. These behaviours are based on the activation of multiple mechanisms such as secreted cell-wall-degrading enzymes, production of antifungal secondary metabolites and induction of plant defence systems. Besides having significant biocontrol activity, C. rosea also functions in the biodegradation of plastic waste, biotransformation of bioactive compounds, as a bioenergy sources and in fermentation. This mini review summarizes information about the biology and various applications of C. rosea and expands on its possible uses.
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Affiliation(s)
- Z-B Sun
- School of Light Industry, Beijing Technology and Business University, Beijing, China.,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - S-D Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Q Ren
- School of Light Industry, Beijing Technology and Business University, Beijing, China
| | - J-L Xu
- School of Light Industry, Beijing Technology and Business University, Beijing, China
| | - X Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - M-H Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Wen Z, Zeng Z, Ren F, Asiegbu FO. The Conifer Root and Stem Rot Pathogen ( Heterobasidion parviporum): Effectome Analysis and Roles in Interspecific Fungal Interactions. Microorganisms 2019; 7:microorganisms7120658. [PMID: 31817407 PMCID: PMC6955712 DOI: 10.3390/microorganisms7120658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion parviporum Niemelä & Korhonen is an economically important basidiomycete, causing root and stem rot disease of Norway spruce (Picea abies (L.) Karst) in Northern Europe. The H. parviporum genome encodes numerous small secreted proteins, which might be of importance for interacting with mycorrhiza symbionts, endophytes, and other saprotrophs. We hypothesized that small secreted proteins from H. parviporum (HpSSPs) are involved in interspecific fungal interaction. To identify HpSSP-coding genes potentially involved, we screened the H. parviporum effectome and compared their transcriptomic profiles during fungal development and in planta tree infection. We further conducted phylogenetic analysis, and identified a subset of hypothetical proteins with nonpredicted domain or unknown function as HpSSPs candidates for further characterization. The HpSSPs candidates were selected based on high-quality sequence, cysteine residue frequency, protein size, and in planta expression. We subsequently explored their roles during in vitro interaction in paired cultures of H. parviporum with ectomycorrhizal Cortinarius gentilis, endophytic Phialocephala sphaeroides, saprotrophs (Mycena sp., Phlebiopsis gigantea, and Phanerochaete chrysosporium), respectively. The transcriptomic profile revealed that a large proportion of effector candidates was either barely expressed or highly expressed under all growth conditions. In vitro dual-culture test showed that P. sphaeroides and C. gentilis were overgrown by H. parviporum. The barrage zone formation or no physical contact observed in paired cultures with the saprotrophs suggest they had either combative interaction or antibiosis effect with H. parviporum. Several HpSSPs individuals were up- or downregulated during the nonself interactions. The results of HpSSPs gene expression patterns provide additional insights into the diverse roles of SSPs in tree infection and interspecific fungal interactions.
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Affiliation(s)
- Zilan Wen
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
| | - Zhen Zeng
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
| | - Fei Ren
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, No. 1 Shuiza Road, Beijing 102300, China
| | - Fred O. Asiegbu
- Faculty of Agriculture and Forestry, P. O. Box 27, Latokartanonkaari 7, University of Helsinki, 00014 Helsinki, Finland; (Z.W.); (Z.Z.); (F.R.)
- Correspondence: ; Tel.: +358-294158109
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Sarrocco S, Mauro A, Battilani P. Use of Competitive Filamentous Fungi as an Alternative Approach for Mycotoxin Risk Reduction in Staple Cereals: State of Art and Future Perspectives. Toxins (Basel) 2019; 11:E701. [PMID: 31810316 PMCID: PMC6950288 DOI: 10.3390/toxins11120701] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Among plant fungal diseases, those affecting cereals represent a huge problem in terms of food security and safety. Cereals, such as maize and wheat, are very often targets of mycotoxigenic fungi. The limited availability of chemical plant protection products and physical methods to control mycotoxigenic fungi and to reduce food and feed mycotoxin contamination fosters alternative approaches, such as the use of beneficial fungi as an active ingredient of biological control products. Competitive interactions, including both exploitation and interference competition, between pathogenic and beneficial fungi, are generally recognized as mechanisms to control plant pathogens populations and to manage plant diseases. In the present review, two examples concerning the use of competitive beneficial filamentous fungi for the management of cereal diseases are discussed. The authors retrace the history of the well-established use of non-aflatoxigenic isolates of Aspergillus flavus to prevent aflatoxin contamination in maize and give an overview of the potential use of competitive beneficial filamentous fungi to manage Fusarium Head Blight on wheat and mitigate fusaria toxin contamination. Although important steps have been made towards the development of microorganisms as active ingredients of plant protection products, a reasoned revision of the registration rules is needed to significantly reduce the chemical based plant protection products in agriculture.
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Affiliation(s)
- Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy;
| | - Antonio Mauro
- International Institute of Tropical Agriculture, P.O. Box 34441 Dar es Salaam, Tanzania;
| | - Paola Battilani
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
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Iqbal M, Dubey M, Broberg A, Viketoft M, Jensen DF, Karlsson M. Deletion of the Nonribosomal Peptide Synthetase Gene nps1 in the Fungus Clonostachys rosea Attenuates Antagonism and Biocontrol of Plant Pathogenic Fusarium and Nematodes. PHYTOPATHOLOGY 2019; 109:1698-1709. [PMID: 31120795 DOI: 10.1094/phyto-02-19-0042-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Secondary metabolites produced by biological control agents may influence the outcome of their interactions with plant pathogenic microorganisms and plants. In the present study, we investigated the role of the nonribosomal peptide synthetase gene nps1 expressed by the biocontrol fungus Clonostachys rosea. A gene expression analysis showed that nps1 was induced during confrontations with the plant pathogenic fungus Botrytis cinerea. Gene deletion strains of nps1 displayed increased growth rates and conidiation. However, the nematicidal activity of culture filtrates from C. rosea Δnps1 strains was significantly weaker than that from wild-type filtrates (P ≤ 0.001); after 24 h of incubation with culture filtrates from nps1 deletion strains, only 13 to 33% of a mixed community of nematodes were dead compared with 42% of nematodes incubated with wild-type culture filtrates. The Δnps1 strains also showed reduced biocontrol efficacy during pot experiments, thus failing to protect wheat seedlings from foot rot disease caused by the plant pathogenic fungus Fusarium graminearum. Furthermore, C. rosea Δnps1 strains were not able to reduce populations of plant-parasitic nematodes in soil or in roots of wheat as efficiently as the wild-type strain. Both C. rosea wild-type and Δnps1 strains increased the dry shoot weight and shoot length of wheat by 20 and 13%, respectively. We showed that NPS1, a putative nonribosomal peptide synthetase encoded by nps1, is a biocontrol factor, presumably by producing a hitherto unknown nonribosomal peptide compound with antifungal and nematicidal properties that contributes to the biocontrol properties of C. rosea.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Viketoft
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
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Ji S, Liu Z, Liu B, Wang Y. Comparative analysis of biocontrol agent Trichoderma asperellum ACCC30536 transcriptome during its interaction with Populus davidiana × P. alba var. pyramidalis. Microbiol Res 2019; 227:126294. [PMID: 31421718 DOI: 10.1016/j.micres.2019.126294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
Abstract
After exposure to with Populus davidiana × P. alba var. pyramidalis, the expression of genes in Trichoderma asperellum were compared in four transcriptomes. The top 20 high expression genes included six heat shock proteins and three hydrophobins, indicating that Trichoderma can rapidly adapt to environment stresses and elicit a plant defense response. The genes, involved in the interaction between Trichoderma and plant, showed an increasing expression level, for example sugar transporters, EPL1s, endoxylanases, pectin lyases, and nitrilases. Interestingly, sugar transporters also showed high expression when T. asperellum was cultured on medium lacking a carbon substrate, which would contribute to T. asperellum's survival and domination in ecological niche competition. And the genes related to mycoparasitism were expressed abundantly following T. asperellum's interaction with PdPap, indicating the PdPap induction could enhance the mycoparasitic ability of T. asperellum. Twelve chitinases and five glucanases showed higher expression in transcriptome Cs, indicating that T. asperellum secretes both types of enzyme before interacting with pathogens, allowing T. asperellum to implement mycoparasitism and obtain more energy. Many novel transcripts were obtained in each transcriptome, which may play important roles in the biocontrol process of T. asperellum. Interestingly, T. asperellum undergo constitutive alternative splicing in the biocontrol process: Seven biocontrol genes were alternative spliced via intron retention. qRT-PCR analysis proved that intron retention is negatively associated with the expression of chitinase, oligopeptide transporters, and beta-lactamase. However, the percentage of MAPK intron retention was quite low, suggesting that intron retention has little effect on the function of MAPK.
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Affiliation(s)
- Shida Ji
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Zhihua Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Bin Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Yucheng Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China.
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Köhl J, Kolnaar R, Ravensberg WJ. Mode of Action of Microbial Biological Control Agents Against Plant Diseases: Relevance Beyond Efficacy. FRONTIERS IN PLANT SCIENCE 2019; 10:845. [PMID: 31379891 PMCID: PMC6658832 DOI: 10.3389/fpls.2019.00845] [Citation(s) in RCA: 333] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/12/2019] [Indexed: 05/19/2023]
Abstract
Microbial biological control agents (MBCAs) are applied to crops for biological control of plant pathogens where they act via a range of modes of action. Some MBCAs interact with plants by inducing resistance or priming plants without any direct interaction with the targeted pathogen. Other MBCAs act via nutrient competition or other mechanisms modulating the growth conditions for the pathogen. Antagonists acting through hyperparasitism and antibiosis are directly interfering with the pathogen. Such interactions are highly regulated cascades of metabolic events, often combining different modes of action. Compounds involved such as signaling compounds, enzymes and other interfering metabolites are produced in situ at low concentrations during interaction. The potential of microorganisms to produce such a compound in vitro does not necessarily correlate with their in situ antagonism. Understanding the mode of action of MBCAs is essential to achieve optimum disease control. Also understanding the mode of action is important to be able to characterize possible risks for humans or the environment and risks for resistance development against the MBCA. Preferences for certain modes of action for an envisaged application of a MBCA also have impact on the screening methods used to select new microbials. Screening of MBCAs in bioassays on plants or plant tissues has the advantage that MBCAs with multiple modes of action and their combinations potentially can be detected whereas simplified assays on nutrient media strongly bias the selection toward in vitro production of antimicrobial metabolites which may not be responsible for in situ antagonism. Risks assessments for MBCAs are relevant if they contain antimicrobial metabolites at effective concentration in the product. However, in most cases antimicrobial metabolites are produced by antagonists directly on the spot where the targeted organism is harmful. Such ubiquitous metabolites involved in natural, complex, highly regulated interactions between microbial cells and/or plants are not relevant for risk assessments. Currently, risks of microbial metabolites involved in antagonistic modes of action are often assessed similar to assessments of single molecule fungicides. The nature of the mode of action of antagonists requires a rethinking of data requirements for the registration of MBCAs.
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Affiliation(s)
- Jürgen Köhl
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
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Gimeno A, Sohlberg E, Pakula T, Limnell J, Keller B, Laitila A, Vogelgsang S. TaqMan qPCR for Quantification of Clonostachys rosea Used as a Biological Control Agent Against Fusarium graminearum. Front Microbiol 2019; 10:1627. [PMID: 31379780 PMCID: PMC6646457 DOI: 10.3389/fmicb.2019.01627] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/02/2019] [Indexed: 11/13/2022] Open
Abstract
Clonostachys rosea is a biological control agent against Fusarium graminearum in small grain cereals and maize. Infections with F. graminearum do not only reduce the yield but, due to the production of mycotoxins, also affect the entire value chain of food and feed. In addition, production of other secondary metabolites such as hydrophobins, also known as gushing inducers, may cause quality challenges for the malting and brewing industry. Sustainable disease control strategies using C. rosea are treatment of infected residues of the previous crop, direct treatment of the actual cereal crop or post-harvest treatment during malting processes. Follow-up of growth and survival of biocontrol organisms during these different stages is of crucial importance. In the current study, we developed a quantitative real-time PCR detection method that amends the currently available culture-dependent techniques by using TaqMan chemistry with a highly specific primer and probe set, targeting the actin gene. We established a sensitive assay that detects the biological control agent down to 100 genome copies per reaction, with PCR efficiencies between 90 and 100%. The specificity of the assay was confirmed against a panel of 30 fungal and 3 bacterial species including 12 members of the Fusarium head blight complex and DNA of barley, maize and wheat. The DNA of C. rosea was detected in Fusarium-infected maize crop residues that were either treated in the laboratory or in the field with C. rosea and followed its DNA throughout the barley malting process to estimate its growth during grain germination. We used a standardized DNA extraction protocol and showed that C. rosea can be quantified in different sample matrices. This method will enable the monitoring of C. rosea during experiments studying the biological control of F. graminearum on cereal crop residues and on cereal grains and will thus contribute to the development of a new disease control strategy.
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Affiliation(s)
- Alejandro Gimeno
- Ecological Plant Protection in Arable Crops, Research Division Plant Protection, Agroscope, Zurich, Switzerland.,Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Elina Sohlberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Tiina Pakula
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Jenni Limnell
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Beat Keller
- Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Arja Laitila
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Susanne Vogelgsang
- Ecological Plant Protection in Arable Crops, Research Division Plant Protection, Agroscope, Zurich, Switzerland
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48
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Killer toxin-like chitinases in filamentous fungi: Structure, regulation and potential roles in fungal biology. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Broberg M, Dubey M, Sun MH, Ihrmark K, Schroers HJ, Li SD, Jensen DF, Brandström Durling M, Karlsson M. Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping. Front Microbiol 2018; 9:2844. [PMID: 30524411 PMCID: PMC6262169 DOI: 10.3389/fmicb.2018.02844] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/05/2018] [Indexed: 01/16/2023] Open
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°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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Affiliation(s)
- Martin Broberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Man-Hong Sun
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Shi-Dong Li
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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50
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Vaz ABM, Fonseca PLC, Badotti F, Skaltsas D, Tomé LMR, Silva AC, Cunha MC, Soares MA, Santos VL, Oliveira G, Chaverri P, Góes-Neto A. A multiscale study of fungal endophyte communities of the foliar endosphere of native rubber trees in Eastern Amazon. Sci Rep 2018; 8:16151. [PMID: 30385829 PMCID: PMC6212449 DOI: 10.1038/s41598-018-34619-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/17/2018] [Indexed: 12/18/2022] Open
Abstract
Hevea brasiliensis is a native hyperdiverse tree species in the Amazon basin with great economic importance since it produces the highest quality natural rubber. H. brasiliensis, in its natural habitat, may harbor fungal endophytes that help defend against phytopathogenic fungi. In this work, we investigated the fungal endophytic communities in two pristine areas in Eastern Amazon (Anavilhanas National Park - ANP and Caxiuanã National Forest - CNF) at different spatial scales: regional, local, individual (tree), and intra-individual (leaflet). Using a culture-based approach, 210 fungal endophytes were isolated from 240 sampling units and assigned to 46 distinct MOTUs based on sequencing of the nrITS DNA. The community compositions of the endophytomes are different at both regional and local scales, dominated by very few taxa and highly skewed toward rare taxa, with many endophytes infrequently isolated across hosts in sampled space. Colletotrichum sp. 1, a probably latent pathogen, was the most abundant endophytic putative species and was obtained from all individual host trees in both study areas. Although the second most abundant putative species differed between the two collection sites, Clonostachys sp. 1 and Trichoderma sp. 1, they are phylogenetically related (Hypocreales) mycoparasites. Thus, they probably exhibit the same ecological function in the foliar endosphere of rubber tree as antagonists of its fungal pathogens.
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Affiliation(s)
- Aline B M Vaz
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Faculdade de Minas (FAMINAS), Belo Horizonte, MG, 31744-007, Brazil
| | - Paula L C Fonseca
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30480-000, Brazil
| | | | - Luiz M R Tomé
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Allefi C Silva
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Mayara C Cunha
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Marco A Soares
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Vera L Santos
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | | | - Priscilla Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Aristóteles Góes-Neto
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
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