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Mukesh Dubey

Mukesh Dubey
Associate Professor (Docent) in Plant Pathology at Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden


My research addresses the fundamental questions related to host-microbe interactions relevant to sustainable crop productions. I use state-of-the-art technologies, including genetics, genomics, metabolomics, and molecular biology to investigate how mycoparasitic and plant beneficial fungi such as those belonging to the genus Trichoderma and Clonostachys interact with their fungal and plant hosts and the environment. My aim is to develop knowledge-based strategies for better integration of theses fungal species into the agricultural production systems for plant health promotion and biological control of fungal plant diseases under climate change.  


Small-RNA based strategies to control fungal plant pathogens- an unexplored mechanism in biocontrol interactions (funded by Formas)

Small RNAs (sRNAs) are noncoding RNA molecules and play a central role in gene expression regulation called gene silencing. sRNAs are emerging as key players in pathogenic and symbiotic fungus-plant interactions by moving between the interacting plant host and the fungus and suppressing recipient cells’ defence response. However, the role of sRNA in mediating mycoparasitic and beneficial-fungus plant interactions remains obscure. Here we aim I) to investigate sRNA-mediated mechanisms regulating mycoparasitic interactions, and II) to expand the understanding of cross-kingdom gene silencing in beneficial fungus-plant interactions. To achieve this aim, we take advantage of the biocontrol fungus Clonostachys rosea, which can live both as a mycoparasite and as a mutualist on plant roots. We will use a combination of genomics, genetics, molecular biology, and microscopy approaches to study how gene silencing functions during interactions between the plant-beneficial fungus Clonostachys rosea and the plant pathogenic fungi Botrytis cinerea and Fusarium graminearum and plant host wheat. The result of this project will fill in the knowledge gaps and produce insights into the mechanism of interaction relevant to biocontrol, which can be applied to formulate sustainable strategies for future crop protection under a changing environment. 

An illustration showing small-RNA based strategies to control fungal plant pathogens- an unexplored mechanism in biocontrol interactions.

Small-RNA based strategies to control fungal plant pathogens- an unexplored mechanism in biocontrol interactions. A: During non-interacting conditions, the biocontrol agent produces a series of sRNAs, keeping part of its genes silenced. B: During the interaction with the fungal host, the sRNAs silence a different set of genes, affecting the regulation of endogenous gene expression and culminating in the production of antagonism-related factors. At the same time, some sRNAs enter the fungal host and hijack its RNA-silencing machinery, downregulating genes involved in virulence or response to the biocontrol agent. C: When the RNA silencing mechanism is impaired, for example in DCL deletion mutants, many sRNAs are not produced, hampering the ability of the biocontrol agent to efficiently respond to the contact with the fungal host.

Harnessing soil–microbe-plant interactions for sustainable wheat production (funded by Formas)

Wheat cultivation faces many emerging challenges, including limited nutrient resources and extreme events of biotic and abiotic stresses due to climate change. Microorganisms can play an important role in plant health promotion and stress resilience by improving nutrient availability and acquisition, by modulating plant growth regulators and by suppressing plant pathogens. The aim of this proposal is to use the genetic diversity of the beneficial fungus Clonostachys rosea to improve the health and climatic resilience of wheat. Our aim is to i) identify C. rosea strains with higher plant health promotion ability under biotic and abiotic stress conditions – with a focus on fusarium foot rot and head blight diseases, and drought stress, ii) identify wheat cultivars ideal for C. rosea application, and iii) investigate the mechanisms for high PHP activity by C. rosea. To achieve the aim we will combine approaches of microbiome, transcriptome and genome-wide association analysis to investigate the mechanisms behind PHP in C. rosea. The findings from this proposal will show how C. rosea can enhance stress resilience in wheat, reduce application of fertilizers and fungicides and improve plant health in wheat production. 

Petri dish and pots with wheat. Photo.

A) Clonostachys rosea strain IK726 on PDA medium. B) The effect of Clonostacnhys rosea on wheat plant growth promotion. Photo: Mukesh Dubey.

Fungal interactions in relation to biological control of plant diseases (funded by SLU)

Fungi occupy diverse ranges of environmental niches, and they closely interact at inter-species and intra-species levels for nutrients and space. Certain fungal species strive to kill other species and feed on the dead mycelia. This interaction and mode of lifestyle represent necrotrophic mycoparasitic interactions and mycoparasitism, respectively. Also, few mycoparasites can colonize plant roots, promote plant health, and induce immune responses (beneficial fungus-plant interactions) against plant pathogens. For these properties, certain of these species are used as biocontrol agents in agriculture and horticulture production systems. I aim to fill in the knowledge gap of mycoparasitic and beneficial fungus-plant interactions using reverse genetics combined with multi-omic approaches, which is of utmost importance to improve the efficacy of these strains under field conditions. 

Six wheat plants with different growth. Photo.

Biocontrol of Fusarium foot and root rot (caused by Fusarium graminearum) on wheat by the fungus Clonostachys rosea. Photo: Mukesh Dubey

Three Petri dishes with fungal mycelia. Photo.

 A) Trichoderma atroviride on PDA medium. B) Trichoderma atroviride wild-type strain can grow over grey mould fungus Botrytis cinerea under in vitro conditions. C), T. atroviride strain lacking Eng18B gene cannot grow over grey mould fungus Botrytis cinerea under in vitro conditions. Photo: Mukesh Dubey.

Mycotoxins and food safety and security in Rwanda: Understanding the biology and epidemiology of maize ear rots for sustainable maize production (funded by Swedish Research Council, VR)

Ear rot (ER) in maize caused by Aspergillus flavus, Fusarium graminearum and Fusarium verticillioides poses a serious threat to food safety and security by lowering the yield and the grain quality by mycotoxin contamination. The current project aims to generate crucial scientific knowledge to formulate strategies for improving maize productivity and quality through ensuring ER disease control. We will use i) a comprehensive approach combining farmers' training and awareness with field surveys on ER occurrence, distribution, and risk factors conducive to disease development and ii) identify genetic factors associated with the virulence determinants in ER pathogens and ER resistance in maize through population genomics and transcriptomics. Since ER pathogens can co-occur, we will iii) investigate whether pathogen co-infection has synergistic or antagonistic effects on ER development, mycotoxin production and plant disease resistance under normal and abiotic stress conditions. This project will provide scientific knowledge vital for improving maize productivity and quality through ensuring ER disease control and extension support services to farmers. The project will be executed through the collaborative efforts of a multi-disciplinary team from Rwanda and Sweden, covering all aspects for a successful implementation of the project.


Course leader/organizer

  • Emerging technologies and their application in sustainable crop production, 2024, PhD course at SLU, 3 ECTs. Course leader.
  • NOVA PhD course 2022, Biological control and the role of plant biomes in plant health, 9-13 May 2022, Älvkarleo, Sweden. Course co-organizer.
  • Plant pathology and Microbial interactions course at UMSA Bolivia, Nov 3-4, 2022. Co-organizer.

Teaching assignments (Teacher)

PhD courses

  • Mycology – its basics and applications, SLU. 
  • NOVA PhD courses

Master courses

  • Plant Pathology (Bl1044), 15 hp, SLU. 
  • Molecular Plant-Microbe Interactions, 15 hp, Stockholm University.
  • Plant Biology for Breeding and Protection (BI1296), 15 hp, SLU. 
  • Sustainable Plant Production-from Molecular to Field Scale (BI1295), 15 hp, SLU. 
  • Plant-Microbe Interactions (BI1354), 15 hp, SLU.
  • Ecology and Management of Diseases and Pests of Forest Trees (SG0225), 15 HP, SLU
  • Parasitology, Mycology and Clinical Infection Biology (3MK012), Uppsala University and SLU, 15hp.

Bachler course

Molecular and Microbial Ecology course, 15 hp, SLU.


PhD students

  • Marisel Mercedes Mamani Mamani, start year 2022, Main supervisor.
  • Alessandra Ruffino, start year 2023, co-supervisor.
  • Bekele Gelena Kelbessa, start year 2022, co-supervisor.
  • Virginia Rigoberta Gonzales Mamani, start year 2022, co-supervisor.
  • Sidhant Chaudhary, start year 2021, co-supervisor.
  • Carol Kålin, start year 2020, co-supervisor.
  • Mudassir Iqbal, start year 2015, co-supervisor.

Visiting PhD students 

  • Nathalie Kamou, 2014. Aristotle University of Thessaloniki, Greece.
  • Maroua Ben Amira, 2016. UCA, UMR PIAF, Clermont-Ferrand, France.
  • Schmidt Ruth, 2017. Department of Microbial Ecology, Netherlands Institute of Ecology, the Netherlands.
  • Awais Khan, 2019. University of Sargodha, Pakistan Collage of Agriculture, Pakistan. 
  • María Illescas Morente, 2022. Department of Molecular Genetics, University of Salamanca, Salamanca, Spain.
  • Georgios Sofianos, 2022. Aristotelian University of Thessaloniki, Thessaloniki, Greece.
  • Siqiao Chen, 2023-2024. Nanjing Agricultural University, Department of Soil Microorganism and Organic Fertilization Science, Nanjing, China. 

Master Students

  • Sebastian Bengtsson, 2016, 30 hp.
  • Umma Fatema, 2016-2017, 45 hp.
  • Emiliano Delli Compagni, 2018, 30 hp, Erasmus+ exchange student, University of Pisa, Italy.
  • Alma Gustavsson Ruus, 2022, 30 hp.
  • Jismy Treesa Sebastian, 2023, 15 hp.
  • Susmita Sigdel, 2024, 30 hp. Erasmus+ exchange student, University of Padua, Padua, Italy.
  • Francesca Sasso, 2024, 30hp. Exchange student, University of Turin.
  • Antonio Zapparata, 2013, 30 hp. Erasmus exchange student, University of Pisa, Italy.
  • Sofia Alvarez Nordström, 2014, 30 hp.
  • Anaís Carpelan, 2020, 45 hp.
  • Esther Kuper, 2021, 30 hp. 
  • Zainab Qayyum, 2022, 30 hp. Erasmus exchange student, Georg-August-Universität, Gottingen, Germany.
  • Jesper Fritzson, 2022, 30 hp.
  • Lekshmi Sudha, 2023, 15 hp.
  • Rosa Ricardo, 2023, 30 hp. Erasmus exchange student, Faculty of Sciences, University of Porto, Portugal.

Bachelor students

  • Ingeborg Zinger, 2016, Exchange student, Hanze University of Applied Science, Netherlands.
  • Ayano Tanaka, 2020, 15 hp.
  • Victor Olsson, 2019, 15 hp.
  • André Åbonde, 2023, 15 hp.

Selected publications

Peer-reviewed publications: 2012-till date

Piombo E, Kelbessa BG, Sundararajan P, Whisson SC, Vetukuri RR and Dubey M (2023). RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents. Frontiers in Microbiology. 14:1076522. doi: 10.3389/fmicb.2023.1076522.

Kälin C, Kolodinska Brantestam A, Arvidsson A-K, Dubey M, Elfstrand M and Karlsson M (2023). Evaluation of pea genotype PI180693 partial resistance towards aphanomyces root rot in commercial pea breeding. Frontiers in Plant Science 14:1114408. doi: 10.3389/fpls.2023.1114408

Piombo E, Guaschino M, Jensen DF, Karlsson M and Dubey M (2023).  Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes. Frontiers in Microbiology, 14:1112673. doi: 10.3389/fmicb.2023.1112673.                        

Kelbessa BG, Dubey M, Catara V, Ghadamgahi F, Ortiz R, Vetukuri RV (2022). Potential of plant growth-promoting rhizobacteria to improve crop productivity and adaptation to a changing climate CABI Reviews,  

Edoardo Piombo, Micol Guaschino, Dan Funck Jensen, Magnus Karlsson and Mukesh Dubey (2023). Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes (2023). Frontiers in Microbiology, 14:1112673.
doi: 10.3389/fmicb.2023.1112673.

Bekele Gelena Kelbessa, Mukesh Dubey, Vittoria Catara, Farideh Ghadamgahi, Rodomiro Ortiz, and Ramesh Raju Vetukuri (2023). Potential of plant growth-promoting rhizobacteria to improve crop productivity and adaptation to a changing climate. CABI Reviews,

Carol Kälin, Anna Berlin, Agnese Kolodinska Brantestam, Mukesh Dubey, Anna-Kerstin Arvidsson, Paul Riesinger, Malin Elfstrand, and Magnus Karlsson (2022). Genetic diversity of the pea root pathogen Aphanomyces euteiches in Europe. Plant Pathology, 2022, 1570-1578.

Piombo E, Vetukuri RR, Sundararajan P, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M (2022). Comparative small RNA and degradome sequencing provide new insights into antagonistic interactions in the biocontrol fungus Clonostachys rosea. Applied and Environmental Microbiology, 10.1128/aem.00643-22. 

Beatriz Gomez-Munoz, Aikaterini Efthymiou, Mukesh Dubey, Jonathan Sølve,Mette Nicolaisen, Dan F. Jensen, Ole Nybroe, John Larsen )2022). Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil. Fungal Biology, 126 (2022) 356e365.

Vahideh Rafiei, Alessandra Ruffino, Kristian Persson Hodén, Anna Tornkvist, Raimondas Mozuraitis, Mukesh Dubey, and Georgios Tzelepis (2022). A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene. Molecular Plant Pathology,  23, 291–303. h t t p s : //d o i .org/10.1111/mpp.13162.

Edoardo Piombo, Ramesh Raju Vetukuri, Anders Broberg, Pruthvi B. Kalyandurg, Sandeep Kushwaha, Dan Funck Jensen, Magnus Karlsson, and Mukesh Dubey (2021). The role of Dicer-dependent RNA interference in regulating mycoparasitic interactions. Microbiology Spectrum, 9: e01099-21.

Ramesh R. Vetukuri, Mukesh Dubey, Pruthvi B. Kalyandurg, Anders S. Carlsson, Stephen C. Whisson and Rodomiro Ortiz (2021). Spray-induced gene silencing: an innovative strategy for plant trait improvement and disease control. Crop Breeding and Applied Biotechnology, 21(S): e387921S11.

Kalyandurg PB, Sundararajan P, Dubey M, Ghadamgahi F, Zahid AM, Whisson SC, Vetukuri RR (2021). Spray-induced gene silencing as a potential tool to control potato late blight disease. Phytopathology, In Press.

Stenberg JA, Sundh I, Becher PG, Björkman C, Dubey M, Egan PA, Friberg H, Gil JF, Jensen DF, Jonsson M, Karlsson M, Khalil S, Ninkovic V, Rehermann G, Vetukuri RR, Viketoft M (2021). When is it biological control? A framework of definitions, mechanisms, and classifications. Journal of Pest Science. 10.1007/s10340-021-01354-7

Amira MB, Faize M, Karlsson M, Dubey M, Frąc M, Panek J, Fumanal B, Gousset-Dupont A, Julien J-L, Chaar H, Auguin D, Mom R, Label P, Venisse J-S (2021). Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations. Biomolecules, 11(2):338.

Mukesh Dubey, Dan Funck Jensen and Magnus karlsson (2020) Functional characterization of the AGL1 aegerolysin in the mycoparasitic fungus Trichoderma atroviride reveals a role in conidiation and antagonism. Molecular Genetics and Genomics. 296(1):131-140.

Martin Broberg#, Mukesh Dubey#, Mudassir Iqbal, Mikael Gudmundssson, Katarina Ihrmark, Hans-Josef Schroers, Dan Funck Jensen, Mikael Brandström, Durling and Magnus Karlsson (2020) Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota,
Hypocreales). Evolutionary Applications. DOI: 10.1111/eva.13134. # joint first author.

Rajiv Chaudhary, Karl Lundén, Kerstin Dalman, Mukesh Dubey,
Miguel Nemesio‑Gorriz, Bo Karlsson, Jan Stenlid1 & Malin Elfstrand (2020) Combining transcriptomics and genetic linkage based information to identify
candidate genes associated with Heterobasidion‑resistance in Norway spruce. Scientific Reports, 10: 12711.

Iqbal M, Broberg M, Haarith D, Broberg A, Bushley KE, Viketoft M, Jensen DF, Dubey M and Karlsson M. (2020) Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping. Evolutionary Applications. 13;9:2264-2283.

Dubey M, Vélëz H, Broberg A Jensen DF and Karlsson M (2020) LysM proteins regulate fungal development and contribute to hyphal protection and biocontrol traits in Clonostachys rosea. Frontiers in Microbiology, 11, 679.

Iqbal M, Dubey M, Broberg A, Viketoft M, Jensen DF and Karlsson M (2019). Deletion of the Non-Ribosomal Peptide Synthetase Gene nps1 in the Fungus Clonostachys rosea Attenuates Antagonism and Biocontrol of Plant Pathogenic Fusarium and Nematodes. Phytopathology, 109(10):1698-1709.

Martin Broberg, Mukesh Dubey, Man-Hong Sun, Katarina Ihrmark, Hans-Josef Schroers, Shi-Dong Li, Dan Funck Jensen, Mikael Brandström Durling, Magnus Karlsson (2018). Out in the cold: Identification of genomic regions associated with cold tolerance in the biocontrol fungus Clonostachys rosea through genome-wide association mapping. Frontiers in Microbiology 9:2844.

Mudassir Iqbal, Mukesh Dubey, Mikael Gudmundsson, Maria Viketoft, Dan Funck Jensen, Magnus Karlsson (2018). Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea. BMC Evolutionary Biology 18:171.  

Lea Atanasova, Mukesh Dubey, Marica Grujić, Mikael Gudmundsson, Cindy Lorenz, Mats Sandgren, Christian P. Kubicek, Dan Funck Jensen and Magnus Karlsson (2018) Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family. BMC Microbiology 18:178.

Umma Fatema, Anders Broberg, Dan Funck Jensen, Magnus Karlsson and Mukesh Dubey (2018). Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea. Scientific Reports, 8:15009.

Ruth Schmidt, Mikael B. Durling, Victor de Jager, Riya C. Menezes,
Erik Nordkvist, Aleˇs Svatoˇs, Mukesh Dubey, Lukas Lauterbach, Jeroen
S. Dickschat, Magnus Karlsson and Paolina Garbeva (2018). Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum. FEMS Microbiology Ecology, 94, 2018, fiy078.

Kristiina Nygren#, Mukesh Dubey#, Antonio Zapparata, Mudassir Iqbal, Georgios D. Tzelepis, Mikael Brandström Durling, Dan Funck Jensen, Magnus Karlsson (2018). The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey. Evolutionary Applications, 11:931-949. #joint first author.

Iqbal M, Dubey M, McEwan K, Menzel U, Andersson Franko M, Viketoft M, Funck Jensen D, Karlsson M. (2018). Evaluation of Clonostachys rosea for control of plant-parasitic nematodes in soil and in roots of carrot and wheat. Phytopathology, 108(1):52-59.

Dubey MK, Jensen DF and Karlsson M (2016). The ABC transporter ABCG29 is involved in H2O2 tolerance and biocontrol traits in the fungus Clonostachys rosea. Molecular Genetics and Genomics 291, 677–686.

Kamou NN, Dubey M, Tzelepis G, Menexes G, Papadakis EN, Karlsson M, Lagopodi AL, and Jensen DF (2016). Investigating the compatibility of the biocontrol agent Clonostachys rosea IK726 with prodigiosin‑producing Serratia rubidaea S55 and henazine‑producing Pseudomonas chlororaphis ToZa7. Archives of Microbiology, 198, 369–377.

Tzelepis G, Dubey, MK, Jensen DF, Karlsson M (2015). Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea. Microbiology 61,1407-1419.

Karlsson M, Durling MB, Choi J, Kosawang C, Lackner G, Tzelepis GD, Nygren K, Dubey MK, Kamou N, Levasseur A, Zapparata A, Wang J, Amby DB, Jensen B, Sarrocco S, Panteris E, Lagopodi AL, Pöggeler S, Vannacci G, Collinge DB, Hoffmeister D, Henrissat B, Lee YH, Jensen DF (2015). Insights on the Evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biology and Evolution 7, 465-480.

Tzelepis, G., Akira Hosomi, A., Hossain, T.J., Hirayama, H., Dubey, M., Jensen, D.F., Suzuki, T., Karlsson, M. (2014). Endo-b-N-acetylglucosamidases (ENGases) in the fungus Trichoderma atroviride: Possible involvement of the filamentous fungi-specific cytosolic ENGase in the ERAD process. Biochemical and Biophysical Research Communications 449, 256-261.

Dubey, M.K., Jensen, D.F. and Karlsson M. (2014). Involvement of an ATP-binding cassette pleotropic drug transporter in xenobiotic tolerance and antagonism in fungal biocontrol agent Clonostachys rosea IK726. Molecular Plant-Microbe Interaction.

Dubey, M.K., Jensen, D.F. and Karlsson M. (2014). The hydrophobins are required for conidial hydrophobicity and plant root colonization in fungal biocontrol agent Clonostachys rosea. BMC Microbiology, 14, 18.

Dubey, M.K., Broberg, A., Jensen, D.F. and Karlsson M. (2013). Role of the methylcitrate cycle in growth, antagonism and induction of systemic defence responses in the fungal biocontrol agent Trichoderma atroviride. Microbiology, 159, 2492-2500.

Dubey, M.K., Broberg, A., Sooriyaarachchi, S., Ubhayasekera, W., Jensen, D.F. and Karlsson M. (2013). The glyoxylate cycle is involved in pleotropic phenotypes, antagonism and induction of plant defence responses in the fungal biocontrol agent Trichoderma atroviride. Fungal Genetics and Biology, 58-59, 33-41.

Dubey, M.K., Ubhayasekera, W., Sandgren, M., Jensen, D.F. and Karlsson M. (2012): Disruption of the Eng18B ENGase gene in the fungal biocontrol agent Trichoderma atroviride affects growth, conidiation and antagonistic ability. PLoS ONE 7(5): e36152.

Book Chapters

Piombo, E., Dubey, M. (July 2022). Computational Analysis of HTS Data and Its Application in Plant Pathology. In: Luchi, N. (eds) Plant Pathology. Methods in Molecular Biology, vol 2536. Humana, New York, NY.

Jensen DF, Dubey M, Jensen B, and Karlsson, M (November 2021). Clonostachys rosea for the control of plant diseases, in Microbial bioprotectants for plant disease management (BDS Publishing). In: Köhl, J. and Ravensberg, W. (ed.), Microbial bioprotectants for plant disease management, Burleigh Dodds Science Publishing


Researcher at the Department of Forest Mycology and Plant Pathology; Division of Plant Pathology
Telephone: +4618-671540
Postal address:
Skoglig mykologi och växtpatologi , Box 7026
750 07 UPPSALA
Visiting address: Almas Allé 5, Uppsala