Microbiome in Plant Virus Infections
Plant viruses are a significant threat to global food security, causing substantial yield losses and economic impacts. Many plant viruses are disseminated by insect vectors, mainly by aphids and planthoppers. The changing climate fosters an increase in insect-transmitted disease outbreaks due to their increased population growth and number of vector generations per year during the longer vegetation periods. The climate change effect has been amplified by a recent EU regulation prohibiting and reducing the outdoor chemical pesticide compounds for growing sustainable and healthy food. Therefore, there is a need for new mitigation measures to reduce the range and economic impact of plant virus outbreaks. An increasing number of studies indicates that plant microbiome may provide protection against virus infections or reduce the severity of infection by changing the plant metabolism.
The general goal of the study is to achieve an understanding of the biology of tritrophic interactions between plants, their endophytes and viruses, particularly with respect to pathogenesis and symbiosis in order to predict and mitigate disease impacts. The objectives of the research project are to understand the differences between the microbiomes of infected and healthy plants in the context of studied viral disease; what are the key microorganisms supporting plant health; how these microbes or their consortia change the plant transcriptome and metabolome; and how the to initiate the assembly of supportive microbiome. Our recent studies have been focused on cereal viruses. Thus, the preferred research subject will be virus diseases of cereal crops, e.g. yellow dwarfing of cereals caused by cereal/barley yellow dwarf viruses, or wheat dwarfing caused by wheat dwarf virus.
The techniques used during the research project will include microbial isolation, cultivation and characterization, extraction of nucleic acids, preparation of sequencing libraries, analysis of the bioinformatic data, the statistical analyses, laboratory experiments with microbiome assembly and virus transmission using insect vectors.
Merike Sõmera (ORCID ID: 0000-0001-9316-0481) is a senior researcher at the Department of Chemistry and Biotechnology, Tallinn University of Technology (TalTech), Estonia. During her PhD, she studied sobemoviruses. Later, she focused on viruses infecting cereal crops and their insect vectors. She has been a guest researcher at the Swedish University of Agricultural Sciences in Uppsala, and at Gembloux, University of Liège in Belgium. She has been involved in the working groups of plant health and virology in several international organizations and networks. Her work bridges the gaps between plant virology, molecular biology and ecology. In addition to the experimental work, she conducts field surveys and utilizes high-throughput sequencing technologies (HTS) to uncover and identify plant viruses. Through this research, she aims to expand the understanding of virus-host interactions, with the potential to improve crop protection and agricultural management practices. Currently, she has one PhD student under supervision (with expected graduation at the end of 2025). She is starting a new research group at TalTech for the studies on plant microbiome role in plant virus infections.
Current research focus: virology, microbiology, crop disease, insect vector, virus transmission
Number of Publications: 31
Key Funding: EUPHRESCO project "Diagnosis and epidemiology of viruses infecting cereal crops"
Awards, memberships: Chair of SG Solemoviridae and Member of Spinareoviridae SG at the ICTV; Plant Health national contact person for EFSA and EPSO; EUPHRESCO scientist of the month: June 2024
Sébastien Massart (ORCID ID: 0000-0002-7153-737X) is a Full Professor of Plant Pathology and Biotechnology at Gembloux Agro-Bio Tech, the Faculty of Bioengineering at the University of Liège, Belgium. His research focuses on plant pathogen diagnostics, plant virus epidemiology and ecology, and plant–microbiota interactions. He has been working with high-throughput sequencing (HTS) technologies for 17 years—initially for research and progressively extending their application to diagnostics. He views research as a collaborative effort mobilizing a network of colleagues and has participated in numerous international projects. He is the co-author of 163 peer-reviewed scientific publications. He has supervised 16 PhD students, and 7 are currently under supervision.
Inga Sarand (ORCID ID: 0000-0002-9517-8965) is a microbiologist currently serving as an Associate Professor at the Department of Chemistry and Biotechnology. With a broad expertise across various fields of microbiology, she has specialized in food microbiology in recent years. Her extensive background provides a solid foundation for her current research, where she focuses on characterizing microbial diversity, stability, and adaptation mechanisms within different food microbiomes, particularly in relation to food quality, safety, and fermentation. Inga also actively contributes to teaching microbiology, bacterial genetics, food microbiology, and hygiene, mentoring the next generation of scientists in these fields. Inga Sarand has supervised 2 PhD students, 4 are under supervision.
University degree (M.Sc.) in microbiology, plant pathology, or a related field, and a keen interest in bioinformatics. Experience with sterile methods and basic molecular methods are necessary. Prior experience in rhizospheric or plant microbiome isolation and characterization by metabarcoding/metagenomics is an advantage. We value accountability and reliability and seek a candidate who is motivated to acquire new skills. The applicant should be curious, self-driven and able to work effectively independently and in a team environment. Good English oral and written communication skills are mandatory.