Mark Paul Rivarez

Balik Scientist, Philippine Genome Center–Visayas and University of the Philippines Visayas, funded by the Department of Science and Technology – Philippine Council for Health Research and Development; Philippines, 2024 

Postdoctoral Research Scholar, Department of Entomology and Plant Pathology, North Carolina State University; USA, 2023 

Balik Scientist, Caraga State University, funded by the Department of Science and Technology – Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development; Philippines, 2022 

Doctoral (Doctor of Science program), National Institute of Biology and Jožef Stefan International Postgraduate School; Slovenia, 2019-2022;  

Secondments: (1) Abiopep, S.L. and Center for Edaphology and Applied Biology of Segura (CEBAS)–CSIC; Murcia, Spain and (2) French National Research Institute for Agriculture, Food and the Environment (INRAE); Bordeaux, France 

Predoctoral (Young Researcher Scholarship program), Institute of Integrative Systems Biology, Spanish National Research Council – University of Valencia; Spain, 2019 

Masters (Master of Science program, major in Plant Pathology, minor in Plant Breeding), University of the Philippines and Institute of Plant Breeding; Philippines, 2015-2018 

Instructor of Plant Pathology and Agricultural Biotechnology, University of the Philippines; Philippines, 2014-2018 

Bachelors (Bachelor of Science program in Agricultural Biotechnology), magna cum laude, University of the Philippines and International Rice Research Institute; Philippines, 2010-2014 

At the Phytopathology + Virology (PPV) Laboratory, led by Dr. Mark Paul Rivarez, we study phytopathogens and viruses beginning in the field, where we diagnose plant diseases and collect diverse samples from crops, arthropods, wild plants or weeds, and the environment (soil and/or water). Our findings are further investigated under controlled conditions in greenhouses or growth chambers – to explore microbes’ biological properties and possible ecological and beneficial roles. Subsequent molecular diagnostics and high-throughput sequencing are performed in the ‘wet’ lab, generating vast datasets that are then processed and interpreted using bioinformatics tools, data mining, and artificial intelligence (AI)-based modeling approaches in the ‘dry’ lab.  

This integrated approach, from field observations to computational analysis, allows us to explore phytopathogen and virus diversity, predict disease emergence and spread, and develop sustainable strategies to protect plant health. 

Our Research Themes: 

(Note: asterisk (*) means Greenhouse or Growth Chambers) 

1.  AgroViroMics Research (Exploration of Agroecosystem Viromes and Microbiomes (discovery and ecological approach))  

Research Goal: To uncover diversity and reservoirs of viruses (and other pathogenic or beneficial microbes) in crops, wild or native/indigenous plants, arthropods, and environment within and at the interface of wild and cultivated agroecosystems in association with disease dynamics using high-throughput sequencing (HTS). 

Work Mode (estimate): Field (30%), GH/GC* (10%), Wet Lab (30%), Dry Lab (30%) 

Techniques: field survey and disease diagnostics, molecular diagnostics, high-throughput sequencing (HTS), bioinformatics 

Publication for reference: In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. Microbiome 11:60. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01500-6 

2.  PhyloEcology Research (Predictive studies on virus evolution and epidemiology using Phylogenetics and Ecological approaches) 

Research Goal:  To proactively track global distribution and spread, host range expansion, and discover new ecological niche of viruses by employing exa-scale datamining of global sequencing databases, and subsequently, examine relationships of host-virus coevolutionary history and their ecology to better predict possible host range expansion, spread, or emergence of detected viruses. 

Work Mode (estimate): Field (0%), GH/GC* (0%), Wet Lab (30%), Dry Lab (70%) 

Techniques: high-throughput sequencing (HTS), bioinformatics, exa-scale datamining, AI-based modeling 

Publication for reference: Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse plants and global sequencing data. Phytopathology® 113:1729-1744. https://apsjournals.apsnet.org/doi/10.1094/PHYTO-12-22-0465-V 

3.  PhytoGuard Research (Sustainable solutions to guard plant health, e.g. biological control for plant pathogens, plant probiotics and stimulants, etc.) 

Research Goal:  To characterize the pathobiological properties or potential beneficial ecological roles of viruses and other microbes from agroecosystems to enhance risk assessment and mitigation strategies for pandemic preparedness. 

Work Mode (estimate): Field (20%), GH/GC* (40%), Wet Lab (30%), Dry Lab (10%) 

Techniques: field survey and disease diagnostics, molecular diagnostics, biological and GH/GC* assays, bioinformatics 

Publication for reference: Influence of native endophytic bacteria on the growth and bacterial crown rot tolerance of papaya (Carica papaya). European Journal of Plant Pathology 161. https://doi.org/10.1007/s10658-021-02345-1 

Interested in becoming a virus hunter or pathogen hunter? Join Us!  

We welcome students and researchers at all levels from high school, undergraduate (Bachelors) to graduate (Masters or PhD), and Postdocs or Visiting Scientists, within and outside UBC or Canada. Our research can be interdisciplinary thus, we likewise welcome students from the computing sciences, chemistry, physics, and engineering.  

Please contact Dr. Mark Paul Rivarez at paul.rivarez@ubc.ca for more information on how you could be a part of our vibrant and diverse team, including information on scholarships and funding opportunities. 

For a full list of publications, visit: Google Scholar.

Note: * co-first authors 

^# (co-)corresponding author(s) 

Rivarez MPS^#, Pecman A, Bačnik K, Carvalho Ferreira OM, Vučurović A, Seljak G, Mehle N, Gutiérrez-Aguirre I, Ravnikar M, Kutnjak D^#. 2023. In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. Microbiome 11:60. [LINK]. 

Rivarez MPS^#, Faure C, Svanella-D. L, Pecman A, Tušek-Ž. M, Schönegger D, De Jonghe K, Blouin A, Rasmussen DA, Massart S, Ravnikar M, Kutnjak D, Marais A, Candresse T^#. 2023. Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse plants and global sequencing data. Phytopathology® 113:1729-1744. [LINK]. 

Fontdevila N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Fox A, Marais A, Trontin C, Kutnjak D, Petter F, Selmi I, Ravnikar M, Botermans M, Aranda M, Boonham N, Tahzima R, Candresse T, Wetzel T, Hernando T, Massart S. 2023. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Frontiers in Microbiology 14. [LINK] 

Ferreira OM^#, Bačnik K, Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Gutiérrez-Aguirre I, Kutnjak D^#. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems. Water Research (accepted for publication). [LINK] 

Rivarez MPS, Kogej Z, Jakoš N, Pecman A, Seljak G, Vučurović A, Mehle N, Ravnikar M, Kutnjak D^#. 2022. First report of Ranunculus white mottle ophiovirus in Slovenia in pepper with yellow leaf curling symptom and in tomato. Plant Disease 106. [LINK] 

Temple C, Blouin A, De Jonghe K, Foucart Y, Gentit P, Botermans M, Westenberg M, Schoen R, Gentit P, Visage M, Verdin E, Wipf-S. C, Ziebell H, Gaafar YZ, Zia A, Yan XH, Richert-P. KR, Ulrich R, Rivarez MPS, Kutnjak D, Vučurović A, Massart S. 2022. Biological and genetic characterization of Physostegia chlorotic mottle virus in Europe through host range, location, and time. Plant Disease 106. [LINK] 

Rivarez MPS, Vućurovič A, Mehle N, Ravnikar M, Kutnjak D^#. 2021. Global advances in tomato virome research: current status and the impact of high-throughput sequencing. Frontiers in Microbiology 12. [LINK] 

Rivarez MPS^#, Parac EP, Dimasingkil SF, Magdalita PM. 2021. Influence of native endophytic bacteria on the growth and bacterial crown rot tolerance of papaya (Carica papaya). European Journal of Plant Pathology 161. [LINK] 

Butković A, González R, Rivarez MPS, Elena SF. 2021. A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in their evolutionary history and degree of host specialization. Virus Evolution 7. [LINK] 

González R, Butković, A, Rivarez MPS, Elena SF. 2020. Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development. Scientific Reports 10. [LINK] 

Balik Scientist Program Awardee of the Department of Science and Technology (DOST), Philippines, 2022 and 2024 

Marie Sklodowska Curie Actions (MSCA) Doctoral Fellow and Early Career Researcher at the National Institute of Biology, Slovenia, 2019-2022 

Becas Jovenes Investigadores (Young Researcher Scholarship) Awardee at the University of Valencia, Spain, 2019 

Member, European Virus Bioinformatics Center. Profile: https://evbc.uni-jena.de/members/paul-rivarez/