Chaverri Research Lab

The Chaverri Research Lab focuses on phytobiomes (plant microbiomes) from wild relatives of economically important crops, understanding their function in natural ecosystems, and the implications for agriculture and conservation. More specifically, we are interested in the role fungi play in natural and agricultural systems. Our research uses multidisciplinary and hierarchical approaches, such as systematics, phylogenetics, evolution, ecology, plant pathology, genomics, and metabolomics, including observational and experimental.


Phytobiomes of coffee plants and their relatives

Coffee crops are being affected like never before by climate change, pests, and diseases. Coffee is mostly produced by low-income countries and small farm holders. Currently, the largest consuming regions (e.g., USA and Europe) are demanding more environmentally friendly agricultural products. This new demand has become challenging for producing countries because the transition from conventional to organic agricultural may be costly and the alternatives based on sound science are limited.

The research in our lab focuses on using the natural microbiota from wild relatives of coffee plants (the family Rubiaceae) in the tropics to search for alternatives to pesticides. More specifically, we are studying the endophytobiome (microorganisms that live inside the healthy tissues of plants; a.k.a. endophytes). We use systematics, genomic and metabolomic tools to predict which endophytic fungi will be able to protect coffee plants against diseases and drought, and at the same time, promote the plant’s growth (biofertilizer, biostimulant, biofungicide). We also apply these fungi to coffee seedlings. This approach is considered by some as analogous to the use of probiotics in humans, as these endophytic fungi improve the plant’s immunity. This ongoing and long-term project is a collaboration with scientists at the University of Costa Rica and the coffee co-op Coopetarrazu, both in Costa Rica. 

Diversity of mycoviruses in fungal endophytes and their cryptic roles in plant health

Microbes are ubiquitous and associated with almost all living organisms. The associations or interactions microbes have with their hosts may range from beneficial to detrimental, and may be direct or indirect. However, considering that there are trillions of microorganisms on Earth, much of that diversity and interactions are unknown. A poorly studied group are viruses. The objective of this project is to begin to discover the diversity of viruses that inhabit fungi (a.k.a. mycoviruses) that live inside plants, the effects of mycoviruses on those fungi, and the indirect interactions and consequences on the plant hosts. One hypothesis of the study is that those mycoviruses serve as an “invisibility cloak”, so that the fungus can penetrate the plant without activating the plant defenses. The project will focus on beneficial and pathogenic fungi that inhabit coffee plants. While some mycoviruses may make a fungus more pathogenic on its plant host, others may make them less pathogenic (=hypovirulent mycoviruses), thus having potential applications in the engineering of those fungi to benefit crops. Plant pathology, mycology, virology, metagenomics, metatranscriptomics, and bioinformatics tools will be used in this project. Collaborators in this project are Dr. James Culver (University of Maryland), Dr. David Paez-Espino (Ancilia Biosciences), and Dr. Max Chavarría (University of Costa Rica and CENIBiot). This project is funded by U.S. National Science Foundation.

The microbiome of two species of sloths in Costa Rica

We are studying the gut microbiome in two-toed (Choloepus hoffmani) and three-toed (Bradypus variegatus) sloths in Costa Rica. The objective of this research is to determine the role microorganisms play in the digestion of plant material. We are using shotgun and targeted amplicon metagenomics, metatranscriptomics, and lignocellulolytic assays to answer our interrogations. This project is a collaboration with scientists at University of Costa Rica and the National Center for Biotechnological Innovations (CeNIBiot; Costa Rica).

Biodegradation of Polychlorinated Biphenyls (PCBs) using fungi

PCBs are prevalent toxic chemicals used in many industrial and commercial applications such as electrical, heat transfer and hydraulic equipment; plasticizers in paints, plastics and rubber products; and pigments, dyes and carbonless copy paper; among others. PCBs have been linked to serious health effects such as cancer and damages to the immune system, reproductive system, nervous system, and endocrine system, among others. In this project we are characterizing fungi from Maryland and assessing their tolerance to PCBs and bioremoval/bioremediation potential. This project is a collaboration with Dr. Birthe Veno Kjellerup (Department of Civil and Environmental Engineering, University of Maryland, College Park, MD).

Chaverri lab members and Course-based Undergraduate
Research Experience students, spring 2024

Current Lab Members

We are always interested in motivated undergraduate, MSc students, and postdocs who want to join the group! Please contact Dr. Chaverri if you are interested in joining!

Abolfazl DadkhanhtehraniDr. Abolfazl Dadkhahtehrani
Visiting Scientist




 Michal Belle
Undergraduate Research Assistant
Biology major

Michal is mostly working with mycoviruses of endophytic fungi.



 Natasha Goldson
Undergraduate Research Assistant
Biology major

Natasha is working with various projects, including plant pathogenic fungi and mycoviruses. She also is the Teaching Assistant for Microbiology I BIOL309 in the spring of 2024.


Former Lab Members

Former Teaching Assistants

  • Cameryn DuBose
  • Rayjeanna Ennis
  • TyNiah Dates

Former MSc student

  • Keona Smith (rotating student for ABMB MSc program)