This research is funded by the USDA-NIFA via the NSF-NIH-USDA joint program in Ecology and Evolution of Infectious Diseases.


 Our overarching research theme is plant disease ecology, chiefly from a community ecology perspective. For example, it has been suggested that some individuals have a microbiome that protects them against infection by pathogens. Working with plant leaves, we can do experiments to test whether this is the case, and if it is, then determine how this protective function of the microbiome operates. The leaf microbiome is dominated by fungi, and accordingly our work incorporates fungal species that range from pathogens to mutualists of the plant. To better understand microbial diversity and interactions within leaves, we are employing high-throughput genomic sequencing approaches as well as field experiments, greenhouse experiments, field surveys, and mathematical models. Our research integrates across levels of biological organization, from the organism to the landscape.

               Fungal Pathogen, Rhizoctonia, presenting symptoms in host, tall fescue (photo: B. Joyner)

About our current project  

      A major frontier in disease ecology is the role of hosts’ non-pathogen symbionts, including commensals and mutualists. Available ecological theory, considered together with mechanistic studies, strongly predict that the species composition of a host’s microbiome will influence the role of that host in pathogen transmission. Yet, this nexus between the microbiome and parasite transmission remains an open frontier for research. To advance on this frontier, we are investigating whether and how interactions among pathogens and mutualists within host individuals (i.e. within the microbiome) scale up to influence pathogen transmission dynamics across the host population. This project takes a mechanistic experimental approach, leveraging a growing ecological and evolutionary model system (the widespread grass tall fescue and its defensive symbiont, the fungal endophyte Epichloë coenophiala). As well as the endophyte, the grass host is commonly coinfected by multiple diverse species of fungal pathogens. Our goal is to characterize the linkage between microbial interactions within host individuals and pathogen transmission dynamics across the host population. We hypothesize that a key component of this linkage is heterogeneity among pathogen individuals. To quantify how such heterogeneity links microbial interactions to transmission rates, we are integrating diverse approaches ranging from field experiments manipulating the composition of the microbiome to transcriptomic analysis of pathogen individuals. This project is in collaboration with a multidisciplinary team with expertise in not only disease ecology, but also fungal biology, theoretical ecology, and evolutionary biology.

A field mesocosm experiment is created using “kiddie pools” (photo: B. Joyner)

Our prior projects include:

The community ecology of viral pathogens – Causes and consequences of coinfection in hosts and vectors

Predicting disease risk from community context and host phenotype: a trait-based approach

The role of pathogens in competition between introduced and native grasses

Joint effects of global change and biological invasions on insect-vectored generalist pathogens

Feedbacks between host community structure and pathogen spread

Microbial plant pathogens as modulators of global change

Host species, tall fescue, in flower (photo: B. Joyner)