**The AGA grants EECG Research Awards each year to graduate and post-doctoral researchers who are at a critical point in their research, where additional funds would allow them to conclude their research project and prepare it for publication. EECG awardees also get the opportunity to hone their science communication and write three posts over their grant tenure for the AGA Blog. In the first in the series, our EECG awardees write about their research and their interests as an ’embarkation’.
About the Author: María Torres-Sánchez is a postdoctoral researcher currently working in the Longo Lab at the University of Florida on the host-pathogen interactions with amphibian species and pathogenic chytrid fungi. As an early career evolutionary biologist, she is broadly interested in the mechanisms that underlie biodiversity and its evolution, especially in amphibians. Her research focuses on the study of selection and adaptation processes, mainly through the analysis of genetic variation and functional genomics. She is fond of observing nature, especially herpetofauna, including birds. Follow María on Twitter @TorresSanchezM and ResearchGate.
Chytridiomycosis is an emerging infectious disease caused by chytrid fungi, and it has decimated amphibian populations worldwide mainly due to the spread of a hypervirulent lineage (Batrachochytrium dendrobatidis Global Panzootic Lineage, Bd GPL) (Scheele et al., 2019; Fisher and Garner, 2020). Amphibian pathogenic chytrids colonize host skin and can severely alter its function and structure, resulting in animal mortality (Van Rooij et al., 2015). Despite this, the response to chytrid fungal outbreaks is highly variable, consequently, it remains unclear how some populations recover and stabilize while others face extinction. Amphibians with intraspecific variation to Bd infection are ideal models to explore the chytridiomycosis triangle, and investigate if host resistance arises from plasticity and co-adaptation processes. Among the amphibian species with variable response to Bd infection is the common coquí frog (Eleutherodactylus coqui), a tree frog endemic to Puerto Rico (Figure 1). This direct-developing frog exhibits disease cycles modulated by different factors (e.g., skin microbial communities) but, mainly, influenced by seasonal environmental conditions (Longo et al., 2015; Longo and Zamudio, 2016). During the warm-wet season, frogs withstand Bd infection, whereas a high percentage of infected frogs (50-60%) die during the cool-dry season. It has been hypothesized that host immunity is suppressed in this adverse season, however, this hypothesis has not been fully tested. Thus, the resistance mechanisms of coquí frogs between seasons and within the cool-dry season remain poorly understood.
We are studying the common coquí-Bd system through the lens of genomics to disentangle the dynamics of this specific chytridiomycosis triangle. Using samples from individuals in a mesocosm infection experiment (Longo and Zamudio, 2016), we extracted DNA (from liver) and RNA (from skin and spleen) to both describe host genetic variation and investigate changes in gene expression profiles across seasons and infection status. We examined the role of genetic variation in disease outcome and uncovered evidence of adaptation using Genotyping by Sequencing. We identified single nucleotide polymorphisms (SNPs) associated to frogs’ initial Bd load and to the infection recovery. Now, we are applying Dual RNA-Seq (Westermann et al., 2012) to quantify differences in gene expression between seasons on both the frog and Bd. Our preliminary results did not show a clear distinction of Bd gene expression between seasons, however we found evidence of potential Bd interference mechanisms on the coquí gene expression pattern. These results suggest that Bd thermal optima (17-25°C) is not affected by seasonal changes, but this climate stress in conjunction with Bd infection might imperil the frog defense responses. We are analyzing the host transcripts to address this question.
To complement our multi-omics approach, we propose an epigenomic experiment to determine if common coquí frogs integrate infection responses into their genomes and respond differently depending on seasonal conditions (Figure 2). We hypothesize that survival to Bd infection during the favorable warm-wet season will induce a protective mechanism whereby frogs would be better suited and equipped to fight Bd later during the cool-dry season. As a consequence, these individuals would have a higher survival probability. We speculate that this mechanism can be driven by DNA methylation processes that control gene expression through epigenetic switch and memory (Flores et al., 2013). We expect to find hypomethylation in upstream control regions (CpG islands) of candidate defense genes (identified in our transcriptomic study) in skin cells after sloughing. These epigenetic changes will allow them to overcome Bd infection during the following seasons.
Our findings will offer a mechanistic explanation to the intraspecific variation in disease response in amphibians persisting with enzootic infections. By combining the data of our Omics studies, we will provide an evolutionary framework to interrogate the Chytridiomycosis triangle that could be applied to any amphibian-chytrid system. At the same time, we will broaden our understanding of declines and persistence of amphibian populations especially in the Americas and the Caribbean, where many species with similar traits have faced extinction due to Bd emergence (Scheele et al., 2019).
Currently, we are planning our field season for this summer 2021 in Puerto Rico. Please, stay tuned!
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