Research Overview

Using bioinformatics, I integrate across -omics approaches to address eco-evolutionary questions related to microbe-microbe, microbe-host and microbe-environment interactions. I work with a variety of research systems ranging from sea to summit and I am particularly drawn to projects involving questions about symbiosis, biogeography, land-to-sea transitions, community assembly, and characterization of understudied lineages (e.g. marine fungi).

Photo of seagrass

Environmental drivers of the seagrass microbiome

A series of projects investigating the potential biotic and abiotic drivers of microbiome assembly in seagrass beds including observing (1) differences across locations within a seagrass patch, (2) differences related to proximity to a marina and (3) succession during ammonification.

Photo of Cassie holding a core containing seagrass; Photo credit: Katy Dynarski

Seagrass-associated fungi

Not a lot is known about the diversity of marine fungi or what role fungi might play in associations with marine plants. This project seeks to survey the taxonomic and functional diversity of seagrass associated fungi and to determine the evolutionary and ecological importance of these associations.

Photo of CA wildflowers; Photo credit: Andrew Latimer

Grassland plant microbiomes

I am collaborating with Dr. Marina LaForgia, a postdoc at UC Davis, to study below-ground plant-microbe feedback loops during competition between native wildflowers and invasive grass species in California grasslands across varying precipitation regimes.

Photo of a crab

Land crab microbiomes

I am collaborating with Dr. Victoria Watson-Zink, a postdoc at Stanford University, to study the gut microbiomes of crabs across a gradient of terrestriality. We are interested in looking for patterns of co-evolution and convergent evolution in the gut microbiomes of land crabs.

Photo of phoronids taken by Ken-ichi Ueda; https://www.flickr.com/photos/ken-ichi/

Phoronid microbiomes

Phoronids are a tiny (~12 species) phyla of marine invertebrates that live inside protective chitinous tubes in the sediment. We sampled phoronids found inside and outside of seagrass beds to investigate their microbiome.

Photo of glassy-winged sharpshooter taken by Beatriz Vindiola

Glassy-winged Sharpshooter

The glassy-winged sharpshooter is a xylem feeding leafhopper, invasive to California and an important agricultural pest. We are working on genome improvements, as well as investigating mechanisms that might lead to insecticide resistance.

Photo of Arkashin Shurf, Kamchatka, Russia taken by Russell Neches; https://www.flickr.com/photos/rneches/

Miscellaneous projects

These are one-off projects. Currently these include (1) recovery of metagenome-assembled genomes (MAGs) from hot springs in Kamchatka, Russia and (2) MAGs from aquariums.

Recent publications

Grasses may alter wildflower microbiomes

Our paper, "Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome", is now published.

Improved genome for Glassy-winged Sharpshooter

Our manuscript decribing our genome improvement efforts, " Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce’s disease" is now out in G3 Genes|Genomes|Genetics.

Global biogeography of the eelgrass mycobiome

Our new paper "Global diversity and biogeography of the Zostera marina mycobiome" is now accepted in AEM.