Research Overview
Using bioinformatics, I integrate across -omics approaches to address questions related to microbe-microbe, microbe-host and microbe-environment interactions. I have expertise working with a variety of research systems ranging from sea to summit and with projects addressing questions about symbiosis, biogeography, community assembly, animal health, and characterization of understudied fungal lineages.
Poultry biosurveillance
At Barnwell Bio, we use metagenomics to analyze environmental samples from poultry production systems, enabling early detection of pathogens and dysbiosis.
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.
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 work sought to survey the taxonomic and functional diversity of seagrass associated fungi and to determine the evolutionary and ecological importance of these associations.
Grassland plant microbiomes
In collaboration with Dr. Marina LaForgia, we studied below-ground plant-microbe feedback loops during competition between native wildflowers and invasive grass species in California grasslands across varying precipitation regimes.
Land crab microbiomes
In collaboration with Dr. Victoria Watson-Zink, we studied the gut microbiomes of crabs across a gradient of terrestriality. We looked for patterns of co-evolution and convergent evolution in the gut microbiomes of land crabs.
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.
Glassy-winged Sharpshooter
The glassy-winged sharpshooter is a xylem feeding leafhopper, invasive to California and an important agricultural pest. We worked on genome improvements, as well as investigating mechanisms that might lead to insecticide resistance.
Insect-associated fungi
Fungi have important roles as insect pathogens and symbionts. Using -omics, we worked to understand the biology behind complicated insect-microbe interactions.
Viruses from extreme environments
Viruses are some of the most prevalent entities on our planet, yet we know relatively little about their diversity. We searched metagenomic data from extreme environments to generate viral catalogs for future ecological work.
Miscellaneous projects
Currently these include (1) recovery of metagenome-assembled genomes (MAGs) from hot springs in Russia and (2) MAGs from aquariums, and (3) genomics of plant-associated bacteria.
Select publications
Environmental biosurveillance in commercial poultry
Our review, "Beyond clinical signs: the case for continuous environmental biosurveillance in commercial poultry production", is now published in Poultry Science.
Metagenomic insight into seagrass-associated fungi
Our paper, "Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales", is published in Microbial Genomics.
Unravelling the evolutionary patterns of symbiosis
Our latest work, "Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives" is out in Aquatic Botany.