Soil is an incredibly important for environmental health and plant health and productivity. Soil is arguably the most diverse ecosystem on the planet exhibiting an amazing array of unknown microbes. Our lab uses nucleotide sequencing techniques and other methods to characterize both taxonomy and functional diversity of microbes in soil. We work with both bacterial and fungal species and use computational methods to extract genomic information from metagenomic and metatranscriptomic sequencing data.


The overall health of plants and their is influenced by microbes, which can be pathogens, mutualists, and commensal organisms. Some microbes may be a pathogen on one plant and a mutualist on another. How are these associations regulated and what is the mode of interaction between plant host and microbe. We use metagenomics, metatranscriptomics, and metaproteomic approaches to address these relationships. Our goal is to understand the mechanisms that regulate plant-associated microbial communities.


Using genome sequencing techniques, we are inspecting the taxonomic and functional diversity from single sequenced genomes and genomes assembled from mixed metagenomic reads. Using these genomes, we’re investigating the role of the pan-genome, including core and accessory genes, in symbiotic and pathogenic relationships with hosts. Candidate genes for these roles include effectors and other small secreted proteins.


We’re investigating the diversity of both ecomycorrhizal and arbuscular mycorrhizal fungi in relation with host plants. This diversity is inferred from molecular and morphological characters, as well as community level diversity through amplicon sequencing and longer contigs and scaffolds acquired from metagenome assembly techniques. We have initiated field, greenhouse, and growth chamber studies to understand these symbioses.