Tree Microbiomes

The microbial communities inside living trees are largely undescribed and unexplored. I am developing methods for tree microbiome analysis, investigating microbial communities and diversity inside trees, and measuring the effects of tree-dwelling microbes on ecosystem processes such as methane uptake and release.

Developing methods for wood microbial analysis

There is no standard method to extract or analyze microbial DNA from wood tissues in living trees. In order to enable analyis of methane-cycling communities and the larger tree microbiome, we have tested and refined methods that allow the isolation of microbial DNA from wood tissues, amplicon sequencing (16S and ITS), and quantification (ddPCR).

A methods paper is in review and a preprint is available here: 

A Method for Sampling the Living Wood Microbiome

Searching for methane-cycling microbes in tree stems

There remains substantial debate about the sources of methane emitted from tree stems (plant vs. soil origin, and plant vs. microbial production). We are quantifying the prevalence and abundance of methanogens and methanotrophs inhabiting living trees, and investigating the relationships of these communities to observed tree-mediated methane emissions.

Exploring the cross-domain microbiome of living trees

Although root- and leaf-associated microbial communities have received substantial attention, we know very little about the non-pathogenic microbial communities that inhabit living trees. We are using genomic tools to understand the structure and diversity of bacterial, archaeal, and fungal communities across tree organs and species in temperate forests.