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 was previously no standard method to extract or analyze microbial DNA from wood tissues in living trees. In order to enable analysis 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).
Our methods paper, which enabled the work below, is available in Methods in Ecology & Evolution:
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. I use genomic tools to understand the structure and diversity of bacterial, archaeal, and fungal communities across organs and species of forest trees., and particularly the microbiome of the wood of living trees—Earth's largest biomass reservoir
Our work has revealed that a single tree can harbor approximately a trillion microbes in its internal aboveground tissues alone, with distinct microbial communities in the heartwood and sapwood. These communities are largely unique to the tree's internal environment and differ markedly from those in other plant tissues and surrounding ecosystems. Notably, the heartwood is a unique ecological niche, hosting specialized archaea and anaerobic bacteria that drive important biogeochemical processes such as methanogenesis and nitrogen fixation. This new frontier in environmental microbiology oresebts many potential opportunities to discover unknown dimensions of biodiversity and its consequences for environmental and ecological health.
A preprint detailing our work is available on BioRxiv (manuscript currently in review): A diverse and distinct microbiome inside living trees.
This work was covered in Science: More than 1 trillion microbes live inside the average tree trunk
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, exploring their role in tree microbial communities, and investigating the relationships of these communities to observed tree-mediated methane emissions.
