Forest trees like the ones in the picture above—an ancient limber pine growing at high elevation in the Rocky Mountains, Colorado—are worlds of ‘hidden’ symbiotic bacteria. Most if not all plants and animals form symbioses with microbes that are essential to their health, yet little is known about the role of such microbes—or microbiomes—especially in natural host populations. Bacteria and fungal microbiome inside and on plants mediate plant traits, with implications not only for individual plants, but for entire ecosystems.  We have a wide and growing list of interests in the plant microbiome; What factors influence the plant microbiome? Do plant microbiomes show biogeography? Are they structured by host species or are they generalists? How are plant-associated microbes transmitted and dispersed? How do endophytes enter the plant?  Do plant microbiomes support plants in stressful environments like nutrient poor soil, through drought and inundation in ephemeral vernal pools, or at the edge of plant species’ distributions?

To answer these questions, we use a combination of DNA sequencing, genomics, metagenomics, growth chamber experiments, and functional assays to study plant microbiomes in several systems including forest trees, vernal pool plants, and herbaceous plants native to the Sierra Nevada.

Much of our work involves foliar nitrogen-fixation in conifers (Moyes et al 2016), supported by the National Science Foundation Dimensions of Biodiversity Program. Why conifers? While there are far more angiosperms on Earth than there are gymnosperms, one division of the gymnosperms—the conifers—still dominate many of the world’s temperate and boreal forest ecosystems. Conifers are remarkably tolerant to a wide range of soils and climates, including infertile dry soil and exposed high elevations. We would like to understand if and how partnerships with bacteria contribute to this ability to thrive where few other plants grow.