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. In my lab, we focus mostly on bacteria called endophytes, that live inside plants. Such bacteria are important to study because they are known to mediate plant traits, with implications not only for individual plants, but for entire ecosystems.

What are endophytes? Endophytes are bacteria or fungi that live inside plants without causing disease. They are found in all land plants, in all tissues, including roots, seeds, flowers, stems, and leaves. Endophytes can directly stimulate plant growth through the production of plant hormones, or protect the plant against disease and abiotic stress. Some bacterial endophytes fix nitrogen.

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.  Do partnerships with bacteria contribute to this ability to thrive where few other plants grow? We are currently researching the bacterial endophytes of a number of Western conifer species, including limber pine, lodgepole pine, Bolander pine, white fir, incense cedar, Engelmann spruce, ponderosa pine, Jeffrey pine, giant sequoia, and coast redwood.

How do we study bacterial endophytes? Studying new bacteria in the environment is tricky since most of them refuse to grow in the lab. We use a combination of bacterial culturing, next-generation genome- and 16S rRNA sequencing to study the bacterial endophytes of (mostly) conifer trees, including their patterns of interaction with the host, their evolution, and the genetic mechanisms underlying the symbiosis.

We find that some conifers are host to consistent,  bacterial communities in their needles (see Carrell and Frank 2014), while others are host to diverse and variable bacterial communities (see Carrell and Frank 2015). We hypothesize that this reflects host species- and site level differences in the level of endophyte-mediated adaptations to the environment. Our findings suggests that some conifers, in some environments, form environment-driven mutualisms. We are currently working on elucidating the mechanisms underlying these mutualizes (see Koskimäki et al. 2015), and the evolutionary relationship between hosts and endophytes. Much of our work involves foliar nitrogen-fixation in conifers (Moyes et al 2016), supported by the National Science Foundation Dimensions of Biodiversity Program.