I’m recruiting a graduate student to work in transmission of foliar microbiomes of forest trees! If you’re interested in microbial ecology, forests, and bioinformatics, please apply to the Quantitative and Systems Biology graduate program at UC Merced.

Also, there is a postdoctoral position available in the Frank lab! Apply here.

The Frank lab is recruiting an exceptional and highly motivated postdoc to work on diversity and function of the conifer foliage microbiome. The successful candidate will contribute to on-going research that seeks to understand the diversity, function, and transmission routes of the microbiome associated with foliage of western high elevation conifers.

Recent findings suggest that both evergreen and deciduous trees have the potential to directly access atmospheric N via N2-fixing bacteria in the foliage. These findings are important to our understanding of how plants in N-limited ecosystems meet their N demand, and to balancing ecosystem N budgets.

Illumina sequencing of the 16S rRNA gene has shown that the conifer microbiome is largely consistent across species and geographic sites, with several potential N2-fixing uncultured taxa dominating the community. The successful candidate will use a combination of enrichment of bacterial cells and DNA; metagenomics and single cell genome (SAG) sequencing; amplification of nitrogenase (nif) genes using PNA PCR blockers to exclude conifer nif homologs; designing and using nif primers for specific groups of bacteria; and bioinformatics analysis of metagenomes and SAGs. Metagenome- and SAG sequencing is performed in collaboration with Tanya Woyke’s group at Joint Genome Institute in Walnut Creek, CA. There are also opportunities for collaborating with Jennifer Pett-Ridge’s group at Lawrence Livermore National Lab for fluorescence in situ hybridization. The project involves sampling lodgepole pine in nearby Yosemite National Park.

Applicants should have a PhD, completed or completion imminent, in microbiology, evolution, genomics, bioinformatics, or related fields. Programming and bioinformatics experience is desirable.

This position begins in January and is funded for 12 months with the possibility of extension for a total of 2 years. Salary is based on the University of California Academic Salary Scales. Prospective applicants should contact Carolin Frank at cfrank3@ucmcerced to discuss the project.

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.