Dimensions of Biodiversity

Our lab is investigating the taxonomic, genetic and functional biodiversity of above-ground bacterial endophytes in subalpine conifers. The project is a collaboration with Lara Kueppers at the Lawrence Berkeley National Lab, Jennifer Pett-Ridge at the Lawrence Livermore National Lab, and Tanja Woyke at the Joint Genome Institute, and is supported by the NSF Dimensions of Biodiversity program.

Our goal is to determine the evolutionary and ecological significance of a novel symbiosis between pine trees and bacteria living inside their foliage as endophytes.

A deeper understanding of how taxonomic, genetic and functional biodiversity of endophytes affects the capability of forest conifers to use nitrogen from the atmosphere has the potential to significantly improve our understanding of the nitrogen cycle and help solve a long-standing ecological mystery: where does the nitrogen come from in conifer forests?

Nitrogen is essential to all life on Earth, but is a growth-limiting nutrient in most ecosystems. For a long time, the only important pathways for nitrogen input to terrestrial ecosystems were thought to be microbes that live in the soil or in a symbiotic relationship with legumes, alders and a few other plants. Recent findings using DNA sequencing indicate that symbiotic endophytes living inside the foliage of high-elevation pines can fix atmospheric nitrogen.

We will investigate how the diversity of endophytes in pine foliage affects the amount of atmospheric nitrogen fixed within the tree. The research focuses on limber pine, a species with a wide climatic, elevational and geographic range. Limber pine grows in the Rocky Mountains from Alberta to New Mexico; in the Great Basin states of Nevada and Utah; and in the Sierra Nevada in California. To understand how endophyte diversity is shaped by the environment and how it shapes the nitrogen cycle in subalpine forests, we will examine the biodiversity of endophytes in limber pine and co-occurring pine species across the limber pine range. Like most bacteria, the endophytes cannot be cultured in the lab. Therefore, cutting-edge methods including DNA sequencing and genome analysis will be integrated with established and highly sensitive methods for detecting and visualizing nitrogen fixing activity inside limber pine tissue.

The research has the potential to radically change our perspective on how some plants acquire nitrogen, and also our understanding of the terrestrial nitrogen cycle. Temperate and boreal coniferous forests accumulate more nitrogen in soil and vegetation than can be explained by known sources of nitrogen, suggesting an unknown biodiversity of nitrogen fixing bacteria exists in these ecosystems.


March 2016 fieldwork at the Ecological Staircase

Below are some photos from our sampling trip to the ecological staircase in Mendocino, California. The staircase consists of five wave-cut terraces formed by glacier, sea and tectonic activity. They derive from the same parent material but differ in age, and consequently, soil fertility and vegetation. We went here to measure the rate of nitrogen fixation in lodgepole- and Bishop pine foliage across terraces, hoping to test if above-ground endophytic fixation rates is facultative and capable of regulating fixation in response to ecosystem nitrogen supply, or alternatively, obligate and fixing at a steady rate regardless of nitrogen availability.

James Kupihea (Frank lab PhD student) and Katy Dynarski (Houlton lab at UC Davis) looking at Bishop pine at one of the higher terraces. P3140207.JPG

James sampling reindeer lichen.P3140223.JPG

Dana Carper (Frank lab PhD student) and James, on the way to one of our sites.P3140214.JPG

Back in Berkeley – mason jars ready for the Acetylene Reduction Assay to measure nitrogenase activity.P3150226.JPG

Lara Kueppers recording data.P3150235.JPG

Dianne Quiroz, a former SULI (Science Undergraduate Laboratory Internships) student in Lara Kueppers’ lab, now a research technician on the project, and the student who led this effort!P3150238.JPG

Carolin Frank injecting acetylene into jars with pine twigs.P3150245.JPG

James, operating a gas-tight syringe.P3150250.JPG

What about lichen…?P3160253.JPG

Paola Saldierna (Frank lab PhD student) measuring the volume of a pine twig.P3150247.JPG

Paola, Dianne and James working with soil samples.P3160254.JPG