Research: Yosemite

The iconic Yosemite National Park (YNP) is among the oldest and most heavily visited protected areas in the world.  Encompassing over 3,000 km2—from the foothills of California’s Sierra Nevada Mountains to their 4,000 m crest—YNP hosts ca. 5 million visitors annually, yet much of the park is designated wilderness with only limited trail access.  Within its boundaries, YNP harbors the headwaters of river systems that supply drinking water and farmwater to California’s millions of citizens and multibillion dollar agricultural industry.  Our research is focused on the microbial ecology of high mountain lakes, which are naturally beautiful and a highlight of Yosemite, but may be sensitive to pollution and climate change.

YNP is located upstream and downwind from the Central Valley of California, an intensive agricultural area that suffers poor air quality and presents a stark contrast—with feedlots, factories, and freeways located ~100 km from the Sierra.  As a consequence, the National Park Service is concerned about transport of atmospheric pollutants into YNP (  High elevations are also expected to rapidly warm, and lakes are considered climate ‘sentinels’ that are sensitive to rising temperatures (Williamson et al. 2009 and references therein).  Changes in carbon fluxes into and out of lakes are a major concern, as lakes are carbon ‘sinks,’ yet can also produce the potent greenhouse gas methane (CH4).

We began sampling along a lake elevation gradient in YNP in 2010, examining multiple aspects of lake biogeochemistry and microbial ecology on a regular basis.  We published our work on nitrification in 2014 (Hayden and Beman 2014, PLOS ONE) and our work on lake microbial community ecology in 2015 (Hayden and Beman 2015, Environmental Microbiology).  One interesting aspect of this latter work was finding high abundances of CH4-cycling organisms in our sequence data.  As a result, our current focus is on CH4 production and consumption in these lakes and we have found high rates of both.  This set the stage for a Joint Genome Institute Community Science Program grant that we received in early 2015.

Our current work is focused on metagenomic analysis of the microbial communities involved in CH4 cycling in high altitude lakes, quantifying rates of CH4 production and consumption, and determining the sensitivity of these processes to different forms of environmental change.

Yosemite info:

Current conditions (roads, weather, webcams, etc.)

Clickable Yosemite weather


Wilderness conditions

Air quality data and webcam

Yosemite HD

Mike is also a co-PI for the Yosemite REU program funded by NSF.  Contact him if you are undergraduate interested in summer research in the Park.

REU program and press release:

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