Monday, September 25, 2017

UW Receives $20 Million Grant for Unprecedented Microbial Research Effort

When people look across Wyoming, they see the variety of terrain, vegetation and other life that make up the state’s landscapes, from plains grasslands and productive farmland to sagebrush-steppe deserts and alpine forests.
What they don’t see are the innumerable bacteria, fungi and other microbes in the soil, water and air that shape life in the Cowboy State.
Over the next five years, University of Wyoming researchers will take an up-close look at those unseen organisms at an unprecedented scale, thanks to a $20 million grant from the National Science Foundation (NSF). And, using cutting-edge techniques including DNA sequencing and computational modeling, the scientists hope to learn the distribution and ecological consequences of microbes, producing insights that will help Wyomingites address a variety of challenges -- from managing rangeland, forest and water resources, to reclaiming areas disturbed by mineral extraction, to improving crop productivity.
In the process, the university expects to stimulate significant economic and business opportunities across the state -- and engage people from elementary school pupils to community college students to business leaders in scientific discovery.
“This grant will allow us to conduct microbial research at a scale that isn’t taking place anywhere else on the planet,” says Bill Gern, UW’s just-retired vice president for research and economic development.
“This will enhance our research capacity and competitiveness along with the state’s workforce and economy, creating intellectual property that can be applied to economic sectors relevant to Wyoming, including the fast-growing field of data science, which has an enormous range of applications,” says Ed Synakowski, Gern’s successor.
The grant was among five announced today (Tuesday) through NSF’s EPSCoR (Established Program to Stimulate Competitive Research) program, which supports efforts to enhance research, science and mathematics education, and workforce development. The award comes on the heels of another five-year, $20 million NSF grant in 2012 -- at the time, the largest research grant in UW history -- that stimulated wide-ranging research into Wyoming’s water resources.
“These investments by NSF promise to yield fundamental understanding in research areas of regional and national importance while catalyzing new educational and training opportunities for students and researchers,” NSF Director France Cordova says. “This year’s EPSCoR awards continue to demonstrate the vitality of scientific inquiry and innovation, which is present in universities and research laboratories across the nation.”
UW President Laurie Nichols says the new grant leverages and complements Wyoming’s investments in high-performance computing and the university’s Science Initiative -- which aims to transform science education across the state while driving innovation and economic progress.
“This grant is an example of how the commitment of the Legislature and the governor to upgrade UW’s scientific infrastructure will pay dividends for the people of Wyoming and our quality of life,” Nichols says. “It touches on all aspects of the university’s three-fold mission of providing top-caliber educational opportunities for our students, conducting research to benefit the state and meeting the needs of Wyoming through service.”
This highly interdisciplinary award, bringing together researchers and educators from multiple UW colleges, is led cooperatively by principal investigators Brent Ewers, Cynthia Weinig and Alex Buerkle, professors of botany; Naomi Ward, associate professor of molecular biology; and Linda van Diepen, assistant professor of ecosystem science and management.

A New Age of Discovery
While the presence of bacteria, fungi and other microbes has been known for centuries, human understanding of the diversity of microbial life -- and its role in human biology, ecology and agriculture -- is still rudimentary, the UW researchers say. That is changing because of major advances in technology, particularly in DNA sequencing and high-performance computing.
“This is an age of discovery in microbiology,” says Buerkle, who studies genetic consequences of evolutionary adaptation. “Just as modern telescopes have given astronomers the ability to see the universe with amazing detail, our new genomic sequencing capabilities have opened a whole new world in the study of life.”
With this grant, UW will be on the cutting edge of using biotechnology to study the natural world. Specifically, the university’s technology in sampling microbes from Wyoming’s landscapes; sequencing the DNA of those microbes; and using computer models of microbial life will be at the forefront of science.
The grant will fund the next generation of equipment for UW’s Advanced Research Computing Center; create new on-campus centers for liquids handling, biogeochemistry and data science; and allow for the hiring of three faculty members, numerous postdoctoral researchers and graduate students, as well as facilitate undergraduate student research.
Sampling of Wyoming soil, plants, water and air will be done at hundreds of sites across the state -- from mountaintops to basin bottoms -- primarily on public lands and in cooperation with private partners. The “pipeline” of sample collection, storage and analysis will involve UW and community college students, K-12 teachers and others. And the resulting Data Science Center will reach across campus and around the state, creating unprecedented opportunities for students to engage in the cutting edge of genomics, the study of the entire DNA sequences of organisms and statistical analyses -- crucial components of the contemporary growth in the economy related to life sciences and data science.
Beyond opportunities in the technology sector, potential benefits for the state include improved knowledge of invasive plants and microbes; improving crop production; improving reclamation of lands disturbed by development; and, in general, managing lands more effectively.
“Any good naturalist can look at a field and see the plants there and understand the life cycle and the interrelated species that live there, but in that same field are hundreds of billions of microscopic living organisms we don’t know much about,” says Weinig, whose research involves evolutionary genetic analysis of adaptation in nature. “By learning about the microbes that are there, and what they do, we will be able to identify functions that might be improved for plants, grazing animals and other users of the land.”
“Once we know what organisms are there, including their genetic capacity, we can figure out how we can make use of them,” says van Diepen, whose research includes the role of soil microbes in restoring forests after wildfire, soil remediation of contaminated mine lands and microbial interactions with invasive plants such as cheatgrass.
Ward adds that the project "applies the same approaches used so successfully to understand the microbial communities associated with the human body.
“Human microbiome studies have provided clear evidence that some microbes are essential for our health, while others predispose us to disease,” she says. “In the same way, this new project will provide information on how some microbial groups support healthy ecosystems, while others are associated with environmental imbalances.”
Why Wyoming?
Wyoming is ideal for research of this nature and scope because of the variety of its lands, including elevation, temperature, moisture and land use, the researchers say. Rapid changes in elevation and soil type often occur over small distances, and these steep gradients will give scientists an excellent window to study the variety of microbes and their functions.
Wyoming also provides unusual access to pristine lands and waters, as well as systems disturbed by resource extraction, dams and water diversions.
The project will train members of the Northern Arapaho and Eastern Shoshone tribes in sample collection and laboratory and statistical analyses of microbiomes from the Wind River Indian Reservation. This work by the two sovereign tribes will not only answer new questions about land management, but also aid in economic development.
In fact, the microbe that Buerkle says launched the biotechnology revolution was discovered in the Mushroom Pool of Yellowstone National Park’s Lower Geyser Basin in Wyoming in 1966. In the mid-1980s, scientists discovered that Thermus aquaticus, which survives in extremely high temperatures, made DNA testing much more practical. This fortuitous discovery led to the biotechnology industry, generating billions of dollars a year and creating scientific breakthroughs in medicine and agriculture.
Bioprospecting for other useful Wyoming microbes could lead to discovery and commercialization of new products, the UW researchers say. And there will be significant entrepreneurial opportunities as a result of associated data science capacity.
“This project will provide a mechanism to counteract the boom-and-bust cycles of Wyoming’s energy-based economy,” says Ewers, who researches how plants control the flow of energy and mass at small and large scales. “This is an opportune time for training and workforce development in data science, with the particular application here to microbial ecology.”

UW Press Release - from Institutional Communications, Chad Baldwin

Tuesday, September 12, 2017

The Only Good Use for a 20-Gauge is Shooting Trees - a fieldtrip reflection

Graduate and undergraduate students spread out across a hillslope as the morning twilight begins to light the valley – armed with shotguns, a drone, and pole pruners. Sounds like the opening of a story told around a campfire. But this is another day in the life of WyCEHG scientists who are going out to measure water stress of trees in the Happy Jack area near Laramie.

Daniel Beverly, an affable PhD Student and his equally friendly field partner a Bernese mountain dog called Aldo are leading the day’s fieldwork. He measures tree stress along a hill’s gradient. Just off trail from the parking lot, the slope is covered with instruments humming away during field season. Wires run across streams, solar panels provide energy to boxes containing multiple wires and curiously shaped objects. While this is a relatively heavily used trail – instrumentation is tucked away. Hummingbirds dart across the slope that pops with midsummer color of yarrow, daisies, yellow paintbrush, sage, and flax flowers.

Calm prevails until the stroke of the hour, every third hour (unless you are a large friendly dog who seems calm throughout the day), when field techs and graduate students jump into action. Coffee and reading are set aside, sample bags are stuffed in pockets, and people begin hiking to the top of the hillslope to collect leaf matter from the sample trees as they work their way down to the valley. Collection methods vary from shooting branches with a 20-gauge shotgun to sawing branches with arborist tools. Volunteers are eager to remove branches using the shotgun, and some have quite good aim. Once a usable sample is removed from each tree, it is bagged and brought down to the field station for processing. The first measurement was recorded at 5:00 am, and this cycle will continue beyond the setting of the sun. This measurement strategy allows the researchers to observe diurnal changes in sap flow.  

Tree sap is the fluid transported in xylem cells of a tree which creates pressure within the tree. In addition to water, sap contains minerals and nutrients. Those presence and quantity of nutrients can determine the health of the tree, but for today’s purposes the sap content in the top third of the tree is what will reveal stress. Drought stress can be seen by applying pressure to a sample of leaf and stem material in a pressure chamber. Once the pressure on the sample becomes great enough to force liquid out of the stem, a quantity is recorded. This occurs for each sample throughout the day. The higher the pressure required to release liquid, the more stressed the tree. On this overcast cool day, Beverly does not predict high pressure readings. Aldo seems quite content to be in the field under these conditions, though it seems the researchers are hoping for a more dramatic temperature flux. 

The team will come back throughout the field season to establish a picture of seasonal stress and the vulnerability of this forest. With a changing climate, researchers will have tools to respond to the forest’s needs and better prioritize species protection. If you find  yourself on the east side of the headquarters trail at Happy Jack, wave hello to the WyCEHG scientists who may be just off the trail collecting data and helping us better understand our local forests.