Discovering Wyoming's Microbiome Through Data

Wyoming researchers are diving deeper into data collection in order to better understand Wyoming’s microbiome. Yet one of the most challenging parts of collecting data is meaningfully sharing it with the public. Dr. Shannon Albeke, with the Wyoming Geographic Information Science Center has developed a data discovery tool that aims to do just that.  

The data discovery tool is an interactive web-map containing the spatial locations of collected data. Users can search the data base with specific filters based on location or the type of data. All of the data is free and open to public access online. 

The map interface of the data discovery tool. The orange points indicate data sets collected in the Medicine Bow and Laramie area.

Development of the tool began a few years ago with the input of WyCEHG data. The hydrological and geophysical data collected during this time will also be useful information for researchers investigating the microbial communities in these areas. 

“Ideally, this would be a one stop shop for researchers and their data to interact across discipline boundaries,” Shannon explains. 

Traditionally, data collection programs like this one have static data sets, but the discovery tool will have live data sets that update every 15 minutes. This is one of the first tools of its kind to include this feature. 

The discovery tool is still in its initial testing phase and will undergo more development. While most of the programming aspects of the tool have been completed, the next focus will be on the interface. Making the data base user friendly and easy to access is an important component of the project.
 
While the data discovery tool is now home to diverse data sets from across Wyoming, Shannon was interested in the tools ability to aid outreach efforts across the state. Shannon has collaborated with Dr. Andrea Burrows on incorporating the Data Discovery Tool into K-12 curriculum across Wyoming. Through her Science Methods class, Dr. Burrows has recruited undergraduate and graduate students to develop lesson plans that relate to microbiology.

"This is a great way to support scientists and teachers, but it's also a learning opportunity for students, soon they will be in the classroom teaching," Andrea says.

Science Methods students display their depiction of cyanobacteria with their microbe art project.

The initial lesson plans include an art project undergraduate students completed in their science methods class. To better understand microbes, the students divide pictures of microbes into three separate sections. Then in groups of three, each student painted a silk screen of their section of the microbe photo. When all three paintings are brought together, they complete the whole picture. Students working on the lesson plan development also proposed including microbiology into topics that are traditional covered in K-12 curriculum by focusing on microbes that exist within the food chain or ecosystem.  

“This is a great experience for students because the lesson plans they create can be used for 4-5 years throughout the grant. Each year new students or teachers can alter and build upon these original lesson plans,” Andrea explains. 

Andrea looks forward to directly relating these lesson plans to the use of the data discovery tool.  Teachers can pick specific microbes to study based on what is in their surrounding locations.

Shannon also mentioned storing imagery of microbes for younger students to view would also be beneficial. Additional modules and functionalities such as this can be incorporated into the data discovery tool to better aid outreach efforts.

With the development of the data discovery tool used in conjunction with outreach efforts, open data available to the public will further encourage more scientific exploration throughout the state. 

Community College Students dig into Applied Research on a Glacier

A bridge building exercise is designed to take one from where they are, to where they want to go. As Wyoming EPSCoR transitions between two large projects, there is an activity spanning both that serves as a bridge and lovely example of applied student learning at the community college level. The Interdisciplinary Climate Change Expedition, or ICCE, is a course taught at Central Wyoming College, which is one of seven community colleges in the state. It culminates in a two-week trek into the Dinwoody Glacier in Wyoming’s Wind River Range on which students engage in active learning and applied research. The glacier, which is one of more than 100 in the range, becomes their classroom and nature their guide. Groups use ground penetrating radar, or GPR, to get a sense of what lies below the snow, they study the microbial ecology of scree fields and emerging landscapes that arrive due to the glacier’s receding. There is an archaeology team and one studying black carbon, as well as a geographical information systems, or GIS, group. Scientific American recently published a science brief on the project, the article can be found here.

During the semester students have the opportunity to learn mountaineering skills, ways to interact with scientific equipment, experiment design, and outdoor leadership through a partnership with the National Outdoor Leadership School.

As we cross the bridge into Microbial Ecology research across the state, ICCE will continue to offer community college students an opportunity to actively research and apply their learning to real world issues. These hands on experiences may create another bridge, the transition from a 2-year school to the University of Wyoming.

This past summer’s ICCE expedition took along some video equipment. Check out their adventures here.

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

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. 

GLEES turns 30!

Guest Post by Elizabeth Traver

On Friday 28 July, the Rocky Mountain Research Station celebrated the 30^th birthday of the Glacier Lakes Ecosystem Experiments Site, or GLEES.  It is located off the Brooklyn Lake Road in the Snowy Range, about 35 west of Laramie.  It was established in 1987 and, since 1989, scientists have been gathering data on everything from water chemistry to soil and air temperature, from relative humidity to solar radiation and wind speeds and directions.  In addition, permanent vegetation plots have been periodically sampled for more than 25 years offering an long-term resource for researchers.

On that Friday, Forest Service folks offered talks on the history and significance of the GLEES site, while others gave mountain tours and talked about the lake cores and vegetation plots as well as the ongoing field research for the National Atmospheric Deposition Program and stream flow measurements.  Another offered tours and talks about the ~100’ scaffold tower that holds a large number of sensors including though which are part of FLUXNET a system of 800 Ameriflux towers that measure a  variety of atmospheric components around the world.  GLEES tower is the windiest and I think the highest in elevation.

After all the tours and talks, everyone headed to the Forest Service cabin located just outside Centennial which has room to house collaborating researches and has both wet and dry labs as well as a site-specific herbarium.  We all enjoyed the cook-out and cake and mingled with both current and retired FS researchers and several from U W who have done many projects within the GLEES area.

Panoramic view of GLEES. Aerial photo (L) and this photo: Josh King, University of Wyoming