Geohackweek: A Five-Day Geospatial Workshop

From November 14 to 18, the University of Washington’s eScience Institute will be hosting a five-day Geohackweek, and you are invited to take part in wide-ranging tutorials, data exploration, software development and community networking—all focused on open source tools to analyze and visualize geospatial data. Among the practical tools and skills addressed will be how to:

•             access, store and manage environmental datasets like climate grids;
•             create beautiful maps and visualizations that are easily shareable;
•             analyze geospatial data, including remote sensing imagery, using spatial statistics and open source packages;
•             use different cloud storage options to host your code and data depending on your needs.
•             and much more!

One workshop that might be of particular interest to SEFS is about Google Earth Engine, which is a free, cloud-based platform for analyzing land-use change that includes well-developed case studies centered on deforestation, among other themes.

While the workshops will predominantly be taught using Python and/or Javascript, the lessons should be accessible to anyone with basic programming language experience, even if it is in another language (R, Matlab, etc). Also, if you want to brush up on Python beforehand, Software Carpentry has great intro workshops they regularly teach in the Puget Sound area.

The application deadline for attending is September 15, 2016, so learn more and get involved!

2016_08_Geohackweek

Summer Campers Have Fun Exploring Biogeochemistry

Last week, we wrote about the new Mission Earth Scout One science camp that one our graduate students, Isabel Carrera Zamanillo, launched this August. The camp offers underrepresented middle and high school students the opportunity to gain hands-on experience in a variety of scientific disciplines, and to help out with the different subjects, Isabel recruited several folks from SEFS to serve as guest scientists for a day. Among the volunteers was SEFS doctoral student Catherine Kuhn, who is part of Professor David Butman’s Landscape Biogeochemistry Lab, and she took her turn leading instruction for the campers on Monday, August 8.

Students practice field sampling for methane and carbon dioxide along Ravenna Creek.

Students practice field sampling for methane and carbon dioxide along Ravenna Creek.

Catherine and her research assistant, SEFS undergrad Rachel Yonemura, taught a lesson about the freshwater carbon cycle and introduced students to the idea of how greenhouse gases can be emitted from lakes, rivers and streams. The lesson also included a section on carbon mapping and different tools that can be used to visualize geospatial data.

Rachel followed up by applying some of the new concepts to urban stream chemistry in Ravenna Creek, which is one of Rachel’s study sites for her senior capstone research. So later that afternoon, the students then practiced field sampling for methane and carbon dioxide at an access site where Ravenna Creek meets the Montlake Slough.

Catherine says the students did an outstanding job collecting field samples, and the Landscape Biogeochemistry Lab team had a great time working with the young scientists in the making.

Photos © Catherine Kuhn.

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Professor Prugh Hits the Field with Current and Future Grad Students

This summer, Professor Laura Prugh has taken two trips to the field—first with one of her current graduate students near Mount Rainer, and then to southeast Alaska with a master’s student who’s joining her lab and starting at SEFS this fall.

Mitch Parsons with a Microtus vole that he captured and ear tagged for mark-recapture density estimation.

Mitch Parsons with a Microtus vole that he captured and ear tagged for mark-recapture density estimation.

For the first excursion in June, Laura spent a few days south of Mount Rainier in Gifford Pinchot National Forest with her current master’s student, Mitch Parsons, and his summer field technician, Aaron Black. Mitch’s project is looking at trophic relationships of reintroduced fishers in the South Cascades. Fishers were reintroduced this past winter, and another round of releases will occur this winter. So Mitch is assessing prey availability using sign surveys and small mammal trapping, and assessing the occupancy of competing carnivores using camera trapping.

Then, two weeks ago Laura traveled to Glacier Bay National Park in southeast Alaska to check out future study sites for her incoming master’s student, Mira Sytsma. Using camera traps, Mira’s project will involve looking at how visitor shore excursions affect the activity of terrestrial wildlife. They spent three days on a research boat with National Park Service Biologist and project collaborator Tania Lewis, and they visited many sites—enjoying amazing wildlife sightings along the way, too, including a wolf with three pups, two brown bears, lots of humpback whales, orcas, sea otters, Stellar sea lions, harbor seals, moose, mountain goats and even a porcupine!

We look forward to hearing how these projects progress!

Photos © Laura Prugh.

Laura (right) and Mira at one of the sites, with their research boat in the background.

Laura (right) and Mira at one of the sites, with their research boat in the background.

 

SEFS Student Leads Mission One Science Camp

This August, SEFS doctoral candidate Isabel Carrera Zamanillo is leading the first-ever Mission Earth Scout One science camp, which will guide more than 35 middle and high school students through four weeks of hands-on STEM activities and exploration.

The idea for the camp came from her time living in Chicago a few years ago, when she created an outreach project called Jugando con la Ciencia (“Playing with Science”) at the Evanston Public Library. Every weekend, the program would invite Hispanic scientists to the library to talk about their work and research with kids and their parents. Isabel, who grew up in Mexico City, also helped with science outreach in the Latino community through the Field Museum and Adler Planetarium, and she had been looking for a similar opportunity in Seattle.

On their first day of the Mission Earth One camp, students ... at the Center for Urban Horticulture.

On their first day of camp on August 1, 2016, the students were out observing birds at the Center for Urban Horticulture.

So when she was offered a chance to help organize the first summer camp for the Northwestern Earth and Space Sciences Pipeline (which is supported by the Washington NASA Space Grant Consortium), she accepted and got approval this past May to host the camp in August. She then began reaching out to underrepresented communities to recruit students who haven’t had as much exposure to science. Mission Earth has an emphasis on bilingual students, as well, and Isabel’s outreach attracted participants from a wide range of backgrounds, including Latino, African, Bosnian and Asian Indian, among others.

“My idea was to create a theme that will combine physics, math, chemistry, engineering, biology and environmental sciences,” she says, so she settled on climate change as the unifying subject.

The students will now get to spend the month learning about climate change through a variety of fun hands-on experiments and field trips. They’ll visits campus labs and the UW Farm, go on excursions to Whidbey Island to look at glaciers, and Tacoma to look at a wastewater treatment plant and learn about biosolids. They’ll start the camp by focusing on understanding nature, interacting with soils and plants—touching, feeling and sensing—and learning the principles of an ecosystem. From there they’ll move on to technology and more abstract concepts, building to the final week, which will feature drones and rockets, remote sensing and GIS. Through everything, the students will get a chance to work closely with scientists and see how science connects to their daily lives.

In addition to Isabel as the main instructor, several other members of SEFS are participating as guest scientists and leading one-day sessions, including Professors Dan and Kristiina Vogt, Sally Brown and Renata Bura; Research Associate Azra Suko and Paper Science Center Manager Kurt Haunreiter; and graduate students Shawn Behling, Catherine Kuhn and Jessica Hernandez. All of them are volunteering their time and materials, which helps remove financial obstacles for students attending the camp. The cost per student, in fact, is only $5 per week, with grant funding covering the rest.

The day camp runs from August 1 to 26, Monday through Friday from 10 a.m. to 2 p.m. It’s going to be an exciting month of discovery for these students, and keep an eye out on August 18 when they’ll be visiting SEFS!

Photo © Isabel Carrera Zamanillo.

Alaska Bear Project: Year Five

Now in its fifth year (and counting), the Alaska Bear Project continues to build momentum. Working in collaboration with Professor Tom Quinn from the School of Aquatic and Fishery Sciences, Professor Aaron Wirsing just returned from Bristol Bay, Alaska, where researchers have been non-invasively studying brown bears hunting along six sockeye salmon spawning streams since 2012. Thus far, they’ve collected more than 2,000 hair samples for genetic analysis using barbed wires strung across the streams, and detected 121 individual bears.

Professor Aaron Wirsing, left, and Professor Tom Quinn on the tundra near one of their bear wires on Whitefish Creek.

Professor Aaron Wirsing, left, and Professor Tom Quinn on the tundra near one of their bear wires on Whitefish Creek.

This year, for the first time, they’ve also been collecting video using motion-activated trail cameras deployed in conjunction with the wires, and elsewhere, on each stream. They’ll be analyzing the videos to explore bear behavioral responses to the wires (e.g., do they learn to avoid them?), and to track the timing and location of different bear behaviors, including foraging and traveling. Working with Anne Hilborn, a doctoral student in Professor Marcella Kelly’s lab at Virginia Tech, they’re also using the videos as a means to better communicate their work and findings to the public.

Below, check out one of their videos from this summer, which provides a great example of the type of footage they’re collecting: a brown bear mother passing by with two cubs!

Photo © Blakeley Adkins; video © Aaron Wirsing.

Grizzly Mom with Two Cubs

Researchers Study Morel Abundance After 2013 Rim Fire

Few mushrooms are as beloved as the morel. From recreational pickers jealously protecting their secret hunting spots, to world-class chefs coveting them for their springtime recipes, morels have acquired an almost mythic status and even have a few festivals in their honor (one in Michigan has been running for 55 years). Yet despite the enormous popularity of morels, surprisingly little research has quantified how the mushrooms respond to one of the greatest disturbances in their natural habitat: a forest fire.

The other coauthors with SEFS ties include Mark Swanson (’99, B.S.; ’07, Ph.D.), now a professor in the School of the Environment at Washington State University, and two former SEFS undergrads, Sienna Hiebert (’12, B.S.), who is running her own business, Lost Creek, LLC, and Tucker Furniss (’11, B.S.), now a graduate student at Utah State.

The other coauthors with SEFS ties include Mark Swanson (’99, B.S.; ’07, Ph.D.), now a professor in the School of the Environment at Washington State University, and two former SEFS undergrads, Sienna Hiebert (’12, B.S.), who is running her own business, Lost Creek, LLC, and Tucker Furniss (’11, B.S.), now a graduate student at Utah State.

Understanding that response is fairly crucial, as morels tend to proliferate most significantly in the first year following a fire. So several researchers—including six with ties to the School of Environmental and Forest Sciences (SEFS)—sought to address that hole in the literature with a new paper just published in Forest Ecology and Management, “Post-fire morel (Morchella) mushroom abundance, spatial structure, and harvest sustainability.”

Led by Professor Andrew Larson (’03, B.S.; ’09, Ph.D.) from the University of Montana, the study provides the most comprehensive picture yet of morel numbers and distribution after a wildfire, as well as the most concrete data to help forest managers set policies for sustainable morel harvesting (which is especially important since the mushrooms grow and are collected almost exclusively in the wild).

The project came together after the Rim Fire in the Sierra Nevada—the third-largest wildfire in California’s history—burned through parts of Yosemite National Park from August to October 2013. Among the affected areas was the Yosemite Forest Dynamics Plot, a long-term research site with years of accumulated data overseen by principal investigators Larson and Professor Jim Lutz (’05, M.S.; ’08, Ph.D.) from Utah State University.

“One of the benefits of a long-term plot is you can layer on additional studies,” says Alina Cansler (’15, Ph.D.), the second author on the study and a research ecologist at SEFS. So the research team was able to assess the morel population alongside other typical post-fire measurements, such as number of trees killed, fuel burned and decrease in forest biomass. Also, at the time of the wildfire, forest managers had backburned part of the area to stop the fire from burning further into Yosemite National Park, but otherwise allowed it to burn naturally under fairly dry fuel conditions—opening a rare opportunity to study a characteristic morel response.

The Findings
The following May, in the spring when morels typically fruit after a fire, the researchers surveyed 1,119 small sample plots in the study area. They found, first of all, an incredible volume of morels, and they estimated the white-fir/sugarpine forests in Yosemite have an average of 1,693 morels per hectare. That translates to 1,083,520 morels per year, given the typical area that burns within that type of forest in Yosemite! Alina notes, moreover, that that is an underestimate of the total number of morels in the park, since morels also fruit after fire in other forest types, and fruiting of some species of morels are not tied to fire.

Alina Cansler discovers a morel in the study area.

Alina Cansler discovers a morel in the study area, which the authors estimate could be home to 4,183 morels per acre.

Two other big discoveries were that the highest occurrence of morels occurred on ground that had been 100-percent burned by the fire, and that the morels were generally found clumped closely together and distributed unevenly across the forest. In the paper, the researchers note that the practical application of this uneven distribution is that “if you find one mushroom, carefully search the area within about 3 m (10 feet) and continue to search out to about 7 m (23 feet), as additional mushrooms are likely to occur in this neighborhood.”

The latter findings will require further research to figure out the mechanisms behind them, says Alina, such as whether mycelial colonies (the belowground parts of the morels) are present in the soil before or after the fire, and how variations in the presence of the mycelium, forest vegetation  and fire severity affect distribution patterns. “We still don’t know exactly what [the morels] are responding to in the environment,” she says. “There’s a lot more work to be done.”

More immediately, though, the paper’s estimation of the number of morels in the forest—coupled with a thorough literature review of similar sites in the Pacific Northwest and Alaska—could have direct management implications. Until now, managers didn’t have a clear picture of how many mushrooms are in the park on a given year. Current regulations in Yosemite limit pickers to one pint of morels a day, yet Alina says this research supports the potential for a more liberal, yet still sustainable, recreational harvest in the park.

“What stands out from this study,” she says, “is that morels are such a culturally important non-timber forest product, yet there had been very few reputable, statistically valid samples of their abundance after fire.”

But this latest research, with its large number of sampling points in an intensively monitored forest plot, fills at least one gap in the literature and provides strong evidence to guide the management of forests with morels—in California and around the Pacific Northwest. Next up: Figuring out precisely how and why morels respond so vigorously after a fire!

Photos © Alina Cansler.

Students: Plant Survey Volunteers Needed!

Looking to pick up some valuable field experience this September? SEFS doctoral student Apryle Craig is recruiting several volunteers to help her survey plants at deer exclosures as part of a study investigating the impacts of recolonizing wolves on deer herbivory! You’ll gain experience with using a GPS, identifying plants, common plant survey techniques, installing trail cameras, repairing large herbivore exclosures, and more—all while spending time out in the forests of northeast Washington.

Job Description
You will be identifying and measuring plants at deer exclosures in Apryle’s study area. This work involves a lot of kneeling, bending and crouching, and surveys require a high attention to detail during repetitive tasks. Volunteers should be comfortable working long days, hiking cross-country across uneven terrain for about a quarter mile at any given time, and carrying large, awkward fencing supplies. The crew will be moving rolls of fencing and cutting wire. Volunteers may also have the opportunity to install trail cameras, review camera footage, and more.

Volunteers must provide their own transportation to the site near Tonasket, Wash. At that point, a shared vehicle will be used to access the survey sites. Volunteers are responsible for their own food.

Dates
Time commitment is flexible, depending on applications received. Please let her know your availability between September 1 and October 5.

How to Apply
Email Apryle with your resume, two references, and your availability from September 1 through October 5. Please indicate if you feel comfortable identifying plants of northeast Washington, and if you have CPR and/or first aid training. No previous field experience required. Plant identification skills are useful but not necessary, and your safety in the field is always the top priority.

Photo © Apryle Craig.

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SEFS Hosts Observable Beehive for the Summer

On Tuesday, July 19, Alison Morrow from King 5 News brought a film crew to shoot some footage of the glass-enclosed observable beehive that we’re hosting this summer as part of the popular course, “Bees, Beekeeping and Pollination” (ESRM 491D for this quarter).

Evan estimates the hive in Winkenwerder is now home to some 4,000 bees.

Evan estimates the hive in Winkenwerder is now home to some 4,000 bees.

The course’s instructor, Evan Sugden, has been teaching the class for years through the Department of Biology, but construction of the new Life Sciences Building forced him and his bees out of their usual home at the Biology Greenhouse. So in addition to relocating six hives to neighborhood backyards around the area, including in Wedgewood and Madison Valley, Evan was able to move the course to a classroom in Winkenwerder Hall to keep the course running.

The observable hive, which has a vent to the outside, is fully safe and secure—for anyone worried about a bee allergy—and provides a wonderful teaching tool for students.

Watch the great segment on King 5, “Homeless honey bees find new home in UW science building,” which includes shots from the classroom and out at one of the neighborhood hives!

Photos © SEFS.

Evan Sugden

Evan Sugden and the observable beehive.

Professor Torgersen Helps Organize Riverscape Workshop in France

From June 22 to 24, USGS Landscape Ecologist and SEFS Affiliate Professor Christian Torgersen co-organized a workshop in Antony, France, “Putting the Riverscape Perspective into Practice: State of the Science and Future Directions in Freshwater Management.”

Sponsored and hosted by Irstea, the French National Research Institute of Science and Technology for Environment and Agriculture, the workshop focused on evaluating applications of the riverscape approach to address challenges for watershed and fisheries managers. The riverscape approach uses theories from landscape ecology and applies them to river ecosystems, and the workshop brought together scientists from Canada, France, Portugal, the United Kingdom and the United States.

Photo © Christian Torgersen.

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Christian Torgersen, back row, second from far right, with the workshop team.

 

 

Director’s Message: Summer 2016

Earlier this summer, I headed out to the field with one of my graduate students to conduct some initial soil sampling on a new set of plots in the San Juan Islands. With the assistance of our cooperators, the work went extremely smoothly, and we were able to catch the morning boat off Waldron Island.

Our good fortune on that trip reminded me of the short-term nature of graduate research programs, and how little room for error we often have with our projects. You generally have only two to five years to complete your whole master’s or doctoral program, which means your research efforts have to be meticulously planned and executed, with as little backtracking as possible. Yet these programs are often a student’s first or second serious research effort, so even with the guidance of a supervisor and graduate committee, errors, delays, missteps and revised study plans are the norm.

Tom collecting samples in Sweden.

Tom collecting samples in Sweden.

Research, especially at the graduate level, is a process of trial and error. It’s about generating a hypothesis based on observation or existing knowledge in the published literature, creating a reasonable set of experiments and experimental methodologies to test the hypothesis, and executing the work in the field, greenhouse or laboratory. This process can be excruciatingly slow for someone on a short timeline, and it requires graduate students to be exceptionally focused and nimble—and willing to absorb a fair amount of surprise—in order to nurture their work to completion.

With time and schedules so compressed, after all, our students don’t get to relax or head home for the summer; they head out into the field. Indeed these months, though deceptively quiet around campus, are often the peak season of research for graduate students. They have to maximize their production in the span of several weeks, knowing that even with the best-planned programs, data collection can go terribly wrong. Whether in the lab or far afield, students can be at the mercy of stochastic events, such as a wildfire (especially last year), animal intervention such as elk browsing on electrical wiring, or a simple human error, such as forgetting to start a data recorder.

For my own MS experience in Montana, I was investigating whether elemental sulfur inoculated with acidifying microbes could enhance soil phosphorus availability for plant uptake in alkaline soils. I used a combination of laboratory, greenhouse and field investigation to test my hypotheses. During my second summer (and only full field season), a farmhand plowed right across our carefully laid research plots, eliminating one out of my three field sites. I was fortunate that our missing data didn’t undermine my overall project, but I’ve never forgotten that my first publication included a table where dashes replaced numbers for that one site.

Still, for all the hang-ups and headaches, the stress of a graduate research program is hugely rewarding and beneficial. Our students learn how to be resourceful and innovative while maintaining the scientific integrity of the original project. They discover that no matter how tired, dirty and hungry you might be on those long field excursions, you can never sacrifice the rigor of your research. You might not have another chance to conduct the study, and you can’t predict how cutting corners will impact your findings. While the pressure can be exhausting in the moment, it breeds precisely the discipline that will make your future research and career successful.

So as I look at the travel request forms from our students this summer, I can’t help but muse about the effort and planning that went into preparing for this field season. Dozens of projects are well underway or just getting started, including programs exploring fire, earthworms and phosphorus cycling in northern Japan; fisher reintroduction in northern Washington; carbon cycling in the Columbia river basin; pollution influence on microarthropods of forest canopies of western Washington; epiphytes and canopy soil development on the Olympic Peninsula; influence of salvage logging on site recovery in eastern Washington; the displacement of passerines (songbirds) by various human activities in Denali National Park in Alaska; and numerous other fascinating projects.

The next couple months offer a precious window of research activity for these graduate students. They’ll be learning on the go, adapting to a host of hiccups and hardships, and shepherding their research through it all. That experience, from the development of their projects to their growth as people and scientists, will be priceless.

Tom DeLuca
School of Environmental and Forest Sciences