Taking Flight: Lisa Hannon Heads South for Research Trip to Costa Rica, Argentina

This past February and March, SEFS doctoral student Lisa Hannon took advantage of a rare opportunity to combine a research visit to Costa Rica with an intensive field course in Argentina studying hymenopterans, the third largest order of insects, including wasps, bees and ants.

Hannon, left, with with fellow HYM Course students from Alaska and Taiwan.

Hannon, left, with with fellow HYM Course students from Alaska and Taiwan.

An NSF Graduate Fellow, Hannon works with SEFS Professor Sharon Doty in the Plant Microbiology Lab, and some of her research involves studying agriculturally important microbes associated with sustainable Coffea arabica production. She also is researching how landscape and farmer practices in coffee plantations impact parasitoid wasp communities, which is important for integrated pest management.

Improving the sustainability of coffee production is a huge research area—whether through reducing the reliance on chemical inputs (e.g. fertilizers, fungicides, herbicides or pesticides), or by maintaining natural areas to provide habitat for native pollinators or parasitoid wasps. Globally, more than 100 million people depend on coffee production for subsistence; in Mexico and Central America alone, the production and processing of coffee employs approximately 8.5 million people.

So for the first leg of her trip in Costa Rica, Hannon spent a week meeting with research collaborators and visiting her coffee plantation field sites. “Usually, I am in the Tarrazú Valley during the rainy season, when there is greater biodiversity of bees and wasps,” says Hannon. “My field sites are located in the cloud forests on Costa Rica’s Pacific slope, so we typically receive three meters of rain while I’m there sampling. So traveling this year during the dry season to see the coffee harvest was a nice change of pace for me.”

Argentine micro-hymenoptera (4 mm)

Argentine micro-hymenoptera (4 mm)

For the second leg, Hannon then continued south to the highlands of northwest Argentina to participate in a professional hymenopteran course, known as HYM Course, sponsored by the Smithsonian Institution. She joined a group of 20 researchers selected to attend; most were from North, Central and South America, but some traveled from as far away as Australia and Angola. Course participants included other graduate students, university professors, laboratory technicians and even two curators from the American Natural History Museum in New York. They received highly specialized training in identifying parasitic and predatory wasps, sawflies, wood wasps, bees and ants—all in a novel and unfamiliar location—and they learned taxonomic identification, advanced field collection methods and specialized preservation techniques.

“This course was a wonderful opportunity not only to receive individualized instruction from expert researchers, but also to meet potential collaborators for future projects,” says Hannon. “I feel very fortunate for being selected to attend.”

Photos © Lisa Hannon.

Hannon sampling in the Sierra Velasco mountains at the former Argentine president’s private hunting lodge.

Hannon sampling in the Sierra Velasco mountains at the former Argentine president’s private hunting lodge.

 

Magical Microbes: Using Natural Endophytes to Remove Environmental Pollutants

A few weeks ago, we reported about a new publication in Environmental Science and Technology that involves several authors in Professor Sharon Doty’s Plant Microbiology Lab. In the paper, “Degradation, Phytoprotection and Phytoremediation of Phenanthrene by Endophyte Pseudomonas putida, PD1,” Research Scientist Zareen Khan and her co-authors—David Roman, Trent Kintz, May delas Alas, Raymond Yap and Professor Doty—demonstrate the ability of willow trees and grasses, inoculated with a specific bacteria, to remove a serious pollutant from the environment.

It’s exciting research, and one of the most impressive angles is that four of the paper’s authors were undergraduates in Doty’s lab while contributing to the project.

Zareen Khan

Research Scientist Zareen Khan, lead author on the recent publication, joined the Doty lab in 2010.

One of those students, David Roman, graduated in 2012 and is now working at an analytical testing laboratory in Seattle. When he first came to SEFS six years ago, he was an older student and says he was eager to get involved in research as quickly as possible. Yet since he was transferring from North Seattle College, he was one of the last to pick courses during his first quarter. That delay ended up being a fortuitous break, though, as he found a late spot in one of Professor Doty’s classes, where he learned about phytoremediation—the use of plants to clean up pollutants from soil and water.

The success of phytoremediation depends on a number of factors, from the type of plant being used to the level of toxicity in the soil, which can stunt or kill a host plant before it can be effective. But one emerging strategy to enhance and accelerate the process—the subject of the paper, and a major focus of the Doty lab—involves inoculating the plants with naturally occurring microbes (endophytes) that live inside plants to create a powerful and mutually beneficial relationship.

Like microorganisms that live within humans, microbes within plants are important for plant health, providing nutrients and increasing stress tolerance, and in some cases detoxifying pollutants the plants take up. Endophytes are a subset of this microbiota that live fully within plants; they do not cause disease, but rather act as symbiotic partners. These microbes have fast generation times and can rapidly evolve abilities to detoxify or metabolize chemicals. Trees like willows and poplars have much slower generation times, but they can use partnerships with these bacteria to help them survive in harsh environments. Specifically, endophyte-assisted phytoremediation couples the better pollutant degradation abilities of microbes with the plant’s ability—via extensive root systems and uptake of air pollutants through leaves—to absorb pollutants from a wide area.

The result is a completely natural environmental scrub, and the concept immediately hooked Roman. “So many people in the environmental science fields are trying to find some way to stave off the carbon wave that is coming—that is already here,” he says. “The thing about phytoremediation is that we’re cleaning up the messes we’ve already made and taking back land we’ve lost.”

David Roman

Roman was especially drawn to the power of these microbes to help reclaim polluted landscapes. “We don’t need to point a finger at anybody,” he says. “The trees don’t care who was here beforehand; they’re just here to help.”

Halfway through his first quarter, Roman approached Doty to see she if needed any extra help in the lab. By the next quarter, she was able to bring him in to assist with a number of projects, and within a month she’d hired him as a lab assistant. Soon he was fully immersed in phytoremediation, spending about 30 hours a week on independent research (ESRM 499), while also going to school full-time and working another 30 hours a week in the Doty lab.

Roman couldn’t get enough of the research, and he especially loved the simplicity and sustainability of using poplars and willows as natural cleaning agents. “The way you plant them,” he says, “is to cut a branch off an existing tree, stick it in the ground, and in a couple months you have an actively working, phytoremediating tree. You’re talking about a very sustainable and functional natural process that doesn’t take a lot of machinery or extra fuel—and it works.”

The subject alone was enough to motivate Roman. But a big part of what makes working in the Doty lab so special, he says, is that undergraduates are given all the tools and freedom to thrive as researchers, from hands-on guidance to collaborative opportunities with fellow students. “Sharon and Zareen really mentored me and were always open for discussions and ideas. You felt supported, and that confidence in your work and really pushes you to do as much as you can.”

By the end of his time with SEFS, in fact, Roman had produced a 26-page research paper of all the experiments he had completed in two-plus years of work—and, of course, gotten his name on his first scientific publication.

“It took me six years to graduate,” he says, “which was wonderful in every way but the bill I got afterwards from Sallie Mae. Yet I wouldn’t have traded my time in the Doty lab for anything.”

Local Applications
Another exciting dimension of phytoremediation is the potential for using the technology right here in Seattle (not to mention its applicability to other polluted and brownfield sites around the world). Managed by Seattle Parks and Recreation, Gas Works Park was originally home to a coal gasification plant that operated from 1906 to 1956. The soil and groundwater at the site remain contaminated by polycyclic aromatic hydrocarbons (PAHs), including phenanthrene, which the Environmental Protection Agency has listed as a “priority pollutant” because of its carcinogenicity and toxicity.

Gas Works Park

Seattle’s Gas Works Park, where a coal gasification plant operated for 50 years until 1956.

Carcinogenic pollutants like phenanthrene are widespread in our environment, but effective technologies to remove them are limited. Common mitigation solutions involve excavation and indefinite storage of the contaminated soil, or capping a site to cover up contaminated areas; both approaches can be expensive, and the latter often involves repeated rounds. Gas Works Park, for instance, was initially capped with 1.5 feet of clean soil, which provides a buffer and removes the threat to park visitors. But occasionally the pollutants seep up near the surface, and the park has to be closed for recapping—which is happening right now—to make it safe again.

That’s what makes Gas Works Park such an ideal test ground. Doty’s lab has isolated a natural microbial endophyte that is able to tolerate and break down phenanthrene while also preserving the host plant. So if willow shrubs are colonized with this bacterium and planted at the park—either all at once, or in sections for several-year intervals—they should be able to solve the park’s contamination problem naturally, permanently and far more cheaply than capping.

Willows are particularly well-suited for the job since they are native to Washington, highly adaptable and can grow five to six feet a year, with rapidly spreading root systems to maximize their reach in absorbing pollutants. Plus, after several years of work, they could be removed and the park restored to its former condition—minus much of the contamination. Yet even if people are adamantly opposed to planting willows, says Doty, they could still inoculate the grass with the same endophytes. The grass might not be as effective as the willows, but it would still begin removing some of the soil contaminants.

Before implementing any of these strategies, though, several big questions would need to be resolved, starting with figuring out what the public and other stakeholders would think about having phytoremediation introduced at Gas Works Park.

Ellen Weir

“The most exciting part for me, by far, is the ability of plant-microbe interactions to accomplish all these different things,” says Weir.

That’s a question one of Professor Doty’s doctoral students, Ellen Weir, is hoping to answer with her research into the social acceptability of phytoremediation. She’s currently collecting direct public input and determining whether the community would be okay with allowing phytoremediation at Gas Works Park—and, if so, under what conditions.

“If we had the same piece of land outside the city, it would be way easier to implement phytoremediation,” she says. But with an iconic park in the heart of Seattle, accounting for the social environment makes the task immensely more nuanced and delicate.

Weir set out several months ago by contacting community groups and putting out bulletins to organize focus groups of four to eight people. She sat down with these groups and had conversations about what phytoremediation is and how it might be implemented at Gas Works. She recorded their thoughts and concerns and used that feedback to develop surveys for a broader subset of the population. She then distributed those surveys by handing them out to park visitors at different times, as she wanted to make sure she was hearing responses from actual users.

So far, she’s heard back from about 140 responders, and Weir says that despite seeing some trepidation about implementing an unfamiliar solution, the reactions overall have been positive and do not preclude the use of phytoremediation. Some of the biggest concerns include whether phytoremediation is a contamination risk to park users, or whether the technology involves the use of any genetic modification (no and no, incidentally). Another worry is that the willows will obstruct the view and traditional experience of the park. More than anything, though, she has learned how invested people are in the long-term health and use of the park, and how much they want to be involved in important decisions regarding its future. “That’s why it’s so critical to take into account the views and perspectives of all stakeholders,” she says.

As she continues to collect the final surveys and analyze her data, Weir hopes to have more concrete results in the next couple months—and when she’s done, she will have filled a major hole in the decision-making process. When she started her research, after all, no one knew what the public thought about phytoremediation as an alternative to capping at Gas Works Park. Now, when Weir’s research is complete, managers will have more information to guide future management decisions at the park, and that could open the door for some magical microbes to do their work.

Photo of Zareen Khan © Sharon Doty; photo of David Roman © Sharon Doty; photo of Gas Works Park © Wikimedia Commons; photo of Ellen Weir © Ellen Weir; photo of lab experiment (below) © David Roman.

Endophytes

Recognition Event: Honorees and Auction Results!

Yesterday afternoon—Monday, May 19—a great crowd of students, staff and faculty gathered in the Forest Club Room for the annual SEFS Recognition Event. It was a high-spirited celebration of our school and community, including the presentation of a number of awards, recognition of retiring faculty (David Ford and Frank Greulich), fantastic catered snacks and enough wine to keep a cruise ship afloat.

Silent Auction

Browsing some terrific options for the Silent Auction.

It also looks like we eclipsed our total from the Silent Auction last year and should raise more than $3,100 for the SEFS Student Scholarship Fund. Nice work, everyone!

In case you missed the fun, below are the honorees for this year’s awards. Congratulations to all of you, and to the many other tremendous nominees!

Staff Member of the Year: Amanda Davis*
Faculty Member of the Year: Sharon Doty*
Graduate Student of the Year: Hyungmin “Tony” Rho*
Undergraduate Student of the Year: Alison Sienkiewicz*

Director’s Award for Faculty Service: Sarah Reichard
Director’s Award for Staff Service: Theresa Santman

The John A. Wott Fellowship in Plant Collection and Curatorship: Eve Rickenbaker
The Richard D. Taber Outstanding Wildlife Conservation Student Award: Kyla Caddey

* Each of these honorees will have his/ her name engraved on a permanent plaque display in Anderson Hall, to be unveiled later this summer.

A HUGE thanks, as well, to everyone who helped pull this event together. Contributions were many and much appreciated, including: Greg Ettl for serving as Master of Ceremonies; Vince Gallucci and Ettl for commemorating departing faculty; Nevada Smith for arranging the catering and door prizes; Abraham Ngu and Amanda Davis for helping set up the room in advance; Michelle Trudeau for impressively folding every single program; Steve West for organizing another spectacular wine tasting; the awards committee for reviewing an exceptionally large and competitive candidate pool; and everyone who donated—and bid on—the wonderful prizes and experiences for the Silent Auction. I know I’m forgetting some important contributors, but know that I appreciated every nudge of help and support. Thank you!

Photos © SEFS.

Silent Auction

SEFS Grad Student Hyungmin Rho Presents Research at Conference in Florida

Hyungmin “Tony” Rho, a second-year doctoral student at the School of Environmental and Forest Sciences (SEFS), recently presented some of his research at the 2013 ASA, CSSA and SSSA International Annual Meetings in Tampa, Fla., November 3-6. A joint meeting of three different societies—the American Society of Agronomy, the Crop Science Society of America, and the Soil Science Society of America—this year’s conference focused on the theme, “Water, Food, Energy & Innovation for a Sustainable World.”

Tony Rho

Tony Rho with rice plants in the Douglas Conservatory at the Center for Urban Horticulture.

Rho, who works with Professor Soo-Hyung Kim in the Plant Ecophysiology Lab, presented his poster, “Bacterial Endophytes Living in Intercellular Spaces of Leaves Lower Leaf Water Potential of Rice (Oryza sativa) Plants,” during the “Crop Physiology and Metabolism” session. His research is funded by USDA-NIFA and is the collaborative work of three labs, including Professors Kim and Sharon Doty at SEFS, both of whom were coauthors for his oral presentation. Other SEFS grad students involved in this research include Evan Henrich and Shyam Kandel.

“I believe these beneficial bacteria could be one of the potential bio-fertilizers in the future that can mitigate the climate change impacts derived from the current agricultural practice of using extensive amounts of nitrogen fertilizers,” says  Rho. “My presentation gave a good glimpse of our novel approach to mitigate climate change impacts, and I got positive feedback from the audience.”

In addition to giving a presentation, Rho attended other sessions about current research trends and got to meet with a wide range of scientists and grad students. “I think it was a perfect opportunity for me to make social and professional connections throughout the conference,” he says, “as well as to introduce myself and my research.”

To assist with the cost of travel and attending the meetings, Rho received financial support from Director’s Student Travel funds at SEFS, and also from the Graduate School Fund for Excellence and Innovation (GSFEI).

Photo of Tony Rho © Tony Rho.

Thesis Defense: Mahsa Khorasani!

Masha KhorasaniThis Friday, May 24, at 11:30 a.m. in Anderson 22, Mahsa Khorasani will be defending her Master’s Thesis: “Cylindrocarpon species in Pacific Northwest Douglas-fir Nurseries: Phylogeny and Effects of Temperature and Fungicides on Mycelial Growth.”

Douglas-fir nurseries play an important economic role in the Pacific Northwest timber industry. However, there are various types of fungi that cause the early death of seedlings and influence regeneration success. One of the destructive fungus root rot pathogens, Cylindrocarpon, causes the loss of seedlings in early stages of their growth.  The objectives of this study were to: (1) identify the species of Cylindrocarpon occurring in three different nurseries in the Pacific Northwest, (2) investigate the effect of temperature on the growth rate of the mycelia of these fungus pathogens in vitro, and (3) determine the influence of some major fungicides on the control these pathogens.

Khorasani’s results have implications for nursery pathology in the identification and control of seedling root rot of Douglas-fir, so come out and learn what she discovered!

Her committee chair is Professor Emeritus Bob Edmonds, and other committee members include Professor Sharon Doty, along with Joseph Ammirati, Willis Littke and Rusty Rodriguez.

Xi Sigma Pi Announces Research Grant Winners for 2013

Xi Sigma PiXi Sigma Pi, the Forestry Honor Society founded at the University of Washington in 1908, is proud to announce the recipients of this year’s research grant funding. After long and hard deliberation, and the careful review of many highly competitive proposals, the following winners were selected:

Two First Place Winners of $500 each:
Oliver Jan, “A mechanistic approach towards lignin char reduction and valorization in catalytic fast pyrolysis through bifunctional Pd/ZSM-5 catalysts” (Faculty Advisor: Fernando Resende)

Luyi Li, “The effects of soil parent material and fertilization treatment on the wood quality of Douglas fir in the Pacific Northwest” (Faculty Advisor: Eric Turnblom)

Second Place Winner of $250:
Sebastian Tramon, “The mystery of conservation outcomes: Looked through institutional lenses” (Faculty Advisor: Clare Ryan)

Undergraduate Research Winner of $250:
Raymond Yap, “Colonization, degradation of Trichloroethylene and comparison of phytotoxicity in plants inoculated with endophyte PDN3″ (Faculty Advisor: Sharon Doty)

Congratulations to all of the grant recipients, and Xi Sigma Pi extends a big thank you to the grant review committee!