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.


See the Signs!

The next time you venture over to the Washington Park Arboretum, you’ll probably notice more than 30 new signs now spread throughout the park to provide way-finding and other educational information to visitors!

Bald Cypress

This “Bald Cypress” sign is one of several additions you’ll find along the new “Pinetum Loop” trail in the Arboretum.

Part of a three-year project involving Seattle Parks and Recreation, the University of Washington Botanic Gardens and the Arboretum Foundation, the signage effort coincides with the opening of two new interpretive trails at the 230-acre Arboretum: the half-mile “Pinetum Loop,” and the one-mile “Lookout Loop.”

These additions address a common suggestion from visitor surveys about providing more information and interpretation of the Arboretum’s collections. Planners took special care during installation, though, to make sure the new signs were as unobtrusive as possible, providing a wealth of educational context without affecting the aesthetic enjoyment of the park.

Of course, we can talk about the new signs and trails all day, but the best way to explore the changes is to head over and see for yourself! To direct your journey, the UW Botanic Gardens has created new trail maps that are available online (in PDF) or in print at the Graham Visitors Center.

For more information about the new signage and trails, contact UW Botanic Gardens Director Sarah Reichard.

Azalea Way

Arboretum to Unveil New Zealand Collection

Coming up on Sunday, September 15, from 11 a.m. to 2 p.m., the public is invited to attend the official dedication of the New Zealand Forest, the most significant addition to the Washington Park Arboretum in decades!

First conceived nearly 10 years ago, the 2-acre New Zealand collection will feature more than 10,000 plants, shrubs and grasses that are found on New Zealand’s South Island. The exhibit—located on a boulder-strewn hillside crisscrossed with rock swales—is the second of five eco-geographic forests to be completed in the Arboretum’s Pacific Connections Garden, which will eventually cover 14 acres and be the largest exhibit of its kind in North America.

New Zealand Forest

The New Zealand Forest under construction this past May.

Construction of the New Zealand Forest cost roughly $2 million, with funding from the Arboretum Foundation and the 2008 Parks and Green Space Levy, and planners are extremely excited to see the garden opened to the public.

“This is our legacy to leave behind for future generations to enjoy, like Azalea Way or the Winter Garden,” says Fred Hoyt, associate director of the University of Washington Botanic Gardens (UWBG), which owns and manages the collections at the Arboretum.

The opening celebration—organized in partnership with the Seattle-Christchurch Sister City Association and the Burke Museum of Natural History and Culture—will pay homage to New Zealand’s culture and ethnobotanical history. The dedication will include a Māori dance troupe from Vancouver, British Columbia, to perform a traditional “haka,” or war dance. Caine Tauwhare, a Māori wood carver who carved the slats for a park bench in the new forest, is also traveling from Christchurch (Seattle’s sister city in New Zealand) for a demonstration. Members of the local Muckleshoot Tribe will be there to greet the Māori, who by custom won’t enter a new land until the native people have welcomed them. (In the lead-up to the formal dedication, the Burke Museum will be highlighting its New Zealand collection, and the Māori dance group and carver will be there on Saturday, September 14, for a separate performance and demo.)

Sunday’s festivities will also include a host of speakers, including speeches from Seattle Mayor Mike McGinn, UW Vice Provost for Global Affairs Jeffrey Riedinger, New Zealand Honorary Consul Rachel Jacobson, and senior officials from the University of Washington Botanic Gardens, Seattle Parks and Recreation, and the Arboretum Foundation.

New Zealand Forest

The New Zealand Forest last week, coming together beautifully in time for the public dedication.

Building the New Zealand Forest has been an enormous collaborative effort that has involved the support of many partners, including Seattle Parks and Recreation, the Arboretum Foundation and The Berger Partnership, the design firm hired for the project. UWBG Director Sarah Reichard and Hoyt have been closely involved in the planning and creation of this new exhibit since its inception, and they’re grateful for all of the community volunteers and energy, as well as the citizens of Seattle for supporting the levy that funded the garden’s infrastructure.

As the New Zealand Forest matures, it will be a spectacular new garden to enjoy at the Arboretum. Visitors will be able to immerse themselves in unfamiliar landscapes—modeled on actual plant communities from the South Island of New Zealand—and discover beautiful plants they’ve never seen before. When you do visit, though, be mindful that many of the plants will be small for a while yet. Of course, that’s part of the joy of a collection like this: It will continue growing and changing for as long as it’s here. “No garden is ever done,” says Reichard, and they will keep adding new plants for years to come.

Check back with UWBG closer to the date for the most updated schedule of activities. The dedication is free and open to the public—no ticket or RSVP required—and will take place at the Pacific Connections meadow at the south end of the Arboretum. There will be live music, a ribbon cutting, cake and lemonade, and tours of the new garden. So come out and explore the New Zealand Forest!

Parking and Transportation
Arboretum Drive will be open to one-way traffic, going south, for the duration of the event. Parking will be permitted along the right-hand side of the drive, as well as in designated Arboretum parking lots. To help reduce traffic, please consider using public transportation, or coming by bike or on foot.

New Zealand Forest
Photos © SEFS.