Round up of ESA conference

The 2017 ESA meeting in Portland, OR, which took place August 6-11, created a flurry of imagination here in Eugene: Roo Vandegrift left with a large hash of approximately 275 live-tweets, Sue Ishaq left with a jumbled pile of hastily scribbled notes in the program book margins, a few of which she has expanded upon, and Ashkaan Fahimipour went away with the inscrutable expression of a mathematical modeler visualizing complex networks in their head. All three presented some of their recent or ongoing work, along with a number of other BioBE members and friends from the UO Institute of Evolution and Ecology.

The meeting started out with a number of engaging science activities, including the Field-to-Collection BioBlitz, which brought conference participants to Forest Park in Portland to collect biological samples for identification and curation. Forest Park is the largest urban forest in the United States, and the biological specimens collected will shed light on the number and types of diversity found there, as well as indicate the success of urban forests at harboring a sustainable level of biodiversity.

The plenary speech was given on Sunday evening, officially opening the conference, and presentations kicked off bright and early on Monday morning. Of the BioBE team, Roo was first to give a presentation on Monday afternoon, on a project led by the recently-defended Dr. Ashley Bateman for her dissertation: Moving Microbes: the dynamics of the skin microbiome in response to environmental exposures. (Revised; listed as “The built environment as a reservoir for transmission and colonization of the skin microbiome.”)

 

 

Erica Hartmann, Assistant Professor at Northwestern University, presented on Tuesday with a compelling talk on the importance of limiting antimicrobial chemicals in synthesized products: Antibiotic resistance and antimicrobial chemicals in the built environment. Antimicrobial chemicals are pervasive in the built and outdoor environments, much more than we realize, yet we have little knowledge of their long-term effect on microorganisms or how this might feed-back onto human health. The full publication can be found here.

Gwynne having a delightful time at her poster.

On Tuesday evening, doctoral candidate Gwynne Mhuireach presented her poster on Fine-scale urban vegetation patterns shape airborne microbial community composition.

Wednesday evening, Sue presented some preliminary data on a project she is finishing up from her post-doc: Soil bacterial diversity in response to stress from farming system, climate change, weed diversity, and wheat streak virus (poster). A more detailed description of her previous work can be found here.

Ashkaan gave a presentation on Thursday on The dynamics of food web assembly: Structure, stability, and trophic cascades.  The study explored how empty ecosystems acquire new species, how the food web develops over time, and how the trophic niches of those colonists can determine the total diversity of the ecosystem or weather disturbances. The large meeting room was well-attended, despite the low total abundance pictured- ecologists don’t seem to like to sit in the front rows.

 

In between our presentations, we filled our days by attending other talks and posters, networking events, and daydreaming about our own science.  We took away valuable perspectives on newly discovered results, considerations for data analysis, or the dynamics of ecological systems, which can be incorporated into our own work to improve how we think about indoor systems and approach problem solving.  You never know when a presentation on shower heads, baboons, or dormant amoeba might give you an idea which will change the way you think.

Looking ahead, we are anticipating attending a number of conferences on microbiology, air quality, building health, architecture, and ecology over the next year. Here are a few of the meetings that are already on our calendars:

Report from the Mycological Society

In July, one of our own, Dr. Roo Vandegrift, went to the annual Mycological Society of America (MSA) meeting, held just outside of Atlanta, Georgia, in the college town of Athens. He went to learn what others in the field are up to, and present work from the BioBE Center. Roo live-tweeted most of the talks he went to; you can find him @MycoRoo on twitter to look back through his experience of the conference, and look up the hashtag #MSA17 or #MSA2017 to see other posts about the conference.

The meeting started with a pre-conference foray: a group of nearly one hundred mycologists loaded into three packed busses and went out to Unicoi State Park for a 3.5 mile hike; collecting mushrooms, ascomycetes, and plant pathogenic fungi all the way. It has apparently been a particularly wet summer in Georgia so far, and the fungal diversity on display was astonishing, particularly coming from Oregon, where our summers are dry and a bit mycologically deprived.

On Monday morning, the day started with the Presidential Address from outgoing president, Dr. Georgiana May, titled “Lucky: A career in mycology.” She gave a rolling account of a career full of lucky breaks and fortuitous moments, which she made the best possible use of with her sharp and grateful mind. She also included a number of historical anecdotes that had the audience in stitches of laughter, and sometimes on the verge of tears. She asked that the contents of her talk remain private, though, so that’s as much detail as I’ll give here.

The first session of talks that I went to was the Ecology & Conservation section, which started with Terry Henkel presenting some amazing work from his lab on the Thelephoralean ectomycorrhizal fungi of a monodominant tropical forest in the Guyana shield region of South America, and how these fungi may be involved in seedling survival and recruitment in this forest. The discussion of this system continued with the next talk in the session, from Terry’s graduate student, Carolyn Delevich, who gave a fascinating discussion of the community assembly of ectomycorrhizal fungi on the roots of these dominant Fabaceae trees, looking at the change in the community over time on the seedlings from one of these mass fruiting events.

There were a number of other excellent talks about mycorrhizal communities, highlighting the cutting edge of molecular techniques in fungal community ecology, host-associated dynamics, and spatial/temporal ecology. Dr. Alija Mujic’s talk on invasion dynamics in mycorrhizal communities of Nothofagus in Patagonia was particularly good.

At the end of that first day, Roo presented his talk: “Impacts of Weatherization on Indoor Fungal Communities“, co-authored with other BioBE personnel, as well as colleagues from the Oregon Research Institute and Northwestern University (Roo Vandegrift, Ashkaan Fahimipour, Jeff Kline, Alejandro Manzo, Dale Northcutt, Jason Stenson, Hannah Wilson, Ryann Crowley, Erica Hartmann, Deborah Johnson-Shelton, G.Z. Brown, Jessica Green, Kevin Van Den Wymelenberg). This talk debuted preliminary data from our EPA-funded study examining a multi-faceted, interdisciplinary dataset combining microbial ecology, indoor air quality, and an extensive survey detailing aspects of health and behavior. Feedback was incredibly positive and encouraging, including some really helpful feedback on biophysical explanations for observed trends in the data.

There were a handful of other talks that stood out as particularly important or impactful. Mara DeMers, from the University of Minnesota, Twin Cities, presented on endophytic fungi in prairie plants, and whether molecular OTUs (or ESVs, for that matter) correspond to species; she asks the question does it matter if they do? She was particularly vexed by the genus Alternaria, which made up most of her endophyte sequences, and appears to be non-resolvable into meaningful groupings via ITS alone — the region is so variable in this group (and other!), that the intra-strain variation is as great as the inter-strain variation, meaning that the same sequence may belong to totally different strains, while very different sequences may belong to extremely closely related individuals. This is an important caution for the field, and one we at the BioBE Center will certainly keep in mind!

Among the amazing talks, excellent company, and stimulating scientific conversations, Dr. Regine Kahmann (from Max Planck Institute for Terrestrial Microbiology) presented the the Karling Lecture, titled “Core Effectors in Smut Fungi: An Amazing Treasure Box.” This was an incredible summary of her life’s work on the molecular mechanisms underlying the pathogenicity and ecology of smut fungi (Ustilagomycota). The careful, methodical, innovative science on display during her talk was breathtaking, and an inspiration.

One other talk strikes me as worth explicit mention here: Jesse Uehling’s discussion of how to re-purpose archived data in new ways. I think there’s an important lesson here; we are generating sequence data much more rapidly than we are currently exhausting the ways that such data can be explored, and the techniques for exploring that data are evolving extremely rapidly. As Jesse says, there may be treasure in that trash!

One idea from her talk that struck me as particularly significant was that the “junk” reads from genomic assemblies are typically reads representing the microbiome of whatever organism was sequenced. It is certainly worth considering that there may be a large quantity of un-examined microbiome data available from a wide range of organisms, if we only go looking through the available raw data. And, the assembly of small bacterial genomes from mixed starting templates has been well demonstrated.

There were many other noteworthy aspects to this meeting; it is worth browsing the #MSA17 tweets if you’re interested. We hope for many more productive, fascinating meetings like this in the future!

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Roo wore a different mushroom-patterned bowtie every day of the meeting. We’re not sure why he was so pleased about this.

BioBE and ESBL are seeking a new Office Manager!

BioBE and ESBL are looking to a hire an office manager to support our teams!  The full position description and application can be found here.

The position will serve as the primary business officer in charge of coordinating and supporting both labs’ fiscal and administrative operations. In this capacity, the OM assists the lab director, research faculty, research staff, and students in developing and executing annual operating plans, conducting budget forecasts, identifying and procuring grants and contracts, building budgets and scopes of work for proposals, managing allocations of space/equipment and staff resources, and participating in and developing sales and client relationships.

As such, we are looking for someone with excellent written and oral communication skills, who can dynamically interface between the biology and building design teams and our administrative needs.  We need someone who has experience in project management and budgeting, who can properly handle confidential information, and who can proactively engage with team members and clients to identify potential conflicts and solutions.  This position will require you to work independently, and may require occasional nights and/or weekends to fulfill special projects or events, as well as the timely interaction with clients.

Minimum Requirements
• Bachelor’s degree from accredited college or university.
• Five or more years of administrative experience, or relevant transferable experience.
• Experience managing a budget, or relevant transferable experience.
• Experience in a lead or supervisory role.

Preferred Qualifications
• Master’s degree or advanced degree in relevant field
• Research and/or grant management experience
• Demonstrated knowledge of regulatory issues related to sponsored projects and an ability to satisfy federal, state and university regulations, while advancing the goal of creating a facilitative environment for faculty research.
• Expertise with Banner and EPCS systems.

BioBE presentations at the ESA meeting next week

The 2017 Ecological Society of America (ESA) conference is being held next week in Portland, OR, at the Oregon Convention Center, and members of the BioBE team will have a strong showing. After the conference, we’ll be sure to have a round-up post with more information on our presentations.

Dr. Roo Vandegrift: OOS 3-4 — Moving Microbes: the dynamics of the skin microbiome in response to environmental exposures. (Revised; listed as “The built environment as a reservoir for transmission and colonization of the skin microbiome.”) Monday, August 7, 2017: 2:30 PM, Portland Blrm 256.

Ashley Bateman1, Roxana Hickey2, Ashkaan K. Fahimipour3, Roo Vandegrift3, Brendan J.M. Bohannan3 and Jessica L. Green3, (1)Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, (2)Phylagen, San Francisco, CA, (3)Institute of Ecology and Evolution, University of Oregon, Eugene, OR

Dr. Erica HartmannOOS 17-9 — Antibiotic resistance and antimicrobial chemicals in the built environment. Tuesday, August 8, 2017: 4:20 PM, Portland Blrm 258.

Erica Hartmann1, Roxana Hickey2, Tiffany Hsu3, Jing Chen4, Clarisse M. Betancourt Román2, Adam J. Glawe1, Jeff Kline5, Kevin Van Den Wymelenberg5, G.Z. (Charlie) Brown5, Rolf U. Halden4, Curtis Huttenhower3 and Jessica L. Green2, (1)Civil and Environmental Engineering, Northwestern University, Evanston, IL, (2)Institute of Ecology and Evolution, University of Oregon, Eugene, OR, (3)Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, (4)Biodesign Center for Environmental Security, Arizona State University, Tempe, AZ, (5)Department of Architecture, University of Oregon, Eugene, OR

Gwynne MhuireachPS 29-166 — Fine-scale urban vegetation patterns shape airborne microbial community composition (poster). Tuesday, August 8, 2017 from 4:30 to 6:30 PM, Exhibit Hall.

Gwynne Mhuireach1, Clarisse Betancourt2, Jessica L. Green3, and Bart R. Johnson4,(1)Department of Landscape Architecture, University of Oregon; Biology and the Built Environment Center, (2)Van Andel Research Institute, Grand Rapids, MI, (3)Institute of Ecology and Evolution, University of Oregon, Eugene, OR, (4)Department of Landscape Architecture, University of Oregon, Eugene, OR

Dr. Sue IshaqPS 31-13 — Soil bacterial diversity in response to stress from farming system, climate change, weed diversity, and wheat streak virus (poster). Wednesday, August 9th from 4:30 to 6:30 pm, Exhibit Hall.

Suzanne L. Ishaq1, Tim Seipel2, Alexandra M. Thornton2, and Fabian Menalled2, (1) University of Oregon, Biology and the Built Environment, (2)Land Resources and Environmental Sciences, Montana State University, Bozeman, MT

Dr. Ashkaan Fahimipour: OOS 43-3 — The dynamics of food web assembly: Structure, stability, and trophic cascades. Thursday, Aug 10, 2:10 pm, Portland Blrm 258. 

Ashkaan will be the opening speaker for this session, which will cover the establishment of interaction ecology as a discipline, particularly focusing on how recent developments contribute to basic understanding of ecological processes at multiple scales and to the solution of environmental problems across the globe. We will begin by providing a synthesis of key processes that act at different temporal and spatial scales to determine the organization of complex systems.

Congratulations to Dr. Ashley Bateman on her defense, next steps!

We made sure to send her off with some Oregon memorabilia.

Last week, BioBE said good-bye and good-luck to Ashley Bateman, who successfully defended her dissertation on May 25th.  Ashley has been with the department for 6 years, as a graduate student in the Institute of Ecology and Evolution at the University of Oregon.  She worked in the labs of Drs. Jessica Green and Brendan Bohannan, studying the human skin microbiome.  Her thesis, entitled “Moving Microbes: The dynamics of microbial transfer and persistence on human skin“, will soon be available through the University of Oregon library.

Starting in 2011, Ashley has had a very distinguished graduate career; in 2012 she received a  National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) award to conduct research on the transfer of microorganisms to human skin from contact sources, in 2013 she was named Outstanding Graduate Student by the UO Institute of Molecular Biology, in 2015 she received the William R. Sistrom Memorial Scholarship Award, and in 2016 she won a scholarship from the Women in Graduate Sciences organization at UO to attend the Pacific Northwest Women in Science Retreat.  She has already co-authored a number of cutting-edge papers, including the investigation of the human microbiome cloud, a meta-analysis on the indoor microbiome, and a review on human hygiene, as well as a number of other previously published and forthcoming articles.  Ashley has also been interviewed and has contributed blog posts on the implications of her work.  From here, she is headed to the University of California, Davis, to attend law school.  BioBE is going to miss her insight, her organizational skills and attention to detail, and her welcoming personality, but we are enthusiastic about the next step in her journey!

ESBL is seeking an Associate Director of Outreach in Portland, OR

The Energy Studies in Buildings Laboratory (ESBL) at the University of Oregon is seeking a new Associate Director of Outreach at the Portland location!

At ESBL, as part of the Department of Architecture, we research how buildings, related transportation and land use systems, climate, and human behavior, determine energy and resource use and impact human health. We develop new materials, components, assemblies, whole buildings, and communities with improved performance. We consult and develop design tools to enable professionals to design more effective buildings and communities. We educate professionals and students, so they develop the knowledge and skills necessary for improving building energy performance and human well-being. Finally, we collaborate with academia, government agencies, utilities, product developers, and the profession. ESBL works closely with the Biology and the Built Environment Center (BioBE) as ESBL Director, Dr. Kevin Van Den Wymelenberg, is Co-director of BioBE.  Examples of our collaborative work include how the shape of a building and its use affects microbial dispersal, or the effect of home weatherization on air quality and the indoor microbiome, and many other studies in our state-of-the-art climate chamber in Portland.

Together, BioBE and ESBL launched the Health+Energy Research Consortium (HERC) in May 2017 with their inaugural meeting, which brings university researchers and building science professionals together to exchange information on the built environment, assess the need for research that can provide answers related to design and health choices, and foster collaborations that benefit both the academic and industry sectors while providing a beneficial impact on human health, building design, and energy sustainability.  The Consortium aims to dramatically reduce energy consumption and maximize human health by conducting research that transforms the design, construction and operation of built environments. Collaboration between innovative industry professionals and academic researchers in the disciplines of architecture, biology, chemistry, engineering, and urban design provides sharp focus to our research agenda and accelerates the impact of our scientific discoveries.

Position Summary
The Department of Architecture seeks a creative and innovative faculty member for a faculty position to teach, secure and conduct research, oversee the Portland ESBL, and to cultivate outreach and engagement. The chosen candidate will support the ESBL director by leading the lab’s Portland-based outreach efforts by securing grants and contracts to fund the lab’s work. Specifically, the candidate will lead the effort to develop the HERC industry-university research consortium (following, in-part, the NSF IUCRC model). S/he will also be expected to contribute to ESBL’s teaching obligations to A&AA students in Portland, possibly including architectural design studios, environmental control systems, and related technical courses. The selected candidate will develop and maintain strong industry support for the University of Oregon HERC, thus this position will have a large outreach component. Finally, the selected candidate will share the obligation to secure and conduct research, technical assistance, and project based education in cooperation with ESBL faculty and staff and associated architectural and engineering professional design teams to support ESBL’s mission.

Minimum Requirements
• Terminal degree from accredited college or university.
• Three or more years of research or outreach administrative experience, or relevant transferable experience.
• Professional training or relevant transferable experience managing a budget.
• Experience in a lead or supervisory role.

The full job posting and application can be found here.

The initial review of applications begins August 1st, 2017, but the position will remain open to application until filled. We look forward to hearing from you!

HERC Recap: Artist Morgan Maiolie

How do you illustrate the microbiome of bacterial, fungal and viral communities to architects, engineers and building equipment manufacturers?  You commission an artist! During the events of Health and Energy Research Consortium, Morgan Maiolie was busy with a brush set to canvas. Associate Professor, and director Van Den Wymelenberg notes “We really wanted to find a way to bring the microbiome to life for the diverse consortium guests, so we decided to invite an artist to complete a live painting that responded to the research presentations.  Morgan Maiolie did an excellent job understanding and translating our scientific findings into her painting.  She made the microbiome vibrant and tangible!”

Morgan describes her inspiration, “The team of research scientists at the Biology and Built Environment Center and Energy Studies in Buildings Laboratory have illuminated the world of living, breathing bacteria swirling in the air around us and this piece visualizes that invisible world.  The researchers made me aware of the key role building design plays in shaping our indoor microbiome. Buildings can act as filters, petri dishes, and wind tunnels.  I wanted the painting to conceptually reveal how bacteria might move into and through a building based on its architecture, systems, and inhabitation.”

To learn more about Maolie and her work, please visit her website: maiolie.com.

This post is part of a blog series sharing information covered at the Health Energy Research Consortium in Portland, OR May 4-5, 2017. 

Daylight Exposure & Microbial Communities Indoors

The microbiome and its relevance to healthy environments was of critical interest at the Health Energy Research Consortium.  Ashkaan Fahimipour, presented BioBE‘s recent investigations in microbial communities and exposure to daylight.

Humans spend most of their time indoors, exposed to bacterial communities found in dust. Understanding what determines the structure of these communities may therefore have relevance for human health. Light exposure in particular is a critical building design consideration and is known to alter growth and mortality rates of many bacterial populations, but the effects of light on the structure of entire dust communities are unclear.

We performed a controlled microcosm experiment designed to parse the effects of filtered solar radiation on the structure of dust microbial communities.

We report that exposure to light per se has marked effects on community diversity, composition and viability, while variation in light dosage or particular wavelengths experienced are associated with nuanced changes in community structure. Our results suggest that architects and lighting professionals designing rooms with more or less access to daylight may play a role in shaping bacterial communities associated with indoor dust.

This post is part of a blog series sharing information covered at the Health Energy Research Consortium in Portland, OR May 4-5, 2017. View the original post on the ESBL blog.

Dr. Sue Ishaq joins the BioBE team!

Hello, readers! I’m Dr. Sue Ishaq, the newest Research Assistant Professor hire in the BioBE center at the University of Oregon.  I’ve been at the center for two weeks now, and I thought I’d introduce myself as I’ll soon be a regular contributor to the center’s research efforts and blog.  I’m a microbial ecologist with a focus on host-associated microbiomes. My baccalaureate and doctorate were both in animal science and nutrition from the University of Vermont, in Burlington.  As a Ph.D. student in the Wright Lab, my work focused on identifying and manipulating the bacteria, methanogens, and protozoa in the rumen of the North American moose.  For the past two years, I was a post-doctoral researcher at Montana State University, in Bozeman.  For one year, I was in the Department of Animal and Range Sciences performing the bioinformatic analyses for multiple host-associated and environmental projects in the Yeoman Lab.  My second year was in the Department of Land Resources and Environmental Sciences in the Menalled Lab, where I was part of a large project investigating the effect of climate change on wheat production.  For my part, this meant assessing the changes to soil bacteria over time and under different climate scenarios.

Here at the BioBE, I’ll be adding my experience in host-associated microbiomes, bacterial ecology, and health, to the growing collaborative research team.  Over the course of the summer, I’ll be writing several grants and organizing new projects that explore how building design, occupancy, pets, and human habits affect human health and the indoor microbiome.  If you happened to have been at the Health + Energy Research Consortium, held in Portland in May, you might have seen me around, and I’ll also be at the Ecological Society of America meeting in Portland, OR in August.  You can follow me on my personal blog and, of course, you can find me on the BioBE blog!

2017 AIA Design & Health Research Consortium Convening

On March 21-22, the BioBE Center team took to Detroit to present “Biology & Buildings: How Indoor Environments Affect Human Health” to the American Institute of Architects Design & Health Research Consortium.  We were encouraged to see the diversity of research blooming at our fellow ACSA schools of architecture. For example, Joseph Kennedy from the NewSchool of Architecture & Design presented fascinating work on natural building materials in a panel discussion with members of the BioBE team. Bita Kash from Texas A&M University presented excellent work on integrating health and design, discussing ideas of fundamental adjacencies in the design process. Every panel was excellent, and the broad concern for integration of empirical methods to design evaluation was wonderful to see.

Most interesting was to learn from leading architecture firms about how they integrate research into their design practices and how they have developed funding models to support this research.  Upali Nanda (@upalinanda) of HKS Architects (Houston) talked about the importance of pooling research resources and openly sharing new knowledge in order to more rapidly progress the field and avoid redundancy.  Jeri Brittin, Director of Research at HDR Architects (Omaha) eloquently described how the research design process shares similarities with the building design process and how she has effectively used this analogy to explain the value of a rigorous research design process to firm decision makers.  Robert Phinney (@rsphinney), Sustainable Design Director at Page Architects (Washington DC), described the uphill climb that many firms face when trying to meaningfully integrate original research into the building design practice, stressing that measurable outcomes and financial metrics dominate the discourse.  What was most encouraging was that all three firm leaders described the immense value to their firms and clients of maintaining a tight relationship with university research and how rewarding it can be to work with academics to leverage their technical skills to help overcome the “pain points” facing their practice.  We couldn’t agree more!

Some of our most rewarding research has been closely linked with practical industry needs. However, there are some challenges that we face in the academy when integrating our work with industry objective.  First and foremost, is to ensure academic integrity when creating the research design to avoid real or perceived biases associated with industry engaged research.  Without this, the research has no value to industry or to science.  Other important considerations is to be nimble enough to complete the research at the “speed of business” and to work out possible concerns with intellectual property.  All of these, and other concerns, can be, and have been overcome.  The result in an opportunity to bring the leading scientific processes and utmost rigor to important problems that face society.  Industry partners can help to focus academic research and help it gain traction to make greater impact more rapidly.  It is for these reasons that we have launched a new industry engagement model here at the University of Oregon.