In mid-October, The Alfred P. Sloan Foundation and The National Academies of Sciences, Engineering and Medicine co-hosted the MoBE 2017 (Microbiology of the Built Environment) Research and Applications Symposium, in Washington, D.C. The meeting brings together researchers, industry professionals, and funders to discuss the state of MoBE research and how to bridge the gap between research and application. Some of the opening remarks to the meeting were given by Paula Olsiewki, Program Director at the Alfred P. Sloan Foundation, who gave a retrospective on the history of MoBE and the process of growing research fields.
A number of BioBE members and collaborators were in attendance and gave presentations, including Jess Green, Co-Director of BioBE, who gave a brief history on the research of BioBE, followed by more detailed narratives on how ventilation and bioaerosols, daylighting, and antimicrobial compounds are driving community structure of the indoor microbiome. Jonathan Eisen, Professor at the University of California, Davis, gave some background on microBEnet and the massive effort to promote microbiology on social media and in education to give our work as much impact as possible. Richard Corsi, Professor at the University of Texas, Austin, who just spent two weeks visiting BioBE, spoke about indoor chemistry and how building design, materials, and the indoor microbiome can all affect the types and concentrations of chemicals indoor- often to the detriment of our health. Kent Duffy, architect at SRG, spoke about how microbial research has impacted architectural design, and how this information can be used to change the way we design spaces.
In addition to presentations on their recent work, a number of meeting participants also sat on several panels to discuss broader issues. For example, “The Myth and Reality of MoBE Manipulation” panel, moderated by Rob Knight, University of California San Diego and featuring Rita Colwell, Jeffrey Siegel, Ilana Brito, and Jessica Green as panelists, discussed the challenges to improving MoBE research and outreach. The panel discussed the need for more basic science and evidence-based applied studies, in order to make more informed decisions on when and how to make interventions.
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.
EcM diversity increases as you move AWAY from the equator — counter to most other diversity trends. But some exceptions, eg Guyana. #MSA2017
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!
ITS OTUs don't map well to species or sections within Alternaria. Variation at the ITS locus doesn't match multi-locus variation. #MSA2017
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.
Mating and pathogenicity are intimately linked in U. maydis. This process happens only inside the plants. #MSA17
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.
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.
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
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 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
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
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.
Postdoc Roxana Hickey presented “Microbial interactions between humans and the built environment” at the 21st Lake Arrowhead Microbial Genomics meeting held in Lake Arrowhead, California on September 18-22, 2016 (slide deck below). The biannual conference hosted more than 100 scientists and featured a variety of speakers (58% of whom were female!) highlighting research on the human microbiome, disease pathogenesis, population and evolutionary genomics, and cutting-edge omics techniques. Jonathan Eisen (UC Davis), a long-time attendee and promoter of the meeting, chaired a session on the built environment microbiome (Storify here) in which Dr. Hickey presented past and present BioBE research. Other talks in the session included microbial community assembly in cheese manufacturing (Rachel Dutton, UC San Diego), a citizen science study of the highly polluted Gowanus Canal in New York City (Elizabeth Hénaff, Mason lab @ Weill Cornell Medicine), community engagement through microbiome research aboard the International Space Station (David Coil, Eisen lab @ UC Davis), and evolution of biofilm formation in response to rising marine temperature (Alyssa Kent, Adam Martiny lab @ UC Irvine).
David Coil summarized each day of talks at the meeting on the microBEnet blog (day 1, 2, 3 and 4), and Jonathan Eisen created several Storify recaps of #LAGM16 tweets (here, here and here). The meeting was the most Twitter-active I (Roxana Hickey) have attended and contributed to yet, which facilitated active discussions with members both at and away from the meeting.
Here are my main three main takeaways from the meeting:
Metagenomics (and other ‘omic’ techniques) is gaining strength and popularity for a variety of applications. These include genome reconstruction across whole communities of microorganisms, strain-level diversity and population genomics, functional analyses, and development of targeted therapeutics and rational probiotics. There were very few amplicon-based studies at this meeting (I noticed a similar trend at the International Symposium on Microbial Ecology #ISME16 last month in Montreal). In addition, the tools used to analyze omics data are plentiful and sophisticated. I was especially impressed by work featured from the labs of Eric Alm (MIT), Jill Banfield (UC Berkeley), Kostas Konstantinidis (Georgia Tech), and Adam Phillippy (NIH).
Many are beating the drum for more reference genomes and cultured isolates. Human-associated bacteria are fairly well-represented in the databases, thanks in large part to the Human Microbiome Project, but for most other environments we have relatively low representation of the resident microbes. This dearth of reference genomes limits our ability to make inferences about the function and ecology of the vast majority of microbes on earth, as was highlighted in a recent update to the tree of life (Hug et al. Nature 2016). More and more scientists are shifting some of their efforts toward cultivation and sequencing of isolates from diverse environments.
Citizen science and community outreach are increasingly popular and wildly successful approaches to microbiome research. I was really excited to learn about the BKBioreactor Project on the Gowanus Canal (which made use of a community biohacker lab in Brooklyn), Project MERCCURI (which relied on crowdsourcing efforts to send microbes to space), and FijiCOMP (a really cool study looking at microbial transmission among members of a community in Fiji). All of these projects promote open access to data and publications. It got me very excited and thinking about ways to incorporate more public outreach in my own research.
Finally, I would be remiss not to mention the stunning fluorescence microscopy images of dental plaque presented by Jessica Mark Welch (Marine Biological Laboratory) illustrating genus-specific bacterial assemblages in the finest of detail (recently published in PNAS). These images are not only beautiful, but they also provide direct insights into physical interactions between populations of bacteria and inform hypotheses about their possible ecological roles in assembly and succession. Would love to see this technique employed in other microbial habitats!
I (Ashley Bateman) recently won a scholarship from the Women in Graduate Sciences organization at the University of Oregon, to attend the 2016 Pacific Northwest Women in Science Retreat. The event was held at Camp Magruder in Rockaway Beach, OR from July 8th-10th. The attendees and workshop leaders featured over 100 women from across the STEM career spectrum, from graduate students, technicians, and post-docs to government and industrial early and late career scientists. The focus of this retreat is on professional skill development and professional networking, especially for and with other women scientists in the region. The retreat featured 3 main workshops: A COACh workshop on the Performing Art of Science Presentations, a Rehearsals for Life: workshop, and a Bragging workshop led by the enthusiastic Judy Giordan. We also heard from and asked questions of a diverse group of women on academic, industrial, and alternative career panels.
Clarisse Betancourt Román and Gwynne Mhuireach have both been awarded scholarships to attend and present their research at the Healthy Buildings 2015 America Conference in Boulder, CO, July 19-22. The mission of the conference is to promote collaboration among built environment researchers and practitioners in order to make buildings healthier and more sustainable. Clarisse and Gwynne will be presenting in a special session focused on Urban and Indoor Environments.
G.Z. Brown of BioBE and Deb Johnson-Shelton of the Oregon Research Institute attended the kickoff meeting of the AIA Design & Health Research Consortium on March 5, 2015. Held at the Robert Wood Johnson Foundation in Princeton, New Jersey, the 11 inaugural university members of the consortium heard from several invited speakers from the fields of architecture and public health. Table discussions were held around the topics of education, metrics, the “internet of things”, resilience and equity, and translation. More on the consortium can be found at http://www.aia.org/practicing/AIAB104553.
The Donald E. Wimber Fund Award was created through the generosity of Carol Cogswell as a memorial to retired University of Oregon biology faculty member Donald Wimber. The award was established to provide support for junior faculty, research associates, or graduate students to travel to conferences to present their research work. Erica will be traveling to ASM.
Last week several members of the BioBE Center visited Boulder, CO for the 3rd annual Microbiology of the Built Environment Conference hosted by the Alfred P. Sloan Foundation. James Meadow presented our recent work on building-scale microbial patterns, the phone-hand connection, and the human microbial cloud. Adam Altrichter presented a poster (see it here) on our ongoing work with the Light Box experiments that Kyla Martichuski put together for a recent symposium at the U of O. Gwynne Mhuireach also presented a poster with an update on the analyses from her study looking at the bacteria in air from parks vs parking lots throughout Eugene. Check out the Storify put together from tweets during the conference to see what folks were talking about all week.