Updates

My first week at the University of Oregon

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My new work home.

Last week was my first week as a Research Assistant Professor in the Biology and the Built Environment Center (BioBE) at the University of Oregon, and my first full week in Eugene.  Combined with the Energy Studies in Buildings Laboratory, our collaborative team of architects and biologists researches how to make buildings more efficient, sustainable, pleasant, and healthy.

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Delta Ponds, along my new bike route to work.

My first day started auspiciously as I charted a new bike route to work, about 4.5 mi of which is along a path snaking next to the Willamette River.  It goes through several parks, and by a few small lakes and swamps which are home to dozens of species of birds, mammals, amphibians, and reptiles.  I haven’t seen any river otters yet, but I have been keeping a close eye out.

Arriving on campus, most of my first day, and first week, were spent visiting the various places around campus to get myself established as a new employee- obtaining my ID card and email address, filing out paperwork, attending orientation, and finding all the coffee places within walking distance of the building.  ESBL is renovating and expanding its offices across several large, pluripotent rooms to accommodate a growing research team, so I got a brand new standing desk, chair, shelving, and computers (on order), all to my specifications.  The flexibility of working position, screen size, and screen angle provided by my new station are comfortable and great for productivity, and it’s neat to design the new space into offices, meeting tables, and storage which are based on our personalized usage needs and preferences.  And of course, there is plenty of space for all the mementos and science toys I’ve accumulated.

Most importantly, my first week was spent acclimating to my new department and getting up to speed on the ongoing and planned projects.  BioBE and ESBL have dozens on ongoing or planned projects on the built environment, with a combination of building and biology facets.  Over the course of the summer, I’ll be writing several grants and organizing new projects that explore how building use, occupancy, and human habits affect human health and the indoor microbiome, as well as contributing to the BioBE blog,  providing building microbiome posts to Give Me the Short Version, and getting some older projects out for publication.  On top of that, I’m looking forward to exploring the Pacific coast and the Northwestern landscape, and availing myself of the Willamette Valley wine industry.

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Photo Credit: Alen Mahic

I accepted a position at the University of Oregon!

I am thrilled to announce that I have formally accepted a position as a Research Assistant Professor of Microbial Ecology at the University of Oregon‘s Biology and the Built Environment Center (BioBE) starting in June in Eugene, Oregon!  BioBE brings together architects and biologists to study how we (and our microbes) interact with the built environment.  Combined with the Energy Studies in Buildings Laboratory, our collaborative team researches how to make buildings more efficient, sustainable, pleasant, and healthy.

Last week, I went to Portland, Oregon for the first ever meeting of the Health and Energy Research Consortium (HERC), which brings together researchers, foundations, consultants, and industry leaders from different fields to discuss these research issues and foster interdisciplinary work in the built environment.  This includes everything from designing lighting control systems that better integrate human behavior and preferences, to understanding how our human microbiomes interact with building materials to create a unique building microbiome that can feed back onto us in a positive or negative way.  More information can be found on the BioBE site, as well as microBEnet.  And of course, I’ll be sure to keep you updated right here.

Lee, Izzy, and I have been in Montana for just over two wonderful years, and while we will miss being just 30 min away from great skiing, we are also excited for this next chapter of our life.  Is it a coincidence that the next chapter is located in wine country and less than an hour from the beach?  Too early to say.  One thing is for sure, though, the friendships and collaborations I’ve made here will continue to be cultivated in the years to come.

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My review on Plant-Microbial Interactions in Agriculture got published!

A few months ago, I was invited to submit an article to the special issue “Plant Probiotic Bacteria: solutions to feed the World” in AIMS Microbiology on the interactions between agricultural plants and microorganisms.  As my relevant projects are still being processed, I chose to write a review of the current literature regarding these interactions, and how they may be altered by different farming practices.  The review is available as open-access here!

“Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity”

A thorough understanding of the services provided by microorganisms to the agricultural ecosystem is integral to understanding how management systems can improve or deteriorate soil health and production over the long term. Yet it is hampered by the difficulty in measuring the intersection of plant, microbe, and environment, in no small part because of the situational specificity to some plant-microbial interactions, related to soil moisture, nutrient content, climate, and local diversity. Despite this, perspective on soil microbiota in agricultural settings can inform management practices to improve the sustainability of agricultural production.

Keywords bacteria; climate change; farming system; fungi; nutrient exchange; pathogens; phytohormones

Citation: Suzanne L. Ishaq. Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity. AIMS Microbiology, 2017, 3(2): 335-353. doi: 10.3934/microbiol.2017.2.335

Fort Ellis inoculation day

Today was a big day out in the field at Fort Ellis: virus inoculation day for the project I’ve been part of, on how farming system can alter reactions to adverse growing conditions (like climate change, weed competition, and disease).  This is the second year of the project, and the fifth year of the larger crop rotation study, so a lot is riding on being able to keep to the schedule.

Spring has been cool and wet here in Montana, which has presented us from being able to do work in the muddy fields but hasn’t slowed down the wheat or the weeds.  If the wheat is too developed when the virus is sprayed, the infection won’t manifest well enough to measure.  Thanks to carefully prepared protocols, seasoned personnel, and a stretch of sunny, dry days, we treated our plots and went home early!

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Harvesting a feast of data

My greenhouse trial on the legacy effects of farming systems and climate change has concluded!  Over this past fall and winter, I maintained a total of 648 pots across three replicate trials (216 trials per).  In the past few weeks, we harvested the plants and took various measurements: all-day affairs that required the help of several dedicated undergraduate researchers.

In case you were wondering why research can be so time and labor intensive, over the course of the trials we hand-washed 648 pot tags twice, 648 plant pots twice, planted 7,776 wheat seeds across two conditioning phases, 1,944 wheat seeds and 1,944 pea seeds for the response phase.  We counted seedling emergence for those seeds every day for a week after each of the three planting dates in each of the three trials (9 plantings all together).  Of those 11,664 plants, we hand-plucked 7,776 seedlings and grew the other 3,888 until harvesting which required watering nearly every day for over four months.  At harvest, we counted wheat tillers or pea flowers, as well as weighed the biomass on those 3,888, and measured the height on 1,296 of them.  And this is only a side study to the larger field trial I am helping conduct!  All told, we have a massive amount of data to process, but we hope to have a manuscript ready by mid-summer – stay tuned!

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Expanding Your Horizons for Girls workshop, MSU 2017

Yesterday I participated in the Expanding Your Horizons for Girls workshop at Montana State University!  EYH brings almost 300 middle-school aged girls from all over Montana for a one-day conference in STEM fields.  Twenty-seven instructors, including myself and other female scientists and educators, ran workshops related to our current research.  My presentations were on “Unlocking the Hidden World of Soil Bacteria”, with the help of undergraduate Genna Shaia from the Menalled Lab.

I gave the girls a brief presentation on microbial ecology, and how bacteria and fungi can affect plants in agricultural soil.  We talked about beneficial versus pathogenic microorganisms, and how different farming strategies can influence soil microbiota.  This was followed by two hands-on activities that they were able to talk home with them.  First, the girls made culture plates from living or sterile soil that was growing wheat or peas to see what kind of microbes they could grow.  Then, they planted wheat seeds in either living or sterile soil so they could track which soil made the seeds germinate faster.

 

The girls were enthusiastic to learn, asked lots of insightful questions, and it was awesome being able to share microbiology with kids who hadn’t given it much thought before!  If you are a woman in STEM, and have the opportunity to participate in a workshop or mentor a young scientist,  it is not only rewarding but can make a huge impact on encouraging women into STEM.

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Slideshow photos: Genna Shaia, reproduced with student permission.