The Biology and the Built Environment center here at the University of Oregon has a blog, and I’ll be writing updates and blog posts for them, as well. I will be cross-posting my posts, but you should also check them out!
Category: Updates
My first week at the University of Oregon
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.
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.
![IMG_20170610_211058_268[1]](https://i0.wp.com/sueishaqlab.org/wp-content/uploads/2017/06/img_20170610_211058_2681.jpg?w=489&h=275&ssl=1 "IMG_20170610_211058_268[1]")
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.
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.
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!
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!
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.
Setting up a soil microbes workshop for Expanding Your Horizons for Girls.
Genna Shaia, undergraduate researcher.
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.
Slideshow photos: Genna Shaia, reproduced with student permission.
A collaborative project on sheep feed efficiency and gut bacteria was published!
I’m pleased to announce that a paper that I contributed to was recently accepted for publication in the Journal of Animal Science!
“Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small intestine-located microbiota”, Katheryn Perea; Katharine Perz; Sarah Olivo; Andrew Williams; Medora Lachman; Suzanne Ishaq; Jennifer Thomson; Carl Yeoman (article here).
Katheryn is an undergraduate at New Mexico Institute of Mining and Technology who received an INBRE grant to support her as a visiting researcher at Montana State University in Bozeman, MT over summer 2016. Here, she worked with Drs. Carl Yeoman and Jennifer Thomson to perform the diversity analysis on the bacteria in the gastrointestinal tract of sheep from a previous study. These sheep had been designated as efficient or inefficient, based on how much feed was needed for them to grow. Efficient sheep were able to grow more with less feed, and it was thought this might be due to hosting different symbiotic bacteria which were better at fermenting fibrous plant material into usable byproducts for the sheep.
Samples from the sheep were collected as part of a larger study on feed efficiency performed by MSU graduate students Kate Perz and Medora Lachman, as well as technicians Sarah Olivo and Andrew Williams, and Katheryn performed the data and statistical analysis using some of my guidelines. This is Katheryn’s first published article, and one I just presented a poster on at the Congress on Gastrointestinal Function in Chicago, IL!
2017 Congress on Gastrointestinal Function
I just got back from my very first Congress on Gastrointestinal Function, 
a small meeting for researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois. The special session this year was on “Early Acquisition and Development of the Gut Microbiota: A Comparative Analysis”. The rest of the sessions opened up the broader topics of gut ecosystem surveillance and modulation, as well as new techniques and products with which to study the effect of microorganisms on hosts and vice versa. The research had a strong livestock animal focus, as well as a human health focus, but we also heard about a few studies using wild animals.
As I’ve previously discussed, conferences are a great way to interact with other scientists. Not only can you learn from similar work, but you can often gain insights into new ways to solve research problems inherent to your system by looking at what people in different fields are trying, something that you might otherwise miss just by combing relevant literature online. A meeting or workshop is also a great place to meet other similarly focused scientists to set up collaborators that span academia, government, non-profit, and industry sectors.
This year, I was excited for one of my abstracts to be accepted as a poster presentation, and honored to have the other upgraded from poster to talk! Stay tuned for details about both of those projects in the coming weeks, and be sure to check this meeting out in April, 2019.
National Employee Appreciation Day!
According to National Day Calendar, it’s National Employee Appreciation Day! Many organizations have an annual Staff Appreciation Day or Week, and rightly so. Research staff in academia, as well as general staff, are often quietly under appreciated. Research staff can be costly, especially because many universities insist that research positions have salary and benefits fully-funded by grants. Many labs thus rely on undergraduate student researchers, who work for minimum wage or might even pay for university “research credits”, to help provide labor.
While many undergraduates find themselves performing unglamorous routine lab maintenance (anything from washing dishes, to pre-weighing commonly used supplies, to dusting, to inventory), as a researcher I can attest to how vital these tasks are. Working in a molecular biology lab, dust and other contaminants had to be minimized and it was extremely helpful to have undergraduates who were able to dust multiple times a day. When culturing bacterial isolates, I would go through hundreds of culturing tubes every week, which all needed to be autoclave sterilized, emptied, washed, and re-sterilized. This was a massive amount of effort unto itself, and I would not have been able to accomplish my culture work without. Perhaps the best example was my study of probiotics in newborn lambs. I had 24 lambs which were only 4 days old, which needed to be fed every 4-5 hours, sometimes by hand, as well as weighed, sampled, and cleaned on a regular basis. Without numerous undergraduate volunteers, I would have found myself sleeping at the barn for two months.
Not only is it polite to appreciate the staff who keep your work moving, but proper gratitude can go a long way towards improving work relationships, job satisfaction, and performance. So get out there and start thanking!
The Ishaq Lab 