Temporal soil bacterial community responses to cropping systems and crop identity in dryland agroecosystems of the Northern Great Plains.

This project was part of the graduate research for master’s student Tindall Ouverson, and is her first manuscript!

Photo of woman in front of mountains

Tindall is a Master’s of Science in the Department of Land Resources and Environmental Sciences at Montana State University. Her graduate advisers are Drs. Fabian Menalled and Tim Seipel. Her research focuses on the response of soil microbial communities to cropping systems and climate change in semiarid agriculture. 

I have been mentoring Tindall as a graduate committee member since she began in fall 2019, teaching her laboratory and analytical skills in microbial ecology, DNA sequencing, and bioinformatic analysis. We first met when she came to visit when I was working in Oregon, and since then have connected remotely. She has a flair for bioinformatics analysis, and a passion for sustainable agricultural development. She plans to defend her thesis in spring 2021, and then to further her career in sustainable agriculture in Montana.

In the Northern Great Plains of the United States, cereal crops, such as wheat, are important economic staples. In this area, climate change is forecasted to increase temperature and decrease precipitation during the summer, which is expected to negatively affect crop production and the management of pests (insects and microbes).  There are numerous reports on the current effects of climate change on agricultural production, as well as how they will be predicted to worsen, such as:

Ouverson, T.,  Eberly, J., Seipel, T., Menalled, F., Ishaq, S.L.2021.Temporal soil bacterial community responses to cropping systems and crop identity in dryland agroecosystems of the Northern Great Plains.  Frontiers in Sustainable Food SystemsNo Impact Factor. Article. This is an invited submission to Plant Growth-Promoting Microorganisms for Sustainable Agricultural Production  special collection.


Industrialized agriculture results in simplified landscapes where many of the regulatory ecosystem functions driven by soil biological and physicochemical characteristics have been hampered or replaced with intensive, synthetic inputs. To restore long-term agricultural sustainability and soil health, soil should function as both a resource and a complex ecosystem. In this study, we examined how cropping systems impact soil bacterial community diversity and composition, important indicators of soil ecosystem health. Soils from a representative cropping system in the semi-arid Northern Great Plains were collected in June and August of 2017 from the final phase of a five-year crop rotation managed either with chemical inputs and no-tillage, as a USDA-certified organic tillage system, or as a USDA-certified organic sheep grazing system with reduced tillage intensity. DNA was extracted and sequenced for bacteria community analysis via 16S rRNA gene sequencing. Bacterial richness and diversity decreased in all farming systems from June to August and was lowest in the chemical no-tillage system, while evenness increased over the sampling period. Crop species identity did not affect bacterial richness, diversity, or evenness. Conventional no-till, organic tilled, and organic grazed management systems resulted in dissimilar microbial communities. Overall, cropping systems and seasonal changes had a greater effect on microbial community structure and diversity than crop identity. Future research should assess how the rhizobiome responds to the specific phases of a crop rotation, as differences in bulk soil microbial communities by crop identity were not detectable.

Framing the discussion of microorganisms as a facet of social equity in human health

In summer 2019, I developed and taught a course on ‘Microbes and Social Equity‘ to the Clark Honors College at the University of Oregon.

In just a four-week course, I introduced 15 undergraduates from the University of Oregon Clark Honors College to microorganisms and the myriad ways in which we need them. More than that, we talked about how access to things, like nutritious foods (and especially fiber), per- and postnatal health care, or greenspace and city parks, could influence the microbial exposures you would have over your lifetime. Inequalities in that access – such as only putting parks in wealthier neighborhoods – creates social inequity in resource distribution, but it also creates inequity in microbial exposure and the effect on your health.

The course assignments were literature review essays on various topics, which were compiled into a single manuscript as the group-based final project for the course. This large version is available as a preprint; however, the published version is more focused (abstract below).

What is next for ‘Microbes and Social Equity’?

Since publishing in November, a number of researchers have connected with me, and we have formed a loose collaboration for “Microbes and Social Equity Part 2”. We have several initiatives in development, and there will be news releases as those coalesce. At this time, we are developing a journal special call, and a series of workshops/mini-symposia, both with the goal of connecting researchers and practitioners. Stay tuned!

Framing the discussion of microorganisms as a facet of social equity in human health.

Suzanne L. Ishaq1,2*, Maurisa Rapp2,3, Risa Byerly2,3, Loretta S. McClellan2, Maya R. O’Boyle2, Anika Nykanen2, Patrick J. Fuller2,4, Calvin Aas2, Jude M. Stone2, Sean Killpatrick2,4, Manami M. Uptegrove2, Alex Vischer2, Hannah Wolf2, Fiona Smallman2, Houston Eymann2,5, Simon Narode2, Ellee Stapleton6, Camille C. Cioffi7, Hannah Tavalire8

  1. Biology and the Built Environment Center,  University of Oregon
  2. Robert D. Clark Honors College, University of Oregon
  3. Department of Human Physiology, University of Oregon
  4. Charles H. Lundquist College of Business, University of Oregon
  5. School of Journalism and Communication, University of Oregon
  6. Department of Landscape Architecture, University of Oregon
  7. Counseling Psychology and Human Services, College of Education, University of Oregon
  8. Institute of Ecology and Evolution, University of Oregon


What do ‘microbes’ have to do with social equity? On the surface, very little. But these little organisms are integral to our health, the health of our natural environment, and even impact the ‘health’ of the environments we have built. Early life and the maturation of the immune system, our diet and lifestyle, and the quality of our surrounding environment can all impact our health. Similarly, the loss, gain, and retention of microorganisms ⁠— namely their flow from humans to the environment and back⁠ — can greatly impact our health and well-being. It is well-known that inequalities in access to perinatal care, healthy foods and fiber, a safe and clean home, and to the natural environment can create and arise from social inequality. Here, we focus on the argument that access to microorganisms as a facet of public health, and argue that health inequality may be compounded by inequitable microbial exposure.

In the Media

  1. ” UMaine prof: Inequity is creating a gut microbe gap.” Mike Tipping and Ben Chin, Maine People’s Alliance. Dec 20, 2019.
  2. Inequity takes a toll on your gut microbes, too.” Sue Ishaq,  The Conversation, Dec 4, 2019.
    1. Picked up by The Telegraph, Alton, Illinois, and other agencies
    2. Included on UMaine news
  3. All people have a right to healthy gut microbes.” Paige Jarreau and Signe Asberg, Lifeapps. Dec 3, 2019.  
  4. Rich People Have Access to Better Microbes Than Poor People, Researchers Say.” Becky Ferreira, Vice. Nov 26, 2019.
  5. Microbiome is a Human Right.” Heather Smith, Sierra. Nov 26, 2019.
  6. Life, liberty—and access to microbes?” Press release for Plos Biology. Nov 19, 2019.

Story picked up by (non-exhaustive list)