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The PRISM Project:
Prairie Root Influences on Soil Microbes


NSF-DEB 1937255: Impacts of plants and communities on soil microbial composition and function across phylogenetic scales

In May 2020, we were awarded funding for a new collaborative research project through NSF’s Rules of Life initiative. Working with colleagues at the Morton Arboretum, San Diego State University, Northern Illinois University, Middle Tennessee State University, and the Lawrence Berkeley National Laboratory, we will study how plants shape the structure and function of soil microbial communities.


We want to understand how root exudates—chemicals that plants release into the soil environment—vary among plants, and how they influence bacteria, archaea, and fungi. The project has several exciting research components and gives us the opportunity to get people involved in science.


What will we do?


First, we will be characterizing the root exudates from dozens of species of tallgrass prairie plants to understand how they vary with plant phylogeny and plant leaf and root traits. We will use those exudates in soil incubation experiments to see how their addition shapes microbial communities and their functions through metagenomic and metatranscriptomic data and metabolic assays.




Next, we will take advantage of an incredible biodiversity experiment, the Ware Field experimental prairie at the Morton Arboretum in Illinois. This NSF-funded experiment consists of over 100 prairie species planted in monoculture plots and in multispecies communities in which phylogenetic and functional trait diversity have been manipulated. This lets us study how soil microbes vary with individual plant species and among diverse plant communities under these controlled conditions.




Lastly, our combined data on plant traits, root exudates, and soil communities can be combined and analyzed using new machine learning approaches like artificial neural networks. With these techniques, we will build predictive models of how new combinations of plant species would shape soil microbial communities. Then we will test those predictions in a field setting using 200 quadrats in a series of restored and remnant prairies at Nachusa Grasslands.


Who is involved?

The project is led by Nick Barber at SDSU, Meghan Midgley and Andrew Hipp at the Morton Arboretum, Wes Swingley at NIU, Trent Northen and Kate Zhlanina at LBNL, and Josh Phillips at MTSU.


We will provide training opportunities across all the project activities.  We will support a postdoc working at Morton and NIU, graduate students at SDSU and MTSU, and undergraduate researchers at all the institutions. Through the three universities, our labs also provide supportive mentoring environments for students traditionally underrepresented in science. SDSU is a Hispanic-Serving Institution, NIU is likely to have HSI status soon, and all three universities have large proportions of first-generation college students. We strive to create labs where all students are safe and supported regardless of their background and have the opportunity to succeed in science.


Outreach is also an important part of this work. Through the Arboretum, we will establish a Lifelong Learnings Program for retired adults. There is already a strong community of volunteers at the Arboretum, including those working at the Ware Experimental Prairie. We will formalize the volunteer program so participants can engage with field and lab activities and interact with scientists and seminar speakers. High school biology students visit the experiment each year to participate in data collection, and that will continue in the coming years, giving hundreds of teenagers the chance to take part in science.



— In July 2021, we fully sampled all 400+ plots at the Morton Arboretum. Keeping with tradition, we scheduled it for a day with 90+ degree heat and high humidity. But it went well, and our team of SDSU, NIU, and Morton Arboretum folks completed the sampling in a single day. It was especially fun working with the arboretum's high school student interns who have quickly become experts in plant identification and ecology.

These samples will be processed at NIU and sent off for sequencing to describe the archaeal, bacterial, and fungal communities in the soil of each plot.

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Many of the plots were in full mid-summer bloom.


Dr. Meghan Midgley sterilizing a scoopula before taking a soil sample from the base of a compass plant plot.


The Ware Field experimental prairie. Each plot is 2m x 2m and contains either a singe plant species, or a combination with known functional and phylogenetic diversity.

— In Summer 2022, our team joined members of Holly Jones's lab for joint soil sampling in conjunction with the CAPER project. We collected soil from almost 200 sampling points at Nachusa that are also vegetation survey points annually, so we will be able to link plant community composition to soil characteristics and microbial community.

Camille Traylor and Mareike Lankhorst (both Barber lab) joined Meghan Midgley's lab to start soil analysis, and Meghan's team measured a wide range of soil parameters that will help us better understand plant-microbe-soil ecosystem linkages.

See pictures from our soil sampling here!

January 2023, our first paper from the project was published in FEMS Microbiology Ecology! We used the amplicons sequencing from sites at Nachusa, which formed someo f the preliminary data for PRISM, to determine how soil bacterial communities changed over time following restoration, and with bison access. We found that bison might be driving soil bacterial succession along a different trajectory compared to similar aged sites where bison are absent.

Here's a PDF of the paper.

Summary 2023, Barber Lab REU student Lydia Duran is looking at some of our first exudate data produced by Kate Zhalnina at LBNL. Kate analyzed exudate samples from ~30 species, across a range of plant families. One of Lydia's first questions will be to determine if plants with larger rootmasses produce a greater volume of root exudates, using total organic carbon measurements of exudate samples.

The background photo on this page is the Ware Field experimental prairie, photographed by Lane Scher.

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