URBAN Trainee Kathryn Atherton Researches Urban Soil Microbiomes

Watch Video: URBAN Trainee Kathryn Atherton Researches Urban Soil Microbiomes

Kathryn Atherton is a PhD Student studying Bioinformatics in the BU URBAN Program. She received a 2021 Early Stage Urban Research Award from the Initiative on Cities (IOC) for her project, “The Impact of Racism on Urban Belowground Biodiversity.”

Read the Q&A with Atherton and watch the video by IOC and URBAN to learn more about her research on soil microbial diversity in cities.

Amelia Murray-Cooper (IOC): Why were you interested in working on this project?

Kathryn Atherton: We have collaborators, Dr. Lucy Hutyra and Ian Smith, and they have been working on investigating trees in Boston for a few years now. They had a great data set looking at how trees are doing in Boston, healthwise, growthwise, and deathwise as compared to rural trees. They have hypotheses about how urban conditions might be impacting these trees, and they found generally that urban trees grow four times as fast but die twice as fast as rural trees.

It really shocked me that there’s that much of a difference between urban and rural trees, and I thought the soil microbiome could explain why this is happening. There are these microbes called mycorrhizal fungi that they participate in symbiosis with, and they’re great for helping trees take up nutrients. They can also protect trees from pathogens just by encapsulating their roots. We found in the past that rural trees have more of these fungi than urban trees. Putting these findings together, I thought we needed to look at how the soil microbiome is changing and how it can explain this massive difference between the health of urban and rural trees.

What are the main takeaways from your findings?

All of our data is still in the soil. We went out and took six different soil samples from underneath a hundred trees, so right now we’re still processing that data. We’re still doing the DNA extraction to find out what exactly is in these soil samples and we’re generally taking soil chemistry data.

Did anything surprise you during your research?

I was focusing on the soil microbiome itself, and about midway through the project, my Co-PI Jennifer Bhatnagar brought up that she had a conversation with someone who studies leaf microbiomes. They had a hypothesis that as you get more urban, the leaf microbiome becomes richer and more diverse, whereas we found that the soil microbiome becomes less diverse. It surprised me that there’s a dichotomy where the urban microbiome shifts from the soil into the leaves, so we’ve also started taking leaf samples and we’re going to analyze the leaf microbiome to see if that hypothesis is true.

I also got to see a lot of the city that I never would have gotten a chance to see had I not done this project. I had never been to Dorchester before and I took samples from underneath Dorchester and Roxbury trees. Something else that was really surprising was the number of people that came up to us and were curious what we were doing. We had a really big pole and it looked like we were pounding it into the ground and then pulling up a bunch of soil, so people were kind of like, “what are you doing?” Once we told them that we were interested in figuring out what is happening to the city’s trees, many people had anecdotal stories like, “there’s a tree in front of my yard that died within five years of planting it,” or “I’ve noticed that this certain kind of tree always seems to die really quickly and I’ve always wondered why.” We had a ton of interest from the community.

What do you hope comes out of this work?

Ideally, we would be able to draw conclusions about how the soil microbiome is impacting the health of trees and then work with the City of Boston to think about management strategies that boost the soil microbiome to benefit trees and increase the amount of mycorrhizal fungi in urban soils. In rural ecosystems, leaves just fall and get decomposed and all of those nutrients go back into the soil. In urban ecosystems, we don’t want those leaves to clog drains and impact our infrastructure so we rake them up. We think that means the soil is getting less of these nutrients, so we have to put in things like fertilizer that aren’t good for these microbes. We would love to test if we transplant leaves from rural areas into urban soil, how might that boost the soil microbiome. The tagline that Jennifer Bhatnagar has said is “Make Boston Decay Again.”

A potential future research opportunity would be taking soil cores and soil samples from rural areas and directly putting those into the urban soil underneath trees to promote the growth of mycorrhizal fungi. We could even potentially engineer our own community that we think can withstand the stress of all the nutrients, pollution, and temperature increases in Boston, so we can get the best community possible growing in Boston.

The IOC has funded over 70 projects to date through the Early State Urban Research Awards. Learn about past projects and learn how to apply for future funding opportunities here.