Urban trees are essential to the health of cities and their residents: they cool neighborhoods, filter pollution from the air, support biodiversity, and improve human well-being. But these benefits depend in part on the tree microbiome, which influences tree health, stress tolerance, and interactions with the environment. As cities expand and environmental stressors like heat, drought, and pollution intensify, we risk disrupting the microbial relationships that trees rely on for growth.
A team of researchers from the Bhatnagar Lab at Boston University recently published a paper in Nature Cities that studied the difference in microbial communities of street trees and non-urban forest trees. By analyzing fungal and bacterial diversity, tree size, and soil properties, their research shows the impacts of urban environmental stressors upon city tree microbiomes.
In this Q&A, senior author on the paper Jenny Bhatnagar, a Boston University associate professor of biology and director of the biogeoscience program, along with first author Kathryn Atherton, former PhD student in BU's bioinformatics & computational biology graduate program, discuss how the microbial communities of city trees can effect, not only trees and plants, but all life in urban settings and what the implications of their research could mean for future green urbanization initiatives.
What is the importance of studying the microbiomes of trees?
Jenny Bhatnagar: Microorganisms are everywhere, and they drive critical ecosystem services such as decomposition, nutrient cycling, tree growth, and carbon sequestration. They can also harm plants and animals by acting as pathogens and by releasing greenhouse gases to the atmosphere. Most work has focused on the built environment of cities (i.e., microbiomes of buildings and indoor spaces) or the microbiome of lawns and parks in cities. However, we are in the very early stages of understanding how urbanization impacts microorganisms.
Kathryn Atherton: Studying how urbanization disrupts the tree microbiome is important because it helps us understand how cities affect the invisible organisms that support tree health and ecosystem services. Trees rely on diverse microbial partners for nutrient cycling, disease resistance, and stress tolerance, especially under harsh urban conditions like heat, drought, and pollution. When those microbial communities are disrupted, trees may become more vulnerable to decline, and the ecological and health benefits they provide to city residents may be reduced. By identifying which microbial functions and symbionts are lost in urban environments, we can design better strategies to maintain healthy urban forests and create cities that are more resilient, equitable, and sustainable.
What's your key research finding?
Jenny Bhatnagar: Everything that can go wrong in a microbiome goes wrong for trees living in cities. They suffer a loss of belowground symbionts (ectomycorrhizal fungi) and potential aboveground symbionts (epiphytes) and an accumulation of plant pathogens and wood rot fungi and bacteria. They also host more animal and human pathogens. Finally, trees in cities host more bacteria that have the capacity to generate nitrous oxide (N2O), a potent greenhouse gas, and fewer methanogens, that consume methane, relative to rural trees. It's a nightmare scenario for an environmental microbiome – a bit of a horror story for our urban trees. The good news is that these shifts are correlated with heat, low soil moisture, low soil organic matter, and soil density, and atmospheric aerosol deposition – things that humans can reverse in cities, if we choose.
You looked at oak trees in your research but are there other trees that might have similar properties?
Jenny Bhatnagar: Oak trees are ectomycorrhizal – meaning that they associate with ectomycorrhizal fungi, a group of about 20,000 fungal species that colonize the roots of live plants and help woody plants live where they do on Earth. Some other plants in urban areas are ectomycorrhizal, so may respond similarly to urbanization. However, many plants are not ectomycorrhizal – they associate with other types of symbiotic fungi, and it is still unclear how the microbiome of those plants is impacted by the urban environment.
What motivated you to do this work?
Jenny Bhatnagar: Some of the most intriguing challenges I have tackled in research were brought to the table by my students, leading to massive expansions of my work into new territory. Urbanization effects on the environmental microbiome is one of them. Katie came to do her PhD in my lab and felt strongly that she wanted to study urbanization impacts on microorganisms, as well as how we could reverse any potential negative effects. We are still working on the reversing part – but Katie drove this new research to understand how cities reshape microscopic communities.
Kathryn Atherton: During the pandemic, I read about how urbanization was linked to higher COVID-19 morbidity, especially in areas with limited green space and poor environmental quality. I wanted to learn more about how we can protect our urban forests. Being a microbial ecologist, I was particularly interested in understanding how urbanization affects the beneficial microbial mutualisms that support tree health and resilience. After discussing with Dr. Bhatnagar, we decided to explore these relationships and what they mean for both trees and people.
Why is it important now to understand microbiomes?
Jenny Bhatnagar: Urban ecosystems are the fastest growing biome on Earth. Worldwide, urban areas are expected double in size by 2050. In the U.S., urbanization is projected to subsume over 20% (118,300 km2) of U.S. Forest land and house 90% of U.S. population by 2050. Yet, we don't fully understand them or what they do to the natural ecosystems they abut and surround. I think that is dangerous, but fixable
Kathryn Atherton: Our work shows that urbanization fundamentally alters the microbial life trees depend on in ways that could compromise their survival and the benefits they provide. That has major consequences for how we think about managing urban forests in a warming, urbanizing world. Understanding these microbial shifts now can help us protect and restore the ecological resilience of urban forests before those systems break down further and ensure that urban nature continues to serve both people and the planet in the decades ahead.
What could change because of your research?
Jenny Bhatnagar: I think that our ability to correlate disruption of tree microbiomes with key environmental factors: soil organic matter, water, temperature, and pollutants – point to key modifications we can make – even to just the soil underneath trees – that could reverse some of the negative effects of urbanization on tree microbiomes.
Can it help city planners decide how to improve green spaces within urban environments?
Kathryn Atherton: Incorporating microbiome considerations into urban forestry policies could improve tree survival rates, enhance ecosystem services like air pollution filtration and carbon capture, and ultimately create more resilient and equitable green spaces. In this way, our findings offer a new biological perspective that can guide smarter, science-informed decisions in urban planning and environmental management.
What's can individuals do to help with this issue?
Jenny Bhatnagar: One easy thing to do is, if you are planting a tree or caring for a tree outside your home –put down mulch. This will increase moisture in soil and potentially encourage growth of tree mutualists (mycorrhizal fungi) belowground that provide stress protection, nutrients, and water to trees.
Kathryn Atherton: I want people to remember that while street trees might look isolated in their sidewalk pits, they don't stand alone: they depend on complex microbial communities that are vulnerable to city stressors. Protecting urban forests means protecting the microbiome, too. I hope city planners, environmental managers, and the public start considering the microbiome as a vital part of urban green space health and invest in strategies that support microbial diversity and function, helping our cities become healthier, cooler, and more resilient.
What are the next steps in this research?
Jenny Bhatnagar: One of the major areas of research that we are moving into is environmental engineering for cities. Cities worldwide are investing millions of dollars in greening initiatives to increase tree cover, but high tree mortality rates lead to massive financial losses and an inability for cities to sequester enough carbon to reach net zero emissions. We think that part of the issue is this loss of mutualists for trees in cities, which opens ecological space for pathogens to grow. Reintroducing fungal root mutualists (i.e., mycorrhizal fungi) has been hugely successful in reducing tree mortality in forests, but urbanization leads to some of the most stressful environmental conditions for mutualists on the planet (e.g., heat, drought, pollution). Nevertheless, these can be reversed with simple modifications to soil structure. I spent my sabbatical studying forest restoration and realized the enormous potential for rewilding tree-associated microbes in urban lands. In summer 2023, I set up our first trial microbiome rewilding experiment, which we are analyzing now.
Kathryn Atherton: While we've identified that urbanization disrupts the tree microbiome and linked this to environmental stressors, we still need to understand which specific factors most strongly predict tree health and growth outcomes. To do this, I'm working on modeling these relationships to pinpoint priority environmental and microbial targets for urban planting and management.
This work was supported by several grants from Boston University including the Patricia McLellan Leavitt Research Award, as well as the following funders: U.S. Department of Agriculture, National Institute of Food and Agriculture, U.S. Department of Energy, National Institute of General Medical Sciences, and National Science Foundation Research Traineeship
