Urban trees lose helpful microbes and gain harmful bacteria

Cities breathe through trees. They cool streets, clean the air, and comfort minds. Yet, few notice the invisible worlds beneath their bark and roots.

Each tree hosts a vast community of microorganisms that shape its health and resilience. As heat, drought, and pollution grow, those microscopic partners face intense stress.

Researchers from the Bhatnagar Lab at Boston University explored how city life reshapes these hidden ecosystems. Their study compares microbial communities in urban street trees and forest trees.

The results reveal how urban stress changes fungal and bacterial balance, affecting not just trees but entire city ecosystems.

Why tree microbiomes matter

“Microorganisms are everywhere, and they drive critical ecosystem services such as decomposition, nutrient cycling, tree growth, and carbon sequestration,” explained Professor Jenny Bhatnagar, senior author of the study.

Kathryn Atherton, the paper’s first author, noted that studying urban microbiomes reveals how cities disrupt those natural systems.

“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,” she said.

Urban trees lose critical microbes

“Everything that can go wrong in a microbiome goes wrong for trees living in cities,” said Bhatnagar.

Urban trees lose crucial fungal allies and gain harmful bacteria and pathogens. Some bacteria even release nitrous oxide, a potent greenhouse gas.

On the bright side, these effects connect to factors like soil quality, temperature, and pollution – elements humans can control. Adjusting urban soil management could help reverse this microbial imbalance.

The team studied oak trees because they rely on ectomycorrhizal fungi, a group that forms deep root partnerships.

Bhatnagar noted that while some urban plants share this trait, others depend on different symbionts, and their responses to city life remain unclear. Understanding these differences could guide future planting choices and conservation methods.

The urgency of now

Bhatnagar credits her students for sparking this line of research. “Urbanization effects on the environmental microbiome is one of them,” she said.

Atherton, inspired during the pandemic, wanted to understand how cities and health intertwine. Her curiosity about microbial mutualisms became the root of this project.

Urban areas are expanding fast. “Worldwide, urban areas are expected to double in size by 2050,” said Bhatnagar.

Yet, our understanding of urban ecosystems lags behind. According to Atherton, the findings reveal deep shifts in microbial life, threatening the survival of trees and the balance of urban nature.

She emphasized that without proactive research and sustainable planning, cities may lose vital ecological functions that keep them livable.

The delicate microbial partnerships beneath urban soil are as essential as the trees themselves – influencing air quality, soil fertility, and even climate resilience. Protecting these invisible ecosystems could determine how cities endure future environmental challenges.

Building resilient urban trees

The study shows that small environmental changes – like improving soil moisture and reducing pollution – can strengthen microbial health.

“Our ability to correlate disruption of tree microbiomes with key environmental factors points to key modifications we can make,” said Bhatnagar.

Atherton noted that city planners should weave microbiome science into their green policies. This approach could improve tree survival, air quality, and carbon capture, making cities more resilient and fair.

She recommends integrating microbial data into urban design to predict which areas need ecological support most. By considering soil microbes alongside vegetation and climate data, planners can design spaces that strengthen environmental networks from the ground up.

This microbial perspective encourages smarter investments in tree health and long-term sustainability. It transforms city planning from surface-level greening to a deeper understanding of the living systems that make cities thrive.

How citizens can help

Bhatnagar’s advice is simple: “If you are planting a tree or caring for a tree outside your home – put down mulch.” It helps soil retain moisture and supports beneficial fungi.

Atherton reminds people that street trees are not alone. “They depend on complex microbial communities that are vulnerable to city stressors,” she said. Protecting trees means protecting those microbes, too.

Restoring urban tree microbes

The team’s next step moves toward “microbiome rewilding.” Bhatnagar believes that restoring lost fungal partners could cut urban tree mortality and boost carbon capture.

Bhatnagar’s lab has begun trials to reintroduce beneficial fungi into urban soils. “I spent my sabbatical studying forest restoration and realized the enormous potential for rewilding tree-associated microbes in urban lands.”

Atherton focuses on modeling environmental and microbial interactions to identify the strongest predictors of tree health. Together, they aim to build cities that sustain both trees and the unseen worlds that keep them alive.

The study is published in the journal Nature Cities.

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