Sunday, October 05, 2025

The essential role of the urban tree microbiome: A key to city health

A new study by Boston University researchers looks at the impact of environmental stressors on the growth of city trees

Boston University

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

Journal

Nature Cities

DOI

10.1038/s44284-025-00322-x

Method of Research

Observational study

Subject of Research

Not applicable

Article Title

Disruption of the oak tree microbiome with urbanization

Article Publication Date

3-Oct-2025

Africa, climate, and food: How to feed a continent without increasing its carbon footprint

An international study compares Africa’s trajectory with China’s and proposes concrete solutions—from water management in rice paddies to modernizing logistics chains—to produce more food without worsening the climate.

The Alliance of Bioversity International and the International Center for Tropical Agriculture

Africa, climate, and foot — image:
*Africa’s agrifood system emits nearly 2.9 billion tonnes of CO₂.*
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Credit: Alliance of Bioversity and CIAT

Africa’s agrifood system emits nearly 2.9 billion tonnes of CO₂ equivalent every year—more than a quarter of global sector emissions. An international study compares Africa’s trajectory with China’s and proposes concrete solutions—from water management in rice paddies to modernizing logistics chains—to produce more food without worsening the climate. These analyses were conducted by researchers Xia Li, Yumei Zhang, Shenggen Fan (China Agricultural University) and Issa Ouedraogo (Alliance of Bioversity International and CIAT)

A growing continent: More mouths to feed, fewer emissions to produce

Africa’s population will reach around 2.5 billion by 2050. This reality translates into a simple but complex challenge: produce more without emitting more. Today, agrifood systems account for nearly a third of global emissions. On the continent, the footprint increased by about 40% between 2000 and 2021, rising from 2.03 to 2.85 Gt CO₂e. This rise has not been uniform: some subregions, such as East and Central Africa, saw faster growth, often linked to expanding croplands and herds. Elsewhere, soil management policies, modest mechanization, and more advanced urbanization slowed the curve—but did not reverse it.

At the heart of this equation, the Congo Basin—the world’s second tropical lung—plays a key role. The steady loss of primary rainforests—several million hectares since the early 2000s—threatens essential carbon sinks and undermines rural livelihoods. Every hectare saved, every farm established without cutting ancient forests, counts twice: for the climate and for local incomes.

Faced with demographic and food pressures, the study underlines an often-forgotten truth: there is no single “Africa,” but many Africas. Agroecological contexts, production systems, water access, and market structures vary greatly. The solution, therefore, is not one uniform “grand plan” but differentiated pathways. In forest zones, the priority is curbing deforestation and restoring landscapes. In pastoral regions, cutting methane from ruminants through better feeding and animal health. In rice plains, managing water and nitrogen to curb emissions without lowering yields. And in urban supply basins, modernizing collection, processing, and transport so that every kilo produced actually reaches a plate.

The good news: these pathways already exist, are being tested, and generate co-benefits (income, jobs, resilience to climate shocks). The challenge now is to accelerate, support, and scale them up.

Forests, rice paddies, livestock: The big three — and the small shifts that change everything

Deforestation remains the largest source of emissions in several Central and West African countries. When dense forest is converted into farmland (cocoa, oil palm, maize) or pasture, the CO₂ stored in trees and soils is released. But the solution is not just to “stop cutting.” It means making forest protection economically rewarding for communities: clear land tenure, agroforestry that integrates trees and crops, zero-deforestation traceability in cocoa–coffee–palm oil chains, payments for ecosystem services, and markets that pay for sustainable quality and origin. Where these conditions are met, producers see real benefits in preserving trees rather than felling them.

In flooded rice paddies, the issue is methane (CH₄). Stagnant water creates conditions that favor its formation. A simple practice, proven in Asia and tested in West Africa, makes a big difference: Alternate Wetting and Drying (AWD). Instead of keeping paddies permanently flooded, farmers alternate wet and drier periods. The result: up to ~30% water savings and up to ~47% less methane in recent pilots, with no yield loss when technical support is provided (irrigation scheduling, leveling, guidance). For family farms, this means less pumping, lower energy bills, and more resilient production in drought-prone seasons.

For livestock, the challenge is enteric fermentation in ruminants. Here too, solutions are within reach: improved forages (nitrogen-fixing legumes, more digestible species), mineral supplements, and animal health (deworming, regular watering, rest). In practice, this leads to more milk and meat per animal, and fewer emissions per liter or kilo. In the Sahel and East Africa, these “climate + income” solutions have already proven effective in pilot projects, with strong interest among pastoralist and agropastoralist communities facing drought and competition over water and pasture.

The common thread of this forest–rice–ruminant trio? Simple technical measures, but backed by solid public support: local extension services, access to credit, land security, and commercial outlets. Without this ecosystem, good practices remain isolated. With it, they become the new norm.

The hidden footprint of our food: Fertilizers, post-harvest losses, and the road to cities

When we think “agricultural emissions,” we imagine the field. But a growing share comes before and after: producing inputs (fertilizers, packaging), storing, processing, packaging, transporting, selling, and managing waste. This “life around the plate” already accounts for nearly a fifth of the global total and is rising with Africa’s urbanization.

Nitrogen fertilizers: They boost productivity but are energy-intensive to produce. Manufacturing ammonia (the basis of urea) emits ≈ 2.4–2.9 t CO₂ per tonne of NH₃. Two complementary tracks are needed. First, greening chemistry (renewable hydrogen, carbon capture and storage). Second, smarter field application (soil diagnostics, split application, cover crops, compost, biofertilizers). The right dose at the right time, combined with cleaner sources, cuts the footprint while protecting yields.
Post-harvest losses: In many value chains (fruits, vegetables, tubers), 20–30% of production is lost between farm and market. This is both a climate and economic waste. Solutions are emerging: shared solar cold rooms, ventilated crates, field sorting, passable roads, real-time market information. Operators such as ColdHubs in Nigeria show large-scale impact: thousands of tonnes saved from loss in one year, higher incomes for producers and traders, safer food for consumers.
Logistics: Intra-regional trade still relies heavily on trucking. To lower emissions per ton-kilometer, trucks must be better loaded, backhauls reduced, refrigeration improved (insulation, efficient engines), fleets renewed, and rail prioritized where electricity is decarbonized. Recognized methods (GLEC/EDF frameworks) help businesses and authorities measure and reduce footprints.

And then there is us, urban consumers. Our choices matter: seasonal products, shorter supply chains when available, simpler packaging, supporting brands and cooperatives that disclose their climate efforts. Added up, these small shifts cut the carbon bill without sacrificing affordability or quality. The hidden footprint is becoming visible—and visibility is the first step to reducing it.

Scaling up: Public policies, finance, and innovation to accelerate change

The good news is that pathways exist. The less good: time is short and scale is lacking. On public policy, several countries are leading the way. In Kenya, a fertilizer subsidy program launched in 2022 via e-vouchers helps farmers secure yields while improving targeting and transparency. The lesson? Involve the private sector, strengthen agronomic support, and include environmental goals (nitrogen management, organic and biofertilizers) to avoid rebound effects. In South Africa, the Climate Change Act (2024) introduces sectoral carbon budgets and aligns the carbon tax with national trajectories—a strong signal for agribusiness, cold chains, and transport, with adaptation plans expected at provincial and municipal levels. At the regional level, the AFR100 initiative commits over 30 countries to restoring 100 million hectares by 2030, increasingly emphasizing ecosystem restoration (e.g., avoiding conversion of natural savannas), trees outside forests, and local value chains.

The keystone remains finance. Adaptation and mitigation needs in agriculture and land use will exceed USD 50 billion per year by 2030. Mobilizing such sums requires bankable, replicable projects: AWD rice systems, solar cold chains, organic fertilization and biofertilizers, landscape restoration, improved forages and animal health, zero-deforestation traceability, low-carbon logistics. Each project must show measurable results: tonnes of CO₂e avoided, liters or kilos produced, losses prevented, jobs created, market share gained for cooperatives, gender impacts (inclusion of women, youth, marginalized groups).

The study suggests a realistic and motivating target: deploy proven technologies to 20% of family farms to generate substantial climate gains in the short term, with co-benefits for incomes, resilience, and soil health. In practice, this means training field advisers, offering tailored credit (small amounts, repayments aligned with farm cycles), securing land access, and opening markets that reward low-carbon and quality production.

The final message is simple: feeding Africa and protecting the climate are not opposing goals. By combining smart public policies, agronomic innovations, and value chain innovations, the continent can slow the growth of its emissions while improving access to safe, nutritious food. The path is clear; the challenge is to move faster, further, together—governments, communities, researchers, producers, businesses, donors, and consumers.

The hidden footprint of our food

The study compares the sources of carbon emissions.

Credit

X.Li; Y.Zhang; S. Fan; I. Ouedraogo

Read the full study Agrifood system carbon emissions and reduction policy: insights from China and Africa published in Frontiers in Agricultural Science & Engineering (vol. 12, 2025) for detailed methodology and policy recommendations.