Microbes That Keep Ecosystems in Balance Can Fall Apart Easily, New Study Finds

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Institute for Systems Biology research shows how microbial teamwork vital to clean water and healthy soils is becoming more fragile

SEATTLE, June 18, 2025 (GLOBE NEWSWIRE) -- Beneath the surface of soil, wetlands, and waterways, microbial communities perform some of the planet's most important - and invisible - work. But research from the Institute for Systems Biology (ISB) reveals that the partnerships microbes rely on to get these jobs done become surprisingly vulnerable to disruption in contaminated environments.

Denitrification: A Microbial Balancing Act

The study, published in The ISME Journal, focuses on denitrification, a critical part of the nitrogen cycle. In this process, microbes work together to convert nitrates into harmless nitrogen gas. In some contexts, such as when nitrate levels exceed a threshold due to fertilizer run-offs, this process fails to function smoothly. As a result, nitrate is partially reduced to nitrous oxide, a potent greenhouse gas that has contributed significantly to the warming of our planet and the depletion of ozone in the atmosphere. 

"Until now, we have had a limited understanding of how this kind of microbial cooperation forms and how resilient it is to stress,” said Dr. Alex Carr, lead author of the study and a postdoctoral fellow in ISB's Baliga Lab. "Through laboratory reconstitution of key players from a natural microbial community, we observed how different strains organized themselves to carry out the multi-step denitrification process.”

This cooperative behavior emerged without human intervention - each strain performing its role in concert with others.

While the microbes and their interactions are resilient to natural environmental changes, harmony proved fragile when there was excess nitrate. In these contaminated environments, when researchers introduced common changes such as oxygen or shifting the nutrient supply, the collaboration broke down, and the community lost its ability to complete the denitrification cycle.

Lasting Consequences for Ecosystems

In some cases, even when original conditions were restored, the system failed to recover.

"These findings are a reminder that, in contaminated environments, microbial ecosystems lose their remarkable capacity of being self-healing machines,” said ISB Professor, Director, and Senior Vice President Dr. Nitin Baliga, senior author of the study. "Even small environmental changes can push them past a tipping point, with long-lasting ecological consequences.”

The implications reach beyond the lab. Denitrifying microbes help keep waterways clean, limit greenhouse gas emissions, and maintain the fertility of agricultural soils. If the microbial partnerships are tuned to operate within the limits of their evolutionary experiences, it raises important questions about how climate change, pollution, and human intervention could rapidly drive such ecosystems to undesirable states and even to the brink of collapse.

The research also carries lessons for the design of microbial systems in engineered settings, such as wastewater treatment facilities or bioremediation efforts. "Simply assembling the right strains may not be enough,” said Carr. "Long-term function depends on keeping the environment stable and the community intact.”

About ISB

Institute for Systems Biology (ISB) is a collaborative and cross-disciplinary non-profit biomedical research organization based in Seattle. We focus on some of the most pressing issues in human health, including aging, brain health, cancer, chronic illness, infectious disease, and more. Our science is translational, and we champion sound scientific research that results in real-world clinical impacts. ISB is an affiliate of Providence, one of the largest not-for-profit healthcare systems in the United States. Follow us online at isbscience.org, and on YouTube, Facebook, LinkedIn, X, Bluesky, and Instagram.

CONTACT: Joe Myxter

Institute for Systems Biology

[email protected]