Hidden dangers in 'acid rain' soils

Acid rain from fossil fuel pollution may be quietly training soil bacteria to become longer-lived, more transmissible, and more deadly, according to a new study in the journal New Contaminants that tracks how a notorious foodborne pathogen rapidly evolved under simulated acid deposition.​​

Acid deposition from burning coal, oil, and other fossil fuels has long been known to damage forests, lakes, and crops, but its impact on disease-causing microbes in soil has been largely overlooked. The new research shows that acid rain can destabilize the native soil microbiome in ways that make it easier for the pathogen Escherichia coli O157:H7 to invade and persist. In global soil metagenomic data from 2,874 sites, the team found that E. coli abundance peaks in mildly acidic soils around pH 5, pointing to soil acidification as a powerful ecological pressure shaping this pathogen’s success.​​

“Pollution is not just stressing ecosystems, it is also giving dangerous bacteria a chance to adapt, spread, and become more harmful to humans,” said senior author Peng Cai of Huazhong Agricultural University. “Our results suggest that acid deposition can act as an unseen accelerator for the evolution of high-risk pathogens.”​​

A 150-day “evolution experiment” in soil

To probe this risk, the researchers ran a 150-day greenhouse experiment using forest soil from Henan Province, China, repeatedly treated with simulated rain at three acidity levels and inoculated with E. coli O157:H7, a major cause of severe foodborne illness. While pathogen numbers declined over time in all treatments, acid rain significantly slowed the die-off, with mildly acidic rain maintaining up to 100 times more bacteria than normal rain at certain time points and leaving several-fold higher populations after five months.​

Surprisingly, the overall composition and diversity of the native bacterial community remained relatively stable, but its internal interaction network changed dramatically. Acid rain and pathogen invasion simplified the network and increased negative interactions, indicating intensified internal competition that weakened the community’s natural “biotic resistance” to invaders and opened ecological space for E. coli O157:H7 to persist.​

From soil survivor to “super colonizer”

By the end of the experiment, the team isolated multiple independently evolved E. coli lineages that had adapted to the acid-stressed soil environment. These strains showed altered colony color, enhanced biofilm formation, and changes in motility, as well as shifts in how they used different carbon sources. When the evolved strains were returned to soil, they outcompeted their ancestor, reaching 6- to 450-fold higher abundances after 60 days, demonstrating a major boost in long-term colonization ability.​

Phenotypic analyses revealed that the most successful lineages balanced moderate biofilm formation with efficient movement, rather than maximizing a single trait. Biofilm and motility together explained most of the variation in soil colonization, showing how acid rain had nudged the pathogen toward an optimized “survival toolkit” for life in disturbed soils.​

Deep genetic rewiring under pollution stress

Gene expression profiling showed that evolved strains switched on a coordinated module of functions that govern movement, biofilm building, chemical communication, and virulence. Key quorum sensing and biofilm regulators sat at the center of a highly connected expression network, tightly linked to motility and pathogenicity genes, indicating a systemic upgrade rather than isolated changes.​

Whole-genome sequencing of the top colonizers revealed that this rapid evolution was driven largely by structural genome changes. Independent lineages shared a convergent chromosomal inversion near an acid-response regulator, while one highly fit strain carried a deletion that removed a major stress-sensing regulatory system thought to restrain biofilm production, potentially freeing downstream virulence and colonization traits from tight control.​

Stronger threats to the food chain and health

Crucially, the evolved environmental adaptations translated directly into greater risk along the food chain and in animals. In lettuce pot experiments mimicking contamination from irrigated soil, evolved strains reached up to eight times higher levels in edible leaves compared with the ancestral strain, indicating a much greater chance of reaching consumers on fresh produce.​

In mouse infection tests, the adapted lineages grew to higher levels in the gut and caused far more severe disease. Mortality rose from about 10 percent in animals exposed to the original strain to around 50 percent for some evolved strains, which produced extensive intestinal damage and lesions beyond the gut. These outcomes matched the observed upregulation of virulence genes, confirming that acid rain–driven adaptation had created not just tougher environmental survivors, but more lethal pathogens.​

Pollution and pathogen evolution: a feedback loop

Together, the results outline a three-step eco-evolutionary cascade: acid deposition destabilizes soil microbial defenses, this disturbance favors the survival and rapid evolution of invading pathogens, and the resulting strains are better at colonizing crops and causing severe disease. The authors argue that industrial pollution and pathogen evolution can form a dangerous positive feedback loop, in which environmental stressors unintentionally train “super pathogens” with heightened public health impact.​​

The study highlights the need to integrate microbial evolution into environmental and food safety risk assessments, especially in regions with ongoing acid deposition and intensive agriculture. Reducing emissions that drive acid rain, the researchers suggest, could help protect not only ecosystems but also human populations from emerging, pollution-fueled disease threats.​​

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Journal reference: Wang L, Wang Y, Xing Y, Gao C, Wu Y, et al. 2025. Acid deposition fuels pathogen risk through a coupled ecological and evolutionary cascade. New Contaminants 1: e012  

https://www.maxapress.com/article/doi/10.48130/newcontam-0025-0012  

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About the Journal:

New Contaminants is an open-access journal focusing on research related to emerging pollutants and their remediation.

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