Deadly bacteria may thrive in warmer soils » Yale Climate Connections

Basgonda Patil, a farmer in western India, needed two weeks in the hospital and over three months of recovery time to get over what he first thought was a common bacterial infection. 

“I felt like I was going to die at any moment,” he recalled of the first 10 days when a high fever was followed by a throat infection. Antibiotics did not help the 56-year-old until the doctor prescribed a dose so strong that Patil asked if he was the subject of an experiment.

Despite his long and near-fatal brush with a resistant strain of bacteria, Patil survived. More than a million other sufferers around the world were not so lucky.

The World Health Organization reported that antimicrobial resistance, or AMR, was responsible for approximately 1.27 million deaths worldwide in 2019. In many countries, doctors and health care workers are noticing a gradual increase in cases where common infections are becoming difficult to treat because bacteria have developed the ability to resist antibiotics.

Resistant bacteria have long been a problem in hospitals, which fight back with tighter sanitation protocols to limit their spread. Scientists are now turning their attention to an overlooked source of resistant bacteria: the soil on farms, which is rich with many tiny living organisms. Climate change may have exacerbated this problem. Scientists know that hotter weather can make soil bacteria carry more resistant genes, and they are trying to understand the reasons why this happens.

Warmer soils boost resistant bacteria

Researchers examined 280 soil bacterial genomes from 44 countries and conducted an experiment in Alaska’s boreal forest where they artificially warmed a field. 

“I was surprised to find that bacteria living in higher temperatures not only have more AMR genes within their genome, but they are also ‘using’ them at an increased rate,” said Melanie Hacopian, a postdoctoral scholar in the Treseder Lab at the University of California, Irvine, who led the study.

This finding indicated that bacteria in warmer environments might gain a survival advantage by actively switching on these resistance genes.

Higher temperatures and certain antimicrobial compounds, like medicines and chemicals that kill bacteria or inhibit their growth, can harm bacterial cells in similar ways, Hacopian added. Both can damage proteins in the cells, weaken their protective walls, or stop important cell processes. When heat and an antimicrobial compound cause the same kind of damage, the stress on the bacteria overlaps. Some bacteria have special genes, called resistance genes, that protect them from this damage. These genes can help them survive not only against heat stress but also from exposure to antimicrobial drugs.

But soil microbes rarely face just one stressor at a time. In Germany, researchers exposed soils to 10 factors, including global warming, drought, heavy metals, salinity, fertilizers, and microplastics, both individually and in random combinations of these eight factors, to investigate their effects on soil microbes.

They found that when multiple factors combine, they favor different types of bacteria and viruses than those typically found in soil. These types are more adaptable and carry more antibiotic resistance genes, which could make soils a bigger source of resistance.

“This happened mainly because bacteria that carry these resistance genes are becoming more common, which naturally increases the number of antibiotic resistance genes in the soil,” said Álvaro Rodriguez del Rio, postdoctoral researcher at the Institute of Biology, Freie University Berlin, Germany, and lead author of this study.

This, he explained, can happen through resistance mechanisms like efflux pumps, which are like tiny brooms or pumps within a bacterial cell that push out harmful substances, such as antibiotics or toxins. Resistance genes can also spread when bacteria share DNA, a process called horizontal gene transfer. Small DNA loops called plasmids carry multiple resistance traits and can move between species, meaning soil bacteria could potentially pass resistance to human pathogens.

“In our study, soils with more plasmids had more resistance genes, showing gene sharing may drive antibiotic resistance,” del Rio said. Widespread antibiotic resistance in soil could pose a threat to human health, Hacopian warned.

Down in the flood

Researchers have found that floodwaters can carry antibiotic-resistant bacteria into the soil. There, they can survive for months, raising the risk of exposure for both humans and animals. Floods also disrupt the balance of soil microbes, decrease oxygen levels, and create favorable conditions for anaerobic bacteria to thrive, some of which can be harmful and resistant to antibiotics.

Following Hurricane Harvey’s flooding of Houston in August 2017, scientists found that the city’s soil contained more bacteria carrying antibiotic resistance genes. This heightened risk persisted for about three to five months after the storm, and 18 months later, levels of these genes had decreased.

For Patil, the dangers of antibiotic-resistant bacteria became painfully real after his fields flooded last year. His wife, Nanda Patil, 45, and son, Abhishek, 19, also fell ill and were hospitalized for 12 days. Nearly 100 others from his remote village in Maharashtra state reported similar symptoms.

“During that time, I was near the fields, trying to save my cattle, and it’s probably something from the field that affected me,” he said.

Researchers say Patil’s suspicion isn’t unfounded. In Xiamen, China, scientists investigated how warmer soil affects the gut bacteria of the invasive giant African snail, a nocturnal species that spends its days buried in soil, making it particularly sensitive to changes in soil temperature. Higher temperatures led to an increase in antibiotic-resistant bacteria in the snails, including human pathogens that carried multiple resistance genes. This finding raises concerns that climate change could accelerate the spread of resistance from the environment to bacteria that infect humans.

Also linking climate change to soil that spreads antibiotic resistance, scientists from southern China reported an increase in specific antibiotic resistance genes. Their study, conducted over five years in forest and plantation ecosystems, simulated a 4°C warming to observe these changes across three seasons.

Overusing antibiotics often backfires

The overuse and misuse of antibiotics, like taking them unnecessarily or in large amounts, give bacteria more opportunities to adapt and develop resistance, making these drugs less effective over time.

David Graham, a professor in the department of biosciences at the U.K.’s Durham University, emphasized that the best way to combat resistance is to prevent its development in the first place. He highlighted more sustainable antibiotic use and fighting pollution, another factor driving resistance. He noted the lack of good diagnostics in many regions of the world, which causes unnecessary or inappropriate antibiotic use: “By improving diagnostics, we can prevent the need for antibiotics, obstructing the spiral towards more antibiotic use.” 

He also stressed that improving sanitation and hygiene in both human and animal health is vital, as stopping resistant bacteria from contaminating water, soil, or crops is much easier than dealing with them after they have spread. 

In India and many other countries, antibiotic regulation is weak, and people often use antibiotics in dairy and chicken farms even when not needed. In these regions, it is easy to buy antibiotics without a doctor’s note, and farmers feel pressure to produce more milk.

Patil said antibiotics have become a common part of cattle’s lives. But drug-resistant bacteria, along with antibiotic residues, can reach humans through milk, meat, and eggs. They can also spread when farmworkers handle animals or animal waste contaminates soil and water. Once these resistant bacteria infect humans, resistance genes can transfer between bacteria, making common infections more difficult to treat. 

To prevent the rise of antibiotic resistance in soil, it may also be important to limit the simultaneous occurrence of multiple environmental stressors, Rodriguez del Rio said. Additionally, Hacopian suggested, “We could improve wastewater treatment technology and slow the leakage of antibiotic residues and heavy metals into the natural environment.” 

This approach would reduce the exposure of soil microbes to harmful stressors, making it less likely for antibiotic resistance genes to be favored and spread.

Climate change could make common infections harder to treat in the future, experts said.

“People aren’t realizing that the antibiotics that once helped them fight infections are silently becoming less effective. Now, even a common bacterial infection can take several days to recover,” Patil warned.