At first glance, Harvard Forest looks like an ordinary forest. Oaks shade the land among small shrubs and other trees, mainly maples, birches and beeches. Dead leaves cover the ground below. What makes this 4,000-acre piece of land in north-central Massachusetts so special is that it’s buried in the ground.
About 10 centimeters below, scientists have installed an underground network of cables – some of which have been active for around 35 years – that warms the forest floor. By continuously heating the ground to 5 degrees Celsius above ambient ground temperature, these cables mimic the global warming effects of climate change for researchers who want to understand what a warmer world could mean for the surrounding ecosystem.
Ecologist Serita Frey of the University of New Hampshire in Durham has certainly noticed changes since she began working at Harvard Forest in 2003. These days, there is more rain and less snow in winter. Summers are drier than before. More and more trees are falling victim to disease and certain invasive species are taking hold. But what’s less visible – and what she wants to learn – is what happens to bacteria, fungi and other microbes that take up residence in the dirt beneath the forest floor.
Microbes, like all life on Earth, are facing global warming. Using underground cables that artificially warm the ground, Frey and his team can collect soil samples to monitor the evolution of microorganisms that have taken up residence in the Harvard Forest soil. They learned, for example, that two decades of warming have changed the populations of bacteria living the topsoil of heated plotsas well as the microbial community composition found in clods of earth.
Overall, human-caused climate change “is changing the composition of the community in terms of who is there,” Frey says. “But we’re also changing its function.”
Scientists have long known that microbes play a crucial role in maintaining levels of carbon and other nutrients in our environment. As microbes decompose dead animal and plant matter, these organisms can both absorb and produce climate-changing gasesincluding carbon dioxide, methane and nitrous oxide. In a warming world, this cycle could begin to take a different form, with serious consequences for other life forms on the planet. Frey is one of many researchers working to understand how climate change will affect microbes — and whether humans can harness them to reduce its impacts.
Carbon in motion
Carbon continually moves through soils, waterways, organisms and the atmosphere in a process called the carbon cycle.
Carbon dioxide enters the atmosphere through respiration
plants (B, E) and animals (C), as well as through man
activities (A).
As microbes break down dead organisms in soil or water (D), they push carbon towards underground reserves (F) or the deep ocean.
But, like animals and plants, microbes can also release carbon into the atmosphere as a byproduct of energy production.
As with soil work, research elsewhere reveals that viruses and other microbes in thawing permafrost can add more carbon to the atmosphere by breaking down previously frozen material. But other microbial capabilities could have the opposite effect and prove beneficial against the consequences induced by climate change. For example, when paired with beneficial soil fungi, plants at risk of habitat loss could get a boost to resist environmental stress or disease.
Understand how microbes respond to warming temperatures, drought, flooding, etc. is essential for identifying strategies that can prevent more carbon from seeping into the atmosphere or help manage transforming ecosystems, says microbial ecologist Jizhong “Joe” Zhou of the University of Oklahoma in Norman. Terrestrial microbes have withstood varying climates for 3.5 billion years. For them, change is the only constant.
Changing communities
About 1,300 miles from the shady terrain of Harvard Forest, tall prairie grasses and small trees cover a vast expanse of rolling hills south of Oklahoma City. Dotting the meadows, long tube-shaped infrared lamps float 1.5 meters above the ground and are distributed evenly across experimental plots, each a few meters wide.
In an experiment led by Zhou at the University of Oklahoma’s Kessler Atmospheric and Ecological Station, or KAEFS, the lamps heat dirt and ambient air to 3 or 4 degrees Celsius above room temperature. As at Harvard Forest, the goal of this experiment is to zoom in on the smallest forms of soil life to see if and how quickly new microbes could take over, in this case, warmer prairie soils.
Experiments at other research sites use outdoor chambers to create warmer experimental plots or, as Harvard Forest does, directly warm the soil. But heating air and soil together is a more realistic way to examine the impact of rising temperatures on underground ecosystems, Zhou says. In nature, “warming usually affects the air first.”
Since the project began in 2009, Zhou and his team have collected a wealth of data. Wires made of a mixture of copper and nickel and placed up to 75 centimeters deep in the ground record the temperature every 15 minutes. The team also regularly measures the water content of the soil and keeps an eye on which plants are growing and how much carbon is in the soil. Each year, when plant growth peaks in September or October, researchers extract a 15-centimeter-deep piece of soil from three locations in each plot to assess the microbial composition.
After about five years of artificial warming, many of the the microbes inhabiting the grassland patches have changedZhou and colleagues reported in 2018 in Climate change. These include bacteria such as Actinobacteria, which help maintain nutrient levels to maintain soil fertility, and Ascomycota fungi, which also help stabilize the soil. These organisms dominated other microbes or disappeared completely at higher temperatures than in control plots. Warming has also pushed these microbial populations change more quickly over time. Population changes that could have occurred naturally over decades occurred in just a few years.
As Zhou and his colleagues continued to monitor the changes for two more years, they found that soil microbial diversity decreased. Fewer species of bacteria and fungi occupied grassland patches that have experienced continued warming and drought. When this happens, the relationships between the remaining species can become more and more complexsometimes forcing them to fight to persist in a changing environment.
“If we look into the future, 15, 20 years, 50 years or 100 years later,” Zhou says, “the whole community might be very different from what it is today.” And as microbial populations fluctuate, so does their role in the ecosystem.
Analysis of differences
Despite everything Zhou and others have learned about the evolution of microbial communities, it’s difficult to determine which organisms do what in their environment. Historically, scientists have not known exactly which microbes live where. This is perhaps not surprising, as our planet could support up to 1,000 billion different species living in very different landscapes.
Because microbes are invisible to the naked eye, scientists must resort to indirect means to study them. Environmental DNA can provide a window into who’s there, says Michael Van Nuland, a Portland, Oregon-based ecologist and evolutionary biologist with the Society for the Protection of Underground Networks. But it can be difficult to know whether this genetic material comes from part of the microbial community as it is today, “or whether you’re capturing remnants of DNA that were floating around in the past.”
It is also difficult to relate the organism to its function. Scientists can find molecular signals in soil that suggest what certain microbes are doing in an ecosystem, but those data don’t easily specify how quickly organisms grow, how they attract carbon and other nutrients into soils, or how they spread through the environment.
Over the past decade, projects aimed at mapping microbes, bacteria and fungi found in soils to viruses that inhabit the oceanshave begun to help researchers fill in some of these gaps. Such reference maps can help researchers document fluctuations in response to temperature changes or storms in certain regions, Van Nuland says.
Van Nuland’s project involves creating an atlas of mycorrhizal fungi, which have symbiotic relationships with a wide range of plants around the world, from crops like corn, wheat and blueberries to common trees like maple and pine. As temperatures rise, these fungi could adapt to the heat or shift their habitat to a more suitable location, even if the trees with which they exist in symbiosis I might not be able to followVan Nuland and colleagues reported in 2024 in the Proceedings of the National Academy of Sciences. Other mushrooms could persist in a state of stresswhile waiting for the return of favorable conditions. Or they might just die.
Fungi help most plants absorb nutrients such as nitrogen and phosphorus and can provide a physical shield against pathogens. The loss of these benefits could have destructive impacts on ecosystems. “It’s not just about understanding how climate change affects a single species,” says Van Nuland. It is also “the network of interactions that these species maintain with other organs isms of the environment that allow them to persist and thrive. We need to take this into account in order to understand how species respond to climate change.”
Disturbed cycles
Warming is just one factor causing changes in microbial life. Other factors affected by climate change, such as precipitation and pollution, can also have unpredictable consequences.
Droughts, for example, are becoming more and more frequent. For the microbes occupying Zhou’s experimental plots in Oklahoma’s prairie landscape, a double whammy of heat and drought is an incentive to become more active and release more carbon into the atmosphere, Zhou and colleagues report in a forthcoming paper in Climate change. But climate change may also lead to more violent and unpredictable torrential rains. In wetter conditions, microbes appear to retain carbon in the soil, the team found.
Although impacts likely vary widely across different ecosystems, the results in Oklahoma suggest that carbon stored in soils could be released as droughts worsen around the world, the researchers say. Future warming could worsen as the natural process of microbial carbon cycling is disrupted. Drylands, which cover about 40 percent of the Earth’s surface, could be particularly vulnerable.
In Harvard Forest, Frey focuses on the dual influence of climate change and pollution. Like many forests in the northeastern United States, Harvard Forest’s soil has historically been rich in nitrogen from human-caused pollution, such as car exhaust and power plant emissions (although atmospheric nitrogen levels have improved over the past decade thanks to the Clean Air Act). But nitrogen is also essential for plant growth, because it allows them to make proteins and carry out photosynthesis.
Unlike warmer temperatures, which cause microbes to work overtime and release more carbon into the atmosphere, additional nitrogen puts the brakes on microbes, slowing decomposition and retaining organic compounds in the soil. Frey believed that adding additional nitrogen to Harvard Forest soils would follow this principle and slow down the microbes, thereby offsetting the carbon they would otherwise emit from artificial heat.
Instead, carbon dioxide emissions from the soil were actually higher in plots treated with both heat and nitrogen compared to just one of these factors, she and her colleagues reported in 2024 in Ecology and evolution of nature. The total amount of carbon in the soil, however, remained about the same.
“There is concern that with warming we will lose carbon from the system, which would deplete soil nutrients,” says Frey. However, it is possible that warming soils and providing additional nutrients could stimulate plant growth in ways that absorb more carbon from the atmosphere. “In systems that are more nutrient rich to begin with and have a lot of nitrogen, perhaps carbon loss will be reduced.”
Because his team’s experimental plots are small, predicting what the results might mean for the carbon budget of the broader ecosystem would require computer simulations, Frey says. At least for now, studies suggest that the Harvard Forest is doing exactly what it’s designed to do and absorbing more carbon than it releases.
Thawing of permafrost
Much of the work analyzing how climate change influences microbes focuses on fungi and bacteria, because they do much of the work of moving nutrients through ecosystems. But viruses can also play a role, working behind the scenes to make sure everything goes smoothly – or at least to their own advantage.
This dynamic is visible in the Arctic, a region that is warming almost four times faster than other parts of the globe. To better understand the effect of climate change on viral communities, some researchers have turned to permafrost, a layer of soil that remains frozen from year to year. When thawing, resurrected bacteria, fungi and other microbes come back to life, breaking down dead plant matter and adding carbon dioxide and methane to the atmosphere. The newly awakened viruses can then attack these microorganisms.
When viruses infect, and sometimes kill, their hosts, they affect the microbes that live in a system, says Akbar Adjie Pratama, a viral ecologist at Friedrich Schiller University in Jena, Germany, and Ohio State University in Columbus. As with other dead organisms, hosts killed by viruses release carbon and other nutrients that are put back into the ecosystem. But this extra carbon could weigh down an already carbon-rich atmosphere.
In 2024, Pratama and colleagues reported in Environmental microbiology that, over a period of seven years, a viral community in permafrost in Sweden remained surprisingly stable. Some of these viruses carried genes that, if the ground thawed, could help degrade carbon in the ecosystem. Some can infect Methanoflorenes archaea, a group of microbes that emit methane into the atmosphere. Understanding the viral controls that naturally control microbes that leak gas, the team wrote, could help researchers find ways to do so artificially.
To uncover the impact of viruses on ecosystems around the world, we need to identify the organisms that viruses infect in permafrost, water and soil, Pratama says. But it is a difficult task. So far, he and his colleagues have managed to link only a small fraction of permafrost viruses to their microbial hosts, and even fewer in groundwater. “How can we draw a meaningful conclusion about the role of viruses when we can only link about 1% of them? Pratama said.
Change for the better
Understanding the roles that viruses and other microbes play in climate change – both the organisms themselves and the processes to which they contribute – helps identify allies who could help humans mitigate some of its effects.
For example, viruses such as soil-dwelling phages that infect carbon- or nitrogen-emitting soil microbes could help reduce greenhouse gas emissions, Pratama says. In places like the Netherlands, where the agricultural industry produces more nitrogen per hectare than most other European Union countries, adding such viruses to the soil could help reduce nitrogen-fueled algae blooms that leach into waterways and degrade water quality.
Mushrooms could also be collaborators. Planting trees to restore forests following wildfire may have a better chance of success if the trees’ fungal partners are also transplanted. “They are ecosystem engineers,” says Van Nuland. “They work across the realms of life to get things done.”
However, beyond hypothetical uses, some scientists have already applied their knowledge of microbes to help stressed coral reefs during marine heatwaves, which are occurring more frequently due to climate change.
Coral reefs are home to diverse algae that display a kaleidoscope of colors and which in turn host a myriad of beneficial microbes. Heat waves cause these algae to produce toxins that not only cause corals to expel them – which we think of as discolored or bleached corals – but also kill some of the good bacteria. In this environment, pathogens can begin to grow. “A whole already bad situation is going to get worse,” says Raquel Peixoto, a marine ecologist at King Abdullah University of Science and Technology in Thuwal, Saudi Arabia.
Peixoto experimented with restoring healthy bacteria to bleached corals to keep these marine animals alive. In 2021, she and her colleagues reported in Scientific advances that the use of probiotics to restore the bacterial community was effective for protecting corals in an aquarium. The team has since tested their probiotic treatment in the wild. During a marine heatwave in 2022, treated corals were healthier than untreated organismsthe researchers reported last year in a paper published on bioRxiv.org.
“We continue to apply [the probiotic treatment] for weeks when the corals are in very poor condition,” says Peixoto. Not only do the corals benefit, but the microbiomes of fish, algae and sponges also improve. “We see in the reef that it makes a difference,” she says.
However, such experiments with microbe-based solutions are still rare and limited. Deploying such solutions to combat climate change would require a significant scale-up of human attempts to create useful microbes. And while it is clear that Earth’s changing climate is altering microbes and their communities, the consequences remain unclear. Regardless of what the future holds, what is certain is that microbes will play a vital role in what is to come.
“Microbes shape and shape our planet, our atmosphere, throughout our existence,” says Peixoto. Microbes as a whole are not going to disappear. “They will evolve, they will be replaced, they will always be there,” she assures. But their role in keeping our planet functioning “is changing.”
