Interactions between microorganisms and climate change

In the Anthropocene era, climate change, attributed to greenhouse gas emissions generated by human activities, causes the alteration of the composition of the planet’s atmosphere, and impacts numerous life forms on Earth. While the effects of climate change on macroscopic processes are well-documented, scientists now emphasize the importance of understanding the links between microorganisms and climate change. Indeed, microorganisms play a key role in the biology of climate change and in the balance of ecosystems. How do they affect climate change? Are they also impacted by climate disruption? Can they be part of the solution to reduce and withstand the negative effects of anthropogenic climate change?

Microorganisms: the omnipresence of the “invisible majority”

Microorganisms are defined as a group of microscopic life forms including bacteria, archaea, protozoa, microalgae, fungi (yeasts and molds), and viruses.

They appeared on Earth over 3.8 billion years ago and have colonized all environments: air, soil, oceans, and even extreme environments such as glacial deserts, hot springs, ocean depths, hypersaline environments, and the Earth’s mantle rocks. Their omnipresence, abundance, and diversity testify to their adaptability and importance in maintaining the balance of ecosystems.

Microorganisms play an essential role in biogeochemical cycles such as the carbon, nitrogen, and methane cycles(1).

Thus, for millions of years, the carbon cycle, in other words the exchange of carbon between different reservoirs such as the atmosphere, the biosphere (including soils), the hydrosphere (primarily oceans), and the lithosphere (rocks), was perfectly regulated. However, since 1850 and the start of the industrial era, this balance has been upset, leading to the changes observed in the climate system.

Human activities such as fossil fuel exploitation (oil, coal, gas), cement production, deforestation, ruminant farming, and the use of nitrogen fertilizers lead to an increase in the concentration of greenhouse gases (carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O)) in the atmosphere, which amplifies the greenhouse effect. The Earth then receives more energy, causing an increase in the global temperature.

Climate change affects microorganisms

Microorganisms are also affected by climate change. “It’s difficult to worry about microorganisms because we don’t see them. But we interact with them every day, and they are crucial for all forms of life on the planet“, emphasizes Ricardo Cavicchioli, a professor at the School of Biotechnology and Biomolecular Sciences (BABS), at the University of New South Wales (Australia). In 2019, more than 1700 biologists warned in the journal Nature(2) of the major repercussions on all living organisms of a disruption of terrestrial microbial flora due to climate change.

Climate change can indeed:

  • Influence the structure, diversity, composition, functions, and distribution of microbial communities.
  • Disrupt interactions between species, forcing them to adapt, migrate, be replaced by other species, or disappear.


Changes in the environment of microorganisms (temperature, acidification, CO2 levels, etc.) can therefore cause disturbances to ecosystems that depend on them.

Agricultural practices can also affect microbial communities in specific ways. Pollution sources such as fertilizers, for example, disturb the composition and function of microbial communities, thereby altering the natural cycles of carbon, nitrogen, and phosphorus transformation.

Today, soil microbial diversity is tending to decline, which has an impact on the functional potential of microbial communities, particularly in supporting plant growth. Plants play a key role in the absorption of CO2.


The consequences are visible even in the oceans, which are rich in micro-organisms. For instance, this is the case of phytoplankton, which is composed of microalgae and photosynthetic bacteria called cyanobacteria. Through photosynthesis, phytoplankton produces more than half of the Earth’s oxygen and consumes half of the CO2. Moreover, it is the primary link in the marine ecosystem food chain. Researchers from the Massachusetts Institute of Technology(3) (MIT – United States) have noted a 10 % decline in phytoplankton productivity in the North Atlantic since the beginning of the industrial era. This decline, which coincides with rising ocean surface temperatures, will affect all oceanic life.

Similarly, ocean acidification, resulting from a decrease in the pH of seawater due to increased dissolved CO2 in the form of carbonic acid, is a growing concern. It has the same origin as global warming, namely anthropogenic CO2 emissions. Ocean acidification lowers the oceanic concentration of calcium carbonates. However, calcium carbonates are essential for many marine organisms for the production and maintenance of the skeletons of planktonic species, corals, urchin shells, and mollusk shells. Once again, the entire marine ecosystem is impacted.

The combination of anthropogenic climatic factors truly constitutes a major threat to coral reefs. According to the IPCC(4), a 2°C temperature increase could thus lead more than 99 % of warm-water coral reefs to disappear by the end of the century. However, the disappearance of corals triggers a cascade of deleterious effects, ranging from the loss of marine ecosystem biodiversity to health hazards for humans, as well as economic issues(4).

Microorganisms have an impact on climate change

The relationship between microorganisms and climate change is two-fold because in natural processes, they both produce and consume the three main gases responsible for 98 % of global warming: carbon dioxide, methane, and nitrous oxide(5).

The increase in human activities today amplifies the production of greenhouse gases by microorganisms through three main microbial processes involved:

  • heterotrophic respiration, which produces CO2;
  • methane production by methanogenic bacteria which convert CO2 into methane (methanogenesis) in anaerobic environments such as wetlands, rice paddies, and the digestive system of ruminants;
  • denitrification, which notably produces N2O, a toxic gas responsible for eutrophication and the acidifying nature of rain. Soil denitrification is intensified by the excessive use of nitrogen fertilizers.

According to a study(6)  conducted by Alon Nissan et al. in 2023, climate change contributed to the acceleration of soil heterotrophic respiration. Heterotrophic respiration corresponds to the process of decomposing organic materials (wood, branches, twigs, plants, dead animals, excrement) in the soil by microorganisms, which then release CO2 in the atmosphere. Researchers have observed that if the soil temperature increases, microbial CO2 emissions also increase, regardless of the climatic zone.

Amplifying phenomena of global warming, such as the increased thaw of permafrost (20 % of the Earth’s surface), further intensify this trend with an impact on greenhouse gas emissions by microorganisms.

Permafrost refers to soils that are perpetually frozen on Earth (Arctic regions). When the soil is permanently frozen, microbial activities are greatly slowed and reduced, and there is very little release of CO2 into the atmosphere due to the very low intensity of respiration and fermentation by soil decomposer microorganisms. Permafrost also contains clathrates, icy structures that contain methane (CH4).

If the temperature rises, some of the permafrost will melt and thus consequently lead to:

  1. The resumption of activity by decomposer microorganisms of organic matter, accelerating the decomposition of vegetation and releasing significant amounts of CO2 into the atmosphere.
  2. The release into the atmosphere of CH4 trapped in the ice, thus accentuating the greenhouse effect and promoting ice melting, which in turn further decreases albedo, amplifying global temperature once more; albedo being the proportion of solar radiation that is reflected back into the atmosphere.

CO2 and CH4 emissions thus exacerbate global warming according to a positive feedback loop.

Finally, certain microorganisms, methanogenic archaea, play a critical role in the global carbon cycle due to their unique ability to produce CH4 under strictly anaerobic conditions, a potent greenhouse gas. Methanogens are present in the rumen of livestock, rice paddies, and manure.

Microorganism-based solutions for climate-resilient agriculture

The microbial flora has seen its density and microbiological activity in soils impacted by intensive agriculture. However, we know that soil microbiota plays a role in soil structuring and plant health. Soil microbiome analysis provides valuable information on soil productivity and disease risks. For climate-resilient crops, in addition to the use of plants from new genetic techniques, the microbiological approach is crucial.

One strategy is to encourage the use of biofertilizers, which contain living or inactive microorganisms that can promote plant growth by increasing their tolerance to unfavorable soil and environmental conditions or by improving their nutrient storage capacity (source FiBL(7)). These biofertilizers help plants better withstand extreme weather conditions such as drought or high temperatures without polluting the environment, unlike some chemical pesticides.

Certain types of microorganisms have the ability to reduce the amount of greenhouse gases, such as methane and nitrous oxide, two powerful greenhouse gases. Nitrogen-fixing bacteria used in the formulation of biofertilizers, for example, are very useful for reducing the use of mineral nitrogen fertilizers (which amplify N2O production). Some strains of non-denitrifying bacteria with higher N2O reductase activities are likely to reduce soil N2O production(8).

Similarly, methane-consuming methanotrophic bacteria are being studied to mitigate methane emissions in highly concentrated environments such as landfills and wetlands (rice paddies, peatlands, etc.). They have gained a growing interest in recent years due to their potential for transforming methane into value-added bioproducts such as biopolymers, ectoine, organic acids, microbial proteins, fatty acids, and lipids, within bioreactors(9). Recent advances in genomics, physiology, and genetic engineering techniques of methanotrophs pave the way for the production of secondary and non-native metabolites of interest.

For soil health, it is also important to decontaminate soils polluted by industrial processes or consumer products that may release toxic chemicals, posing a serious threat to food security. To solve this problem, it is necessary to accelerate the restoration of disturbed agricultural lands. Bioremediation is an effective treatment to prevent agricultural soil pollution (hydrocarbons, oil, heavy metals, pesticides, dyes, etc.). It relies on the ability of microorganisms to remove pollutants, notably thanks to their enzymes that allow them to use environmental contaminants as food. Today, thanks to microorganisms derived from genetic engineering, degradation capacities can be improved, thus encompassing a wider range of chemical contaminants.

Carbon sequestration by microorganisms

Soils contain three times more carbon than the atmosphere and play a major role in the fight against climate change(10).

Did you know that there are more microbes in a teaspoon of soil than there are people in the world? Scientists have discovered that microbial communities store much more carbon in the soil than they release through their metabolism. By promoting the decomposition and stabilization of soil organic matter, microorganisms help trap carbon in the soil, thereby reducing the amount of carbon dioxide (CO2) released in the atmosphere. Fungal microorganisms are valuable in this regard. A recent study(11) estimated that mycorrhizal fungi, which are crucial for soil health and plant growth, stored 36 % of fossil fuel emissions in the soil.

Many research efforts also focus on developing techniques for CO2 sequestration and its valorization using the potential of yeasts and bacteria.

CO2 sequestration using microorganisms as catalysts has the dual advantage of:

  1. being a green and sustainable approach to reducing global warming.
  2. being able to simultaneously produce value-added chemicals, biofuels, or bioplastics, for example.

In an article entitled “Engineering microorganisms for enhanced CO2 sequestration“, Guipeng Hu et al. discuss recent advances in improving CO2 fixation by microorganisms and reducing CO2 release by microorganisms(12). By using metabolic engineering strategies, the efficiency of CO2 fixation can be increased in both autotrophic and heterotrophic microorganisms. At the same time, CO2 release can be reduced by rearranging cellular metabolism to improve carbon conservation.

In conclusion, in the face of current anthropogenic and climatic disturbances, understanding and harnessing the potential of microorganisms appears to be a crucial pathway for developing strategies to mitigate climate change and restore degraded environments. Advances in biotechnology, particularly metabolic and genetic engineering, offer promising prospects for improving the resilience of agricultural systems and soil health, while contributing to more effective carbon sequestration. It is essential to continue supporting research in this field to better predict and manage the future impacts of climate change, while highlighting the vital ecological functions that microorganisms fulfill on our planet.


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