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Microbiomes: the unseen majority of tiny little things

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We cannot see, hear or sense them, yet, they are everywhere. We are talking about microbiomes, those microbial communities made up of bacteria, viruses, fungi and other single-cellular species that are the oldest living things on earth. Even though we can’t sense them, they come in armies of quadrillions. While they are active in the intestines of humans and animals, they also colonise plants, roots and foods. They live above or below the surfaces of soil, water, and even in the air.

The Covid pandemic has demonstrated how mighty tiny little things can be, as the SARS-CoV-2 virus has dominated international politics over the last two years. Louis Pasteur, the godfather of modern microbiology, has already said about the microbes: “They have the last word.”

Is this true? Since the beginning of the Covid crisis, we have seen a rise in awareness of research into viral life in nature and its transmission potential. Yet, many researchers have stressed the need to map out the entirety of microbiome life. In particular, knowledge has increased about the activities of microbiomes in another world theatre: climate change.

Diverse microbiomes turn oceans, soils and forests into the most efficient natural carbon sinks

A major contributor to human-induced climate change is the abundance of carbon dioxide (CO2) in the atmosphere. Forests, soils and oceans are the most significant natural carbon sinks: plants and soils, with the help of microbes and sunlight, take up the carbon dioxide from the air and convert it to build up food, feed and green biomass. At the same time, they release oxygen into the air and trap CO2 in the terrestrial and marine ecosystems. Unsurprisingly, these huge natural CO2 recycling and storage systems play a big role in the climate discussion.

Currently, terrestrial ecosystems of plants and soils remove three gigatonnes of CO2 every year. Almost the same amount of CO2 is absorbed by phytoplankton and marine sediments in the ocean. “This treasure might not last forever”, points out Prof. Andreas Richter, microbiologist and terrestrial ecosystem researcher at the University of Vienna. He states that “the capabilities will depend heavily on the availability of nutrients and the productivity of our natural systems.”

Microbiologists warn humanity: prevent loss of microbial biodiversity

Thousands of researchers and research organisations in the scientific community of microbiologists have signed a ‘Consensus Statement‘ warning humanity about the alarming and unprecedented rates of plant and animal extinction as a result of human activity, and also about losses in microbial biodiversity. According to them, “the abundance and diversity of microorganisms underlie their role in maintaining a healthy global ecosystem. Simply put, the microbial world constitutes the life support system of the biosphere. A major concern is that changes in microbial biodiversity and activities will affect the resilience of all other organisms and hence their ability to respond to climate change”. The scientists recommend that microbiome research become more involved in climate change research programmes.

Microbiomes play several roles

Seas and soils are the ‘engine rooms’ of organic growth, with marine phytoplankton, terrestrial plants and microbes acting as primary biomass producers through sunlight photosynthesis. Plants and microbiomes absorb CO2 from the air and energy from sunlight, which they then metabolise during their growth processes. In exchange, they release oxygen into the atmosphere.

Other groups of microbiomes are secondary producers, which act as an interface during processes of recycling, decomposition and demineralising plant remnants. Broad varieties of microorganisms govern the global carbon cycles. When decomposing, microbiomes release part of the plants’ CO2 uptake, including methane gases, back into the atmosphere. At the same time, other microbes fix carbon from plant particles in the layers of soils, including in the rhizosphere (the region of soil surrounding plant roots which is under the influence of the root). Marine microorganisms in the seas can bury CO2 by binding it to organic matter particles and sinking the marine sediments on the sea floor.

Rising temperatures and high CO2 concentrations in the air affect biological processes in the oceans and on land. Plant growth, dispersal in ecosystems and microbial composition shift as temperatures rise, and environments either adapt or fall out of balance. This has further impact on oxygen and greenhouse gas release capabilities.

The marine microbiome is a key marker for climate change

Although the complex feedback mechanisms are not yet fully understood, it is clear that the marine microbiome is highly responsive to climate change.

Prof. Antje Boetius, geomicrobiologist and director of the German Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research:With rising temperatures, it looks like the biological carbon pump gets weaker, as does the physical pump. Along with sea-ice melting and loss of multiyear ice, specific microbes may even disappear because of the lack of ice. The microbes are the fastest biological markers we have in nature, they are highly responsive to environmental dynamics. Microbiome research is vital because once we understand the links between community composition, biogeochemical functions and environmental dynamics, we can predict what will happen to the ocean’s role as carbon sink. There is an increasing body of evidence that the change of marine single-cell species marks climate change, including consequences for the food webs“. – Read Antje Boetius’ full interview

Studies have indicated growing global changes and instability in phytoplankton in specific regions and specific phytoplankton groups. However, long-term data and global ocean measurement infrastructure are widely lacking. Prof. Boetius, therefore, proposes an increase in field research to assess the ‘oceans’ productivity’, including innovative microbiome-based technologies to mitigate climate change.

The increase of coastal vegetation and the support for whale reproduction, including their role as fertilisers of phytoplankton, are seen as potential solutions. In 2022, the ‘United Nations Decade of Ocean Sciences‘ listed more than 470 actions to support the sustainable development of marine ecosystems globally.

Warming will lead to an increase in soil carbon loss: more CO2 emissions, less food security

In global forest ecosystems, shifts are caused not only through heat damage to macro life, but also by systemic microbial changes affecting carbon soil storage capacities.

Tom Crowther, professor of geoecology at the Swiss Federal Institute of Technology, ETH Zürich: “Northern forests, for example, are dominated by fungi, whereas bacterial webs dominate in the southern tropical forests. Tropical forests have faster carbon cycles causing higher emission rates. With global warming, cold-adapted regions like the Arctic are heating up fastest, and the microbiome is likely to respond. Consequently, we estimated that warming is stimulating microbial activity in the Arctic and sub-Arctic regions, enhancing the loss of carbon from soils. We estimated that these increased soil carbon losses could increase carbon emissions by 12-15 %. The warmer the climate, the more soil carbon emissions we are likely to see”. – Read Tom Crowther’s full interview

Prof. Crowther observes and investigates global microbial biogeography and geochemistry. He believes that restoring ecosystems, including increased microbial biodiversity above and below soil surfaces, will help to improve carbon storage capacities, with peatlands being the frontrunner as terrestrial sinks.


The UN’s Food and Agriculture Organization encourages the restoration of degraded agricultural land by building up microbial diverse humus layers to improve the soil’s sustainable productivity.

Furthermore, the ‘4 per 1000 Initiative‘, a platform that came out of the UN World Climate Congress COP21, promotes the annual increase of carbon fixation in soils by 0.4%, with the goal of capturing and storing massive amounts of carbon on agricultural land. They also want to ensure global food security by 2050.

Prof. Richter maintains hope for the future. According to him, more solutions and new technologies for additional and stable systems to remove and store CO2 will become increasingly available: “Improved microbial soil biochemistry would be an option for better carbon storage. We also estimate to see strong effects of binding organic materials to minerals. When high-molecular carbon is fixed by minerals or by enhanced weathered sandstone, the microbes can’t recycle it anymore. It could become a century’s chance for a very stable soil-carbon sink.”

Related content:
Prof. Antje Boetius: ‘Being at the pulse of the ocean to better understand its role in climate change’
Prof. Tom Crowther: ‘Microbial soil life is crucial for climate regulation’

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