Periodic Reporting for period 4 - SomSOM (Self-organisation of microbial soil organic matter turnover)
Okres sprawozdawczy: 2023-11-01 do 2025-04-30
Soil is one of the largest carbon stores on Earth, holding more carbon than the atmosphere and all plants combined. A major reason for this is the work of soil microbes—tiny organisms that break down plant material. When they do this, some of the carbon is released back into the air as CO2, but another part is transformed into microbial by-products. These by-products can become protected within the soil’s structure, where they are stored for long periods of time.
Over thousands of years, this microbial activity has both kept the C cycle between land and atmosphere in balance, and built up enormous reserves of carbon in soils. However, we still don’t fully understand the processes that govern how microbes break down and transform organic matter and their response to ongoing environmental change. One reason is that these activities happen at very small scales—in microscopic pores and on the surfaces of soil particles—where countless microbes interact in complex ways.
This makes the soil microbiome a complex system: it is made up of countless individual units that constantly interact. From physics and mathematics, we know that such systems often display “emergent behavior” or “self-organization,” where new patterns and properties arise that cannot be explained by looking at individual components alone. Yet, it has been unclear whether such dynamics also matter for soil microbial ecosystems and how they influence soil carbon cycling under environmental change.
Our project found evidence that complex systems behavior is central to soil functioning. Microbial communities are organized at the scale of tiny soil aggregates, and their structure is closely tied to the properties of organic matter found there. Their interactions create non-linear feedbacks, which can give rise to tipping points, where small changes in microbial or environmental properties trigger sudden and lasting shifts in how the soil system is organized and how it functions.
By showing that self-organization and emergent behavior play a role in soil carbon cycling, our work highlights the importance of treating soils as complex systems. This perspective is essential for predicting how soils will respond to environmental change - and how they will shape Earth’s carbon balance in the future.
Over thousands of years, this microbial activity has both kept the C cycle between land and atmosphere in balance, and built up enormous reserves of carbon in soils. However, we still don’t fully understand the processes that govern how microbes break down and transform organic matter and their response to ongoing environmental change. One reason is that these activities happen at very small scales—in microscopic pores and on the surfaces of soil particles—where countless microbes interact in complex ways.
This makes the soil microbiome a complex system: it is made up of countless individual units that constantly interact. From physics and mathematics, we know that such systems often display “emergent behavior” or “self-organization,” where new patterns and properties arise that cannot be explained by looking at individual components alone. Yet, it has been unclear whether such dynamics also matter for soil microbial ecosystems and how they influence soil carbon cycling under environmental change.
Our project found evidence that complex systems behavior is central to soil functioning. Microbial communities are organized at the scale of tiny soil aggregates, and their structure is closely tied to the properties of organic matter found there. Their interactions create non-linear feedbacks, which can give rise to tipping points, where small changes in microbial or environmental properties trigger sudden and lasting shifts in how the soil system is organized and how it functions.
By showing that self-organization and emergent behavior play a role in soil carbon cycling, our work highlights the importance of treating soils as complex systems. This perspective is essential for predicting how soils will respond to environmental change - and how they will shape Earth’s carbon balance in the future.
In this project, we studied how soil microbes “self-organize” across different spatial scales. Our goal was to uncover how their interactions shape the way organic matter is broken down and how carbon is stored or released from soils.
At the microscopic scale, we combined experiments and computer models to study how microbes cooperate to break down complex substances such as cellulose or chitin. We found that microbes face important trade-offs: they must invest in enzymes to unlock food sources, but the effectiveness of these enzymes depends strongly on soil structure. Tiny soil pores can limit enzyme activity even more than the microbes’ own biology. These trade-offs create thresholds, where small changes in conditions can cause abrupt shifts in microbial activity.
At a slightly larger scale, we examined microbial communities in millimeter-sized soil aggregates. By analyzing both the microbes present and the chemistry of the aggregates, we discovered that the soil microbiome is highly structured and diverse at small scales. Some microbial groups are associated with “fresh” organic matter, while others are linked to more decomposed material. These findings show how soil structure shapes microbial communities, and how microbial evolution and ecology are tied to the state of organic matter at fine scales.
We also explored network analysis, a method commonly used to study microbial co-occurrence patterns. Our theoretical work revealed that the environmental context and sampling strategy strongly influence these networks. Importantly, we showed that smaller sampling units (like individual aggregates) preserve ecological signals better than large, mixed samples, which can blur the patterns.
At the ecosystem scale, we studied long-term field experiments. In Austrian grasslands, we found that 70 years of nutrient depletion caused complex shifts in soil fungi, linked to changes in plant communities and soil chemistry. In Iceland, we examined soils along a natural geothermal warming gradient. Here, microbial activity and soil carbon showed non-linear responses to warming, suggesting that soils may pass critical tipping points under environmental change.
Overall, our project demonstrates that soil microbial ecosystems behave like complex systems, showing self-organization, trade-offs, feedbacks, and tipping points. These findings advance our understanding of how soils function and how they may respond to global change.
Dissemination of results
The project’s results were shared through peer-reviewed publications, conference presentations, and preprints on BioRxiv. Some findings are already published in international peer-reviewed journals (e.g. Nature Geoscience, ISME Journal, PLOS Computational Biology), while others are under review, and available as preprints on BioRxiv. The work has been presented on conferences, both within the soil science community and at interdisciplinary meetings on complex systems and mathematical modeling.
At the microscopic scale, we combined experiments and computer models to study how microbes cooperate to break down complex substances such as cellulose or chitin. We found that microbes face important trade-offs: they must invest in enzymes to unlock food sources, but the effectiveness of these enzymes depends strongly on soil structure. Tiny soil pores can limit enzyme activity even more than the microbes’ own biology. These trade-offs create thresholds, where small changes in conditions can cause abrupt shifts in microbial activity.
At a slightly larger scale, we examined microbial communities in millimeter-sized soil aggregates. By analyzing both the microbes present and the chemistry of the aggregates, we discovered that the soil microbiome is highly structured and diverse at small scales. Some microbial groups are associated with “fresh” organic matter, while others are linked to more decomposed material. These findings show how soil structure shapes microbial communities, and how microbial evolution and ecology are tied to the state of organic matter at fine scales.
We also explored network analysis, a method commonly used to study microbial co-occurrence patterns. Our theoretical work revealed that the environmental context and sampling strategy strongly influence these networks. Importantly, we showed that smaller sampling units (like individual aggregates) preserve ecological signals better than large, mixed samples, which can blur the patterns.
At the ecosystem scale, we studied long-term field experiments. In Austrian grasslands, we found that 70 years of nutrient depletion caused complex shifts in soil fungi, linked to changes in plant communities and soil chemistry. In Iceland, we examined soils along a natural geothermal warming gradient. Here, microbial activity and soil carbon showed non-linear responses to warming, suggesting that soils may pass critical tipping points under environmental change.
Overall, our project demonstrates that soil microbial ecosystems behave like complex systems, showing self-organization, trade-offs, feedbacks, and tipping points. These findings advance our understanding of how soils function and how they may respond to global change.
Dissemination of results
The project’s results were shared through peer-reviewed publications, conference presentations, and preprints on BioRxiv. Some findings are already published in international peer-reviewed journals (e.g. Nature Geoscience, ISME Journal, PLOS Computational Biology), while others are under review, and available as preprints on BioRxiv. The work has been presented on conferences, both within the soil science community and at interdisciplinary meetings on complex systems and mathematical modeling.
This project advanced the understanding of soil microbial ecosystems by applying a complex systems perspective to soil carbon cycling, an approach rarely used in this field. Previous research had described microbial roles in decomposition and stabilization of organic matter but had not addressed whether emergent behaviors such as self-organization—well established in physics and mathematics—also govern soil functioning.
Our work provided first evidence that complex systems dynamics shape soil carbon turnover. We showed that microbial interactions are shaped by trade-offs and soil structure, leading to thresholds in organic matter breakdown. At the aggregate and ecosystem scale, we found that microbial communities are spatially organized and respond to environmental change in non-linear ways, revealing potential tipping points.
By integrating concepts from microbial ecology, soil science, and complex systems theory, this project established a new framework to understand and predict how soils respond to environmental change. This represents a significant step beyond the state of the art in soil research.
Our work provided first evidence that complex systems dynamics shape soil carbon turnover. We showed that microbial interactions are shaped by trade-offs and soil structure, leading to thresholds in organic matter breakdown. At the aggregate and ecosystem scale, we found that microbial communities are spatially organized and respond to environmental change in non-linear ways, revealing potential tipping points.
By integrating concepts from microbial ecology, soil science, and complex systems theory, this project established a new framework to understand and predict how soils respond to environmental change. This represents a significant step beyond the state of the art in soil research.