In our recent study, “Microbial carbon metabolism is linked to organic matter chemistry across soil systems”, published in Communications Earth & Environment, we could show across a geoclimatic grassland gradient that carbon metabolism of soil microbes (i.e. the rates at which the microbes grow and respire, and their efficiency of carbon use) is linked to the chemistry of their potential food source - extractable organic matter. This is an exciting finding, because it indicates that the chemical composition of organic matter can potentially help us to understand and predict the fate of carbon across different ecosystems. And it shows the insights that soil gradient studies can provide for one of the greatest challenges in soil science: bridging across scales.
The great challenge of stratified knowledge1
The soil organic carbon cycle is commonly conceptualized at three fundamentally different spatial scales2–6.
(1) The microscale, where most biogeochemical processes take place: e.g., chemical interactions stabilize organic matter on mineral surfaces, and microbes grow, respire and interact. The microscale is therefore the scale at which we study the fundamental mechanisms that underly the soil organic carbon cycle.
(2) The mesoscale, where most processes in soil biogeochemistry are commonly measured. Many analytical procedures use milligrams to grams of soil material to quantify pools and fluxes of C and nutrients, or to characterize microbial communities. Field experiments to understand mechanisms in plant-soil systems are commonly conducted in plots of several meters. As a result, most information that feeds into macroscale models is measured at the mesoscale.
(3) Lastly, the macroscale, which ranges from kilometers to the global system. At this scale, entire landscapes and phenomena such as land use or climate change are studied, and it is this scale at which policy making needs to be informed. How should we manage soil systems? How will soil systems respond to global change? How do soil systems affect global change?
However, the study of soil organic carbon dynamics at separate scales sometimes causes a “stratified” understanding of the carbon cycle, because it is not always easy to integrate and consolidate our knowledge from different scales.
Using gradient studies to bridge across scales1
Upscaling, and with this the transfer of concepts and mechanisms across these three different scales (typically from smaller to larger spatial scales) is therefore a major challenge in soil science and related fields. To inform policy making and predict the future, it is crucial to learn which micro- and mesoscale mechanisms should be represented at the macroscale. This is not easy7–9, because on the one hand processes that emerge at larger scales can be the result from a complex interaction of processes at smaller scales. On the other hand, not all mechanisms and controls translate from the micro- and mesoscale to the macroscale.
The three main scales at which soil organic carbon cycling is studied, and the quest to find mechanisms that bridge across scales. Modified from1.
One -sometimes overlooked- tool with which we can inform upscaling are gradient studies. Natural gradients can be used to investigate whether the effects of hypothesized mechanisms are reflected at the macroscale and whether the mechanisms in question therefore actually matter at the macroscale. To this end, we can measure the micro- or mesoscale processes of interest (or their proxies) along macroscale gradients. In combination with underlying mechanistic knowledge, this approach allows to evaluate whether the micro- and mesoscale mechanisms cause relevant patterns at the macroscale, and whether they are therefore likely to translate to the macroscale.
Microbial food preferences and organic matter chemistry matter across scales
A growing body of studies propose mechanisms that link organic matter chemistry to soil microbial carbon turnover. While the idea itself is not entirely new, evidence if and how this matters at the macroscale is still scarce. In our paper “Microbial carbon metabolism is linked to organic matter chemistry across soil systems” we set out to test these ideas with a well-described gradient of 33 mineral topsoils from Chilean grasslands. Together with partners from the Umweltforschungszentrum in Leipzig, Germany, we applied ultra-high resolution LC FT-ICR mass spectrometry to gain the best possible insights into the chemistry of extracted organic matter from these soils. After overcoming analytical challenges in the laboratory and lending statistical procedures that are commonly applied in the analysis of infrared spectra, we were able to link this data with measurements of microbial growth, respiration and carbon use efficiency.
Colorful soil samples getting ready for incubation (Image: Daniel Wasner).
Our results show clearly that microbial carbon metabolism is linked to organic matter chemistry and – put simply- , that these linkages and the resulting soil microbe’s food preferences might translate to the macroscale! Our data further suggests that these links function in ways that are largely consistent with mechanistic concepts that have already been developed and tested at the micro- and mesoscale. This is great news and allows us to conclude that information on the chemical composition of bioavailable organic matter can provide insights into the processes which govern the fate of carbon across different ecosystems.
Answering this question opens several promising avenues for future research. Which biochemical pathways are most central to the coupling of organic matter chemistry and microbial carbon metabolism? And if such pathways can be identified, could they serve as simple yet robust proxies to predict soil microbial carbon turnover across diverse soils? Addressing these questions could provide a mechanistic bridge between microscale processes and macroscale patterns of soil carbon turnover, ultimately improving our ability to predict carbon cycling at the macroscale.
References
1. These paragraphs are based on Chapter 1 in: Wasner, D. Mechanisms that link climate, soil properties and microbes to macroscale soil organic carbon dynamics: Insights from a geoclimatic gradient. (ETH Zurich, Zurich, 2024). doi:https://doi.org/10.3929/ethz-b-000672416. In this chapter, you find numerous references to further authors who have discussed these ideas.
2. Hinckley, E. S., Wieder, W., Fierer, N. & Paul, E. Digging Into the World Beneath Our Feet: Bridging Across Scales in the Age of Global Change. EoS Transactions 95, 96–97 (2014).
3. O’Rourke, S. M., Angers, D. A., Holden, N. M. & McBratney, A. B. Soil organic carbon across scales. Global Change Biology 21, 3561–3574 (2015).
4. Wieder, W. R. et al. Explicitly representing soil microbial processes in Earth system models. Global Biogeochemical Cycles 29, 1782–1800 (2015).
5. Blankinship, J. C. et al. Improving understanding of soil organic matter dynamics by triangulating theories, measurements, and models. Biogeochemistry 140, 1–13 (2018).
6. Pachepsky, Y. & Hill, R. L. Scale and scaling in soils. Geoderma 287, 4–30 (2017).
7. Hall, E. K. et al. Understanding how microbiomes influence the systems they inhabit. Nat Microbiol 3, 977–982 (2018).
8. Baveye, P. C. et al. Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain. Front. Microbiol. 9, 1929 (2018).
9. Doetterl, S. et al. A landscape-scale view of soil organic matter dynamics. Nat Rev Earth Environ 6, 67–81 (2025).