Principal Investigators

At a Glance

To understand the complicated role stored carbon plays in global climate, Princeton researchers are investigating three important areas. The first two research highlights focus on the role clay minerals play in storing carbon, and how this carbon might be released as a result of, respectively, microorganisms and the dynamic interplay of water molecules. The third highlight looks at how moisture affects organic carbon decomposition in two key areas, iron-redox cycling and carbon sequestration by rock weathering. These highlights are important because there is more carbon locked up in soils than there is in the atmosphere. Understanding the processes by which soils store – and other factors might release – this carbon is crucial to any implementation of emissions cuts as required by the Paris Climate Accords.

Howard Stone, Judy Yang and Ian Bourg in the lab
In the soils lab, left to right, Howard Stone, Judy Yang and Ian Bourg studying 4D images that reveal mechanisms of clay-carbon protection and release. (Photo courtesy of Howard Stone)


Research Highlight 1

Clay minerals have long been assumed to protect organic matter from decomposition. They do this by absorbing and retaining organic matter in soil despite accelerated rates of decomposition caused by global warming. However, field measurements show that after small molecular-size biodegradable sugars (e.g., root exudates) were input into soil, the amount of soil carbon decreased significantly in a short period of time (such as days). This suggests that clay-associated carbon may be released, which would accelerate climate change.

Scientists need a more detailed understanding of the carbon sorption and release processes to accurately predict global climate, and potentially suggest carbon mitigation strategies. Such an understanding, however, is hindered by lack of technology to measure the carbon distribution inside clay aggregates in real time. Such real time measurement is critical because the organic matter sorption and release can occur in only a matter of days.

The researchers used laponite, a synthetic and transparent smectite clay made from natural minerals, to provide the first 4-D observation (three spatial dimensions plus time) of the organic matter sorption-release processes inside transparent clay micro-aggregates. The results show that, unlike “small” molecular-size sugars, which can be adsorbed to and desorbed from clay reversibly, “large” molecular-size organic matter is irreversibly sorbed to clay. It is physically separated from bacteria, which cannot penetrate the nano-size pores of clay micro-aggregates.

Figure 3.1 below shows how “large”-size organic matter is irreversibly sorbed to clay aggregates (the solid gray-to-black curve). The curve represents the amount of “large”-size organic matter in clay, and the adjacent images “a-e” are the confocal microscopy snapshots of the micro-aggregates at different times. The fluorescent organic matter is green, and the silver color indicates the outer surface of the clay aggregate. The dashed gray-to-black curve shows the reversible sorption of a “small” molecular-size sugar (glucose) for comparison.

Figure 3.1.
This figure shows how “large”-size organic matter is irreversibly sorbed to clay aggregates (the solid gray-to-black curve).

The researchers visualized the sorption and release of carbon from clay micro-aggregates in the presence of bacteria and extracellular enzymes. They observed that enzymes can penetrate aggregates and break down the irreversibly sorbed organic matter into smaller sizes. The organic matter is then released, becoming available to bacteria outside the aggregate. The integrated conceptual model shown in Figure 3.2 summarizes this process. The results explain the intensified release of mineral-protected carbon observed in the field. Results further suggest that bacteria and extracellular enzymes play important roles in soil carbon dynamics, yet they have not been fully represented in current global soil carbon predictive models. Based on the results of this study (Yang et al. 2020), the authors suggest an improved global soil carbon predictive model.

Figure 3.2.
An integrated conceptual model for interactions between clay, carbon, microbes, and exoenzymes is proposed. Note: drawing not to scale.


Research Highlight 2

The researchers used supercomputers provided by the US Department of Energy to carry out the first large-scale atomistic simulation of a hydrated clay aggregate (Underwood and Bourg, 2020). The purpose was to gain insight into the environment that exists within clay aggregates. The researchers generated an aqueous suspension of 30 clay nanoparticles with dimensions and crystal structures similar to the clay used in the previous Research Highlight. The modeled systems were then slowly hydrated during a 150 ns simulation, at a computational cost of several million hours of CPU time (Figure 3.3). Simulation results (including first-of-a-kind predictions of total suction as a function of porosity) showed that hydrated clay aggregates equilibrated with pure water should spontaneously phase-separate into dense nanoporous regions (where organic molecules may become physically “protected”) and microporous regions (where water can flow and soil bacteria can live). Simulation results further showed that water molecules and adsorbed ions remain remarkably mobile even in dense clay aggregates if the system remains water-saturated. But their mobility decreases rapidly once drying begins as air bubbles invade the medium. This process is similar to the impact of drying on bacterial metabolism.

Figure 3.3.
Molecular dynamics simulation snapshots during the progressive dehydration of a 25 x 25 x 40 nm clay-water systems containing 30 smectite nanoparticles. Yellow, red, light blue, and pink spheres show clay Si, O, Al, and Mg atoms; dark blue spheres show exchangeable Na ions; water molecules are not shown.


Research Highlight 3

Hydrologic variability modulates the interactions between organic matter, clay and rock minerals. As a result, actual carbon fluxes and residence time differ from those observed in controlled simulations and laboratory experiments. To bridge this gap, researchers developed a dynamical system to analyze the coupling between iron and carbon dynamics in the soil root zone as driven by soil moisture. Emphasis was placed on the interaction of soil organic matter, the Fe-reducing population, the iron Fe2+-Fe3+ cycling, and the soil moisture level, which controls the redox rates (Figure 3.4). Similar to what has been observed in a tropical forest, the results suggest that soil moisture and litterfall rates are the primary drivers of iron fluctuations at daily-to-seasonal temporal scales. This contributes to improved quantification of the role of the soil iron cycle in the decomposition of the organic matter.

Figure 3.4.
Schematic of iron-redox cycling in soils and its effect on organic carbon decomposition.
After Calabrese et al. (submitted, 2019).

The research led to the discovery of an optimum regime for regenerating Fe3+ electron acceptors for iron reduction in upland soils (Calabrese et al. 2019). In the predominantly oxic, upland soils, periods of high wetness trigger anaerobic processes such as iron (Fe) reduction within the soil microsites. This has implications for organic matter decomposition, the fate of pollutants, and nutrient cycling. In fluctuating O2 conditions, Fe reduction is maintained by the re-oxidation of ferrous iron, which renews the electron acceptor, Fe3+, for microbial Fe reduction. When optimal conditions are not replicated, the duration of the oxic or the anoxic phase limits the regeneration of Fe3+ or its reduction rate, respectively. The average duration of the oxic and anoxic intervals is linked to the frequency and mean depth of precipitation events that drive the dynamics of soil moisture. This is illustrated in Figure 3.5, where a tropical (Luquillo CZO) and a subtropical (Calhoun CZO) forest are compared. The tropical site maintains a high potential for iron reduction throughout the year, due to quick and frequent transitions between oxic and anoxic conditions. By contrast, seasonality strongly affects the subtropical site, which limits iron reduction to winter and early-spring months with higher precipitation and lower evaporative demand.

Figure 3.5.
Soil moisture (a) duration of anoxic conditions (b) iron reduction phase (c) Reduced iron concentration. After Calabrese et al. (d) Temporal evolution of Fe2+ over the course of a year (the inset show details of the iron-redox cycles in March) (submitted, 2019).

Chemical weathering occurs when minerals dissolve during contact between meteoric water and the continental crust. Hydrologic controls on this process are responsible for the production and percolation of carbonates that are sequestered in oceans. It is important for scientists to understand how environmental conditions, such as climate and geology, affect chemical weathering rates for the long-term stability of such crucial areas as the Critical Zone. Understanding chemical weathering is also crucial to estimate the effectiveness of the so-called enhanced mineralization techniques proposed in geoengineering for carbon mitigation (e.g., Hartmann et al., 2013). The researchers applied the Pi-theorem of dimensional analysis to available datasets to show that a strong relation between chemical depletion, precipitation and potential evapotranspiration underlines the primary role of wetness on chemical weathering of parent materials (Figure 3.6). They estimated the spatial distribution of chemical depletion fraction and found that, globally, soils are 50% chemically depleted, 60% of the land is in kinetic-limited conditions, while only 10% is supply-limited. The remaining 30% of the land is in a transitional regime and susceptible to changes in wetness.

Figure 3.6.
Global data of normalized weathering rates as a function of Dryness Index, DI (potential evapotranspiration rate divided by mean rainfall rate). Calabrese and Porporato (in preparation).



Calabrese, S., D. Barcellos, A. Thompson, and A.M. Porporato, 2019. Optimal hydrologic regime for regenerating Fe electron acceptors for iron reduction in upland soils. Biogeochemistry (submitted).

Calabrese S., and A. Porporato, Mineral weathering controlled by wetness (submitted).

Calabrese, S., and A. Porporato, 2019. Impact of ecohydrological fluctuations on iron-redox cycling. Soil Biology and Biochemistry 133: 188-195.

Hartmann, J., A.J. West, P. Renforth, P. Köhler, C.L. De La Rocha, D.A. Wolf-Gladrow, H.H. Dürr, and J. Scheffran, 2013. Enhanced chemical weathering as a geoengineering strategy to reduce atmospheric carbon dioxide, supply nutrients, and mitigate ocean acidification. Reviews of Geophysics, 51(2), pp.113-149.

Underwood, T.R., and I.C. Bourg, 2020. Large-scale molecular dynamics simulation of the dehydration of a suspension of smectite clay nanoparticles. Journal of Physical Chemistry C, 124:3702-3714. (

Willemsen, J.A.R., S.C.B. Myneni, and I.C. Bourg, 2019. Molecular dynamics simulations of the adsorption of phthalate esters on smectite clay surfaces. Journal of Physical Chemistry C, 123: 13624-13636. (

Yang, J.Q., X. Zhang, I.C., Bourg, and H.A. Stone, 2020. 4D imaging reveals mechanisms of clay-carbon protection and release (in preparation).