Why Soil Structure Matters
Soil structure—the arrangement of soil particles into aggregates and the pore spaces between them—is arguably the most important physical property of soil. It controls:
- Water infiltration and storage: Well-structured soils absorb and retain water effectively
- Root growth: Aggregated soils allow easier root penetration and exploration
- Gas exchange: Pore networks enable oxygen delivery to roots and microbes
- Carbon sequestration: Aggregates physically protect organic matter from decomposition
- Erosion resistance: Stable aggregates resist breakdown by water and wind
Yet soil structure is systematically omitted from Earth System Models and most pedotransfer functions, which rely primarily on texture (sand, silt, clay percentages). Our research demonstrates why this omission matters and how to account for structure in models and predictions.
Key Research Areas
1. Aggregate Formation & Stability
Soil aggregates form through complex interactions between:
- Biological agents: Roots, fungal hyphae, microbial polysaccharides
- Chemical bonds: Clay-organic matter interactions, polyvalent cations
- Physical processes: Wetting-drying cycles, freeze-thaw
We investigate how different factors contribute to aggregate stability across size classes:
- Macroaggregates (>250 μm): Primarily stabilized by roots and fungal hyphae
- Microaggregates (53-250 μm): More persistent, stabilized by organo-mineral complexes
- Silt and clay (<53 μm): Individual particles and micro-microaggregates
2. Carbon Distribution Across Aggregate Fractions
Soil organic carbon (SOC) is not uniformly distributed. Using physical fractionation techniques, we separate soils by:
- Size: Large vs. small aggregates
- Density: Light organic matter vs. dense mineral-associated carbon
Cover Crop Effects on Carbon Distribution
Our studies using stable isotopes (δ¹³C) and spectroscopy (NEXAFS, EXAFS) reveal:
- Cover crops rapidly incorporate new plant material into macroaggregates
- New carbon is more "plant-like" (phenolic resonance) compared to no-cover controls
- Cover crop carbon appears across all density fractions, not just light organic matter
- Iron oxide crystallinity may increase with cover cropping, affecting C stabilization
3. Pore Size Distribution & Hydraulic Implications
Soil structure creates a hierarchy of pore sizes:
- Macropores (>75 μm): Between aggregates; rapid water transmission and drainage
- Mesopores (0.2-75 μm): Plant-available water storage
- Micropores (<0.2 μm): Within aggregates; water held too tightly for plants
We measure pore size distribution using:
- Water retention curves analyzed via inverse modeling
- Mercury intrusion porosimetry
- X-ray computed tomography (collaborations)
Our findings show that conservation practices (no-till, cover crops) alter pore size distribution in ways that:
- Increase infiltration rates (more macropores)
- Marginally improve water storage
- Enhance gas diffusion
4. Management Effects on Structure
Long-term field experiments (24+ years) allow us to quantify how agricultural practices affect soil structure:
Tillage Effects:
- Standard tillage disrupts aggregates, reducing macroporosity
- No-till preserves or enhances aggregate stability over time
- Structural benefits take years to manifest (5-10+ years)
Cover Cropping:
- Increases root biomass and exudation, promoting aggregation
- More impact on macroaggregate formation than total SOC stocks (short-term)
- Effects visible after just one season in macroaggregate fraction
Irrigation Method:
- High-efficiency irrigation may reduce structural development compared to furrow irrigation
- Wetting-drying cycles important for aggregation; reduced cycles may limit structure formation
Soil Structure in Earth System Models
We've demonstrated that systematic omission of soil structure from Earth System Models (ESMs) has significant consequences:
Local vs. Global Effects
At local scales:
- Including structure significantly alters infiltration-runoff partitioning
- Affects recharge predictions in wet, vegetated regions
- Changes water availability for plants
At global scales:
- Coarse spatial resolution of ESMs masks local structure effects
- Current ESMs can't simulate intense, short rainfall where structure matters most
- Global climate implications remain elusive in current models
Advanced Characterization Methods
Spectroscopic Approaches
We use synchrotron-based techniques to probe carbon chemistry and iron speciation:
- Carbon NEXAFS: Identifies aromatic vs. aliphatic carbon, carboxylic groups
- Iron EXAFS: Determines iron oxide mineralogy and crystallinity
These techniques reveal that cover crops and conservation practices alter not just carbon quantity but also its chemistry and protection mechanisms.
Isotope Tracing
Using natural δ¹³C differences between C3 (most crops) and C4 (corn) plants, we trace:
- How quickly new carbon enters different aggregate fractions
- Whether old or new carbon is preferentially lost
- Turnover times for carbon in different pools
Practical Implications
Carbon Sequestration
While soil carbon credits and offsets generate interest, our research urges caution:
- Short-term (1 season) cover cropping may not increase bulk SOC stocks
- Carbon is redistributed among fractions rather than simply accumulated
- Long-term commitments (decades) needed for measurable sequestration
- Co-benefits (improved water infiltration, erosion control) may be more reliable than carbon credits
Resilience to Climate Extremes
Well-structured soils with stable aggregates better withstand:
- Intense rainfall without erosion or crusting
- Drought periods with maintained pore networks
- Freeze-thaw cycles without structural collapse
Recent Publications
- Composition and Persistence of Soil Organic Matter Along Eroding and Depositional Transects in Buried vs. Modern Soil Layers: A Case of the Brady Paleosol at Wauneta, Nebraska.Dolui, M., Nel, T., Phillips, L. M., McMurtry, A. R., Moreland, K. C., Tfaily, M., … Berhe, A. A.Geoderma (under Review), (accepted). 2026.
Abstract
Paleosols form when soils are buried through deposition by aeolian, colluvial, alluvial, or other processes. Burial of former topsoil isolates soil organic matter (SOM) from surface conditions, allowing carbon to accumulate and potentially remain stable for millennia. In this study, SOM composition, distribution, and persistence were analyzed in the Brady Soil of Nebraska, USA, to compare SOM spatial variability in modern and buried soils, as well as the impact of erosional exposure on SOM stability. The Brady Soil, formed as a surface soil during the Pleistocene-Holocene transition and now a paleosol buried up to 6 m deep (or more) by loess deposition during the Holocene, was sampled along burial (up to 5.8 m depth) and erosional (up to 1.8 m depth) transects to compare SOM dynamics in different geomorphic settings. Fourier Transform Infrared Spectroscopy (FTIR) and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) were used to analyze SOM composition, while δ¹³C isotope analyses identified SOM sources, and radiocarbon values were used to estimate turnover rates. Results confirmed a vegetation shift from C3 to C4 plants after Brady Soil formation, reflecting warming climatic conditions. Increasing SOM age and decreasing δ¹³C and δ¹⁵N values with depth indicated slowing of decomposition rate in buried soils. Higher pH in the Brady Soil suggested greater base cation content, supporting SOM stabilization through organo-mineral associations and aggregate formation. However, exposure of the Brady Soil due to surface erosion caused faster SOM turnover. This result suggested susceptibility of buried SOM to losses via decomposition upon erosional exposure, possibly accelerated by priming in response to modern SOM inputs. These findings highlight the potential loss of carbon stocks in buried soils under future climate change, as shifts in soil physicochemical properties may destabilize long-preserved SOM.BibTeX
@article{p2025-Dolui-Geoderma, title = {Composition and Persistence of Soil Organic Matter Along Eroding and Depositional Transects in Buried vs. Modern Soil Layers: A Case of the Brady Paleosol at Wauneta, Nebraska}, language = {en}, journal = {Geoderma (under review)}, author = {Dolui, Manisha and Nel, Teneille and Phillips, Laura M. and McMurtry, Abbygail R. and Moreland, Kimber C. and Tfaily, Malak and McFarlane, Karis Jensen and Mason, Joseph A. and Marin-Spiotta, Erika and de Graaff, Marie-Anne and Ghezzehei, Teamrat A. and Berhe, Asmeret Asefaw}, pages = {(accepted)}, year = {2026}, research-theme = {soil-structure} } - Soil Structure Changes Under Conservation Management Enhance Carbon Mineralization in Irrigated Croplands.AlvarezSagrero, J., Chacon, S. S., Mitchell, J., & Ghezzehei, T. A.Vadose Zone Journal. 2026.
Abstract
BibTeX
@article{p2025-Alvarez, title = {Soil Structure Changes Under Conservation Management Enhance Carbon Mineralization in Irrigated Croplands}, language = {en}, journal = {Vadose Zone Journal}, author = {AlvarezSagrero, Jennifer and Chacon, Stephany S and Mitchell, Jeffrey and Ghezzehei, Teamrat A.}, pages = {}, doi = {10.1002/vzj2.70065}, year = {2026}, research-theme = {soil-structure, rhizosphere, sustainable-agriculture} } - Soil Organic Matter Stabilization by Polyvalent Cations in a Buried Alkaline Soil.Dolui, M., Nel, T., Chacon, S., Phillips, L. M., McMurtry, A. R., Moreland, K. C., … Berhe, A. A.JGR Biogeosciences (Under Review), (accepted). 2026.
Abstract
Buried paleosols can store large quantities of organic carbon (C), much of which persists for millennia due to isolation from surface processes that promote decomposition. Subsoil organic matter (SOM) persistence is often enhanced by mineral associations and ionic conditions — particularly high clay content and polyvalent cations — that limit microbial degradation and leaching. However, the vulnerability of these deep C stocks under erosion or environmental change remains poorly understood. This study investigates controls on SOM stabilization in the Brady paleosol and overlying modern soils across contrasting geomorphic settings in the Great Plains of Nebraska, where Late Quaternary loess deposition and erosion created a sequence of buried and exposed paleosols. We sampled soils along burial and erosional toposequences and analyzed their physicochemical properties and radiocarbon-based persistence of occluded particulate organic matter (oPOM) and mineral fractions (MF). Brady Soil showed greater persistence (lower Fm) of oPOM and MF than modern soils, particularly under burial. This was linked to higher silt and clay content, elevated electrical conductivity, and increased exchangeable calcium and magnesium content, supporting roles for organo-mineral interactions, flocculation, and carbonate cementation. In modern soils, SOM persistence and C content were more strongly tied to pH and cation exchange capacity. Erosional exposure reduced SOM stability and promoted geochemical convergence toward modern surface soils. These findings show that burial enhances SOM persistence via multiple stabilization mechanisms, while erosion increases subsoil C vulnerability. Our results underscore the importance of geomorphic and geochemical context in predicting soil C stability under environmental change.BibTeX
@article{Dolui2025, author = {Dolui, Manisha and Nel, Teneille and Chacon, Stephanie and Phillips, Laura M. and McMurtry, Abbygail R. and Moreland, Kimber C. and McFarlane, Karis Jensen and Mason, Joseph A. and Marin-Spiotta, Erika and de Graaff, Marie-Anne and Ghezzehei, Teamrat A. and Berhe, Asmeret Asefaw}, title = {Soil Organic Matter Stabilization by Polyvalent Cations in a Buried Alkaline Soil}, journal = {JGR Biogeosciences (Under review)}, year = {2026}, pages = {(accepted)}, doi = {}, research-theme = {soil-structure} }
- Environmental Variability and Moisture-Temperature Coupling Reveal Continental-Scale Controls on Soil Respiration.Rojas, Y. T. P., & Ghezzehei, T. A.JGR-Biogeosciences (under Review).
Abstract
Understanding how temporal patterns of moisture variability control biogeochemical responses remains a fundamental challenge in Earth system science. Jensen’s inequality provides a mathematical framework for quantifying when episodic environmental events dominate over mean conditions. We applied this framework to continental-scale AmeriFlux data (134.5 million hourly observations from 2,004 soil moisture sensors) to quantify how moisture distribution patterns control soil respiration responses across environmental gradients. Sensors in dry regions show large Jensen’s inequality effects (median temporal averaging difference of -63.6%) because they experience highly skewed moisture distributions where brief wet periods drive disproportionate respiratory responses. Wet regions show minimal effects (median -27.1%) because they have more uniform moisture distributions. Data density analysis reveals that sensors operating at θ≈0.05 exhibit severe temporal averaging effects, while sensors at θ≈0.45 show minimal effects, demonstrating the mechanistic basis for where ecosystems operate on the moisture-respiration relationship. Climate gradient analysis shows systematic transitions from severe effects in arid systems to moderate effects in humid systems. Depth analysis reveals that surface soils experience maximum episodic event importance while deeper soils show reduced effects due to environmental buffering. Moisture-temperature coupling demonstrates systematic negative correlations in water-limited systems, indicating that environmental co-variation modulates biogeochemical responses. Jensen’s inequality emerges as a diagnostic tool for identifying when moisture variability patterns dominate biogeochemical processes, with continental-scale patterns revealing fundamental controls on episodic event importance across ecosystems.BibTeX
@article{2025-PerezRojas, title = {Environmental Variability and Moisture-Temperature Coupling Reveal Continental-Scale Controls on Soil Respiration}, language = {en}, journal = {JGR-Biogeosciences (under review)}, author = {Rojas, Yulissa T. Perez and Ghezzehei, Teamrat A.}, pages = {}, research-theme = {water-flow, soil-structure} } - Two Decades of Conservation Agriculture Enhances Soil Structure, Carbon Sequestration, and Water Retention in Mediterranean Soils.Alvarez-Sagrero, J., Berhe, A. A., Chacon, S. S., Mitchell, J. P., & Ghezzehei, T. A.Soils, EGUsphere [Preprint].
Abstract
Conservation agriculture offers a pathway for enhancing soil health with climate co-benefits in Mediterranean agricultural systems. This study examined long-term impacts of combining no-till management with cover cropping over 20 years in California’s Central Valley, providing rare insights into soil system equilibrium under sustained conservation management. We assessed soil physical, chemical, and structural properties comparing reduced tillage with cover crops to standard tillage without cover crops, employing density fractionation and spectroscopic analysis to understand carbon protection mechanisms. After two decades, conservation agriculture achieved dynamic equilibrium characterized by fundamental shifts in carbon stabilization pathways. Water-stable aggregate analysis revealed the most pronounced management effects, with conservation practices exhibiting 136% greater stability, indicating substantial improvements in soil structural integrity. These structural enhancements corresponded with a reorganization of carbon protection mechanisms, demonstrating that physical protection within aggregates becomes a dominant carbon stabilization pathway under long-term conservation management. Mineral-associated organic carbon saturation analysis revealed that both management systems remained well below theoretical maximum capacity, indicating substantial remaining potential for carbon sequestration even after reaching equilibrium. Physical property improvements included 15% lower bulk density and 13% greater water retention at field capacity. Our findings demonstrate that two decades of conservation agriculture fundamentally transforms soil functioning through aggregate-mediated physical protection.BibTeX
@article{2025-AlvarezSagrero, title = {Two Decades of Conservation Agriculture Enhances Soil Structure, Carbon Sequestration, and Water Retention in Mediterranean Soils}, language = {en}, journal = {Soils, EGUsphere [preprint]}, author = {Alvarez-Sagrero, Jennifer and Berhe, Asmeret Asefaw and Chacon, Stephany S. and Mitchell, Jeffrey P. and Ghezzehei, Teamrat A.}, doi = {10.5194/egusphere-2025-6047}, pages = {}, research-theme = {sustainable-agriculture, soil-structure, water-flow} }
Related Research
Key Methods
- Wet sieving for aggregate fractionation
- Density separation (heavy liquids)
- Carbon NEXAFS spectroscopy
- Iron EXAFS spectroscopy
- Stable isotope analysis (δ¹³C)
- Water retention for pore size distribution
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