Soil Structure, Aggregation & Carbon

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.

Paleosols formed by the burial of topsoil during landscape evolution can sequester substantial amounts of soil organic carbon (SOC) over millennia due to protection from surface disturbances. We investigated the moisture sensitivity of buried SOC storage in the Brady paleosol, a loess-derived soil in Nebraska, USA, where historical aeolian deposition during the Pleistocene–Holocene transition buried soils up to 6 m deep. Topsoils from erosional (up to 1.8 m depth) and depositional (up to 5.8 m depth) transects were incubated under two moisture regimes – continuous wetting (60 % water-holding capacity) and repeated drying–rewetting – to assess SOM vulnerability to changing hydrologic conditions. SOC decomposition rates modeled from CO2 fluxes were consistently higher in erosional than depositional settings, with surface re-exposure of Brady soils enhancing microbial accessibility and destabilization. A two-pool model showed that >96 % of SOC was stored in a slow-cycling pool, particularly in deeply buried soils where stabilization was linked to mineral association, fine particles, and Ca-mediated flocculation. However, this pool decomposed more rapidly in shallower Brady soils (higher turnover rate relative to buried soil), reflecting increased microbial responsiveness to surface-driven processes. Drying–rewetting cycles caused greater SOC losses from Brady soils than continuous wetting, despite the dominance of the slow pool and depletion of labile SOC. These cycles also accelerated fast pool decay in modern soils and erosional transects, whereas burial dampened variability in Brady soils. Although continuous wetting increased overall decay in burial transects during the incubation period, wet–dry cycles destabilized the slow pool, which may result in greater long-term SOC loss. Together, these results underscore the importance of burial depth, geomorphic context, and moisture regime in shaping the long-term vulnerability of ancient SOC under climate change.

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.

Keywords: Erosion, Paleosols, Soil organic matter composition, Soil carbon persistence, Subsoil

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.

We conducted two 64-day incubation experiments to assess how locally produced almond-shell biochar influences soil physical and hydraulic properties. Biochar was created using slow pyrolysis at different temperatures (350 °C or 700 °C), separated into different particle sizes (<250 μm or 1–2 mm), and applied at 10 ton/ha or 60 ton/ha to a coarse-textured soil. While our analysis shows that biochar yielded greater cation exchange capacity (CEC) and specific surface area (SSA) with increasing pyrolysis temperature and finer particle size, its contributions to improving soil hydraulic properties were marginal. In the first experiment, the addition of biochar at high rates slightly improved water stable aggregate (WSA) (3.8%–5.3% increase) but has no effect on saturated hydraulic conductivity (Ksat). Soil respiration measured throughout the experiment were not significantly different among treatments. In the second experiment, the addition of biochar increased soil infiltration rate at the initial stage (8.18E–4 cm/s), but this effect diminished over time. WSA was lower for biochar amended soil and lowest at high application rates (5%–21% reduction). Cumulative carbon dioxide (CO2) flux varied between biochar particle sizes and rates. Additionally, a significant difference between the two experiments was also observed, with cumulative CO2 (38%–56% greater) and WSA (11%–40%) being inversely correlated. Our findings suggest that almond-shell derived biochar has a limited impact on arable loamy sand soil properties, specifically for water retention under short-term conditions.

A long-term annual crop study in Five Points, California, shows that the combined use of no-tillage, surface residue retention, and cover crops improves soil health compared to conventional practices common to the region. Several chemical, biological, and physical soil health indicators were improved when these practices were combined. Our data suggest that farmers stand to gain multiple synergistic benefits from the integrated use of these practices by increasing soil structural stability, water infiltration and storage, and agroecosystem biodiversity, and improving the efficiencies of the carbon, nitrogen, and water cycles of their production systems.

The growing water scarcity jeopardizes crop production for global food security, a problem poised to worsen under climate change–induced drought. Amending soils with locally derived biochar from pyrolyzed agricultural residues may enhance soil moisture retention and resilience, in addition to climate change mitigation. However, prior studies on the hydrologic benefits of biochar focused on optimal moisture, not water-limited conditions where biochar’s large wettable surface area could aid plants and microbes. We hypothesized that biochars differing in feedstocks would positively augment soil moisture and respiration, with overall impacts most beneficial under drier conditions. Using water vapor sorption isotherms, we used film theory to estimate the specific surface area (SSA) of biochars. We then modeled and tested the moisture retention of a coarse-textured soil amended with biochar. Additionally, a 109-day lab incubation experiment was also conducted to examine biochar effects on respiration across a moisture range spanning optimal to wilting point. Among seven tested biochars, almond shell biochar significantly increased soil moisture and yield the second highest SSA. Despite drying treatments, the amended soil maintained higher respiration than the control, indicating enhanced biological activity. The results demonstrate biochars counter drying effects in coarse soils through physical and biological mechanisms linked to increased sorptive capacity. Our findings contribute to the development of sustainable water and waste management strategies tailored to the needs of California Central Valley, where the potential for biochar application is substantial. Above all, our research fills a crucial gap by providing context-specific insights that can inform the effective utilization of locally produced biochars in the face of increasing water scarcity and excess biomass challenges.

Growing interest in human-excreta derived fertilizers requires more information on their agronomic relevance. In this study, we measured the nitrogen (N) and phosphorus (P) mineralization from fresh urine, stored urine, urine-enriched biochar prepared with either fresh or stored urine, and feces-derived compost application in a 90-day aerobic loam soil incubation. Soils were extracted for available N at days 0, 5, 10, 20, 30, 60, and 90, while soils were extracted for four biologically relevant P pools at days 0, 30, 60, and 90. We found that N in urine applied alone was immediately bioavailable, supplying nearly all the 200 kg-N ha-1 applied, while urine-enriched biochar supplied approximately half of the N applied. Feces-derived compost application led to a slow release of mineral N. Feces-derived compost application stimulated substantial native soil P mining, while urine-P was likely rapidly immobilized. These results are relevant to container-based sanitation and other source-separated sanitation endeavors, and researchers and producers interested in human excreta-derived fertilizers. Future research should explore, among other things, different urine-enriched biochar preparations and the co-application of urine-based fertilizers and feces-derived compost.

Keywords: ecological sanitation, nitrogen, phosphorus, organic fertilizer, sustainable agriculture, container-based sanitation, compost, urine

Uncertainty in the global carbon (C) budget has been reduced for most stocks, though it remains incomplete by not considering aquatic and transitional zone carbon stocks. A key issue preventing such complete accounting is a lack of available C data within these aquatic and aquatic-terrestrial transitional ecosystems. Concurrently, quantifiable results produced by restoration practices that explicitly target C stock accumulation and sequestration remain inconsistent or undocumented. To support a more complete carbon budget and identify impacts on C stock accumulation from restoration treatment actions, we investigated C stock values in a Mediterranean-montane riparian floodplain system in California, USA. We quantified the C stock in aboveground biomass, large wood, and litter in addition to the C and total nitrogen in the upper soil profile (5 cm) across 23 unique restoration treatments and remnant old-growth forests. Treatments span 40 years of restoration actions along seven river kilometers of the Cosumnes River, and include process-based (limited intervention), assisted (horticultural planting and other intensive restoration activities), hybrid (a combination of process and assisted actions), and remnant (old-growth forests that were not created with restoration actions) sites. Total C values measured up to 1100 Mg ha−1 and averaged 129 Mg ha−1 with biomass contributing the most to individual plot measurements. From 2012 to 2020, biomass C stock measurements showed an average 32 Mg ha−1 increase across all treatments, though treatment specific values varied. While remnant forest plots held the highest average C values across all stocks (336 Mg ha−1), C values of different stocks varied across treatment type. Process-based restoration treatments held more average biomass C (120 Mg ha−1) than hybrid (23 Mg ha−1) or assisted restoration treatments (50 Mg ha−1), while assisted restoration treatments held more average total C in soil and litter (58 Mg ha−1) than hybrid (35 Mg ha−1) and process-based restoration treatments (37 Mg ha−1). Regardless of treatment type, time was a significant factor for all C stock values. These findings support a more inclusive global carbon budget and provide valuable insight into restoration treatment actions that support C stock accumulation.

Keywords: Riparian floodplain, Floodplain restoration, Biomass, Soil carbon, Large Wood, Nature-based solutions, Multi-benefit restoration

Manure is a leading source of methane (CH4), nitrous oxide (N2O), and ammonia (NH3) emissions, and alternative manure management practices can help society meet climate goals and mitigate air pollution. Recent studies show that biochar-composting can substantially reduce emissions from manure. However, most studies test only one type of biochar applied at a single application rate, leading to high variation in emission reductions between studies. Here, we measured greenhouse gas and NH3 emissions during biochar-composting of dairy manure with biochar applied at 5% or 20%, by mass, and made from walnut shells, almond shells, or almond clippings. We found little difference in emissions between biochar type. However, we found that the 20% application rates increased CH4 emissions and decreased N2O and NH3 emissions, resulting in a net reduction in global warming potential (GWP). We attribute this result to biochar increasing the formation of compost aggregates, which likely acted as anaerobic reactors for methanogenesis and complete denitrification. Biochar may have further fueled CH4 production and N2O consumption by acting as an electron shuttle within aggregates. We recommend lower application rates, as we found that the 5% treatments in our study led to a similar reduction in GWP without increasing CH4 emissions.

Keywords: ammonia, biochar, climate change mitigation, composting, livestock, manure, methane, nitrous oxide

Aggregation is a vital characteristic of soil structure that affects its physical and biogeochemical properties. Aggregation results from the cohesion of primary minerals with organic or inorganic constituents. It depends on the dynamic balance between binding and fragmentation. There are two classes of aggregation. Mechanical aggregates are formed instantly by external forces and are often unstable. Hierarchical aggregates result from slow binding and are stable. Characterization of aggregation includes size, shape, stability, configuration, and their arrangement within soil. The nature of hierarchical aggregation is inferred from size separation of aggregates. Aggregate stability indicates their ability to persist under disruptive forces.

Keywords: Aeration, Aggregate, Cementation, Clod, Imaging, Organic matter, Rhizosheath, Rhizosphere, Root, Sequestration, Soil health, Tillage, X-racy CT

Finding feasible solutions for sustainable food production is challenging. Here we try to understand the balance between crop productivity and ecological stewardship using agroecological-based soil management strategies. We evaluated the potential of different organic materials such as dairy manure compost and different biochar manure co-composts, derived locally from agricultural wastes, to enhance soil ecosystem services. We assessed their potential impact on soil moisture and nutrient retention, greenhouse gas emissions, and crop productivity using data collected from an outdoor tomato column study. Results from the experiment showed potential of biochar co-composts to positively affect soil health by lessening loss of essential nutrients such as NO3−-N and NH4+-N, sustained tomato yield, and uphold crop water use efficiency. However, yield response to soil organic amendment is constrained by external factors such as irrigation strategies, with treatments under deficit irrigation greatly impacted. Overall, we observed a positive effect of adding biochar manure co-composts to soil, although best management practices are needed to optimize crop productivity and avoid unintentional consequences.

Organic amendments, such as compost and biochar, mitigate the environmental burdens associated with wasting organic resources and close nutrient loops by capturing, transforming, and resupplying nutrients to soils. While compost or biochar application to soil can enhance an agroecosystem’s capacity to store carbon and produce food, there have been few field studies investigating the agroecological impacts of amending soil with biochar co-compost, produced through the composting of nitrogen-rich organic material, such as manure, with carbon-rich biochar. Here, we examine the impact of biochar co-compost on soil properties and processes by conducting a field study in which we compare the environmental and agronomic impacts associated with the amendment of either dairy manure co-composted with biochar, dairy manure compost, or biochar to soils in a winter wheat cropping system. Organic amendments were applied at equivalent C rates (8 Mg C ha−1). We found that all three treatments significantly increased soil water holding capacity and total plant biomass relative to the no-amendment control. Soils amended with biochar or biochar co-compost resulted in significantly less greenhouse gas emissions than the compost or control soils. Biochar co-compost also resulted in a significant reduction in nutrient leaching relative to the application of biochar alone or compost alone. Our results suggest that biochar co-composting could optimize organic resource recycling for climate change mitigation and agricultural productivity while minimizing nutrient losses from agroecosystems.

Soil structure is a key attribute of soil quality and health that significantly impacts water infiltration. Structure can be significantly altered by natural or anthropogenic drivers including soil management practices and can in turn impact soil infiltration. Those changes in soil structure are often complex to quantify and can lead to conflicting impacts on water infiltration into soils. Here, we present a narrative systematic review (SR) of the impacts of soil structure on water infiltration. Based on inclusion and exclusion criteria, as well as defined methods for literature search and data extraction, our systematic review led to a total of 153 papers divided into two sets: experimental (131) and theoretical (22) papers. That implied a significant number of in-situ and field experiments that were conducted to assess the impacts of soil structure on water infiltration under the influence of different land uses and soil practices. Analysis of the metadata extracted from the collected papers revealed significant impacts of soil structure on water infiltration. Those effects were further attributed to land use and management, where we demonstrate the impact of three unique categories: soil amendments, crop management and tillage. Furthermore, significant correlations were established between infiltration rate and soil structural properties, with R2 values ranging from 0.51 to 0.80 and for saturated hydraulic conductivity and soil structural properties, with R2 values ranging from 0.21 to 0.78. Finally, our review highlighted the significant absence of and the need for theoretical frameworks studying the impacts of soil structure on water infiltration.

Keywords: Soil structure, Soil infiltration, Pedotransfer functions, Infiltration capacity

Subsurface carbon stocks are a prime target for efforts to increase soil carbon storage for climate change mitigation and improving soil health. However, subsurface carbon (C) dynamics are not well understood, especially in soils under long term intensive agricultural management. We compared subsurface C dynamics in tomato-corn rotations after 25 years of differing C and nutrient management in the California Central Valley: CONV (mineral fertilizer), CONV+WCC (mineral fertilizer + cover crops) and ORG (composted poultry manure + cover crops). Our results showed a  19 Mg/ha increase in SOC stocks down to 1 m under ORG systems, no significant SOC increases under CONV+WCC or CONV systems, and the accumulation of carboxyl rich C in the subsurface (60–100 cm) horizons of all systems. Systems also had greater amounts of aromatic carbon in the order ORG>CONV+WCC>CONV. We identified a potential interaction between cover crops and compost, theorizing that increased macropores from cover crop roots facilitate the transport of soluble C and nutrients into the subsurface, thereby increasing stocks. These results demonstrate the potential for subsurface carbon storage in tilled agricultural systems and highlight a potential pathway for increasing carbon transport and storage in subsurface soil layers.

To meet the requirements of California’s Sustainable Groundwater Management Act, there is a critical need for crop production strategies with less reliance on irrigation from surface and groundwater sources. One strategy for improving agricultural water use efficiency is reducing tillage and maintaining residues on the soil surface. We evaluated high residue no-till versus standard tillage in the San Joaquin Valley with and without cover crops on the yields of two crops, garbanzo and sorghum, for 4 years. The no-till treatment had no primary or secondary tillage. Sorghum yields were similar in no-till and standard tillage systems while no-till garbanzo yields matched or exceeded those of standard tillage, depending on the year. Cover crops had no effect on crop yields. Soil cover was highest under the no-till with cover crop system, averaging 97% versus 5% for the standard tillage without cover crop system. Our results suggest that garbanzos and sorghum can be grown under no-till practices in the San Joaquin Valley without loss of yield.

Most soil hydraulic information used in Earth System Models (ESMs) is derived from pedo-transfer functions that use easy-to-measure soil attributes to estimate hydraulic parameters. This parameterization relies heavily on soil texture, but overlooks the critical role of soil structure originated by soil biophysical activity. Soil structure omission is pervasive also in sampling and measurement methods used to train pedotransfer functions. Here we show how systematic inclusion of salient soil structural features of biophysical origin affect local and global hydrologic and climatic responses. Locally, including soil structure in models significantly alters infiltration-runoff partitioning and recharge in wet and vegetated regions. Globally, the coarse spatial resolution of ESMs and their inability to simulate intense and short rainfall events mask effects of soil structure on surface fluxes and climate. Results suggest that although soil structure affects local hydrologic response, its implications on global-scale climate remains elusive in current ESMs.

Increasing soil organic carbon (SOC) stocks in agricultural soils can contribute to stabilizing or even lowering atmospheric greenhouse gas (GHG) concentrations. Cover crop rotation has been shown to increase SOC and provide productivity benefits for agriculture. Here we used a split field design to evaluate the short-term effect of cover crop on SOC distribution and chemistry using a combination of bulk, isotopic, and spectroscopic analyses of size-and density-separated soil aggregates. Macroaggregates (>250 µm) incorporated additional plant material with cover crop as evidenced by more negative δ13C values (−25.4‰ with cover crop compared to −25.1‰ without cover crop) and increased phenolic (plant-like) resonance in carbon NEXAFS spectra. Iron EXAFS data showed that the Fe pool was composed of 17–21% Fe oxide with the remainder a mix of primary and secondary minerals. Comparison of oxalate and dithionite extractions suggests that cover crop may also increase Fe oxide crystallinity, especially in the dense (>2.4 g cm−3) soil fraction. Cover crop δ13C values were more negative across density fractions of bulk soil, indicating the presence of less processed organic carbon. Although no significant difference was observed in bulk SOC on a mass per mass basis between cover and no cover crop fields after one season, isotopic and spectroscopic data reveal enhanced carbon movement between aggregates in cover crop soil

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.