Conservation agriculture practices like no-tillage and cover cropping are promoted for rebuilding soil health and sequestering carbon, but their effectiveness in irrigated systems remains questioned. We hypothesized that improved soil structure under conservation practices could inadvertently stimulate microbial respiration upon wetting, potentially offsetting carbon gains. After 19 years of reduced tillage with cover crops (conservation tillage with cover crops [CTCC]) versus standard tillage with no cover crops (STNC), we found CTCC increased surface (0-5 cm) soil carbon by 50%, nitrogen by 83%, and air-filled porosity by up to 2.5-fold (580%) at high water potentials. However, CTCC respiration rates increased over 100% under wet conditions (-0.25 to -2 kPa) in 0- to 5-cm depth, likely due to the formation of macropores that become microbial hotspots upon rewetting, accelerating carbon cycling. Normalized respiration showed that each unit of soil carbon under CTCC was mineralized at nearly triple the rate observed under STNC when soils were wet, with this effect decreasing substantially with declining soil moisture and at 5-10 cm. Future work should focus on irrigation intensity and the possibility of amplifying this effect, constraining net carbon accrual despite the overall benefits of conservation practices. Our findings highlight that soil structure-moisture-microbe interactions represent a critical frontier for optimizing conservation agriculture for carbon sequestration, requiring a balanced approach to tillage, organic inputs, and irrigation management to minimize rapid carbon losses.

Abstract Cover crops are widely promoted for soil health benefits, yet their effectiveness in Mediterranean semiarid climates remains poorly understood. We conducted 3‐year on‐farm trials across California's Central Valley to evaluate cover crop impacts on soil carbon dynamics and related soil health indicators in representative annual cropping systems. Sites included summer legume cover crops in the Sacramento‐San Joaquin Delta (San Joaquin County), winter mixed species in Fresno County cotton (Gossypium barbadense L. or Gossypium hirsutum L.) production, and winter legume cover crops in Sutter County vegetable systems. Soil carbon responses varied dramatically by site and depth, challenging assumptions about universal benefits. At the Delta site, summer cover crops unexpectedly decreased surface carbon stocks by 60%–85% compared to fallow, likely due to increased soil disturbance and irrigation‐enhanced respiration. Conversely, the Mendota site showed significant carbon increases at 30‐ to 90‐cm depths, suggesting potential for deeper carbon storage when surface conditions are highly disturbed. The Sutter site maintained carbon equilibrium while avoiding problematic N 2 O emissions despite nitrogen inputs from legume cover crops. Beyond carbon, cover crops delivered important co‐benefits including reduced soil salinity, improved water infiltration, and enhanced soil structure. These findings reveal that cover crop success in Mediterranean climates depends on site‐specific factors and management practices, suggesting the need for locally adapted strategies rather than universal recommendations.

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 (CTCC) to standard tillage without cover crops (STNC), 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 CTCC exhibiting 136% greater stability than STNC, indicating substantial improvements in soil structural integrity. These structural enhancements corresponded with a reorganization of carbon protection mechanisms: CTCC disproportionately enriched the occluded light fraction (44.1% vs. 35.4% of total recovered carbon in STNC), 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 (11.5% vs. 7.4% saturation for CTCC and STNC, respectively), indicating substantial remaining potential for carbon sequestration even after reaching equilibrium. Physical property improvements under CTCC included 15% lower bulk density and 13% greater water retention at field capacity, though benefits were concentrated in the surface horizon. Our findings demonstrate that two decades of conservation agriculture fundamentally transforms soil functioning through aggregate-mediated physical protection, while creating substantial improvements in soil structural integrity and water retention capacity. This mechanism shift represents a new soil system equilibrium that maintains enhanced functionality and continued carbon sequestration potential in Mediterranean agricultural systems.

The potential of terminating cover crops with a roller-crimper is of increasing interest. A two-year (2020/21 and 2021/22) study was conducted in Fresno, CA, USA. Five cover crop treatments (rye (Secale cereale L.) alone, ultra-high diversity mix, multiplex cover crop mix, fava bean (Vicia faba L.) + phacelia (Phacelia tanacetifolia Benth.), and rye + field pea (Pisum sativum L.) + purple vetch (Vicia americana Muhl. Ex Willd.)) were planted in November, roller-crimped in April, and silage maize (Zea mays L.) was strip-till planted in the residue in May. Cover crop kill, soil cover by residue, weed cover, amount of organic residue, and silage maize yield were recorded. The roller-crimper resulted in 95 to 100% kill of the cover crops. Soil cover at maize canopy closure (mid-July) was approximately 90% in the rye plots while it was 30 to 70% in the other treatments. The fava bean + phacelia cover crop disintegrated the most rapidly. Weed cover was <5% in all the treatments until maize canopy closure. The cover crops added 6.7 to 14 MT ha−1 of residue. Maize silage yield was similar across the treatments. Therefore, in this study, cover crops were successfully terminated by the roller-crimper, allowing successful strip-till establishment and production of silage maize.

Policy and market incentives are rapidly expanding to promote soil organic carbon (SOC) sequestration in global croplands. Evidence suggests that long-term increases in SOC can influence both crop yield and nitrogen (N) fertilizer requirements, with the potential to help address two important sustainability challenges. However, increases in SOC may also trigger higher soil nitrous oxide (N2O) emissions, which would represent an important tradeoff for climate change mitigation. We tested the hypothesis that long-term increases in SOC are associated with higher crop yields and fertilizer N use efficiency (NUE), but at the cost of higher N2O emissions. Wheat was grown in two soils (SOClow and SOChigh) under three N fertilizer rates (0, 100, and 200 kg N ha-1) in a mesocosm experiment. Soils were obtained (0-25 cm) from a 22-yr field experiment on no-till and cover cropping in California. Results indicate that total biomass and grain yield were higher for SOClow than SOChigh at 100 kg N ha-1 but not the other N levels. Crop N uptake was also 28% greater for SOClow at 200 kg N ha-1, resulting in higher overall NUE. Soil N2O emissions increased for SOChigh by 25-112% compared to SOClow, likely due to long-term changes in labile C and N pools, microbial activity, and soil structure influencing porosity and gas diffusion. While there are well-documented crop and environmental benefits from enhancing SOC in agricultural soils, results from this study suggest that changes in soil N2O emissions should be considered to accurately determine net GHG emission reductions.

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.

California farmers who use reduced-disturbance tillage and winter cover cropping can boost production and improve soil health. However, some farmers are hesitant to try these conservation practices due to uncertainty about whether planting winter cover crops will deplete soil moisture in already drought-stricken regions. Our study addresses these concerns by looking at how long-term reduced-disturbance tillage and winter cover cropping, compared to fallowed soils with standard tillage, affected soil moisture. Although we found a statistical difference in total soil water content, the difference was only about 0.3 inches of water per foot of soil. On average, the soil water content of the top 0–96 inches was highest for the reduced-disturbance fields with winter cover crops. This was especially evident during our driest field season, from November 1, 2017, to March 15, 2018, when cumulative rainfall was only 1.9 inches. Our findings show that winter cover cropping and reduced-disturbance tillage can improve soil without depleting soil water levels in row crops.

Soil organic carbon (SOC) is closely tied to soil health. However, additional biological indicators may also provide insight about C dynamics and microbial activity. We used SOC and the other C indicators (potential C mineralization, permanganate oxidizable C, water extractable organic C, and beta-glucosidase enzyme activity) from the North American Project to Evaluate Soil Health Measurements to examine the continental-scale drivers of these indicators, the relationships among indicators, and the effects of soil health practices on indicator values. All indicators had greater values at cooler temperatures, and most were greater with increased precipitation and clay content. The indicators were strongly correlated with each other at the site-level, with the strongest relationship between SOC and permanganate oxidizable C. The indicator values responded positively to decreased tillage, inclusion of cover crops, application of organic nutrients, and retention of crop residue, but not the number of harvested crops in a rotation. The effect of decreased tillage on the C indicators was generally greater at sites with higher precipitation. The magnitude and direction of the response to soil health practices was consistent across indicators within a site but measuring at least two indicators would provide additional confi-dence of the effects of management, especially for tillage. All C indicators responded to management, an essential criterion for evaluating soil health. Balancing the cost, sensitivity, interpretability, and availability at commercial labs, a 24-hr potential C mineralization assay could deliver the most benefit to measure in conjunction with SOC.

Cover crops are widely advocated for increasing soil organic carbon (SOC) levels, thereby benefiting soil health improvement and climate change mitigation. Few regional-scale studies have robustly explored SOC stocks under cover cropping, due to limited long-term experiments. We used the unique experimental data from the North American Project to Evaluate Soil Health Measurements conducted in 2019 to address this issue. This study included 19 agricultural research sites with 36 pairs of cover cropping established between 1896 and 2014. Explanatory variables related to site-specific environmental conditions and management practices were collected to identify and prioritize contributing factors that affect SOC stocks with cover crops, by coupling the Boruta algorithm and structural equation modeling. Overall, cover crops significantly (P < 0.05) improved several indicators of soil health, including greater SOC (concentration: +8%; stock: +7%), total nitrogen (+8%), waterstable aggregates (+15%), and potential carbon mineralization (+34%), on average, compared to no cover crop control. Likewise, on average, cover crops sequestered SOC 3.55 Mg C ha-1 (0-15 cm depth), with a sequestration rate of 0.24 Mg C ha-1 yr-1. In addition, we found climate (Hargreaves climatic moisture deficit) was important in explaining the variation of SOC stocks with cover crops, followed by soil properties (e.g., soil clay content). In terms of management practices, cover crop type had a significant positive (0.36) effect on SOC stocks, with non-legumes showing a greater impact, compared to legumes and mixtures. Crop rotational diversity also had a positive (0.28) effect on SOC accumulation. Our findings suggested that integrating non-legume cover crops into diverse crop rotation is likely to be a promising strategy to maximize SOC stocks with cover crops across North America.

Farmers, scientists, and other soil health stakeholders require interpretable indicators of soil hydraulic function. Determining which indicators to use has been difficult because of measurement disconformity, spatial and temporal variability, recently established treatments, and the effect of site characteristics on management practice differences. The North American Project to Evaluate Soil Health Measurements includes 124 sites uniformly sampled across a range of soil health management practices in North America in 2019. We compare and recommend indicators of hydraulic function that best characterize soil health. We assessed the relationship of each indicator to a suite of soil inherent properties and climate variables, the response of each indicator to soil health management practices, the effect that soil inherent properties (clay content, sand content, and pH) and climatic variables (10-yr mean annual precipitation and temperature) had on response to management practices, and the relationship among the responses of the indicators to soil health management practices. Field capacity measured on intact cores (theta(FC_INTACT)) was the best measure of soil hydraulic function, because it responded to management, represents a direct measure of soil hydraulic function, is proximal to stakeholder values, and its response to management was not significantly influenced by inherent and climatic variables. Other suitable indicators are bulk density, soil organic carbon (SOC), and aggregate stability, which are not direct measures of soil hydraulic function but do respond to management and may be practical in situations in which measuring theta(FC_INTACT) is not. This study informs selection of soil health indicators to measure soil hydraulic function.

Currently accepted pedotransfer functions show negligible effect of management-induced changes to soil organic carbon (SOC) on plant available water holding capacity (theta(AWHC)), while some studies show the ability to substantially increase theta(AWHC) through management. The Soil Health Institute's North America Project to Evaluate Soil Health Measurements measured water content at field capacity using intact soil cores across 124 long-term research sites that contained increases in SOC as a result of management treatments such as reduced tillage and cover cropping. Pedotransfer functions were created for volumetric water content at field capacity (theta(FC)) and permanent wilting point (theta(PWP)). New pedotransfer functions had predictions of theta(AWHC) that were similarly accurate compared with Saxton and Rawls when tested on samples from the National Soil Characterization database. Further, the new pedotransfer functions showed substantial effects of soil calcareousness and SOC on theta(AWHC). For an increase in SOC of 10 g kg(-1) (1%) in noncalcareous soils, an average increase in theta(AWHC) of 3.0 mm 100 mm(-1) soil (0.03 m(3) m(-3)) on average across all soil texture classes was found. This SOC related increase in theta(AWHC) is about double previous estimates. Calcareous soils had an increase in theta(AWHC) of 1.2 mm 100 mm(-1) soil associated with a 10 g kg(-1) increase in SOC, across all soil texture classes. New equations can aid in quantifying benefits of soil management practices that increase SOC and can be used to model the effect of changes in management on drought resilience.

As fresh water supplies become more unreliable, variable and expensive, the water-related implications of sustainable agriculture practices such as cover cropping are drawing increasing attention from California's agricultural communities. However, the adoption of winter cover cropping remains limited among specialty crop growers who face uncertainty regarding the water use of this practice. To investigate how winter cover crops affect soil water and evapotranspiration on farm fields, we studied three systems that span climatic and farming conditions in California's Central Valley: processing tomato fields with cover crop, almond orchards with cover crop, and almond orchards with native vegetation. From 2016 to 2019, we collected soil moisture data (3 years of neutron hydroprobe and gravimetric tests at 10 field sites) and evapotranspiration measurements (2 years at two of 10 sites) in winter cover cropped and control (clean-cultivated, bare ground) plots during winter months. Generally, there were not significant differences in soil moisture between cover cropped and control fields throughout or at the end of the winter seasons, while evapo-transpirative losses due to winter cover crops were negligible relative to clean-cultivated soil. Our results suggest that winter cover crops in the Central Valley may break even in terms of actual consumptive water use. California growers of high-value specialty crops can likely adopt winter cover cropping without altering their irrigation plans and management practices.

We studied the long-term impact of contrasting tillage and cover cropping systems on soil structure and hydraulic properties. Complete water retention and conductivity curves for the top (0–5 cm) and subsurface (20–25 cm) soils were characterized and contrasted. Dynamic water storage and retention were evaluated using numerical simulations in HYDRUS-2D software. Compared with standard-till (ST) and no-cover-crop (NO) systems, soils under no-till (NT) and cover cropping (CC) systems showed improved soil structure in terms of pore size distribution (PSD). Changes in hydraulic conductivity (K) under these systems led to an increased infiltration rate and water retention. However, NT and CC plots had lower water content at field capacity (33 kPa suction) and lower plant-available water (PAW) compared with ST and NO plots. Numerical simulations, however, showed that NT and CC plots have higher water storage (albeit marginal in magnitude) and water availability following irrigation. Because the numerical simulations considered retention and conductivity functions simultaneously and dynamically through time, they allow the capture of hydraulic states that are arguably more relevant to crops. The study concludes that the long-term practices of NT and CC systems were beneficial in terms of changes to the PSD. NT and CC systems also marginally improved soil water conductivity and storage at the plot scale.

Potential carbon mineralization (Cmin) is a commonly used indicator of soil health, with greater Cmin values interpreted as healthier soil. While Cmin values are typically greater in agricultural soils managed with minimal physical disturbance, the mechanisms driving the increases remain poorly understood. This study assessed bacterial and archaeal community structure and potential microbial drivers of Cmin in soils maintained under various degrees of physical disturbance. Potential carbon mineralization, 16S rRNA sequences, and soil characterization data were collected as part of the North American Project to Evaluate Soil Health Measurements (NAPESHM). Results showed that type of cropping system, intensity of physical disturbance, and soil pH influenced microbial sensitivity to physical disturbance. Furthermore, 28% of amplicon sequence variants (ASVs), which were important in modeling Cmin, were enriched under soils managed with minimal physical disturbance. Sequences identified as enriched under minimal disturbance and important for modeling Cmin, were linked to organisms which could produce extracellular polymeric substances and contained metabolic strategies suited for tolerating environmental stressors. Understanding how physical disturbance shapes microbial communities across climates and inherent soil properties and drives changes in Cmin provides the context necessary to evaluate management impacts on standardized measures of soil microbial activity.

The fungal genus Fusarium contains plant pathogens, mutualists, and commensalists. Because nonpathogenic Fusarium strains can contribute to disease suppression in soil by competition or induced plant resistance, identifying factors that influence the abundance of nonpathogenic strains could lead to strategies that enhance plant-beneficial interactions and deter pathogen invasion. We developed a Fusarium-specific high-throughput translation elongation factor 1α (EF-1α) amplicon-sequencing method with subspecies resolution. Newly designed primers enabled reads to be joined for improved quality metrics after Illumina MiSeq sequencing. By including the ‘oligotyping’ program in our bioinformatic workflow, we reconstructed Fusarium EF-1α haplotypes with 100% accuracy. We conducted simulated crop rotation experiments in soil infested with the strawberry pathogen Fusarium oxysporum f. sp. fragariae ( Fof) and the following treatments: strawberry, blackberry, raspberry, lettuce, broccoli, and fallow. We profiled root Fusarium communities with EF-1α amplicons and observed that nonpathogenic strains of F. oxysporum did not colonize crops uniformly; some strains exhibited asymptomatic host preferences. In susceptible strawberry roots, >90% of sequences corresponded to Fof. Bulk soil communities of Fusarium were remarkably stable and had minimal treatment-dependent effects after 1 year. Similarly, in a long-term agricultural research experiment, 18 years of conservation tillage and cover cropping did not lead to bulk soil Fusarium communities that were significantly different than controls. Although the roots of rotation crops can augment the abundance of nonpathogenic F. oxysporum strains, their abundance in bulk soil is unlikely to be altered after a single year. Climate and soil physicochemical properties may have a greater effect on Fusarium community structure.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Aggregate stability is a commonly used indicator of soil health because improvements in aggregate stability are related to reduced erodibility and improved soil-water dynamics. During the past 80 to 90 years, numerous methods have been developed to assess aggregate stability. Limited comparisons among the methods have resulted in varied magnitudes of response to soil health management practices and varied influences of inherent soil properties and climate. It is not clear whether selection of a specific method creates any advantage to the investigator. This study assessed four commonly used methods of measuring aggregate stability using data collected as part of the North American Project to Evaluate Soil Health Measurements. The methods included water stable aggregates using the Cornell Rainfall Simulator (WSACASH), wet sieved water stable aggregates (WSAARS), slaking captured and adapted from SLAKES smart-phone image recognition software (STAB10), and the mean weight diameter of water stable aggregates (MWD). Influence of climate and inherent soil prop-erties at the continental scale were analyzed in addition to method responses to rotation diversity, cash crop count, residue management, organic nutrient amendments, cover crops, and tillage. The four methods were moderately correlated with each other. All methods were sensitive to differences in climate and inherent soil properties between sites, although to different degrees. None measured significant effects from rotation diversity or crop count, but all methods detected significant increases in aggregate stability resulting from reduced tillage. Significant increases or positive trends were observed for all methods in relation to cover cropping, increased residue retention, and organic amendments, except for STAB10, which expressed a slightly negative response to organic amendments. Considering these results, no single method was clearly superior and all four are viable options for measuring aggregate stability. Therefore, secondary considerations (e.g., cost, method availability, increased sensitivity to a specific management practice, or minimal within-treatment variability) driven by the needs of the investigator, should determine the most suitable method.

Cover crops and reduced tillage are two elements of conservation agriculture with potential to support larger and more diverse soil biological communities. Soil macrofauna can be indicators of soil quality and can regulate multiple soil functions, but their response to cover crop adoption in temperate regions is not well studied. We evaluated soil macrofauna communities and related soil quality metrics in response to a 16-year winter cover crop and tillage trial located in the San Joaquin Valley of California, USA. The most abundant taxa were Coleoptera (beetles) and Lumbricidae (earthworms), with average densities ranging between 5 and 318 beetles m−2 and 65–480 earthworms m−2 depending on sample date and treatments. Overall macrofauna abundance increased by 93% with the addition of cover crops in rotation, and 50% with the elimination of tillage. Taxonomic richness increased by 48% with cover crops in treatments managed without tillage, though there was no effect of cover crops under standard tillage. Macrofauna abundance was positively related to total soil carbon, water infiltration, and soil aggregate stability. Macrofauna community composition was best explained by soil carbon, water stable aggregate fraction, and cover crop usage. Agricultural management practices that foster soil biological communities may support biodiversity and improve environmental outcomes critical for sustainable food production.

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.

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops.Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.