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California agriculture will undergo significant transformations over the next few decades in response to climate extremes, environmental regulation and policy encouraging environmental justice, and economic pressures that have long driven agricultural changes. With several local climates suited to a variety of crops, periodically abundant nearby precipitation, and public investments that facilitated abundant low-priced irrigation water, California hosts one of the most diverse and productive agroecosystems in the world. California farms supply nearly half of the high-nutrient fruit, tree nut, and vegetable production in the United States. Climate change impacts on productivity and profitability of California agriculture are increasing and forebode problems for standard agricultural practices, especially water use norms. We highlight many challenges California agriculture confronts under climate change through the direct and indirect impacts on the biophysical conditions and ecosystem services that drive adaptations in farm practices and water accessibility and availability. In the face of clear conflicts among competing interests, we consider ongoing and potential sustainable and equitable solutions, with particular attention to how technology and policy can facilitate progress.

BACKGROUND: Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation. RESULTS: Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of - 25 to - 75 kPa at a soil depth of 30 cm which reduced biomass by 30-55% and grain yield by 1-92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks. CONCLUSIONS: Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.

Introduction: Integrated crop-livestock systems (ICLS) use animals to graze crop residues or cover crops before planting fresh produce and provide ecosystem services to support organic vegetable production. However, there is a risk of foodborne pathogen transfer to fresh produce because grazing may introduce enteric foodborne pathogens into the soil via animal feces, which may subsequently be transferred to the produce. Methods: To examine the effect of cover crop use and the risk of cover crop grazing on the contamination of soil and produce by foodborne pathogens in ICLS, a three-year (2019–2021) experimental study was conducted in organically managed plots, which were assigned three different treatments (fallow without cover crop or grazing, cover crop without grazing, or cover crop with grazing by sheep) in a maize/tomato rotation. During the three years of the experiment, a total of 184 pre- and post-graze fecal samples and 96 samples of tomatoes were collected to test for foodborne pathogens (Escherichia coli O157, non-O157 Shiga toxin-producing Escherichia coli (STEC), and Listeria (L.) monocytogenes). Soil samples were collected monthly until 126–171 days after grazing (824 in total) to examine the presence of foodborne pathogens, and generic E. coli (MPN/g) was quantified to compare its persistence among the three treatments. Results and Discussion: We did not detect any foodborne pathogens from harvested tomatoes in 2020 and 2021. One non-O157 STEC positive soil sample (0.1%, 1/824) was detected in the fallow treatment, and one L. monocytogenes-positive (1.1%, 1/92) was detected from the post-graze fecal samples. When assessing proportions of generic E. coli positive and counts of generic E. coli in the soil samples using mixed effect zero-inflated negative binomial models, soil samples collected in the graze cover crop treatment plot showed significant increases in the counts of generic E. coli until 61–82 days post grazing, but no difference was observed after 96–123 days, compared to the baseline of the fallow treatment. Findings from generic E. coli counts support the use of the United States Department of Agriculture (USDA) National Organic Program (NOP) 90- or 120-day interval rule between applying raw manure and harvesting in organic farming into ICLS. Additionally, we confirmed that commercial organic compost application before cover crop seeding in the winter had no significant effect on the proportions and counts of generic E. coli in the soil of the following growing seasons. This longitudinal field trial confirmed that the effect of sheep grazing on foodborne pathogen contamination in ICLS is minimal but further studies comparing the genetic associations between fecal and soil samples would be necessary to distinguish the source of foodborne pathogen contamination.

The strategic use of ruminant grazing in perennial cropland is steadily increasing throughout Mediterranean perennial agroecosystems. Integrated sheep-vineyard (ISV) management, where small ruminant livestock graze on understory vegetation, is viewed by some practitioners as a feasible transition opportunity to facilitate less petrochemically intensive vineyard understory management. However, our knowledge of soil carbon dynamics associated with grazing in perennial integrated crop-livestock (ICL) agroecosystems is notably limited, especially within Mediterranean climate contexts. Here, we use a series of on-farm paired surveys to assess soil ecosystem habitat and resource conditions related to SOC flux and storage in vineyards utilizing sheep-integration (ISV) and conventional understory management techniques (CONV). Our results show that long-term grazing increased the quantity of active, labile, and soluble carbon (C) within ISV soils, with much higher quantities of microbial biomass carbon (MBC). Vineyard soils with sheep grazing also showed increases in phospholipid fatty acid (PLFA) biomarkers, particularly amongst core functional groups related to decomposition. Soil microbial communities under ISV had higher C mineralization rates as well as higher carbon use-efficiency, as indicated by less CO2-C respired relative to the size of the MBC pool. Whereas inorganic soil nitrogen (N) and phosphorous (P) were also higher under ISV, microbial communities showed distinct metabolic investment strategies related to nutrient acquisition, with lower P-cycling enzyme activity and higher N-cycling enzyme activity. Additionally, ISV resulted in an increase in subsoil SOC storage, including higher quantities of physicochemical stabilization in the mineral-associated organic carbon (MAOC) pool of the deepest measured subsoil layer (30–45 cm). We observed no differences in soil structure indicators between treatments nor differences in the carbon fractions associated with four distinct aggregate size categories. We propose a framework to explain observed shifts in SOC dynamics of perennial ICL systems that include i) deposition of C and nutrient inputs with higher lability and solubility; ii) ruminant-induced decoupling of C from N and P, resulting in increased nutrient bioavailability; and iii) altered soil microbial metabolic strategies with more efficient biomass accumulation. These findings show strong potential of strategically applied ICL grazing to enhance soil functioning and increase SOC storage in Mediterranean perennial agroecosystems.

Domestication and breeding have affected interactions between plants and their microbiomes in ways that are only beginning to be understood but may have important implications for recruitment of rhizosphere microorganisms, particularly under stress conditions. We investigated the responses of a modern maize (Zea mays subsp. mays) cultivar and its wild relative, teosinte (Z. mays subsp. parviglumis), to different phosphate availabilities. We appraised responses of the plant-microbial holobiont to phosphate stresses by profiling root exudate metabolomes, and microbial communities in the root endosphere and rhizosphere. We also performed plate assays to quantify phosphate-solubilizing microorganisms from the rhizosphere. Although root exudate metabolite profiles were distinct between the teosinte and modern maize under high phosphate, both plants shifted exudate compositions in response to phosphate stress toward a common metabolite profile. Root and rhizosphere microbial communities also responded significantly to both plant type and the phosphate availability. A subset of bacterial and fungal taxa were differentially abundant under the different phosphate conditions, with each of the three conditions favoring different taxa. Both teosinte and maize rhizospheres harbored phosphate-solubilizing microorganisms under all growth conditions. These results suggest that the root exudation response to phosphate stress was conserved through the domestication of maize from teosinte, shifting exudation levels of specific metabolites. Although microbial communities also shifted, plate-based assays did not detect selective recruitment of phosphate solubilizers in response to phosphate availability.

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.

Climate models project greater weather variability over the coming decades. High yielding systems that can maintain stable crop yields under variable environmental scenarios are critical to enhance food security. However, the effect of adding a trophic level (i.e. herbivores) on the long-term stability of agricultural systems is not well understood. We used a 16-year dataset from an integrated soybean-beef cattle experiment to measure the impacts of grazing on the stability of key crop, pasture, animal and whole-system outcomes. Treatments consisted of four grazing intensities (10, 20, 30 and 40 cm sward height) on mixed black oat (Avena strigosa) and Italian ryegrass (Lolium multiflorum) pastures and an ungrazed control. Stability of both human-digestible protein production and profitability increased at moderate to light grazing intensities, while over-intensification or absence of grazing decreased system stability. Grazing did not affect subsequent soybean yields but reduced the chance of crop failure and financial loss in unfavorable years. At both lighter and heavier grazing intensities, tradeoffs occurred between the stability of herbage production and animal live weight gains. We show that ecological intensification of specialized soybean systems using livestock integration can increase system stability and profitability, but the probability of win-win outcomes depends on management.

Plant-microbe interactions in the rhizosphere influence rates of organic matter mineralization and nutrient cycling that are critical to sustainable agricultural productivity. Agricultural intensification, particularly the introduction of synthetic fertilizer in the USA, altered the abundance and dominant forms of nitrogen (N), a critical plant nutrient, potentially imposing selection pressure on plant traits and plant-microbe interactions regulating N cycling and acquisition. We hypothesized that maize adaptation to synthetic N fertilization altered root functional traits and rhizosphere microbial nutrient cycling, reducing maize ability to acquire N from organic sources. Six maize genotypes released pre-fertilizer (1936, 1939, 1942) or post-fertilizer (1984, 1994, 2015) were grown in rhizoboxes containing patches of 15N-labelled clover/vetch residue. Multivariate approaches did not identify architectural traits that strongly and consistently predicted rhizosphere processes, though metrics of root morphological plasticity were linked to carbon- and N-cycling enzyme activities. Root traits, potential activities of extracellular enzymes (BG, LAP, NAG, urease), abundances of N-cycling genes (amoA, narG, nirK, nirS, nosZ) and uptake of organic N did not differ between eras of release despite substantial variation among genotypes and replicates. Thus, agricultural intensification does not appear to have impaired N cycling and acquisition from organic sources by modern maize and its rhizobiome. Improved mechanistic understanding of rhizosphere processes and their response to selective pressures will contribute greatly to rhizosphere engineering for sustainable agriculture.

Domestication and agricultural intensification dramatically altered maize and its cultivation environment. Changes in maize genetics (G) and environmental (E) conditions increased productivity under high-synthetic-input conditions. However, novel selective pressures on the rhizobiome may have incurred undesirable tradeoffs in organic agroecosystems, where plants obtain nutrients via microbially mediated processes including mineralization of organic matter. Using twelve maize genotypes representing an evolutionary transect (teosintes, landraces, inbred parents of modern elite germplasm, and modern hybrids) and two agricultural soils with contrasting long-term management, we integrated analyses of rhizobiome community structure, potential microbe-microbe interactions, and N-cycling functional genes to better understand the impacts of maize evolution and soil management legacy on rhizobiome recruitment. We show complex shifts in rhizobiome communities during directed evolution of maize (defined as the transition from teosinte to modern hybrids), with a larger effect of domestication (teosinte to landraces) than modern breeding (inbreds to hybrids) on rhizobiome structure and greater impacts of modern breeding on potential microbe-microbe interactions. Rhizobiome structure was significantly correlated with plant nutrient composition. Furthermore, plant biomass and nutrient content were affected by G x E interactions in which teosinte and landrace genotypes had better relative performance in the organic legacy soil than inbred and modern genotypes. The abundance of six N-cycling genes of relevance for plant nutrition and N loss pathways did not significantly differ between teosinte and modern rhizospheres in either soil management legacy. These results provide insight into the potential for improving maize adaptation to organic systems and contribute to interdisciplinary efforts toward developing resource-efficient, biologically based agroecosystems.

Reduced insect pest populations found on long-term organic farms have mostly been attributed to increased biodiversity and abundance of beneficial predators, as well as to changes in plant nutrient content. However, the role of plant resistance has largely been ignored. Here, we determine whether host plant resistance mediates decreased pest populations in organic systems and identify potential underpinning mechanisms. We demonstrate that fewer numbers of leafhoppers (Circulifer tenellus) settle on tomatoes (Solanum lycopersicum) grown using organic management as compared to conventional. We present multiple lines of evidence, including rhizosphere soil microbiome sequencing, chemical analysis and transgenic approaches, to demonstrate that changes in leafhopper settling between organically and conventionally grown tomatoes are dependent on salicylic acid accumulation in plants and mediated by rhizosphere microbial communities. These results suggest that organically managed soils and microbial communities may play an unappreciated role in reducing plant attractiveness to pests by increasing plant resistance.

There is an urgent need to develop climate smart agroecosystems capable of mitigating climate change and adapting to its effects. In California, high commodity prices and increased frequency of drought have encouraged orchard turnover, providing an opportunity to recycle tree biomass in situ prior to replanting an orchard. Whole orchard recycling (WOR) has potential as a carbon (C) negative cultural practice to build soil C storage, soil health, and orchard productivity. We tested the potential of this practice for long term C sequestration and hypothesized that associated co-benefits to soil health will enhance sustainability and resiliency of almond orchards to water-deficit conditions. We measured soil health metrics and productivity of an almond orchard following grinding and incorporation of woody biomass vs. burning of old orchard biomass 9 years after implementation. We also conducted a deficit irrigation trial with control and deficit irrigation (-20%) treatments to quantify shifts in tree water status and resilience. Biomass recycling led to higher yields and substantial improvement in soil functioning, including nutrient content, aggregation, porosity, and water retention. This practice also sequestered significantly higher levels of C in the topsoil (+5 t ha-1) compared to burning. We measured a 20% increase in irrigation water use efficiency and improved soil and tree water status under stress, suggesting that in situ biomass recycling can be considered as a climate smart practice in California irrigated almond systems.

Production systems that feature temporal and spatial integration of crop and livestock enterprises, also known as integrated crop-livestock systems (ICLS), have the potential to intensify production on cultivated lands and foster resilience to the effects of climate change without proportional increases in environmental impacts. Yet, crop production outcomes following livestock grazing across environments and management scenarios remain uncertain and a potential barrier to adoption, as producers worry about the effects of livestock activity on the agronomic quality of their land. To determine likely production outcomes across ICLS and to identify the most important moderating variables governing those outcomes, we performed a meta-analysis of 66 studies comparing crop yields in ICLS to yields in unintegrated controls across 3 continents, 12 crops, and 4 livestock species. We found that annual cash crops in ICLS averaged similar yields (-7% to +2%) to crops in comparable unintegrated systems. The exception was dual-purpose crops (crops managed simultaneously for grazing and grain production), which yielded 20% less on average than single-purpose crops in the studies examined. When dual-purpose cropping systems were excluded from the analysis, crops in ICLS yielded more than in unintegrated systems in loamy soils and achieved equal yields in most other settings, suggesting that areas of intermediate soil texture may represent a "sweet-spot" for ICLS implementation. This meta-analysis represents the first quantitative synthesis of the crop production outcomes of ICLS and demonstrates the need for further investigation into the conditions and management scenarios under which ICLS can be successfully implemented.

Root exploitation of soil heterogeneity and microbially mediated rhizosphere nutrient transformations play critical roles in plant resource uptake. However, how these processes change under water-saving irrigation technologies remains unclear, especially for organic systems where crops rely on soil ecological processes for plant nutrition and productivity. We conducted a field experiment and examined how water-saving subsurface drip irrigation (SDI) and concentrated organic fertilizer application altered root traits and rhizosphere processes compared to traditional furrow irrigation (FI) in an organic tomato system. We measured root distribution and morphology, the activities of C-, N-, and P-cycling enzymes in the rhizosphere, the abundance of rhizosphere microbial N-cycling genes, and root mycorrhizal colonization rate under two irrigation strategies. Tomato plants produced shorter and finer root systems with higher densities of roots around the drip line, lower activities of soil C-degrading enzymes, and shifts in the abundance of microbial N-cycling genes and mycorrhizal colonization rates in the rhizosphere of SDI plants compared to FI. SDI led to 66.4% higher irrigation water productivity than FI, but it also led to excessive vegetative growth and 28.3% lower tomato yield than FI. Our results suggest that roots and root-microbe interactions have a high potential for coordinated adaptation to water and nutrient spatial patterns to facilitate resource uptake under SDI. However, mismatches between plant needs and resource availability remain, highlighting the importance of assessing temporal dynamics of root-soil-microbe interactions to maximize their resource-mining potential for innovative irrigation systems.

BackgroundRhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.ResultsHost selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.ConclusionsPlant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

Increasing soil organic carbon (SOC) via organic inputs is a key strategy for increasing long-term soil C storage and improving the climate change mitigation and adaptation potential of agricultural systems. A long-term trial in California's Mediterranean climate revealed impacts of management on SOC in maize-tomato and wheat-fallow cropping systems. SOC was measured at the initiation of the experiment and at year 19, at five depth increments down to 2 m, taking into account changes in bulk density. Across the entire 2 m profile, SOC in the wheat-fallow systems did not change with the addition of N fertilizer, winter cover crops (WCC), or irrigation alone and decreased by 5.6% with no inputs. There was some evidence of soil C gains at depth with both N fertilizer and irrigation, though high variation precluded detection of significant changes. In maize-tomato rotations, SOC increased by 12.6% (21.8 Mg C/ha) with both WCC and composted poultry manure inputs, across the 2 m profile. The addition of WCC to a conventionally managed system increased SOC stocks by 3.5% (1.44 Mg C/ha) in the 0-30 cm layer, but decreased by 10.8% (14.86 Mg C/ha) in the 30-200 cm layer, resulting in overall losses of 13.4 Mg C/ha. If we only measured soil C in the top 30 cm, we would have assumed an increase in total soil C increased with WCC alone, whereas in reality significant losses in SOC occurred when considering the 2 m soil profile. Ignoring the subsoil carbon dynamics in deeper layers of soil fails to recognize potential opportunities for soil C sequestration, and may lead to false conclusions about the impact of management practices on C sequestration.

Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines' rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

Adaptive management practices that maximize yields while improving yield resilience are required in the face of resource variability and climate change. Ecological intensification such as organic farming and cover cropping are lauded in some studies for fostering yield resilience, but subject to criticism in others for their low productivity. We implemented a quantitative framework to assess yield resilience, emphasizing four aspects of yield dynamics: yield, yield stability, yield resistance (i.e., the ability of systems to avoid crop failure under stressful growing conditions), and maximum yield potential. We compared the resilience of maize-tomato rotation systems after 24 years of irrigated organic, cover cropped, and conventional management in a Mediterranean climate, and identified crop-specific resilience responses of tomato and maize to three management systems. Organic management maintained tomato yields comparable to those under conventional management, while increasing yield stability and resistance. However, organic and cover cropped system resulted in 36.1% and 35.8% lower maize yields and reduced yield stability and resistance than the conventional system. Our analyses suggest that investments in ecological intensification approaches could potentially contribute to long-term yield resilience, however, these approaches need to be tailored for individual crops and systems to maximize their benefits, rather than employing one-size-fits-all approaches.

Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO3-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.

Amplicon sequencing of 16S, ITS, and 18S regions of microbial genomes is a commonly used first step toward understanding microbial communities of interest for human health, agriculture, and the environment. Correlation network analysis is an emerging tool for investigating the interactions within these microbial communities. However, when data from different habitats (e.g., sampling sites, host genotype, etc.) are combined into one analysis, habitat filtering (co-occurrence of microbes due to habitat sampled rather than biological interactions) can induce apparent correlations, resulting in a network dominated by habitat effects and masking correlations of biological interest. We developed an algorithm to correct for habitat filtering effects in microbial correlation network analysis in order to reveal the true underlying microbial correlations. This algorithm was tested on simulated data that was constructed to exhibit habitat filtering. Our algorithm significantly improved correlation detection accuracy for these data compared to Spearman and Pearson correlations. We then used our algorithm to analyze a two real data sets of 16S variable region amplicon sequences that were expected to exhibit habitat filtering. Our algorithm was found to effectively reduce habitat effects, enabling the construction of consensus correlation networks from data sets combining multiple related sample habitats.

Agroecosystems are on both the receiving and contributing ends of increasingly demanding climatic and environmental conditions. Maintaining productive systems under resource scarcity and multiplicative stresses requires precise monitoring and systems-scale planning. By incorporating ecological resilience into agroecosystems research we can gain valuable insight into agroecosystem identity, change, responsivity, and performance under stress, but only if we move away from resilience as a mere touchstone concept. Using the productivity, stability, resistance, and recovery of system processes as a basic framework for resilience monitoring, we propose quantitative research approaches to tackle the continuing lack of biophysical, field-scale indicators needed to lend insight into dynamic resilience variables and mechanisms. We emphasize the importance of considering productive functions, sources of system regulation and disturbance, and cross-scale interactions when applying resilience theory to agroecosystems. Agroecosystem resilience research requires understanding of multiple scales and speeds of influence both above and below the focal scale. When these considerations are addressed, resilience theory can add tangible value to agroecosystems research, both for the purposes of monitoring current systems and of planning future systems that can reconcile productivity and sustainability goals.

Hulls and shells are an abundant by-product from almond production with potential as an organic matter amendment (OMA). A combination of incubation study and field research was conducted in 2019–2021 to evaluate the impacts of three practices in combination on orchard soils' C and N cycling, including a 210-day period of laboratory incubation with hulls and shells, and field sampling of orchard soils with and without historic applications of green waste compost as an OMA; with hulls and shells and with and without off-ground harvest where orchard soils remain undisturbed year round. Hulls and shells increased microbial biomass carbon in the field study by 248 μg g−1 dry soil after one year (p < 0.001) and during incubation, and increased cumulative respiration in soils with and without historic OMA (p < 0.001). Historic OMA resulted in double the total soil organic carbon (SOC) and total nitrogen (TN) compared to soil without resulting in significantly higher respiration and N mineralization when amended with hulls and shells. The decomposition of hull and shell biomass following surface application progressed at similar rates in the laboratory and field (1.7 g kg−1 d−1 during incubation (R2 = 0.84) and 1.3 g kg−1 d−1 in the field trial (R2 = 0.91). Our results highlight the suitability of hulls and shells as a by-product source of OMA for improving soil health in orchards with historic OMA and transitioning to organic matter management. [ABSTRACT FROM AUTHOR]

The effect of domestication and modern breeding on aboveground traits in maize (Zea mays) has been well-characterized, but the impact on root systems and the rhizosphere remain unclear. The transition from wild ecosystems to modern agriculture has focused on selecting traits that yielded the largest aboveground production with increasing levels of crop management and nutrient inputs. Root morphology, anatomy, and ecophysiological processes may have been affected by the substantial environmental and genetic shifts associated with this transition. As a result, root and rhizosphere traits that allow more efficient foraging and uptake in lower synthetic input environments might have been lost. The development of modern maize has led to a shift in microbiome community composition, but questions remain as to the dynamics and drivers of this change during maize evolution and its implications for resource acquisition and agroecosystem functioning under different management practices. Better understanding of how domestication and breeding affected root and rhizosphere microbial traits could inform breeding strategies, facilitate the sourcing of favorable alleles, and open new frontiers to improve resource use efficiency through greater integration of root development and ecophysiology with agroecosystem functioning.

Cropping sequence diversification provides a systems approach to reduce yield variations and improve resilience to multiple environmental stresses. Yield advantages of more diverse crop rotations and their synergistic effects with reduced tillage are well documented, but few studies have quantified the impact of these management practices on yields and their stability when soil moisture is limiting or in excess. Using yield and weather data obtained from a 31-year long term rotation and tillage trial in Ontario, we tested whether crop rotation diversity is associated with greater yield stability when abnormal weather conditions occur. We used parametric and non-parametric approaches to quantify the impact of rotation diversity (monocrop, 2-crops, 3-crops without or with one or two legume cover crops) and tillage (conventional or reduced tillage) on yield probabilities and the benefits of crop diversity under different soil moisture and temperature scenarios. Although the magnitude of rotation benefits varied with crops, weather patterns and tillage, yield stability significantly increased when corn and soybean were integrated into more diverse rotations. Introducing small grains into short corn-soybean rotation was enough to provide substantial benefits on long-term soybean yields and their stability while the effects on corn were mostly associated with the temporal niche provided by small grains for underseeded red clover or alfalfa. Crop diversification strategies increased the probability of harnessing favorable growing conditions while decreasing the risk of crop failure. In hot and dry years, diversification of corn-soybean rotations and reduced tillage increased yield by 7% and 22% for corn and soybean respectively. Given the additional advantages associated with cropping system diversification, such a strategy provides a more comprehensive approach to lowering yield variability and improving the resilience of cropping systems to multiple environmental stresses. This could help to sustain future yield levels in challenging production environments.

Introduction: Integrated crop-livestock systems (ICLS) use animals to graze crop residues or cover crops before planting fresh produce and provide ecosystem services to support organic vegetable production. However, there is a risk of foodborne pathogen transfer to fresh produce because grazing may introduce enteric foodborne pathogens into the soil via animal feces, which may subsequently be transferred to the produce. Methods: To examine the effect of cover crop use and the risk of cover crop grazing on the contamination of soil and produce by foodborne pathogens in ICLS, a three-year (2019-2021) experimental study was conducted in organically managed plots, which were assigned three different treatments (fallow without cover crop or grazing, cover crop without grazing, or cover crop with grazing by sheep) in a maize/tomato rotation. During the three years of the experiment, a total of 184 pre- and post-graze fecal samples and 96 samples of tomatoes were collected to test for foodborne pathogens (Escherichia coli O157, non-O157 Shiga toxin-producing Escherichia coli (STEC), and Listeria (L.) monocytogenes). Soil samples were collected monthly until 126-171 days after grazing (824 in total) to examine the presence of foodborne pathogens, and generic E. coli (MPN/g) was quantified to compare its persistence among the three treatments. Results and Discussion: We did not detect any foodborne pathogens from harvested tomatoes in 2020 and 2021. One non-O157 STEC positive soil sample (0.1%, 1/824) was detected in the fallow treatment, and one L. monocytogenespositive (1.1%, 1/92) was detected from the post-graze fecal samples. When assessing proportions of generic E. coli positive and counts of generic E. coli in the soil samples using mixed effect zero-inflated negative binomial models, soil samples collected in the graze cover crop treatment plot showed significant increases in the counts of generic E. coli until 61-82 days post grazing, but no difference was observed after 96-123 days, compared to the baseline of the fallow treatment. Findings from generic E. coli counts support the use of the United States Department of Agriculture (USDA) National Organic Program (NOP) 90- or 120-day interval rule between applying raw manure and harvesting in organic farming into ICLS. Additionally, we confirmed that commercial organic compost application before cover crop seeding in the winter had no significant effect on the proportions and counts of generic E. coli in the soil of the following growing seasons. This longitudinal field trial confirmed that the effect of sheep grazing on foodborne pathogen contamination in ICLS is minimal but further studies comparing the genetic associations between fecal and soil samples would be necessary to distinguish the source of foodborne pathogen contamination. [ABSTRACT FROM AUTHOR]

Introduction: Irrigation management dramatically alters soil water availability and distribution and could impact soil microbial communities and carbon (C) and nitrogen (N) cycling to an even greater degree than observed in rainfed systems. Adoption of subsurface drip irrigation (SDI) in California's Mediterranean agroecosystems provides agronomic benefits but wets only a portion of the soil volume near the root zone, leaving the rest dry throughout the growing season. In contrast, traditional furrow irrigation (FI) has periodic wetting events with more homogenous moisture distribution. With conversion to precision irrigation methods, how will the microbiome respond to changes moisture availability, and how is their response influenced by soil C and N resource levels? Methods: In a field experiment in California, we compared SDI and FI's effects on microbial communities and evaluated how long-term organic and conventional management systems impact outcomes. Throughout the growing season, soil samples were collected at two depths (0-15, 15-30 cm) and three distances from bed center (10, 25, 45 cm) where the drip tape is located. Results: At harvest, soils irrigated using SDI had lower microbial biomass C (MBC) than under FI at the surface and showed a build-up of soluble C and N relative to MBC at the bed edge, indicating reduced microbial uptake. Community composition at the bed edge also diverged between SDI and FI, favoring Actinobacteria in the former and Acidobacteria and Gemmatimonadetes in the latter. Regardless of irrigation type, dry areas of the bed had the highest alpha diversity indices. Response to SDI was similar in organic and conventional systems, though organic had higher MBC, DOC, and relative abundance of Proteobacteria and fungal lipids, regardless of irrigation. Discussion: Prolonged dry conditions in SDI appeared to limit microbial access to resources and changed community composition. As seen in non-agricultural systems, the severity and frequency of moisture changes, adaptation of the communities, and resource availability affect microbial response. Decoupling of C and N pools in dry surface soils under SDI may increase the potential for losses of DOC and nitrate with the first winter rains in this Mediterranean climate. [ABSTRACT FROM AUTHOR]