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Inefficient nitrogen (N) fertilization and irrigation have led to unhealthy nitrate levels in groundwater bodies of agricultural areas in California. Simultaneously, high commodity prices and drought have encouraged perennial crop growers to turnover less-productive orchards, providing opportunities to recycle tree biomass in situ and to use high-carbon (C) residues to conserve soil and water resources. Although climate change adaptation and mitigation benefits of high-C soil amendments have been shown, uncertainties remain regarding the benefits and trade-offs of this practice for N cycling and retention. We used established almond [Prunus dulcis (Mill.) D. A. Webb] orchard trials on Hanford fine sandy loam with short-term and long-term biomass recycling legacies to better understand the changes in N dynamics and retention capacity associated with this practice. In a soil column experiment, labeled N fertilizer was added and traced into various N pools, including microbial biomass and inorganic fractions in soil and leachate. Shifts in microbial communities were characterized using the abundance of key N cycling functional genes regulating nitrification and denitrification processes. Our findings showed that, in the short term, biomass recycling led to N immobilization within the orchard biomass incorporation depth zone (0-15 cm) without impacts on N leaching potential. However, this practice drastically reduced nitrate leaching potential by 52%, 10 yr after biomass incorporation without an increase in N immobilization. Although the timing of these potential benefits as a function of microbial population and C and N biogeochemical cycles still needs to be clarified, our results highlight the potential of this practice to meaningfully mitigate nitrate discharges into groundwater while conserving soil resources.

Habitat diversification has been shown to positively influence a variety of ecosystem services to agriculture, including biological control of arthropod pests. The impact of increased biodiversity tends to be species specific though, and practices therefore need to be developed on a case-by-case basis for each cropping system. In perennial systems, numerous studies have demonstrated that cover crops can have positive impacts on soil quality and other ecosystem services, such as pollination and pest management. However, few studies have focused on the use of cover crops to enhance pest control in almond orchards, especially winter cover crops. The primary pest of almonds in North America is navel orangeworm, Amyelois transitella Walker, which overwinter as larva or pupa on remnant nuts, many of which remain on the orchard soil surface. In the spring, first flight adults subsequently use these remnant nuts as reproductive substrate. An experiment was conducted to evaluate the influence of two distinct winter cover crop mixtures on overwintering mortality and spring egg deposition of A. transitella. Remnant nuts placed into cover crop plots produced fewer adult A. transitella in the spring, suggesting increased overwintering mortality. Additionally, spring egg deposition was reduced on remnant nuts in the cover crops, possibly due to the ground covers interfering with host location and access. In this way, winter cover crops appear to contribute to the reduction of A. transitella populations in the orchard by altering abiotic and physical conditions, although studies to document specific mechanisms are still needed.

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.

Inoculation of crop plants with beneficial root-associated microorganisms may be a useful strategy for sustainable intensification of agriculture. In recent years, interest has grown in using rhizo...

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.

Summary A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Although empirical evidence remains sparse, management strategies that increase environmental sustainability, such as increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize yields in intensively managed grain systems. More diverse rotations increased maize yields over time and across all growing conditions (28.1% on average), including in favorable conditions (22.6%). Notably, more diverse rotations also showed positive effects on yield under unfavorable conditions, whereby yield losses were reduced by 14.0%–89.9% in drought years. Systems approaches to environmental sustainability and yield resilience, such as crop-rotation diversification, are a central component of risk-reduction strategies and should inform the enablement of policies.

Permanent crops like almond (Prunus dulcis) require significant water inputs for economic yields and long-term productivity. This demand creates a challenge in drought-prone regions like California. Use of organic matter amendments (OMA) can improve water use efficiency by conserving soil moisture and reducing tree water stress. The majority of almond orchards in California are no-till with irrigation targeted on a narrow tree berm where OMA is applied as surface mulch. We examined the effects of composted dairy manure (CM) and the timing of its application on soil moisture, soil water retention and tree water status in a young orchard planted in 2014. Treatments including Fall-applied CM (October 2015 and 2016), Spring-applied CM (April 2016 and 2017) and an unamended control were monitored during the 2016 and 2017 growing seasons. Fall-applied CM was more readily incorporated in soil organic matter of the 0–60 cm rooting zone as evidenced by significantly greater soil organic carbon (SOC) for Fall versus Spring-applied CM in 2016 (p

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.

There is an urgent need to develop resilient agroecosystems capable of helping smallholder farmers adapt to climate change, particularly drought. In East Africa, diversification of maize-based cropping systems by intercropping with grain and tree legumes may foster productivity and resilience to adverse weather conditions. We tested whether intercropping enhances drought resistance and crop and whole-system yields by imposing drought in monocultures and additive intercrops along a crop diversity gradient—sole maize (Zea mays), sole pigeonpea (Cajanus cajan), maize-pigeonpea, maize-gliricidia (Gliricidia sepium, a woody perennial), and maize-pigeonpea-gliricidia—with and without fertilizer application. We developed and tested a novel low-cost, above-canopy rainout shelter design for drought experiments made with locally-sourced materials that successfully reduced soil moisture without creating sizeable artifacts for the crop microenvironment. Drought reduced maize grain yield under fertilized conditions in some cropping systems but did not impact pigeonpea grain yield. Whole-system grain yield and theoretical caloric and protein yields in two intercropping systems, maize-pigeonpea and maize-gliricidia, were similar to the standard sole maize system. Maize-pigeonepea performed most strongly compared to other systems in terms of protein yield. Maize-pigeonpea was the only intercrop that consistently required less land than its corresponding monocultures to produce the same yield (Land Equivalent Ratio >1), particularly under drought. Despite intercropping systems having greater planting density than sole maize and theoretically greater competition for water, they were not more prone to yield loss with drought. Our results show that maize-pigeonpea intercropping provides opportunities to produce the same food on less land under drought and non-drought conditions, without compromising drought resistance of low-input smallholder maize systems.

Integrated crop–livestock systems are a form of sustainable intensification of agriculture that rely on synergistic relationships between plant and animal system elements to bolster critical agroecosystem processes, with potential impacts on resilience to weather anomalies. We simulated productivity dynamics in an integrated cover crop grazing agroecosystem typical of southern Brazil to gain a better understanding of the impacts of livestock integration on system performance, including future productivity and resilience under climate change. Long-term historical simulations in APSIM showed that the integrated system resulted in greater system-wide productivity than a specialized control system in 77% of simulated years. Although soybean yields were typically lower in the integrated system, the additional forage and livestock production increased total system outputs. Under simulated future climate conditions [representative concentration pathway 8.5 (RCP8.5) scenario from 2020 to 2060], integrated system productivity exceeded specialized system productivity in 95% of years despite declines in average soybean yield and aboveground cover crop biomass production. While the integrated system provided a productivity buffer against chronic climate stress, its resilience to annual weather anomalies depended on disturbance type and timing. This study demonstrates the utility of process-based models for exploring biophysical proxies for resilience, as well as the potential advantages of livestock integration into cropland as a sustainable intensification strategy.

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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., Synthetic nitrogen (N) fertilizers have fundamentally changed the availability of this critically important plant nutrient in agricultural systems, replacing organic sources such as compost and cover crops. Decades of plant breeding have created maize varieties that are highly productive under synthetic nitrogen fertilization, but potential trade-offs for uptake of organic nitrogen were unclear. Using a small panel of maize genotypes, we find minimal impacts of modern breeding on maize root traits, interactions between roots and associated microorganisms that regulate organic matter breakdown and transformations, and uptake of organic nitrogen from cover crops.

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.

Losses of nitrogen from agriculture are a major threat to environmental and human health at local, regional and global scales. Emerging evidence shows that climate change and intensive agricultural management will interact to increase the harmful effects and undermine current mitigation efforts. Identifying effective mitigation strategies and supporting policies requires an integrated understanding of the processes underlying potential agricultural nitrogen responses to climate change. In this Review, we describe these processes, propose a set of multi-scale principles to guide research and policy for decreasing nitrogen losses in the future, and describe the economic factors that could constrain or enable their implementation. Climate change and intensive agricultural management will interact to increase nitrogen (N) losses from agriculture. This Review analyses the processes underlying potential agricultural N responses to climate change, proposes a set of principles to help decrease N losses in the future and describes the economic factors that could affect their implementation.

Subsurface drip (SSD) irrigation is becoming increasingly prevalent in drought-prone irrigated agroecosystems thanks to greater yields and irrigation water productivity (IWP) and decreased weed pressure. However, potential tradeoffs for soil health and biogeochemical cycles remain unclear, especially in organic systems that rely on soil ecosystem services and biological processes for productivity. Gains in IWP and weed control were evaluated with respect to shifts in soil biological and physicochemical parameters in an organic processing tomato (Solanum lycopersicum L.) agroecosystem. Yield, IWP, and spatial distribution of soil resources and microbial processes were measured in furrow and SSD irrigated organic processing tomato on long term organic fields. Higher IWP and lower weed density under SSD confirm known benefits, while altered distributions of inorganic N, salinity, microbial activity, and C/N cycling enzyme activities as a function of shifts in soil moisture highlight the far-reaching impacts of irrigation management on soil organic C (SOC) and N dynamics regulating resource availability. Decreased macroaggregate formation and greater unprotected C under SSD indicate that altered soil wetting patterns may reduce the C sequestration potential of irrigated land. Previously unknown tradeoffs should be integrated to develop irrigation strategies that maintain current and future sustainability and productivity of organic tomato agroecosystems.

In Ontario, Canada, acreage of red clover (Trifolium pratense L.) intercropped with winter wheat (Triticum aestivum L. em. Thell) has declined, despite well-documented soil and yield benefits. The decline has resulted from increasing prevalence of stand non-uniformity, which has been attributed in part to soil moisture deficits. We examined whether there are genotypic differences in drought response between red clover varieties. A double-cut (Belle) and a single-cut variety (Altaswede) were grown under four different durations of drought (4, 8, 12 and 16 days below 15% relative soil water content, RSWC). Shoot dry weight, shoot relative water content (RWC), leaf area and crown water content were measured in control, drought and drought + recovery treatments. Belle used significantly more water during soil moisture deficit and had greater leaf area, shoot dry weight and RWC compared to Altaswede. In contrast, Altaswede had significantly higher survival rates than Belle, attributed to maintenance of meristematic tissue viability in the crown where re-growth, after shoot tissue desiccation, can occur. By demonstrating genotypic variation in survival strategies of red clover, traits can be identified for the development of improved varieties. Varieties with higher survival rates during drought will result in more uniform stands and increased utilization of red clover for environmental and yield benefits.

Across the world, an increasing number of farmers are piloting agroecological systems. The recoupling of crops and livestock is one type of agroecological practice that has potential to help reduce the use of off-farm inputs, improve soil quality, and reduce costs for farmers. Yet, a major part of the world's agricultural landscapes remain dominated by conventional specialized crop and livestock practices. In particular, grazing animals in perennial cropping systems may reduce pesticide and fuel use, decrease labor, and build soil organic carbon and soil fertility. In this study, we examined adopters and non-adopters’ perceptions of a niche system, integrated sheep-vineyard systems (ISVS) in California. We aimed at understanding the conditions under which ISVS, a specific case of ICLS (integrated crop-livestock systems), could be mainstreamed. We then contextualized these interviews using the Multi-Level Perspective framework to analyze the levers favoring or impeding mainstreaming of this niche system. We considered both pull factors arising from changes in the landscape, and push factors arising through decentralized, grassroot processes. Our inductive analysis is a promising first insight into farmers’ perceptions and motivations toward ISVS adoption in California, considering both vineyard managers and contractors (i.e. shepherds renting their sheep to vineyard managers). We found a positive perception of ISVS among both current adopters and non-adopters regarding the potential agronomic, environmental and economic benefits of these practices. All adopters were satisfied with this system as they experienced labor and fuel savings, soil quality improvement and marketing advantages. Local push factors (bottom-up levers emerging from the niche systems) were highlighted by interviewees as contributing to adoption. Push factors identified include knowledge exchange and networking between vineyard managers and developing marketing pathways for “carbon-positive” wool, meat and wine products. However, some pull factors (macro-economic and policy levers acting as top-down levers) could help move the system beyond limited adoption. We point out biotechnical and socio-economic research avenues to encourage the scaling-up of ISVS and ICLS more broadly. On the biotechnical dimension, we recommend continuing and scaling-out system experiments to redesign vineyards considering sheep integration and evaluate the effect of grazing on soil quality and fire management. On the socio-economic dimension, we encourage the exploration of relevant spatial scenarios through co-design of collaborative arrangements between vineyard managers and contractors at the landscape level. Greater research on the social, environmental and economic services provided by ISVS is urgently needed to inform state and federal agricultural policies, including whether such systems should be supported through payment for ecosystem services and as part of environmental good practices and fire safety recommendations.

Climate change adaptation requires building agricultural system resilience to warmer, drier climates. Increasing temporal plant diversity through crop rotation diversification increases yields of some crops under drought, but its potential to enhance crop drought resistance and the underlying mechanisms remain unclear. We conducted a drought manipulation experiment using rainout shelters embedded within a 36-year crop rotation diversity and no-till experiment in a temperate climate and measured a suite of soil and crop developmental and eco-physiological traits in the field and laboratory. We show that diversifying maize-soybean rotations with small grain cereals and cover crops mitigated maize water stress at the leaf and canopy scales and reduced yield losses to drought by 17.1 ± 6.1%, while no-till did not affect maize drought resistance. Path analysis showed a strong correlation between soil organic matter and lower maize water stress despite no significant differences in soil organic matter between rotations or tillage treatments. This positive relationship between soil organic matter and maize water status was not mediated by higher soil water retention or infiltration as often hypothesized, nor differential depth of root water uptake as measured with stable isotopes, suggesting that other mechanisms are at play. Crop rotation diversification is an underappreciated drought management tool to adapt crop production to climate change through managing for soil organic matter.

© 2017 Elsevier Ltd Crops and livestock play a synergistic role in global food production and farmer livelihoods. Increasingly, however, crops and livestock are produced in isolation, particularly in farms operating at the commercial scale. It has been suggested that re-integrating crop and livestock systems at the field and farm level could help reduce the pollution associated with modern agricultural production and increase yields. Despite this potential, there has been no systematic review to assess remaining knowledge gaps in both the social and ecological dimensions of integrated crop and livestock systems (ICLS), particularly within commercial agricultural systems. Based on a multi-disciplinary workshop of international experts and additional literature review, we assess the current knowledge and remaining uncertainties about large-scale, commercial ICLS and identify the source of remaining knowledge gaps to establish priorities for future research. We find that much is understood about nutrient flows, soil quality, crop performance, and animal weight gain in commercial ICLS, but there is little knowledge about its spatial extent, animal behavior or welfare in ICLS, or the tradeoffs between biodiversity, pest and disease control, greenhouse gas (GHG) mitigation, and drought and heat tolerance in ICLS. There is some evidence regarding the economic outcomes in commercial ICLS and supply chain and policy barriers to adoption, but little understanding of broader social outcomes or cultural factors influencing adoption. Many of these knowledge gaps arise from a basic lack of data at both the field and system scales, which undermines both statistical analysis and modeling efforts. Future priorities for the international community of researchers investigating the tradeoffs and scalability of ICLS include: methods standardization to better facilitate international collaborations and comparisons, continued social organization for better data utilization and collaboration, meta-analyses to answer key questions from existing data, the establishment of long term experiments and surveys in key regions, a portal for citizen science, and more engagement with ICLS farmers.

Breeding towards root-centric ideotypes can be a relatively quick trait-based strategy to improve crop resource use efficiency. Irrigated agriculture represents a crucial and expanding sector, but its unique parameters require traits distinct from previously proposed rainfed ideotypes. We propose a novel irrigated ideotype that integrates traits across multiple scales to enhance resource use efficiency in irrigated agroecosystems, where resources are concentrated in a relatively shallow 'critical zone'. Unique components of this ideotype include rapid transplant recovery and establishment, enhanced exploitation of localized resource hotspots, adaptive physiological regulation, maintenance of hydraulic conductivity, beneficial rhizosphere interactions, and salinity/waterlogging avoidance. If augmented by future research, this target could help to enhance agricultural sustainability in irrigated agroecosystems by guiding the creation of resource-efficient cultivars.

Arbuscular mycorrhizal fungi (AMF) are mutualistic fungi that play important roles in plant nutrition and soil ecosystem functions. While AMF are known to benefit diverse host plants under a range of conditions, little is known about their presence in commercial almond orchards and how frequently used management practices regulate AMF root colonisation. A large-scale survey of almond orchards in the Central Valley of California was conducted to determine the extent of mycorrhizal associations with roots and the impact of orchard management practices and soil properties on AMF root colonisation rates. The roots in all orchards were colonised, with an overall average rate of 64.4%. Organically managed orchards had higher AMF root colonisation rates (73.2%) as compared with conventionally managed orchards (62.1%), primarily due to the presence of soil vegetative cover rather than organic matter inputs. Choice of rootstock and fumigation had only marginal effects while inoculation at planting increased AMF root colonisation of young trees by 27% compared to non-inoculated control. These results highlighted the ubiquitous presence of AMF in commercial almond orchards and significant interacting influences of common management practices on AMF root colonisation under field conditions. Further research into the functional implications of mycorrhizal associations in these orchards will help guide the development of management practices that increase AMF abundance and root colonisation to improve the sustainability of this rapidly expanding industry.

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 2m, taking into account changes in bulk density. Across the entire 2m 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% (21.8MgC/ha) with both WCC and composted poultry manure inputs, across the 2m profile. The addition of WCC to a conventionally managed system increased SOC stocks by 3.5% (1.44MgC/ha) in the 0-30cm layer, but decreased by 10.8% (14.86MgC/ha) in the 30-200cm layer, resulting in overall losses of 13.4MgC/ha. If we only measured soil C in the top 30cm, 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 2m 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.

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.

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.

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.

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.

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 NO(3)-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.

While characteristics of semi-arid climates place limitations on soil organic carbon (SOC) storage, there is opportunity and urgency for increasing the quality and long-term persistence of cropland SOC content within these agroecosystems. Livestock re-integration into cropland shows potential to improve semi-arid agroecosystem functioning through shifts in biogeochemical processes and the facilitation of multiple ecosystem services involved in carbon and nutrient cycling and use-efficiency. Here we review the characteristics of grazing-based Integrated Crop-Livestock (ICL) systems and how various associated management practices may interplay with semi-arid agroecological and biogeochemical dynamics to influence soil microbial ecology and SOC accumulation and stabilization. We argue that livestock re-integration holds notable potential to increase cropland SOC through controls on landscape net primary productivity, allocation of biomass belowground, efficient recycling of residual crop nutrients, and soil biological activity related to a suite of soil ecosystem services. Achieving the full SOC accumulation potential of ICL management will require site-specific consideration of feedbacks between herbivory, soil microbial ecology, soil disturbance, and forage species interactions. Future research should focus on optimizing plant-soil-grazer feedbacks and understanding of mechanistic drivers of ICL system outcomes to optimize the design and management of semi-arid regional ICL systems for enhanced SOC quality and persistence.

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.

Pasture degradation hinders livestock production and ecosystem services that support rural smallholder communities throughout Latin America. Silvopastoral systems, with improved pasture cultivars (especially Brachiaria spp.) and multipurpose trees, offer a promising strategy to restore soils and improve livelihoods in the region. However, studies evaluating the impact of such systems on pasture productivity and soil health under realistic smallholder constraints are lacking. We evaluated the impact of improved pasture grass and tree establishment on a suite of soil health indicators in actively grazed, low-input, farmer-managed silvopastoral systems. In August 2013, paired pasture treatments (improved grass with trees vs. traditional pastures) were established on nine farms with similar land-use histories near Matagalpa, Nicaragua. On each farm, one treatment was left as traditional pasture with naturalized grass (Hyparrhenia rufa), while the adjacent treatment was sown with the improved grass (Brachiaria brizantha cv. Marandu) and planted with tree saplings without fertilizer. In August 2015, we measured standing biomass and a suite of chemical, biological, and physical soil health variables. Improved silvopastoral systems with B. brizantha produced more standing grass biomass and supported higher levels of earthworm populations and permanganate oxidizable carbon (POXC) compared to the traditional control. Correlations suggest that earthworms and POXC were associated with incipient improvements to soil aggregate stability and water holding capacity. We report measurable improvements to soil health just two years following the establishment of improved pasture systems under common smallholder management practices and suggest that these systems, even with minimal fertility inputs, have the potential to enhance regional sustainability.

Diversity in crop rotations regulates the ecologic processes active in maintaining and improving agricultural productivity in a changing climate. This review explores how rotation diversity influences water and nitrogen (N) use efficiencies in temperate, rainfed, arable cropping systems through linkages between water and N dynamics. We consider impacts of diversification on mechanisms spanning scales from crop to agroecosystem, including shifts in cycling, retention, and losses of water and N and changes in crop demand and foraging capacity. We integrate crop, soil, and microbial processes and their dynamics over the length of the crop rotation to better understand the potential of temporal diversification to improve resource use efficiency. We close by identifying knowledge gaps and research priorities. Systems approaches are critically needed to better assess the environmental and agronomic impact of crop rotation diversification under different climate scenarios and optimize rotations for current and future production constraints. Increasing rotation complexity to improve water and N use efficiencies will also promote other ecosystem services provided by biodiverse landscapes, helping build cropping systems that benefit from and foster the conservation of natural resources and ecosystem services.

International audience; AbstractCommercial-scale integrated crop-livestock systems intensify land use by combining complementary agricultural enterprises and leveraging synergistic ecosystem services to achieve both productive and environmental outcomes. Although widely implemented in southern Brazil as an annual beef/soybean rotation, tradeoffs such as competing soil water use between pasture and crop phases may result from seasonal grazing in this system. We compared soil water and plant physiological variables in the crop phase of an integrated annual beef-soybean system managed with no-till and best grazing practices with those of an ungrazed cover crop control as part of a long-term experiment in southern Brazil. A mixed black oat (Avena strigosa Schreb.) and Italian ryegrass (Lolium multiflorum Lam.) pasture was either grazed by beef cattle to 20-cm sward height or left as an ungrazed cover crop in the winter, and direct-planted to soybean (Glycine max [L.] Merr.) in the summer. Although soybean yields did not differ between grazed and ungrazed treatments, soil matric potential was on average 25% lower across depths and growth stages in plots that had been grazed during winter. Soybeans in grazed plots also exhibited up to 34% lower light-use efficiency and a 2-week slower time to physiological maturation than soybeans in plots that had not been previously grazed. These results describe for the first time the differential crop growing conditions and crop physiological responses created after 16 years of integration with grazing animals. As integrated crop-livestock systems grow in importance in commercial production settings, this research can inform adaptive management practices to ensure the sustainability of these systems into the future and under a variety of environmental conditions.

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 real data set of 16S-V4 amplicon sequences that was 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.