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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...

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.

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.

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.

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.

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.

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.

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.

Roots are notoriously difficult to study. Soil is both a visual and mechanical barrier, making it difficult to track roots in situ without destructive harvest or expensive equipment. We present a customizable and affordable rhizobox method that allows the non-destructive visualization of root growth over time and is particularly well-suited to studying root plasticity in response to localized resource patches. The method was validated by assessing maize genotypic variation in plasticity responses to patches containing (15)N-labeled legume residue. Methods are described to obtain representative developmental measurements over time, measure root length density in resource-containing and control patches, calculate root growth rates, and determine (15)N recovery by plant roots and shoots. Advantages, caveats, and potential future applications of the method are also discussed. Although care must be taken to ensure that experimental conditions do not bias root growth data, the rhizobox protocol presented here yields reliable results if carried out with sufficient attention to detail.

Biofertilizers are promoted as a strategy for sustainable intensification of agriculture, but their efficacy varies widely among published studies and it is unclear whether they deliver the promised benefits. Studies are commonly conducted under controlled conditions prior to deployment in the field, yet the predictive value of such studies for field-scale productivity has not been critically examined. A meta-analysis was conducted using a novel host crop-specific approach to evaluate the agronomic potential of bacterial biofertilizers for maize. Yield increases tended to be slightly higher and more variable in greenhouse studies using field soil than in the field, and greenhouse studies poorly predicted the influence of moderating climate, soil and taxonomic variables. We found greater efficacy of Azospirillum spp. and lower efficacy of Bacillus spp. and Enterobacter spp. under field conditions. Surprisingly, biofertilizer strains with confirmed plant-growth-promoting traits such as phosphorus solubilization, nitrogen fixation and phytohormone production in vitro were associated with lower yields in the field than strains not confirmed to possess these traits; only 1-aminocyclopropane-1-carboxylate deaminase synthesis increased yields. These results indicate the need for a novel biofertilizer development framework that integrates information from native soil microbial communities and prioritizes field validation of results.

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.

A common agronomic recommendation is under-seeding red clover to wheat in the corn–soy–wheat rotation. As a leguminous cover crop, red clover boosts agro-ecological resilience and productivity through nitrogen fixation, as well as non-nitrogen-related contributions, such as soil temperature and moisture regulation; reduction of erosion, runoff, and leaching; weed suppression; and interruption of pest and disease cycles. The objective of this paper is to propose a system that extends red clover usage into the corn phase of the corn–soy–wheat rotation as a living mulch. The system incorporates strip-tillage, strip-mowing, as well as banded herbicide and fertilizer application in order to maximize productivity and minimize competition. We analyzed the feasibility of this proposal by examining red clover’s adequacy for the proposed system in comparison with other broadleaf, leguminous cover crops, and assessed potential agro-ecological benefits. We considered logistical components of the proposition, including the use of strip-tillage, the application of precision technology, as well as the opportunity for further technological developments. We found that the proposed system has potential to increase agro-ecological sustainability, resilience, and the overall productivity of this three-year rotation. Thus, this easily-implemented practice should be formally studied.

Continuously flooded rice systems are a major contributor to global rice production and food security. Allowing the soil to dry periodically during the growing season (such as with alternate wetting and drying irrigation - AWD) has been shown to decrease methane emissions, water usage, and heavy metal accumulation in rice grain. However, the effects of AWD on rice yields are variable and not well understood. A two-year study was established to quantify the impacts of a range of treatments differing in AWD severity (degree of soil drying between flooding events) on yield (as well as factors that may affect yields), soil hydrology in the soil profile, and grain arsenic (As) concentrations relative to a continuously flooded control (CF). Three AWD treatments of increasing severity were imposed between full canopy cover (around 45 days after sowing) and 50% heading: AWD-Safe (field was reflooded when the perched water table reached 15 cm below the soil surface) and AWD35 and AWD25 (field was reflooded when the soil volumetric water content at 0–15 cm depth reached 35% and 25%, respectively). During the drying periods, the 0–15 cm soil layer in the AWD-Safe remained saturated, whereas in AWD35 and AWD25 the soil dried to the desired volumetric water contents. In contrast, soil moisture at 25–35 cm below the soil surface was similar across all treatments. Yield was not reduced in any of the AWD treatments, compared to the CF control. There were no consistent differences in yield components, 13C discrimination, and N dynamics. Results suggest that the availability of water and the presence of roots at the 25–35 cm soil depth during the drying periods ensured that the crop did not suffer drought stress and thus yields were maintained. Grain As concentration in the AWD-Safe treatment was similar to that in the CF control but decreased by 56–68% in AWD35 and AWD25. AWD-Safe is often promoted as a means of practicing AWD without reducing yields; however, in this study this practice did not reduce grain As concentration because the soil did not reach an unsaturated state. These findings demonstrate that knowledge of surface and subsurface hydrology, and the root system are important for understanding the potential of AWD.

Many of the foods we eat today look very different than they did in the past. Corn, or maize, did not exist 10,000 years ago: it descended from a weedy grass with tiny hard-shelled seeds that we would not recognize as corn kernels. That wild ancestor of corn, called teosinte, grew in mixtures of many other plants, instead of grows in cornfields like today. Big changes between teosinte and corn that we can see aboveground lead us to think that there have been changes belowground too. Plants form partnerships with microbes, such as bacteria and fungi, to get the nutrients that they need to grow. Scientists are finding that microbes near the roots of teosinte are different than microbes that live around corn roots. Understanding how corn’s microbe partners have changed can help us make corn varieties that are better for the environment.

In light of the environmental challenges ahead, resilience of the most abundant field crop production systems must be improved to guarantee yield stability with more efficient use of nitrogen inputs, soil and water resources. Along with genetic and agronomic innovations, diversification of northern agro-ecosystems using inter-seeded legumes provides further opportunities to improve land management practices that sustain crop yields and their resilience to biotic and abiotic stresses. Benefits of legume cover crops have been known for decades and red clover (Trifolium pratense) is one of the most common and beneficial when frost-seeded under winter wheat in advance of maize in a rotation. However, its use has been declining mostly due to the use of synthetic fertilizers and herbicides, concerns over competition with the main crop and the inability to fully capture red clover benefits due to difficulties in the persistence of uniform stands. In this manuscript, we first review the environmental, agronomic, rotational and economical benefits associated with inter-seeded red clover. Red clover adaptation to a wide array of common wheat-based rotations, its potential to mitigate the effects of land degradation in a changing climate and its integration into sustainable food production systems are discussed. We then identify areas of research with significant potential to impact cropping system profitability and sustainability.

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.

There is interest in discovering root traits associated with acclimation to nutrient stress. Large root systems, such as in adult maize, have proven difficult to be phenotyped comprehensively and over time, causing target traits to be missed. These challenges were overcome here using aeroponics, a system where roots grow in the air misted with a nutrient solution. Applying an agriculturally relevant degree of low nitrogen (LN) stress, 30-day-old plants responded by increasing lengths of individual crown roots (CRs) by 63%, compensated by a 40% decline in CR number. LN increased the CR elongation rate rather than lengthening the duration of CR growth. Only younger CR were significantly responsive to LN stress, a novel finding. LN shifted the root system architectural balance, increasing the lateral root (LR)-to-CR ratio, adding ∼70 m to LR length. LN caused a dramatic increase in second-order LR density, not previously reported in adult maize. Despite the near-uniform aeroponics environment, LN induced increased variation in the relative lengths of opposing LR pairs. Large-scale analysis of root hairs (RHs) showed that LN decreased RH length and density. Time-course experiments suggested the RH responses may be indirect consequences of decreased biomass/demand under LN. These results identify novel root traits for genetic dissection.

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.

Background There was ancient human selection on the wild progenitor of modern maize, Balsas teosinte, for decreased shoot branching (tillering), in order to allow more nutrients to be diverted to grain. Mechanistically, the decline in shoot tillering has been associated with selection for increased expression of the major domestication gene Teosinte Branched 1 (Tb1) in shoot primordia. Therefore, TB1 has been defined as a repressor of shoot branching. It is known that plants respond to changes in shoot size by compensatory changes in root growth and architecture. However, it has not been reported whether altered TB1 expression affects any plant traits below ground. Previously, changes in dosage of a well-studied mutant allele of Tb1 in modern maize, called tb1-ref, from one to two copies, was shown to increase tillering. As a result, plants with two copies of the tb1-ref allele have a larger shoot biomass than heterozygotes. Here we used aeroponics to phenotype the effects of tb1-ref copy number on maize roots at macro-, meso- and micro scales of development. Results An increase in the tb1-ref copy number from one to two copies resulted in: (1) an increase in crown root number due to the cumulative initiation of crown roots from successive tillers; (2) higher density of first and second order lateral roots; and (3) reduced average lateral root length. The resulting increase in root system biomass in homozygous tb1-ref mutants balanced the increase in shoot biomass caused by enhanced tillering. These changes caused homozygous tb1-ref mutants of modern maize to more closely resemble its ancestor Balsas teosinte below ground. Conclusion We conclude that a decrease in TB1 function in maize results in a larger root system, due to an increase in the number of crown roots and lateral roots. Given that decreased TB1 expression results in a more highly branched and larger shoot, the impact of TB1 below ground may be direct or indirect. We discuss the potential implications of these findings for whole plant coordination of biomass accumulation and maize domestication.

Numerous transgenes have been reported to increase rice drought resistance, mostly in small-scale experiments under vegetative-stage drought stress, but few studies have included grain yield or field evaluations. Different definitions of drought resistance are currently in use for field-based and laboratory evaluations of transgenics, the former emphasizing plant responses that may not be linked to yield under drought. Although those fundamental studies use efficient protocols to uncover and validate gene functions, screening conditions differ greatly from field drought environments where the onset of drought stress symptoms is slow (2-3 weeks). Simplified screening methods, including severely stressed survival studies, are therefore not likely to identify transgenic events with better yield performance under drought in the target environment. As biosafety regulations are becoming established to allow field trials in some rice-producing countries, there is a need to develop relevant screening procedures that scale from preliminary event selection to greenhouse and field trials. Multilocation testing in a range of drought environments may reveal that different transgenes are necessary for different types of drought-prone field conditions. We describe here a pipeline to improve the selection efficiency and reproducibility of results across drought treatments and test the potential of transgenic rice for the development of drought-resistant material for agricultural purposes.