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Agriculture is a designed system with the largest areal footprint of any human activity. In some cases, the designs within agriculture emerged over thousands of years, such as the use of rows for the spatial organization of crops. In other cases, designs were deliberately chosen and implemented over decades, as during the Green Revolution. Currently, much work in the agricultural sciences focuses on evaluating designs that could improve agriculture's sustainability. However, approaches to agricultural system design are diverse and fragmented, relying on individual intuition and discipline-specific methods to meet stakeholders' often semi-incompatible goals. This ad-hoc approach presents the risk that agricultural science will overlook nonobvious designs with large societal benefits. Here, we introduce a state space framework, a common approach from computer science, to address the problem of proposing and evaluating agricultural designs computationally. This approach overcomes limitations of current agricultural system design methods by enabling a general set of computational abstractions to explore and select from a very large agricultural design space, which can then be empirically tested.

Increasing soil organic carbon (SOC) stocks is increasingly targeted as a key strategy in climate change mitigation and improved ecosystem resiliency. Agricultural land, a dominant global land use, provides substantial challenges and opportunities for global carbon sequestration. Despite this, global estimates of soil carbon sequestration potential often exclude agricultural land and estimates are coarse for regions in the Global South. To address these discrepancies and improve estimates, we develop a hybrid, data-augmented database approach to better estimate the magnitude of SOC sequestration potential of agricultural soils. With high-resolution (30 m) soil maps of Africa developed by the International Soils Database (iSDA) and Malawi as a case study, we create a national adjustment using site-specific soil data retrieved from 1160 agricultural fields. We use a benchmark approach to estimate the amount of SOC Malawian agricultural soils can sequester, accounting for edaphic and climatic conditions, and calculate the resulting carbon gap. Field measurements of SOC stocks and sequestration potentials were consistently larger than iSDA predictions, with an average carbon gap of 4.42 ± 0.23 Mg C ha

Cover cropping is considered a cornerstone practice in sustainable agriculture; however, little attention has been paid to the cover crop production supply chain. In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 3.8% (median 2.0%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.5% and 11.9%, respectively. The latter land requirement is comparable to the annual amount of maize grain lost to disease in the U.S. We highlight avenues for reducing these high land use costs., In this Perspective, Bryan Runck and colleagues discuss an often-overlooked consequence of scaling up cover cropping – a cornerstone of sustainable agriculture. Using published seed yield data from common cover crops, they demonstrate the potentially large land use cost and discuss ways for reducing this cost.

Microorganisms play essential roles in agricultural systems, and their abundance, diversity and activity can be influenced by management practices. Crop rotational diversity is known to influence both soil microorganisms and crop productivity, yet the specific contributions of microorganisms to rotational benefits are unknown. To facilitate monitoring soil biological processes that support vigorous and high yielding crops, we studied maize (Zea mays L.) and soybean (Glycine max L.), and their associated microorganisms within a two-year maize-soybean rotation and within four-year crop rotations with varying crop sequences. We hypothesized that rhizosphere microbial communities are strong predictors of crop productivity contingent on rotational diversity and previous crop legacy. Sampling at seedling and flowering stages, we assessed rhizosphere bacterial and fungal communities, soil and plant tissue nutrients, aboveground biomass, and yield. Rhizosphere communities varied with rotational diversity and previous crop legacy. Concurrently, maize and soybean yield and biomass were approximately 15–25% larger in more diverse rotations and with different crop legacies, but there were no crop rotational effects on tissue or soil nutrients. Yield differences across rotational diversity or previous crop legacy were better predicted when microbial communities were considered. Fungal communities predicted lower maize seedlings biomass when following soybean, and lower soybean seedling biomass when following maize, independent of rotational diversity. Further, for maize, fungal communities predicted lower maize yield in the maize-soybean rotation, while in the four-year diverse rotations, bacterial communities predicted maize recovery from a soybean legacy by flowering. These results suggest that benefits of four-year rotations in maize and soybean production are driven by changes in plant pathogenic communities.

Emerging biotechnologies, such as genome editing, may revolutionize agricultural development through rapid and precise genetic manipulation of a wide range of crop traits without having to transfer foreign DNA [1]. If so, these new genetic‐engineering (GE) technologies can help to generate crop varieties to address critical challenges in agricultural development, such as climate resilience or nutrient uptake, or diet‐related problems in nutrition and health in poorer countries. However, society must also be protected from potential harmful effects of genetically manipulated crops on the environment, human health, or social welfare. Governance of these crops must therefore balance agricultural developments with risk assessment and prevention of potential harm. > …genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed Presently, genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed. Influential groups concerned with the potential hazards of such crops view this situation with growing alarm, which has created tensions with the academic community and regulatory agencies [2]. Both the USA and the European Commission are currently reviewing the governance of crops produced by genome editing and other new technologies. On the US side, at least, the review process appears unlikely to result in governance approaches that will satisfy parties that are concerned with either over‐ or under‐regulation of such crops, and tension and conflicts about them are likely to heighten. We propose an alternative approach for governance of these crops that may help to defuse tensions and enable exploration of genome editing technologies’ potential while protecting society from harm: a cooperative governance network. Such networks have performed well in …

Managing the soil nitrogen (N) cycle is a major component of agricultural sustainability. Soil functional zone management (zonal management) is a novel agroecological strategy for managing row-crop agroecosystems. It may improve the efficiency of soil N cycling compared with conventional and no-tillage approaches, by managing the timing and location (crop row vs inter-row) of key soil N cycling processes. We compared N mineralization and availability during the period of maize peak N demand in crop rows and inter-rows in zonal management and conventional chisel plow tillage systems at four sites across the US Corn Belt over three growing seasons. Under zonal management, potential N mineralization and N availability during crop peak N demand were significantly greater in crop rows, where the majority of crop roots are found, compared with inter-rows. Averaged across all site-years, plant-available N in zonal management crop rows was 46 mg kg −1 compared with 21 mg kg −1 in inter-rows. In contrast, in conventional tillage, potential N mineralization and N availability were greater in inter-rows compared with crop rows; averaged across all site-years, plant-available N in conventional tillage crop rows was 24 mg kg −1 compared with 51 mg kg −1 in inter-rows. The results demonstrate that the active management of crop residues under zonal management can enhance the spatiotemporal efficiency of soil N cycling processes, by concentrating N mineralization and availability close to crop roots in synchrony with crop developmental needs. Zonal management therefore has potential to increase crop N-use efficiency compared with conventional tillage, and thereby reduce the impacts of row-crop agricultural production on water resources and greenhouse gas emissions that result from N leaching and denitrification.

Zonal tillage (e.g. ridge tillage, RT) separates management of row and inter-row positions, while non-zonal tillage (e.g. chisel plough, CP) applies management uniformly across a field. This may have large effects on soil hydrothermal properties, affecting soil processes and crop development. We examined the effects of RT versus CP on soil hydrothermal conditions under maize (Zea mays L.) at four sites spanning the US Corn Belt over two growing seasons (2012–2013). We also investigated whether RT, as a result of changes in hydrothermal conditions, could stimulate greater soil nitrogen (N) availability during peak maize N demand. We captured wide variation in soil types and climates, allowing us to generalise tillage effects across a large environmental gradient. Continuous hydrothermal measurements were taken in the centre of row and inter-row positions. Soil cores collected shortly after maize six leaf stage (V6) were analysed for plant-available N and potentially mineralisable N (PMN). We hypothesised: 1) in spring CP and RT both produce warm, dry seedbeds with equivalent accumulations of growing degree days (GDD), but later in season RT holds greater soil moisture, providing better conditions for cover or relay crop establishment; 2) Hydrothermal properties of RT rows are distinct from RT inter-rows, while CP rows and inter-rows are indistinguishable; 3) RT promotes greater soil N mineralisation and availability in crop rows compared with CP. Results largely confirmed all hypotheses. In early spring, rows were drier in RT than CP, and both were similar in warmth (i.e. in accumulated GDD). From V6 to tasselling, CP accumulated more GDD than RT in inter-rows, while row positions remained similar; RT maintained greater soil moisture across both positions. From tasselling to harvest, RT inter-rows held greater soil moisture than CP, but accumulated fewer GDD. Both tillage systems showed zonation of soil moisture between planting and harvest (inter-rows moister than rows); the magnitude of zonation was greatest in RT. Plant-available N and PMN were greater in RT compared with CP at V6, suggesting RT increases synchrony of soil N availability with crop requirements. The results demonstrate that zonal tillage can integrate the seedbed benefits of conventional tillage with increased soil moisture retention across a wide range of climates and soil types. Increased moisture retention may help buffer agricultural systems against drought, and improve seedbed conditions for cover and relay crops in late summer and early autumn, thus potentially improving both sustainability and production in these systems.

Since the mid-20th century, crop breeding has driven unprecedented yield gains. Breeders generally select for broadly- and reliably-performing varieties that display little genotype-by-environment interaction (GxE). In contrast, ecological theory predicts that across environments that vary spatially or temporally, the most productive population will be a mixture of narrowly adapted specialists. We quantified patterns of broad and narrow adaptation in modern, commercial maize (Zea mays L.) hybrids planted across 216 site-years, from 1999-2018, for the University of Illinois yield trials. We found that location was the dominant source of yield variation (44.5%), and yearly weather was the smallest (1.7%), which suggested a benefit for reliable performance in narrow biophysical environments. Varieties displayed a large "home field advantage" when growing in the location of best performance relative to other varieties. Home field advantage accounted for 19% of GxE and provided a yield increase of 1.01 ± 0.04 Mg ∙ ha-1 (7.6% relative to mean yield), yet was both smaller than predicted by a null model and unchanged across time. This counterfactual suggests that commercial breeding programs have missed an opportunity to further increase yields by leveraging local adaptation. Public breeding programs may pursue this opportunity by releasing specialist varieties that perform reliably in narrow environments. As seed sources are increasingly privatized and consolidated, this alternate strategy may compliment private breeding to support global food security.

Common buckthorn (Rhamnus cathartica) is an important invasive shrub in North American forests, where it is thought that the plant’s retention of green leaves during autumn canopy senescence helps it succeed in deciduous understory habitat. This trait results in loss of nitrogen (N) in N-rich leaf litter, which has led some workers to suggest buckthorn may foster associative N-fixation in soil. We examined this possibility in an oak woodland understory in eastern Minnesota using the acetylene reduction assay to compare apparent nitrogenase activity in soils collected from beneath buckthorn individuals with soils collected from a canopy species (Quercus spp.), an important understory shrub (Prunus serotina), and non-vegetated areas. Buckthorn and non-buckthorn soils differed in variability of acetylene reduction (AR) rates, with buckthorn values covering a range 10× the range of non-buckthorn soils. Mean AR also differed between buckthorn and non-buckthorn soils, but the direction and magnitude of the difference varied with sampling location. Estimates of N inputs calculated from our data suggest that AR values at the high end of the buckthorn-associated range are biologically significant. Our results represent the first measurement of AR activity associated with common buckthorn, and are consistent with the hypothesis that this plant supports associative N fixation under some conditions. Suggestions for follow-up studies are provided.

The X-linked inhibitor of apoptosis protein (XIAP) is a zinc metalloprotein that has recently been implicated in copper homeostasis. XIAP mediates apoptosis via the inhibition of caspase enzymes through multiple baculovirus IAP repeat (BIR) domains, wherein zinc is coordinated by three cysteine amino acids and one histidine amino acid. XIAP binds copper ions directly at one or more unspecified sites, indicating that the protein may function as a copper sensor. We report the copper-binding properties of an XIAP construct containing the BIR2 and BIR3 domains. Absorption and emission spectroscopic measurements show that XIAP exhibits only a low-to-moderate affinity for Cu(II), but a strong affinity for Cu(I). Cu(I) is observed to bind at multiple sites within the BIR2 and BIR3 domains, including the CXXC motifs of the zinc structural sites and multiple BIR2 surface sites. Mutagenesis-based experiments reveal that surface cysteine residues mediate binding in the BIR2 domain and induce protein oligomerization under elevated copper concentrations. These results constitute the first spectroscopic evidence of copper-XIAP interactions.

Increasingly, funding agencies are investing in integrated and transdisciplinary research to tackle “grand challenge” priority areas, critical for sustaining agriculture and protecting the envi -ronment. Coordinating multidisciplinary research teams capable of addressing these priority areas, however, presents its own unique set of chal-lenges, ranging from bridging across multiple dis -ciplinary perspectives to achieve common ques-tions and methods to facilitating engagement in holistic and integrative thinking that promotes linkages from scholarship to societal needs. We propose that structural equation modeling (SEM) can provide a powerful framework for synergizing multidisciplinary research teams around grand challenge issues. Structural equation modeling can integrate both visual and statistical expres-sion of complex hypotheses at all stages of the research process, from planning to analysis. Three elements of the SEM framework are par-ticularly beneficial to multidisciplinary research teams; these include (i) a common graphical lan-guage that transcends disciplinary boundaries, (ii) iterative, critical evaluation of complex hypoth -eses involving manifest and latent variables and direct and indirect interactions, and (iii) enhanced opportunities to discover unanticipated interac-tions or causal pathways as empirical data are tested statistically against the model. Using our ongoing multidisciplinary, multisite field inves-tigation of climate change adaptation and miti-gation in annual row crop agroecosystems as a case study, we demonstrate the value of the SEM framework for project design, coordination, and implementation and provide recommendations for its broader application as a means to more effectively engage and address issues of critical societal concern.R.G. Smith, L.W. Atwood, A.B. Daly, and A.S. Grandy, Dep. of Natural Resources and the Environment, Univ. of New Hampshire, Durham, NH 03824; A.S. Davis, USDA-ARS Global Change and Photosynthesis Research Unit, Urbana, IL 61801; N.R. Jordan and P. Ewing, Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN 55108; M.C. Hunter, and D.A. Mortensen, Dep. of Plant Science, The Pennsylvania State Univ., University Park, PA 16802; R.T. Koide, Dep. of Biology, Brigham Young Univ., Provo, UT 84602; D. Kane and S.S. Snapp, Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI 48824; M. Li, Dep. of Crop Sciences, Univ. of Illinois, Urbana, IL 61801; Y. Lou and A.C. Yannarell, Dep. of Natural Resources and Environmental Sciences, Univ. of Illinois, Urbana, IL 61801; K.A. Spokas, USDA-ARS Soil and Water Management Research Unit, St. Paul, MN 55108. Received 19 July 2013. *Corresponding author (richard.smith@unh.edu).

Diversification of agroecological systems to enhance agrobiodiversity is likely to be critical to advancing environmental, economic, and social sustainability of agriculture. Temperate-zone agroecological systems that are currently organized for production of summer-annual crops can be diversified by integration of fallow-season and perennial crops. Integration of such crops can improve sustainability of these agroecological systems, with minimal interference with current agricultural production. Importantly, these crops can provide feedstocks for a wide range of new bio-products that are forming a new agricultural bioeconomy, potentially providing greatly increased economic incentives for diversification. However, while there are many fallow-season and perennial crops that might be used in such a “bioeconomic” strategy for diversification, most are not yet well adapted and highly-marketable. Efforts are underway to enhance adaptation and marketability of many such crops. Critically, these efforts require a strategic approach that addresses the inherent complexity of these projects. We outline a suitable approach, which we term “sustainable commercialization”: a coordinated innovation process that integrates a new crop into the agriculture of a region, while intentionally addressing economic, environmental and social sustainability challenges via multi-stakeholder governance. This approach centers on a concerted effort to coordinate and govern innovation in three critical areas: germplasm development, multifunctional agroecosystem design and management, and development of end uses, supply chains, and markets. To exemplify the approach, we describe an ongoing effort to commercialize a new fallow-season crop, field pennycress (Thlaspi arvense L.).

There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating decimetre-scale spatial and temporal heterogeneity, SFZM attempts to foster greater soil biodiversity and integrate complementary soil processes at the sub-field level. Such integration maximizes soil services by creating zones of ‘active turnover’, optimized for crop growth and yield (provisioning services); and adjacent zones of ‘soil building’, that promote soil structure development, carbon storage and moisture regulation (regulating and supporting services). These zones allow SFZM to secure existing agricultural productivity while avoiding or minimizing trade-offs with soil ecosystem services. Moreover, the specific properties of SFZM may enable sustainable increases in provisioning services via temporal intensification (expanding the portion of the year during which harvestable crops are grown). We present a conceptual model of ‘virtuous cycles’, illustrating how increases in crop yields within SFZM systems could create self-reinforcing feedback processes with desirable effects, including mitigation of trade-offs between yield maximization and soil ecosystem services. Through the creation of functionally distinct but interacting zones, SFZM may provide a vehicle for optimizing the delivery of multiple goods and services in agricultural systems, allowing sustainable temporal intensification while protecting and enhancing soil functioning.