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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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Suggested Citation:"5 Soils." National Academies of Sciences, Engineering, and Medicine. 2018. Science Breakthroughs to Advance Food and Agricultural Research by 2030. Washington, DC: The National Academies Press. doi: 10.17226/25059.
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5 Soils 1. INTRODUCTION Fertile soils are among the greatest natural assets of the U.S. agricultural system. These include highly productive types of soils (e.g., mollisols and alfisols) that cover more than 30 percent of the coun- try (USDA, 1999; see Figure 5-1). The importance of maintaining the nation’s agricultural soils cannot be overstated: Soils are the basis of the nation’s capacity to produce unparalleled crop yields and bountiful pasturelands, and for all practical purposes, are a finite resource. Soil formation is a slow, primarily geo- logical process augmented by activity of biota living in soil, with formation rates in the productive U.S. heartland averaging a little over one-tenth of a millimeter per year (Cruse et al., 2013). Many agricultural and other land-use practices cause physical, biological, and chemical degradation of soil that weakens its ability to support plant life and to provide ecosystems services. These conditions exacerbate the negative effects of weather and climate on soil stability and quality and contribute to water and air pollution (NRC, 2010; ITPS, 2015; NSTC, 2016). Future agricultural productivity to meet the needs of a growing world population can be possible only if the nation’s fertile soils are maintained, which mandates protecting soils from erosion and degradation and efficiently managing vital crop nutrients. FIGURE 5-1 Dominant Soil Orders of the United States. SOURCE: USDA NRCS, 1999. 70 Prepublication Copy

Soils The capacity for soils to support crop production and buffer the environment against perturbations such as climate change, drought, flood, and environmental pollution are a result of the ongoing, sophisti- cated interplay of their physical, chemical, and biological components. As agricultural production intensi- fies, an advanced understanding of these dynamics under different management regimes and weather conditions is critical. This advanced understanding will require (1) the development and use of sensing technologies, biological strategies, and integrated systems approaches to maintain depth and quality of existing fertile soils and restoration of degraded soils; (2) the combined use of novel sensing technologies, data analytics, precision plant breeding, and land management practices that significantly increase and optimize nutrient-use efficiency; and (3) supporting a healthy soil microbiome, which is instrumental to a wide range of soil ecosystem services including nutrient production and bioavailability, breakdown of toxicants, and resilience to pests, pathogens, and other stressors such as climate variability and drought. This chapter describes a vision for a research strategy that will enable producers to sustain and enhance soil vitality for food production. 2. CHALLENGES America’s soils require stewardship. Threats to soil and consequently to food productivity fall into three broad categories: (1) soil sustainability, (2) soil quality, and (3) nutrient availability. The future for a vibrant, resilient U.S. food production enterprise depends on understanding and taking action to address these threats. 2.1 Soil Sustainability A primary challenge facing soil sustainability in the United States is erosion, a form of soil degrada- tion that causes the displacement of the upper layers of soil by wind and water. Although soil erosion oc- curs under natural conditions, human activity on the land accelerates that process. Some agricultural prac- tices, including conventional tillage, allowing cleared soil to remain uncovered, crop specialization (e.g., monoculture) with limited rotations or diversity, overuse of pesticides and fertilizers, and poor irrigation management are associated with soil erosion and the breakdown of soil structure relative to the rate of soil formation (NRC, 2010; ITPS, 2015; NSTC, 2016). Extreme weather events and associated flooding fur- ther erode soil (Nearing et al., 2004). Erosion not only displaces soil, but it also depletes soil organic matter (SOM) and reduces soil quali- ty, fertility, and water-holding capacity (Magdoff and van Es, 2009) and thus reduces crop yields (den Biggelaar et al., 2004; Fenton et al., 2005). The results can be costly, with estimates ranging from hun- dreds of millions (Crosson, 2007) to tens of billions of dollars in the United States alone (Pimentel et al., 1995). Globally, erosion and the degradation of soil quality has led to the abandonment of approximately one-third of the world’s arable land (UNCCD, 2017). Soil loss and erosion is not a new challenge, but has not yet been sufficiently addressed. Effective approaches to reduce soil erosion include no-till techniques; use of perennial, sod-forming crops; and use of cover crops (Montgomery, 2007; Magdoff and van Es, 2009). However, adoption of soil conservation practices are not widespread in the United States. In the United States alone, soil on cultivated cropland is estimated to be eroding at an average annual rate of ~2- 5 tons/acre, with some regions losing soil at even greater rates, especially following severe weather events (Handelsman and Liautaud, 2016). However, the annual rate of soil formation is only on the order of 0.1 to 0.5 ton/acre. In the 1950s the United States developed guidelines for “tolerable” soil loss (Montgom- ery, 2007), but given the slow rate of soil formation, these guidelines with respect to long-term soil sus- tainability are under question. Without coordinated action, it has been posited that the United States is on track to run out of topsoil before the end of the 21st century (Handelsman and Liautaud, 2016). Prepublication Copy 71

Science Breakthroughs to Advance Food and Agricultural Research by 2030 2.2 Soil Health The degradation of soil health1 is caused by a wide range of interacting agricultural and nonagricul- tural factors. These include loss of nutrients and soil organic carbon through erosion and contamination through overuse of pesticides and fertilizers, increased salinization and acidification (NRC, 2010), and biologically by increases in soil-borne pathogens. A key component of a healthy, fertile soil is soil organic carbon (SOC)—the major component of SOM—that serves as a key nutritional resource for plants and microbes. Although Earth's soils are a rich reservoir of carbon, with twice the amount of carbon than is held in the atmosphere and more than three times the amount of carbon held in vegetation, current agricultural practices have a predominantly detri- mental impact on SOC. Intensive tillage practices cause declines of SOC stocks due to oxidation of or- ganic matter, destruction of soil aggregates, and reduction in water infiltration (Olson et al., 2014a). Cul- tivation has been shown to significantly reduce SOC stocks by 30 perecent when tilling native prairie and forest soils of the north-central United States (Lal, 1999). Loss of SOC due to erosion is more pronounced on sloping land areas, due to drainage from the soil. SOC stocks declines are also predicted to be exacer- bated by climate change with severe implications for future agricultural productivity (Weismeir et al., 2016). Although agricultural expansion has resulted in modest increases of SOC in naturally infertile areas through practices such as liming, weed control and fertilizer application (Spera et al., 2016), the potential to restore lost SOC is limited for most agricultural areas. Sanderman et al. (2017) estimated a global car- bon debt due to agriculture of 116 Pg C for the top 2 m of soil, with the rate of loss increasing over the past 200 years. These losses are similar to carbon losses from vegetation due to deforestation. Hotspots for SOC loss are found in most major cropping regions and grazing lands around the world, including in the United States (see Figure 5-2). The prevalence of diseases causing soilborne pathogens (seedling, vascular, and root rot diseases) is another important dimension of soil health. Disease contributes heavily to crop losses. The persistence of disease-causing pathogens is influenced by abiotic and biotic soil components and by agricultural practic- es (such as irrigation, tillage, and fertilization). Some management practices, such as crop rotation, have been shown to help avoid pathogen selection (Katan, 2017). In degraded soils or under continuous mono- culture practices the beneficial members of the rhizosphere community are sometimes unable to maintain a biological barrier to pathogens that thrive as a result (Lal, 2004; Busby et al., 2017). 2.3 Nutrient Availability Nutrient availability in adequate amount, time, and place is key to success for any agricultural pro- duction system. Farmers rely heavily on chemical fertilizers to provide key plant macro- and micronutri- ents. Together with improved plant genetics, fertilizer use has generated enormous increases in crop productivity in recent decades. Unfortunately, continued dependence on chemical fertilizers to provide essential nutrients is unsustainable. The use of chemical fertilizers is causing well-documented negative consequences for the environment, including eutrophication, groundwater contamination, soil acidifica- tion, soil biodiversity loss, and the buildup of chemicals toxic to humans and animals (NRC, 2010). The amount of nutrients naturally present in soils varies widely, and generally is insufficient to sup- port high demands of crop production. For example, nitrogen, which is widely available in the atmosphere but more limited in soil, frequently becomes the first nutrient constraint on crop production (Lal and Stewart, 2017). The Haber-Bosch process has enabled the production of synthetic nitrogen fertilizer from atmospheric nitrogen (N2) (Erisman et al., 2008). Overreliance and excessive application of synthetic ni- 1 Also referred to as soil quality, soil health is the capacity of soils to function as living systems, with ecosystem and land use boundaries, to sustain plant and animal productivity, maintain or enhance water and air quality, and promote plant and animal health (FAO, 2008). 72 Prepublication Copy

Soils trogen to ensure sufficient nitrogen supply for crops has, however, led to a significant reduction in global nitrogen-use efficiency (NUE),2 from 68 percent in the 1960s to below 50 percent today (Lassaletta et al., 2014). Nitrogen is highly mobile in soils, and hence any amount applied that exceeds the crop uptake re- sults in its loss. Too little nitrogen application leads to lower crop productivity, world hunger and malnu- trition, and soil degradation (Sanchez and Swaminathan, 2005; Zhang et al., 2015; Lal and Stewart, 2017). Applying too much nitrogen results in environmental pollution and in the subsequent negative im- pacts on ecosystem health and human health (Jerett et al., 2009; Avnery et al., 2011; Robertson et al., 2013; Zhang et al., 2015). Low NUE accounts for significant economic and environment loss, human health impacts, and a contribution of over 67 percent of the N2O emissions into the atmosphere. Many estimate that current levels of nitrogen fertilizer use have far exceeded the planetary boundaries (de Vries et al., 2013; Steffen et al., 2015), leading to increased calls for precision approaches to improve NUE. FIGURE 5-2 Global distribution of cropping and grazing in 2010. A. Color gradients indicate proportion of land use for crop production (red) and grazing (green) B. Histogram of SOC loss (Mg C ha-ah geez1), with positive values indicating loss and negative values indicating gains in SOC. SOURCE: Sanderman et al., 2017. 2 Nitrogen-use efficiency is defined as the ratio between the amount of fertilizer nitrogen removed from the field by the crop and the amount of fertilizer nitrogen applied (Saravia et al., 2016). Prepublication Copy 73

Science Breakthroughs to Advance Food and Agricultural Research by 2030 Phosphorus is another essential nutrient for plant growth. However, the amount of phosphorus natu- rally present in soil varies. To compensate for deficiencies in bioavailable soil phosphorus, rock phos- phate is normally applied to soil as fertilizer. There is growing concern among some experts that world- wide stock of rock phosphate is rapidly depleting (Gilbert, 2009). As a result, advanced approaches to reuse phosphorus in waste products such as sewage sludge and manure will be critically important along- side the implementation of precision management practices that reduce the application of fertilizer. Rock phosphate is also a source of environmental contaminants such as cadmium, lead, chromium, nickel, manganese, and copper, which are toxic to soil, animal, and human health (Faridullah et al., 2017). The tendency to over apply phosphorus (and other nutrients) to compensate for insufficient bioavailability of the individual nutrient components exacerbates negative environmental impacts. Phosphorus in fertilizer often binds with soil minerals so that it becomes unavailable to plants or is lost through runoff. Depend- ing on land use and management practice, such runoff losses are as high as 42 percent (Hart et al., 2004), and upon reaching aquatic systems can result in environmental degradation due to eutrophication. Continued reliance on chemical fertilizers as the dominant source of nutrients threatens the vitality of the soils on which agriculture relies and the long-term sustainability of the agricultural enterprise. Change will require new advances in identifying less harmful sources of nutrients, new approaches to im- prove the bioavailability of nutrients, and new mechanisms to recycle nutrients such as phosphorus from waste streams. These new sources and approaches are likely to enhance fertilizer use efficiency if accom- panied by determining the “right” approaches of what, when, where, how much, and how fertilizers are applied. 3. OPPORTUNITIES From the perspective of the sustainable uses of soil, the objective is to keep soil healthy, in places where it is needed, and to maximize its ability to provide essential goods and services, whether that is in crop production, water filtration, or carbon sequestration. An understanding of those processes, including the role of the soil microbiome in them, could help inform management of the status of the soil resource. Novel tools are emerging to probe, measure, monitor, and analyze soil and its characteristics in all of its complexity, from the molecular level to the ecosystem scale. Such tools, coupled with new approaches to farmer engagement and technology adoption, will enable both scientists and the farming community to sustainably maximize the benefits of soil resources. 3.1 Leveraging Advances in Microelectronics, Sensing, and Modeling Soil ecosystems are marked by chemical, biological, and physical reactions that are affected by ex- ternal perturbations such as weather or tillage, and the changes caused by these forces on soils have been documented over time. However, “visualizing” dynamic soil processes in real time has been an elusive goal in soil science, much less acquiring that information from a wide range of locations and under differ- ent environmental conditions and a diversity of management practices. Now, achieving that goal has the potential to become a reality, if the scientific community can facilitate the convergence of several fields of science and technology to build the tools that can enable this capability. With progress in wireless communications and the miniaturization of electronic devices, coupled with advances in chemical, molecular, and optics signaling platforms, it is now possible to conceive of networks of sensor arrays positioned in situ on and below the soil surface across a farm field—potentially across many farm fields—that would actively measure the biological, chemical, and physical reactions taking place in the soil. These advances will provide the potential to acquire data about soils (erosion, moisture, nutrient content, biological activity, etc.) at the temporal and spatial resolution that are needed to inform improved models of soil ecosystems and to enable implementation of site-specific management practices that reverse soil and nutrient loss. In the specific case of soil erosion, there is an opportunity to integrate high-resolution remote sensing, GPS, and GIS to survey soils and identify areas where soil loss- es are in need of specific conservation practices (Sahu et al., 2015). For example, fusion of high- 74 Prepublication Copy

Soils resolution LISS III and PAN satellite imagery was used to make decisions about vegetative barriers to prevent soil erosion and to preserve soil moisture. Tiwari (2004) suggested bioengineering measures to reduce soil loss in areas of high to very high risk of soil erosion. Application of sensor arrays, in situ and remote, would transmit data wirelessly to receiving devices aboveground, connected to computers for collation and analysis of the data collected. Next-generation sensors, when fully developed and integrated into improved data decision models, will revolutionize our capability to deploy solutions in near real time and, in many cases prior to the visible damage to plants (i.e., when they are asymptomatic), For example: georeferenced in situ soil sensors widely distributed across a farm may provide a measure of soil and plant nutrient status as a colored geospatial map, allow- ing farmers to site-specifically and variably apply nutrients, optimize inputs, and maximize output (Koch et al., 2004). Having this kind of information would vastly expand fundamental knowledge about the drivers of soil dynamics. A better understanding of those dynamics in relation to crop production could give rise to actionable information for farmers, with the detail, speed, and affordability that currently do not exist. In the most expansive form envisioned, networks of arrays would produce high-resolution maps of biogeo- chemical activity—essentially, a dynamic “weather map” for the soils across the nation that would fill a missing gap in models of nutrient cycling, greenhouse gas production, and carbon storage. 3.2 Leveraging Advances in Soil Microbiology, Omics, Synthetic Biology, and Computational Biology to Harness Beneficial Properties of the Soil Microbiome Soils have an incredible diversity of microbial life (Thompson et al., 2017), with billions of micro- bial cells and thousands to millions of taxa per gram (Torsvik et al., 2002; Knietch et al., 2003; Gans et al., 2005; Roesch et al., 2007; Jansson, 2011). Several soil microorganisms have previously been shown to improve plant growth, through growth stimulation, nutrient provision, or through disease suppression (Toyoto and Watanabe, 2013; Bhardwaj et al., 2014; Courty et al., 2015; de Souza et al., 2015; Mus et al., 2016; Baez-Rogelio et al., 2017; Gupta et al., 2017). However, the vast majority of soil microbes and their potential beneficial functions remain to be discovered. Therefore, an opportunity is to gain a better understanding of this rich resource of soil microbial biodiversity and to exploit beneficial functions of the soil microbiome to not only optimize crop productivity, but also to provide other beneficial ecosystem services, such as sequestration of organic carbon and increasing water retention. Greater understanding of the diversity and importance of microbes individually and collectively is now emerging, owing in part to the research field and tools of metagenomics3 and associated omics tech- nologies (Biteen et al., 2016). These omics data have the potential to be leveraged to inform the develop- ment and design of new microbial products, including combinations of microorganisms (consortia) that might be more resilient to environmental stress, as components of targeted biofertilizer and biocontrol formulations. A specific example is to exploit the ability of arbuscular mycorrhizal fungi and associated bacteria to mobilize and increase the bioavailability of soil phosphorus to plants (Hinsinger et al., 2015). Another opportunity is to use synthetic biology approaches for custom design of rhizosphere microbiomes that are optimally suited to enhance productivity of a specific crop under a given soil type and climate regime (Busby et al., 2017). In addition, by exploration of the omics data generated from soil microbi- omes, there is the opportunity to use this knowledge to exploit and custom-design microbial species and enzymes for new processes, such as new pathways for affordable and sustainable nitrogen fertilizer pro- duction (Liu et al., 2017). 3 Metagenomics is a field of science that involves genome-level characterization and understanding of microbes and their communities, through high-throughput studies that incorporate methods from genomic and other omics studies (NRC, 2007). Prepublication Copy 75

Science Breakthroughs to Advance Food and Agricultural Research by 2030 Finally, research is currently under way to elucidate the “metaphenome” of the soil microbiome, that is, the functions carried out, or phenotypes, of the microbiome, as a totality of the genetic expression of the collective microorganisms, in response to environmental conditions and available resources (Jansson and Hofmockel, 2018). By examining how the physiology, metabolism, and interactions of the soil mi- crobiome change in response to a perturbation, such as moisture, investigators hope to develop predictive models of the microbiomes’ behavior and state. This research will be an important dovetail with other new powerful methods of measuring the collective environmental response of the soil at higher scales. In summary, this opportunity will build on the convergence of soil microbiology, metagenomics and other omics, synthetic biology, and computational biology, together with advances in more traditional disciplines, including microbial physiology, fermentation, and formulation of seed/soil inoculants. The committee notes the recent publication of opportunities for microbiome research across differ- ent agencies in the United States that is much in line with our own recommendations, Interagency Strate- gic Plan for Microbiome Research, FY2018-2022 (MIWG, 2018). This plan included a strategy for ma- nipulating the soil/plant microbiome to increase crop productivity, with specific recommendations to advance knowledge of the microbiome, including determining their functions and how they contribute to soil sustainability. It is too early to judge the success of this unified strategy; however, the committee supports the call for increased funding in microbiome science to support these potentially important ad- vances in knowledge. 3.3 Integrating Social Sciences on Technology Adoption and Farmer Engagement into Soil Health Research Research on soil loss and sustainability is fairly advanced. Some of the existing transformative tools and practices that better protect soils include reduced, modified, or no-tillage methods (also called “con- servation tillage”), crop rotations, use of cover crops; split application of fertilizer; dripline irrigation, and controlled or slow release of nutrients. Most of these methods not only prevent or reduce soil loss and degradation, but also have other environmental benefits such as carbon sequestration (Bernoux et al., 2006; Lal et al., 2007; Olson et al., 2014b; Poeplau and Don, 2015) and economic benefits, such as reduc- ing costs of labor and production (Allmaras and Dowdy, 1985; Mitchel et al., 2009; Vitale et al., 2011). Pairing known methods to reduce soil loss with site-specific soil sensors and models has the potential to become a powerful breakthrough approach to addressing erosion. However, U.S. farmers have not been successful in adopting some, much less all, of these soil conservation approaches (Mitchell et al., 2007; Bossange et al., 2016; Carlisle, 2016; Ulrich-Schad et al., 2017). The development of near-term technolo- gy and best management practices will require convergence of agronomy and social science research on technology adoption and farmer engagement. A variety of factors influence the adoption of new technology and approaches to land management specifically regarding soils (e.g., reduced-till strategies and higher precision fertilization practices). Re- search suggests that the most prominent barriers include economics (affordability of new tools, labor, or change in methods), education (availability and accessibility of learning resources), social networks (community support networks to facilitate technology adoption), and farmer perceptions about the bene- fits of adopting new approaches. Carlisle (2016) provides a comprehensive review of research on each these barriers and emphasizes that their influence on farmer decision-making vary according to geograph- ic, economic, and social contexts. A missing element, however, is research on engagement – involving farmers in development of tools and methods that reduce soil loss and promote soil health, and in the de- velopment of education and policy incentives to support technology adoption. Research on effective en- gagement strategies for the introduction of new technologies is rapidly expanding (Kleinman et al., 2007; Nisbet et al., 2009; Philbrick and Barandiaran, 2009; Sclove, 2010; Rask and Worthington, 2015). Bring- ing the science of engagement into research on and development of strategies that encourage technology adoption opens new opportunities for addressing the suite of challenges associated with soil loss and deg- radation. 76 Prepublication Copy

Soils 4. GAPS We currently lack the essential knowledge required to manage agricultural soil ecosystems to obtain their full potential. Recognition that soil’s geophysical dimensions are highly influenced by its living components has brought to the forefront a need for better understanding of the interplay of soil’s biologi- cal attributes with its physical and chemical components. Major knowledge gaps to be filled include the following. 4.1 Influence of Cropping Systems and Amendments on Soil Properties Sufficient understanding of the physical and chemical properties of soil at appropriate temporal and spatial scales to model, manage, and predict changes in agricultural soil ecosystems is needed. In addi- tion, better information is needed on how different cropping systems and amendments, such as manure, influence the soil texture, water storage capacity, resistance to erosion, and SOM retention. We also need understanding of the interactions between soil physical, chemical, and biological properties and the ability of the soil microbiome to facilitate soil aggregation and soil carbon retention. 4.2 Interactions Between Soil Ecosystems, Nutrient Bioavailability, and Crop Productivity SOM pools can provide significant amount of nutritional needs, (particularly mineral nitrogen needs) of the crop throughout the growing season. However, there are no reliable techniques to quantify and account for nitrogen supplied to the crop from mineralization of SOM. A better understanding is needed of nutrient distribution in space, time, and depth and how it contributes to crop nutritional needs, particularly mineral nitrogen needs throughout the growing season. Better information on the role of the microbiome with respect to nutrient cycling; including increasing nitrogen-use efficiency, increasing bio- availability of soil phosphorus, and cycling of SOM is needed. In addition, a better molecular-level under- standing is needed of soil biogeochemistry and the influence of specific enzymes, metabolites, and signal- ing molecules on crop productivity. 4.3 Interactions Between Soil Ecosystems and Climate Climate change will impact soil organic carbon flux to the atmosphere and cycling of other nutri- ents. Although these functions are vitally important for plant growth and sustainability of life on our plan- et, the mechanistic details are largely unknown. Currently, studies of bulk processes involved in organic carbon turnover in soil, such as decomposition and respiration, reflect the sum of myriads of specific met- abolic processes carried out by interacting members of the soil community. An understanding is needed of the biogeochemical pathways involved in SOC decomposition and greenhouse gas emission, and how changes in environmental conditions influence those processes. Ultimately, this knowledge can lead to better management practices for sequestering soil SOC and preventing carbon loss from the system. 5. BARRIERS TO SUCCESS 5.1 Insufficient Tools and Techniques to Measure, Model, and Manage Soil Ecosystem Services Carried Out by the Soil Microbiome Because of the high physical heterogeneity and biological diversity of soils, it has been a significant challenge to obtain relevant measures of ecosystem services carried out by the soil microbiome. Current technologies are largely based on high-throughput sequencing or measures of bulk processes (such as soil respiration), and are insufficient to decode the functional relevance of the soil microbiome at relevant scales (Biteen et al., 2016; Blaser et al., 2016). Although metagenomics datasets provide a bounty of phy- logenetic and functional information, deciphering the roles of microbial genes and gene products has Prepublication Copy 77

Science Breakthroughs to Advance Food and Agricultural Research by 2030 proven to be difficult due to the high microbial diversity in soil (Blaser et al., 2016; Jansson and Hof- mockel, 2018). Also, it is challenging to generalize findings from one soil system to another because of the differences in soil characteristics, parent materials, climate, and other factors that shape soils. Thus, to fully understand, predict, and harness beneficial microbes for agricultural purposes, more research is needed across several different science disciplines, including soil microbiology and microbial ecology, combined with computational biology and advanced omics and imaging technologies. This multidiscipli- nary approach is necessary to elucidate the molecular mechanisms underpinning soil–microbe–plant in- teractions and to determine how to optimize beneficial interactions to improve agricultural production. 5.2 Limited Development and Deployment of Modern Sensor Technologies to Assess Soil Properties Across Different Scales of Resolution Sensors have been deployed for decades to measure parameters of interest in agriculture, for exam- ple, sensing soil moisture to decide the time to irrigate crops or monitoring weather for crop planting. Many of these sensing methodologies, however, provide only a point measure. Recent advances in preci- sion agriculture have brought innovative tools and implements to farmers, enabling them to manage farm inputs at a much finer scale than ever before. Currently, farmers’ ability to precision-manage is limited by their capability to precision-measure. There is a growing need to measure multiple soil and plant proper- ties at a very high frequency and data density, in heterogeneous space and time. This requires develop- ment of novel active and passive sensors that provide diagnostic measures of soil and crop properties of interest rapidly, reliably, nondestructively, in situ, in motion, and that provide near-real-time information to farmers and scientists to increase efficiency of farming practices. However, the development and deployment of advanced materials that can provide soil data at the molecular level or nanoscale, including biological sensors, is still in its infancy. Sensors are also needed, but have not yet been developed that (a) can be buried indefinitely in the subsurface of soil; (b) can cap- ture chemical signals that enable “imaging” of the rhizosphere; and (c) can wirelessly transmit data through the soil substrate to aboveground receivers. Depending on which process or reaction for which a measurement is sought, a chemical-biological-optical-electrical signaling platform must be devised. The sensors would need to be reliable, miniaturized, energy efficient, and of low cost, enabling them to be arranged in arrays. Such sensors might include plants themselves connected to microelectronic detection systems potentially coupled with remote sensing devices. It may also include the development and appli- cation of live microbial biosensors, for example, that are engineered using synthetic biology tools to pro- duce a recordable signal in response to specific soil nutrient levels and/or needs of the growing plant (Xu et al., 2013; Wang et al., 2017; Lindemann et al., 2017). 5.3 Lack of Soil Data Commons to Share Data, Analytical Methods, and Models There is a need to integrate and share soil physical, chemical, and biological data to harness the in- tellectual capital of scientists from multiple disciplines (from microbiology to data analytics) to translate data into meaningful knowledge. A common infrastructure with open access could be similar to the Na- tional Cancer Institute’s Genomic Data Commons4 or the Human Cell Atlas Data Coordination Platform.5 A centralized community-driven platform for depositing and sharing data does not yet exist for the soil sciences, and this holds the field back. In addition, translating data into meaningful knowledge and, ulti- mately, management decisions requires the development of computational tools that integrate models of crop nitrogen demand with soil nitrogen supply to inform decision support tools that are the basis of pre- cision agriculture. Such advances are necessary to realize the complete potential of the Five-R approach 4 See https://gdc.cancer.gov. 5 See https://www.humancellatlas.org/data-sharing. 78 Prepublication Copy

Soils for precision agriculture—having the right input, at the right time, at the right place, in the right amount, and in the right manner (Khosla, 2010). 6. RECOMMENDATIONS FOR NEXT STEPS Emerging science—including sensor engineering, data science, and microbiology—shows consider- able promise for developing advanced tools to better assess, monitor, and enhance agricultural soils. The transformation from knowledge to action will require sustained investments in research and its associated infrastructure, such as unified data sharing and analysis platforms. Also, research efforts will need to be conducted through transdisciplinary collaborations that involve not only soil scientists, but also engineers, microbiologists, ecologists, and data scientists, among others. The committee identified the following high-priority goals that, with adequate support for research, have the potential to be achieved within the next decade:  Maintain depth and health of existing fertile soils and restore degraded soils through adoption of best agronomic practices, combined with the use of new sensing technologies, biological strate- gies, and integrated systems approaches.  Significantly increase and optimize nutrient-use efficiency (especially nitrogen) through the inte- gration of novel sensing technologies, data analytics, precision plant breeding, and land manage- ment practices.  Create more productive and sustainable crop production systems by identifying and harnessing the soil microbiome’s capability to produce nutrients, increase nutrient bioavailability and im- prove plant resilience to environmental stress and disease.  Improve the transfer of technology and practices to farmers to reduce soil loss through converg- ing research in soil sciences, technology adoption, and community engagement. REFERENCES Allmaras, R. R., and R.H. Dowdy. 1985. Conservation tillage systems and their adoption in the United States. Soil & Tillage Research. 5:197-222. Avnery, S., D. L. Mauzerall, J. Liu, and L. W. Horowitz. 2011. Global crop yield reductions due to surface ozone exposure: 2. Year 2030 potential crop production losses and economic damage under two scenarios of O3 pol- lution. Atmospheric Environment 45(13):2297-2309. Baez‐Rogelio, A., Y. E. Morales‐García, V. Quintero‐Hernández, and J. Muñoz‐Rojas. 2017. Next generation of microbial inoculants for agriculture and bioremediation. Microbial Biotechnology 10(1):19-21. Bernoux M., Cerri C.C., Cerri C.E.P., Neto M.S., Metay A., Perrin A.-S., et al. 2006. Cropping systems, carbon se- questration and erosion in Brazil, a review. Agronomy for sustainable development 26:1-8. Bhardwaj, D., M. W. Ansari, R. K. Sahoo, and N. Tuteja. 2014. Biofertilizers function as key player in sustainable ag- riculture by improving soil fertility, plant tolerance and crop productivity. Microbial Cell Factories 13(1):66. Biteen, J. S., P. C. Blainey, Z. G. Cardon, M. Chun, G. M. Church, P. C. Dorrestein, S. E. Fraser, J. A. Gilbert, J. K. Jansson, R. Knight, J. F. Miller, A. Ozcan, K. A. Prather, S. R. Quake, E. G. Ruby, P. A. Silver, S. Taha, G. van den Engh, P. S. Weiss, G. C. L. Wong, A. T. Wright, and T. D. Young. 2016. Tools for the microbiome: Nano and beyond. ACS Nano 10(1):6-37. Blaser, M. J., Z. G. Cardon, M. K. Cho, J. L. Dangl, T. J. Donohue, J. L. Green, R. Knight, M. E. Maxon, T. R. Northen, K. S. Pollard, E. L. Brodie. 2016. Toward a predictive understanding of Earth’s microbiomes to ad- dress 21st century challenges. mBio 7(3):e00714-16. Bossange, A.V., Knudson, K.M., Shrestha, A., Harben, R., and J.P. Mitchell. 2016. The potential for conservation tillage adoption in the San Juaquin Valley, California: a qualitative study of farmer perspectives and opportu- nities for extension. PLoS One 11(12): e0167612. Busby, P. E., C. Soman, M. R. Wagner, M. L. Friesen, J. Kremer, A. Bennett, M. Morsy, J. A. Eisen, J. E. Leach, and J. L. Dangl. 2017. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology 15(3):e2001793. Prepublication Copy 79

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For nearly a century, scientific advances have fueled progress in U.S. agriculture to enable American producers to deliver safe and abundant food domestically and provide a trade surplus in bulk and high-value agricultural commodities and foods. Today, the U.S. food and agricultural enterprise faces formidable challenges that will test its long-term sustainability, competitiveness, and resilience. On its current path, future productivity in the U.S. agricultural system is likely to come with trade-offs. The success of agriculture is tied to natural systems, and these systems are showing signs of stress, even more so with the change in climate.

More than a third of the food produced is unconsumed, an unacceptable loss of food and nutrients at a time of heightened global food demand. Increased food animal production to meet greater demand will generate more greenhouse gas emissions and excess animal waste. The U.S. food supply is generally secure, but is not immune to the costly and deadly shocks of continuing outbreaks of food-borne illness or to the constant threat of pests and pathogens to crops, livestock, and poultry. U.S. farmers and producers are at the front lines and will need more tools to manage the pressures they face.

Science Breakthroughs to Advance Food and Agricultural Research by 2030 identifies innovative, emerging scientific advances for making the U.S. food and agricultural system more efficient, resilient, and sustainable. This report explores the availability of relatively new scientific developments across all disciplines that could accelerate progress toward these goals. It identifies the most promising scientific breakthroughs that could have the greatest positive impact on food and agriculture, and that are possible to achieve in the next decade (by 2030).

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