Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils.

Background: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils. Results: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs. Conclusions: We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.

Distinct, direct and climate-mediated environmental controls on global particulate and mineral-associated organic carbon storage.

Identifying controls on soil organic carbon (SOC) storage, and where SOC is most vulnerable to loss, are essential to managing soils for both climate change mitigation and global food security. However, we currently lack a comprehensive understanding of the global drivers of SOC storage, especially with regards to particulate (POC) and mineral-associated organic carbon (MAOC). To better understand hierarchical controls on POC and MAOC, we applied path analyses to SOC fractions, climate (i.e., mean annual temperature [MAT] and mean annual precipitation minus potential evapotranspiration [MAP-PET]), carbon (C) input (i.e., net primary production [NPP]), and soil property data synthesized from 72 published studies, along with data we generated from the National Ecological Observatory Network soil pits (n = 901 total observations). To assess the utility of investigating POC and MAOC separately in understanding SOC storage controls, we then compared these results with another path analysis predicting bulk SOC storage. We found that POC storage is negatively related to MAT and soil pH, while MAOC storage is positively related to NPP and MAP-PET, but negatively related to soil % sand. Our path analysis predicting bulk SOC revealed similar trends but explained less variation in C storage than our POC and MAOC analyses. Given that temperature and pH impose constraints on microbial decomposition, this indicates that POC is primarily controlled by SOC loss processes. In contrast, strong relationships with variables related to plant productivity constraints, moisture, and mineral surface availability for sorption indicate that MAOC is primarily controlled by climate-driven variations in C inputs to the soil, as well as C stabilization mechanisms. Altogether, these results demonstrate that global POC and MAOC storage are controlled by separate environmental variables, further justifying the need to quantify and model these C fractions separately to assess and forecast the responses of SOC storage to global change.

Cover Crop Cultivar, Species, and Functional Diversity is Reflected in Variable Root Exudation Composition.

Cover cropping has emerged as a sustainable alternative to traditional crop rotational practices, yet the effects of variable root exudation from cover crop species and cultivars within species remains unclear. Here, we assess the chemical heterogeneity of root exudates from 16 commonly used cover crop species as well as 3 distinct cultivars of hairy vetch. Plants were grown hydroponically and analyzed via nontargeted gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), and targeted LC-MS/MS to evaluate patterns in root exudate composition across species and functional plant type. Overall, root exudation profiles are heterogeneous across crop species and cultivars. Species within legumes stand out as a unique functional group of plants capable of producing distinct chemical environments rich with complex secondary metabolites, such as triterpenoid saponins (soyasaponins), isoflavonoids, and flavonoids.

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function.

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.

Deficit irrigation impacts on greenhouse gas emissions under drip-fertigated maize in the Great Plains of Colorado.

Precise water and fertilizer application can increase crop water productivity and reduce agricultural contributions to greenhouse gas (GHG) emissions. Regulated deficit irrigation (DI) and drip fertigation control the amount, location, and timing of water and nutrient application. Yet, few studies have measured GHG emissions under these practices, especially for maize (Zea mays L.). The objective was to quantify N2 O and CO2 emission from DI and full irrigation (FI) within a drip-fertigated maize system in northeastern Colorado. During two growing seasons of measurement, treatments consisted of mild, moderate, and extreme DI and FI. Deficit irrigation was managed based on growth stage so that full evapotranspiration (ET) was met during the yield-sensitive reproductive stage, but less than full crop ET was applied during the late vegetative and maturation growth stages. In the first year, mild DI (90% ET) reduced N2 O emissions by 50% compared with FI. In the second year, compared with FI, moderate DI (69-80% ET) reduced N2 O emissions by 15%, and extreme DI (54-68% ET) reduced N2 O emissions by 40%. Only extreme DI in the second year significantly reduced CO2 emissions (by 30%) compared with FI. Mild DI reduced yield-scaled emissions in the first year, but moderate and extreme DI had similar yield-scaled emissions as FI in the second year. The surface drip fertigation resulted in total GHG emissions that were one-tenth of literature-based measurements from sprinkler-irrigated maize systems. This study illustrates the potential of DI and drip fertigation to reduce N2 O and CO2 emissions in irrigated cropping systems.

COVID-19 and the agri-food system in the United States and Canada.

Agri-food supply chains in North America have become remarkably efficient, supplying an unprecedented variety of items at the lowest possible cost. However, the initial stages of the COVID-19 pandemic and the near-total temporary loss of the foodservice distribution channel, exposed a vulnerability that many found surprising. Instead of continued shortages, however, the agri-food sector has since moved back to near normal conditions with prices and production levels similar to those typically observed in years prior to the pandemic. Ironically, the specialization in most food supply chains designed for "just-in-time" delivery to specific customers with no reserve capacity, which led to the initial disruptions, may have also been responsible for its rapid rebound. A common theme in assessing the impacts across the six commodities examined is the growing importance of understanding the whole supply chain. Over the longer term, a continuation of the pandemic could push the supply chain toward greater consolidation of firms and diversification of products given the increasing option value of maintaining flexibility. Other structural changes will be felt through input markets, most notably labour, as the trend toward greater automation will continue to accelerate as a response to meeting concerns about a consistent supply of healthy and productive workers. The economic fall out from the pandemic may lead to greater concentration in the sector as some firms are not able to survive the downturn and changes in consumer food buying behaviour, including movement toward online shopping and enhanced demand for attributes associated with resiliency, such as local. On the other hand, online shopping may provide opportunities for small producers and processors to shorten supply chains and reach customers directly. In the long term, COVID-19 impacts on global commerce and developing country production are more uncertain and could influence poverty reduction. While COVID-19's impacts on North American agriculture should have minimal effect on the Sustainable Development Goals (SDGs) through food prices, the ongoing global trends in trade and agribusiness accelerated by the pandemic are relevant for achievement of the SDGs.

Management of cover crops in temperate climates influences soil organic carbon stocks: a meta-analysis.

Increasing the quantity and quality of plant biomass production in space and time can improve the capacity of agroecosystems to capture and store atmospheric carbon (C) in the soil. Cover cropping is a key practice to increase system net primary productivity (NPP) and increase the quantity of high-quality plant residues available for integration into soil organic matter (SOM). Cover crop management and local environmental conditions, however, influence the magnitude of soil C stock change. Here, we used a comprehensive meta-analysis approach to quantify the effect of cover crops on soil C stocks from the 0-30 cm soil depth in temperate climates and to identify key management and ecological factors that impact variation in this response. A total of 40 publications with 181 observations were included in the meta-analysis representing six countries across three different continents. Overall, cover crops had a strong positive effect on soil C stocks (P < 0.0001) leading to a 12% increase, averaging 1.11 Mg C/ha more soil C relative to a no cover crop control. The strongest predictors of SOC response to cover cropping were planting and termination date (i.e., growing window), annual cover crop biomass production, and soil clay content. Cover crops planted as continuous cover or autumn planted and terminated led to 20-30% greater total soil C stocks relative to other cover crop growing windows. Likewise, high annual cover crop biomass production (>7 Mg·ha-1 ·yr-1 ) resulted in 30% higher total soil C stocks than lower levels of biomass production. Managing for greater NPP by improving synchronization in cover crop growing windows and climate will enhance the capacity of this practice to drawdown carbon dioxide (CO2 ) from the atmosphere across agroecosystems. The integration of growing window (potentially as a proxy for biomass growth), climate, and soil factors in decision-support tools are relevant for improving the quantification of soil C stock change under cover crops, particularly with the expansion of terrestrial soil C markets.

Science-graphic art partnerships to increase research impact.

Graphics are becoming increasingly important for scientists to effectively communicate their findings to broad audiences, but most researchers lack expertise in visual media. We suggest collaboration between scientists and graphic designers as a way forward and discuss the results of a pilot project to test this type of collaboration.

Managing nitrogen through cover crop species selection in the U.S. mid-Atlantic.

Cover crops have the potential to be agricultural nitrogen (N) regulators that reduce leaching through soils and then deliver N to subsequent cash crops. Yet, regulating N in this way has proven difficult because the few cover crop species that are well-studied excel at either reducing N leaching or increasing N supply to cash crops, but they fail to excel at both simultaneously. We hypothesized that mixed species cover crop stands might balance the N fixing and N scavenging capabilities of individual species. We tested six cover crop monocultures and four mixtures for their effects on N cycling in an organically managed maize-soybean-wheat feed grain rotation in Pennsylvania, USA. For three years, we used a suite of integrated approaches to quantify N dynamics, including extractable soil inorganic N, buried anion exchange resins, bucket lysimeters, and plant N uptake. All cover crop species, including legume monocultures, reduced N leaching compared to fallow plots. Cereal rye monocultures reduced N leaching to buried resins by 90% relative to fallow; notably, mixtures with just a low seeding rate of rye did almost as well. Austrian winter pea monocultures increased N uptake in maize silage by 40 kg N ha-1 relative to fallow, and conversely rye monocultures decreased N uptake into maize silage by 40 kg N ha-1 relative to fallow. Importantly, cover crop mixtures had larger impacts on leaching reduction than on maize N uptake, when compared to fallow plots. For example, a three-species mixture of pea, red clover, and rye had similar maize N uptake to fallow plots, but leaching rates were 80% lower in this mixture than fallow plots. Our results show clearly that cover crop species selection and mixture design can substantially mitigate tradeoffs between N retention and N supply to cash crops, providing a powerful tool for managing N in temperate cropping systems.

Climate Change Impacts on Yields and Soil Carbon in Row Crop Dryland Agriculture.

Dryland agroecosystems could be a sizable sink for atmospheric carbon (C) due to their spatial extent and level of degradation, providing climate change mitigation. We examined productivity and soil C dynamics under two climate change scenarios (moderate warming, representative concentration pathway [RCP] 4.5; and high warming, RCP 8.5), using long-term experimental data and the DayCent process-based model for three sites with varying climates and soil conditions in the US High Plains. Each site included a no-till cropping intensity gradient introduced in 1985, with treatments ranging from wheat-fallow ( L.) to continuous annual cropping and perennial grass. Simulations were extended to 2100 using data from 16 global circulation models to estimate uncertainty. Simulated yields declined for all crops (up to 50% for wheat), with small changes after 2050 under RCP 4.5 and continued losses to 2100 under RCP 8.5. Of the cropped systems, continuous cropping had the highest average productivity and soil C sequestration rates (78.1 kg C ha yr from 2015 to 2045 under RCP 4.5). Any increase in soil C for cropped rotations was realized by 2050, but grassland treatments increased soil C (up to 69%) through 2100, even under RCP 8.5. Our simulations indicate that reduced frequency of summer fallow can both increase annualized yields and store more soil C. As evapotranspiration is likely to increase, reducing fallow periods without live vegetation from dryland agricultural rotations may enhance the resilience of these systems to climate change while also increasing soil C storage and mitigating carbon dioxide emissions.