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Agriculture contributes nearly a quarter of global greenhouse gas (GHG) emissions, which is motivating interest in adopting certain farming practices that have the potential to reduce GHG emissions or sequester carbon in soil. The related GHG emission (including N2O and CH4) and changes in soil carbon stock are defined here as “agricultural carbon outcomes”. Accurate quantification of agricultural carbon outcomes is the basis for achieving emission reductions for agriculture, but existing approaches for measuring carbon outcomes (including direct measurements, emission factors, and process-based modeling) fall short of achieving the required accuracy and scalability necessary to support credible, verifiable, and cost-effective measurement and improvement of these carbon outcomes. Here we propose a foundational and scalable framework to quantify field-level carbon outcomes for farmland, which is based on the holistic carbon balance of the agroecosystem: Agroecosystem Carbon Outcomes = Environment (E) × Management (M) × Crop (C). Following a comprehensive review of the scientific challenges associated with existing approaches, as well as their tradeoffs between cost and accuracy, we propose that the most viable path for the quantification of field-level carbon outcomes in agricultural land is through an effective integration of various approaches (e.g. diverse observations, sensor/in-situ data, and modeling), defined as the “System-of-Systems” solution. Such a “System-of-Systems” solution should simultaneously comprise the following components: (1) scalable collection of ground truth data and cross-scale sensing of environment variables (E), management practices (M), and crop conditions (C) at the local field level; (2) advanced modeling with necessary processes to support the quantification of carbon outcomes; (3) systematic Model-Data Fusion (MDF), i.e. robust and efficient methods to integrate sensing data and models at each local farmland level; (4) high computation efficiency and artificial intelligence (AI) to scale to millions of individual fields with low cost; and (5) robust and multi-tier validation systems and infrastructures to ensure solution fidelity and true scalability, i.e. the ability of a solution to perform robustly with accepted accuracy on all targeted fields. In this regard, we provide here the detailed scientific rationale, current progress, and future research and development (R&D) priorities to achieve different components of the “System-of-Systems” solution, thus accomplishing the Environment×Management×Crop framework to quantify field-level agricultural carbon outcomes.

Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.

A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

Invasive plants can increase soil nitrogen (N) pools and accelerate soil N cycling rates, but their effect on gross N cycling and nitrous oxide (N2 O) emissions has rarely been studied. We hypothesized that perennial pepperweed (Lepidium latifolium) invasion would increase rates of N cycling and gaseous N loss, thereby depleting ecosystem N and causing a negative feedback on invasion. We measured a suite of gross N cycling rates and net N2 O fluxes in invaded and uninvaded areas of an annual grassland in the Sacramento-San Joaquin River Delta region of northern California. During the growing season, pepperweed-invaded soils had lower microbial biomass N, gross N mineralization, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification-derived net N2 O fluxes (P

Methane (CH4) is a potent greenhouse gas that is both produced and consumed in soils by microbially mediated processes sensitive to soil redox. We evaluated the classical conceptual model of peatland CH4 dynamics—in which the water table position determines the vertical distribution of methanogenesis and methanotrophy—versus an emerging model in which methanogenesis and methanotrophy can both occur throughout the soil profile due to spatially heterogeneous redox and anaerobic CH4 oxidation. We simultaneously measured gross CH4 production and oxidation in situ across a microtopographical gradient in a drained temperate peatland and ex situ along the soil profile, giving us novel insight into the component fluxes of landscape-level net CH4 fluxes. Net CH4 fluxes varied among landforms (p

Microbial transformations of nitrogen (N) largely determine whether N is retained in ecosystems via net primary productivity or lost via gaseous emissions and leaching. The controls on soil N cycling are often studied at single locales, making it difficult to predict N cycling at regional to global scales. We hypothesized that contemporary soil properties exhibit consistent relationships with instantaneous gross N cycling rates across diverse biomes that create a continuum in these properties. We measured ex situ gross N cycling rates and soil properties at 33 study sites representing five biome classifications in California including deserts, grasslands, shrublands, forest, and wetlands. Desert soils had significantly lower total N, organic carbon (C), microbial biomass N, and soil moisture as well as higher pH than all other biomes, whereas forests and wetlands had significantly lower soil nitrate (NO3−) concentrations (P

Sea level rise will change inundation regimes in salt marshes, altering redox dynamics that control nitrification - a potential source of the potent greenhouse gas, nitrous oxide (N2 O) - and denitrification, a major nitrogen (N) loss pathway in coastal ecosystems and both a source and sink of N2 O. Measurements of net N2 O fluxes alone yield little insight into the different effects of redox conditions on N2 O production and consumption. We used in situ measurements of gross N2 O fluxes across a salt marsh elevation gradient to determine how soil N2 O emissions in coastal ecosystems may respond to future sea level rise. Soil redox declined as marsh elevation decreased, with lower soil nitrate and higher ferrous iron in the low marsh compared to the mid and high marshes (P

Salt marshes currently play an important role as filters for upslope nitrogen (N) inputs. This could change in the future with sea level rise, warming and eutrophication, which are expected to favor monocultures over diverse plant communities. We explored patterns in gross N cycling, dissimilatory nitrate (NO3-) reduction to ammonium (NH4+) (DNRA), and denitrification in a salt marsh soil under two typical redox conditions (aerobic and anaerobic), and in soils under plant communities manipulated to simulate potential future composition (forb and graminoid monocultures). Natural salt marsh soils exhibited high potential gross N mineralization rates. Averaging 50.4 6 5.7 lg N g-1 d-1 under aerobic conditions; rates declined to 23.6 6 3.4 lg N g-1 d-1 under an N2 headspace. Microbial NH4+ uptake and gross nitrification together accounted for only 14 % of gross N mineralization. Nitrogen retention via DNRA and microbial uptake greatly exceeded N losses via denitrification. Gross nitrification rates were greater in the forb and graminoid monocultures than in the control. This effect may be mediated by the lower plant biomass in the monocultures than in the control, which may have reduced competition between plants and nitrifiers for NH4+. Soil NO3- concentrations and net nitrous oxide (N2O) fluxes were greatest for the forb monoculture, likely due to higher soil oxygen (O2) concentrations in these plots. Our results suggest that salt marsh soils with a diverse plant community have high potential rates of N mineralization and microbial N retention, and the establishment of forb monocultures could lead to greater ecosystem N losses.

Accurately quantifying and predicting the reactive transport of nitrate (NO3− ${{\text{NO}}_{3}}^{-}$) in hydrologic systems continues to be a challenge, due to the complex hydrological and biogeochemical interactions that underlie this transport. Recent advances related to time‐variant water age have led to a new method that probes water mixing and selection behaviors using StorAge Selection (SAS) functions. In this study, SAS functions were applied to investigate storage, water selection behaviors, and NO3− ${{\text{NO}}_{3}}^{-}$ export regimes in a tile‐drained corn‐soybean field. The natural abundance stable nitrogen and oxygen isotopes of tile drainage NO3− ${{\text{NO}}_{3}}^{-}$ were also measured to provide constraints on biogeochemical NO3− ${{\text{NO}}_{3}}^{-}$ transformations. The SAS functions, calibrated using chloride measurements at tile drain outlets, revealed a strong young water preference during tile discharge generation. The use of a time‐variant SAS function for tile discharge generated unique water age dynamics that reveal an inverse storage effect driven by the activation of preferential flow paths and mechanically explain the observed variations in NO3− ${{\text{NO}}_{3}}^{-}$ isotopes. Combining the water age estimates with NO3− ${{\text{NO}}_{3}}^{-}$ isotope fingerprinting shed new light on NO3− ${{\text{NO}}_{3}}^{-}$ export dynamics at the tile‐drain scale, where a large mixing volume and the lack of a strong vertical contrast in NO3− ${{\text{NO}}_{3}}^{-}$ concentration resulted in chemostatic export regimes. For the first time, NO3− ${{\text{NO}}_{3}}^{-}$ isotopes were embedded into a water age‐based transport model to model reactive NO3− ${{\text{NO}}_{3}}^{-}$ transport under transient conditions. The results of this modeling study provided a proof‐of‐concept for the potential of coupling water age modeling with NO3− ${{\text{NO}}_{3}}^{-}$ isotope analysis to elucidate the mechanisms driving reactive NO3− ${{\text{NO}}_{3}}^{-}$ transport. Plain Language Summary: Accurately quantifying the transport and transformation of NO3− ${{\text{NO}}_{3}}^{-}$ in hydrologic systems continues to be a challenging task. In this study, we combined water age modeling with NO3− ${{\text{NO}}_{3}}^{-}$ isotope analysis to understand how hydrological processes, microbial reactions, and management practices interact to control NO3− ${{\text{NO}}_{3}}^{-}$ loss from a tile‐drained agricultural field. While water age is an important descriptor of how water flows through hydrologic systems, NO3− ${{\text{NO}}_{3}}^{-}$ isotopes contain unique information about NO3− ${{\text{NO}}_{3}}^{-}$ sources and microbial reactions that produce, consume, and recycle NO3− ${{\text{NO}}_{3}}^{-}$ during hydrologic transport. Therefore, the coupled use of water age modeling and NO3− ${{\text{NO}}_{3}}^{-}$ isotopes provides complementary information about water flow and microbial NO3− ${{\text{NO}}_{3}}^{-}$ cycling. Results from this study show that tile discharge was fed by younger stored water flowing through big soil pores when the tile drained system was wet. Based on the measured NO3− ${{\text{NO}}_{3}}^{-}$ isotopes, we were able to discern key microbial NO3− ${{\text{NO}}_{3}}^{-}$ cycling reactions that occurred during the transport of NO3− ${{\text{NO}}_{3}}^{-}$ with water, which, in turn, provided important evidence to confirm the dominant mechanism that controls how water flows at the tile‐drain scale. Our finding suggests that combining water age modeling with NO3− ${{\text{NO}}_{3}}^{-}$ isotopes is a promising way forward for modeling coupled water and NO3− ${{\text{NO}}_{3}}^{-}$ transport. Key Points: StorAge Selection‐based water age modeling revealed a strong preference for young water and an inverse storage effect during tile discharge generationNitrate export regime was modulated by an interplay between water mixing, flow path activation, and the vertical distribution of soil nitrateCombining water age modeling with nitrate isotope analysis has the potential to improve the modeling of reactive nitrate transport [ABSTRACT FROM AUTHOR]