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At least 109 records · Page 6

Changes in microbial community and network structure precede shrub degradation in a desert ecosystem

Large-scale restoration is intended to promote ecological recovery. Improvements in plant and microbial conditions, however, may slow or even reverse in late succession. To better understand long-term restoration outcomes and underlying drivers of successional pathways, we tracked plant, bacterial and fungal, and soil conditions across a 40-year shrub plantation that was intended to stabilize desertified land in northern China. Here, we found that planted Haloxylon ammodendron shrubs developed and then subsequently became degraded after 30–40 years. Bacterial abundance and α-diversity were much higher than those of fungi, but no significant differences in composition and structure were found in different plantation ages. In contrast, the dominant taxa of fungal communities shifted from symbiotroph and saprotroph species towards pathotroph species with increased soil nutrients in the plantation chronosequence after two decades. The changes in fungal dominant species led to a transition in microbial network structure and function, with an increase in negative linkages among taxa that began in the middle stages of succession. Changes in fungal community structure had direct and indirect negative effects on shrub leaf physiology, root activity, and biomass. Our results highlight the preceding role of a breakdown in soil microbial community composition and network structure on the degradation of shrub performance in long-term desert succession. Our study emphasizes the importance of understanding soil-microbial-plant linkages on restoration outcomes, and mechanisms that can slow or reverse the recovery of ecosystems.

Bacterial and fungal community composition↗

A multi-objective optimization model for cropland design considering profit, biodiversity, and ecosystem services

More sustainable agricultural methods are needed to alleviate the decreases in biodiversity and ecosystem services that have occurred because of industrial agriculture. One such method is the inclusion of alternative crops into croplands that can support biodiversity, reduce erosion and chemical runoff, and sequester carbon in the soil. However, the question of where such crops should be planted to balance competing economic and environmental objectives remains open. To this end, we develop a mixed-integer quadratically constrained program to optimize the layout of a cropland considering economic, biodiversity, greenhouse gas emissions, and water quality objectives. We include spatially varying fertilization as a decision variable in addition to crop establishment location. We further include the effect of core area and edges between different crops on biodiversity. To demonstrate the applicability of the model, we apply it to an example field, showing how the optimal cropland design changes as a decision-maker prioritizes different objectives and as edges have different impacts on biodiversity.

54 ENVIRONMENTAL SCIENCES↗

Feasibility of Formulating Ecosystem Biogeochemical Models From Established Physical Rules

Abstract To improve the predictive capability of ecosystem biogeochemical models (EBMs), we discuss the feasibility of formulating biogeochemical processes using physical rules that have underpinned the many successes in computational physics and chemistry. We argue that the currently popular empirically based approaches, such as multiplicative empirical response functions and the law of the minimum, will not lead to EBM formulations that can be continuously refined to incorporate improved mechanistic understanding and empirical observations of biogeochemical processes. Instead, we propose that EBM parameterizations, as a lossy data compression problem, can be better formulated using established physical rules widely used in computational physics and chemistry, and different biogeochemical processes can be more robustly integrated within a reactive‐transport framework. Through several examples, we demonstrate how mathematical representations derived from physical rules can improve understanding of relevant biogeochemical processes and enable more effective communication between modelers, observationalists, and experimentalists regarding essential questions, such as what measurements are needed to meaningfully inform models and how can models generate new process‐level hypotheses to test in empirical studies. Finally, while empirical models with more parameters are often less robust, physical rules‐based models can be more robust and show lower predictive equifinality, stemming from their enhanced consistency in representations of processes, interactions and spatial scaling.

54 ENVIRONMENTAL SCIENCES↗

TARP Identifying Critical Thresholds for Acute Response of Plants and Ecosystems to Water Stress at Walker Branch Watershed, 2002-2005

This dataset contains data from a manipulative field study aimed at identifying critical thresholds for acute response of plants and ecosystems to water stress (TARP) that took place at Walker Branch Watershed in Oak Ridge, Tennessee from 2002-2005 (2002-06-20 to 2005-12-16). The study used understory tents for the removal of 100% of the growing-season throughfall and stem flow, to provide data on the impact of acute drought on mechanisms responsible for growth and mortality of deciduous forest canopy trees representative of common plant functional types (Liriodendron and Quercus). Through three years of manipulation (2003, 2004 and 2005; pretreatment measurements in 2002) various measures of tree response to surface moisture deficits were recorded including root and leaf traits, plant nonstructural carbohydrates status, hourly sapflow, basal area, and periodic observations of foliar photosynthesis and conductance. Additionally, environmental data such as air and soil temperature, soil water content, and soil matric potential were recorded. This dataset contains data 16 files in comma-separate (*.csv) format. Additional metadata are provided: 16 data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

basal area↗

Representing cropping systems with the MEMS 2 ecosystem model

Abstract Croplands have been the focus of substantial investigation due to their considerable potential for sequestering carbon. Understanding the potential for soil organic carbon (SOC) sequestration and necessary management strategies will be enabled with accurate process‐based models. Accurately representing crop growth and agricultural practices will be critical for realistic SOC modeling. The MEMS 2 model incorporates a current understanding of SOC formation and stabilization, measurable SOC pools, and deep SOC dynamics and is seen as a highly promising tool to inform management intervention for SOC sequestration. Thus far, MEMS 2 has been developed to represent grasslands. In this study, we further developed MEMS 2 to model annual grain crops and common agricultural practices, such as irrigation, fertilization, harvesting, and tillage. Using four Ameriflux sites, we demonstrated an accurate simulation of crop growth and development. Model performance was strong for simulating aboveground biomass (index of agreement [d] range of 0.89–0.98) and green leaf area index (dfrom 0.90 to 0.96) across corn, soybean, and winter wheat. Good agreement with observations was also achieved for net ecosystem CO 2 exchange (dfrom 0.90 to 0.96), evapotranspiration (dfrom 0.91 to 0.94), and soil temperature (dof 0.96), while discrepancy with the available soil water content data remain (dfrom 0.14 to 0.81 at four depths to 100 cm). While we will continue model testing and improvement, MEMS 2 (version 2.14) has now demonstrated its ability to effectively simulate the growth of common grain crops and practices.

Agriculture↗

Evapotranspiration Partitioning Using Flux Tower Data in a Semi-Arid Ecosystem

Information about evapotranspiration (ET) and its components, that is, evaporation and transpiration, is crucial for a wide range of water and ecosystem management applications. However, partitioning ET into its two components is often challenging because of their spatiotemporal variabilities and lack of process understanding. This study developed a machine learning (ML) framework to shed light on ET processes and assess the relative importance of different drivers by incorporating hydrometeorology and biomass productivity variables. The Shapley Additive Explanations (SHAP) approach was applied to enhance explainability and rank the importance of ET drivers and their components. A total of 62 variables covering hydrometeorological and biomass productivity dimensions were considered from the Reynolds Creek Critical Zone Observatory (CZO) station in Idaho. The variable importance assessment identified the leading drivers individually for evaporation, transpiration and ET (soil water content for evaporation, vapour pressure deficit for transpiration and soil water content for ET). The results further highlighted the value of combining hydrometeorological and biomass productivity variables to achieve better predictability of ET processes.

54 ENVIRONMENTAL SCIENCES↗

Field–scale evaluation of ecosystem service benefits of bioenergy switchgrass

Purpose-grown perennial herbaceous species are nonfood crops specifically cultivated for bioenergy production and have the potential to secure bioenergy feedstock resources while enhancing ecosystem services. This study assessed soil greenhouse gas emissions (CO 2 and N 2 O), nitrate (NO 3 -N) leaching reduction potential, evapotranspiration (ET), and water-use efficiency (WUE) of bioenergy switchgrass (Panicum virgatum L.) in comparison to corn (Zea mays L.). The study was conducted on field-scale plots in Urbana, IL, during the 2020–2022 growing seasons. Switchgrass was established in 2020 and urea-fertilized at 56 kg N ha –1 year –1 . Corn management followed best management practices for the US Midwest, including no-till and 202 kg N ha –1 year –1 fertilization, applied as urea–ammonium nitrate (32%). Our results showed lower direct N 2 O emissions in switchgrass compared to corn. Although soil CO 2 emissions did not differ significantly during the establishment year, emissions in subsequent years were over 50% higher in switchgrass than in corn, likely due to increased belowground biomass, which was over five times higher in switchgrass. Nitrate-N leaching decreased as the switchgrass stand matured, reaching 80% lower than in corn by the third year. Differences in ET and WUE between corn and switchgrass were not significant; however, results indicate a trend toward reduced WUE in switchgrass under drought, driven by lower aboveground biomass production. Our study demonstrates that switchgrass can be implemented at a commercial scale without negatively impacting the hydrological cycle, while potentially reducing N losses through nitrate-N leaching and soil N 2 O emissions, and enhancing belowground C storage.

09 BIOMASS FUELS↗

Interactive effects of precipitation, temperature, and grazing pressure on the net ecosystem carbon balance of grazing lands across the continental United States

Grazing lands cover approximately one-third of the contiguous United States, support much of the nation's beef production, and are an important component of the U.S. terrestrial carbon budget. In this study, we quantified net ecosystem carbon balance (NECB), the net status of grazing lands as a carbon sink (C-sink) or source (C-source) and a key determinant of soil health and productivity. Our primary objective was to synthesize multiple years of annual NECB across heterogeneous grazing lands across the continental U.S and evaluate annual NECB against physical drivers (mean annual precipitation (MAP), mean annual temperature (MAT), vegetation, and moisture condition) and management practices (grazing pressure index (GPI) and fertilization history). We hypothesized that (1) NECB is higher in mesic and fertilized grasslands; (2) NECB increases with MAP and MAT but decreases with GPI; and (3) interactive effects exist among MAP, MAT, and GPI. Using carbon fluxes measured by eddy covariance towers and methane emissions including both enteric methane and manure derived from stocking rates across seven USDA Long-term Agroecosystem Research Network sites, we found: (1) grazing lands were a C-sink or carbon neutral at most sites; (2) vegetation type, moisture conditions, or fertilization had no significant effect on NECB; (3) NECB increased with MAP and MAT, but decreased with a higher GPI; and (4) MAT had a significant positive effect on NECB when MAP exceeded 750 mm (greater water availability). The effect of GPI on NECB was significantly negative when MAP was below 1000 mm, significantly negative when MAT < 12 °C and significantly positive when MAT > 16 °C. Thus, most grazing lands in our study acted as C-sinks unless water deficit, low temperature, or heavy grazing were interactively present. Understanding how climate and management influence NECB of grazing lands is key to maintaining resilient agroecosystems that secure beef production and sustain rural prosperity.

LTAR↗

Using stable isotopes to inform water resource management in forested and agricultural ecosystems

Present and future climatic trends are expected to markedly alter water fluxes and stores in the hydrologic cycle. In addition, water demand continues to grow due to increased human use and a growing population. Sustainably managing water resources requires a thorough understanding of water storage and flow in natural, agricultural, and urban ecosystems. Measurements of stable isotopes of water (hydrogen and oxygen) in the water cycle (atmosphere, soils, plants, surface water, and groundwater) can provide information on the transport pathways, sourcing, dynamics, ages, and storage pools of water that is difficult to obtain with other techniques. However, the potential of these techniques for practical questions has not been fully exploited yet. Here, we outline the benefits and limitations of potential applications of stable isotope methods useful to water managers, farmers, and other stakeholders. We also describe several case studies demonstrating how stable isotopes of water can support water management decision-making. Finally, we propose a workflow that guides users through a sequence of decisions required to apply stable isotope methods to examples of water management issues. We call for ongoing dialogue and a stronger connection between water management stakeholders and water stable isotope practitioners to identify the most pressing issues and develop best-practice guidelines to apply these techniques.

54 ENVIRONMENTAL SCIENCES↗

Overlooked cooling effects of albedo in terrestrial ecosystems

Radiative forcing (RF) resulting from changes in surface albedo is increasingly recognized as a significant driver of global climate change but has not been adequately estimated, including by Intergovernmental Panel on Climate Change (IPCC) assessment reports, compared with other warming agents. Here, we first present the physical foundation for modeling albedo-induced RF and the consequent global warming impact (GWI Δα ). We then highlight the shortcomings of available current databases and methodologies for calculating GWI Δα at multiple temporal scales. There is a clear lack of comprehensive in situ measurements of albedo due to sparse geographic coverage of ground-based stations, whereas estimates from satellites suffer from biases due to the limited frequency of image collection, and estimates from earth system models (ESMs) suffer from very coarse spatial resolution land cover maps and associated albedo values in pre-determined lookup tables. Field measurements of albedo show large differences by ecosystem type and large diurnal and seasonal changes. As indicated from our findings in southwest Michigan, GWI Δα is substantial, exceeding the RF Δα values of IPCC reports. Inclusion of GWI Δα to landowners and carbon credit markets for specific management practices are needed in future policies. We further identify four pressing research priorities: developing a comprehensive albedo database, pinpointing accurate reference sites within managed landscapes, refining algorithms for remote sensing of albedo by integrating geostationary and other orbital satellites, and integrating the GWI Δα component into future ESMs.

54 ENVIRONMENTAL SCIENCES↗

Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes

Drylands cover one-third of the Earth’s surface and are one of the largest terrestrial sinks for methane. Understanding the structure–function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors—water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m 2 h −1 , peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum , two Methylobacter , and uncultivated Methylococcaceae ). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum . Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Integrating ORNL’s HPC and Neutron Facilities with a Performance-Portable CPU/GPU Ecosystem

We explore the development of a performance-portable CPU/GPU ecosystem to integrate two of the US Department of Energy’s (DOE’s) largest scientific instruments, the Oak Ridge Leadership Computing facility and the Spallation Neutron Source (SNS), both of which are housed at Oak Ridge National Laboratory. We select a relevant data reduction workflow use-case to obtain the differential scattering cross-section from data collected by SNS’s CORELLI and TOPAZ instruments. We compare the current CPU-only production implementation using the Garnet Python multiprocess package based on the Mantid C++ framework against our proposed CPU/GPU implementation that uses the LLVM-based, just-in-time Julia scientific language and the JACC.jl performance-portable package. Two proxy apps were developed: (i) an app for extracting relevant Mantid kernels (MDNorm) in C++ and (ii) the Julia MiniVATES.jl miniapp. We present performance results for NVIDIA A100 and AMD MI100 GPUs and AMD EPYC 7513 and 7662 CPUs. The results provide insights for future generations of data reduction software that can embrace performance portability for an integrated research infrastructure across DOE’s experimental and computational facilities.

Hahn, Steven↗

Wildfire smoke impacts lake ecosystems

Abstract Wildfire activity is increasing globally. The resulting smoke plumes can travel hundreds to thousands of kilometers, reflecting or scattering sunlight and depositing particles within ecosystems. Several key physical, chemical, and biological processes in lakes are controlled by factors affected by smoke. The spatial and temporal scales of lake exposure to smoke are extensive and under‐recognized. We introduce the concept of the lake smoke‐day, or the number of days any given lake is exposed to smoke in any given fire season, and quantify the total lake smoke‐day exposure in North America from 2019 to 2021. Because smoke can be transported at continental to intercontinental scales, even regions that may not typically experience direct burning of landscapes by wildfire are at risk of smoke exposure. We found that 99.3% of North America was covered by smoke, affecting a total of 1,333,687 lakes ≥10 ha. An incredible 98.9% of lakes experienced at least 10 smoke‐days a year, with 89.6% of lakes receiving over 30 lake smoke‐days, and lakes in some regions experiencing up to 4 months of cumulative smoke‐days. Herein we review the mechanisms through which smoke and ash can affect lakes by altering the amount and spectral composition of incoming solar radiation and depositing carbon, nutrients, or toxic compounds that could alter chemical conditions and impact biota. We develop a conceptual framework that synthesizes known and theoretical impacts of smoke on lakes to guide future research. Finally, we identify emerging research priorities that can help us better understand how lakes will be affected by smoke as wildfire activity increases due to climate change and other anthropogenic activities.

54 ENVIRONMENTAL SCIENCES↗

Body size and early marine conditions drive changes in Chinook salmon productivity across northern latitude ecosystems

Disentangling the influences of climate change from other stressors affecting the population dynamics of aquatic species is particularly pressing for northern latitude ecosystems, where climate‐driven warming is occurring faster than the global average. Chinook salmon (Oncorhynchus tshawytscha) in the Yukon‐Kuskokwim (YK) region occupy the northern extent of their species' range and are experiencing prolonged declines in abundance resulting in fisheries closures and impacts to the well‐being of Indigenous people and local communities. These declines have been associated with physical (e.g., temperature, streamflow) and biological (e.g., body size, competition) conditions, but uncertainty remains about the relative influence of these drivers on productivity across populations and how salmon–environment relationships vary across watersheds. To fill these knowledge gaps, we estimated the effects of marine and freshwater environmental indicators, body size, and indices of competition, on the productivity (adult returns‐per‐spawner) of 26 Chinook salmon populations in the YK region using a Bayesian hierarchical stock‐recruitment model. Across most populations, productivity declined with smaller spawner body size and sea surface temperatures that were colder in the winter and warmer in the summer during the first year at sea. Decreased productivity was also associated with above average fall maximum daily streamflow, increased sea ice cover prior to juvenile outmigration, and abundance of marine competitors, but the strength of these effects varied among populations. Maximum daily stream temperature during spawning migration had a nonlinear relationship with productivity, with reduced productivity in years when temperatures exceeded thresholds in main stem rivers. These results demonstrate for the first time that well‐documented declines in body size of YK Chinook salmon were associated with declining population productivity, while taking climate into account.

54 ENVIRONMENTAL SCIENCES↗

Consistent time allocation fraction to vegetation green-up versus senescence across northern ecosystems despite recent climate change

Extended growing season lengths under climatic warming suggest increased time for plant growth. However, research has focused on climatic impacts to the timing or duration of distinct phenological events. Comparatively little is known about impacts to the relative time allocation to distinct phenological events, for example, the proportion of time dedicated to leaf growth versus senescence. We use multiple satellite and ground-based observations to show that, despite recent climate change during 2001 to 2020, the ratio of time allocated to vegetation green-up over senescence has remained stable [1.27 (± 0.92)] across more than 83% of northern ecosystems. This stability is independent of changes in growing season lengths and is caused by widespread positive relationships among vegetation phenological events; longer vegetation green-up results in longer vegetation senescence. These empirical observations were also partly reproduced by 13 dynamic global vegetation models. Our work demonstrates an intrinsic biotic control to vegetation phenology that could explain the timing of vegetation senescence under climate change.

54 ENVIRONMENTAL SCIENCES↗

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

ABSTRACT Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the Brachypodium distachyon rhizosphere in an EcoFAB using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments. IMPORTANCE We report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.

Priya, Shweta↗

Mojo: MLIR-based Performance-Portable HPC Science Kernels on GPUs for the Python Ecosystem

We explore the performance and portability of the novel Mojo language for scientific computing workloads on GPUs. As the first language based on the LLVM’s Multi-Level Intermediate Representation (MLIR) compiler infrastructure, Mojo aims to close performance and productivity gaps by combining Python’s interoperability and CUDA-like syntax for compile-time portable GPU programming. We target four scientific workloads: a seven-point stencil (memory-bound), BabelStream (memory-bound), miniBUDE (compute-bound), and Hartree–Fock (compute-bound with atomic operations); and compare their performance against vendor baselines on NVIDIA H100 and AMD MI300A GPUs. We show that Mojo’s performance is competitive with CUDA and HIP for memory-bound kernels, whereas gaps exist on AMD GPUs for atomic operations and for fast-math compute-bound kernels on both AMD and NVIDIA GPUs. Although the learning curve and programming requirements are still fairly low-level, Mojo can close significant gaps in the fragmented Python ecosystem in the convergence of scientific computing and AI.

Godoy, William [ORNL] (ORCID:0000000225905178)↗

Data for "Field-scale Evaluation of Ecosystem Service Benefits of Bioenergy Switchgrass"

Purpose-grown perennial herbaceous species are nonfood crops specifically cultivated for bioenergy production and have the potential to secure bioenergy feedstock resources while enhancing ecosystem services. This study assessed soil greenhouse gas emissions (CO2 and N2O), nitrate (NO3-N) leaching reduction potential, evapotranspiration (ET), and water-use efficiency (WUE) of bioenergy switchgrass ( Panicum virgatum L.) in comparison to corn ( Zea mays L.). The study was conducted on field-scale plots in Urbana, IL, during the 2020–2022 growing seasons. Switchgrass was established in 2020 and urea-fertilized at 56 kg N ha−1 year−1. Corn management followed best management practices for the US Midwest, including no-till and 202 kg N ha−1 year−1 fertilization, applied as urea–ammonium nitrate (32%). Our results showed lower direct N2O emissions in switchgrass compared to corn. Although soil CO2 emissions did not differ significantly during the establishment year, emissions in subsequent years were over 50% higher in switchgrass than in corn, likely due to increased belowground biomass, which was over five times higher in switchgrass. Nitrate-N leaching decreased as the switchgrass stand matured, reaching 80% lower than in corn by the third year. Differences in ET and WUE between corn and switchgrass were not significant; however, results indicate a trend toward reduced WUE in switchgrass under drought, driven by lower aboveground biomass production. Our study demonstrates that switchgrass can be implemented at a commercial scale without negatively impacting the hydrological cycle, while potentially reducing N losses through nitrate-N leaching and soil N2O emissions, and enhancing belowground C storage.

field data↗