Rodrigo Vargas

University of Delaware | UDel UD · Department of Plant and Soil Sciences

Forest soils and canopies are major components of ecosystem CO2 and CH4 fluxes. In contrast, less is known about coarse woody debris and living tree stems, both of which function as active surfaces for CO2 and CH4 fluxes. We measured CO2 and CH4 fluxes from soils, coarse woody debris, and tree stems over the growing season in an upland temperate fo...

The net ecosystem exchange (NEE) is the difference between ecosystem CO2 assimilation and CO2 losses to the atmosphere. Ecosystem respiration (Reco), the efflux of CO2 from the ecosystem to the atmosphere, includes the soil-to-atmosphere carbon flux (i.e., soil respiration; Rsoil) and aboveground plant respiration. Therefore, Rsoil is a fraction of...

Aims Soils provide key ecosystem services and directly control ecosystem functions; thus, there is a need to define the reference state of soil functionality. Most common functional classifications are vegetation-centered, such as plant functional types (PFTs), and neglect soil characteristics and processes. We propose Soil Functional Types (SFTs)...

Environmental observatory networks (EONs) are coordinated efforts to provide knowledge that ultimately delivers transformational ecological science from regional to global scales. We used ecosystem functional types (EFTs), a time-varying land surface classification, as an alternative way to characterize ecosystem functional heterogeneity based on c...

The metabolic activity of water-limited ecosystems is strongly linked to the timing and magnitude of precipitation pulses that can trigger disproportionately high (i.e., hot-moments) ecosystem CO 2 fluxes. We analyzed over 2-years of continuous measurements of soil CO 2 efflux (Fs) under vegetation (Fs veg) and at bare soil (Fs bare) in a water-lim...

Soil respiration (Rs), the soil‐to‐atmosphere flux of CO2, is a dominant but uncertain part of the carbon cycle, even after decades of study. This review focuses on progress in understanding Rs from laboratory incubations to global estimates. We survey key developments of in situ ecosystem‐scale Rs observations and manipulations, synthesize Rs meta...

Methane dynamics within salt marshes are complex because vegetation types, temperature, oscillating water levels, and changes in salinity and redox conditions influence CH4 production, consumption, oxidation, and emissions. These non‐linear and complex interactions among variables affect the traditionally expected functional relationships and prese...

Tropical Dry Forest (TDF) is a distinctive ecosystem characterized by distinct seasonal changes, primarily composed of deciduous trees adapted to endure prolonged drought periods. Obtaining ecosystem-scale flux measurements using the Eddy Covariance (EC) technique is crucial for comprehending the spatiotemporal dynamics of interactions between the...

A data-driven method is presented for improving sampling designs from times series (1D approach) or spatial arrays (2D approach) of digital information. We present the autocorrelated conditioned Latin Hypercube Sampling (acLHS). This method combines a conditioned Latin Hypercube (cLHS) to obtain a representative sample of the joint probability dist...

Information on forest extent and tree cover is required to evaluate the status of natural resources, conservation practices, and environmental policies. The challenge is that different forest definitions, remote sensing-based (RSB) products, and data availability can lead to discrepancies in reporting total forest area. Consequently, errors in fore...

Application of the best available science to improve quantification of greenhouse gas (GHG) emissions at regional and national scales is key to climate action. Here, we present a two‐decade (2000–2019) GHG (CO2, CH4, and N2O) budget for Mexico derived from multiple products. Data from the National GHG Inventory, global observations, and the scienti...

The frequency and persistence of tidal inundation varies along the coastal terrestrial-aquatic interface, from frequently inundated wetlands to rarely inundated upland forests. This inundation gradient controls soil and sediment biogeochemistry and influence the exchange of soils and sediments from terrestrial to aquatic domains. Although a rich li...

Soil CO2 efflux represents a complex interplay of biological and physical processes that result in the production and transfer of CO2 from soils to the atmosphere. Temperature has been widely recognized as a critical factor regulating soil CO2 efflux and is commonly utilized in deterministic empirical models to predict this important flux for the c...

Tidal salt marshes produce and emit CH 4 . Therefore, it is critical to understand the biogeochemical controls that regulate CH 4 spatial and temporal dynamics in wetlands. The prevailing paradigm assumes that acetoclastic methanogenesis is the dominant pathway for CH 4 production, and higher salinity concentrations inhibit CH 4 production in salt...

Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades o...

Transferable and mechanistic understanding of cross-scale interactions is necessary to predict how coastal systems respond to global change. Cohesive datasets across geographically distributed sites can be used to examine how transferable a mechanistic understanding of coastal ecosystem control points is. To address the above research objectives, d...

Process‐based land surface models are important tools for estimating global wetland methane (CH4) emissions and projecting their behavior across space and time. So far there are no performance assessments of model responses to drivers at multiple time scales. In this study, we apply wavelet analysis to identify the dominant time scales contributing...

Soil CO 2 efflux involves complex biological and physical processes that contribute to the production and transport of CO 2 from soils to the atmosphere. Temperature is widely used in deterministic empirical models, but these approaches cannot fully capture the complexity of the temperature-soil CO 2 efflux relationship due to environmental drivers...

Wetlands are responsible for 20%–31% of global methane (CH4) emissions and account for a large source of uncertainty in the global CH4 budget. Data‐driven upscaling of CH4 fluxes from eddy covariance measurements can provide new and independent bottom‐up estimates of wetland CH4 emissions. Here, we develop a six‐predictor random forest upscaling mo...

We made a commitment to better include underrepresented members of our community in the publication pipeline of JGR: Biogeosciences. This commitment consists of regular updates on our policies and practices, and concrete actions we intend to implement over the next year. So far, our progress to tackle biases and ensure equitable research in the bio...

Methane dynamics within salt marshes are complex because vegetation types, temperature, oscillating water levels, and changes in salinity and redox conditions influence CH4 production and emission. These non-linear and complex interactions among variables affect the traditionally expected functional relationships and present challenges for interpre...

Infrequent and small precipitation (PPT) events characterize PPT patterns in semiarid grasslands; however, plants and soil microorganisms are adapted to use the unpredictable small pulses of water. Several studies have shown short-term responses of carbon and nitrogen mineralization rates (called the "priming effect" or the Birch effect) stimulated...

Tidal channels are biogeochemical hotspots that horizontally exchange carbon (C) with marsh platforms, but the physiochemical drivers controlling these dynamics are poorly understood. We hypothesized that C‐bearing iron (Fe) oxides precipitate and immobilize dissolved organic carbon (DOC) during ebb tide as the soils oxygenate, and dissolve into th...

How sea level rise (SLR) alters carbon (C) dynamics in tidal salt marsh soils is unresolved. Changes in hydrodynamics could influence organo-mineral associations, influencing dissolved organic carbon (DOC) fluxes. As SLR increases the duration of inundation, we hypothesize that lateral DOC export will increase due to reductive dissolution of C-bear...

One of the largest challenges with soil information around the world is how to harmonize archived soil data from different sources and how to make it accessible to soil scientist. In Ecuador, there have been two major projects that have provided soil information, but the methodology of these projects, although comparable, did not coincide, especial...

Quantifying the role of soils in nature-based solutions requires accurate estimates of soil greenhouse gas (GHG) fluxes. Technological advances allow us to measure multiple GHGs simultaneously, and now it is possible to provide complete GHG budgets from soils (i.e., CO2, CH4, and N2O fluxes). We propose that there is a conflict between the convenie...

Mangrove wetlands play an essential role as blue carbon ecosystems. However, worldwide they also face imminent threats caused by anthropogenic activities and climate change. Mangroves in the semiarid region of the Gulf of California are highly vulnerable to both threats. In this study, we present eddy covariance measurements of net ecosystem exchan...

Precipitation (PPT) patterns in semiarid grasslands are characterized by infrequency and small PPT events; however, plants and soil microorganisms are adapted to use the unpredictable small pulses of water. Several studies have shown short-term responses of carbon and nitrogen mineralization rates (called the priming effect or the Birch effect) sti...

Salt marsh ecosystems are underrepresented in process‐based models due to their unique location across the terrestrial–aquatic interface. Particularly, the role of leaf nutrients on canopy photosynthesis (FA) remains unclear, despite their relevance for regulating vegetation growth. We combined multiyear information of canopy‐level nutrients and ed...

Tidal salt marsh soils can be a dynamic source of greenhouse gases such as carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), as well as sulfur-based trace gases such as carbon disulfide (CS2) and dimethylsulfide (DMS) which play roles in global climate and carbon–sulfur biogeochemistry. Due to the difficulty in measuring trace gases in...

Continental North America has been found to be a carbon (C) sink over recent decades by multiple studies employing a variety of estimation approaches. However, several key questions and uncertainties remain with these assessments. Here we used results from an ensemble of 19 state‐of‐the‐art dynamic global vegetation models from the TRENDYv9 project...

One of the largest challenges with soil information around the world is how to harmonize archived soil data from different sources and how make it usable to extract knowledge. In Ecuador there have been two major projects that provided soil information, whose methodology, although comparable, did not coincide, especially regarding the structure of...

Soil nitrogen (N) is an important driver of plant productivity and ecosystem functioning; consequently, it is critical to understand its spatial variability from local‐to‐global scales. Here, we provide a quantitative assessment of the three‐dimensional spatial distribution of soil N across the United States (CONUS) using a digital soil mapping app...

Quantifying the role of soils in nature-based solutions require accurate estimates of soil greenhouse gas (GHG) fluxes. Technological advances allow to simultaneously measure multiple GHGs and now is possible to provide complete GHG budgets from soils (i.e., CO2, CH4 and N2O fluxes). We propose that there is a conflict between the convenience of si...

Tidal wetlands are comprised of complex interdependent pathways where measurements of carbon exchange are often scale dependent. Common data collection methods (i.e., chambers and eddy covariance) are inherently constrained to different spatial and temporal scales which could generate biased information for applications of carbon accounting, identi...

Soil moisture is an important parameter that regulates multiple ecosystem processes and provides important information for environmental management and policy decision-making. Spaceborne sensors provide soil moisture information over large areas, but information is commonly available at coarse resolution with spatial and temporal gaps. Here, we pre...

The development of several large‐, “continental”‐scale ecosystem research infrastructures over recent decades has provided a unique opportunity in the history of ecological science. The Global Ecosystem Research Infrastructure (GERI) is an integrated network of analogous, but independent, site‐based ecosystem research infrastructures (ERI) dedicate...

Tidal salt marsh soils can be a dynamic source of greenhouse gases such as carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), as well as sulfur-based trace gases such as carbon disulfide (CS2) and dimethylsulfide (DMS) which play roles in global climate and carbon-sulfur biogeochemistry. Due to the difficulty in measuring trace gases in...

RESUMEN El carbono orgánico de los suelos (COS) es uno de los almacenes más importantes de los ecosistemas terrestres, por lo que la estimación de este almacén y sus flujos (dinámica) en México permite la generación de escenarios de intervención para analizar el impacto de políticas públicas, además de dar soporte a la implementación de mercados de...

The terrestrial carbon cycle is a major source of uncertainty in climate projections. Its dominant fluxes, gross primary productivity (GPP), and respiration (in particular soil respiration, R S ), are typically estimated from independent satellite-driven models and upscaled in situ measurements, respectively. We combine carbon-cycle flux estimates...

This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology tra...

Key Points The impact of our journal is enhanced when a representative pool of contributors participates in the process of scientific publication Increasing reviewer and editor diversity is the best opportunity we have to remove bias from the peer review process Key priorities to expand and diversify our editorial, reviewing, and publishing communi...

To trust findings in computational science, scientists need workflows that trace the data provenance and support results explainability. As workflows become more complex, tracing data provenance and explaining results become harder to achieve. In this paper, we propose a computational environment that automatically creates a workflow execution's re...

Estudios sobre la variación espacial del carbono orgánico del suelo (COS) son indispensables para mejorar el conocimiento sobre el ciclo global del carbono. Este trabajo documenta el desarrollo de un mapa digital de COS para México a 1 m de profundidad y 90 m de resolución espacial representativo del periodo 1991-2009. Un ensamble de árboles de reg...

Study region Delaware, USA and its surrounding watersheds. Study focus An ensemble using multiple Kernel K-nearest neighbors (KKNN) models was trained to predict daily grids of SSM at 100-meter resolution based on SSM estimates from the European Space Agency’s Climate Change Initiative Soil Moisture Product, terrain data, soil maps, and local mete...

Time series of wetland methane fluxes measured by eddy covariance require gap-filling to estimate daily, seasonal , and annual emissions. Gap-filling methane fluxes is challenging because of high variability and complex responses to multiple drivers. To date, there is no widely established gap-filling standard for wetland methane fluxes, with regar...

Water is a crucial factor controlling the fate and processing of soil organics. Water commonly flows through the vadose zone via preferential flow pathways, resulting in nonuniform and rapid infiltration. Hence, a large portion of the soil matrix is bypassed. Preferential flow paths, often associated with well-connected macropore networks (>300 μm...

C4 plants frequently experience high light and high temperature conditions in the field, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridi...

Tidal marshes store large amounts of carbon; however, little is known about the patterns, magnitudes, and biophysical drivers that regulate CO2 efflux from these ecosystems. Due to harsh environmental conditions (e.g., flooding), it is difficult to measure continuous soil CO2 efflux in tidal marshes. These data are necessary to inform empirical and...

Methane (CH4) emissions from natural landscapes constitute roughly half of global CH4 contributions to the atmosphere, yet large uncertainties remain in the absolute magnitude and the seasonality of emission quantities and drivers. Eddy covariance (EC) measurements of CH4 flux are ideal for constraining ecosystem-scale CH4 emissions due to quasi-co...

The exchange of multiple greenhouse gases (i.e., CO2 and CH4) between tree stems and the atmosphere represents a knowledge gap in the global carbon cycle. Stem CO2 and CH4 fluxes vary across time and space and is unclear which are their individual or shared drivers. Here we measured CO2 and CH4 fluxes at different stem heights combining manual (biw...

Humid tropical forests play a dominant role in the functioning of Earth but are under increasing threat from changes in land use and climate. How forest vulnerability varies across space and time and what level of stress forests can tolerate before facing a tipping point are poorly understood. Here, we develop a tropical forest vulnerability index...

Salt marshes constitute an important terrestrial-aquatic interface that remains underrepresented in Earth System Models due to constraining biophysical controls and spatially limited land cover. One promising approach to improve representativeness is the application of proximal remote sensing to generate phenological information, yet we lack detail...

Measurements of atmospheric ammonia (NH3) concentrations and fluxes are limited in coastal regions in the eastern U.S. In this study, continuous and high temporal resolution measurements (5s) of atmospheric NH3 concentrations were recorded using a cavity ring‐down spectrometer in a temperate tidal salt marsh at the St Jones Reserve (Dover, DE). Mic...

Large datasets of greenhouse gas and energy surface-atmosphere fluxes measured with the eddy-covariance technique (e.g., FLUXNET2015, AmeriFlux BASE) are widely used to benchmark models and remote-sensing products. This study addresses one of the major challenges facing model-data integration: To what spatial extent do flux measurements taken at in...

Soil respiration (Rs), the efflux of CO2 from soils to the atmosphere, is a major component of the terrestrial carbon cycle, but is poorly constrained from regional to global scales. The global soil respiration database (SRDB) is a compilation of in‐situ Rs observations from around the globe that has been consistently updated with new measurements...

While wetlands are the largest natural source of methane (CH4) to the atmosphere, they represent a large source of uncertainty in the global CH4 budget due to the complex biogeochemical controls on CH4 dynamics. Here we present, to our knowledge, the first multi‐site synthesis of how predictors of freshwater wetland CH4 fluxes (FCH4) vary across we...

Soil moisture is key for understanding soil–plant–atmosphere interactions. We provide a soil moisture pattern recognition framework to increase the spatial resolution and fill gaps of the ESA-CCI (European Space Agency Climate Change Initiative v4.5) soil moisture dataset, which contains > 40 years of satellite soil moisture global grids with a spa...

Salt marshes are large carbon reservoirs as part of blue carbon ecosystems. Unfortunately, there is limited information about the net ecosystem (NEE) and methane (CH4) exchange between salt marshes and the atmosphere to fully understand their carbon dynamics. We tested the influence of biophysical drivers by plant phenological phases (i.e., Greenup...

Wetland methane (CH 4 ) emissions ( $${F}_{{{CH}}_{4}}$$ F C H 4 ) are important in global carbon budgets and climate change assessments. Currently, $${F}_{{{CH}}_{4}}$$ F C H 4 projections rely on prescribed static temperature sensitivity that varies among biogeochemical models. Meta-analyses have proposed a consistent $${F}_{{{CH}}_{4}}$$ F C H 4...

Environmental observatory networks (EONs) provide information to understand and forecast the spatial and temporal dynamics of Earth's biophysical processes. Consequently, representativeness analyses are important to provide insights for improving EONs' management, design, and interpretation of their value‐added products. We assessed the representat...

Over the past decade, Brazil has experienced severe droughts across its territory, with important implications for soil moisture dynamics. Soil moisture variability has a direct impact on agriculture, water security and ecosystem services. Nevertheless, there is currently little information on how soil moisture across different biomes responds to d...

C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the...

Turfgrass is an important component of the urban landscape frequently considered as an alternative land cover to offset anthropogenic CO2 emissions. However, quantitative information of the potential to directly remove CO2 from the atmosphere by turfgrass systems is lacking, especially in the tropics. Most assessments have considered the carbon acc...

Although drylands cover >40% of the land surface, models of ecosystem gross primary productivity (GPP) generally have been designed for mesic temperate ecosystems. Arguably, GPP models often lack a good representation of vegetation phenology, particularly not estimating the ecosystem effects of the prolonged foliage senescence which may be common i...

Methane (CH4) emissions from natural landscapes constitute roughly half of global CH4 contributions to the atmosphere, yet large uncertainties remain in the absolute magnitude and the seasonality of emission quantities and drivers. Eddy covariance (EC) measurements of CH4 flux are ideal for constraining ecosystem-scale CH4 emissions, including thei...

Over the last 100 years a shifting human population has seen large proportions of people relocating from rural agricultural regions to urban and suburban areas. Extensive development within these modified lands has altered soils and natural vegetative cover which directly affects many biophysical processes. The current study examines over 4 years o...

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-toatmosphere CO2 flux, commonly though imprecisely termed soil respiration (RS), is one of the largest car...

Soil moisture is key for quantifying soil-atmosphere interactions. We provide a soil moisture pattern recognition framework to increase the spatial resolution and fill gaps of the ESA-CCI (European Space Agency-Climate Change Initiative v4.5) soil moisture dataset, which contains more than 40 years of satellite soil moisture global grids with a spa...