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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

New soil carbon sequestration with nitrogen enrichment: a meta-analysis

Background and aims: Through agriculture and industry, humans are increasing the deposition and availability of nitrogen (N) in ecosystems worldwide. Carbon (C) isotope tracers provide useful insights into soil C dynamics, as they allow to study soil C pools of different ages. In this study we evaluated to what extent N enrichment affects soil C dynamics in experiments that applied C isotope tracers. Methods: Using meta-analysis, we synthesized data from 35 published papers. We made a distinction between “new C” and “old C” stocks, i.e., soil C derived from plant C input since the start of the isotopic enrichment, or unlabeled, pre-existing soil C. Results: Averaged across studies, N addition increased new soil C stocks (+30.3%), total soil C stocks (+6.1%) and soil C input proxies (+30.7%). Although N addition had no overall, average, effect on old soil C stocks and old soil C respiration, old soil C stocks increased with the amount of N added and respiration of old soil C declined. Nitrogen-induced effects on new soil C and soil C input both decreased with the amount of extraneous N added in control treatments. Conclusion: Although our findings require additional confirmation from long-term field experiments, our analysis provides isotopic evidence that N addition stimulates soil C storage both by increasing soil C input and (at high N rates) by decreasing decomposition of old soil C. Furthermore, we demonstrate that the widely reported saturating response of plant growth to N enrichment also applies to new soil C storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition

Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. Furthermore, during a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data and scripts associated with the manuscript "Encoding Diel Hysteresis and the Birch Effect in Dryland Soil Respiration Models through Knowledge-Guided Deep Learning"

This package contains the data and scripts used in "Encoding Diel Hysteresis and the Birch Effect in Dryland Soil Respiration Models through Knowledge-Guided Deep Learning" (Jiang et al., 2022). The data.zip file contains the flux tower and automated chamber observations used for developing the deep learning model for modeling soil respiration. The scripts.zip file contains the Jupyter notebooks and python scripts for preprocessing the data, training the deep learning models, and postprocessing the results. The src.zip contains the source code for training the deep learning model, performing mutual information analysis, and plotting functions. The trained_models.zip contains multiple folders used for hosting the trained deep-learning models and the associated soil respiration predictions. The whole process is performed using python. We include the REAMD.md to document the python package requirements.Soil respiration in dryland ecosystems is challenging to model due to its complex interactions with environmental drivers. Knowledge-guided deep learning provides a much more effective means of accurately representing these complex interactions than traditional Q10-based models. Mutual information analysis revealed that future soil temperature shares more information with soil respiration than past soil temperature, consistent with their clockwise diel hysteresis. We explicitly encoded diel hysteresis, soil drying, and soil rewetting effects on soil respiration dynamics in a newly designed Long Short Term Memory (LSTM) model. The model takes both past and future environmental drivers as inputs to predict soil respiration. The new LSTM model substantially outperformed three Q10-based models and the Community Land Model when reproducing the observed soil respiration dynamics in a semi-arid ecosystem. The new LSTM model clearly demonstrated its superiority for temporally extrapolating soil respiration dynamics, such that the resulting correlation with observational data is up to 0.7 while the correlations of both Q10-based models and the Community Land Model (CLM) are less than 0.4. Our results underscore the high potential for knowledge-guided deep learning to replace Q10-based soil respiration modules in Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Experimental warming and drying increase older carbon contributions to soil respiration in lowland tropical forests

Tropical forests account for over 50% of the global terrestrial carbon sink, but climate change threatens to alter the carbon balance of these ecosystems. We show that warming and drying of tropical forest soils may increase soil carbon vulnerability, by increasing degradation of older carbon. In situ whole-profile heating by 4 °C and 50% throughfall exclusion each increased the average radiocarbon age of soil CO 2 efflux by ~2–3 years, but the mechanisms underlying this shift differed. Warming accelerated decomposition of older carbon as increased CO 2 emissions depleted newer carbon. Drying suppressed decomposition of newer carbon inputs and decreased soil CO 2 emissions, thereby increasing contributions of older carbon to CO 2 efflux. These findings imply that both warming and drying, by accelerating the loss of older soil carbon or reducing the incorporation of fresh carbon inputs, will exacerbate soil carbon losses and negatively impact carbon storage in tropical forests under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Reproductive and leaf litterfall fluxes in forest ecosystem sites globally (1950-2022)

Forest allocation of net primary productivity (NPP) to reproduction is poorly quantified globally, despite its critical role in forest regeneration and a well-supported trade-off with allocation to growth. Although field measurements of total NPP are rare, our work finds that a proxy for reproductive carbon allocation constructed from leaf (L) and reproductive (R) litterfall fluxes, R/(R+L), is strongly correlated with R/NPP, facilitating analysis across a wide range of sites where biometric estimates of NPP are not available (R² = 0.85; Hanbury-Brown et al., 2022, Ward et al., in prep). To investigate relationships between ecosystem-scale reproductive allocation (RA) and climate, soil fertility, and stand age gradients, we conducted a literature search and synthesized 824 observations of annual average leaf and reproductive litterfall fluxes across forest sites globally. The zip file includes 1) a folder Data/ containing the litterfall data ("GlobalForestRA_data.csv") and metadata ("GlobalForestRA_metadata.doc") files. The data file includes geographic coordinates, long-term mean annual temperature and precipitation (1970-2000, extracted from WorldClim2.1), leaf and reproductive litterfall fluxes, sampling interval and protocols, forest characteristics (dominant leaf morphology, information pertaining to forest age and successional stage, and disturbance history) and soil properties (% sand, %silt, %clay, total phosphorus (P), nitrogen (N), cation exchange capacity (CEC) and pH) extracted from SoilGrids250 and from on-site measurements, where available. The metadata file contains information about each variable reported in the data file, including data sources, processing methods, and all references. The Data folder contains two additional files used to create Figure 1; these are described in greater detail in the README.2) R scripts GloalForestRA_analysis.r and GlobalForestRA_SI.r and a folder /Functions used to produce results, figures, and tables in the manuscript Ward et al. (in press)3) a README file describing how the data and R scripts can be used to reproduce statistical results, figures, and tables found in the manuscript. Ward et al. (in press)This repository can also be found at: https://github.com/r-ward/Global_Analysis_ForestRA.Ward, R.E., Zhang-Zheng, H. Aernethy, K., Adu-Bredu, S., Arroyo, L., Bailey, A. et al. (in press). Forest age rivals climate to explain reproductive allocation patterns in forest ecosystems globally. Ecology Letters. Hanbury-Brown, A.R., Ward, R.E. & Kueppers, L.M. (2022). Forest regeneration within Earth system models: current process representations and ways forward. New Phytol., 235, 20–40.Ward et al. (2025), Forest age rivals climate to explain reproductive allocation patterns in forest ecosystems globally, in prep.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Whole-Ecosystem Warming Increases Plant-Available Nitrogen and Phosphorus in an Ombrotrophic Bog

Warming is expected to increase the net release of carbon from peatland soils, contributing to future warming. This positive feedback may be moderated by the response of peatland vegetation to rising atmospheric [CO 2 ] or to increased soil nutrient availability. We asked whether a gradient of whole-ecosystem warming (from + 0 °C to + 9 °C) would increase plant-available nitrogen and phosphorus in an ombrotrophic bog in northern Minnesota, USA, and whether elevated [CO 2 ] would modify the nutrient response. We tracked changes in plant-available nutrients across space and through time and in comparison with other nutrient pools, and assessed whether nutrient warming responses were captured by a point version of the land-surface model, ELM-SPRUCE. We found that warming exponentially increased plant-available ammonium and phosphate, but that nutrient dynamics were unaffected by elevated [CO 2 ]. The warming response increased by an order of magnitude between the first and fourth year of the experimental manipulation, perhaps because of dramatic mortality of Sphagnum mosses in the surface peat of the warmest treatments. However, neither the magnitude nor the temporal dynamics of the responses were captured by ELM-SPRUCE. Here, relative increases in plant-available ammonium and phosphate with warming were similar, but the response varied across raised hummocks and depressed hollows and with peat depth. Plant-available nutrient dynamics were only loosely correlated with inorganic and organic porewater nutrients, likely representing different processes. Future predictions of peatland nutrient availability under climate change scenarios must account for dynamic changes in nutrient acquisition by plants and microbes, as well as microtopography and peat depth.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

ESI-FTICR-MS Analysis of Organic Matter during Incubations with Nitrogen Addition, Teller Road Site, Seward Peninsula, Alaska

This dataset contains the results of the molecular characterization of water-extractable organic matter collected during soil microcosm incubations of tundra soil. The microcosms contained soil collected in April 2017 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (“Toeslope”) and Intensive Site 5 (“Plateau”). The incubations were conducted under an atmosphere of N2 at 8°C for 55 days, with or without addition of ammonium chloride (NH4Cl). Soils were extracted with deionized water and extracted using Bond Elut PPL cartridges prior to analysis. Molecular characterization was performed using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI- FTICR-MS). Two data files are provided with this dataset. The first is the summary, by soil type and treatment, of the mass spectrometry results for formulas (as a % of the total) containing C, H, and O only, and with N, S, and other elements. These formulas were then grouped into nine biochemical classes of compounds based on O:C and H:C ratios. The second file provides soil sample characteristics and the processed high-resolution mass spectrometry results by soil type and treatment.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A Unified Framework to Reconcile Different Approaches of Modeling Transpiration Response to Water Stress: Plant Hydraulics, Supply Demand Balance, and Empirical Soil Water Stress Function

Plant responses to water stress is a major uncertainty to predicting terrestrial ecosystem sensitivity to drought. Different approaches have been developed to represent plant water stress. Empirical approaches (the empirical soil water stress (or Beta) function and the supply-demand balance scheme) have been widely used for many decades; more mechanistic based approaches, that is, plant hydraulic models (PHMs), were increasingly adopted in the past decade. However, the relationships between them—and their underlying connections to physical processes—are not sufficiently understood. This limited understanding hinders informed decisions on the necessary complexities needed for different applications, with empirical approaches being mechanistically insufficient, and PHMs often being too complex to constrain. Here we introduce a unified framework for modeling transpiration responses to water stress, within which we demonstrate that empirical approaches are special cases of the full PHM, when the plant hydraulic parameters satisfy certain conditions. We further evaluate their response differences and identify the associated physical processes. Finally, we propose a methodology for assessing the necessity of added complexities of the PHM under various climatic conditions and ecosystem types, with case studies in three typical ecosystems: a humid Midwestern cropland, a semi-arid evergreen needleleaf forest, and an arid grassland. Notably, Beta function overestimates transpiration when VPD is high due to its lack of constraints from hydraulic transport and is therefore insufficient in high VPD environments. With the unified framework, we envision researchers can better understand the mechanistic bases of and the relationships between different approaches and make more informed choices.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Impact of Drought on Ecohydrology of Southern California Grassland and Shrubland

Abstract Through their rooting profiles and water demands, plants affect the distribution of water in the soil profile. Simultaneously, soil water content controls plant development and interactions within and between plant communities. These plant-soil water feedbacks might vary across plant communities with different rooting depths and species composition. In semiarid environments, understanding these differences will be essential to predict how ecosystems will respond to drought, which may become more frequent and severe with climate change. In this study, we tested how plant-soil water feedbacks responded to drought in two contrasting ecosystem types—grassland and shrubland—in the coastal foothills of southern California. During years 5–8 of an ongoing precipitation manipulation experiment, we measured changes in plant communities and soil moisture up to 2 m depth. We observed different water use patterns in grassland and shrubland communities with distinct plant functional types and water use strategies. Drought treatment did not affect perennial, deep-rooted shrubs because they could access deep soil water pools. However, mid-rooted shrubs were sensitive to drought and experienced decreased productivity and die-off. As a result, water content actually increased with drought at soil depths from 50–150 cm. In grassland, biomass production by annual species, including annual grasses and forbs, declined with drought, resulting in lower water uptake from the surface soil layer. An opportunistic “live fast, die young“ life strategy allowed these species to recover quickly once water availability increased. Our results show how drought interacts with plant community composition to affect the soil water balance of semiarid ecosystems, information that could be integrated into global scale models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)

ABSTRACT Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effects of Vegetation on Fluxes of Nitric Oxide, Nitrogen Dioxide, and Nitrous Oxide in a Mixed Deciduous Forest Clearing

Atmosphere-terrestrial exchange of nitrogen oxides, such as nitric oxide (NO), nitrogen dioxide (NO2) and nitrous oxide (N2O), plays an important role in controlling atmospheric composition and the radiative forcing of Earth’s atmosphere. In this study, the impact of vegetation ground cover on NOx (NOx = NO + NO2) and N2O fluxes in a deciduous forest clearing was studied using dynamic flow chambers located on three experimental plots with differing vegetation ground cover. Microbial emissions of NO and N2O were observed throughout the measurement period, while NO2 was exclusively deposited. Vegetation had no observable impact on NO2 deposition. Under dry conditions, total measured nitrogen emissions were numerically similar across all plots, although the N2O:NO ratio was higher for plots containing plants. Vegetation elevates soil water content through enhanced water retention, a condition that favors denitrification and more N2O production, relative to NO. Two rain events induced pulses of NO and N2O that were higher for bare soil compared to the vegetated plots. Lower NO and N2O emissions in plant-containing chambers stemmed from enhanced root uptake of N following rewetting, which diminished the amount of N substrate available for microbial NO and N2O production. The sensitivity of soil N emissions to vegetation ground cover highlights the need for more studies that investigate this effect over a wide range of ecosystems and to include vegetation effects in future parameterizations of soil NOx and N2O used in atmospheric models. This dataset includes processed data collected from 4 dynamic flux chambers and 17 sensors. Data includes ambient gas measurements made 1 m from the surface and soil flux measurements of NO, NO2, N2O, ozone (O3) and carbon dioxide (CO2). Also included is a suite of meteorological (air temperature, humidity, pressure) and soil parameters (water filled pore space, soil temperature). Refer to the readme for more information about each of the data sets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Soil microbiome resilience to short-term (30 days, 90 days) and long-term (1000 days) drought

This dataset contains data used for the paper "Drought duration does not impact soil microbiome resilience". The Related References will be updated with a full citation when available. Increasing global droughts exert large but poorly understood effects on the microbial communities and ecology of soil. Microbial communities generally show resilience and return to pre-drought conditions when short-term droughted soils are rewet; soils exposed to long-term drought, however, often show a lag upon rewetting, after which microbial communities may or may not return to their pre-stressed conditions. Though short-term droughts have been widely studied, long-term drought manipulation experiments remain rare, especially those that compare microbial response to short-term and long-term drought in tandem. We conducted a 1000-day drought simulation in controlled laboratory conditions with soil cores collected from a tidal freshwater ecosystem in Washington state, USA, and subsequently exposed them to rewetting for two weeks. We also included short-term (30-day and 90-day) drought and rewet treatments to directly compare microbial community and organic matter responses across drought durations. We found distinct microbial taxa belonging to Firmicutes and Actinobacteria enriched after the 1000-day drought, but not after the short-term droughts. While we hypothesized that the microbial community would recover from a short-term drought after rewetting to resemble pre-drought conditions, our results revealed community dissimilarities between rewet and pre-drought conditions across all drought durations. These findings suggest unique microbial life history strategies within certain microbial phyla that make them successful colonizers during an extended drought period, and the influence of environmental and physiological context on microbial responses to rewetting. The 16SrRNA gene amplicon dataset contains processed DNA sequences in the form of an ASV table with raw unrarefied read counts and representative sequences in .fasta format as described in the ESS-DIVE amplicon sequence reporting format (https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format/instructions). The Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) dataset consists of processed files containing presence absence data of molecular formulae and molecular characterization of FTICR resolved peaks. The Nuclear Magnetic Resonance (NMR) dataset contains files relevant to NMR spectra and peaks. A sample key file and a sample metadata file is included for the FTICR/NMR and 16S dataset respectively.

1000-day drought↗
DOE OSTI2021

Root Influences on Mobilization and Export of Mineral-bound Soil Organic Matter

Biogeochemical cycles within mountainous watersheds are key regulators of ecosystem carbon storage and downstream nutrient loadings, and they have shown to be particularly vulnerable to climate change impacts. Increasing temperature and persistent droughts have already dramatically changed vegetation cover across the mountainous western US, with unknown consequences for soil carbon and nutrient cycles belowground. What remains elusive is to what extent associated changes in root-soil interactions may mobilize the vast pool of organic matter (OM) that has been stabilized by associations with minerals for centuries or millennia. Although plant root-driven OM mobilization from minerals may be a central control on carbon loss and nutrient export, such mechanisms are currently missing from conceptual and numerical models. The overall objective of this Exploratory Project is to identify the biogeochemical mechanisms by which roots destabilize mineral-associated organic matter (MAOM) and the cumulative impact on carbon and nutrient fate. To accomplish this goal, we integrated well-controlled laboratory experiments with in-field measurements and a scalable modeling approach. First, we conducted model system experiments to assess the vulnerability of MAOM to exudate-mediated mechanisms. Our results show that common root exudates effectively destabilize MAOM not only through direct, ligand-driven mobilization mechanisms, but also indirect, microbially-mediated mechanisms relying on secondary metabolites and enzymes. We further found that OM bound to poorly crystalline Fe and Al (hydr)oxides is more vulnerable to exudate-induced destabilization than OM bound to more crystalline phases, particularly in response to direct, ligand-promoted mechanisms. These findings demonstrate that the stability of MAOM is not just a function of their inherent properties, but also will depend in large parts on the ability of plant roots and microbes to produce exudates capable of triggering suitable mobilization mechanisms. We further employed a well-controlled rhizobox approach, combining advanced microsensor and mass spectrometry techniques, to resolve spatiotemporal variations in the composition and availability of exudates along single growing roots of grasses. Our results show that the composition of functionally relevant exudate compounds varies at extremely short time scales, seemingly shifting from ligands such as aromatic acids around root tips to less reactive metabolites such as amino acids around mature root segments. These results suggest a prevalence of direct MAOM mobilization mechanisms around the root tip, while indirect MAOM mobilization strategies may dominate around more mature root segments. Additionally, we utilized microsensor measurements in rhizoboxes to parameterize a rhizosphere (hydro)biogeochemistry reactive transport model (eSTOMP-ROOTS). The resulting model was used to assess how root exudations affects the stability of MAOM. Model simulations show that diel pulses of root exudation are strong enough to cause oscillations in biogeochemical conditions—particularly in pH, oxygen concentrations, and microbial activity— that repeatedly disrupt MAOM. Finally, we assessed field-scale impacts of root-driven MAOM destabilization over short and long time scales. A combination of in-field incubations and field-based characterizations showed that MAOM may not only be vulnerable to seasonal variations in root activity, but also to root-driven weathering over pedogenic time scales. In sum, results from our Exploratory Award highlight the strong control plant roots exert on MAOM mobilization and, thus, on the potential for carbon and nutrient export from watersheds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Reduce Revenue Versus Increase Expenditure: Fires and Plant Invasion Drive Soil Carbon Loss With Different Mechanisms in a Mediterranean Shrubland

Fires and plant invasions threaten Mediterranean ecosystems substantially, particularly in the context of changing climate. Our study utilized a data-model integration approach to assess the response of soil organic carbon (SOC) to fires and plant invasion under three Shared Socio-Economic Pathway (SSP) scenarios (SSP1-26, SSP2-45, and SSP5-85). We parameterized the CLM-Microbe model and then investigated the individual and interactive impacts of fires and plant invasion on soil C by comparing factorial simulations of initialization (fire/no wildfire in 2021), fire module on/off, and with and without plant invasion during 2023–2100 in a Mediterranean ecosystem. The simulations indicated a marked C loss due to the 2021 wildfire, projected fires, and plant invasion across all future climate scenarios. Specifically, the 2021 wildfire, projected fires, and plant invasion reduced the SOC (0–30 cm) by 0.12, 0.26, and 0.15 kg C m −2 under SSP1-26, 0.12, 0.30, and 0.12 kg C m −2 under SSP2-45, and 0.12, 0.24, and 0.13 kg C m −2 under SSP5-85, respectively. However, fires and plant invasion decreased SOC through distinct mechanisms. The effects of the 2021 wildfire occurred due to its negative legacy on soil microbial community and, thus, litter accumulation, suppressing the formation of soil carbon via decomposition. Influences of projected fires happen via consuming fuel and suppressing carbon input to soils. In contrast, the impacts of plant invasions were due to enhanced microbial respiration, leading to C loss. In conclusion, these findings emphasize the need for tailored C sequestration strategies considering the disparate effects of fires and plant invasions in the Mediterranean climate.

microbe↗
DOE OSTI2021

Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Forest Age Rivals Climate to Explain Reproductive Allocation Patterns in Forest Ecosystems Globally

ABSTRACT Forest allocation of net primary productivity (NPP) to reproduction (carbon required for flowers, fruits, and seeds) is poorly quantified globally, despite its critical role in forest regeneration and a well‐supported trade‐off with allocation to growth. Here, we present the first global synthesis of a biometric proxy for forest reproductive allocation (RA) across environmental and stand age gradients from a compiled dataset of 824 observations across 393 sites. We find that ecosystem‐scale RA increases ~60% from boreal to tropical forests. Climate shows important non‐linear relationships with RA, but is not the sole predictor. Forest age effects are comparable to climate in magnitude (MAT: ß = 0.24,p = 0.021; old growth forest: ß = 0.22,p < 0.001), while metrics of soil fertility show small but significant relationships with RA (soil pH: ß = 0.07,p = 0.001; soil N: ß = −0.07,p = 0.001). These results provide strong evidence that ecosystem‐scale RA is mediated by climate, forest age, and soil conditions, and is not a globally fixed fraction of positive NPP as assumed by most vegetation and ecosystem models. Our dataset and findings can be used by modellers to improve predictions of forest regeneration and carbon cycling.

Environmental Sciences & Ecology↗
DOE OSTI2022

A Process‐Model Perspective on Recent Changes in the Carbon Cycle of North America

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 to improve these estimates and study the drivers of its interannual variability. Our results show that North America has been a C sink with a magnitude of 0.37 ± 0.38 (mean and one standard deviation) PgC year —1 for the period 2000–2019 (0.31 and 0.44 PgC year —1 in each decade); split into 0.18 ± 0.12 PgC year —1 in Canada (0.15 and 0.20), 0.16 ± 0.17 in the United States (0.14 and 0.17), 0.02 ± 0.05 PgC year —1 in Mexico (0.02 and 0.02) and 0.01 ± 0.02 in Central America and the Caribbean (0.01 and 0.01). About 57% of the new C assimilated by terrestrial ecosystems is allocated into vegetation, 30% into soils, and 13% into litter. Losses of C due to fire account for 41% of the interannual variability of the mean net biome productivity for all North America in the model ensemble. Finally, we show that drought years (e.g., 2002) have the potential to shift the region to a small net C source in the simulations (—0.02 ± 0.46 PgC year —1 ). Our results highlight the importance of identifying the major drivers of the interannual variability of the continental-scale land C cycle along with the spatial distribution of local sink-source dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

CRISPR-based engineering of phages for in situ bacterial base editing

Investigation of microbial gene function is essential to the elucidation of ecological roles and complex genetic interactions that take place in microbial communities. While microbiome studies have increased in prevalence, the lack of viable in situ editing strategies impedes experimental progress, rendering genetic knowledge and manipulation of microbial communities largely inaccessible. Here, we demonstrate the utility of phage-delivered CRISPR-Cas payloads to perform targeted genetic manipulation within a community context, deploying a fabricated ecosystem (EcoFAB) as an analog for the soil microbiome. First, we detail the engineering of two classical phages for community editing using recombination to replace nonessential genes through Cas9-based selection. We show efficient engineering of T7, then demonstrate the expression of antibiotic resistance and fluorescent genes from an engineered λ prophage within an Escherichia coli host. Next, we modify λ to express an APOBEC-1-based cytosine base editor (CBE), which we leverage to perform C-to-T point mutations guided by a modified Cas9 containing only a single active nucleolytic domain (nCas9). We strategically introduce these base substitutions to create premature stop codons in-frame, inactivating both chromosomal ( lacZ ) and plasmid-encoded genes (mCherry and ampicillin resistance) without perturbation of the surrounding genomic regions. Furthermore, using a multigenera synthetic soil community, we employ phage-assisted base editing to induce host-specific phenotypic alterations in a community context both in vitro and within the EcoFAB, observing editing efficiencies from 10 to 28% across the bacterial population. The concurrent use of a synthetic microbial community, soil matrix, and EcoFAB device provides a controlled and reproducible model to more closely approximate in situ editing of the soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗