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DOE OSTI2023

Accounting for herbaceous communities in process‐based models will advance our understanding of “grassy” ecosystems

Abstract Grassland and other herbaceous communities cover significant portions of Earth's terrestrial surface and provide many critical services, such as carbon sequestration, wildlife habitat, and food production. Forecasts of global change impacts on these services will require predictive tools, such as process‐based dynamic vegetation models. Yet, model representation of herbaceous communities and ecosystems lags substantially behind that of tree communities and forests. The limited representation of herbaceous communities within models arises from two important knowledge gaps: first, our empirical understanding of the principles governing herbaceous vegetation dynamics is either incomplete or does not provide mechanistic information necessary to drive herbaceous community processes with models; second, current model structure and parameterization of grass and other herbaceous plant functional types limits the ability of models to predict outcomes of competition and growth for herbaceous vegetation. In this review, we provide direction for addressing these gaps by: (1) presenting a brief history of how vegetation dynamics have been developed and incorporated into earth system models, (2) reporting on a model simulation activity to evaluate current model capability to represent herbaceous vegetation dynamics and ecosystem function, and (3) detailing several ecological properties and phenomena that should be a focus for both empiricists and modelers to improve representation of herbaceous vegetation in models. Together, empiricists and modelers can improve representation of herbaceous ecosystem processes within models. In so doing, we will greatly enhance our ability to forecast future states of the earth system, which is of high importance given the rapid rate of environmental change on our planet.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Bioenergy for climate change mitigation: Scale and sustainability

Many global climate change mitigation pathways presented in IPCC assessment reports rely heavily on the deployment of biomass for bioenergy, often used in conjunction with carbon capture and storage (BECCS). We review the literature on bioenergy, including the modelling of bioenergy in integrated assessment models (IAMs) and bottom-up modelling and non-modelling studies on the implications of bioenergy use. We summarise the limitations of existing modelling studies and what is known about the potential co-benefits and adverse side-effects of bioenergy systems. We find that the implications of bioenergy supply on mitigation and other sustainability criteria are context dependent and influenced by feedstock, management regime, climatic region, scale of deployment and the counterfactual land use and energy system. However, due to limitations of the existing models, and uncertainty over the future context with respect to the many variables that influence availability of biomass and land resources, it is not possible to precisely quantify the sustainability implications for different scales of bioenergy implementation. Given these uncertainties, the dependence on large-scale deployment of bioenergy in mitigation scenarios carries risks. The deployment of bioenergy technologies and the evolution of biomass supply chains at a scale that achieves significant mitigation and carbon sequestration requires integrative policies, coordinated institutions and improved governance mechanisms. As a result, bioenergy, and the use of land to produce biomass, is an essential part of many climate mitigation strategies but there are limits to its use due to trade-offs with sustainability.

09 BIOMASS FUELS↗

DOE OSTI2020

Chemical plasticity in the fine root construct of Quercus spp. varies with root order and drought

ne roots of trees exhibit high plasticity to adapt to environmental stress. Although the morphological and physiological plasticity of roots has been well studied, less explored are the accompanying changes in the chemical plasticity of fine roots, which regulates both root function and soil carbon sequestration. We investigated the changes in quantity, composition and localization of compounds in different fine root orders of Quercus alba and Quercus rubra subjected to drought stress. The total quantity of lignins varied only by root orders where distal (1+2) orders had lower lignin compared to higher orders. However, the 1+2 orders had higher guaiacyl lignin and bound phenolics, which provide greater protection from environmental stress. Unlike lignins, drought altered the quantity and composition of tannins. In Q. alba, the ellagitannins decreased in the 1+2 orders exposed to drought. The lower content of ellagitannins with antimicrobial properties reveals a strategic adaptive response by fine roots to facilitate symbiotic association, as evidenced by the higher colonization of ectomycorrhizal fungi, which help in drought tolerance. Our study revealed that the chemical construct of different heteropolymers varied differently across root orders when exposed to drought, indicating the importance of chemical plasticity of fine roots to adapt to environmental stress

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Accelerated sea-level rise is suppressing CO 2 stimulation of tidal marsh productivity: A 33-year study

Accelerating relative sea-level rise (RSLR) is threatening coastal wetlands. However, rising CO 2 concentrations may also stimulate carbon sequestration and vertical accretion, counterbalancing RSLR. A coastal wetland dominated by a C 3 plant species was exposed to ambient and elevated levels of CO 2 in situ from 1987 to 2019 during which time ambient CO 2 concentration increased 18% and sea level rose 23 cm. Plant production did not increase in response to gradually rising ambient CO 2 concentration during this period. Elevated CO 2 increased shoot production relative to ambient CO 2 for the first two decades, but from 2005 to 2019, elevated CO 2 stimulation of production was diminished. The decline coincided with increases in relative sea level above a threshold that hindered root productivity. While elevated CO 2 stimulation of elevation gain has the potential to moderate the negative impacts of RSLR on tidal wetland productivity, benefits for coastal wetland resilience will diminish in the long term as rates of RSLR accelerate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth’s surface environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Cretaceous sequence stratigraphy of the northern Baltimore Canyon Trough: Implications for basin evolution and carbon storage

We evaluate the Cretaceous stratigraphy and carbon sequestration potential of the northern Baltimore Canyon Trough (NBCT) using >10,000 km of multi-channel seismic profiles integrated with geophysical logs, biostratigraphy, and lithology from 29 offshore wells. We identify and map six sequences resolved primarily at the stage level. Accommodation was dominated by thermal and non-thermal subsidence, though sequence boundaries correlate with regional and global sea-level changes, and the record is modified by igneous intrusion, active faulting, and changes in sediment supply and sources. Our stratigraphic maps illustrate a primary southern (central Appalachian) Early Cretaceous source that migrated northward during the Aptian and Albian. During the Cenomanian, sedimentation rates in the NBCT increased and depocenters shifted northward and landward. We show that deposition occurred in three phases: (1) earlier Cretaceous paleoenvironments were primarily terrestrial indicated by variable amplitude, chaotic seismic facies, serrated gamma logs, and heterolithic sandstones and mudstones with terrestrial microfossils; (2) the Albian to Cenomanian was dominated by deltaic paleoenvironments indicated by blocky, funnel-shaped, gamma-ray logs and clinoforms characterized by continuous high-amplitude seismic reflections with well-defined terminations; and (3) the Cenomanian and younger was marine shelf, inferred from mudstoneprone lithologies, peak gamma-ray values in well logs, and foraminiferal evidence. Long-term transgression and maximum water depths at the Cenomanian/Turonian boundary correlative with Ocean Anoxic Event 2 were followed by a regression and relative sea-level fall. We show that porous and permeable sandstones of three Aptian to Cenomanian highstand systems tracts are high-volume reservoirs for supercritical CO 2 storage that are confined by overlying deep water mudstones.

58 GEOSCIENCES↗

DOE OSTI2021

Reactive Flows in Porous Media: Challenges in Theoretical and Numerical Methods

We review theoretical and computational research, primarily from the past 10 years, addressing the flow of reactive fluids in porous media. The focus is on systems where chemical reactions at the solid–fluid interface cause dissolution of the surrounding porous matrix, creating nonlinear feedback mechanisms that can often lead to greatly enhanced permeability. Here, we discuss insights into the evolution of geological forms that can be inferred from these feedback mechanisms, as well as some geotechnical applications such as enhanced oil recovery, hydraulic fracturing, and carbon sequestration. Until recently, most practical applications of reactive transport have been based on Darcy-scale modeling, where averaged equations for the flow and reactant transport are solved. We summarize the successes and limitations of volume averaging, which leads to Darcy-scale equations, as an introduction to pore-scale modeling. Pore-scale modeling is computationally intensive but offers new insights as well as tests of averaging theories and pore-network models. We include recent research devoted to validation of pore-scale simulations, particularly the use of visual observations from microfluidic experiments.

wormhole formation↗

DOE OSTI2024

Modeling Framework for the Assessment of a Sustainable Hydrogen Production and Supply Chain Network in California

The cost-effective and sustainable deployment of hydrogen supply and demand networks, especially in large economic regions like California, can be challenging considering the spatial-temporal availability and variability of the different actors across the network such as production processes, distribution modes, and end-users. In this presentation, we will provide an overview and demonstration of a modeling framework used to assess the environmental, economic, and human health impacts of plausible hydrogen production and supply chain networks in California. Scenarios focus on green hydrogen production pathways using water electrolysis and biomass gasification. End-use applications included in the model are transit, medium and heavy-duty trucking, port authorities, and power and aviation companies that currently consume natural gas, diesel, and aviation fuel for their day-to-day operation. Representative locations for hydrogen production and end-use are based on recent projections of the hydrogen economy in California. All mass and energy flows, as well as estimated emissions, are based on H2A process model designs and projections of technology performance, literature review, and LBNL process, economic and life cycle modeling, and not on company data for the sake of this presentation. Human health impacts are included following methodologies developed for the University of California Irvine HyDeal project. Life cycle phases associated with hydrogen production include feedstock preparation (water and biomass), energy production and consumption (renewable, grid, and combination of renewable and grid electricity), maintenance (chemical utilization in electrolysis and natural gas combustion in gasification), carbon sequestration, hydrogen storage (compression and liquefaction), and distribution (truck and pipeline). We apply the framework utilizing California specific emission factors, financial data, and human health damages and explore the impact of network characteristics on results. Example variations include: the inclusion of policy incentives or not, different representations of the electricity grid and source, electrolysis versus gasification versus combinations of both for production, liquefaction versus compression based on producer capacity cutoffs, transportation truck versus pipeline based on existing infrastructure, and ultimate end use. Comparison of these different scenarios can help inform future projects by demonstrating the trade-offs among environmental, economic, and human health impacts. This model, automated in R, is a starting platform upon which new analysis, modeling capabilities, locations, and emission factors can be rapidly tested and integrated.

Zaki, Mohammed Tamim↗

DOE OSTI2023

Semi-Analytical Leakage Solutions for Aquifers (SALSA) v1

SALSA is a semi-analytical modeling tool that can provide assessments of pressure perturbations and brine leakage because of fluid injection and extraction activities in sedimentary basins. Sedimentary basins typically contain vertical sequences of near-horizontal aquifers separated by less-permeable aquitards. In the context of geologic carbon sequestration (GCS), while aquitards are relied upon to contain injected buoyant free-phase CO2 and limit inter-aquifer brine flow, the large number of leaky wells (e.g., unused/unsuccessful exploration wells, or improperly plugged water or oil/gas wells) that are present in sedimentary basins creates concerns for potential leakage and groundwater contamination. The mathematical theory and solution method included in SALSA is presented in our recent manuscript under review. SALSA is the first to account for the coupled leakage through aquitards and leaky wells, with geologic pressurization sources. SALSA based on semi-analytical solutions can be computationally very efficient for problems containing many injection and leaky wells in multilayered sedimentary systems, compared to any numerical simulation software requiring local mesh refinement around each well to obtain accurate results. Therefore, stakeholders (e.g., regulators, operators) for site screening, injection and post-injection pressure behavior and assessing leakage risks can use SALSA as a fast-predictive tool in GCS applications in multilayered aquifer systems.

Cihan, Abdullah↗

DOE OSTI2021

pnnl/SOSAT

State of Stress Analysis Tool (for carbon sequestration). The SOSAT tool provides value during GCS site screening and characterization phases to target collection of specific additional data to constrain uncertainties in geomechanical risk and to help operators to make informed decisions during the operational phase (Appriou et al., 2019). The capability represented in SOSAT, therefore, helps build stakeholder confidence that geomechanical risks are understood and manageable

Central, PNNL Developer↗

DOE OSTI2023

TReactMech v4.217

TReactMech couples geomechanical processes (poroelasticity, failure, and inelastic strain) with multiphase nonisothermal flow (derived from TOUGH2) and reactive geochemical transport. At its core is the reactive-transport code TOUGHREACT v4.13. TReactMech is an efficient hybrid parallel simulator, solving the geomechanics using finite elements and MPI/PetSc, the multiphase flow using integrated finite difference and MPI/PETSc, and the reactive chemistry using OpenMP. The advantages of TReactMech are in its multiphase flow capabilities (e.g., supercritical CO2, supercritical water, air) and parallel geomechanics including full 3-D stress tensor, shear and tensile failure, coupled to porosity and permeability changes. It is backwardly compatible with TOUGH2 and TOUGHREACT v4.13, allowing for easier transitions between the codes. TReactMech can be used to simulate many natural and engineered subsurface systems, including geothermal reservoirs, borehole heat exchangers, geologic carbon sequestration, geologic storage of nuclear waste, groundwater resources, weathering, sediment diagenesis, seafloor hydrothermal circulation, hydrofracturing in unconventional reservoirs, and injection/production-induced surface deformation.

Sonnenthal, Eric↗

DOE OSTI2022

T2Well/EOS7NC (EOS7NC) v1.0Beta

T2Well/EOS7NC extends TOUGH2/EOS7C to include the choice of any three of a variety of non-condensable gas components and adds the coupled well-reservoir capability of T2Well. T2Well/EOS7NC is applicable to geologic carbon sequestration, CO2-enhanced gas recovery, compressed air energy storage, geologic hydrogen storage, and other subsurface porous-media injection/withdrawal processes involving non-condensable gases. The advantage of T2Well/EOS7NC over TOUGH2/EOS7C is that TOUGH2/EOS7C is restricted to modeling CO2 or N2, a gas tracer, and CH4 whereas T2Well/EOS7NC can model and three non-condensable gas components chosen from a long list within the code. In addition, T2Well provides the coupled well-reservoir capability.

Oldenburg, Curtis↗

DOE OSTI2021

Experimental study correlating damage and permeability in concrete using confined, flattened Brazilian disks

This research experimentally studies coupled hydro-mechanical relationships using flattened Brazilian disks under confinement, with concurrent permeability measurements and acoustic emission monitoring. A series of tests are performed on concrete, as representative samples of brittle geo-materials, under a range of confining stresses between 2.76 and 13.79 MPa. Acoustic emission data is used to quantify damage and identify damage thresholds. Damage is then correlated to pre-peak changes in permeability. The advancement of models that couple transport properties to mechanical responses are of interest in the fields of carbon sequestration, hydrofracking, production of geothermal energy, induced seismicity, and underground nuclear waste storage, and these experiments validate a novel experimental approach towards investigating hydro-mechanical relationships.

Boyce, S.↗

DOE OSTI2024

Carbon-Storing Structural Material Based on Wastewater-Cultivated Chlorella Sorokiniana

Microalgae cultivation is a promising technology for carbon sequestration and wastewater remediation. It is economically and logistically critical to find viable applications for the large quantities of produced biomass. In current research, a structural material is developed by using nearly 100% Chlorella sorokiniana. The otherwise non-cohesive microalgae cells are first surface-activated and then compacted under a relatively high pressure. The resulting material is a dense solid, stronger than typical steel-reinforced concrete in flexural tests. The processing procedure is simple and fast, and the setup is scalable. This technique may be useful for next-generation green construction and provide a use-case for sustainable microalgae biomass.

Yi, Haozhe↗

DOE OSTI2022

Transformation and gene editing in the bioenergy grass Miscanthus

Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.

09 BIOMASS FUELS↗

DOE OSTI2023

Machine learning-based inversion for acoustic impedance with large synthetic training data: Workflow and data characterization

Where wells are sparse or training data are difficult to label with high-quality wireline-derived impedance logs, machine learning (ML)-based inversion of acoustic impedance typically depends on small training data sets, leading to biased prediction. We have advanced a novel workflow that applies large synthetic seismic training data to reduce facies-related bias. Using a geologically realistic model as the truth model, we randomly select sparse seed wells to perform sequential Gaussian simulation (SGS) for impedance models of the same geometry and simulate facies variability. We implement random forest regression on 30 features extracted from the synthetic volume. We observe that more seed wells tend to reduce facies-induced bias by sampling more types of facies, resulting in a better prediction. We then focus on the responses of SGS models to facies changes, the number of seed wells necessary for a useful synthetic model, and how much a synthetic model can help ML-based inversion. Here, we observe that the SGS synthetic training model outperforms well-direct training in general. For modeled clastic shore-zone systems in Miocene Gulf of Mexico, two or more seed wells are necessary for a significant reduction of root-mean-square error and outliners, and improvement of facies imaging. In a field-data test, we apply a similar workflow to quantitatively predict acoustic impedance, which is then converted to a sand-volume map at a high-frequency sequence (10–100 m), revealing detailed facies and sandstone patterns. Such results are valuable in many geologic and engineering applications, such as hydrocarbon and CO 2 reservoir prospecting, reserve estimation, simulation, etc.

3D seismic↗

DOE OSTI2020

Seismic response to paleo-sand dunes in the Nugget Sandstone Formation, southwestern Wyoming

We have analyzed a 3D seismic survey acquired for a carbon sequestration project on top of the Moxa Arch in southwestern Wyoming. We observed a zone of discontinuous reflectors on vertical slices of seismic amplitude volume, whereas, the northwest–southeast lineations were observed on the time slices. We performed a seismic to well tie that suggested that the lineations occur within the Nugget Sandstone. The Nugget Sandstone is an eolian sandstone deposit of Early Jurassic age, deposited as a subtropical dune field, and equivalent to the Navajo Sandstone of southwestern Utah. Petrophysical analysis indicates that the Nugget Sandstone is dominated by clean sandstone (70%–80%), whereas evaporites, including halite and anhydrite, are present in certain zones. Previous outcrop studies on the Navajo Sandstone indicate the wind direction to be predominantly northeast–southwest. Seismic attributes, including coherence and curvature, displayed on stratal slices within the Nugget Sandstone interval indicate the presence of lineations in the northwest–southeast direction with irregular spacing. These lineations are approximately perpendicular to the inferred dominant wind direction. We computed the dominant wind direction from the average azimuth of the lineations as seen on the curvature attribute in the Nugget Sandstone interval. Geological feature: Eolian sand dunes with interdunal evaporites Seismic appearance: Parallel lineations with irregular spacing on seismic attribute horizon slices Alternative interpretations: Canyons at continental slopes; slope failures Features with a similar appearance: Marine bars; contourites Formation: The Nugget Sandstone — equivalent to the Navajo Sandstone Age: Early Jurassic Location: Moxa Arch, Wyoming Seismic data: Obtained by the University of Wyoming with U.S. DOE funding Contributors: Dhruv Agrawal, Brady Lujan, Sumit Verma, Shuvajit Bhattacharya, and Subhashis Mallick Analysis tools: Coherence and curvature attributes; seismic inversion; petrophysical inversion

Geochemistry & Geophysics↗

DOE OSTI2022

Data for Transformation and Gene Editing in the Bioenergy Grass Miscanthus

Miscanthus, a C4 member of the family Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies Miscanthus x giganteus and its parental species M. sacchariflorus and M. sinensis . Use of biotechnology-based procedures to genetically improve miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.

Biomass Analytics↗