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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2025

Simulating Marine Ecosystem Dynamics and Biogeochemical Cycling With Multiple Plankton Functional Types

Current representations of marine ecosystems in Earth System Models are greatly simplified, neglecting key interactions between dynamic food webs, biogeochemistry, and climate change. We use the Marine Biogeochemistry Library code base within the Community Earth System Model 2.2.2 to create an expanded ecosystem model with eight phytoplankton groups and four zooplankton size classes (MARBL-8P4Z). Incorporating more specific plankton types and size classes has the potential to capture a wider range of possible behaviors of the ecosystem, its complex interactions with biogeochemistry, and its feedback to climate change. It also permits stronger observational constraints, including in situ group-specific biomass and various observational estimates of plankton community composition. MARBL-8P4Z broadly captures observed global-scale patterns in biomass and community composition for both phytoplankton and zooplankton, with a good performance in simulating broad biogeochemistry fields. The model shows comparable spatial patterns and magnitudes to the observed picophytoplankton biomass (Prochlorococcus, Synechococcus, picoeukaryotes), and captures the seasonal cycle of mesozooplankton biomass. Picophytoplankton groups and microzooplankton dominate biomass and production in oligotrophic, subtropical regions, while nano-phytoplankton, diatoms and the larger zooplankton groups prevail at higher latitudes and within upwelling zones. The model simulates reasonable energy transfer efficiency through the food web, with tight linkages between the phytoplankton community composition, zooplankton grazing, and carbon export, with the potential to link to fisheries models. Thus, MARBL-8P4Z has the potential to account for key climate-driven ecological shifts in the plankton that will modify ocean biogeochemistry in the future.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Dryland feedbacks to future climate change: how species mortality and replacement will affect coupled biogeochemical cycles and energy balance (Final Technical Report)

The overall goal of the dryland climate manipulation experiment is to improve our understanding and ability to forecast dryland responses to increasing temperatures and altered precipitation regimes. Drylands cover over 40% of Earth’s terrestrial surface and are predicted to increase in size 11-23% by 2100. Yet our understanding of this vast biome, which exchanges enormous amounts of CO 2 and energy with the atmosphere, is exceedingly poor. This project aims to transform and improve that understanding in order to reduce uncertainty and increase the confidence with which we can make global predictions of future climate. We focus on both above- and belowground processes, and explore temperature controls over critical aspects of carbon and nutrient cycling for dryland plants, soil, and microbes. We have 60 climate manipulation plots where plants (from above the canopy) and soils are warmed using infrared lamps and where precipitation has been altered using targeted watering regimes. We have measured myriad aspects of plant physiology, morphology, carbon exchange, energy exchange, and phenology, as well as analogous climate-induced changes to biological soil crusts and soil microbial communities. Our goals are to investigate temperature responses and acclimation potential of dryland plant and soil processes. Concurrent soil incubation experiments complement the in-situ soil warming component and enable more controlled mechanistic investigations of temperature response on microbial function. Automated soil CO 2 efflux chambers within the plots provide phenomenal opportunity to improve our understanding of dryland CO 2 exchange with the atmosphere and are coupled with plant CO 2 exchange measurements. The project has been exceptionally successful, with 35 peer-reviewed publications (and more in review), including in high-profile journals such as Nature Climate Change and PNAS. We have given over fifty presentations on the work and it has been featured in many high-profile media outlets, such as Discover Magazine and on NPR.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Impacts of sulfonic acids on fungal manganese oxide production

Microbial manganese (Mn) oxidation plays a critical role in Mn(III/IV) oxide formation in modern day environmental systems. These oxidation processes and resulting biominerals are sensitive to aqueous conditions, such as pH and dissolved constituent concentrations. With Mn and sulfur (S) biogeochemical cycling closely linked in many environmental systems, and dissolved organic sulfur comprising a substantial pool of total sulfur in several environments, the impact of dissolved organic sulfur compounds on Mn redox processes is important to consider. Sulfonic acids, environmentally ubiquitous organosulfur compounds, play substantial roles in S cycling in many natural and contaminated systems. Research to assess the effects of these abundant sulfonic acids on Mn biogeochemical cycling, microbial Mn oxidation processes, and Mn biominerals is needed for understanding and predicting the impact of coupled S and Mn biogeochemical cycles, particularly in environments with dynamic redox gradients or in anthropogenically contaminated systems. Further, with research on microbial and abiotic Mn oxidation processes often using aminosulfonic acids to control pH, understanding the impact of such sulfonic acids on microbial Mn oxidation processes is critical. Several recent studies found that commonly used zwitterionic N substituted aminosulfonic acids, known as Good’s buffers, such as HEPES and MES, can alter abiotic birnessite sheet structures. Here we investigate the impact of two sulfonic acids with broad applications to natural and contaminated sites as well as laboratory settings (HEPES and MES) on fungal Mn oxidation relative to a carbonate buffer and a buffer-free control by three Ascomycete fungi known to oxidize Mn(II): Stagonospora sp. SRC1lsM3a, Paraphaeosphaeria sporulosa AP3s5–JAC2a, and Plectosphaerella cucumerina DS2psM2a2. Structural analyses of the products show that sulfonic acids promote Mn oxidation by P. cucumerina, producing hexagonally symmetric phyllomanganates analogous to hexagonal birnessite or c–disordered H + birnessite [(Ca,Na,K)(Mn 4+ ,Mn 3+ ,$\square$)O 2 nH 2 O], with solid–associated Mn(II) bound to vacancy sites and biomass, while in their absence almost all Mn remains as either aqueous Mn(II) or solid–associated Mn(II) bound to biomass. In contrast, sulfonic acids exert the opposite effect on Mn oxidation by P. sporulosa, with their presence suppressing Mn(II) oxidation to Mn(IV), likely leading to the formation of mycogenic bixbyite (Mn 3+ 2 O 3 ) while the buffer–free control forms a poorly crystalline phyllo- or tectomanganate. Meanwhile, all treatments exert a minimal effect on Mn(II) uptake from solution and Mn oxidation with Stagonospora sp., with all experimental systems and controls forming poorly crystalline, hexagonally symmetric phyllomanganates. The fact that the sulfonic acids here studied exert similar effects on Mn oxidation, but substantially different effects for each fungus, suggests they affect Mn oxidation via mechanistically similar pathways that are likely dependent on interactions with fungal exudates (which vary from species to species) or specific fungal Mn oxidation processes. Interestingly, for all fungi, MES increases Mn(III) in the resulting biominerals, while the carbonate buffer consistently decreases Mn(III). Further, these results clearly demonstrate that sulfonic acids not only alter Mn oxide structures, as has been previously noted in abiotic studies, but can interfere with Mn oxidation reactions themselves, highlighting the incredible sensitivity of both Mn oxide structures and the Mn oxidation process to the aqueous environment.

58 GEOSCIENCES↗
DOE OSTI2024

Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling

Abstract Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change–induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.

Nelson, Amelia R.↗
DOE OSTI2023

Matrix Approach to Accelerate Spin-Up of CLM5

Numerical models have been developed to investigate and understand responses of biogeochemical cycle to global changes. Steady state, when a system is in dynamic equilibrium, is generally required to initialize these model simulations. However, the spin-up process that is used to achieve steady state pose a great burden to computational resources, limiting the efficiency of global modeling analysis on biogeochemical cycles. This study introduces a new Semi-Analytical Spin-Up (SASU) to tackle this grand challenge. We applied SASU to Community Land Model version 5 and examined its computational efficiency and accuracy. At the Brazil site, SASU is computationally 7 times more efficient than (or saved up to 86% computational cost in comparison with) the traditional native dynamics (ND) spin-up to reach the same steady state. Globally, SASU is computationally 8 times more efficient than the accelerated decomposition spin-up and 50 times more efficient than ND. In summary, SASU achieves the highest computational efficiency for spin-up on site and globally in comparison with other spin-up methods. It is generalizable to wide biogeochemical models and thus makes computationally costly studies (e.g., parameter perturbation ensemble analysis and data assimilation) possible for a better understanding of biogeochemical cycle under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Arctic Shrub Expansion, Plant Functional Trait Variation, and Effects on Belowground Carbon Cycling (Final Technical Report)

Terrestrial ecosystems are undergoing dramatic changes in response to climate warming, and these changes are expected to feedback to the atmosphere, potentially altering the trajectory of future climate change. Feedbacks from Arctic ecosystems are a major concern because the Arctic is projected to warm significantly in the 21 st century and because >50% of global belowground organic carbon is stored in permafrost and overlying soils. Warming-driven release of this carbon could drastically increase atmospheric greenhouse gas concentrations and accelerate climate warming. Plant communities are also responding to warming, as evidenced by the widely documented increase in woody-shrub growth and “greening” across much of the Arctic tundra biome. This vegetation shift may offset or amplify warming by altering carbon cycling. The direction and magnitude of shrub effects remain highly uncertain, however, due to limited understanding of the consequences of shrub expansion for belowground carbon cycling and simplification of these relationships in models. The major shrubs expanding in the Arctic (Betula, Salix, and Alnus) vary widely with respect to aboveground and belowground traits (e.g., tissue production and chemistry, rooting depth, microbial symbionts), and may also exhibit substantial intraspecific variation in these traits in response to environmental conditions. Such variation is likely to have profound implications for soil carbon cycling. The overarching goal of this project was to improve process-based understanding of the influence of shrub expansion on carbon cycling to enable improved representation of carbon dynamics in ecosystem and Earth system models. We investigated how plant functional traits vary among shrub genera, respond to environmental conditions, and affect belowground carbon and nutrient cycling by quantifying relationships among functional traits and biogeochemical cycling along edaphic gradients nested within a climate gradient in the Alaskan tundra. We found consistent differences in leaf and root traits among shrub genera and between shrubs and a widespread sedge species, indicating diverse nutrient acquisition strategies and belowground impacts among different arctic shrubs. We also found striking differences in trait values among individuals within the same species or genera within sites. Soil parameters were more important than climate parameters for predicting size and leaf trait variation, and root trait responses were less dependent on climate overall. For all but one root trait, including parameters representing aboveground traits improved the predictive ability of models. These results demonstrate that tundra shrub traits vary considerably at local scales and soil factors drive this variation, especially belowground. Furthermore, leveraging information about aboveground traits and soil conditions can improve predictions of how belowground traits will respond to climate change. Despite these differences, soil carbon and nitrogen pools in the active layer did not vary among plots dominated by different shrub or sedge genera. Instead, pool sizes generally decreased from warmer to colder sites, consistent with a productivity gradient. Patterns of isotopic N composition indicate that shrubs tighten nitrogen cycling via nitrogen resorption or immobilization of shrub litter. Overall, these results suggest that further identifying the specific shrub genera in the tundra landscape will ultimately provide better predictions of belowground dynamics across the changing arctic. We also performed simulation experiments with the Terrestrial Ecosystem Model (TEM) incorporated in the Predictive Ecosystem Analyzer (PEcAn) framework, treats model parameters as probability distributions, estimates parameters based on a synthesis of available field data, and then quantifies both model sensitivity and uncertainty to a given parameter or suite of parameters. We performed simulations across different types of tundra, including shrub tundra. One key finding was that both model sensitivity and uncertainty to a given parameter could vary within the same type of tundra, but in a different geographical location, such as over the climate gradient of shrub tundra described above. We organized a special session at the annual meeting of the Ecological Society of America in August 2019 to disseminate our results, refine recommendations for model improvement, and initiate collaborations to implement these recommendations in existing models of tundra carbon dynamics at ecosystem to Earth system scales. Our results support DOE near-term priorities by providing mechanistic insights into the role of vegetation change in the terrestrial carbon cycle in a region that is inadequately represented in Earth system models. Current models reduce the complexity of Arctic vegetation to a small number of plant functional types (PFTs). This approach implicitly assumes that each PFT represents the average ecological function of its constituent species, thus ignoring the effects of trait variation on biogeochemical cycling and potentially leading to large uncertainty in the sign and magnitude of ecosystem feedbacks to climate. By quantifying variation of plant functional traits across broad gradients of climatic and edaphic conditions and elucidating the linkages of such variation with carbon and nutrient cycling, our results illustrate the need and create a foundation for further developing trait-based modeling approaches that allow the traits of PFTs to vary as a function of environmental conditions. These approaches should improve the capacity of simulation models to offer insights into ecosystem carbon dynamics associated with novel plant communities in a rapidly changing Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Advancing the understanding of coastal disturbances with a network-of-networks approach

Coastal ecosystems are at the nexus of many high priority challenges in environmental sciences, including predicting the influences of compounding disturbances exacerbated by climate change on biogeochemical cycling. Extreme events such as hurricanes, flooding, landslides, and wildfires influence biogeochemical cycling in these systems. However, while research in coastal science is fundamentally transdisciplinary – as drivers of biogeochemical and ecological processes often span scientific and environmental domains – traditional place-based approaches are still often employed to understand coastal ecosystems. In this perspective, we argue that integration among distributed research sites from a macrosystem perspective is crucial to understand how compounding disturbances affect coastal ecosystems. We identify a roadmap for the implementation of an integrated network-of-networks framework that leverages existing research network sites in coastal ecosystems to advance continental-scale process understanding for studying extreme events and global change. We also identify specific ways that existing research efforts can maximize mutual benefit, and where additional infrastructure investments might increase return-on-investment along the coast, using the coastal continental US as a case study.

Myers-Pigg, Allison N. [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2022

Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition

To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from correlational evidence, such as virus-driven changes in microbial abundances, viral auxiliary metabolic genes, and links with soil physiochemical properties. To more directly test the impact of soil viruses on carbon cycling during plant litter decomposition, we added concentrated viral community suspensions to complex litter decomposer communities in 40-day microcosm experiments. Microbial communities from two New Mexico alpine soils, Pajarito (PJ) and Santa Fe (SF), were inoculated onto grass litter on sand, and three treatments were applied in triplicate to each set of microcosms: addition of buffer (no added virus), live virus (+virus), or killed-virus (+killed-virus) fractions extracted from the same soil. Significant differences in respiration were observed between the +virus and +killed-virus treatments in the PJ, but not the SF microcosms. Bacterial and fungal community composition differed significantly by treatment in both PJ and SF microcosms. Combining data across both soils, viral addition altered links between bacterial and fungal diversity, dissolved organic carbon and total nitrogen. Overall, we demonstrate that increasing viral pressure in complex microbial communities can impact terrestrial biogeochemical cycling but is context-dependent.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Understanding and Predictability of Integrated Mountain Hydroclimate (Workshop Report)

Mountainous systems cover approximately 23% of Earth’s land and are distributed across all continents. They can capture and store atmospheric moisture that is then cycled through the terrestrial surface and subsurface system, released to downstream communities, and cycled back to the atmosphere. Mountain hydroclimate—characterized by steep gradients, geological, ecological, and biogeochemical diversity—is influenced by topographic forcing and elevated warming and susceptible to large subseasonal to multidecadal variability and rapid changes. Terrestrial hydrological and biogeochemical cycles also experience cascading effects from global warming impacts, such as multidecadal declines in mountain snowpack, longer growing seasons, and increased frequency and severity of extreme events like droughts and wildfires. However, little is known about the effects of these impacts and their feedbacks on climate systems and surface-subsurface compartments. Also unknown are the full implications of changing hydroclimate and extreme events on hydro biogeochemical cycles across atmosphere, terrestrial, and human systems in mountain regions and beyond. This knowledge gap is critical, given human reliance on mountain systems for stable water supply and quality. Mountain systems’ increasing vulnerability to climate change and human perturbations motivates the need to improve understanding of integrated mountain hydroclimate (IMHC) systems and their feedbacks and impacts on humans across scales. However, due to large heterogeneity and strong gradients, coupled natural-human processes in mountain regions present significant challenges for observations, modeling, predictions, and projections. Motivated by gaps in mountain hydroclimate understanding, observations, and modeling and the need for credible projections of future changes, the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program organized a virtual workshop on “Understanding and Predictability of Integrated Mountain Hydroclimate.” Sponsored by BER’s Earth and Environmental Systems Sciences Division (EESSD), the workshop aimed to inform and catalyze EESSD’s growing interests in enhancing predictive understanding of IMHC. Organizers structured the workshop to identify (1) knowledge gaps, (2) observational and modeling challenges, (3) short-term (1 to 3 years) and long-term (10 years and beyond) research opportunities, and (4) strategies for fostering collaboration and coordination. To address the outstanding challenges of IMHC, the workshop included two sessions organized by disciplinary, cross-disciplinary, and crosscutting science topics. The disciplinary and cross-disciplinary topics focused on essential IMHC elements: atmosphere, terrestrial, and human systems and their interactions. Breakout sessions on disciplinary and cross-disciplinary topics facilitated identification of crosscutting topics and central emerging themes. Session 1 focused on connecting existing DOE investments to accelerate progress related to scientific challenges in understanding mountain hydroclimate. In Session 2, participants further explored key Session 1 takeaways through the lens of multiagency collaborations and coordination.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Basin scale distributions of dissolved manganese, nickel, zinc and cadmium in the Mediterranean Sea

Samples for dissolved trace metal concentrations were collected during GEOTRACES expedition GA04-N in summer/spring in the Mediterranean Sea, starting in the Atlantic Ocean and sampling both deep basins of the Mediterranean Sea. Outflow of Mediterranean Outflow Water leads to elevated concentrations of Mn, Ni and Zn in the Atlantic Ocean, but a concentration minimum in the Atlantic distribution of Cd. Nevertheless, when comparing the in- and outflow, the Mediterranean is a net source of Cd to the Atlantic Ocean. Surface concentrations of Mn, Ni, Zn and Cd are elevated in the Mediterranean relative to the Atlantic Ocean where Ni and Cd gradually increased along the eastward surface water flow path, Zn reached a homogenous concentration in the order of 1 to 1.5 nM, and Mn displayed a patchy surface distribution. The observed differences are attributable to the different dynamics of their biogeochemical cycling, notably the partitioning between the dissolved and particulate phases due to biological uptake, scavenging and possibly organic complexation. The elevated surface concentrations of Mn, Ni, Zn and Cd in the Mediterranean are derived from atmospheric deposition, where most likely Zn and Cd are mainly sourced from anthropogenic origin, Mn mostly from lithogenic origin and Ni from both anthropogenic and lithogenic origin. Dissolved Zn and Cd, as well as phosphate and nitrate, display striking inter-basin fractionations with elevated concentrations in the deep water of the western basin compared to the deep eastern basin, without a coinciding increase in the apparent oxygen utilization. Given that physical circulation or contribution from biogenic particulate metals cannot explain the elevated dissolved concentrations, an external non-biological source is required. This source is most likely a vertical flux of metal laden particles dissolving through the water column of the western Mediterranean where these particles, most likely from anthropogenic origin, are derived from either atmospheric deposition or particulate material deposited on the continental shelves that makes its way into the deep basin. Furthermore, to confirm or detect trends in dissolved metal concentrations in the deep basin, regular basin wide assessments of the trace metal distributions in the Mediterranean are needed. The distributions of Mn, Ni, Zn and Cd in the Sea of Marmara illustrate that all of these metals can be affected by anthropogenic surface sources and highlight the different susceptibilities of the dissolved metal distributions to supply from remineralization, and to removal through scavenging. This study provides a first baseline to assess future changes and underlines that the Mediterranean marine environment is susceptible to anthropogenic disturbances, with varying effects for different metals due to differing source strengths and biogeochemical cycles.

58 GEOSCIENCES↗
DOE OSTI2023

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Scaling Global Warming Impacts on Ocean Ecosystems: Lessons From a Suite of Earth System Models

An important technique used by climate modelers to isolate the impacts of increasing greenhouse gasses on Earth System processes is to simulate the impact of an abrupt increase in carbon dioxide. The spatial pattern of change provides a “fingerprint” that is generally much larger than natural variability. Insofar as the response to radiative forcing is linear (the impact of quadrupling CO 2 is twice the impact of doubling CO 2 ) this fingerprint can then be used to estimate the impact of historical greenhouse gas forcing. However, the degree to which biogeochemical cycles respond linearly to radiative forcing has rarely been tested. In this paper, we evaluate which ocean biogeochemical fields are likely to respond linearly to changing radiative forcing, which ones do not, and where linearity breaks down. We also demonstrate that the representation of lateral mixing by mesoscale eddies, which varies significantly across climate models, plays an important role in modulating the breakdown of linearity. Globally integrated surface rates of biogeochemical cycling (primary productivity, particulate export) respond in a relatively linear fashion and are only moderately sensitive to mixing. By contrast, the habitability of the interior ocean (as determined by hypoxia and calcite supersaturation) behaves non-linearly and is very sensitive to mixing. This is because the deep ocean, as well as certain regions in the surface ocean, are very sensitive to the magnitude of deep wintertime convection. The cessation of convection under global warming is strongly modulated by the representation of eddy mixing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Terrestrial laser scanning data (Levels 0 and 1) from Urban Biogeochemistry Pilot Project sites, Knoxville, Tennessee, Jul 2024 - Jul 2025

This data package contains data from terrestrial laser scanning (TLS) at five urban park sites in Knoxville, Tennessee, USA. All parks include open-grown and/or closed-canopy trees and mixed nearby land use. These study sites were established as part of the Urban Biogeochemistry Pilot Project, which has an overall goal of better understanding how hydrobiogeochemical cycling is altered within the human environment. These five sites represent a gradient of urbanization, and were instrumented to understand hydrological and biogeochemical cycling (e.g., soil moisture, soil physical properties and biogeochemistry, tree transpiration, species type). The TLS data archived here were collected to provide detailed, three-dimensional information about forest structure. Specifically, data were collected to allow tree- and stand-level characterization of woody structure and leaf area. TLS scans were placed to capture the area around trees with sap flow sensors, and as much of a 50 m radius area around the meteorological station as possible given site property limits. Derived products will allow upscaling of water content and transpiration data. This data package contains the following data: - High-level files document further details of the campaign and data package: 1_CampaignSummary.csv provides details about the campaign and study site, 2_ScanAreasDetail.csv provides details about each separate scan area (groups of scans post-processed into a single point cloud), 3_TerrestrialLidarSensor.csv provides further technical details about the Riegl VZ-400i TLS sensor, TLS_CSV_dd.csv is a CSV Data Dictionary providing information about the fields in CSV files following the ESS-DIVE CSV File Formatting Guidelines Reporting Format, TLS_flmd.csv is a File Level Metadata file providing information about each file in the data package following the ESS-DIVE File Level Metadata Reporting Format, and README.txt is a text file describing the overall project and file structure. - Level 0 data are the raw data (.PROJ folders) as recorded by the Riegl VZ-400i TLS instrument before scan co-registration and post-processing with the Riegl's proprietary RiSCAN PRO software, which requires a license. - Level 1 data contain post-processed, co-registered data from each scan area. The "PointClouds" folder for each scan area contains a .las file with 1 cm resolution point cloud data exported from RiSCAN PRO. These are the main files likely to be of interest to most users and can be further processed with any software capable of manipulating .las files (e.g. Python, R CloudCompare). The "Project Information" folder contains log files from post-processing in RiSCAN PRO that may be of interest to users who want to see detailed records of post-processing, including all PDF reports generated by RiSCAN PRO. The "ScanPositions" folder contains information about the final position of all TLS scans, after post-processing, in multiple formats. The file ScanPositions_*.csv provides final geo-referenced scan positions, and the file SOP_backup_*.csv can be used in RiSCAN PRO to restore the co-registered scan positions if users wish to re-process raw data (Level 0 .PROJ folders) with RiSCAN PRO software (e.g., subsample to a different resolution, exclude a certain scan position, or apply different filters on reflectance or deviation values) without redoing time-consuming co-registration steps.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quantifying microbial roles in environmental iron oxidation via an integrated kinetics, `omics and metabolic modeling study (Final Report)

Iron oxyhydroxides are extremely reactive components of environmental systems, and therefore exert a strong influence on biogeochemical cycles. These oxyhydroxides strongly adsorb many biologically-relevant elements, including organic carbon and phosphate, as well as a wide range of metals including uranium and actinide species. Thus, the formation mechanism of iron oxyhydroxides are key to understanding both nutrient and contaminant cycling. Microorganisms can catalyze iron oxidation and promote the formation of Fe biominerals and thus are increasingly recognized as important players in biogeochemical cycling. However, it is completely unknown how much of environmental iron oxidation is biologically mediated versus abiotic, and various challenges in studying microbial iron oxidation have hindered accurate incorporation into hydrobiogeochemical models. The overarching goal of our work was to quantify and constrain microbial iron oxidation rates and use ‘omics to gain insight into the controls on this process, while developing tools to enable integration of biotic iron oxidation into hydrobiogeochemical models. Our work focused on the Savannah River Site (SRS) in South Carolina, where extensive microbial iron oxidation has been observed. At Tims Branch, part of the Argonne National Laboratory Wetland Hydrobiogeochemistry Science Focus Area (Argonne SFA), where groundwater discharges into a stream, iron-oxidizing microbial mats form and appear to be a major sink of uranium. In the wetlands that surround Tims Branch, there are wide swaths of iron microbial mats and flocs (mobilized mat). We measured biotic and abiotic iron oxidation rates using mats and water sampled from these sites and found that iron oxidation is primarily carried out by chemolithotrophic microorganisms. The resulting rate constants can be incorporated into models. These mats were characterized by metagenomics and metatranscriptomics, which showed that aerobic chemolithotrophs were the dominant iron-oxidizing bacteria (FeOB), and these included Gallionellaceae and Leptothrix, and possibly Rhodoferax, which is known as an Fe-reducer but may also oxidize Fe(II). This demonstrated that diverse FeOB can coexist and suggests that there are a range of niches and therefore drivers of chemolithotrophic iron oxidation. Analysis of reconstructed genomes strongly suggests that a major factor in diversity is carbon source, as genomes contained varied pathways for autotrophy and heterotrophy. We performed an in-depth analysis of Leptothrix ochracea genomes, since this sheath-former is one of the primary mat builders, yet its physiology remained unresolved. A combination of genomics, transcriptomics, and metabolic modeling suggest that L. ochracea grows mixotrophically using a combination of Fe(II) and organics for energy and both inorganic and organic carbon to create biomass. This contrasts with the largely autotrophic Gallionellaceae (Gallionella, Sideroxydans, and Ferriphaselus) also present in the mats and flocs. Remarkably, multiple FeOB, both Leptothrix and Gallionellaceae, showed activity in response to Fe(II) in live mat incubations. We tracked the gene expression of individual MAGs to Fe(II) and found that various autotrophic and heterotrophic FeOB responded to Fe(II), increasing expression of both carbon fixation and organic utilization genes. The results of the integrated field, kinetics, and omics studies give detailed insight into 1) the taxa that oxidize Fe, and 2) how they connect Fe, C, and N cycles. Towards the goal of connecting omics data to hydrobiogeochemical models, we worked with the KBase team to create a template metabolic model for chemolithotrophic iron oxidation. We initially modeled the well-characterized isolate Gallionellaceae Sideroxydans lithotrophicus, and also applied the model to the mixotroph L. ochracea. In all, we have characterized diverse FeOB in a representative wetland system and solved key problems that enable better incorporation of iron-oxidizing microbes into hydrobiogeochemical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa , dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L 2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix . Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix , and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Vertical movement of soluble carbon and nutrients from biocrusts to subsurface mineral soils

Dryland ecosystems can be constrained by low soil fertility. Within drylands, the soil nutrient and organic carbon (C) cycling that does occur is often mediated by soil surface communities known as biological soil crusts (biocrusts), which cycle C and nutrients in the top ca. 0–2 cm of soil. However, the degree to which biocrusts are influencing soil fertility and biogeochemical cycling in deeper, subsurface mineral soils is unclear. The movement of dissolved resources from biocrusts to deeper soil layers in leachate may be one of the main mechanisms through which biocrust fertility is transferred downward towards deeper microbial communities and plant roots occurring within mineral soil. Here, in this study, we examined the role of biocrust leachate in contributing to subsurface nutrient and soluble C pools and subsurface microbial cycling. We collected biocrusts from three biocrust successional stages and explored resource pools in situ at multiple soil depths, while collecting leachate and measuring nutrient and organic C concentrations and metabolite composition from each successional stage in the laboratory. After four leachate collections, we conducted an incubation of mineral soil collected from below each biocrust successional stage to measure heterotrophic microbial CO 2 flux and biomass. Overall, our findings observed that the degree of nutrient and C connectivity between biocrusts and the sub-crust mineral soil depended on the biocrust successional stage and the element being considered, and the influence of biocrust successional stage on mineral soil CO 2 flux is likely related to long-term resource build up. Together, our results suggest that the influence of biocrust leachate on subsurface mineral soil is complex and context dependent, but, over longer time periods and at later successional stages, can have measurable effects on dryland soil biogeochemical cycling with feedbacks to resource availability and CO 2 flux.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗