SEARCH · Search NASA

Results for “ecological process”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Allometric Trophic Networks From Individuals to Socio-Ecosystems: Consumer–Resource Theory of the Ecological Elephant in the Room

A well-known parable is that of the blind men studying an elephant each of which assert the elephant is the part they first hold in their hands, e.g., “rope!” says the tail holder while the leg holder asserts “tree!” The various subdisciplines of ecology appear similar in that we each engage in our enthusiastic but at least somewhat myopic study with remarkably limited agreement or even discussion about the overall system which we all study. Allometric trophic network (ATN) theory offers a path out of this dilemma by integrating across scales, taxa, habitats and organizational levels from physiology to ecosystems based on consumer-resource interactions among co-existing organisms. The network architecture and the metabolic and behavioral processes that determine the structure and dynamics of these interactions form the first principles of ATN theory, which in turn provides a synthetic overview and powerfully predictive framework for ecology from organisms to ecosystems. Beyond ecology, ATN theory also synthesizes eco-evolutionary and socio-ecological research still largely based on consumer-resource mechanisms but respectively integrated with different processes including natural selection and market mechanisms. This paper briefly describes foundations, advances, and future directions of ATN theory including predicting an ecosystem’s phenotype from its community’s genotype in order to accelerate more predictive and unified understanding of the complex systems studied by ecologists and other environmental scientists.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean

ABSTRACT Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus . Furthermore, all Bermanella encoded and expressed genes for non-gaseous n -alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment. IMPORTANCE Microbial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based ‘omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.

Howe, Kathryn L.↗

DOE OSTI2025

Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here. In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry. Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

DOE OSTI2025

Ecological connectivity and in-kind mitigation in a regulatory decision framework: A case study with an amphibian habitat specialist

Ecological connectivity is critical to the survival and long-term viability of populations but is often overlooked in regulatory frameworks. We integrated landscape-level processes into a mitigation strategy for impacts to aquatic resources on the U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) in eastern Tennessee. Wetlands on the ORR, which contain significant breeding populations of the imperiled four-toed salamander (Hemidactylium scutatum) and tubercled rein orchid (Platanthera flava var. herbiola), will be impacted by construction of an environmental waste disposal facility under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA). Here, we used a modified Kepner-Tregoe decision analysis to select general mitigation options that balanced regulatory requirements and interest group perspectives. We emphasized habitat connectivity through models that prioritized an area's importance to natural area connectivity (centrality) and maintenance of population structure for an affected habitat specialist (four-toed salamanders). We also emphasized in-kind mitigation through the preservation and enhancement of ecologically similar resources and the translocation and establishment of a new subpopulation of four-toed salamanders elsewhere on the ORR. We ultimately released over 500 juvenile salamanders that originated from the impacted site into the chosen mitigation wetlands. By doing so under the constraints of a time-sensitive CERCLA remediation effort and exceeding its substantive requirements, this work underscores feasibility. Ecological connectivity and the conservation of species that are not afforded explicit regulatory processes can be effectively and efficiently integrated into environmental decision-making and land use planning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Transient disease dynamics across ecological scales

Analyses of transient dynamics are critical to understanding infectious disease transmission and persistence. Identifying and predicting transients across scales, from within-host to community-level patterns, plays an important role in combating ongoing epidemics and mitigating the risk of future outbreaks. Moreover, greater emphases on non-asymptotic processes will enable timely evaluations of wildlife and human diseases and lead to improved surveillance efforts, preventive responses, and intervention strategies. Here, we explore the contributions of transient analyses in recent models spanning the fields of epidemiology, movement ecology, and parasitology. In addition to their roles in predicting epidemic patterns and endemic outbreaks, we explore transients in the contexts of pathogen transmission, resistance, and avoidance at various scales of the ecological hierarchy. Examples illustrate how (i) transient movement dynamics at the individual host level can modify opportunities for transmission events over time; (ii) within-host energetic processes often lead to transient dynamics in immunity, pathogen load, and transmission potential; (iii) transient connectivity between discrete populations in response to environmental factors and outbreak dynamics can affect disease spread across spatial networks; and (iv) increasing species richness in a community can provide transient protection to individuals against infection. Ultimately, we suggest that transient analyses offer deeper insights and raise new, interdisciplinary questions for disease research, consequently broadening the applications of dynamical models for outbreak preparedness and management.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Climate Change Risks to Freshwater Subsistence Fisheries in Arctic Alaska: Insights and Uncertainty from Broad Whitefish Coregonus nasus

Arctic freshwater ecosystems and fish populations are largely shaped by seasonal and long-term watershed hydrology. In this paper, we hypothesize how changing air temperature and precipitation will alter freeze and thaw processes, hydrology, and instream habitat to assess potential indirect effects, such as the change to the foraging and behavioral ecology, on Arctic fishes, using Broad Whitefish Coregonus nasus as an indicator species. Climate change is expected to continue to alter hydrologic pathways, flow regimes, and, therefore, habitat suitability, connectivity, and availability for fishes. Warming and lengthening of the growing season will likely increase fish growth rates; however, the exceedance of threshold stream temperatures will likely increase physiological stress and alter life histories. We expect these changes to have mixed effects on Arctic subsistence fishes and fisheries. Management and conservation approaches focused on preserving the processes that create heterogeneity in aquatic habitats, genes, and communities will help maintain the resilience of Broad Whitefish and other important subsistence fisheries. Long-term effects are uncertain, so filling scientific knowledge gaps, such as identifying important habitats or increasing knowledge of abiotic variables in priority watersheds, is key to understanding and potentially mitigating likely impacts to Arctic fishes in a rapidly changing landscape.

60 APPLIED LIFE 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 OSTI2021

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO 2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO 2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO 2 concentration. In conclusion, our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

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 OSTI2024

A Test of Functional Balance Theory for Wetland Biomass Allocation in a Global Change Experiment

Abstract Forecasts of root growth and carbon sequestration under global change are compromised by uncertainty in how plants will allocate biomass between above and belowground pools. Here, we develop a simple model to assess whether functional balance theory can explain a complex biomass allocation response observed in a brackish marsh under experimental warming and elevated CO 2 . Our model shows how treatment‐driven changes in nitrogen supply and demand can explain divergent observations of root growth (i.e., maximum responses under intermediate warming and elevated CO 2 ). The model also reveals a surprising interaction between warming and eutrophication, where enhanced N loading to coastal marshes may reduce adverse impacts of warming on root growth. Our findings provide a mechanistic basis for incorporating biomass allocation into forecast models of marsh evolution. They also provide a general example of using ecological theory to decompose complex net responses observed in multi‐factor global change experiments into constituent processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

A Numerical Modeling Framework for Flocculation and Cohesive Sediment Transport in the Wave Bottom Boundary Layer

Flocculation, a critical process in coastal and estuarine systems, plays a significant role in sediment transport, nutrient cycling, and ecological health. This study develops a cohesive sediment transport modeling framework tailored to the wave bottom boundary layer under dilute and equilibrium conditions, explicitly incorporating flocculation effects via a Population Balance Equation (PBE). Using Direct Numerical Simulation, six baseline cases, each with a distinct sediment concentration profile resulting from a constant settling velocity and critical erosion shear stress, are generated to drive the PBE flocculation model for given floc yield strength and stickiness. Results reveal that flocculation significantly influences sediment concentration profiles promoting three distinct stages, well‐mixed, transition to lutocline, and well‐developed lutocline. At low concentrations with well‐mixed profiles, cohesive floc properties are less significant, and turbulence is a main flocculation driver. In contrast, as concentration increases, cohesive floc properties become crucial, facilitating lutocline formation. Here, the analysis also highlights limitations of depth‐averaged settling velocity as a parameterization. It is suitable for well‐mixed and transitional profiles but fails in well‐developed lutoclines, where empirical formulations that explicitly incorporate turbulent shear rate and sediment concentration better capture variability. This study underscores the necessity of incorporating flocculation effects into sediment transport models to enhance predictions of sediment dynamics in wave bottom boundary layers.

Penaloza‐Giraldo, Jorge A. [Oak Ridge National Lab↗

DOE OSTI2022

Tank Waste LDR Organics Data Summary for Sample-and-Send (Rev.1A)

The presence of organic chemicals regulated under the Resource Conservation and Recovery Act (RCRA) Land Disposal Restrictions (LDR) adds complexity to treating and disposing of the low activity fraction of Hanford tank waste if a low temperature treatment method such as grouting is used (SRNL-STI-2020-00228). The complexity arises from the fact that the baseline vitrification method is considered by the Washington State Department of Ecology (Ecology) as providing adequate thermal treatment for organics; a status not automatically extended to a lowtemperature process, such as solidifying the waste in a cementitious waste form. In addition, the Environmental Protection Agency (EPA) LDR program is intended to ensure that wastes are properly treated prior to disposal. Proper treatment makes hazardous waste less harmful to groundwater by reducing the mobility and/or toxicity of the hazardous constituents in the waste. EPA guidance indicates that stabilization/solidification of waste for organics could be considered impermissible dilution under the LDR dilution prohibition. In addition, waste storage activities at Hanford have required transferring and blending waste within the tank system and these activities have potentially altered the concentrations of the hazardous constituents. The LDR dilution prohibition found in 40 Code of Federal Regulations (CFR) 268.3 states that “… no generator, transporter, handler, or owner or operator of a treatment, storage, or disposal facility shall in any way dilute a restricted waste or the residual from treatment of a restricted waste as a substitute for adequate treatment …”. Hence, if LAW is to be treated using low temperature stabilization (such as cementation), then it is important to demonstrate both how past storage activities have contributed to the removal (by vacuum evaporation), or destruction (by in situ decomposition) of the LDR organics and how future retrieval and waste feed preparation will contribute to their removal (by filtration and ion exchange). Demonstrating these processes helps validate that cementation without additional organic treatment does not necessarily represent impermissible dilution. To aid in implementing cementitious solidification of Low Activity Waste (LAW), WRPS has been developing a regulatory and processing LDR treatment variance strategy termed “Sampleand-Send” that relies, in part, on demonstrating that in situ decomposition reactions along with historic evaporation of tank waste has destroyed or removed most of the LDR organics possibly associated with Hanford Tank Waste (SRNL-STI-2020-00582, SRNL-STI-2021-00453, SRNL-STI-2022-00391). Under the Sample-and-Send concept, Hanford tank waste would be retrieved, processed through a Tank-Side Cesium Removal-like system, and staged as a candidate feed that would then be sampled to confirm the waste acceptance criteria is met for solidification in an LAW cementitious treatment facility. If it can be shown that LDR organics are at concentrations below the waste acceptance criteria (WAC) for cementitious stabilization and have been sufficiently removed (by historic evaporation or by filtration and ion exchange during Cs removal), destroyed (by historic in situ decomposition), or are not soluble in LAW above the WAC then additional organic treatment is not needed prior to creating a cementitious final waste form and the concept of Sample-and-Send would be proposed to establish a non-rulemaking site-specific treatment variance using the specified method of treatment “STABL” to remove sampling requirements of the waste form after treatment. Waste not meeting the WAC could either be routed to the Hanford Waste Treatment and Immobilization Plant for LAW vitrification, or further processed by evaporation or chemical oxidation before solidifying in a cementitious waste form. A key component in implementing the Sample-and-Send strategy is identifying which of the 207 LDR organic compounds associated with the RCRA Part A permit application waste codes for the Double Shell Tanks (DSTs) and Single Shell Tanks (SSTs) and any applicable Underlying Hazardous Constituents (UHCs) from 40 CFR 268.48 should be considered as potentially present and thus subject to regulation. In addition, it is also necessary to understand the solubility volatility, and reactivity of these compounds in LAW to identify which of the potentially present LDR organic compounds are not soluble above regulatory levels or are likely to have been removed by historic evaporation or destroyed by in situ decomposition reactions. If there are potentially present LDR organic compounds that have not been removed or destroyed and are soluble above regulatorily significant concentrations then a treatability variance may be needed for these species to eliminate any concerns pertaining to impermissible dilution. The spreadsheet accompanying this calculation report contains the data and logic computations needed to screen the list of 207 LDR organics associated with Hanford tank waste to identify those potentially present and to indicate which compounds may need to be included in a treatability variance.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Fossil Corals With Various Degrees of Preservation Can Retain Information About Biomineralization-Related Organic Material

Scleractinian corals typically form a robust calcium carbonate skeleton beneath their living tissue. This skeleton, through its trace element composition and isotope ratios, may record environmental conditions of water surrounding the coral animal. While bulk unrecrystallized aragonite coral skeletons can be used to reconstruct past ocean conditions, corals that have undergone significant diagenesis have altered geochemical signatures and are typically assumed to retain insufficient meaningful information for bulk or macrostructural analysis. However, partially recrystallized skeletons may retain organic molecular components of the skeletal organic matrix (SOM), which is secreted by the animal and directs aspects of the biomineralization process. Some SOM proteins can be retained in fossil corals and can potentially provide past oceanographic, ecological, and indirect genetic information. Here, we describe a dataset of scleractinian coral skeletons, aged from modern to Cretaceous plus a Carboniferous rugosan, characterized for their crystallography, trace element composition, and amino acid compositions. We show that some specimens that are partially recrystallized to calcite yield potentially useful biochemical information whereas complete recrystalization or silicification leads to significant alteration or loss of the SOM fraction. Our analysis is informative to biochemical-paleoceanographers as it suggests that previously discounted partially recrystallized coral skeletons may indeed still be useful at the microstructural level.

58 GEOSCIENCES↗

DOE OSTI2022

It takes a village: using a crowdsourced approach to investigate organic matter composition in global rivers through the lens of ecological theory

Though community-based scientific approaches are becoming more common, many scientific efforts are conducted by small groups of researchers that together develop a concept, analyze data, and interpret results that ultimately translate into a publication. Here, we present a community effort that breaks these traditional boundaries of the publication process by engaging the scientific community from initial hypothesis generation to final publication. We leverage community-generated data from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to study organic matter composition through the lens of ecological theory. This community endeavor will use a suite of paired physical and chemical datasets collected from 97 river corridors across the globe. With our first step aimed at ideation, we engaged a community of scientists from 20 countries and 60 institutions, spanning disciplines and career stages by holding a virtual workshop (April 2021). In the workshop, participants generated content for questions, hypotheses, and proposed analyses based on the WHONDRS dataset. These ideation efforts resulted in several narratives investigating different questions led by different teams, which will be the basis for research articles in a Frontiers in Water collection. Currently, the community is collectively analyzing, interpreting, and synthesizing these data that will result in seven crowdsourced articles using a single, existing WHONDRS dataset. The use of a shared dataset across articles not only lowers barriers for broad participation by not requiring generation of new data, but also provides unique opportunities for emergent learning by connecting outcomes across studies. Here we will explain methods used to enable this community endeavor aimed to promote a greater diversity of thinking on river corridor biogeochemistry through community science.

Borton, Mikayla A.↗

DOE OSTI2023

Leaf angle as a leaf and canopy trait: Rejuvenating its role in ecology with new technology

Abstract Life on Earth depends on the conversion of solar energy to chemical energy by plants through photosynthesis. A fundamental challenge in optimizing photosynthesis is to adjust leaf angles to efficiently use the intercepted sunlight under the constraints of heat stress, water loss and competition. Despite the importance of leaf angle, until recently, we have lacked data and frameworks to describe and predict leaf angle dynamics and their impacts on leaves to the globe. We review the role of leaf angle in studies of ecophysiology, ecosystem ecology and earth system science, and highlight the essential yet understudied role of leaf angle as an ecological strategy to regulate plant carbon–water–energy nexus and to bridge leaf, canopy and earth system processes. Using two models, we show that leaf angle variations have significant impacts on not only canopy‐scale photosynthesis, energy balance and water use efficiency but also light competition within the forest canopy. New techniques to measure leaf angles are emerging, opening opportunities to understand the rarely‐measured intraspecific, interspecific, seasonal and interannual variations of leaf angles and their implications to plant biology and earth system science. We conclude by proposing three directions for future research.

Yang, Xi↗

DOE OSTI2022

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Columbia River Surface Water and Pore Water Unaligned FTICR-MS Data Associated with “Using Community Assembly Metrics from Metacommunity Ecology to Understand Environmental Metabolomes”

Surface water and pore water samples were collected at five sites along a shoreline transect of the Columbia River, southeastern WA, USA in 2017. This dataset is comprised of (1) high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) and (2) a metadata csv file. The FTICR-MS files are .xml, and the data package includes instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user’s specific needs. The data are associated with the publication “Using community assembly metrics from metacommunity ecology to understand environmental metabolomes” that will be published in Nature Communications (Danczak et al.). The study aimed to investigate gaps in understanding the spatiotemporal organization of environmental metabolomes to improve the ability to predict ecosystem function. Associated sequencing data will be published via NCBI. The access information for NCBI and the publication DOI will be added to this abstract when they are available. Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists

Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as “leftover scavengers” and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes.

59 BASIC BIOLOGICAL SCIENCES↗