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DOE OSTI2023

Aligning theoretical and empirical representations of soil carbon-to-nitrogen stoichiometry with process-based terrestrial biogeochemistry models

Soil carbon-nitrogen (C:N) stoichiometry acts as a control over decomposition and soil organic matter formation and loss, making it a key soil property for understanding ecosystem dynamics and projected ecosystems responses to global environmental change. However, the controls of soil C:N and how they respond to increasing pressures from global change agents are not fully understood. The “foundational” controls on soil C:N, namely plant and microbial C:N, have been used to predict soil C:N, but fail to accurately simulate all ecosystems and may be insufficient for predictions under global environmental change. Here we present an “emerging” representation of controls of soil C:N that includes plant-microbe-mineral feedbacks that have been shown to regulate soil C:N. We argue that including representation of these emerging drivers in process-based terrestrial biogeochemistry models, which include biological N fixation, mycorrhizae, priming, root exudation of organic acids, and mineralogy (including soil texture, mineral composition, and aggregation), will improve mechanistic representation of soil C:N and associated processes. Such improvements will produce models that will better simulate a variety of ecological states and predict soil C:N when global changes modify plant-microbe-mineral interactions. Here, we align our empirical understanding of controls of soil C:N with those controls represented in models, identifying contexts where emerging drivers might be particularly important to represent (e.g., priming and root exudation in nutrient-limited conditions) and areas of future work. Additionally, we show that implementing emerging drivers of soil C:N results in different simulated outcomes at steady state and in response to elevated atmospheric CO2. Our review and preliminary simulations support the need to incorporate emerging drivers of soil C:N into process-based terrestrial biogeochemistry models, allowing for both theoretical exploration of mechanisms and potentially more accurate predictions of land biogeochemical responses to global change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Investigating the eco‐evolutionary response of microbiomes to environmental change

Abstract Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free‐living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome–functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Cellulose Nanocrystals’ Role in Critical Mineral Beneficiation: Dual Aggregate-Dispersant Behavior Supports Environmentally Benign Nickel Processing

Environmentally unsustainable and toxic chemical flocculants and dispersants from nickel (Ni) processing contribute to industrial effluents that greatly impact biodiversity and aquatic life. Despite the industry’s efforts to reduce its ecological footprint—primarily due to the lack of commercially available biodegradable, environmentally benign, and non-toxic reagents—these reagents continue to harm natural ecosystems. Chemicals used during the processing operations often target a specific unit operation that negatively affects downstream operations. In this study, we discover the concentration-dependent behavior of cellulose nanocrystals (CNCs) as a dispersant and flocculant, avoiding the use of various harmful chemicals in the nickel processing stages. Electrophoretic, optical brightfield microscopy, and quartz crystal microbalance-dissipation studies detected charge neutralization behavior by renewable and biodegradable CNCs, which can greatly benefit Ni processing operations. Microflotation experiments demonstrated that CNCs enhanced Ni recovery from 62 to 77 wt.% and concentrate grade from 15 to 20 wt.%. Settling and turbidity studies demonstrated the dual flocculant-dispersant behavior of CNCs resulting from the alignment of CNC fibers along the octahedral brucite basal and amphoteric edge plane of serpentine. CNCs can be used as dispersants during froth flotation to improve Ni beneficiation and as post-processing flocculants for tailings management and dewatering, which is one of the major environmental and social concerns facing the mining and mineral processing industry. This study paves the way for CNCs to be used as flocculants and dispersants in a range of industries from healthcare to pharmaceuticals to semiconductor devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1989

Controlled Ecological Life Support System

The NASA CELLS program is based upon the integration of biological and physiochemical processes in order to produce a system that will produce food, a breathable atmosphere, and potable water from metabolic and other wastes. The CELSS concept is described and a schematic system diagram is provided. Central to the CELSS concept is the Plant Growth Chamber, where green plant photosynthesis produces food, and aids in the production of oxygen and water. Progress to date at the Breadboard Facility at the Kennedy Space Center is summarized. The Breadboard Facility will implement the basic techniques and processes required for a CELSS based on photosynthetic plant growth in a ground-based system of practical size and results will be extrapolated to predict the performance of a full-sized system. Current available technology and near-future forecasts for plant growth techniques (focusing on maximum productivity), food sources (to select optimal CELSS plants), and waste management and contaminant control are discussed.

Averner, Maurice M.↗

DOE OSTI2024

Using Knowledge-Guided Machine Learning To Assess Patterns of Areal Change in Waterbodies across the Contiguous United States

Lake and reservoir surface areas are an important proxy for freshwater availability. Advancements in machine learning (ML) techniques and increased accessibility of remote sensing data products have enabled the analysis of waterbody surface area dynamics on broad spatial scales. However, interpreting the ML results remains a challenge. While ML provides important tools for identifying patterns, the resultant models do not include mechanisms. Thus, the “black-box” nature of ML techniques often lacks ecological meaning. Using ML, we characterized temporal patterns in lake and reservoir surface area change from 1984 to 2016 for 103,930 waterbodies in the contiguous United States. We then employed knowledge-guided machine learning (KGML) to classify all waterbodies into seven ecologically interpretable groups representing distinct patterns of surface area change over time. Many waterbodies were classified as having “no change” (43%), whereas the remaining 57% of waterbodies fell into other groups representing both linear and nonlinear patterns. This analysis demonstrates the potential of KGML not only for identifying ecologically relevant patterns of change across time but also for unraveling complex processes that underpin those changes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Coordinated resource allocation to plant growth–defense tradeoffs

Summary Plant resource allocation patterns often reveal tradeoffs that favor growth (G) over defense (D), or vice versa. Ecologists most often explain G–D tradeoffs through principles of economic optimality, in which negative trait correlations are attributed to the reconciliation of fitness costs. Recently, researchers in molecular biology have developed ‘big data’ resources including multi‐omic (e.g. transcriptomic, proteomic and metabolomic) studies that describe the cellular processes controlling gene expression in model species. In this synthesis, we bridge ecological theory with discoveries in multi‐omics biology to better understand how selection has shaped the mechanisms of G–D tradeoffs. Multi‐omic studies reveal strategically coordinated patterns in resource allocation that are enabled by phytohormone crosstalk and transcriptional signal cascades. Coordinated resource allocation justifies the framework of optimality theory, while providing mechanistic insight into the feedbacks and control hubs that calibrate G–D tradeoff commitments. We use the existing literature to describe the coordinated resource allocation hypothesis (CoRAH) that accounts for balanced cellular controls during the expression of G–D tradeoffs, while sustaining stored resource pools to buffer the impacts of future stresses. The integrative mechanisms of the CoRAH unify the supply‐ and demand‐side perspectives of previous G–D tradeoff theories.

Monson, Russell K.↗

DOE OSTI2022

Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean

Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on “who is doing what, where, and how?”, this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory—determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

AmeriFlux US-xSJ NEON San Joaquin Experimental Range (SJER)

This is the AmeriFlux version of the carbon flux data for the site US-xSJ NEON San Joaquin Experimental Range (SJER). Site Description - Located at The San Joaquin Experimental Range, in the western foothills of the Sierra Nevada, this 18.2 kilometer terrestrial field site is a mix of open woodlands, shrubs and grasslands with low density cattle grazing. SJER is an ecosystem research experimental area. It was originally conceived as a cooperative interdisciplinary research center to identify cost-effect methods of commercial livestock production in the annual grass-oak pine woodlands, while maintaining the integrity of the ecosystem. More recently, research objectives have expanded and diversified to include research projects making contributions to our knowledge of the patterns and processes working in this ecosystem.

Network), NEON (National Ecological Observatory↗

DOE OSTI2023

AmeriFlux FLUXNET-1F US-xSJ NEON San Joaquin Experimental Range (SJER)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xSJ NEON San Joaquin Experimental Range (SJER). This is the FLUXNET version of the carbon flux data for the site US-xSJ NEON San Joaquin Experimental Range (SJER) produced by applying the standard ONEFlux (1F) software. Site Description - Located at The San Joaquin Experimental Range, in the western foothills of the Sierra Nevada, this 18.2 kilometer terrestrial field site is a mix of open woodlands, shrubs and grasslands with low density cattle grazing. SJER is an ecosystem research experimental area. It was originally conceived as a cooperative interdisciplinary research center to identify cost-effect methods of commercial livestock production in the annual grass-oak pine woodlands, while maintaining the integrity of the ecosystem. More recently, research objectives have expanded and diversified to include research projects making contributions to our knowledge of the patterns and processes working in this ecosystem.

Network), NEON (National Ecological Observatory↗

DOE OSTI2024

Using Knowledge-Guided Machine Learning To Assess Patterns of Areal Change in Waterbodies across the Contiguous United States

58 GEOSCIENCES↗

NASA NTRS1987

Activation of a controlled ecological life support system (CELSS) breadboard facility - Wheat growth studies

NASA's Controlled Ecological Life Support System (CELSS) will include subsystems for biomass production, food processing, and waste management in space. This paper discusses the CELSS Breadboard program, which is a research project for integration and evaluation of concepts and techniques of the CELSS facility, with special attention given to the Biomass Production Chamber (BPC). The design of the BPC and of its subsystems for nutrient delivery, atmospheric control, and computer control are discussed together with the subsystem control and monitoring parameter requirements. Results from preliminary wheat-growth tests in the BPC are included.

Knott, William M.↗

NASA NTRS2018

Atmospheric Trace Gas (NO2 and Ozone) Dynamics over Coastal Waters near Polluted Urban Regions

At the interface between the land, oceans, and atmosphere, coastal regions are highly dynamic environments, characterized by strong variability in both water and air quality. Variability in atmospheric composition is associated with highly variable anthropogenic emissions, as well as complex meteorological processes that influence the circulation and accumulation of atmospheric pollutants at the land-ocean interface. Assessing the spatial and temporal dynamics of atmospheric pollutants, aerosols, and absorbing trace gases in coastal areas is critical for improving modeling of coastal tropospheric air quality, developing accurate satellite retrievals of coastal ocean color and biological processes, determining impacts of atmospheric pollution on human health, and assessing the ecological implications of atmospheric pollutant deposition for coastal terrestrial and aquatic ecosystems.Here, we present new measurements of atmospheric trace gas (NO2, and ozone) dynamics across a range of estuarine and coastal waters near urban regions. Measurements were conducted from research vessels using NASA's shipboard Pandora spectrometers, as part of recent multidisciplinary, multiplatform field campaigns, including the 2016 KORUS OC/AQ field campaign in the Yellow Sea and East Sea/Sea of Japan, the 2017/2018 OLWETS field campaign in the Chesapeake Bay estuary, and the 2018 LISTOS field campaign in the Long Island Sound. Shipboard measurements over these coastal waters were integrated with measurements from a ground-based Pandora network to examine differences in air quality over the land and over the ocean. Measurements were combined with air-parcel back-trajectory simulations to determine the origin of air masses over the coastal ocean. Comparisons with satellite retrievals of atmospheric composition reveal the benefits and limitations of polar-orbit satellite observations in capturing variability in atmospheric pollution gradients over land-water boundaries.

Tzortziou, Maria↗

DOE OSTI2021

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

ABSTRACT Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

The impact crater as a habitat: effects of impact processing of target materials

Impact structures are a rare habitat on Earth. However, where they do occur they can potentially have an important influence on the local ecology. Some of the types of habitat created in the immediate post-impact environment are not specific to the impact phenomenon, such as hydrothermal systems and crater lakes that can be found, for instance, in post-volcanic environments, albeit with different thermal characteristics than those associated with impact. However, some of the habitats created are specifically linked to processes of impact processing. Two examples of how impact processing of target materials has created novel habitats that improve the opportunities for colonization are found in the Haughton impact structure in the Canadian High Arctic. Impact-shocked rocks have become a habitat for endolithic microorganisms, and large, impact-shattered blocks of rock are used as resting sites by avifauna. However, some materials produced by an impact, such as melt sheet rocks, can make craters more biologically depauperate than the area surrounding them. Although there are no recent craters with which to study immediate post-impact colonization, these data yield insights into generalized mechanisms of how impact processing can influence post-impact succession. Because impact events are one of a number of processes that can bring localized destruction to ecosystems, understanding the manner in which impact structures are recolonized is of ecological interest. Impact craters are a universal phenomenon on solid planetary surfaces, and so they are of potential biological relevance on other planetary surfaces, particularly Mars.

Environment↗

NASA NTRS2007

High Spatial Resolution Thermal Infrared Remote Sensing Data for Analysis of the Atlanta, Georgia, Urban Heat Island Effect and Its Impacts on the Environment

The twenty-first century is the first "urban century" according to the United Nations Development Program. The focus of cities reflects awareness of the growing percentage of the world's population that lives in urban areas. In environmental terms, cities are the original producers of many of the global problems related to waste disposal, air and water pollution, and associated environmental and ecological challenges. Expansion of cities, both in population and areal extent, is a relentless process. In 2000, approximately 3 billion people representing about 40% of the global population, resided in urban areas. Urban population will continue to rise substantially over the next several decades according to UN estimates, and most of this growth will Occur in developing countries. The UN estimates that by 2025, 60% of the world's population will live in urban areas. As a consequence, the number of"megacities" (those cities with populations of 10 million inhabitants or more) will increase by 100 by 2025. Thus, there is a critical need to understand urban areas and what their impacts are on environmental, ecological and hydrologic resources, as well as on the local, regional, and even global climate. One of the more egregious side effects of urbanization is the increase in surface and air temperatures that lead to deterioration in air quality. In the United States, under the more stringent air quality guidelines established by the U.S. Environmental Protection Agency in 1997, nearly 300 counties in 34 states will not meet these new air quality standards for ground level ozone. Mitigation of the urban heat island (UHI) effect is actively being evaluated as a possible way to reduce ground ozone levels in cities and assist states in improving air quality. Foremost in the analysis of how the UHI affects air quality and other environmental factors is the use of remote sensing technology and data to characterize urban land covers in sufficient detail to quantifiably measure the impact of increased urban heating on air quality. The urban landscape impacts surface thermal energy exchanges that determine development of the UHI. This paper will illustrate how we are using high spatial remote sensing data collected over the Atlanta, Georgia metropolitan area in conjunction with other geographic information, to perform a detailed urban land cover classification and to determine the contribution of these land covers to the urban heat island effect. Also, the spatial arrangement of the land covers and the impact on urban heating from these selected patterns of development are evaluated. Additionally, this paper will show how these data are being used as inputs to improve air quality modeling for Atlanta, including potential benefits from UHI mitigation.

Quattrochi, Dale A.↗

DOE OSTI2020

Risk to ecological resources following remediation can be due mainly to increased resource value of successful restoration: A case study from the Department of Energy's Hanford Site

Several nations are faced with the need to remediate large contaminated sites following World War II, the Cold War, and abandoned industrial sites, and to return them to productive land uses. In the United States, the Department of Energy (DOE) has the largest cleanup challenge, and its Hanford Site in the state of Washington has the most extensive and most expensive cleanup task. Ideally, the risk to ecological resources on remediation sites is evaluated before, during, and after remediation, and the risk from, or damage to, ecological resources from contaminants should be lower following remediation. In this paper, we report the risk to ecological resources before, during, and as a consequence of remediation on contaminated units requiring cleanup, and then examine the causes for changes in risk by evaluating 56 cleanup evaluation units (EUs) at the Hanford Site. In this case, remediation includes a restoration phase. In general, the risk to ecological and eco-cultural resources is currently not discernible or low at most contaminated units, increases during remediation, and decreases thereafter. Remediation often causes physical disruption to ecosystems as it reduces the risk from exposure to contaminants. Most new remediation projects at the Hanford Site include ecological restoration. Ecological restoration results in the potential for the presence of higher quality resources after remediation than currently exists on these contaminated lands and facilities. Although counter-intuitive, our evaluation of the risk to ecological resources following remediation indicated that a significant percentage of units (61%) will be at increased risk in the post-remediation period. This increased risk is due to DOE's successful remediation and restoration that results in a higher percent of native vegetation and higher ecological value on the sites in the post-remediation period than before. These newly-created resources can then be at risk from post-remediation activities. Risks to these new higher quality resources include the potential for spread of invasive species and of noxious grasses used in previous cleanup actions, disruption of ecosystems (including those with state or federally listed species and unique ecosystems), compaction of soil, use of pesticides to control invasive species, and the eventual need for continued monitoring activities. Thus, by greatly improving the existing habitat and health of eco-receptors, and maintaining habitat corridors between high quality habitats, the ecological resources in the post-remediated units are at risk unless care is taken to protect them. Many of the negative effects of both remediation and future monitoring (or other future land uses) can be avoided by planning and management early in the remediation process. We suggest DOE and other agencies convene a panel of managers, remediation scientists, regulators, environmental and ecological scientists, Native Americans, economists, and the public to develop a generic list of performance metrics for the restoration phase of remediation, including evaluation of success, which could be applied across the DOE complex.

54 ENVIRONMENTAL SCIENCES↗