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Results for “ecosystem functioning”

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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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here, in this work, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

ENVnet provides a global molecular resource of dissolved organic matter

Dissolved organic matter (DOM) is an important component of Earth's carbon cycle and one of the planet's most chemically diverse pools, yet the molecular structures of its constituents remain largely unresolved. This limitation has hindered our ability to link DOM composition to microbial processes and ecosystem function. Here we present ENVnet, a global molecular repository built from tandem mass spectrometry data collected across 13 terrestrial and aquatic environment types, including 419 newly generated samples that expand publicly available DOM metabolomics data and cover previously underrepresented environments. By computationally deconvolving chimeric mass spectra, a longstanding challenge in environmental metabolomics, we recover high-quality fragmentation data for >22,000 distinct molecular features (defined by a specific precursor mass and fragmentation pattern). Using ENVnet, we uncover conserved and environment-specific molecular patterns in DOM composition and underlying biogeochemical processes. We also use molecular features encoded in ENVnet to train predictive models of DOM persistence, allowing molecular-level assessment of microbial turnover in independent systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

California wildfire spread derived using VIIRS satellite observations and an object-based tracking system

Changing wildfire regimes in the western US and other fire-prone regions pose considerable risks to human health and ecosystem function. However, our understanding of wildfire behavior is still limited by a lack of data products that systematically quantify fire spread, behavior and impacts. Here we develop a novel object-based system for tracking the progression of individual fires using 375 m Visible Infrared Imaging Radiometer Suite active fire detections. At each half-daily time step, fire pixels are clustered according to their spatial proximity, and are either appended to an existing active fire object or are assigned to a new object. This automatic system allows us to update the attributes of each fire event, delineate the fire perimeter, and identify the active fire front shortly after satellite data acquisition. Using this system, we mapped the history of California fires during 2012–2020. Our approach and data stream may be useful for calibration and evaluation of fire spread models, estimation of near-real-time wildfire emissions, and as means for prescribing initial conditions in fire forecast models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Aerobic bacterial methane synthesis

Significance Observations summarized herein contribute to an ongoing paradigm shift in microbial ecology, documenting an emergent property of ecosystem function that further challenges the perception that biogenic methane (CH 4 ) production is strictly an anaerobic process. Relevant metabolites, a model bacterial isolate, gene, and enzyme are identified, and we show how this property can conceivably be broadly distributed in the biosphere and contribute to global CH 4 emissions. Scientifically, this study will enable lines of investigation that will expand our understanding of CH 4 synthesis and emission in nature and illustrates how CH 4 synthesis may actually serve as a nexus for the C and N cycles in nature.

Wang, Qian↗
DOE OSTI2021

A novel construct for scaling groundwater–river interactions based on machine-guided hydromorphic classification

Hydrologic exchange between river channels and adjacent subsurface environments is a key process that influences water quality and ecosystem function in river corridors. Predictive numerical models are needed to understand responses of river corridors to environmental change and to support sustainable watershed management. We posit that systematic hydromorphic classification provides a scaling construct that facilitates extrapolation of outputs from local-scale mechanistic models to reduced-order models applicable at reach and watershed scales. This in turn offers the potential to improve large-scale predictions of river corridor hydrobiogeochemical processes. Here we present a new machine-guided hydromorphic classification methodology that addresses the key requirements of this objective, and we demonstrate its application to a segment of the Columbia River in the northwestern United States. The resulting hydromorphic classes form spatially coherent and physically interpretable hydromorphic units that exhibit distinct behaviors in terms of distributions of subsurface residence times (a primary control on critical biogeochemical reactions). This approach forms the basis of ongoing research that is evaluating the formulation of reduced-order models and transferability of results to other river reaches and larger scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Response of salt intrusion in a tidal estuary to regional climatic forcing

Abstract Salinity distribution in a large tidal estuary is subject to estuarine adjustment under the influences of multiple physical drivers such as freshwater pulses and sea level rise, and is crucial to upstream water quality, aquaculture, and ecosystem functions of the estuary. To better understand the estuarine salinity response to climate change, the unstructured-grid Finite Volume Community Ocean Model was implemented to simulate the salt intrusion in the Delaware Bay Estuary. The model was first validated by multiple observational data sets and subsequently applied in an idealized setting to examine the response of salt front to freshwater pulses in high flow conditions, followed by a long-term drought condition supported by a multi-decadal streamflow drought analysis in the estuary. The model results showed that after the freshwater pulses the salt front location moved further upstream with sea level rise. Under the simulated long-term drought condition, the adjustment timescale of salt intrusion varies nonlinearly with sea level rise. With a significant increase in sea level rise, the adjustment timescale starts to decrease. This shift suggests a transition into a different regime where the estuary becomes more stratified, as indicated by an increasing bulk Simpson number with rising sea levels.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Improved methods to assess the effect of bacteria on germination of fungal spores

Abstract Bacterial-fungal interactions (BFI) play a major role on ecosystem functioning and might be particularly relevant at a specific development stage. For instance, in the case of biological control of fungal pathogens by bacteria, a highly relevant kind of BFI, in-vitro experiments often assess the impact of a bacterium on the inhibition of actively growing mycelia. However, this fails to consider other stages of plant infection such as the germination of a spore or a sclerotium. This study aims to present novel experimental platforms for in-vitro experiments with fungal spores, in order to assess the effect of bacteria on germination and fungal growth control, to recover the metabolites produced in the interaction, and to enhance direct visualisation of BFI. Botrytis cinerea, a phytopathogenic fungus producing oxalic acid (OA) as pathogenicity factor, was used as model. Given that oxalotrophic bacteria have been shown previously to control the growth of B. cinerea, the oxalotrophic bacteria Cupriavidus necator and Cupriavidus oxalaticus were used as models. The experiments performed demonstrated the suitability of the methods and confirmed that both bacteria were able to control the growth of B. cinerea, but only in media in which soluble OA was detected by the fungus. The methods presented here can be easily performed in any microbiology laboratory and are not only applicable to screen for potential biocontrol agents, but also to better understand BFI.

Estoppey, Aislinn↗
DOE OSTI2024

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition

Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates for 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits, thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes that suggested—as a trade-off—a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait–trade-offs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Microbial inoculants for soil restoration: A Risk-Proportional Stewardship Framework Integrating Strain-Resolved Genomics and Adaptive Governance

Global soil degradation and increasing reliance on chemical inputs threaten agricultural sustainability, driving interest in microbial inoculants as tools for soil restoration. These biological products have the potential to enhance nutrient cycling, improve soil structure, and support plant resilience, but their environmental release raises important safety and stewardship considerations. Here, we propose a risk-proportional framework for the responsible deployment of microbial inoculants grounded in release-based stewardship. The framework integrates genome-resolved strain identification, exclusionary hazard screening, bioassay-based risk triage, ecological testing under realistic conditions, and monitored field deployment. Drawing on evidence from microbial ecology and invasion biology, we highlight how inoculants can alter resident microbial communities, influence ecosystem function, and, in some cases, facilitate gene flow, underscoring the need for risk assessment. We further outline a federated, genome-informed data infrastructure to support traceability, cross-jurisdiction learning, and adaptive management. Together, this approach provides a scalable and scientifically grounded pathway to balance innovation and safety, enabling microbial technologies to contribute to soil restoration and climate-resilient agriculture.

Edlund, Anna [OATH Inc]↗
DOE OSTI2020

Intra‐species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus

Summary Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra‐species variation between four isolates of the ECM fungus Pisolithus microcarpus , in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis . We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate‐specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles of ECM fungi and their host interactions.

Plett, Krista L.↗
DOE OSTI2022

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Abstract Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant‐associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long‐term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil‐depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co‐occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal‐fungal links and an increase of bacteria–bacteria links with increasing depth in all crops, particularly in the root microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Tidal–hydrological dynamics of water temperature across freshwater forested wetlands on the northeastern Pacific coast

Abstract Tidal freshwater forests were once extensive across temperate coastlines, but loss and fragmentation have made estimation of their ecosystem functions challenging. We measured water temperature for 2 years in three Sitka spruce tidal forests, a restoration site, and an adjacent emergent marsh on the Columbia River, Washington, United States. We assessed spatial variability of water temperature within sites including the effects of hydrology, differences among bay and tributary tidal forests, and differences between the tidal forests and the mainstem Columbia, the restoration site, and the emergent marsh. The tidal forests nearest to the bay had lower interior water temperatures than their channel confluences by up to 2.5°C (weekly median temperature) and 2.0°C (weekly maximum temperature), with most cooling occurring during the low‐flow months of July–September. Tributary sites had maximum temperatures up to 1.9°C cooler than bay sites and 4.2°C cooler than the mainstem. Temperatures in the two bay sites decreased by −0.16°C/100 m and −0.07°C/100 m, on average. The restoration site had the smallest within‐site temperature gradient. Differences in maximum temperatures were greatest when tidal range was low, while higher tidal ranges were associated with warmer and more variable site interiors relative to their confluences. These results suggest that water temperatures in these tidal forests can provide temperature refugia for cold water biota including salmon.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region

1. LiDAR data are being increasingly used to provide a detailed characterization of the vertical profile of forests. This characterization enables the generation of new insights on the influence of environmental drivers and anthropogenic disturbances on forest structure as well as on how forest structure influences important ecosystem functions and services. Unfortunately, extracting information from LiDAR data in a way that enables the spatial visualization of forest structure, as well as its temporal changes, is challenging due to the high dimensionality of these data. 2. In this study, we show how the Latent Dirichlet Allocation model applied to LiDAR data (LidarLDA) can be used to identify forest structural types and how the relative abundance of these forest types changes throughout the landscape. The code to fit this model is made available through the open-source r package LidarLDA in github. We illustrate the use of LidarLDA both with simulated data and data from a large-scale fire experiment in the Brazilian Amazon region. 3. Using simulated data, we demonstrate that LidarLDA accurately identifies the number of forest types as well as their spatial distribution and absorptance probabilities. For the empirical data, we found that LidarLDA detects both landscape-level patterns in forest structure as well as the strong interacting effect of fire and forest fragmentation on forest structure based on the experimental fire plots. More specifically, LidarLDA reveals that proximity to forest edge exacerbates the impact of fires, and that burned forests remain structurally different from unburned areas for at least 7 years, even when burned only once. Importantly, LidarLDA generates insights on the 3D structure of forest that cannot be obtained using more standard approaches that just focus on top-of-the-canopy information (e.g. canopy height models based on LiDAR data). 4. By enabling the mapping of forest structure and its temporal changes, we believe that LidarLDA will be of broad utility to the ecological research community.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Improving leaf spring phenology modelling for temperate tree species: An integration of the Farquhar–Medlyn photosynthesis model with the optimality‐based approach

Spring leaf phenology in temperate tree species is highly sensitive to climate change and significantly affects plant photosynthetic performance, resource utilization, competition and trophic interactions, thereby impacting various ecosystem functions. Although optimality-based (OPT) approaches for modelling spring phenology are increasingly recognized, the optimal representation of the underlying principle (balancing photosynthesis gains with chilling risks) remains controversial. Here, we integrated a coupled Farquhar–Medlyn photosynthesis model into an existing OPT model, and termed the resulting model R-OPT, and evaluated its performance using the PEP725 dataset, which includes 409,144 site-species-year records from across Europe. Our results show that R-OPT outperforms both the default OPT and non-optimality-based models (e.g. the chilling-forcing trade-off and growing degree day models). This improved performance is consistent within and across five focal tree species but varies by region: R-OPT excels in lowland, moist environments but is less effective in high-altitude, cold, and dry areas, possibly due to an incomplete representation of environmental constraints on photosynthetic carbon gain in these regions. Our research advances leaf spring phenology modelling by emphasizing an optimality principle that balances photosynthetic carbon gain with chilling risk, improving the representation of plant photosynthesis processes and enhancing understanding of environmental factors influencing phenology in the context of climate change.

coupled Farquhar–Medlyn photosynthesis model↗
DOE OSTI2024

Microbial Evolution Drives Adaptation of Substrate Degradation on Decadal to Centennial Time Scales Relevant to Global Change

ABSTRACT Understanding microbial adaptation is crucial for predicting how soil carbon dynamics and global biogeochemical cycles will respond to climate change. This study employs the DEMENT model of microbial decomposition, along with empirical mutation and dispersal rates, to explore the roles of mutation and dispersal in the adaptation of soil microbial populations to shifts in litter chemistry, changes that are anticipated with climate‐driven vegetation dynamics. Following a change in litter chemistry, mutation generally allows for a higher rate of litter decomposition than dispersal, especially when dispersal predominantly introduces genotypes already present in the population. These findings challenge the common idea that mutation rates are too low to affect ecosystem processes on ecological timescales. These results demonstrate that evolutionary processes, such as mutation, can help maintain ecosystem functioning as the climate changes.

Abs, Elsa↗