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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data from a four-day long microcosm experiment addressing the destabilization of artificial mineral-associated organic matter by model root exudates embedded in a soil matrix from the Rocky Mountain Biological Laboratory (Gothic, CO, USA), 2019

This dataset provides data collected during a four-day long laboratory soil microcosm experiment testing the efficacy of root exudate-driven mineral-associated organic matter destabilization. This dataset contains four data files in comma-separate values (*.csv). The files provide the metadata and the experimental results on microbial respiration, MAOM-derived respiration, and sequential mineral-extractions. This data was used to produce the figures in Bölscher et al., 2026. The results of the experiment can be found in the open access article Bölscher et al., 2026 (https://doi.org/10.1016/j.soilbio.2026.110276). Abstract: Mineral-associated organic matter (MAOM) is often considered stable, but root exudates can destabilize MAOM via various pathways. Theory and model system studies suggest that direct MAOM destabilization by strong ligands, like oxalic acid, or reducing agents, like catechol, is more effective than indirect, microbial-mediated MAOM destabilization, stimulated by less reactive compounds like glucose. Here, we demonstrate that the presence of a soil matrix alters the efficacy of exudate-driven MAOM destabilization pathways. Glucose and catechol destabilized significantly greater amounts of MAOM from ferrihydrite and aluminum hydroxide (Al (OH)3) embedded in a soil matrix than oxalic acid. Our findings indicate that indirect, microbial-mediated MAOM destabilization may play a larger role than direct MAOM destabilization in soil environments.

Destabilization↗
DOE OSTI2024

2024 OES-Environmental 2024 State of the Science Report, Chapter 3: Marine Renewable Energy: Stressor-Receptor Interactions

Determining the potential effects of marine renewable energy (MRE) development on the ocean requires consideration of how each component of a tidal, wave, riverine, or other MRE system might affect marine animals, habitats that support marine communities, or processes that make up essential oceanographic and ecological systems. Researchers around the world have been assessing the potential effects of MRE deployments and operations using a variety of instruments, models, analytical methods, and approaches. The most common approach, and the one followed throughout this report, is the framework of stressor-receptor interactions (Boehlert & Gill 2010), where stressors are the components of an MRE device and associated system that may cause stress, injury, or death to a marine animal, habitat, or ecosystem. The receptors are the species, their habitats, and the oceanographic and ecological processes that support them.

16 TIDAL AND WAVE POWER↗
DOE OSTI2024

2024 OES-Environmental 2024 State of the Science Report, Chapter 9: Beyond Single Marine Renewable Energy Devices: A System-wide Effects Approach

Global expansion of renewable energy, including marine renewable energy (MRE) technology development is necessary to mitigate the effects of climate change, facilitate a sustainable transition from carbon-based energy sources, and satisfy national energy security needs using locally produced electricity (European Commission 2022; IPCC 2023; IRENA 2020). As MRE engineering and research continue to focus on designing devices for deployment in nearshore and offshore waters around the world, researchers are also examining potential environmental effects on marine animals, habitats, and ecosystem processes. To date, the focus has been on interactions between small numbers of MRE devices (1-6) and the environment, such as collisions between animals and turbine blades, the effects of underwater noise and electromagnetic field (EMF) emissions, changes in habitats and oceanographic processes, risk of entanglement of animals, and displacement of animals (Boehlert & Gill 2010; Copping & Hemery 2020) (see Chapter 3).

16 TIDAL AND WAVE POWER↗
DOE OSTI2024

2024 OES-Environmental 2024 State of the Science Report, Chapter 11: Summary and Path Forward

The 2024 State of the Science report has brought together the most up-to-date information on potential environmental effects of marine renewable energy (MRE) development on marine animals, habitats, and ecosystem processes, as well as social and economic systems, using information that is publicly available as well as expert input. The report has been reviewed by over 56 experts. The reviewers provided in excess of one thousand comments during the drafting of the report that have been addressed in this version. The OES-Environmental country representatives from the 16 participating countries helped to scope the entirety of the report and provided valuable contributions to all chapters. The input from these contributors and reviewers has resulted in the most complete compendium of research and monitoring findings possible. While there is new and exciting research underway that should further illuminate the risks of MRE stressor-receptor interactions in the near future, suppositions and incomplete results from unpublished studies were not included in order to maintain the integrity, and decrease the uncertainty, of the messages in this report

16 TIDAL AND WAVE POWER↗
DOE OSTI2024

Body size and early marine conditions drive changes in Chinook salmon productivity across northern latitude ecosystems

Disentangling the influences of climate change from other stressors affecting the population dynamics of aquatic species is particularly pressing for northern latitude ecosystems, where climate‐driven warming is occurring faster than the global average. Chinook salmon (Oncorhynchus tshawytscha) in the Yukon‐Kuskokwim (YK) region occupy the northern extent of their species' range and are experiencing prolonged declines in abundance resulting in fisheries closures and impacts to the well‐being of Indigenous people and local communities. These declines have been associated with physical (e.g., temperature, streamflow) and biological (e.g., body size, competition) conditions, but uncertainty remains about the relative influence of these drivers on productivity across populations and how salmon–environment relationships vary across watersheds. To fill these knowledge gaps, we estimated the effects of marine and freshwater environmental indicators, body size, and indices of competition, on the productivity (adult returns‐per‐spawner) of 26 Chinook salmon populations in the YK region using a Bayesian hierarchical stock‐recruitment model. Across most populations, productivity declined with smaller spawner body size and sea surface temperatures that were colder in the winter and warmer in the summer during the first year at sea. Decreased productivity was also associated with above average fall maximum daily streamflow, increased sea ice cover prior to juvenile outmigration, and abundance of marine competitors, but the strength of these effects varied among populations. Maximum daily stream temperature during spawning migration had a nonlinear relationship with productivity, with reduced productivity in years when temperatures exceeded thresholds in main stem rivers. These results demonstrate for the first time that well‐documented declines in body size of YK Chinook salmon were associated with declining population productivity, while taking climate into account.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Assessing the Potential Impact of River Chemistry on Arctic Coastal Production

The Arctic coastal margin receives a disproportionately large fraction of the global river discharge. The bio-geochemistry of the river water as it empties into the marine environment reflects inputs and processes that occur as the water travels from its headwaters. Climate-induced changes to Arctic vegetation and permafrost melt may impact river chemistry. Understanding the impact of river nutrients on coastal marine production, and how this may change in the future, are important for resource managers and community members who monitor and rely on coastal food resources. Using the Energy Exascale Earth System Model we explore the impact of timing and river nutrient concentrations on primary production in each coastal Arctic region and then assess how this influences secondary production and particle fluxes supporting the benthic food web. Our results indicate that while the concentration of Arctic river nitrogen can have a significant impact on annual average nitrogen and primary production in the coastal Arctic, with production increases of up to 20% in the river influenced interior Seas, the timing of the river nutrient inputs into the marine environment appears less important. Bloom timing and partitioning between small and large phytoplankton were minimally impacted by both river nutrient concentration and timing, suggesting that in general, coastal Arctic ecosystem dynamics will continue to be primarily driven by light availability, rather than nutrients. Under a doubling river nutrient scenario, the percentage increase in the POC flux to the benthos on river influenced Arctic coastal shelves was 2-4 times the percentage increase in primary production, suggesting changes to the river nutrient concentration has the potential to modify the Arctic food web structure and dynamics. Generally, the nutrient-induced changes to primary production were smaller than changes previously simulated in response to ice reduction and temperature increase. However, in the Laptev Sea, the production increase resulting from a doubling of river nutrients exceeded the production increase simulated with an atmospheric warming scenario. Dissolved organic carbon is presently poorly represented in the model so its impact on production is hard to simulate. Applying established relationships between modeled DOC, total DOC, and light absorption we illustrate that DOC could play a very important role in modulating production. Our findings highlight the importance of developing more realistic river nutrient and discharge forcing for Earth System Models such that their impact on the critical Arctic coastal domain can be more adequately resolved.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes

Phage–bacteria interactions shape ecology and biogeochemistry across biomes. Resistance, arising from their evolutionary arms race, is well documented for receptor mutations, but other resistance mechanisms and their ecological implications remain unexplored. Here we isolated, sequenced and characterized 13 phage-resistant mutants of marine Cellulophaga baltica (Flavobacteriia). Mechanistically, mutations in surface proteins provided broad and complete extracellular resistance against multiple phages through decreased adsorption. Intracellular mutations affecting serine, glycine and threonine metabolism produced narrower resistance against a single phage, permitting viral DNA replication, and, in one mutant, were shown to be lipid mediated. Putative ecosystem impacts inferred from in vitro experiments include: (1) altered carbon utilization for all mutants, but especially by surface ones, (2) increased metabolite secretion for one modelled intracellular mutant (including experimentally verified acetate) and (3) increased ‘stickiness’ for all mutants, with surface mutants also sedimenting faster. Our findings highlight new resistance mechanisms and suggest that the phage–host arms race could result in ecosystem-level biogeochemical impacts in marine microorganisms.

Urvoy, Marion [Ohio State University]↗
DOE OSTI2022

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus . Results Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Sparagon, Wesley J. (ORCID:0000000296274174)↗
DOE OSTI2026

The 2025 “Hacking Limnology” Workshop Series and DSOS Virtual Summit: A Half Decade of Data‐Intensive Aquatic Science

The 5th Aquatic Ecosystem MOdeling Network—Junior (AEMON-J) “Hacking Limnology” Workshop and 6th Virtual Summit: Incorporating Data Science and Open Science in the Aquatic Sciences (DSOS) convened 21–25 July 2025. As in previous years (Fig. 1; Meyer and Zwart 2020; Meyer et al. 2021b, 2021c, 2022, 2024), the virtual workshops and summit were free of charge, the content was formatted to allow for broad engagement from a globally distributed audience, and workshop materials and recordings were made available on the AEMON-J/DSOS archive (Meyer et al. 2021a). In contrast to previous years, which primarily focused on inland aquatic ecosystems, this year's workshops and summit showcased a notable plurality of ecosystem types, with workshops spanning marine, riverine, and lacustrine environments. The weeklong event brought together researchers and practitioners interested in the nexus of data science, open science, and the aquatic sciences, hosting between 47 and 65 attendees at a single time and a higher number of registrants (n = 389), who might opt to access the material asynchronously.

Meyer, Michael F. [US Geological Survey, Portland,↗
DOE OSTI2024

Wetlands Delineation Report and Classification: PNNL – Sequim (formerly MSL) Estuary Wetland Delineation

The Pacific Northwest National Laboratory (PNNL) – Sequim, historically known as the Marine Sciences Laboratory (MSL) in Sequim, Washington, is managed and operated by Battelle on behalf of the U.S. Department of Energy (DOE) Pacific Northwest Site Office (PNSO). The site provides capabilities for future energy research, climate change effects analyses, wetland and coastal ecosystem restoration, other environmental research involving marine resources and hosts the only marine research facilities in the Department of Energy National Laboratory Complex. In order to support campus development, maintenance, and potential research activities, a wetland delineation was conducted on the northern portion of campus in accordance with state and federal wetland regulations. This technical report details out the delineation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria

Chemical cues mediate interactions between marine phytoplankton and bacteria, underpinning ecosystem-scale processes including nutrient cycling and carbon fixation. Phage infection alters host metabolism, stimulating the release of chemical cues from intact plankton, but how these dynamics impact ecology and biogeochemistry is poorly understood. Here we determine the impact of phage infection on dissolved metabolite pools from marine cyanobacteria and the subsequent chemotactic response of heterotrophic bacteria using time-resolved metabolomics and microfluidics. Metabolites released from intact, phage-infected Synechococcus elicited strong chemoattraction from Vibrio alginolyticus and Pseudoalteromonas haloplanktis, especially during early infection stages. Sustained bacterial chemotaxis occurred towards live-infected Synechococcus, contrasted by no discernible chemotaxis towards uninfected cyanobacteria. High-throughput microfluidics identified 5′-deoxyadenosine and 5′-methylthioadenosine as key attractants. Our findings establish that, before lysis, phage-infected picophytoplankton release compounds that attract motile heterotrophic bacteria, suggesting a mechanism for resource transfer that might impact carbon and nutrient fluxes across trophic levels.

Henshaw, Richard J↗
DOE OSTI2020

Phage-specific metabolic reprogramming of virocells

Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.

Environmental Sciences & Ecology↗
DOE OSTI2023

Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities

Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6–35 °C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

2020 State of the Science Report, Chapter 6: Changes in Benthic and Pelagic Habitats Caused by Marine Renewable Energy Devices

Most marine renewable energy (MRE) devices must be attached to the seafloor in some way, either through gravity foundations, pilings, or anchors, and with mooring lines, transmission cables, and devices themselves in the water column. Physical changes in benthic and pelagic habitats have the potential to alter species occurrence or abundance at a localized scale, lead to some level of habitat loss, provide opportunities for colonization by non-native species, alter patterns of ecological succession, modify ecosystem functioning, and affect behavioral responses of marine organisms. The transformation of the seafloor and/or water column habitat to new hard substratum because of the presence of the MRE devices may also lead to artificial reef effects or changes in animal behavior. While there is no indication that MRE devices affect marine habitats differently than other structures currently and historically placed in the ocean, regulators and stakeholders may continue to have concerns. https://tethys.pnnl.gov/publications/state-of-the-science-2020-chapter-6-habitat-changes

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Tsdat: An Open-Source Data Standardization Framework for Marine Energy and Beyond

Many organizations are tasked with the collection and processing of large quantities of data from various measurement devices. Data reported from these sources are often not interoperable with datasets and software used by analysts and other organizations in the same domain, introducing barriers for collaboration on large-scale projects. This poses a particular problem for cross-device comparisons and machine learning applications, which rely on large quantities of data from multiple sources. To address these challenges, the open-source Time-Series Data Pipelines (Tsdat) Python framework was developed by Pacific Northwest National Laboratory, with strategic guidance and direction provided by the National Renewable Energy Laboratory and Sandia National Laboratories to facilitate collaboration and accelerate advancements in the marine energy domain through the development of an open-source ecosystem of tools. This paper will describe the Tsdat framework and the data standards within which it operates. A beta version of Tsdat has been released and is being used by several projects in marine energy, wind energy, and building energy systems.

big data↗
DOE OSTI2022

Minimizing Ecological Impacts of Marine Energy Lighting

Marine energy is poised to become an important renewable energy contributor for the U.S., but widespread deployment of the technology hinges on its benefits outweighing the potential ecological impacts. One stressor marine energy installations introduce is light, which is known to cause varying responses among wildlife and has not yet been addressed as an environmental concern. This review discusses requirements and regulations for similar structures and how lighting design choices can be made to meet these requirements while minimizing environmental consequences. More practical guidance on implementing lighting for marine energy is needed, as well as updated guidelines to reflect technological and research advances. Known responses of wildlife to light are introduced in addition to how the responses of individuals may lead to ecosystem-level changes. The impact of light associated with marine energy installations can be reduced by following basic guidance provided herein, such as removing excess lighting, using lights with high directionality, and employing controls to reduce light levels. Continued research on animal responses to light, such as findings on minimum light levels for animal responses, alongside the development of highly-sensitivity spectral characterization capabilities can further inform lighting guidelines for deploying future open ocean marine energy devices.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Dissolved Organic Carbon in Coastal Waters: Global Patterns, Stocks and Environmental Physical Controls

Abstract Dissolved organic carbon (DOC) in coastal waters is integral to biogeochemical cycling, but global and regional drivers of DOC are still uncertain. In this study we explored spatial and temporal differences in DOC concentrations and stocks across the global coastal ocean, and how these relate to temperature and salinity. We estimated a global median coastal DOC stock of 3.15 Pg C (interquartile range (IQR) = 0.85 Pg C), with median DOC concentrations being 2.2 times higher than in open ocean surface waters. Globally and seasonally, salinity was the main driver of DOC with concentrations correlated negatively with salinity, without a clear relationship to temperature. DOC concentrations and stocks varied with region and season and this pattern is likely driven by riverine inputs of DOC and nutrients that stimulate coastal phytoplankton production. Temporally, high DOC concentrations occurred mainly in months with high freshwater input, with some exceptions such as in Eastern Boundary Current margins where peaks are related to primary production stimulated by nutrients upwelled from the adjacent ocean. No spatial trend between DOC and temperature was apparent, but many regions (19 out of 25) had aligned peaks of seasonal temperature and DOC, related to increased phytoplankton production and vertical stratification at high temperatures. Links of coastal DOC with salinity and temperature highlight the potential for anthropogenic impacts to alter coastal DOC concentration and composition, and thereby ecosystem status.

Lønborg, Christian [Section for Marine Diversity a↗
DOE OSTI2022

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.

Cohen, Natalie R.↗