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

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Depth-resolved carbon dioxide and methane concentrations in 522 lakes, ponds, and reservoirs worldwide

Lakes, ponds, and reservoirs (hereafter: “lakes”) are important sources of the greenhouse gases carbon dioxide (CO 2 ) and methane (CH 4 ). Emissions of CO 2 and CH 4 from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO 2 and CH 4 measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.

Rabaey, Joseph S. [University of Minnesota, Duluth↗
DOE OSTI2021

Soil gas probes for monitoring trace gas messengers of microbial activity

Abstract Soil microbes vigorously produce and consume gases that reflect active soil biogeochemical processes. Soil gas measurements are therefore a powerful tool to monitor microbial activity. Yet, the majority of soil gases lack non-disruptive subsurface measurement methods at spatiotemporal scales relevant to microbial processes and soil structure. To address this need, we developed a soil gas sampling system that uses novel diffusive soil probes and sample transfer approaches for high-resolution sampling from discrete subsurface regions. Probe sampling requires transferring soil gas samples to above-ground gas analyzers where concentrations and isotopologues are measured. Obtaining representative soil gas samples has historically required balancing disruption to soil gas composition with measurement frequency and analyzer volume demand. These considerations have limited attempts to quantify trace gas spatial concentration gradients and heterogeneity at scales relevant to the soil microbiome. Here, we describe our new flexible diffusive probe sampling system integrated with a modified, reduced volume trace gas analyzer and demonstrate its application for subsurface monitoring of biogeochemical cycling of nitrous oxide (N 2 O) and its site-specific isotopologues, methane, carbon dioxide, and nitric oxide in controlled soil columns. The sampling system observed reproducible responses of soil gas concentrations to manipulations of soil nutrients and redox state, providing a new window into the microbial response to these key environmental forcings. Using site-specific N 2 O isotopologues as indicators of microbial processes, we constrain the dynamics of in situ microbial activity. Unlocking trace gas messengers of microbial activity will complement -omics approaches, challenge subsurface models, and improve understanding of soil heterogeneity to disentangle interactive processes in the subsurface biome.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2025

Exploring prokaryotic diversity in permafrost-affected soils of Ladakh’s Changthang region and its geochemical drivers

Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R 2 = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).

16S rRNA↗
DOE OSTI2021

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H 2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Wildfire aerosol deposition likely amplified a summertime Arctic phytoplankton bloom

Summertime wildfire activity is increasing in boreal forest and tundra ecosystems in the Northern Hemisphere. However, the impact of long range transport and deposition of wildfire aerosols on biogeochemical cycles in the Arctic Ocean is unknown. Here, we use satellite-based ocean color data, atmospheric modeling and back trajectory analysis to investigate the transport and fate of aerosols emitted from Siberian wildfires in summer 2014 and their potential impact on phytoplankton dynamics in the Arctic Ocean. We detect large phytoplankton blooms near the North Pole (up to 82°N in the eastern Eurasian Basin). Our analysis indicates that these blooms were induced by the northward plume transport and deposition of nutrient-bearing wildfire aerosols. We estimate that these highly stratified surface waters received large amounts of wildfire-derived nitrogen, which alleviated nutrient stress in the phytoplankton community and triggered an unusually large bloom event. Our findings suggest that changes in wildfire activity may strongly influence summertime productivity in the Arctic Ocean.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids

Abstract The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNATyr gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.

Bhattacharjee, Ananda S.↗
DOE OSTI2026

Rapid organic carbon spiraling in a headwater stream linked with streamflow, biogeochemistry, and canopy phenology

Headwater streams are abundant worldwide and important to global biogeochemical cycles, serving as critical processors and transporters of C. C spiraling is a useful way to understand the retention and mineralization of organic C (OC) in streams. However, analyses of seasonal and interannual variability in OC spiraling are currently limited. In this study, we aimed to understand the temporal patterns and driving mechanisms of OC spiraling, which will inform our understanding of future OC changes under climate change. We used 7 y of daily data in a small headwater stream (Walker Branch, Tennessee, USA) to assess seasonal and interannual variability in OC spiraling length (S OC ) and mineralization velocity (v fOC ), as well as their potential related variables. On average, S OC in Walker Branch was ~10× shorter than in previously studied small streams, indicating strong connections between the water column and the benthic environment where OC mineralization mostly takes place. OC spiraling was faster during the more biologically active periods of spring and autumn compared with more elongated OC spiraling in summer and winter, when OC retention was lower and downstream transport was higher. Gross primary production (GPP) was most strongly related to S OC and v fOC . Photosynthetically active radiation (PAR) and NO 3 − were also positively and negatively related to v fOC , respectively. Trends toward earlier and longer canopy cover and reduced GPP and PAR may result in longer S OC and slower v fOC , reducing localized instream processing of OC and potentially shunting more OC downstream. However, long-term observations indicate reduced NO 3 − at Walker Branch, suggesting opposing effects to those of GPP and PAR, leading to faster v fOC and greater OC retention. Time-series analyses of OC spiraling in streams can enhance our understanding of current and future responses of OC processing and downstream transport to climate change, as well as implications for downstream OC dynamics.

biological activity↗
DOE OSTI2021

Dynamic global vegetation models underestimate net CO 2 flux mean and inter-annual variability in dryland ecosystems

Despite their sparse vegetation, dryland regions exert a huge influence over global biogeochemical cycles because they cover more than 40% of the world surface (Schimel 2010 Science 327 418–9). It is thought that drylands dominate the inter-annual variability (IAV) and long-term trend in the global carbon (C) cycle (Poulter et al 2014 Nature 509 600–3, Ahlstrom et al 2015 Science 348 895–9, Zhang et al 2018 Glob. Change Biol. 24 3954–68). Projections of the global land C sink therefore rely on accurate representation of dryland C cycle processes; however, the dynamic global vegetation models (DGVMs) used in future projections have rarely been evaluated against dryland C flux data. Here, we carried out an evaluation of 14 DGVMs (TRENDY v7) against net ecosystem exchange (NEE) data from 12 dryland flux sites in the southwestern US encompassing a range of ecosystem types (forests, shrub- and grasslands). We find that all the models underestimate both mean annual C uptake/release as well as the magnitude of NEE IAV, suggesting that improvements in representing dryland regions may improve global C cycle projections. Across all models, the sensitivity and timing of ecosystem C uptake to plant available moisture was at fault. Spring biases in gross primary production (GPP) dominate the underestimate of mean annual NEE, whereas models' lack of GPP response to water availability in both spring and summer monsoon are responsible for inability to capture NEE IAV. Errors in GPP moisture sensitivity at high elevation forested sites were more prominent during the spring, while errors at the low elevation shrub and grass-dominated sites were more important during the monsoon. We propose a range of hypotheses for why model GPP does not respond sufficiently to changing water availability that can serve as a guide for future dryland DGVM developments. Our analysis suggests that improvements in modeling C cycle processes across more than a quarter of the Earth's land surface could be achieved by addressing the moisture sensitivity of dryland C uptake.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Overcoming persistent challenges in putting environmental flow policy into practice: a systematic review and bibliometric analysis

The implementation of environmental flows (e-flows) aims to reduce the negative impacts of hydrological alteration on freshwater ecosystems. Despite the growing attention to the importance of e-flows since the 1970s, actual implementation has lagged. Therefore, we explore the limitations in e-flows implementation, their systemic reasons, and solutions. We conducted a systematic review and a bibliometric analysis to identify peer-reviewed articles published on the topic of e-flows implementation research in the last two decades, resulting in 68 research and review papers. Co-occurrence of terms, and geographic and temporal trends were analyzed to identify the gaps in environmental water management and propose recommendations to address limitations on e-flows implementation. We identify the underlying causes and potential solutions to such challenges in environmental water management. The limitations to e-flow implementation identified were categorized into 21 classes. The most recognized limitation was the competing priorities of human uses of water (n = 29). Many secondary limitations, generally co-occurring in co-causation, were identified as limiting factors, especially for implementing more nuanced and sophisticated e-flows. The lack of adequate hydrological data (n = 24) and ecological data (n = 28) were among the most mentioned, and ultimately lead to difficulties in starting or continuing monitoring/adaptive management (n = 28) efforts. The lack of resource/capacity (n = 21), experimentation (n = 19), regulatory enforcement (n = 17), and differing authorities involved (n = 18) were also recurrent problems, driven by the deficiencies in the relative importance given to e-flows when facing other human priorities. In order to provide a clearer path for successful e-flow implementation, system mapping can be used as a starting point and general-purpose resource for understanding the sociohydrological problems, interactions, and inherited complexity of river systems. Secondly, we recommend a system analysis approach to address competing demands, especially with the use of coupled water-energy modeling tools to support decision-making when hydropower generation is involved. Such approaches can better assess the complex interactions among the hydrologic, ecological, socioeconomic, and engineering dimensions of water resource systems and their effective management. Lastly, given the complexities in environmental water allocation, implementation requires both scientific rigor and proven utility. Consequently, and where possible, we recommend a move from simplistic flow allocations to a more holistic approach informed by hydroecological principles. To ease conflicts between competing water demands, water managers can realize more 'pop per drop' by supporting key components of a flow regime that include functional attributes and processes that enhance biogeochemical cycling, structural habitat formation, and ecosystem maintenance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Synthetic soils for ecological and synthetic biology applications

Soils are heterogeneous and dynamic systems characterized by complex physical, chemical, and biological interactions. Understanding these interactions is critical, as they influence plant productivity, global biogeochemical cycles, and ecosystem resilience. While ecologists have long studied soils in field, greenhouse, and laboratory settings, their complexity and heterogeneity make it challenging to pinpoint key properties driving biological processes and derive mechanistic insights. Advancements in synthetic biology, which seeks to engineer and control biological processes in soils, have increased the demand for standardized and controllable experimental platforms. These platforms, referred to here as ‘synthetic soils’, are systems designed to reproduce selected physicochemical characteristics of natural soils in a simplified and defined format, allowing scientists to systematically change soil physicochemical properties (i.e. texture, mineralogy, pH) to study how biological components (i.e. microbes, plants, soil fauna, etc.) respond to, modify, or interact within these controlled environments. This review explores existing synthetic soils, their advantages, limitations, and applications in ecology and synthetic biology, and discusses potential directions for their future development.

artificial soils↗
DOE OSTI2024

Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake

Giant viruses (GVs; Nucleocytoviricota) impact the biology and ecology of a wide range of eukaryotic hosts, with implications for global biogeochemical cycles. Here, we investigated GV niche separation in highly stratified Lake A at the northern coast of Ellesmere Island, Nunavut, Canada. This lake is composed of a layer of ice-covered freshwater that overlies saltwater derived from the ancient Arctic Ocean, and it therefore provides a broad gradient of environmental conditions and ecological habitats, each with a distinct protist community and rich assemblages of associated GVs. The upper layer (mixolimnion) had measurable light and oxygen, and contained diverse GVs linked to photosynthetic protists, indicating adaptation to surface biotic and abiotic conditions. In contrast, the saline lower layer (monimolimnion), lacking oxygen and light, hosted GVs associated with predicted heterotrophic protists, some of which are known for a predatory lifestyle, and with several viral genes suggesting adaptation to deep-water anaerobic conditions. Our observations underscore the coupling between physical and chemical gradients, microeukaryotes and their associated GVs in Lake A, and provide insight into the potential for GVs to directly and indirectly impact host metabolism. There were similarities between the genetic composition of GVs and the metabolic processes of their potential hosts, implying co-evolution and niche-adaptation within the lake habitats. Notably, we found a greater presence of viral rhodopsins in deeper water layers, suggesting an evolutionary relationship with potential hosts capable of supplementing their energetic needs to thrive in low energy, anoxic conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Abstract Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Electroactive biofilms: how microbial electron transfer enables bioelectrochemical applications

Abstract Microbial biofilms are ubiquitous. In marine and freshwater ecosystems, microbe–mineral interactions sustain biogeochemical cycles, while biofilms found on plants and animals can range from pathogens to commensals. Moreover, biofouling and biocorrosion represent significant challenges to industry. Bioprocessing is an opportunity to take advantage of biofilms and harness their utility as a chassis for biocommodity production. Electrochemical bioreactors have numerous potential applications, including wastewater treatment and commodity production. The literature examining these applications has demonstrated that the cell–surface interface is vital to facilitating these processes. Therefore, it is necessary to understand the state of knowledge regarding biofilms’ role in bioprocessing. This mini-review discusses bacterial biofilm formation, cell–surface redox interactions, and the role of microbial electron transfer in bioprocesses. It also highlights some current goals and challenges with respect to microbe-mediated bioprocessing and future perspectives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗
DOE OSTI2020

High-throughput mapping of the phage resistance landscape in E. coli

Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Substrate quality drives fungal necromass decay and decomposer community structure under contrasting vegetation types

Fungal mycelium is increasingly recognized as a central component of soil biogeochemical cycling, yet our current understanding of the ecological controls on fungal necromass decomposition is limited to single sites and vegetation types. By deploying common fungal necromass substrates in a temperate oak savanna and hardwood forest in the midwestern USA, we assessed the generality of the rate at which high- and low-quality fungal necromass decomposes; further, we investigated how the decomposer ‘necrobiome’ varies both across and within sites under vegetation types dominated by either arbuscular or ectomycorrhizal plants. In this work, the effects of necromass quality on decay rate were robust to site and vegetation type differences, with high-quality fungal necromass decomposing, on average, 2.5 times faster during the initial stages of decay. Across vegetation types, bacterial and fungal communities present on decaying necromass differed from bulk soil microbial communities and were influenced by necromass quality. Moulds, yeasts and copiotrophic bacteria consistently dominated the necrobiome of high-quality fungal substrates. Synthesis. We show that regardless of differences in decay environments, high-quality fungal substrates decompose faster and support different types of decomposer micro-organisms when compared with low-quality fungal tissues. These findings help to refine our theoretical understanding of the dominant factors affecting fast cycling components of soil organic matter and the microbial communities associated with rapid decay.

59 BASIC BIOLOGICAL SCIENCES↗