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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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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Predominance of Methanomicrobiales and diverse hydrocarbon–degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome–resolved metabolisms

Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin. Our analyses resulted in the recovery of over 40 metagenome-assembled genomes (MAGs) from eight coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. Further, the data presented herein provides novel insights into Appalachian Basin coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Metagenome‐Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain

Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. In conclusion, the SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Expanded Diversity of Microbial Groups Capable of Anaerobic Pyrite Reduction and Assimilation of Dissolution Products

Pyrite, the most abundant iron sulfide mineral in the Earth's crust, has traditionally been considered as a sink for iron and sulfur in the absence of oxygen. Recent research, however, has shown that anaerobic methanogenic archaea can reductively dissolve pyrite and assimilate its products as sources of iron and sulfur. This study explores whether other anaerobic bacteria, including fermentative, nitrate-, iron oxide-, fumarate-, and sulfate-respiring bacteria, can also reduce pyrite and use its dissolution products as sources of iron and sulfur. Results indicate that heterotrophic bacteria respiring fumarate or sulfate, or fermenting organic carbon, can reduce pyrite and assimilate released iron and sulfur. In contrast, nitrate- or iron oxide-respiring cells did not reduce pyrite, suggesting that microbial pyrite reduction is metabolism-specific. All strains capable of reducing pyrite could also use mackinawite as an iron and sulfur source. With the exception of fermentative Bacteroides, strains did not require direct contact with pyrite to reduce the mineral, indicating extracellular electron transfer via electron shuttles. These findings expand the known diversity of microbial groups capable of pyrite reduction and highlight the mineral's lability in various anaerobic environments, with potential implications for the biogeochemical cycles of iron, sulfur, carbon, and oxygen.

58 GEOSCIENCES↗
DOE OSTI2025

Surface Texture of Macroplastic Pollution in Streams Alters the Physical Structure and Diversity of Biofilm Communities

ABSTRACT Biofilms can develop on nearly any surface, and in aquatic ecosystems they are essential components of biogeochemical cycles and food webs. Plastic waste in waterways is a new type of surface for biofilm colonisation. To analyse the influence of plastic pollution on the development and diversity of microbial freshwater biofilms that colonised them, we incubated 388 cm 2 veneers of high‐density polyethylene (HDPE) with two veneer textures, smooth and rough, and tulip tree wood ( Liriodendron tulipifera ), in three rural headwater streams at the Savannah River Site (Aiken, SC, USA). We collected biofilms from veneers after 14, 28 and 56 days of incubation and analysed 16S rRNA genes and biofilm properties. We found that plastic negatively affected species richness of biofilms compared with wood, but that evenness was greatest on rough textured HDPE. Beta diversity was primarily influenced by stream site. Beta diversity differed more between wood and plastic veneers than with plastic surface texture and became more different over time. Wood had nine times more biomass than rough HDPE and 40 times more biomass than smooth HDPE. Given the projected increase of macroplastic pollution in aquatic ecosystems, our findings emphasise the need to further understand its effects on biofilm characteristics.

Lopez Avila, Fabiola [Odum School of Ecology Unive↗
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↗
DOE OSTI2024

Nitrogen availability and summer drought, but not N:P imbalance, drive carbon use efficiency of a Mediterranean tree-grass ecosystem

All ecosystems contain both sources and sinks for atmospheric carbon (C). A change in their balance of net and gross ecosystem carbon uptake, ecosystem-scale carbon use efficiency (CUE ECO ), is a change in their ability to buffer climate change. However, anthropogenic nitrogen (N) deposition is increasing N availability, potentially shifting terrestrial ecosystem stoichiometry towards phosphorus (P) limitation. Depending on how gross primary production (GPP, plants alone) and ecosystem respiration (R ECO , plants and heterotrophs) are limited by N, P or associated changes in other biogeochemical cycles, CUE ECO may change. Seasonally, CUE ECO also varies as the multiple processes that control GPP and respiration and their limitations shift in time. We worked in a Mediterranean tree-grass ecosystem (locally called ‘dehesa’) characterized by mild, wet winters and summer droughts. We examined CUE ECO from eddy covariance fluxes over 6 years under control, +N and + NP fertilized treatments on three timescales: annual, seasonal (determined by vegetation phenological phases) and 14-day aggregations. Finer aggregation allowed consideration of responses to specific patterns in vegetation activity and meteorological conditions. We predicted that CUE ECO should be increased by wetter conditions, and successively by N and NP fertilization. Milder and wetter years with proportionally longer growing seasons increased CUE ECO , as did N fertilization, regardless of whether P was added. Using a generalized additive model, whole ecosystem phenological status and water deficit indicators, which both varied with treatment, were the main determinants of 14-day differences in CUE ECO . The direction of water effects depended on the timescale considered and occurred alongside treatment-dependent water depletion. Overall, future regional trends of longer dry summers may push these systems towards lower CUE ECO .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Role of Forest Carbon Change in Shaping Future Land Use and Land Cover Change

Global change, particularly the changes in atmospheric CO 2 concentration, climatic variables, and nitrogen deposition, has been widely recognized and examined to have worldwide impacts on forest carbon. However, its influence on forest area required to meet the demand for timber and carbon storage and subsequent land use and land cover change (LULCC) is rarely studied. This study explores the role of global change-driven forest carbon change in shaping future global LULCC projections and investigates underlying drivers. We incorporated the global change impacts on forest carbon from the Canadian Land Surface Scheme Including Biogeochemical Cycles model simulations (driven by meteorological forcing projections from two Earth system models [ESMs]) into the Global Change Analysis Model, under three combinations of shared socioeconomic pathways and representative concentration pathways (SSP126, SSP370, and SSP585). Including forest carbon change decreases the projected expansion of managed forest and managed pasture, reduces the loss of unmanaged pastures and forests, and provides more cropland. The relative change in managed forest by 2100 is -4.0%, -21.7%, and -31.9%, under SSP126, SSP370, and SSP585, respectively, when forest carbon change is considered. CO 2 fertilization is the dominant driver, increasing forest vegetation and soil carbon by 37% and 4.1%, and leading to 78.6% of the total area with a change in land use types by 2100 under SSP585. In comparison, climate change reduces forest vegetation and soil carbon by -3.5% and -0.8%, influencing 23.9% of the total area with a change in land use types by 2100 under SSP585, while nitrogen deposition has minor impacts. Using meteorological forcing data from two ESMs leads to similar impacts of forest carbon change on LULCC in terms of sign and trend but different magnitudes. This study highlights the large impact of forest carbon change on shaping future LULCC dynamics and the critical role of CO 2 fertilization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A functional trait framework for integrating nitrogen‐fixing cover crops into short‐rotation woody crop systems

Abstract Developing approaches to simultaneously maximize short‐rotation woody crop (SRWC) productivity while minimizing footprints associated with intensive management is imperative to profitable and sustainable bioenergy production systems. Intercropping nitrogen (N)‐fixing cover crops in SRWC systems is an overlooked approach to sustainably intensify SRWC production by increasing N availability using less environmentally costly inputs. Here, we discuss how functional traits (e.g., seasonal activity, lifespan, leaf habit, soil exploration) of cover crops and SRWCs may interact through space and time influencing access to light, water, and nutrients to provide a framework for successful integration of cover crops into SRWCs. Next, we summarize the literature on intercropping forest plantations with N‐fixing cover crops to identity research gaps and outline future research needs and opportunities. And then, using empirical N demand and productivity data from SRWCs and cover crop N inputs from the literature, we illustrate how SRWC leaf habit (conifer evergreens and deciduous hardwoods) would influence successful integration of cover crops and potential N fixation. We estimate that integrating cover crops into SRWCs could supply 27% and 72% of the N demand across a 10‐year rotation for an evergreen and a deciduous hardwood, respectively. These figures suggest these integrated SRWC systems may approach a virtual minimal external N input when other biogeochemical cycles are considered. The guiding principles presented here are grounded in ecological theory and provide a framework for sustainable intensification of forest production.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The diatom Fragilariopsis cylindrus : A model alga to understand cold-adapted life

Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands

Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. Here, to evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota

Methane is a potent greenhouse gas, largely produced by methanogenic archaea, contributing to Earth’s dynamic climate and biogeochemical cycles. In the past decade, metagenomics revealed that lineages outside of the Euryarchaeota superphylum encode genes for methanogenesis. This was recently confirmed through the cultivation of two classes of methanogenic Thermoproteota. Thus far, all methanogens within the Thermoproteota are predicted or were shown to be methylotrophic. The only exception to this are the Nezhaarchaea, for which metagenomic predictions suggest they are CO 2 -reducing methanogens. Here, we demonstrate methanogenic activity in a third class of Thermoproteota, the Methanonezhaarchaeia. Contrary to genomic predictions for this class, we cultivated a methylotrophic species, Candidatus Methanonezhaarchaeum fastidiosum YNP3N, highlighting the importance of testing metagenomic hypotheses through experimentation. We investigate the metabolic diversity of Methanonezhaarchaeia, including metabolic modifications accompanying frequent loss of methanogenesis in this class. This highlights gaps in our understanding of the biochemistry, diversity, and evolution of thermoproteotal methanogens and their contributions to carbon cycling.

Kohtz, Anthony J. [Montana State Univ., Bozeman, M↗
DOE OSTI2020

Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO 2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, here we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment. IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs’ β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thermal adaptation of soil microbial growth traits in response to chronic warming

ABSTRACT Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5°C above ambient temperature with unheated controls for 30 years. We hypothesized that Alphaproteobacteria from warmed plots have (i) less temperature-sensitive growth rates; (ii) higher optimum growth temperatures; and (iii) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22°C to 37°C in 2–3°C increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range. IMPORTANCE Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

PioABC-Dependent Fe(II) Oxidation during Photoheterotrophic Growth on an Oxidized Carbon Substrate Increases Growth Yield

Microorganisms that carry out Fe(II) oxidation play a major role in biogeochemical cycling of iron in environments with low oxygen. Fe(II) oxidation has been largely studied in the context of autotrophy. Here, we show that the anoxygenic phototroph, Rhodopseudomonas palustris CGA010, carries out Fe(II) oxidation during photoheterotrophic growth with an oxidized carbon source, malate, leading to an increase in cell yield and allowing more carbon to be directed to cell biomass. We probed the regulatory basis for this by transcriptome sequencing (RNA-seq) and found that the expression levels of the known pioABC Fe(II) oxidation genes in R. palustris depended on the redox-sensing two-component system, RegSR, and the oxidation state of the carbon source provided to cells. This provides the first mechanistic demonstration of mixotrophic growth involving reducing power generated from both Fe(II) oxidation and carbon assimilation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Magnetotactic Bacteria Accumulate a Large Pool of Iron Distinct from Their Magnetite Crystals

ABSTRACT Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that form intracellular nanoparticles of magnetite (Fe 3 O 4 ) or greigite (Fe 3 S 4 ) in a genetically controlled manner. Magnetite and greigite synthesis requires MTB to transport a large amount of iron from the environment. Most intracellular iron was proposed to be contained within the crystals. However, recent mass spectrometry studies suggest that MTB may contain a large amount of iron that is not precipitated in crystals. Here, we attempted to resolve these discrepancies by performing chemical and magnetic assays to quantify the different iron pools in the magnetite-forming strain Magnetospirillum magneticum AMB-1, as well as in mutant strains showing defects in crystal precipitation, cultivated at various iron concentrations. All results show that magnetite represents at most 30% of the total intracellular iron under our experimental conditions and even less in the mutant strains. We further examined the iron speciation and subcellular localization in AMB-1 using the fluorescent indicator FIP-1, which was designed for the detection of labile Fe(II). Staining with this probe suggests that unmineralized reduced iron is found in the cytoplasm and associated with magnetosomes. Our results demonstrate that, under our experimental conditions, AMB-1 is able to accumulate a large pool of iron distinct from magnetite. Finally, we discuss the biochemical and geochemical implications of these results. IMPORTANCE Magnetotactic bacteria (MTB) produce iron-based intracellular magnetic crystals. They represent a model system for studying iron homeostasis and biomineralization in microorganisms. MTB sequester a large amount of iron in their crystals and have thus been proposed to significantly impact the iron biogeochemical cycle. Several studies proposed that MTB could also accumulate iron in a reservoir distinct from their crystals. Here, we present a chemical and magnetic methodology for quantifying the iron pools in the magnetotactic strain AMB-1. Results showed that most iron is not contained in crystals. We then adapted protocols for the fluorescent Fe(II) detection in bacteria and showed that iron could be detected outside crystals using fluorescence assays. This work suggests a more complex picture for iron homeostasis in MTB than previously thought. Because iron speciation controls its fate in the environment, our results also provide important insights into the geochemical impact of MTB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Differential Response of Bacterial Microdiversity to Simulated Global Change

Microbial communities play an integral role in global biogeochemical cycling, but our understanding of how global change will affect microbial community structure and functioning remains limited. Microbiome analyses typically aggregate large amounts of genetic diversity which may obscure finer variation in traits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages

Very little is known about sea ice microbes despite the significant role played by sea ice in the global oceans as well as microbial input into biogeochemical cycling. Studies on the sea ice viruses have been typically limited to -omics-based approaches and microscopic examinations of sea ice samples.

59 BASIC BIOLOGICAL SCIENCES↗