Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Archaea”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth, provide nutrients, or confer pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and assembled stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. Here, this review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.

Clauer, Phillip [Massachusetts Inst. of Technology↗
DOE OSTI2025

Thermostable Enzyme Variants in the Lower Mevalonate Pathway Improve Isoprenoid Production by Cell-Free Biocatalysis

Cell-free biocatalysis is a rapidly evolving field with great potential for sustainably producing valuable chemicals. Some challenges in cell-free biocatalysis include reaction longevity, enzyme stability, and the cost of the biocatalysts. Here, the challenge of enzyme instability was addressed by employing thermophilic enzymes to improve the productivity of the lower mevalonate pathway, using limonene as an example isoprenoid product. The Classical mesophilic mevalonate pathway was compared to a newly assembled set of thermophilic enzymes comprising the Archaea I mevalonate pathway. The thermophilic pathway enzymes were thermostable to at least 60 °C and exhibited a 6× longer operating lifetime at 22 °C. Thus, despite lower initial activity rates at ambient temperature, the thermophilic pathway was longer-lived and resulted in a more productive cell-free reaction overall, achieving 1.7× higher yield of limonene compared to using enzymes from mesophiles. Moreover, the thermostable pathway retained activity for longer with the challenge of solvent exposure, namely, ethanol and isoprenol, which broadens the scope of accessible substrates and/or products in cell-free reactions employing this pathway. Altogether, we showed significant improvement in the stability and productivity of the lower mevalonate pathway, which will enable more efficient cell-free biosynthesis of isoprenoid products. This represents a valuable strategy to increase the robustness of cell-free systems by carefully sourcing biocatalysts from thermophilic organisms, which have proven to be resilient to challenges unique to cell-free reaction systems.

09 BIOMASS FUELS↗
DOE OSTI2026

Nanoarchitectonic Semiconductor–Bio Hybrid Systems with Enhanced Charge Transfer for Hydrogen Peroxide Production

Nanoarchitectonics offers a systematic approach to creating an artificial framework by integrating different multiscale components such as semiconductor lattices and biological substances. However, most nanoarchitectonic abiotic-biotic hybrid systems have intrinsic limitations in imparting nonequilibrium biological features into semiconductor lattices at the nanoscale. Here, in this study, we report a new nanoarchitectonic system integrating bismuth oxychloride (BiOCl) nanosheets with purple membrane (PM) patches. PM is an archaeal subcellular fraction capable of unidirectionally transferring photogenerated charge carriers to its surroundings at the nanoscale independent of archaeal metabolism and retaining this dynamic functionality after isolation from living archaea. Microscopy, spectroscopy, electrochemical, and synchrotron X-ray scattering analyses verify that the nanoarchitectonic hybridization between BiOCl and PM generates a vertical heterostructure, thereby enhancing photogenerated charge-carrier dynamics and enabling the associated photocatalytic capacity. The resulting PM-BiOCl hybrid nanosheets efficiently convert dioxygen into hydrogen peroxide through a two-electron and two-proton transfer process under ambient conditions while simultaneously converting ethylene glycol into value-added chemicals. This study presents a nanoarchitectonic approach that leverages the photogenerated charge-carrier dynamics of the archaeal subcellular fractions to modulate the optoelectronic and catalytic capacity limitations of semiconductors.

catalysis↗
DOE OSTI2024

Methanogens implicated by DNA evidence

Here, this Genome Watch article highlights recent findings that expand the known diversity of methanogenic archaea and the metagenomic evidence that led to their identification and cultivation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days

In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22–1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus

Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N 2 O) emissions, although biochemical origins of this N 2 O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH 2 OH) to dioxygen (O 2 ) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N 2 via reaction with NH 2 OH and dimerization with itself to yield N 2 O. These results afford one plausible enzymatic origin for N 2 O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.

Voland, Robert W. (ORCID:0000000201061257)↗
DOE OSTI2025

An electron-bifurcating “plug” to a protein nanowire in tungsten-dependent aldehyde detoxification

Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacteriumAcetomicrobium mobile.The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation.

Science & Technology - Other Topics↗
DOE OSTI2026

Cryogenic electron tomography by the numbers: Charting underexplored lineages in structural cell biology

Imaging cells and their interactions across the whole biosphere with molecular-scale resolution is key for understanding structure–function relations. Cryogenic electron tomography (cryo-ET) is a powerful method for obtaining this critical information. However, cryo-ET studies are challenging and often limited to a small number of cell types per study. Here, we collate cryo-ET data from hundreds of cells and tissues across the biosphere to i) identify emerging methodological trends, ii) pinpoint strategies to reduce imaging time and costs, iii) quantitatively compare methods for cell freezing and sectioning, and iv) census cryo-ET species coverage across all domains of life. Comparing the fraction of cellular material within a single lamella across all domains of life reveals an order of magnitude difference between eukaryotes (1%) compared to bacteria (9%) and archaea (14%). We calculate the fraction of cellular material which can be imaged using distinct sectioning methods on multicellular communities and tissues—identifying serial lift-out as a powerful approach for obtaining more complete cellular depictions. Finally, we show that the biodiversity of current cryo-ET studies is 2 to 3 orders of magnitude lower than in sequence libraries and 4 to 5 lower than the total predicted on Earth. Our analyses reveal major evolutionary lineages which remain critically understudied and highlight where future cryo-ET research would be most impactful.

HPF↗
DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗
DOE OSTI2025

Sulfide stress tolerance as a controller of methane production in temperate wetlands

Abstract Wetlands are a major source of methane emissions and contribute to the observed increase in atmospheric methane over the last 20 years. Methane production in wetlands is the final step of carbon decomposition performed by anaerobic archaea. Although hydrogen/carbon dioxide and acetate are the substrates most often attributed to methanogenesis, other substrates—such as methylated compounds—may additionally play important roles in driving methane production in wetland systems. Here we conducted mesocosm experiments combined with genome-resolved metatranscriptomics to investigate the impact of diverse methanogenic substrate amendment on methanogenesis in two high methane-emitting wetlands with distinct geochemistry, termed P7 and P8. Methanol amendment resulted in high methane production at both sites, whereas acetate and formate amendment only stimulated methanogenesis in P7 mesocosms, where aqueous sulfide concentrations were lower. In P7 sediments, formate amendment fueled acetogenic microbes that produced acetate, which was subsequently utilized by acetoclastic methanogens. In contrast to expression profiles in P7 mesocosms, active methylotrophic methanogen genomes from P8 showed increased expression of genes related to membrane remodeling and DNA damage repair, indicative of stress tolerance mechanisms to counter sulfide toxicity. Methylotrophic methanogenesis generates higher free energy yields than acetoclastic methanogenesis, which likely enables allocation of more energy toward stress responses. These findings contribute to the growing body of literature highlighting methylotrophic methanogenesis as an important methane production pathway in wetlands. By using less competitive substrates like methanol that provide greater energy yields, methylotrophic methanogens may invest in physiological strategies that provide competitive advantages across a range of environmental stresses.

Environmental Sciences & Ecology↗
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

Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

ABSTRACT The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long‐term established pastures in the Amazon. Machine learning‐derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein‐coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein‐coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long‐term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long‐term established pastures with implications for the C and N cycles.

carbon and nitrogen cycles↗
DOE OSTI2025

A metagenomic perspective on the microbial prokaryotic genome census

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Composition and in situ structure of the Methanospirillum hungatei cell envelope and surface layer

Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo–electron tomography, we visualized the S-layer lattice surroundingMethanospirillum hungatei, a methanogenic archaeon. Though more compact than known structures,M. hungatei’s S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer’s cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment.M. hungateicell’s end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.

Science & Technology - Other Topics↗
DOE OSTI2025

Redox conduction facilitates direct interspecies electron transport in anaerobic methanotrophic consortia

Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) form syntrophic partnerships in marine sediments to consume greenhouse gas methane. While direct interspecies electron transport is proposed to enable ANME/SRB symbiosis, its electrochemical properties remain uncharacterized. Here, using sediment-free enrichment cultures, we measured the electron transport capabilities of marine consortia under physiological conditions. Diverse ANME/SRB consortia exhibited high dry conductance close to electrogenic biofilms. This conductance diminished upon exposure to heat or oxygen but was preserved following paraformaldehyde fixation, indicating a biomolecular origin for this electric charge transfer. Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively. Generator-collector measurements further demonstrated that these redox components facilitate electron transport over micrometer-scale distances, sufficient to link archaeal and bacterial partners. Collectively, our results establish that marine ANME/SRB symbiosis uses redox conduction, consistent with multiheme cytochromec, for direct interspecies electron transport.

Science & Technology - Other Topics↗
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 OSTI2025

Aerosol biome of a cafeteria and medical facility in Los Alamos, New Mexico, USA

Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Floodplain nitrifiers harbor the genetic potential for utilizing a wide range of organic nitrogen compounds

Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (ure) and at least one urea transporter ( utp, urt, dur3 ). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase ( cynS ), nitrilase ( nit1 ), omega-amidase ( nit2 ), nitrile hydratase ( nthA ), and genes related to purine degradation, including biuret hydrolase ( biuH ), oxamic transcarbamylase ( allFGH ), and catabolic carbamate kinase ( allK ). AOA often encoded an uncharacterized amidohydrolase collocated with biuH , rather than allophanate hydrolase ( atzF ). A small number of AOA encoded atzF , functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes ( trtA, biuH , and atzH ), and in comammox, these genes were also collocated with allFGHK . The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members.

floodplain↗