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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Predicting stress response and improved protein overproduction in Bacillus subtilis

Abstract Bacillus subtilis is a well-characterized microorganism and a model for the study of Gram-positive bacteria. The bacterium can produce proteins at high densities and yields, which has made it valuable for industrial bioproduction. Like other cell factories, metabolic modeling of B. subtilis has discovered ways to optimize its metabolism toward various applications. The first genome-scale metabolic model (M-model) of B. subtilis was published more than a decade ago and has been applied extensively to understand metabolism, to predict growth phenotypes, and served as a template to reconstruct models for other Gram-positive bacteria. However, M-models are ill-suited to simulate the production and secretion of proteins as well as their proteomic response to stress. Thus, a new generation of metabolic models, known as metabolism and gene expression models (ME-models), has been initiated. Here, we describe the reconstruction and validation of a ME model of B. subtilis , i JT964-ME. This model achieved higher performance scores on the prediction of gene essentiality as compared to the M-model. We successfully validated the model by integrating physiological and omics data associated with gene expression responses to ethanol and salt stress. The model further identified the mechanism by which tryptophan synthesis is upregulated under ethanol stress. Further, we employed i JT964-ME to predict amylase production rates under two different growth conditions. We analyzed these flux distributions and identified key metabolic pathways that permitted the increase in amylase production. Models like i JT964-ME enable the study of proteomic response to stress and the illustrate the potential for optimizing protein production in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 ( ZmCIPK15 )

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Characterization of Histophilus somni sialic acid uptake mutant (Δ nanP -Δ nanU ) using a mouse septicemia and mortality model

Histophilus somni is an important pathogen of the bovine respiratory disease complex, yet the mechanisms underlying its virulence remain poorly understood. It is known that H. somni can incorporate sialic acid into lipooligosaccharide (LOS), and sialylated H. somni is more resistant to phagocytosis and complement-mediated killing by serum compared to non-sialylated bacteria in vitro. However, the virulence of non-sialylated H. somni has not been evaluated in vivo using an animal model. In this study, we investigated the contribution of sialic acid to virulence by constructing an H. somni sialic acid uptake mutant (ΔnanP-ΔnanU) and comparing the parent and mutant strains in a mouse septicemia and mortality model. Intraperitoneal challenge of mice with wildtype H. somni (1 × 10 8 colony forming units/mouse, CFU) was lethal to all animals. Mice challenged with three different doses (1, 2, or 5 × 108 CFU/mouse) of an H. somni ΔnanP-ΔnanU sialic acid uptake mutant exhibited survival rates of 90 %, 60 %, and 0 % respectively. High-performance anion exchange chromatography analyses revealed that LOS prepared from both parent and the ΔnanP-ΔnanU mutant strains of H. somni were sialylated. These findings suggest the presence of de novo sialic acid synthesis pathway, although the genes associated with de novo sialic acid synthesis (neuB and neuC) were not identified by genomic analysis. The lower attenuation in mice is most likely attributed to the sialylated LOS of H. somni nanPU mutant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identification of a pathway for electron uptake in Shewanella oneidensis

Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO 2 and renewable electricity. Theoretically EET could do this with an efficiency comparable to H 2 -oxidation but without the need for a volatile intermediate and the problems it causes for scale up. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-1, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Optimal production of Phanerochaete chrysosporium manganese peroxidases and Trametes sp. C30 laccase hybrid Lac131 in Aspergillus niger for lignin bioconversion

Background Incorporating the production of related ligninolytic enzymes into industrial filamentous fungus Aspergillus niger will enhance the bioconversion of lignocelluloses to various chemical products. Results In this study, transgenic expression of Phanerochaete chrysosporium manganese peroxidases (mnps) and Trametes sp. C30 laccase hybrid Lac131 (lac131) were examined and optimized in A. niger 11414 prtT∆ strain. Five mnps (mnp1, mnp2, mnp3, mnp4, and mnp5) and lac131 genes were expressed separately or in combination. The transgenic strain containing the entire mnp2 genomic coding sequence (gmnp2) exhibited the highest mnP activity among the five mnp over-expression strains in the modified minimal medium (mMM) with addition of 5 g/L bovine hemoglobin (bHg). We examined the effects of hemin and bHg on mnP production in the gmnp2 strain cultures and found that at least 1 g/L bHg was required, while hemin was not. Culture conditions for mnP production were further optimized for the gmnp2 strain and the highest mnP activities were detected in the cultures grown at 25 °C and 200 rpm with an initial pH of 4.5. Effects of soy protein, skim milk, and bovine serum albumin on mnP production were investigated; 5 g/L of soy proteins or skim milk had comparable effects to 2.5 g/L bHg, while cultures with bovine serum albumin had diminished mnP activity. Disruption of both prtT and vsm1 substantially augmented the mnP production and its activity reached 575 U/L. Trametes sp. C30 laccase hybrid lac131 was strongly expressed in either A. niger gmnp2 (1975 U/L) or 11414prtT∆ (3895 U/L) strain. Both mnP and laccase in the culture supernatants effectively decolorized selected phenolic compounds (dyes) and cleaved tagged model lignin dimers. Conclusion The mnP was successfully produced in A. niger by optimizing the culture conditions and host strain. Co-expression of all four mnp genes in the same expression host by multiplex CRISPR will lead to the mnP production reaching levels comparable to P. chrysosporium, while only requiring 36 h at 25 °C. The Lac131 activity in transgenic A. niger strain is 4- to 7-times higher than that in previous studies. Co-production of mnP and laccase in A. niger will enhance the lignin bioconversion efficiency.

Aspergillus niger↗
DOE OSTI2025

Microbiomes of frozen blood plasma samples reveal potential pathogens in wild birds and rodents

The lack of genomic data on pathogens from wildlife severely limits our ability to track transmission patterns and trace the origins of an outbreak. There are currently millions of wildlife samples in biobanks around the world, including blood samples. Blood has traditionally been viewed as a sterile environment in healthy individuals, but recent evidence suggests that this is not the case, especially for wild animals. Our goal was to determine whether frozen plasma samples can be surveyed using 16S sequencing to provide information about potential hosts for pathogens for a more complete understanding of disease systems. We sequenced blood plasma from wild North American deer mice ( Peromyscus maniculatus ) and American kestrels ( Falco sparverius ) that were cryogenically stored for 7 and 13 years, respectively, and compared two DNA extraction kits. The kestrel samples contained a very high number of reads that could not be identified to phylum compared to the mouse samples. The two kits differed in the phyla and genera that were detected, and the Zymo kit, which is optimized for plasma and serum, produced more high-quality reads for both kestrel and mouse samples. We identified several pathogenic genera, including Mycoplasma, Escherichia-Shigella , and Bartonella . Sequencing blood samples for pathogens could potentially have broad applications for identifying important reservoir hosts for pathogen transmission and provide a reduced set of species on which to follow up.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Comparative Assessment of Severe Acute Respiratory Syndrome Coronavirus 2 Variants in the Ferret Model

The continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans necessitates evaluation of variants for enhanced virulence and transmission. We used the ferret model to perform a comparative analysis of four SARS-CoV-2 strains, including an early pandemic isolate from the United States (WA1), and representatives of the Alpha, Beta, and Delta lineages. While Beta virus was not capable of pronounced replication in ferrets, WA1, Alpha, and Delta viruses productively replicated in the ferret upper respiratory tract, despite causing only mild disease with no overt histopathological changes. Strain-specific transmissibility was observed; WA1 and Delta viruses transmitted in a direct contact setting, whereas Delta virus was also capable of limited airborne transmission. Viral RNA was shed in exhaled air particles from all inoculated animals but was highest for Delta virus. Prior infection with SARS-CoV-2 offered varied protection against reinfection with either homologous or heterologous variants. Notable genomic variants in the spike protein were most frequently detected following WA1 and Delta virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Polar algae flaunt their zinc assets

Metal ions have been at the centre of pivotal points in the evolution of extant life. Oxygen-evolving photosynthesis, which irrevocably reshaped the geochemistry and biology of our planet, has an absolute requirement for metal ions to harvest light, split water and transfer electrons. Access to abundant oxygen then led to the propagation of organisms capable of oxidative metabolism, a process that is also dependent on metal ions for electron transfer and reduction of molecular oxygen. Because of the essential links between metal ions and the proteins that require them to function, as well as changes in metal bioavailability through time, metals have shaped the trajectories that evolution can take. Iron typically steals this show, but with access to whole-genome sequences and transcriptomes, the imprint that zinc has made on biology is coming into focus. Writing in Nature Ecology & Evolution, Ye and colleagues present new insights into the complex connections between zinc bioavailability, adaptation of algae to the polar oceans and the evolution of regulatory networks. By combining field and laboratory-based analyses, the authors suggest that expanded families of zinc-binding proteins have enabled the green alga Microglena sp. YARC to flourish in the harsh conditions of the polar Southern Ocean (Fig. 1). As the waters where this alga occurs are known for their enrichment of zinc, the authors further propose that availability of this metal ion was directly responsible for successful microalgal colonization of polar oceans. To test this hypothesis, the authors compare meta-transcriptomes collected from pole-to-pole and find positive correlations between higher copy numbers for transcripts encoding putative zinc-binding proteins, higher latitudes, lower surface temperatures and dissolved zinc.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Deep Learning‐Assisted Automated Single Cell Electroporation Platform for Effective Genetic Manipulation of Hard‐to‐Transfect Cells

Abstract Genome engineering of cells using CRISPR/Cas systems has opened new avenues for pharmacological screening and investigating the molecular mechanisms of disease. A critical step in many such studies is the intracellular delivery of the gene editing machinery and the subsequent manipulation of cells. However, these workflows often involve processes such as bulk electroporation for intracellular delivery and fluorescence activated cell sorting for cell isolation that can be harsh to sensitive cell types such as human‐induced pluripotent stem cells (hiPSCs). This often leads to poor viability and low overall efficacy, requiring the use of large starting samples. In this work, a fully automated version of the nanofountain probe electroporation (NFP‐E) system, a nanopipette‐based single‐cell electroporation method is presented that provides superior cell viability and efficiency compared to traditional methods. The automated system utilizes a deep convolutional network to identify cell locations and a cell‐nanopipette contact algorithm to position the nanopipette over each cell for the application of electroporation pulses. The automated NFP‐E is combined with microconfinement arrays for cell isolation to demonstrate a workflow that can be used for CRISPR/Cas9 gene editing and cell tracking with potential applications in screening studies and isogenic cell line generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2025

MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers

AbstractProfiling the taxonomic and functional composition of microbes using metagenomic (MG) and metatranscriptomic (MT) sequencing is advancing our understanding of microbial functions. However, the sensitivity and accuracy of microbial classification using genome– or core protein-based approaches, especially the classification of eukaryotic organisms, is limited by the availability of genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel approach that applies multiple hypervariable marker genes to profile fungal communities from MGs and MTs. This approach utilizes the hypervariable regions of ITS and large subunit (LSU) rRNA genes for fungal identification with high sensitivity and resolution. Simultaneously, we propose a computational pipeline (MicroFisher) to optimize and integrate the results from classifications using multiple hypervariable markers. To test the performance of our method, we applied MicroFisher to the synthetic community profiling and found high performance in fungal prediction and abundance estimation. In addition, we also used MGs from forest soil and MTs of root eukaryotic microbes to test our method and the results showed that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. Overall, MicroFisher serves as a novel pipeline for classification of fungal communities from MGs and MTs.

Wang, Haihua↗
DOE OSTI2026

HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria

Bacteriophages are ubiquitous in nature, but relatively few have been isolated and characterized compared to the number of bacterial strains. Phage biotechnology applications benefit from a diverse library of isolated phages to kill or transfer genetic material to a bacterium of interest. However, scaling up phage discovery for diverse bacterial hosts can be time-consuming and costly. Here, we developed an approach to capture novel phages for multiple bacterial strains in parallel from an environmental sample using commercially available 0.2-μM filter plates. Using this High-throughput Phage Isolation Platform (HtPIP), 12 novel phages were isolated spanning 9 diverse bacterial host genera. Eleven of the isolated phages define new phage species, with nine also defining new genera. The HtPIP was used to discover both DNA and RNA phages, including a Tectiviridae infecting Pseudomonas putida mt-2 and a Leviviricetes infecting a Microbacterium isolate, which represents the first cultured RNA phage infecting a host outside of Proteobacteria. Using a metagenomic approach, we demonstrate that the HtPIP captures a higher proportion of novel phages compared to traditional low-throughput methods.

High-throughput↗
DOE OSTI2021

Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering

Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Here, our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

FAIR to WISE (F2W) v1.0.0

FAIR to WISE (F2W) is an iterative, large-language model (LLM) driven pipeline that turns unstructured research PDFs into structured, queryable knowledge graphs (KGs). Core features include schema-driven extraction to a LinkML model; full provenance capture; ontology-grounded enrichment (e.g., chemical validation and ChEBI lookup); graph construction to JSON-LD with stable IDs; and KG-RAG question answering with evidence-aware retrieval. The system is engineered for reproducibility and accessibility (open-source Ollama models, temperature=0, NVTX/Nsight profiling) with robust QA (relation verification, deduplication, and deterministic outputs). Primary uses are literature-to-KG automation, knowledge-grounded Q&A, and experimental steering support. We demonstrate the approach in organic photovoltaics, where the pipeline ingests papers, builds a domain KG, and evaluates answers against expert competency questions to guide experimental planning and interpretation. Compared with off-the-shelf LLMs and ad-hoc NLP tools, F2W addresses ontology gaps and reduces hallucination risk by grounding responses in extracted evidence and enforcing schema constraints; it also offers deterministic, provenance-linked outputs and open, cost-aware deployment. Evidence-aware ranking further improves answer quality over pure vector search.

Abramov, David [Lawrence Berkeley National Laborat↗
DOE OSTI2020

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency

Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including Nocardiopsis and Kocuria in hydrophilic and Streptomyces and Cutibacterium in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms

The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry.

16S RNA↗