SEARCH · Engineering Papers

Results for “consortia”

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.

SourceResearch connectionFrom yearThrough year

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

At least 55 records · Page 3

All sources NASA NTRS DOE OSTI

NASA NTRS2002

Achievements of the DOT-NASA Joint Program on Remote Sensing and Spatial Information Technologies: Application to Multimodal Transportation

This report presents three-year accomplishments from the national program on Commercial Remote Sensing and Geospatial Technology (CRSGT) application to transportation, administered by the U.S. Department of Transportation (U.S. DOT) in collaboration with the National Aeronautics and Space Administration (NASA). The joint program was authorized under Section 5113 of the Transportation Equity Act for the 21st Century (TEA-21). This is the first national program of its type focusing on transportation applications of emerging commercial remote sensing technologies. U.S. DOT's Research and Special Programs Administration manages the program in coordination with NASA's Earth Science Enterprise's application programs. The program focuses on applications of CRSGT products and systems for providing smarter and more efficient transportation operations and services. The program is performed in partnership with four major National Consortia for Remote Sensing in Transportation (NCRST). Each consortium focuses on research and development of products in one of the four priority areas for transportation application, and includes technical application and demonstration projects carried out in partnership with industries and service providers in their respective areas. The report identifies products and accomplishments from each of the four consortia in meeting the goal of providing smarter and more efficient transportation services. The products and results emerging from the program are being implemented in transportation operations and services through state and local agencies. The Environmental Assessment and Application Consortium (NCRST-E) provides leadership for developing and deploying cost effective environmental and transportation planning services, and integrates CRSGT advances for achieving smarter and cost effective corridor planning. The Infrastructure Management Consortium (NCRST-I) provides leadership in technologies that achieve smarter and cheaper ways of managing transportation infrastructure assets, operation, and inspection, and integrates CRSGT advances for achieving infrastructure security. The Traffic Flow Consortium (NCRST-F) provides leadership to develop new tools for regional traffic flow management including heavy vehicles and intermodal flow of freight, and integrates CRSGT advances for complementing and extending the reach of ITS user services. The Safety, Hazards and Disasters (NCRST-H) provides leadership for deploying remote sensing technology to locate transportation hazards and improve disaster recovery, and integrates CRSGT advances for application to protect transportation systems from terrorism. The DOT-NASA team is proud to present this report of accomplishments on products and results emerging from the joint program for application to transportation practice.

Source record↗

NASA NTRS1991

Waste treatment integration in space

The circumstances and criteria for space-based waste treatment bioregenerative life-support systems differ in many ways from those needed in terrestrial applications. In fact, the term "waste" may not even be appropriate in the context of nearly closed, cycling, ecosystems such as those under consideration. Because of these constraints there is a need for innovative approaches to the problem of "materials recycling". Hybrid physico-chemico-biological systems offer advantages over both strictly physico-chemico or biological approaches that would be beneficial to material recycling. To effectively emulate terrestrial cycling, the use of various microbial consortia ("assemblies of interdependent microbes") should be seriously considered for the biological components of such systems. This paper will examine the use of consortia in the context of a hybrid-system for materials recycling in space.

Waste Management/methods↗

NASA NTRS2004

Evaluation of Performance of Five Parallel Biological Water Proce

The objective of the work entitled Molecular Characterization of Eubacteria in a Biological Water Processor was to gain an understanding of the microbial diversity and species stability of the consortia that inhabit an anoxic bioreactor and to correlate those factors with functional performance, mechanical reliability, and stability. The evaluation was divided into four studies. During Study 1, replicate biological water processor (BWP) systems were operated to evaluate variability in the microbial diversity over time as a function of the initial consortia used for inoculation of the BWP reactors. Study 2 was designed to investigate the impact of an inoculum source on BWP performance. Study 3 was a modification of Study 2 where the impact of inoculum on BWP performance from inoculation until steady state operations was monitored. In Study 4, the reactors were divided into three different operational periods, based on the operational periods of the integrated water recovery test at the Johnson Space Center (JSC) in 2001.

Vega, Leticia M.↗

DOE OSTI2025

CarbStor: Development, Analysis and Modification of Carbon Storing Model Soil Communities

Soil microbial communities carry out a number of key processes including plant growth promotion, bioremediation and cycling of nutrients. Carbon cycling is among the most important of these nutrients that are metabolized and processed by the soil microbial community. Many of the carbon inputs are converted to alternative organic forms of carbon that can be used by plants or act as biomass for microbial growth. However, inorganic forms of carbon can also be produced by soil microbial communities including calcium carbonate (CaCO 3 ). Production of calcium carbonate is beneficial for the ecosystem in several ways: it can stabilize soils and improve soil health, especially denser soils with high clay content, it can act as a method of bioremediation, it can serve as an alternative carbon source for plants and it can be a way to store carbon in soil in a stable, inorganic manner for the long term. While the chemistry surrounding individual species carrying out this process is well known what is lacking is an understanding of how species interact in a community to drive carbonate production. As all microbial species in soil exist in a community setting gaining this knowledge is critical to our predicting and controlling this microbial phenotype to greatly improve soil health. The CarbStor project is focused on developing, analyzing and modifying defined microbial soil consortia that express phenotypes at both the species and community level to convert carbon into recalcitrant stable sources such as precipitated carbonate or microbial necromass. To take full advantage of the soil community for this process we will need to fill several key knowledge gaps (KG), three of which are the focus of CarbStor. KG1: Whether and to what degree microbial communities can be developed that produce precipitated carbon via microbial metabolism. KG2: What interspecies interactions drive the individual member phenotypes in defined communities that lead to carbon precipitation. KG3: How can these interactions be modified to enhance carbon sequestration beyond what native communities are capable of. We hypothesize that in a carbon sequestering community only a subset of species will express phenotypes related to carbon storage processes. We also hypothesize that these phenotypes are expressed as a result of interactions with other species in the community that are not involved in carbon storage processes and that these interactions can be harnessed to enhance community carbon sequestration.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Synthetic microbial communities: Bridging research and application in second-generation bioenergy feedstock microbiomes

The sustainable production of purpose-grown bioenergy feedstocks is essential in transitioning away from fossil fuels. Synthetic communities (SynComs) are consortia of microorganisms that can be used as biological interventions to support objectives like plant growth and stress tolerance. This review examines the state of knowledge regarding microbiomes and SynComs of second-generation bioenergy feedstocks, focusing on the rhizosphere. We first provide an overview of second-generation feedstocks, including switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), sorghum (Sorghum spp.), sugarcane (Saccharum spp.), and poplar (Populus spp.), and summarize our current understanding of their plant-soil-microbiome ecology. We next discuss considerations in the objectives, design, and evaluation of SynComs to enhance feedstock production, and then critically review the literature around their use. Our literature analysis revealed that SynCom performance varied substantially between controlled pilot experiments and field trials, possibly due to system complexity that could not be fully considered in their design and pilot evaluation. We identified a gap in the use of SynComs to support the unique sustainability objectives of biofuel feedstock agriculture, presenting an opportunity to leverage these additional microbial traits in SynCom designs. Finally, we emphasize the importance of targeted research to identify the ecological principles that govern the assembly, activation, and persistence of microbes in the feedstock rhizosphere, thereby enhancing our capacity to manage microbiomes under diverse environmental conditions and ensure their functionality. Beyond biofuels, SynComs are a promising microbiome management strategy for crop production; however, an ecologically informed design and evaluation of SynComs are advised.

SynCom↗

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

Quorum-driven microbial consortium for Bioplastic production from agro-waste

Microbial consortia have high relevance in natural environments. Here we present the production of polyhydroxyalkanoates (PHA) from agro-industrial residues by a synthetic interkingdom consortium formed by the saprotrophic fungus Ophiostoma piceae CECT 20146, which encodes a wide range of lignocellulolytic enzymes, and a natural PHA producer, Pseudomonas putida KT2440. Two agro-industrial residues were utilized: Brewer's Spent Grain (BSG) as a carbon/nitrogen source and biofilm scaffold and waste cooking oil (WCO) as a carbon source for PHA synthesis. Through biochemistry, microscopy, and omics analyses, it is shown that P. putida accumulates up to 40.2% of intracellular PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells. An interactive Shiny application has also been developed for an easy visualization and comprehension of all the transcriptomics and metabolomics data: https://jgf-bioinformatics.shinyapps.io/Visualization_app/. These results support the increased PHA production of the consortium by an induction of gene phaG, which redirects intermediaries of the fatty acid biosynthesis to PHA precursors, and the repression of the PHA depolymerase phaZ in P. putida. The trophic interaction between microorganisms seems to rely on the citric acid produced by O. piceae and the glycerol liberated from WCO, which can both be consumed by P. putida. Bioreactor scale-up experiments allowed a 3.3-fold increase in the PHA concentration in the consortium (6.7 g·L-1) without pretreatment or sterilization of the substrates, laying the groundwork for the implementation of an industrial consolidated bioprocess (CBP).

Bacteria↗

DOE OSTI2025

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism

Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular methods. Here, in this study, we describe a technical innovation combining bioorthogonal non-canonical amino acid tagging (BONCAT), stable isotope probing, and metaproteomics to improve the recovery of proteins from active community members and track isotope incorporation. Both click chemistry-enabled cell-sorting and direct protein pulldown coupled to metaproteomics improved recovery of isotopically labeled proteins during acetate oxidation within a full-scale anaerobic digester. Resulting labeled protein expression profiles revealed elevated activity of a rare and uncharacterized syntrophic bacterium belonging to the family Natronincolaceae. BONCAT-based capture of newly translated proteins provided direct molecular evidence for the expression of a previously hypothesized oxidative glycine pathway for syntrophic acetate oxidation by this microorganism, showcasing the potential of targeted metaproteomics to characterize rare and active cells central to community metabolism in natural and engineered ecosystems.

Friedline, Skyler [Univ. of British Columbia, Vanc↗

DOE OSTI2025

Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter

Abstract The in vivo continuous evolution system OrthoRep (orthogonal replication) is a powerful strategy for rapid enzyme evolution inSaccharomyces cerevisiaethat diversifies genes at a rate exceeding the endogenous genome mutagenesis rate by several orders of magnitude. However, it is difficult to neofunctionalize genes using OrthoRep partly because of the way selection pressures are applied. Here we combine OrthoRep with optogenetics in a selection strategy we call OptoRep, which allows fine-tuning of selection pressure with light. With this capability, we evolved a truncated form of the endogenous monocarboxylate transporterJEN1 (JEN1t)into a de novo mevalonate importer. We demonstrate the functionality of the evolvedJEN1t(JEN1t Y180C/G ) in the production of farnesene, a renewable aviation biofuel, from mevalonate fed to fermentation media or produced by microbial consortia. This study shows that the light-induced complementation of OptoRep may improve the ability to evolve functions not currently accessible for selection, while its fine tunability of selection pressure may allow the continuous evolution of genes whose desired function has a restrictive range between providing effective selection and cellular viability.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs

Abstract Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2024

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Overexpression of RuBisCO form I and II genes in Rhodopseudomonas palustris TIE-1 augments polyhydroxyalkanoate production heterotrophically and autotrophically

ABSTRACT With the rising demand for sustainable renewable resources, microorganisms capable of producing bioproducts such as bioplastics are attractive. While many bioproduction systems are well-studied in model organisms, investigating non-model organisms is essential to expand the field and utilize metabolically versatile strains. This investigation centers on Rhodopseudomonas palustris TIE-1, a purple non-sulfur bacterium capable of producing bioplastics. To increase bioplastic production, genes encoding the putative regulatory protein PhaR and the depolymerase PhaZ of the polyhydroxyalkanoate (PHA) biosynthesis pathway were deleted. Genes associated with pathways that might compete with PHA production, specifically those linked to glycogen production and nitrogen fixation, were deleted. Additionally, RuBisCO form I and II genes were integrated into TIE-1’s genome by a phage integration system, developed in this study. Our results show that deletion of phaR increases PHA production when TIE-1 is grown photoheterotrophically with butyrate and ammonium chloride (NH 4 Cl). Mutants unable to produce glycogen or fix nitrogen show increased PHA production under photoautotrophic growth with hydrogen and NH 4 Cl. The most significant increase in PHA production was observed when RuBisCO form I and form I & II genes were overexpressed, five times under photoheterotrophy with butyrate, two times with hydrogen and NH 4 Cl, and two times under photoelectrotrophic growth with N 2 . In summary, inserting copies of RuBisCO genes into the TIE-1 genome is a more effective strategy than deleting competing pathways to increase PHA production in TIE-1. The successful use of the phage integration system opens numerous opportunities for synthetic biology in TIE-1. IMPORTANCE Our planet has been burdened by pollution resulting from the extensive use of petroleum-derived plastics for the last few decades. Since the discovery of biodegradable plastic alternatives, concerted efforts have been made to enhance their bioproduction. The versatile microorganism Rhodopseudomonas palustris TIE-1 (TIE-1) stands out as a promising candidate for bioplastic synthesis, owing to its ability to use multiple electron sources, fix the greenhouse gas CO 2 , and use light as an energy source. Two categories of strains were meticulously designed from the TIE-1 wild-type to augment the production of polyhydroxyalkanoate (PHA), one such bioplastic produced. The first group includes mutants carrying a deletion of the phaR or phaZ genes in the PHA pathway, and those lacking potential competitive carbon and energy sinks to the PHA pathway (namely, glycogen biosynthesis and nitrogen fixation). The second group comprises TIE-1 strains that overexpress RuBisCO form I or form I & II genes inserted via a phage integration system. By studying numerous metabolic mutants and overexpression strains, we conclude that genetic modifications in the environmental microbe TIE-1 can improve PHA production. When combined with other approaches (such as reactor design, use of microbial consortia, and different feedstocks), genetic and metabolic manipulations of purple nonsulfur bacteria like TIE-1 are essential for replacing petroleum-derived plastics with biodegradable plastics like PHA.

Ranaivoarisoa, Tahina Onina↗

DOE OSTI2025

Separate, separated, and together: the transcriptional program of the Clostridium acetobutylicum-Clostridium ljungdahlii syntrophy leading to interspecies cell fusion

ABSTRACT Syntrophic cocultures (hitherto assumed to be commensalistic) of Clostridium acetobutylicum and Clostridium ljungdahlii , whereby CO 2 and H 2 produced by the former feed the latter, result in interspecies cell fusion involving large-scale exchange of protein, RNA, and DNA between the two organisms. Although mammalian cell fusion is mechanistically dissected, the mechanism for such microbial-cell fusions is unknown. To start exploring this mechanism, we used RNA sequencing to identify genes differentially expressed in this coculture using two types of comparisons. One type compared coculture to the two monocultures, capturing the combined impact of interactions through soluble signals in the medium and through direct cell-to-cell interactions. The second type compared membrane-separated versus -unseparated cocultures, isolating the impact of interspecies physical contact. While we could not firmly identify specific genes that might drive cell fusion, consistent with our hypothesized model for this interspecies microbial cell fusion, we observed differential regulation of genes involved in C. ljungdahlii’s autotrophic Wood-Ljungdahl pathway metabolism and genes of the motility machinery. Unexpectedly, we also identified differential regulation of biosynthetic genes of several amino acids, and notably of arginine and histidine. We verified that they are produced by C. acetobutylicum and are metabolized by C. ljungdahlii to its growth advantage. These and other findings, and notably upregulation of C. acetobutylicum ribosomal-protein genes, paint a more complex syntrophic picture and suggest a mutualistic relationship, whereby beyond CO 2 and H 2 , C. acetobutylicum feeds C. ljungdahlii with growth-boosting amino acids, while benefiting from the H 2 utilization by C. ljungdahlii . IMPORTANCE The construction and study of synthetic microbial cocultures is a growing research area due to the untapped potential of defined multi-species industrial bioprocesses and the utility of defined cocultures for generating insight into complex, undefined, natural microbial consortia. Our previous work showed that coculturing C. acetobutylicum and C. ljungdahlii leads to a unique metabolic phenotype (production of isopropanol) and heterologous cell fusion events. Here, we used RNAseq to explore genes involved in and impacted by these fusions. First, we compared gene expression in coculture to each monoculture. Second, we utilized a transwell system to compare gene expression in mixed cocultures to cocultures with both species physically separated by a permeable membrane, isolating the impact of interspecies “touching” on the transcriptome. This study deepens our mechanistic understanding of the C. acetobutylicum-C. ljungdahlii coculture phenotype, laying the groundwork for reverse genetic studies of heterologous cell fusion in Clostridium cocultures.

Willis, Noah B. (ORCID:0009000689365955)↗

DOE OSTI2026

Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation

Microbially induced calcium carbonate precipitation (MICP) holds potential for use in soil stabilization and carbon sequestration, with the overall efficiency of the process being a major determinant for use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such precipitation remain poorly characterized. To address this gap, we developed a four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Microbacterium sp., and Bacillus toyonensis), termed carbon storing consortium - A (CSC-A), that is capable of MICP. Prior work shows that MICP production is higher in CSC-A compared to the sum of carbonate produced by each member, suggesting carbonate production is driven by consortium dynamics. To that end we used a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of niche specialization by B. toyonensis and Microbacterium, while metatranscriptomic analysis suggests R. qingshengii is a keystone species during growth in urea. By comparing individual species’ metabolomes to the metabolic profile of a shared well of precipitated metabolites, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types to search the KEGG reactome highlighted a network centered around glutamine metabolism and branched chain amino acid biosynthesis under regulation during CSC-A growth in urea. Succinate metabolism was also a major node in this network and laboratory assays confirmed that increasing the amount of succinate in the growth medium leads to increased carbonate precipitation by CSC-A, a critical confirmation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortia to carbonate precipitation.

carbon storing consortium - A (CSC-A)↗

DOE OSTI2025

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

The denitrifying bacterium Thauera sp . MZ1T, a common member of microbial communities in wastewater treatment facilities, can produce different compounds from a range of carbon (C) and nitrogen (N) sources under aerobic and anaerobic conditions. In these different conditions, Thauera modifies its metabolism to produce different compounds that influence the microbial community. In particular, Thauera sp . MZ1T produces different exopolysaccharides with floc-forming properties, impacting the physical disposition of wastewater consortia and the efficiency of nutrient assimilation by the microbial community. Under N-limiting conditions, Thauera sp . MZ1T decreases its growth rate and accelerates the accumulation of polyhydroxyalkanoate-related (PHA) compounds including polyhydroxybutyrate (PHB), which plays a fundamental role as C and energy storage in this β-proteobacterium. However, the metabolic mechanisms employed by Thauera sp . MZ1T to assimilate and catabolize many of the different C and N sources under aerobic and anaerobic conditions remain unknown. Systems biology approaches such as genome-scale metabolic modeling have been successfully used to unveil complex metabolic mechanisms for various microorganisms. Here, we developed a comprehensive metabolic model (M-model) for Thauera sp . MZ1T ( i Thauera861), consisting of 1,744 metabolites, 2,384 reactions, and 861 genes. We validated the model experimentally using over 70 different C and N sources under both aerobic and anaerobic conditions. i Thauera861 achieved a prediction accuracy of 95% for growth on various C and N sources and close to 85% for assimilation of aromatic compounds under denitrifying conditions. The M-model was subsequently deployed to determine the effects of substrates, oxygen presence, and the C:N ratio on the production of PHB and exopolysaccharides (EPS), showing the highest polymer yields are achieved with nucleotides and amino acids under aerobic conditions. This comprehensive M-model will help reveal the metabolic processes by which this ubiquitous species influences communities in wastewater treatment systems and natural environments.

Tec-Campos, Diego (ORCID:0000000188194150)↗

DOE OSTI2025

Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site

The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O 2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data and scripts associated with a manuscript modeling microbial regulation of priming effects

This data package is associated with the publication “Modeling Microbial Regulatory Feedback in Organic Matter Decomposition Identifies Copiotrophic Traits as Key Drivers of Positive Priming” published as a preprint on BioRXiv by Ahamed et al. (2026); https://doi.org/10.1101/2024.08.11.607483. The package contains MATLAB scripts and saved simulation outputs used to implement a cybernetic model of microbial regulation during complex organic matter (OM) decomposition governing priming effects. It includes models of (i) single microbial functional groups (copiotrophic or oligotrophic degraders) and (ii) binary consortia composed of degraders and non-degraders with contrasting or common growth traits. Simulation results were generated using Monte Carlo analyses, with randomized key model parameters across a range of environmental mixing fractions of complex and labile OM. The dataset was created to provide a transparent and reusable computational framework for systematically exploring how microbial growth traits, metabolic regulation, and community composition influence OM decomposition dynamics and priming effects. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes the variable definitions. This package includes: (1) annotated MATLAB code implementing the system of ordinary differential equations and cybernetic control laws; (2) saved output files containing data (e.g., biomass, substrates, enzyme levels, priming metrics); and (3) scripts for processing saved outputs and regenerating figures. Specifically, the data package contains three main MATLAB scripts: runPrimingModel.m, runPlotData.m, and runPlotSuppFigS1.m, along with this readme and supporting documentation. Users should begin with runPrimingModel.m, which contains the annotated code implementing the system of ordinary differential equations and cybernetic control laws. This script runs the Monte Carlo simulations of microbial OM decomposition and allows users to modify microbial trait definitions, adjust parameter distributions, or define new community configurations. Simulation outputs are automatically saved as .mat files in the folder named SavedData, which stores all pre-generated results included in this package. The second script, runPlotData.m, reads files from the SavedData folder and processes them to regenerate the figures presented in the manuscript. The third script, runPlotSuppFigS1.m, specifically generates Figure S1 in the Supplementary Material of the manuscript. The package also includes the aforementioned files in non-proprietary .txt format. If users intend to use them, they should first save the files in their respective .m or .mat formats prior to execution in MATLAB.

Biomass concentration↗