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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Solvent selection for a biomass-to-bioproduct pipeline through integrated reductive catalytic fractionation and microbial funneling

The growing significance of lignin-first biorefineries, which focus on upgrading the aromatics resulting from lignin depolymerization, presents opportunities for bioproduct synthesis using microbial strains capable of funneling a diverse array of phenolics into a single commodity chemical. In this study, we evaluated a biomass-to-bioproduct pipeline involving the reductive catalytic fractionation (RCF) of poplar biomass followed by biological funneling with a Novosphingobium aromaticivorans strain that produces 2-pyrone-4,6-dicarboxylic acid (PDC), a potential bioplastic precursor. Considering the impact of solvent on RCF reactor operating pressure, and the potential inhibitory effects of solvent on downstream microbial funneling, we performed an analysis of six pure solvents, namely methanol, ethanol, isopropanol, isobutanol, 1,4-dioxane and ethylene glycol, and different variations of their aqueous mixtures comprising 5 to 50 vol% water. For each pure solvent and solvent/water system, we measured phenolic monomer yields in the RCF process and PDC yields from the phenolic monomers. We then developed correlation models that relate phenolic monomer yields from RCF-derived samples to Hansen solubility parameters to determine solvent descriptors that contribute to high yields. Furthermore, we developed an integrated biorefinery system to estimate the minimum selling price (MSP) of PDC and the associated carbon footprint to identify solvent systems with better costs and sustainability metrics. These analyses resulted in the 50 vol% methanol/water system being identified as optimal because it reduces RCF reactor pressure and is compatible with microbial funneling with N. aromaticivorans. This solvent system produced 63 g PDC per kg biomass (264 g PDC per kg lignin) from 85 g phenolic monomers per kg biomass at a reduced reactor pressure of 48 bar (reduced by 26% compared to our previous poplar-to-PDC pipeline). The MSP for this system is $\$$13.98 per kg of purified PDC (carbon footprint of 1.47 kg CO 2 e per kg), which is about 24% lower than a previously described poplar-to-PDC pipeline and 46% lower than a lignin-to-PDC pipeline that used pure methanol as the solvent. The results from this study illustrate improvements that can be made in lignocellulosic biorefineries that are compatible with the hybrid chemical and biological processes needed to gain value from lignin.

Sripada, Sarada [Great Lakes Bioenergy Research Ce↗
DOE OSTI2025

Tunable and Degradable Dynamic Thermosets from Compatibilized Polyhydroxyalkanoate Blends

Polyhydroxyalkanoates (PHAs) are versatile, biobased polyesters that are often targeted for use as degradable thermoplastic replacements for polyolefins. Given the substantial chemical diversity of PHA, their potential as cross-linked polymers could also enable similar platforms for reversible, degradable thermosets. In this work, we genetically engineered Pseudomonas putida KT2440 to synthesize poly(3-hydroxybutyrate-co-3-hydroxyundecenoate) (PHBU), which contains both 3-hydroxybutyrate and unsaturated 3-hydroxyundecenoate components. To reduce the brittleness of this polymer, we physically blended PHBU with the soft copolymer poly(3-hydroxydecanonate-co-3-hydroxyundecenoate) in mass ratios of 1:3, 1:1, and 3:1. Upon observing varying degrees of immiscibility by scanning electron microscopy, we installed dynamic boronic ester cross-links via thiol–ene click chemistry, which resulted in compatibilized dynamic thermoset blends ranging in hard, medium, and soft rubber or elastomer thermomechanical profiles. These dynamic thermoset blends were subjected to controlled biological degradation experiments in freshwater conditions, achieving timely mass loss despite the cross-linked architectures. Overall, this work highlights a two-component platform for the production of degradable and reprocessable dynamic thermoset blends suitable for several classes of cross-linked polymer technologies from tailored, biological PHA copolymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Catabolic Powerhouse for Biorefineries: Characterization and Engineering Erwinia spp. Strain LJJL01 to Produce Bioproducts

Nonmodel microbial hosts can efficiently biotransform unconventional organic feedstocks into advanced bioproducts, leveraging their superior metabolic capabilities and resilience to process-relevant physicochemical conditions. In this study, we domesticated Erwinia spp. strain. LJJL01 (Er LJJL01) as a potent microbial chassis to advance the emerging biorefinery strategy for the valorization of lignin-rich biomass and plastic, thereby enabling the circular economy. The strain exhibits remarkable chemical tolerance and can biofunnel various substrates, including sugars, acids, polyols, and aromatics, in minimal salt media to produce native fine chemicals such as acetoin, 2,3-butanediol, and lactic acid. As a proof of concept, engineering this strain with advanced genetic tools enables the production of tailored high-value chemicals, such as cis,cis-muconate from plastic-derived terephthalate and polyhydroxybutyrate from lignocellulosic hydrolysate. We established Er LJJL01 as a potent microbial chassis for the green synthesis of bioproducts from unconventional organic feedstocks.

09 BIOMASS FUELS↗
DOE OSTI2025

Warming is Associated With More Encoded Antimicrobial Resistance Genes and Transcriptions Within Five Drug Classes in Soil Bacteria: A Case Study and Synthesis

ABSTRACT The effect of warming on anti‐microbial resistance (AMR) genes in the environment has critical implications for public health but is little studied. We collected published soil bacterial genomes from the BV‐BRC database and tested the correlation between reported optimal growth temperature and the number of encoded AMR genes. Furthermore, we tested the relationship between temperature and AMR gene transcription in a natural ecosystem by analysing soil transcriptomes from a warming manipulation experiment in an Alaskan boreal forest. We hypothesised that there is a positive relationship between warming and AMR prevalence in gene content in bacterial genomes and transcriptomic sequences, and that this effect would vary by drug class. Regarding the bacterial genomes, we found a positive relationship between the fraction of encoded AMR genes and the reported optimal temperature of soil bacteria. The drug classes tetracycline and lincosamide/macrolide/streptogramin had the strongest positive relationship with reported optimal temperature. For the case study in a natural ecosystem, we found 61 significantly upregulated AMR gene‐associated transcripts spanning eight drug classes in warmed plots. In the Alaskan soil samples, we found that warming elicited the strongest positive effect on transcripts targeting lincosamide/streptogramin, beta‐lactam and phenicol/quinolone antibiotics. Overall, higher temperatures were linked to AMR gene prevalence.

Hacopian, Melanie T. [Department of Ecology and Ev↗
DOE OSTI2026

The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus

Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress—such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.

Biological and medical sciences↗
DOE OSTI2025

From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing

Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering, DNA synthesis, and genomic editing. However, to access the massive potential of microbial production, a vast parametric space remains to be investigated to optimize these biobased processes for a robust bioeconomy. Here, we review the current state of the art, some key challenges and possible solutions. We see a critical role of automation, high-throughput technologies, self-driving and cloud labs, and data management to enable Artificial Intelligence/Machine Learning and mechanistic models to overcome the design space challenges and accelerate the development of novel bio-based solutions. Accurate models will expedite the development and scale-up of engineered microbes for a range of final products from many starting materials.

Petzold, Christopher J↗
DOE OSTI2025

Identification and Mitigation of Inhibitory Substances Contained in High-Salinity Crude Glycerol Generated from Biodiesel Production for Polyhydroxyalkanoate Synthesis by Haloferax mediterranei

High-salinity crude glycerol generated from biodiesel production poses significant challenges to microbial valorization due to inhibitory ingredients that severely limit microbial growth. This study identified and mitigated inhibitory substances contained in high-salinity glycerol sludge to enable its conversion to polyhydroxyalkanoates (PHAs) by the extreme halophilic archaeon Haloferax mediterranei. The long-chain fatty acids (LCFAs) were consistently identified as the primary inhibitors by liquid chromatography−mass spectrometry, Fourier transform infrared spectroscopy, and ultraviolet−visible spectroscopy. Acid precipitation at pH 2 efficiently removed these LCFAs, substantially reducing the required feedstock dilution from 23 to 3 times, improving PHA titer by 40%. Furthermore, this dilution reduction also increased the feedstock salinity utilization, achieving a 46% reduction in external salt supplementation for H. mediterranei growth. In contrast, overliming and arrested anaerobic digestion were confirmed to be ineffective in inhibitor removal. This study provides deep insights into inhibitor chemistry and presents acid precipitation as an effective pretreatment strategy for waste valorization of highsalinity crude glycerol.

LC-MS↗
DOE OSTI2026

Biochemical approaches for synthesis of performance-advantaged polymers from lignocellulosic biomass

Lignocellulose is an abundant renewable feedstock for production of sustainable fuels, chemicals, and materials. The structural complexity of lignocellulose provides key material properties and inspires the design of advanced materials. However, this same complexity also presents challenges for conversion of lignocellulosic biomass into new materials with consistent properties. Conventional physical and chemical strategies for valorization of biomass to new materials are often limited by the technical challenges of precisely manipulating complex feedstocks, sensitivity to feedstock variability, and associated costs. In contrast, biological approaches are capable of selectively manipulating complex architectures under mild conditions. Recent advances demonstrate the potential of biological and hybrid biochemical methods to tailor biomass-derived polymers and generate new materials. This review provides an overview of biological strategies to valorize lignocellulosic biomass into novel materials, highlighting approaches for in planta engineering, biochemical modification of natural biomass polymers, microbial funneling of deconstructed biomass, and direct biosynthesis of novel polymers. In combination, these approaches open new avenues for the synthesis of performance-advantaged materials from lignocellulosic biomass.

Qian, Liangyu [ORNL] (ORCID:0009000212029938)↗
DOE OSTI2024

A Novel Integrated Fermentation Process with Engineered Microbial Consortia for Butanol Production from Lignocellulose Sugars without CO 2 Emission

The goal of this project was to develop a synthetic microbial consortium consisting of a lactic acid bacterium, a carboxydotrophic acetogen, and a solventogenic clostridia for the production of n butanol, an advanced biofuel and industrial chemical, from lignocellulose sugars (mainly glucose and xylose) and formate (produced from CO 2 by electrochemical reduction) in an integrated bioprocess (biorefinery), which can provide an effective solution to the technical challenges in developing energy and carbon optimized synthesis for the bioeconomy and achieve the program objectives of ARPA-E. The project focused on the design, modeling and construction of synthetic microbial consortia consisting of three bacterial species to maximize carbon conversion and butanol production with a 100% theoretical product yield from glucose and zero or negative CO 2 emission.

09 BIOMASS FUELS↗
DOE OSTI2025

Evolutionary and functional relationships between plant and microbial C 1 metabolism in terrestrial ecosystems

One-carbon (C 1 ) metabolism, centered on the universal methyl donor S-adenosyl methionine (SAM), plays critical roles in biosynthesis, redox regulation, and stress responses across plants and microbes. A recently proposed photosynthetic C 1 pathway links SAM methyl groups directly to RuBisCO-mediated CO 2 assimilation and integrates with nitrogen and sulfur metabolism. Light-dependent SAM synthesis may regulate the methylation of biopolymers and specialized metabolites and help mitigate photorespiratory stress under elevated temperature and drought. Phylogenetic analysis of two core enzymes suggests evolutionary continuity from methylotrophic microbes to land plants, supporting microbial origins via endosymbiotic gene transfer. Beyond intracellular roles, C 1 metabolism drives biosphere–atmosphere exchange via gases such as methane, methanol, formic acid, and formaldehyde, and numerous specialized volatiles synthesized through SAM methylation. S-methylmethionine, a mobile C 1 metabolite, may mediate phloem transport of reduced sulfur, nitrogen, and methyl groups, linking above- and belowground C 1 cycling in plants. Advances in real-time gas sensing now allow the high-frequency quantification of C 1 fluxes from leaves, stems, and soils, highlighting C 1 metabolism as a critical and underrecognized component of terrestrial carbon and nutrient cycling. Given its microbial ancestry and the production of diverse volatile biosignatures, C 1 metabolism may also offer unique insights into life's origins and biosignature detection on exoplanets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Photothermal Properties of Nanostructured Black Titanium Dioxide for Targeted Cellular and Microbial Elimination

Heterophase black titanium dioxide (hB-TiO 2 ), characterized by broadened near-infrared (NIR) absorption, has emerged as a promising photothermally active nanomaterial. This study focused on the synthesis of nanoscale hB-TiO 2 and its evaluation as a multifunctional agent for photothermal therapy (PTT). The purity and composition of the mixed-phase nanoscale hB-TiO 2 were demonstrated by X-ray diffraction, and the morphology of nanoparticles was imaged by transmission electron microscopy. Extensive additional characterization was conducted to validate the optoelectronic properties. The material was further evaluated in biological systems using NIH 3T3-GFP fibroblasts and the fungus Candida albicans. Nanoscale hB-TiO 2 exhibited good biocompatibility in the absence of laser irradiation and effectively ablated both NIH 3T3-GFP cells and C. albicans following 20 min of laser exposure. This noninvasive treatment strategy leverages NIR-responsive materials to induce localized hyperthermia. The findings provide grounds for the use of selectively induced hyperthermia, which could be employed for the targeted destruction of cells or fungi with minimal impact on surrounding tissue if the material is functionalized with specific targeting groups and delivered to cells or fungal infections.

Irradiation↗
DOE OSTI2026

Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas mobilis by Molecular Simulation

The conversion of lignocellulosic biomass into biofuels and bioproducts by microbial biorefineries is central to a sustainable chemical industry. Zymomonas mobilis is one such biorefinery chassis and is resistant to ethanol stress, leading to its use in biomass conversion to biofuels and bioproducts. However, Z. mobilis growth is often inhibited by organic acids, aldehydes, alcohols, ketones, and amides found in biomass hydrolysate. The resulting slow growth inhibits production and as a result drives up the price for the resulting products. One hypothesis is that these molecules interact with or disrupt the bacterial membrane, triggering stress responses and hindering growth. To test this hypothesis at the molecular level, we employ all-atom molecular dynamics (MD) simulations to investigate lignocellulose-derived small molecules and their impact on a biologically relevant Z. mobilis membrane model. Simulations were conducted across a range of inhibitor concentrations from 0 to 2.5 mol %, analyzing key membrane properties such as area per lipid (APL), membrane thickness, lipid-order parameter (−S CH ), lateral diffusion coefficient (D xy ), and permeability coefficient (Pm). From simulation, we observed altered membrane structure and dynamics at these modest small molecule concentrations commonly found in hydrolysates. Generally, the membranes become thinner, with a higher area per lipid and lower-order parameter as the small molecule concentration increases. These trends are stronger for more hydrophobic molecules with greater hydrophobic bulk, as isobutanol, propanol, and propanoic acid showed greater membrane perturbations as the concentration increased compared to other small molecules. Tracking small molecule distributions directly in our equilibrium simulations allows us to determine concentration-dependent free energy profiles for these molecules. While the trends are noisy, generally the barriers to crossing the membrane decrease as the concentration increases, indicating that the membranes become leakier as small molecule concentrations rise. Comparing between native Z. mobilis membranes with hopanoids and membranes sharing the same phospholipid composition but without hopanoids, hopanoids stabilize and order the membrane for smaller molecules to maintain membrane structure but appear insufficient for larger hydrophobic molecules like isobutanol. These findings provide a mechanistic understanding of how small molecules found in biomass degradation streams interact with the Z. mobilis membrane, offering valuable insights for future strain engineering efforts to optimize biofuel and bioproduct synthesis from biomass feedstocks by highlighting limits to small molecule tolerance. This knowledge can guide the modification of membrane composition to develop more robust microbes, thereby improving microbial survival and yields in industrial contexts.

Singh, Nitin Kumar [Michigan State Univ., East Lan↗
DOE OSTI2025

Carbon cycling across ecosystem succession in a north temperate forest: Controls and management implications

Despite decades of progress, much remains unknown about successional trajectories of carbon (C) cycling in north temperate forests. Drivers and mechanisms of these changes, including the role of different types of disturbances, are particularly elusive. To address this gap, we synthesized decades of data from experimental chronosequences and long-term monitoring at a well-studied, regionally representative field site in northern Michigan, USA. Our study provides a comprehensive assessment of changes in above- and belowground ecosystem components over two centuries of succession, links temporal dynamics in C pools and fluxes with underlying drivers, and offers several conceptual insights to the field of forest ecology. Our first advance shows how temporal dynamics in some ecosystem components are consistent across severe disturbances that reset succession and partial disturbances that slightly modify it: both of these disturbance types increase soil N availability, alter fungal community composition, and alter growth and competitive interactions between short-lived pioneer and longer-lived tree taxa. Further, these changes in turn affect soil C stocks, respiratory emissions, and other belowground processes. Second, we show that some other ecosystem components have effects on C cycling that are not consistent over the course of succession. For example, canopy structure does not influence C uptake early in succession but becomes important as stands develop, and the importance of individual structural properties changes over the course of two centuries of stand development. Third, we show that in recent decades, climate change is masking or overriding the influence of community composition on C uptake, while respiratory emissions are sensitive to both climatic and compositional change. In synthesis, we emphasize that time is not a driver of C cycling; it is a dimension within which ecosystem drivers such as canopy structure, tree and microbial community composition change. Changes in those drivers, not in forest age, are what control forest C trajectories, and those changes can happen quickly or slowly, through natural processes or deliberate intervention. Stemming from this view and a whole-ecosystem perspective on forest succession, we offer management applications from this work and assess its broader relevance to understanding long-term change in other north temperate forest ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Diacylglycerol enantiomer selectivity of diacylglycerol acyltransferases highlights metabolic specialization in triacylglycerol synthesis across the tree of life

Triacylglycerols are the major energy storage lipids in plants, animals, and microorganisms, and are predominantly produced by acyl-CoA:diacylglycerol (DAG) acyltransferases (DGATs). Two enantiomers of the DAG substrate, sn -1,2 and sn -2,3, can be produced by different biological mechanisms; however, little is known about which species produce each enantiomer, the selectivity of DGAT isoforms for either enantiomer, or whether DGAT enantiomer selectivity varies across organisms. Here, DAG enantiomer selectivity of DGAT1 and DGAT2 was measured from eight seed plants, two mammals, one oleaginous yeast, and one photosynthetic microalga using enantiomer-specific in vitro DGAT assays. Across most plants, DGAT1 favored sn -1,2-DAG, whereas DGAT2 preferentially utilized sn -2,3-DAG. However, there were several exceptions. Mammalian DGAT1, DGAT2, and microbial DGAT1s efficiently used both DAG enantiomers, while microbial DGAT2s had unique selectivity. The selectivity of several DGATs for combined acyl-CoA and DAG enantiomer molecular species were also evaluated for biotechnical applications. Therefore, DGAT DAG enantiomer selectivity is common yet strongly dependent on lineage and isoform and likely shaped in part by species-specific metabolic context of triacylglycerol synthesis, turnover, and remodeling. This work expands our understanding of DGAT function and establishes a foundation for leveraging enantiomer-selective acyltransferases in metabolic engineering of tailored lipid products.

Arabidopsis thaliana↗
DOE OSTI2026

Growth-associated polyhydroxybutyrate accumulation in Azospira suillum PS during aerobic and perchlorate respiration

Polyhydroxyalkanoates (PHAs) are widespread microbial storage polymers increasingly recognized for roles beyond carbon and energy storage, including redox homeostasis and stress physiology. While PHA accumulation is classically associated with stationary-phase metabolism under severe nutrient imbalance, comparatively little is known about growth-associated PHA synthesis in facultative anaerobes with unusual respiratory strategies. Here, we investigated polyhydroxybutyrate (PHB) metabolism in Azospira suillum PS, a genetically tractable perchlorate-reducing bacterium capable of both aerobic and anaerobic respiration. Using physiological growth experiments, targeted gene deletions, PHB extractions, and intracellular redox measurements, we examined PHB accumulation under varying respiratory and nutrient conditions. We demonstrate that PHB accumulates during exponential growth under moderately nitrogen-limited conditions, both aerobically and during perchlorate respiration, representing a rare example of growth-associated PHB synthesis under anaerobic conditions. Genomic analysis revealed four phaC homologs, one of which could not be deleted under the experimental conditions tested and co-localized with phaB and phaR. Redox profiling further revealed a strong positive correlation between PHB accumulation and intracellular NADPH/NADP+ ratios. Together, these findings expand the physiological contexts in which PHB synthesis is known to occur and highlight perchlorate-respiring bacteria as underexplored model systems for studying growth-integrated carbon and redox storage strategies.

Meier, David A O↗
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 OSTI2025

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signalling that share mechanistic features with human antiviral systems1. In these pathways, including cyclic oligonucleotide-based antiphage signalling systems (CBASSs) and type III CRISPR systems in bacteria and cyclic GMP–AMP synthase–stimulator of interferon genes (cGAS–STING) in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response2, 3–4. Here, in an unexpected inversion of this process, we show that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that represses a toxic effector. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful defence strategy against virus-mediated immune suppression, expanding our understanding of the role of oligonucleotides in immunity.

Doherty, Erin E↗
DOE OSTI2025

Microbes display broad diversity in cobamide preferences

ABSTRACT Cobamides, the vitamin B 12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli , Sinorhizobium meliloti , and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to those of previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function. IMPORTANCE Nearly all bacteria are found in microbial communities with tens to thousands of other species. Molecular interactions such as metabolic cooperation and competition are key factors underlying community assembly and structure. Cobamides, the vitamin B 12 family of enzyme cofactors, are one such class of nutrients, produced by only a minority of prokaryotes but required by most microbes. A unique aspect of cobamides is their broad diversity, with nearly 20 structural forms identified in nature. Importantly, this structural diversity impacts growth as most bacteria that have been tested show preferences for specific cobamide forms. We measured cobamide-dependent growth in several model bacteria and compared the results to those of previous analyses of cobamide preference. We found that cobamide preferences vary widely across bacteria, showing the importance of characterizing these aspects of cobamide biology to understand the impact of cobamides on microbial communities.

Mok, Kenny C. (ORCID:0000000252276987)↗