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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Active microbial biomass decreases, but microbial growth potential remains similar across soil depth profiles under deeply-vs. shallow-rooted plants

Climate-smart land management practices that replace shallow-rooted annual crop systems with deeply-rooted perennial plants can contribute to soil carbon sequestration. However, deep soil carbon accrual may be influenced by active microbial biomass and their capacity to assimilate fresh carbon at depth. Incorporating active microbial biomass, dormancy, and growth in microbially-explicit models can improve our ability to predict soil's capacity to store carbon. But, so far, the microbial parameters that are needed for such modeling are poorly constrained, especially in deep soil layers. Here, we used a lab incubation experiment and growth kinetics model to estimate how microbial parameters vary along 240 cm of soil depth in profiles under shallow- (soy) and deeply-rooted (switchgrass) plants 11 years after plant cover conversion. We also assessed resource origin and availability (total organic carbon, 14 C, extractable organic carbon, specific UV absorbance of K 2 SO 4 extractable organic C, total nitrogen, total dissolved nitrogen) along the soil profiles to examine associations between soil chemical and biological parameters. Even though root biomass was greater and rooting depth was deeper under switchgrass than soy, resource availability and microbial growth parameters were generally similar between vegetation types. Instead, depth significantly influenced soil chemical and biological parameters. For example, resource availability and total and relative active microbial biomass decreased with soil depth. Decreases in the relative active microbial biomass coincided with increased lag time (response time to external carbon inputs) along the soil profiles. Even at a depth of 210–240 cm, microbial communities were activated to grow by added resources within a day. Maximum specific growth rate decreased to a depth of 90 cm and then remained consistent in deeper layers. Our findings show that >10 years of vegetation and rooting depth changes may not be long enough to alter microbial growth parameters, and suggest that at least a portion of the microbial community in deep soils can grow rapidly in response to added resources. Our study determined microbial growth parameters that can be used in microbially-explicit models to simulate carbon dynamics in deep soil layers.

14C↗
DOE OSTI2024

Advancing quantitative models of soil microbiology, ecology, and biochemistry

Rapid advances in soil biology are increasingly reflected in mathematical models. From molecular to global scales, models contribute to fundamental understanding and prediction of critical soil processes, such as carbon sequestration. Recent models explicitly incorporate microbial control over soil carbon and nutrient cycling, an approach that offers greater biological realism but raises new challenges in model parameterization and stability. Although they have proliferated at community and ecosystem scales, microbial-explicit models have yet to be incorporated into most Earth system models. Applying soil models across scales requires integration with data to support parameterization and validation using approaches such as Bayesian data assimilation. In conclusion, to catalyze future progress, we recommend breaking down barriers between modeling and empirical disciplines while broadening access to the computational infrastructure that supports soil biological modeling.

Xie, Wally↗
DOE OSTI2025

Biotransformation of Pesticides across Biological Systems: Molecular Mechanisms, Omics Insights, and Biotechnological Advances for Environmental Sustainability

The widespread application of pesticides such as organophosphates, organochlorides, and triazines in modern agriculture has led to their notable presence in soils, water bodies, and food chains, raising concerns about persistence, bioaccumulation, and adverse effects on nontarget organisms. Biotransformation, the enzymatic transformation of xenobiotic compounds by microorganisms, plants, and animals, plays a pivotal role in the degradation and detoxification of these chemicals. This review provides a comprehensive examination of the mechanisms, key enzyme classes (e.g., hydrolases, oxidoreductases, transferases), and environmental factors influencing pesticide biotransformation across different biological systems. Recent advances in omics technologies have revolutionized the understanding of microbial and plant metabolism, while synthetic biology offers opportunities for engineering enhanced degradation capabilities. The environmental fate of transformation products is also discussed, together with a critical analysis of challenges, unresolved questions, and future research directions, offering a holistic perspective on pesticide biotransformation as a key process for mitigating chemical pollution.

Biotransformation↗
DOE OSTI2022

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables

Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host–associated and engineered systems. Notably, in spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population–level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week–over–week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage–associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re–examined in the context of ecological history and microbiome responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site

Microbial pathogens bind host complement regulatory proteins to evade the immune system. The bacterial pathogen Neisseria meningitidis, or meningococcus, binds several complement regulators, including human Factor H (FH). FH binding protein (FHbp) is a component of two licensed meningococcal vaccines and in mice FHbp elicits antibodies that inhibit binding of FH to FHbp, which defeat the bacterial evasion mechanism. However, humans vaccinated with FHbp develop antibodies that enhance binding of FH to the bacteria, which could limit the effectiveness of the vaccines. In the present study, we show that two vaccine-elicited antibody fragments (Fabs) isolated from different human subjects increase binding of complement FH to meningococcal FHbp by ELISA. The two Fabs have different effects on the kinetics of FH binding to immobilized FHbp as measured by surface plasmon resonance. The 1.7- and 2.0-Å resolution X-ray crystal structures of the Fabs in complexes with FHbp illustrate that the two Fabs bind to similar epitopes on the amino-terminal domain of FHbp, adjacent to the FH binding site. Superposition models of ternary complexes of each Fab with FHbp and FH show that there is likely minimal contact between the Fabs and FH. Collectively, the structures reveal that the Fabs enhance binding of FH to FHbp by altering the conformations and mobilities of two loops adjacent to the FH binding site of FHbp. In addition, the 1.5 Å-resolution structure of one of the isolated Fabs defines the structural rearrangements associated with binding to FHbp. The FH-enhancing human Fabs, which are mirrored in the human polyclonal antibody responses, have important implications for tuning the effectiveness of FHbp-based vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus

Microbial conversion of biomass relies on a complex combination of enzyme systems promoting synergy to overcome biomass recalcitrance. Some thermophilic bacteria have been shown to exhibit particularly high levels of cellulolytic activity, making them of particular interest for biomass conversion. These bacteria use varying combinations of CAZymes that vary in complexity from a single catalytic domain to large multi-modular and multi-functional architectures to deconstruct biomass. Since the discovery of CelA from Caldicellulosiruptor bescii which was identified as one of the most active cellulase so far identified, the search for efficient multi-modular and multi-functional CAZymes has intensified. One of these candidates, GuxA (previously Acel_0615), was recently shown to exhibit synergy with other CAZymes in C. bescii, leading to a dramatic increase in growth on biomass when expressed in this host. GuxA is a multi-modular and multi-functional enzyme from Acidothermus cellulolyticus whose catalytic domains include a xylanase/endoglucanase GH12 and an exoglucanase GH6, representing a unique combination of these two glycoside hydrolase families in a single CAZyme. These attributes make GuxA of particular interest as a potential candidate for thermophilic industrial enzyme preparations. Here, we present a more complete characterization of GuxA to understand the mechanism of its activity and substrate specificity. In addition, we demonstrate that GuxA exhibits high levels of synergism with E1, a companion endoglucanase from A. cellulolyticus. We also present a crystal structure of one of the GuxA domains and dissect the structural features that might contribute to its thermotolerance.

09 BIOMASS FUELS↗
DOE OSTI2026

The anaerobic fungus Caecomyces churrovis produces H 2 via a non-bifurcating NADH-dependent enzyme complex

ABSTRACT Hydrogenosomes are mitochondria-derived organelles that produce ATP and H 2 to support energy metabolism in anaerobic eukaryotes. H 2 production allows reoxidation of reduced cofactors generated during fermentative metabolism; however, the metabolic mechanisms for H 2 production in anaerobic eukaryotes remains incompletely understood. In particular, it remains unclear whether anaerobic fungi (AF) hydrogenosomes use a ferredoxin-dependent pathway or a distinct mechanism to regenerate NAD(P) + and link electron transfer to H 2 formation. Here, by combining genomic search, proteomic analysis, and enzymology, we reveal the molecular mechanism for H 2 production in the AF strain Caecomyces churrovis . Our enzyme assays on the organelle fraction of C. churrovis revealed the activity of H 2 :NAD + oxidoreductase but not pyruvate:ferredoxin oxidoreductase, which is usually linked to H 2 formation. We identified genes encoding [FeFe] hydrogenase (Hyd) and NADH dehydrogenase subunits E and F (NuoE, NuoF) in C. churrovis , and confirmed their expression in the isolated hydrogenosomal fractions by proteomic analysis. Combining the individually purified enzymes, we found Hyd and NuoEF proteins formed H 2 directly from NADH independently of ferredoxin, functioning as a non-bifurcating NADH-dependent enzyme rather than an electron-bifurcating enzyme. We identified homologs of hydrogenosomal NuoE, NuoF, and Hyd in many other AF, indicating this pathway is commonly shared among the AF. This work demonstrates the existence of a non-bifurcating NADH-dependent enzyme complex in eukaryotes. Moreover, this complex could potentially be exploited as a target for controlling AF H 2 production and altering fungal metabolism. IMPORTANCE H 2 production is a prominent feature of anaerobic energy metabolism, yet our understanding of eukaryotic mechanisms remains limited. Anaerobic fungi (AF) are key decomposers of lignocellulose and contribute to hydrogen flux in anaerobic environments. Although it has been more than 40 years since the H 2 production from AF was first reported, the molecular mechanism for hydrogenosomal H 2 production and redox balance remains unclear. We demonstrate that AF produce H 2 from NADH utilizing a non-bifurcating NADH-dependent enzyme complex rather than an electron-bifurcating, ferredoxin-dependent variant. We show that this enzyme complex is conserved across multiple AF lineages and thus demonstrate the occurrence of a non-bifurcating NADH-dependent enzyme in eukaryotes. This discovery expands our understanding of eukaryotic hydrogenosomal metabolism, reveals a previously unknown strategy for redox balancing, and highlights potential targets for manipulating H 2 production. These insights have broad implications for microbial energy metabolism, anaerobic ecosystems, and bioengineering of H 2 -producing systems.

Zhang, Bo [Department of Chemical Engineering, Uni↗
DOE OSTI2021

Perennial grass bioenergy cropping systems: Impacts on soil fauna and implications for soil carbon accrual

ABSTRACT Perennial grass energy crop production is necessary for the successful and sustainable expansion of bioenergy in North America. Numerous environmental advantages are associated with perennial grass cropping systems, including their potential to promote soil carbon accrual. Despite growing research interest in the abiotic and biotic factors driving soil carbon cycling within perennial grass cropping systems, soil fauna remain a critical yet largely unexplored component of these ecosystems. By regulating microbial activity and organic matter decomposition dynamics, soil fauna influence soil carbon stability with potentially significant implications for soil carbon accrual. We begin by reviewing the diverse, predominantly indirect effects of soil fauna on soil carbon dynamics in the context of perennial grass cropping systems. Since the impacts of perennial grass energy crop production on soil fauna will mediate their potential contributions to soil carbon accrual, we then discuss how perennial grass energy crop traits, diversity, and management influence soil fauna community structure and activity. We assert that continued research into the interactions of soil fauna, microbes, and organic matter will be important for advancing our understanding of soil carbon dynamics in perennial grass cropping systems. Furthermore, explicit consideration of soil faunal effects on soil carbon can improve our ability to predict changes in soil carbon following perennial grass cropping system establishment. We conclude by addressing the major knowledge gaps that should be prioritized to better understand and model the complex connections between perennial grass bioenergy systems, soil fauna, and carbon accrual.

sustainability↗
DOE OSTI2023

Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system

The terrestrial serpentinite-hosted ecosystem known as “The Cedars” is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars (‘Paeni-Cedars’), Alishewanella sp. BS5-314 (‘Ali-BS5-314’), and Anaerobacillus sp. CMMVII (‘Anaero-CMMVII’). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7–10 (minimum pH tested was 7), temperatures 20–40°C, and 0–3% NaCl concentration. The addition of 10–20 mM CaCl 2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10–12 and temperatures 10–40°C, with limited growth observed 1–5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9–12, with the addition of 0.01–1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

UT-GOM2-2 Preliminary Report: Terrebonne Basin Northern Gulf of Mexico, 30 July-28 September 2023

In the summer and fall of 2023, the Gulf of Mexico Deepwater Hydrate Coring Expedition (UT-GOM2-2) drilled, cored, made downhole measurements, and analyzed samples from the seafloor to the base of the gas hydrate stability zone in one location (Site H, WR313) in the Terrebonne basin, deepwater Gulf of Mexico. Analyses of data and samples from the expedition will inform biological, geochemical, and geomechanical models to constrain the role of gas hydrates in the carbon cycle and the potential for gas hydrates as an energy resource. Pressure and conventional cores were collected continuously to a depth of 155.1 meters below the seafloor (mbsf). At deeper depths, cores were taken periodically from hydrate-bearing sands and their bounding muds to a total depth of 861.3 mbsf. 162.6 m of conventional core and 54.8 m of pressure core were obtained. Twelve temperature measurements were made between 27.1 and 144.5 mbsf to determine the geothermal gradient. At the seafloor, more than 4 m of sandy silt of unknown origin was encountered. Beneath this sand, to a depth of ~200 mbsf, the section was composed of interbedded mud and biogenic carbonate ooze. The biogenic ooze correlated to low density and high porosity intervals observed in the previously acquired logging while drilling (LWD) data and as measured. Calcareous nannofossil biostratigraphy constrains the entire record to the Pleistocene (< 0.91 million years) with a pronounced increase in sedimentation rate with depth. Beneath 200 mbsf, the section was predominantly composed of mud with two thicker, hydrate-bearing coarse-grained intervals, which are commonly known as the Blue and Orange sands. The dissolved gas concentration was quantified from pressure cores. In the shallow section, dissolved methane concentration increased below the sulfate-methane transition zone (SMTZ) and reaches saturation (the limit of solubility for methane) at 147 mbsf. Gas expansion was very common in conventional and depressurized pressure (conventionalized) cores below the SMTZ. At deeper depths, the methane concentration within muds bounding the Blue and Orange reservoirs was generally found to be less than saturation. The dissolved and hydrate gas composition is consistent with a microbial source, containing greater than 99.99% methane and only trace concentrations of ethane, propane, and butane. The methane to ethane ratio (C 1 /C 2 ) and the methane to ethane plus propane (C 1 /(C 2 +C 3 )) decrease with depth down to at least 678 mbsf, mainly driven by the increase in ethane with depth. It is unclear if this trend continues through the Orange sand interval. The δ 13 C isotopic signature of methane ranges between -69.9 and -78.5 ‰ Vienna Pee Dee Belemnite (VPDB). Pressure core recovery of all sandy intervals was poor. However, pressure core logs of the Orange sand show intervals of low density and high velocity, which are indicative of high hydrate saturation. One core from within the Orange sand was composed of interbedded graded sandy silt and mud. The sandy silts from this core are composed of mainly quartz and feldspar with some lithics. Most of the recovered pressure core samples are maintained at near in-situ pressure and temperature (within the hydrate stability field) at the University of Texas Pressure Core Center awaiting analysis. In the shallow section, samples will be used to determine the flux of organic carbon through the basin system, find the rate at which that carbon was consumed, and understand the microbial population responsible for these processes. In the deeper section, samples from in and around the hydrate reservoirs will be used to determine the petrophysical properties of the reservoir and bounding seals in these systems.

03 NATURAL GAS↗
DOE OSTI2025

Expedition UT-GOM2-2 Site H

Pressure and conventional cores were collected at Site H of the Walker Ridge Protracted Area Block 313 in the Terrebonne Basin, deepwater Gulf of America (Gulf of Mexico) during the University of Texas (UT) Deepwater Hydrate Coring Expedition (UT-GOM2-2). Pressure and conventional cores were collected continuously to a depth of 155.1 meters below the seafloor (mbsf). At deeper depths, cores were taken periodically from hydrate-bearing sands and their bounding muds to a total depth of 861.3 mbsf. 162.6 m of conventional core and 54.8 m of pressure core were recovered. Twelve temperature measurements were made between 27.1 and 144.5 mbsf to determine the geothermal gradient. At the seafloor, more than 4 m of sandy silt of unknown origin was encountered. Beneath this sand, to a depth of about 200 mbsf, the section was composed of interbedded mud and biogenic carbonate ooze. The ooze correlated to low density and high porosity intervals observed in the previously acquired logging while drilling (LWD) data and as measured. These ooze intervals also correspond to lighter sediment color, increased Ca content based on X-ray florescence (XRF) core scanning, and increased calcareous nannofossil abundance. Calcareous nannofossil biostratigraphy constrains the entire record to the Pleistocene (< 0.91 million years), with a pronounced increase in sedimentation rate with depth. Below 200 mbsf, the section was predominantly composed of mud with two thicker, hydrate-bearing coarse-grained intervals, which are commonly known as the Blue and Orange sands. The dissolved gas concentration was quantified from pressure cores. In the shallow section, dissolved methane concentration increased below the sulfate-methane transition zone (SMTZ) and reaches saturation (the limit of solubility for methane) at 147 mbsf. Gas expansion was very common in conventional and depressurized pressure (conventionalized) cores below the SMTZ. At deeper depths, the methane concentration within muds bounding the Blue and Orange reservoirs was generally found to be less than saturation. The dissolved and hydrate gas composition is consistent with a microbial source, containing greater than 99.99% methane and only trace concentrations of ethane, propane, and butane. The methane to ethane ratio (C1 /C2 ) and the methane to ethane plus propane (C1 /(C2 +C3 )) decrease with depth down to at least 678 mbsf, mainly driven by the increase in ethane with depth. It is unclear if this trend continues through the Orange sand interval. The δ13C isotopic signature of methane ranges between -69.9 and -78.5 ‰ relative to the Vienna Pee Dee Belemnite (VPDB) standard. Pressure core recovery in sandy intervals was poor. However, pressure core logs of the Orange sand show intervals of low density and high velocity, which are indicative of high hydrate saturation. One pressure core was degassed and the average hydrate saturation in the core was determined to be 24%. One core from within the Orange sand was composed of interbedded graded sandy silt and mud. The sandy silts from this core are composed of mainly quartz and feldspar with some lithics. Most of the recovered pressure core samples are maintained at near in-situ pressure and temperature (within the hydrate stability field) at the University of Texas Pressure Core Center awaiting analysis. In the shallow section, samples will be used to determine the flux of organic carbon through the basin system, find the rate at which that carbon was consumed, and understand the microbial population responsible for these processes. In the deeper section, samples from in and around the hydrate reservoirs will be used to determine the petrophysical properties of the reservoir and bounding seals in these systems.

03 NATURAL GAS↗
DOE OSTI2022

Trait relationships of fungal decomposers in response to drought using a dual field and laboratory approach

Abstract Decomposer fungi play a fundamental role in terrestrial ecosystem dynamics. In the southwestern United States, climate change is causing more frequent and severe droughts, which may alter fungal community composition and activity. Investigating relationships between fungal traits may improve the prediction of fungal responses to drought. In this dual field and laboratory experiment, we examine whether trade‐offs occur between traits associated with drought. Specifically, we test the hypothesis that fungi sort into lifestyles specializing in growth y ield, resource a cquisition, and drought s tress tolerance (“YAS” framework). For the field experiment, we constructed microbial “cages” containing sterilized litter and 1 of 10 fungal isolates. These cages were placed in long‐term drought and control plots in a southern Californian grassland for 6 and 12 months. We measured fungal hyphal length per unit litter mass loss for growth yield, the potential activities of four extracellular enzymes for resource acquisition, and the ability to grow in the drought versus control plots for drought stress tolerance. We compared these results with a laboratory microcosm experiment constructed with the same fungal isolates and that measured the same fungal traits. The field experiment corroborated our laboratory results, in that no trade‐offs were observed between growth yield and resource acquisition traits. However, in contrast to the laboratory experiment, drought tolerance was negatively related to extracellular enzyme activity and growth yield in the field, implying a trade‐off. Despite this observed trade‐off in the field, growth yield was not hindered by drought. We propose a modification to the YAS framework, by combining the growth yield and resource acquisition lifestyles, which may be more appropriate for this arid system. This joint laboratory and field approach contextualizes a theoretical framework in microbial ecology and improves understanding of fungal community response to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Salinity and hydraulic retention time induce membrane phospholipid acyl chain remodeling in Halanaerobium congolense WG10 and mixed cultures from hydraulically fractured shale wells

Bacteria remodel their plasma membrane lipidome to maintain key biophysical attributes in response to ecological disturbances. For Halanaerobium and other anaerobic halotolerant taxa that persist in hydraulically fractured deep subsurface shale reservoirs, salinity, and hydraulic retention time (HRT) are important perturbants of cell membrane structure, yet their effects remain poorly understood. Membrane-linked activities underlie in situ microbial growth kinetics and physiologies which drive biogeochemical reactions in engineered subsurface systems. Hence, we used gas chromatography–mass spectrometry (GC–MS) to investigate the effects of salinity and HRT on the phospholipid fatty acid composition of H. congolense WG10 and mixed enrichment cultures from hydraulically fractured shale wells. We also coupled acyl chain remodeling to membrane mechanics by measuring bilayer elasticity using atomic force microscopy (AFM). For these experiments, cultures were grown in a chemostat vessel operated in continuous flow mode under strict anoxia and constant stirring. Our findings show that salinity and HRT induce significant changes in membrane fatty acid chemistry of H. congolense WG10 in distinct and complementary ways. Notably, under nonoptimal salt concentrations (7% and 20% NaCl), H. congolense WG10 elevates the portion of polyunsaturated fatty acids (PUFAs) in its membrane, and this results in an apparent increase in fluidity (homeoviscous adaptation principle) and thickness. Double bond index (DBI) and mean chain length (MCL) were used as proxies for membrane fluidity and thickness, respectively. These results provide new insight into our understanding of how environmental and engineered factors might disrupt the physical and biogeochemical equilibria of fractured shale by inducing physiologically relevant changes in the membrane fatty acid chemistry of persistent microbial taxa. GRAPHICAL ABSTRACT Salinity significantly alters membrane bilayer fluidity and thickness in Halanaerobium congolense WG10.

03 NATURAL GAS↗
DOE OSTI2021

Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. Here, we have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hydrogen production from full-strength corn stover fermentation effluent in single-chamber replaceable-cathode microbial electrolysis cells

Lignocellulosic residual biomass generated by the agricultural sector is an abundant feedstock for biohydrogen production via dark fermentation. However, this process is intrinsically inefficient, converting only ~30% of the reductant energy into H2 and leaving substantial amounts of reduced byproducts. These byproducts, mostly found in the fermentation effluents, can be further valorized in microbial electrolysis cells (MECs) to enhance the overall H2 recovery. However, current MEC configurations are typically dual- or single-chamber systems, yet both suffer from key inefficiencies. Dual-chamber systems rely on proton exchange membranes that are costly and prone to rapid biofouling, whereas single-chamber, membraneless systems are limited by reduced productivity due to H2 recycling and methanogenic consumption In this study, three single-chamber, 50-mL replaceable-cathode microbial electrolysis cells (RC-MECs) were 3D-printed and equipped with a physical separator to isolate anode and cathode compartments and limit H2 migration. Full-strength milled corn stover (MCS) fermentation effluent (COD of ~23.8 g-COD/L) was treated in fed-batch mode over two operational periods spanning 21 (Run 1) and 80 (Run 2) days. The RC-MECs exhibited comparable performance in both runs: after biofilm maturation, current densities exceeded 100 A/m²_cathode, COD removal reached up to 43%. Notably, extended RC-MECs operation led to a substantial methanogenic activity with the CH4 fraction in the cathode gas increasing to as high as 80% of the total biogas. Additions of a methanogenesis inhibitor 2-bromoethanesulfonate (2-BES) produced transient increases in hydrogen yields (11.51 and 5.12 L-H2/L_reactor/day in Runs 1 and 2, respectively); however, sustained 2-BES addition in subsequent cycles reduced total biogas production, decreased COD removal, and led to volatile fatty acid accumulation. Overall, single-chamber MECs can treat high-strength dark fermentation effluents while improving H2 recovery, but methanogenesis remains a key bottleneck, and complete long-term inhibition may be operationally unsustainable.

Hydrogen Production↗
DOE OSTI2025

Accumulation of Soil Microbial Necromass Controlled by Microbe–Mineral Interactions

Soil organic matter (SOM) is a key reservoir for global carbon (C), supporting soil fertility and influencing greenhouse gas emissions. Microbial residues, composed of dead cells and cellular fragments, are major contributors to SOM formation. Yet, mechanisms by which minerals enhance the accumulation of microbial residues remain poorly understood. Here, we used 13 C-labeled glucose in a year-long incubation to trace microbial residue in sandy and silty soils. Across both soils, approximately 89% of retained microbial 13 C was recovered in the fine (<53 μm) mineral-associated organic matter (MAOM) pool. Within this pool, the light MAOM fraction, enriched in poorly crystalline Fe minerals, held 4.3 times more 13 C than the heavy, phyllosilicate-dominated MAOM fraction, despite accounting for only 17.2% of the total MAOM mass and 12.3% of the total soil mass. Along with 13 C enrichment, the light MAOM fraction showed greater abundance of N-containing groups, e.g., (amides and amino groups), indicative of microbial-derived compounds like proteins and amino sugars. Fe oxides in light MAOM from both soils were spatially dispersed. Microbial residue accumulation was greater in finer-textured silty soil. These findings demonstrate that mineral composition and texture jointly regulate microbial necromass accrual, highlighting light MAOM as a key pool for enhancing soil C storage.

13C isotope labeling↗
DOE OSTI2021

A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae

Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a variety of defined characteristics in order to achieve a well-regulated genetic network for high production efficiency. Galactose-inducible (GAL) expression systems, composed of GAL promoters and multiple GAL regulators, have been widely used for protein overexpression and pathway construction in S. cerevisiae. However, the function of each element in synthetic promoters and how they interact with GAL regulators are not well known. Here, a library of synthetic GAL promoters demonstrate that upstream activating sequences (UASs) and core promoters have a synergistic relationship that determines the performance of each promoter under different carbon sources. We found that the strengths of synthetic GAL promoters could be fine-tuned by manipulating the sequence, number, and substitution of UASs. Core promoter replacement generated synthetic promoters with a twofold strength improvement compared with the GAL1 promoter under multiple different carbon sources in a strain with GAL1 and GAL80 engineering. These results represent an expansion of the classic GAL expression system with an increased dynamic range and a good tolerance of different carbon sources. In this study, the effect of each element on synthetic GAL promoters has been evaluated and a series of well-controlled synthetic promoters are constructed. By studying the interaction of synthetic promoters and GAL regulators, synthetic promoters with an increased dynamic range under different carbon sources are created.

59 BASIC BIOLOGICAL SCIENCES↗