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At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly

Pseudomonas alloputida KT2440 (formerly P. putida) has become both a well-known chassis organism for synthetic biology and a model organism for rhizosphere colonization. Here, we describe a CRISPR interference (CRISPRi) system in KT2440 for exploring microbe–microbe interactions in the rhizosphere and for use in industrial systems. Our CRISPRi system features three different promoter systems (XylS/P m , LacI/P lac , and AraC/P BAD ) and a dCas9 codon-optimized for Pseudomonads, all located on a mini-Tn7-based transposon that inserts into a neutral site in the genome. It also includes a suite of pSEVA-derived sgRNA expression vectors, where the expression is driven by synthetic promoters varying in strength. We compare the three promoter systems in terms of how well they can precisely modulate gene expression, and we discuss the impact of environmental factors, such as media choice, on the success of CRISPRi. We demonstrate that CRISPRi is functional in bacteria colonizing the rhizosphere, with repression of essential genes leading to a 10–100-fold reduction in P. alloputida cells per root. Finally, we show that CRISPRi can be used to modulate microbe–microbe interactions. When the gene pvdH is repressed and P. alloputida is unable to produce pyoverdine, it loses its ability to inhibit other microbes in vitro. Furthermore, our design is amendable for future CRISPRi-seq studies and in multispecies microbial communities, with the different promoter systems providing a means to control the level of gene expression in many different environments.

Bacteria↗
DOE OSTI2023

Terrestrial carbon dynamics in an era of increasing wildfire

In an increasingly flammable world, wildfire is altering the terrestrial carbon balance. However, the degree to which novel wildfire regimes disrupt biological function remains unclear. Here, we synthesize the current understanding of above and below ground processes that govern carbon loss and recovery across diverse ecosystems. In this study, we find that intensifying wildfire regimes are increasingly exceeding biological thresholds of resilience, causing ecosystems to convert to a lower carbon-carrying capacity. Growing evidence suggests that plants compensate for fire damage by allocating carbon below ground to access nutrients released by fire, while wildfire selects for microbial communities with rapid growth rates and the ability to metabolize pyrolyzed carbon. Determining controls on carbon dynamics following wildfire requires integration of experimental and modeling frameworks across scales and ecosystems. Fire severity is expected to increase as a result of warming. This will potentially amplify climate change due to its impact on the carbon cycle. This Review discusses ecosystem carbon loss and recovery following wildfire, and highlights where further work is needed to inform model predictions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Complete biosynthesis of QS-21 in engineered yeast

QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans. However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis. Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host’s native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families—a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases—from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure–activity relationship, and will thus enable the rational design of potent vaccine adjuvants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Editorial: Exogenous carbon-based materials in soil ecosystems

Various exogenous carbon-based materials (ECMs) such as crop straw, biochar, carbon-based nano-fertilizer, and microplastics have accumulated in soil ecosystems. These ECMs may cause direct and indirect impacts on soil properties, processes, productivity, and health, thus potentially changing the function and stability of soil ecosystems. However, large knowledge gaps still exist on ECMs in soil ecosystems, including their accumulation, interactions with soil components, and potential ecological impacts and risks. Therefore, more efforts are needed to further understand the impacts especially the long-term effects of ECMs in soil ecosystems. By generating new knowledge, this Research Topic aims to improve the understanding of the effects of ECMs on soil ecosystems, including soil quality, nutrient cycling, microbial ecology, crop growth, environmental health and ecological risk.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration

Anoxic microsites are potentially important but unresolved contributors to soil organic carbon (C) storage. How anoxic microsites vary with soil management and the degree to which anoxic microsites contribute to soil C stabilization remain unknown. Sampling from four long-term agricultural experiments in the central United States, we examined how anoxic microsites varied with management (e.g., cultivation, tillage, and manure amendments) and whether anoxic microsites determine soil C concentration in surface (0–15 cm) soils. We used a novel approach to track anaerobe habitat space and, hence, anoxic microsites using DNA copies of anaerobic functional genes over a confined volume of soil. No-till practices inconsistently increased anoxic microsite extent compared to conventionally tilled soils, and within one site organic matter amendments increased anaerobe abundance in no-till soils. Across all long-term tillage trials, uncultivated soils had ~2–4 times more copies of anaerobic functional genes than their cropland counterparts. Finally, anaerobe abundance was positively correlated to soil C concentration. Even when accounting for other soil C protection mechanisms, anaerobe abundance, our proxy for anoxic microsites, explained 41% of the variance and 5% of the unique variance in soil C concentration in cropland soils, making anoxic microsites the strongest management-responsive predictor of soil C concentration. Our results suggest that careful management of anoxic microsites may be a promising strategy to increase soil C storage within agricultural soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Hypersaline sapropels act as hotspots for microbial dark matter

Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions. Furthermore, the polyphasic approach combined deep coverage SSU rRNA gene amplicon sequencing and bioinformatics with RT-qPCR and physicochemical investigations. We found that sapropels developed an analogous elemental milieu and harbored prokaryotes affiliated with fifty-nine phyla, among which the most abundant were Proteobacteria , Bacteroidetes and Chloroflexi . Containing thirty-two candidate divisions and possibly undocumented prokaryotic lineages, the hypersaline sapropels were found to accommodate one of the most diverse and novel ecosystems reported to date and may contribute to completing the phylogenetic branching of the tree of life.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Early Cyanobacteria and the Innovation of Microbial Sunscreens

Metabolism drives life; therefore, understanding how and when various branches of metabolism evolved provides a critical piece to understanding how life has integrated itself into the geochemical cycles of our planet over billions of years. Although the most transformative metabolisms that have significantly altered the trajectory of Earth are inherently linked to primary metabolism, natural products that stem from specialized metabolic pathways are also key components to many auxiliary facets of life. Cyanobacteria are primarily known as the original inventors of oxygenic photosynthesis, using sunlight to split water to create our dioxygen-filled atmosphere; however, many of them also have evolved to produce small molecules that function as sunscreens to protect themselves from ultraviolet radiation. Determining when cyanobacteria first evolved the ability to biosynthesize such compounds is an important piece to understanding the rise of oxygen and the eventual success of the phylum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Decomposition decreases molecular diversity and ecosystem similarity of soil organic matter

Soil organic matter (SOM) is comprised of a diverse array of reactive carbon molecules, including hydrophilic and hydrophobic compounds, that impact rates of SOM formation and persistence. Despite clear importance to ecosystem science, little is known about broad-scale controls on SOM diversity and variability in soil. Here, we show that microbial decomposition drives significant variability in the molecular richness and diversity of SOM between soil horizons and across a continental-scale gradient in climate and ecosystem type (arid shrubs, coniferous, deciduous, and mixed forests, grasslands, and tundra sedges). The molecular dissimilarity of SOM was strongly influenced by ecosystem type (hydrophilic compounds: 17%, P < 0.001; hydrophobic compounds: 10% P < 0.001) and soil horizon (hydrophilic compounds: 17%, P < 0.001; hydrophobic compounds: 21%, P < 0.001), as assessed using metabolomic analysis of hydrophilic and hydrophobic metabolites. While the proportion of shared molecular features was significantly higher in the litter layer than subsoil C horizons across ecosystems (12 times and 4 times higher for hydrophilic and hydrophobic compounds, respectively), the proportion of site-specific molecular features nearly doubled from the litter layer to the subsoil horizon, suggesting greater differentiation of compounds after microbial decomposition within each ecosystem. Together, these results suggest that microbial decomposition of plant litter leads to a decrease in SOM α-molecular diversity, yet an increase in β-molecular diversity across ecosystems. The degree of microbial degradation, determined by the position in the soil profile, exerts a greater control on SOM molecular diversity than environmental factors, such as soil texture, moisture, and ecosystem type.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Safety Evaluation of Nitric Acid Reactions with Polysaccharides

The hazards of polysaccharides in a transuranic (TRU) waste drum exposed to nitric acid (HNO3) and metal nitrate salts have been evaluated, based on considerations of how complex nitrogen redox cycles carry out the aqueous phase oxidation of alcohols and related organic functional groups. Of particular emphasis is how these exothermic reactions, coupled with a positive feedback loop inherent to nitrogen redox chemistry, can initiate an autocatalytic thermal runaway and explosive gas generation. This poses the most significant hazard for a TRU waste drum under ambient conditions where acidic solution may be present, either in small quantities as free liquid or sorbed within a solid matrix. Regarding specific mechanistic details, nitric acid is an extremely potent oxidant but is remarkably inert, rarely interacting directly with oxidizable substrates, instead exerting its vast potential energy through lower oxidation state reactants such as nitrogen dioxide (NO 2 ) and nitrous acid (HNO 2 ). These lower oxidation states of nitrogen are generated from the slow self-decomposition of nitric acid, as a result of which oxidation reactions involving nitric acid that have not been preloaded with these reactants commonly experience a quiescent induction period. It is the end of this induction period when exothermic reactivity increases rapidly that the system is most vulnerable to autocatalytic thermal runaway. Metal nitrate salts promote this ambient temperature solution chemistry (cf. traditional oxidizer properties of metal nitrate salts, which operate in the solid state at elevated temperatures) by releasing nitric acid into the system. Although less reactive than alcohols by virtue of extensive hydrogen bonding, carbohydrates are oxidized by nitric acid through the same fundamental mechanisms, potentially proceeding through a series of oxidation steps. For polymeric carbohydrates (polysaccharides) the chemistry is complicated by a variety of competing side reactions, including acid-catalyzed hydrolytic depolymerization to more reactive (ultimately monomeric) units, as well as other degradation reactions promoted by radical mechanisms. For this reason, polysaccharides that are more susceptible to hydrolysis such as starches are more reactive than cellulose, with the attendant microbial population in starch based kitty litter adding a special aspect of reactivity. A spectrum of nitrogen containing gas products is generated from polysaccharide oxidation by nitric acid depending on the reaction conditions - for example, fuel lean mixtures tend towards producing more oxidized gases such as NO 2 , and thus favor an autocatalytic cycle, relative to fuel rich conditions that produce lower oxidation state gases such as nitrous oxide (N 2 O). These nitrogen based gases may be accompanied by variable quantities of carbon dioxide (CO 2 ), which may be generated from small molecule (e.g., oxalic acid) oxidation or from decarboxylation of previously oxidized functional groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken in 2017 in June (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) in an active meander (Meander C) of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (15-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (50-88 cm depth below surface). Sediments were homogenized from the ~10 cm cores for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0151851. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 405 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Extracting Natural Biosurfactants from Humus Deposits for Subsurface Engineering Applications

Environmentally benign, economical, and effective surfactants and additives are needed in engineering subsurface energy recovery processes. Biosurfactants have some advantages over chemically synthesized surfactants, but the high costs of microbial-biosynthesis limit their applications in subsurface engineering. In this work, we propose to use naturally occurring biosurfactants contained within Earth's readily available and inexpensive humus deposits for subsurface engineering applications. We collected humus samples of different types from four different regions, and developed a simple method for extracting natural biosurfactant (NBS) using only four common chemicals. The average NBS extraction yields are 16 ± 3% of the raw humus. No significant differences in elemental composition and functional group chemistry were found among the NBS extracted from humus of different origins, suggesting that any humus deposit can be used for NBS extraction. Measurements of interfacial tensions between air-water and supercritical (sc) CO 2 -water interfaces indicate that the NBS is a highly effective surfactant. NBS has good foaming ability. Preliminary tests with only 0.5 mass % NBS in the aqueous phase (no other additives) yielded scCO 2 -in-water foams of 83% foam quality. The apparent viscosity of 13 cP measured at a shear rate of 2320 s -1 indicates that much higher viscosities are achievable at lower shear rates. Finally, these results suggest that NBS merits further research and development for potential applications in subsurface energy production.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Microbial Evolution Drives Adaptation of Substrate Degradation on Decadal to Centennial Time Scales Relevant to Global Change

ABSTRACT Understanding microbial adaptation is crucial for predicting how soil carbon dynamics and global biogeochemical cycles will respond to climate change. This study employs the DEMENT model of microbial decomposition, along with empirical mutation and dispersal rates, to explore the roles of mutation and dispersal in the adaptation of soil microbial populations to shifts in litter chemistry, changes that are anticipated with climate‐driven vegetation dynamics. Following a change in litter chemistry, mutation generally allows for a higher rate of litter decomposition than dispersal, especially when dispersal predominantly introduces genotypes already present in the population. These findings challenge the common idea that mutation rates are too low to affect ecosystem processes on ecological timescales. These results demonstrate that evolutionary processes, such as mutation, can help maintain ecosystem functioning as the climate changes.

Abs, Elsa↗
DOE OSTI2024

Functional-type modeling approach and data-driven parameterization of methane emissions in wetlands (Final Technical Science Report)

Our goals are to improve understanding and quantitative representation of the multiple processes that affect methane emissions at a high (patch level, vertically detailed) spatial resolution, and translate this understanding to improved modeling capability of coastal wetland fluxes using the E3SM Land Model (ELM v1) wetland CH4 biogeochemistry module. We propose an experimental approach to identify and parameterize uncertainties in ELM. Understanding of methane emissions can be improved along three conceptual axes: (i) horizontal (ecohydrological patch resolution), (ii) vertical (through the depth of the soil column), and (iii) process level (e.g., resolving microbial pathways, vegetation specific transport pathways). Along each of the three axes, we will characterize, quantify, and model, the key ecological, hydrological, and meteorological controls of methane (CH4) flux heterogeneity in four model coastal wetlands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Response of soil nutrient pools and microbiomes to recurrent wildfire disturbance and varying burn severities in a mixed conifer forest

Wildfire is a pervasive disturbance in mixed-conifer forests, yet the relative influence of fire recurrence versus burn severity on soil biogeochemistry and microbial communities remains poorly quantified. We examined a natural gradient of fire history (0–3 prior fires) and burn severity (low–high) spanning 50 yr in a mixed-conifer ecosystem to assess how repeated fire shapes soil carbon (C) and nitrogen (N) pools, their isotopic signatures, mineral and particulate fractions, microbial community composition, carbon-use, CO₂ fluxes, and vegetation cover. Successive fires produced progressively higher bare-ground percentages and lower tree cover, which were tightly linked to declines in microbial diversity and reductions bulk %C, and %N. δ 13 C increased with fire frequency, indicating preferential loss of labile C through combustion or enhanced microbial oxidation, thereby explaining the observed net soil-C decline. Conversely, δ 15 N decreased and pH increased as tree density declined, reflecting altered N cycling and reduced acidification in post-fire soils. Fire recurrence, more than severity, corresponded with a marked shift in the bacterial community: for example, Xanthobacteraceae—key N-fixers and C-cyclers—diminished, while N-fixing Bacillaceae increased, underscoring the tightly coupled nature of soil nutrient dynamics and microbiome composition after repeated burns. Our results demonstrate that fire recurrence appears to be a stronger driver of post-fire soil ecosystem responses in this mixed-conifer forest, influencing both abiotic nutrient pools and the functional potential of the soil microbiome. These findings provide a more enhanced assessment and understanding to date of the biogeochemical consequences of repeated wildfire disturbance that can be used to inform management strategies aimed at preserving soil health in fire-prone landscapes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Geothermally warmed soils reveal persistent increases in the respiratory costs of soil microbes contributing to substantial C losses

Increasing temperatures can accelerate soil organic matter decomposition and release large amounts of CO 2 to the atmosphere, potentially inducing positive warming feedbacks. Alterations to the temperature sensitivity and physiological functioning of soil microorganisms may play a key role in these carbon (C) losses. Geothermally active areas in Iceland provide stable and continuous soil temperature gradients to test this hypothesis, encompassing the full range of warming scenarios projected by the Intergovernmental Panel on Climate Change for the northern region. We took soils from these geothermal sites 7 years after the onset of warming and incubated them at varying temperatures and substrate availability conditions to detect persistent alterations of microbial physiology to long-term warming. Seven years of continuous warming ranging from 1.8 to 15.9 °C triggered a 8.6–58.0% decrease on the C concentrations in the topsoil (0–10 cm) of these sub-arctic silt-loam Andosols. The sensitivity of microbial respiration to temperature (Q 10 ) was not altered. However, soil microbes showed a persistent increase in their microbial metabolic quotients (microbial respiration per unit of microbial biomass) and a subsequent diminished C retention in biomass. After an initial depletion of labile soil C upon soil warming, increasing energy costs of metabolic maintenance and resource acquisition led to a weaker capacity of C stabilization in the microbial biomass of warmer soils. This mechanism contributes to our understanding of the acclimated response of soil respiration to in situ soil warming at the ecosystem level, despite a lack of acclimation at the physiological level. Furthermore, persistent increases in the respiratory costs of soil microbes in response to warming constitute a fundamental process that should be incorporated into climate change-C cycling models.

58 GEOSCIENCES↗
DOE OSTI2022

Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands

Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. Here, to evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an intense dinoflagellate bloom in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16S rRNA amplicon libraries from samples collected on 41 dates. The dataset also includes 88 18S rRNA amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom. Accompanying the sequence data are chemical and biological measurements associated with each sample. These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.

59 BASIC BIOLOGICAL SCIENCES↗