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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cytochrome Nanowire XRD

Microbial metabolism plays an important role in the global cycling of carbon, nutrients, and metals. Recent discovery of microorganisms sharing energy using direct electrical connections might represent a prominent strategy by which anaerobic microorganisms interact with the diversity of environments. The purpose of the proposed research is to apply these newly developed principles of electron exchange in microbial communities to the study of biogeochemical cycling in climate and subsurface systems. Previous studies revealed that soil bacteria Geobacter sulfurreducens produce conductive pili nanofilaments that facilitate long-range electron transport to extracellular electron acceptors and other cells. This discovery has already transformed our understanding of the function of microbial communities in diverse environments, making basic contributions to microbial ecology and helping to improve practical applications such as increasing current output of microbial fuel cells and enhancing the conversion of organic waste to methane. Microbial electron exchange via pili may also contribute to methane production in terrestrial environments that are major sources of atmospheric methane. However, the mechanism of electron transport through pili is not well understood. Initial studies have suggested that pili exhibit metallic-like conductivity similar to conducting polymer polyaniline. However, these studies were limited to electrical measurements. X-ray diffraction studies have suggested that aromatic amino acids tyrosine and phenylalanine are closely packed in pili. But these studies used homology modeling to predict the pilus assembly and information about the number of monomers in each pilus assembly unit and their organization are still lacking. The central hypothesis of this proposal is aromatics in pili enable intermolecular electron delocalization due to pi-stacking that can give rise to metallic-like conductivity. By analyzing pili structure using infrared scattering-scanning near field optical microscope (IR s-SNOM) and combining with solution NMR, Focused Ion Beam (FIB and computational capabilities, this work will provide comprehensive understanding of the conduction mechanism from a structure-function perspective. The specific aims are: 1) With infrared scattering scanning near field optical microscope (IR s-SNOM), image the organization and density of pilin monomers and pH-induced conformational changes in a pilus filament. 2) With solution NMR, resolve pH-induced structural changes in the pilin monomer. 3) Using Focused Ion Beam (FIB), draw electrodes on single pili to measure their conductivity. 4) With computational modeling using the NWChem, simulate the effect of environment on the electronic properties of pili as a function of pH. The proposed work will gain the nanoscale insight into the structure of the pili, as the basis for understanding interspecies electrical communications. The improved understanding will be harnessed to accelerate bioenergy production and bioremediation using pili as well as for predictive modeling of carbon cycling in diverse environments to reach the central goals of DOE-BER to develop sustainable energy sources, regulate the contaminants in the subsurface and understand the effects of greenhouse gas emissions on biosphere. The proposed studies will provide design principles for engineering of electrical interactions among these communities by manipulating the amino acid composition of pili. Moreover, these studies will identify the forces that maintain the function of these communities in the face of environmental perturbation. Therefore, these studies will help to address the need "to incorporate process understanding of biogeochemical cycling into a scalable hierarchy of predictive capabilities" specified in EMSL's Science Themes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller “active core” subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

Community Structure and Diversity↗
DOE OSTI2025

Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient

Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.

Biological and medical sciences↗
DOE OSTI2023

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. Here, we showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Biological Mechanisms May Contribute to Soil Carbon Saturation Patterns: Modeling Archive

This Modeling Archive is in support of a TES-SFA publication “Biological Mechanisms May Contribute to Soil Carbon Saturation Patterns” (Craig et al., 2021). We ran and evaluated a multi-assumption soil organic carbon (SOC) model to investigate whether alternative assumptions regarding constraints on soil microbial biomass could lead to soil carbon saturation patterns. We developed this model in the Multi-Assumption Architecture and Testbed (MAAT, https://github.com/walkeranthonyp/MAAT, tag: v1.2.1_Craig2021; Walker et al. 2018). Using MAAT, we embedded three alternative hypotheses in a microbially explicit three-pool SOC model: 1) the efficiency of mineral-associated SOC formation decreases as mineral-associated SOC approaches a maximum value (“Mineral saturation”), 2) the microbial biomass turnover rate increases with increasing microbial biomass (“Density-dependent turnover”), and 3) community carbon use efficiency decreases as microbial biomass increases toward an upper limit (“Density-dependent growth”). We ran a factorial combination of these hypotheses resulting in eight models for three different classes of model (linear decay, Michaelis-Menten decay, or reverse Michaelis-Menten decay), resulting in 24 models, 12 of which are presented or discussed in the related publication. Models were parameterized using values from previous studies with similar models (Wang et al. 2013, Wieder et al. 2014, Li et al. 2014, Georgiou et al. 2017, Hassink and Whitmore 1997) and ran to an approximate steady state (200 years) at six (6) different C input rates corresponding to 0.5, 1, 2, 4, 7, and 10 times the default input value. Further model details are available in the related publication. This archive contains output from three MAAT simulations, and scripts to run these simulations and process and plot the data. Simulations are labeled “lin”, “MM_highKm”, and “RMM_highKm” reflecting factorial runs for linear, Michealis-Menten, and reverse Michaelis-Menten models, respectively. This archive contains: • 3 R scripts prepended with “init_MAAT_” to initialize runs (1 for each simulation), • 1 csv file containing years over which to run simulations (“met_year.csv”), • 1 bash script (.bs) to run MAAT, • 6 XML files that are output from MAAT describing a run (2 for each simulation), • 3 model output csv files prepended by “out_” (1 for each simulation), and • 1 analysis R script for reproducing figures 3 and 4 in Craig et al. 2021. See included user guide (Craig_2021_modeling_archive_20210315.pdf) for file organization details.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Soil microbiome predictability increases with spatial and taxonomic scale

Soil microorganisms shape ecosystem function, yet it remains an open question whether we can predict the composition of the soil microbiome in places before observing it. Furthermore, it is unclear whether the predictability of microbial life exhibits taxonomic- and spatial-scale dependence, as it does for macrobiological communities. Here, we leverage multiple large-scale soil microbiome surveys to develop predictive models of bacterial and fungal community composition in soil, then test these models against independent soil microbial community surveys from across the continental United States. We find remark- able scale dependence in community predictability. The predictability of bacterial and fungal communities increases with the spatial scale of observation, and fungal predictability increases with taxonomic scale. These patterns suggest that there is an increasing importance of deterministic versus stochastic processes with scale, consistent with findings in plant and animal communities, suggesting a general scaling relationship across biology. Biogeochemical functional groups and high-level taxonomic groups of microorganisms were equally predictable, indicating that traits and taxonomy are both powerful lenses for understanding soil communities. Here, by focusing on out-of-sample prediction, these findings suggest an emerging generality in our understanding of the soil microbiome, and that this understanding is fundamentally scale dependent

Biogeography↗
DOE OSTI2023

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Abstract Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Soil viruses: Understudied agents of soil ecology

Over the past couple decades there has been intense exploration of the soil microbiome using modern sequencing and bioinformatics approaches. These studies have revealed a vast diversity of microorganisms across a variety of habitats (Thompson et al., 2017) and how differences in the environment, for example with climate change, influence the soil microbial community composition (Jansson and Hofmockel, 2020). The focus of these studies has primarily been on microbial cellular organisms, including bacteria, archaea and fungi. By contrast, in depth study of soil viruses has been largely neglected, until recently. There are several reasons that soil viruses are less studied, including difficulties with extraction of viruses from soil particles, difficulties with classification of soil viruses based on microscopic imaging, and reliance on the small proportion of microbial hosts that can be cultivated. Now that comprehensive soil metagenomes are available the current trend has been to survey the metagenomes for viral sequences. This approach has revealed that soil viruses are incredibly abundant, highly diverse, and largely uncharacterized (Paez-Espino et al., 2016). This so-called ‘viral dark matter’ presents an incredible research opportunity for the future. Here I will highlight some of these potential research avenues based on what is known to date.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices

ABSTRACT Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding. IMPORTANCE Ecosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Biotechnology & Applied Microbiology↗
NASA NTRS2016

Xeropreservation of Functionalized Lipid Biomarkers in Hyperarid Soils in the Atacama Desert

Our understanding of long-term organic matter preservation comes mostly from studies in aquatic systems. In contrast, taphonomic processes in extremely dry environments are relatively understudied and are poorly understood. We investigated the accumulation and preservation of lipid biomarkers in hyperarid soils in the Yungay region of the Atacama Desert. Lipids from seven soil horizons in a 2.5 meter vertical profile were extracted and analyzed using GC-MS ( Gas Chromatography-Mass Spectrometry) and LC-MS (Liquid Chromatography-Mass Spectrometry). Diagnostic functionalized lipids and geolipids were detected and increased in abundance and diversity with depth. Deeper clay units contain fossil organic matter (radiocarbon dead) that has been protected from rainwater since the onset of hyperaridity. We show that these clay units contain lipids in an excellent state of structural preservation with functional groups and unsaturated bonds in carbon chains. This indicates that minimal degradation of lipids has occurred in these soils since the time of their deposition between more than 40,000 and up to 2 million years ago. The exceptional structural preservation of biomarkers is likely due to the long-term hyperaridity that has minimized microbial and enzymatic activity, a taphonomic process we term xeropreservation (i.e. preservation by drying). The degree of biomarker preservation allowed us to reconstruct major changes in ecology in the Yungay region that reflect a shift in hydrological regime from wet to dry since the early Quaternary. Our results suggest that hyperarid environments, which comprise 7.5 percent of the continental landmass, could represent a rich and relatively unexplored source of paleobiological information on Earth.

Xeropreservation↗
DOE OSTI2021

Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N 2 O) from the tropics. Toward closing these knowledge gaps, in this study we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N 2 O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N 2 O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ~45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following “wet-up”, when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO 2 efflux following wet-up of seasonally dry soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Life history strategies of soil bacterial communities across global terrestrial biomes

The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Finally, our findings provide a trait-based framework to compare life history strategies of soil bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

Biological degradation and composition of inedible sweetpotato biomass

Many challenges are presented by biological degradation in a bioregenerative Controlled Ecological Life Support System (CELSS) as envisioned by the U.S. National Aeronautics and Space Administration (NASA). In the studies conducted with biodegradative microorganism indigenous to sweetpotato fields, it was determined that a particle size of 75 microns and incubation temperature of 30 degrees C were optimal for degradation. The composition of the inedible biomass and characterization of plant nutrient solution indicated the presence of potential energy sources to drive microbial transformations of plant waste. Selected indigenous soil isolates with ligno-cellulolytic or sulfate-reducing ability were utilized in biological studies and demonstrated diversity in ability to reduce sulfate in solution and to utilize alternative carbon sources: a lignin analog--4-hydroxy, 3-methoxy cinnamic acid, cellulose, arabinose, glucose, sucrose, mannitol, galactose, ascorbic acid.

Vegetables/chemistry/metabolism↗
DOE OSTI2020

A genomic catalog of Earth’s microbiomes

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Microbial ecology of extreme environments: Antarctic yeasts and growth in substrate-limited habitats

The high, dry valleys of the Ross Desert of Antarctic, characterized by extremely low temperatures, aridity and a depauperate biota, are used as an analog of the postulated extreme climates of other planetary bodies of the Solar System to test the hypothesis that if life could be supported by Ross, it might be possible where similar conditions prevail. The previously considered sterility of the Ross Desert soil ecosystem has yielded up an indigenous yeast, Cryptoccus vishniacci, which is able to resist the extremes of cold, wet and dry freezing, and long arid periods, while making minimal nutritional demands on the soil.

Vishniac, H. S.↗
DOE OSTI2024

Impact of storage and extraction methods on peat soil microbiomes

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.

Science & Technology - Other Topics↗