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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

BSSD Performance Metric report: LLNL Soil Microbiome SFA (Q1 2021)

The LLNL “Microbes Persist” Soil Microbiome Scientific Focus Area (SFA) seeks to determine how microbial soil ecophysiology, population dynamics, and microbe-mineral-organic matter interactions regulate the persistence of microbial residues and the formation of soil carbon. Our SFA research program is now four years old; it evolved and benefited from previously-funded BSSD projects in the Firestone (UCB), Banfield (UCB), Sullivan (OSU) and Hungate (NAU) labs. We use stable isotope probing in combination with ‘omics to measure how changing water regimes shape activity of individual microbial populations and ecophysiological traits that affect the fate of microbial and plant C. Using measures of population dynamics and microbiome-mineral interactions, we are working to synthesize both genomescale and ecosystem-scale models of soil organic matter (SOM) turnover, to predict the long-aspired connection between soil microbiomes and fate of soil C.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides

Fatty alcohols (FOHs) are important feedstocks in the chemical industry to produce detergents, cosmetics, and lubricants. Microbial production of FOHs has become an attractive alternative to production in plants and animals due to growing energy demands and environmental concerns. However, inhibition of cell growth caused by intracellular FOH accumulation is one major issue that limits FOH titers in microbial hosts. In addition, identification of FOH-specific exporters remains a challenge and previous studies towards this end are limited. To alleviate the toxicity issue, we exploited nonionic surfactants to promote the export of FOHs in Rhodosporidium toruloides, an oleaginous yeast that is considered an attractive next-generation host for the production of fatty acid-derived chemicals. Our results showed FOH export efficiency was dramatically improved and the growth inhibition was alleviated in the presence of small amounts of tergitol and other surfactants. As a result, FOH titers increase by 4.3-fold at bench scale to 352.6 mg/L. With further process optimization in a 2-L bioreactor, the titer was further increased to 1.6 g/L. The method we show here can potentially be applied to other microbial hosts and may facilitate the commercialization of microbial FOH production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming

The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal

Enhanced biological phosphorus removal (EBPR) is an economically and environmentally significant wastewater treatment process for removing excess phosphorus by harnessing the metabolic physiologies of enriched microbial communities. We present a genome-resolved metagenomic data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.

McDaniel, Elizabeth A.↗
DOE OSTI2021

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

Understanding CRISPR-Cas systems—the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks—is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical ‘rich-get-richer’ mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data for "Soil carbon dynamics during drying vs. rewetting: Importance of antecedent moisture conditions"

This dataset contains data used for the paper "Soil carbon dynamics during drying vs. rewetting: importance of antecedent moisture conditions". The Related References field will be updated with a full citation when available.Soil moisture influences soil carbon dynamics, including microbial growth and respiration. The response of such ‘soil respiration’ to moisture changes is generally assumed to be linear and reversible, i.e. to depend only on the current moisture state. Current models thus do not account for antecedent soil moisture conditions when determining soil respiration or the available substrate pool. We conducted a laboratory incubation to determine how the antecedent conditions of drought and flood influenced soil organic matter (SOM) chemistry, bioavailability, and respiration. We sampled soils from an upland coastal forest, Beaver Creek, WA USA, and subjected them to drying and rewetting treatments. For the drying treatment, field moist soils were saturated and then dried to 75, 50, 35, and 5 % saturation. In the rewetting treatment, field moist soils were air-dried and then rewet to 35, 50, 75, and 100 % saturation. We measured respiration and water extractable organic carbon (WEOC) concentrations and used 1H-NMR and FT-ICR-MS to characterize the WEOC pool across the treatments. The drying vs. wetting treatment strongly influenced SOM bioavailability, as rewet soils (with antecedent drought) had greater WEOC concentrations and respiration fluxes compared to the drying soils (with antecedent flood). In addition, air-dry soils had the highest WEOC concentrations, and the NMR-resolved peaks showed a strong contribution of protein groups in these soils. Both NMR and FT-ICR-MS analyses indicated increased contribution of complex aromatic groups/molecules in the rewet soils, compared to the drying soils. We suggest that drying introduced organic matter into the WEOC pool via desorption of aromatic molecules and/or by microbial cell lysis, and this stimulated microbial mineralization rates. Our work indicates that even short-term shifts in antecedent moisture conditions can strongly influence soil C dynamics at the core scale. The predictive uncertainties in current soil models may be reduced by a more accurate representation of soil water and C persistence that includes a mechanistic and quantitative understanding of the impact of antecedent moisture conditions.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv and .txt format, which can be accessed and processed using MS Excel or R. NMR data are provided as raw output data (accessed in Bruker TopSpin or MestreNova) as well as the MestreNova-processed files. This archive can also be accessed on GitHub at https://github.com/kaizadp/hysteresis_and_soil_carbon (DOI: 10.5281/zenodo.4432885).

1H-NMR↗
DOE OSTI2025

Underground Hydrogen Storage: Transforming Subsurface Science into Sustainable Energy Solutions

As the global economy moves toward net-zero carbon emissions, large-scale energy storage becomes essential to tackle the seasonal nature of renewable sources. Underground hydrogen storage (UHS) offers a feasible solution by allowing surplus renewable energy to be transformed into hydrogen and stored in deep geological formations such as aquifers, salt caverns, or depleted reservoirs, making it available for use on demand. This study thoroughly evaluates UHS concepts, procedures, and challenges. This paper analyzes the most recent breakthroughs in UHS technology and identifies special conditions needed for its successful application, including site selection guidelines, technical and geological factors, and the significance of storage characteristics. The integrity of wells and caprock, which is important for safe and efficient storage, can be affected by the operating dynamics of the hydrogen cycle, notably the fluctuations in pressure and stress within storage formations. To evaluate its potential for broader adoption, we also examined economic elements such as cost-effectiveness and the technical practicality of large-scale storage. We also reviewed current UHS efforts and identified key knowledge gaps, primarily in the areas of hydrogen–rock interactions, geochemistry, gas migration control, microbial activities, and geomechanical stability. Resolving these technological challenges, regulatory frameworks, and environmental sustainability are essential to UHS’s long-term and extensive integration into the energy industry. This article provides a roadmap for UHS research and development, emphasizing the need for further research to fully realize the technology’s promise as a pillar of the hydrogen economy.

25 ENERGY STORAGE↗
DOE OSTI2023

A Continental-Scale Estimate of Soil Organic Carbon Change at NEON Sites and Their Environmental and Edaphic Controls

Current carbon cycle models focus on the effects of climate and land-use change on primary productivity and microbial-mineral dependent carbon turnover in the topsoil, while less attention has been paid to vertical soil processes and soil-dependent response to land-use change along the profile. In this study, a spatial-temporal analysis was used to estimate soil organic carbon (SOC) change in topsoil/A horizon and subsoil/B horizon at National Ecological Observatory Network (NEON) sites, USA over 30 years. To separate the effects of land-use, environmental, and edaphic factors on SOC change, space-for-time substitution was used in combination with the Continuous Change Detection and Classification algorithm and Structural Equation Modeling. Results showed that (a) under natural vegetation, Spodosols and Inceptisols found in the eastern NEON sites had substantial topsoil SOC accumulation (+0.4 to +1.2 Mg C ha –1 year –1 ), while Inceptisols and Andisols in the west had a comparable magnitude of topsoil SOC loss (–0.5 to –1.8 Mg C ha –1 year –1 ); (b) Mollisols and Alfisols in the Central Plains sites were susceptible to significant SOC loss under farming and grazing; (c) Runoff/erosion and leaching potential, vertical translocation, and mineral sorption were the most important factors controlling SOC variation across the NEON sites. Our work could be used to parameterize ecosystem models simulating SOC change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Comparison of Microbial Profiling and Tracer Testing for the Characterization of Injector-Producer Interwell Connectivities

Insufficient understanding of the microbial communities and associated microbial processes in geological reservoirs hinders the utilization of this rich data source for improved resource management. In this study, along with four interwell tracer tests at a 1478-m deep fractured crystalline-rock aquifer, we analyzed the microbial communities in the injected and produced water by high-throughput sequencing. The microbial community similarities across boreholes during an interwell flow scenario frequently encountered in reservoir development was explored. Despite the significant tracer recoveries (~30%) in all tracer tests and the cumulatively >100,000 L of exogenous water (carrying exogenous microbes) injected into the 10-m-scale reservoir, the overall structure of produced-fluid microbiome did not increasingly resemble that of the injectate. However, producers with better connectivity with the injector (based on tracer test results) did have more amplicon sequence variants (ASVs) that overlapped with those in the injectate. We identified possible drivers behind our observations and verified the practicality of repeated microbial sampling in the context of reservoir characterization and long-term monitoring. We highlight that injector-producer microbial profiling could provide insights on the relative connectivities across different producers with a given injector, and that the associated logistical needs may be comparable or even less than that of classic tracer tests.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Root Influences on Mobilization and Export of Mineral-bound Soil Organic Matter

Biogeochemical cycles within mountainous watersheds are key regulators of ecosystem carbon storage and downstream nutrient loadings, and they have shown to be particularly vulnerable to climate change impacts. Increasing temperature and persistent droughts have already dramatically changed vegetation cover across the mountainous western US, with unknown consequences for soil carbon and nutrient cycles belowground. What remains elusive is to what extent associated changes in root-soil interactions may mobilize the vast pool of organic matter (OM) that has been stabilized by associations with minerals for centuries or millennia. Although plant root-driven OM mobilization from minerals may be a central control on carbon loss and nutrient export, such mechanisms are currently missing from conceptual and numerical models. The overall objective of this Exploratory Project is to identify the biogeochemical mechanisms by which roots destabilize mineral-associated organic matter (MAOM) and the cumulative impact on carbon and nutrient fate. To accomplish this goal, we integrated well-controlled laboratory experiments with in-field measurements and a scalable modeling approach. First, we conducted model system experiments to assess the vulnerability of MAOM to exudate-mediated mechanisms. Our results show that common root exudates effectively destabilize MAOM not only through direct, ligand-driven mobilization mechanisms, but also indirect, microbially-mediated mechanisms relying on secondary metabolites and enzymes. We further found that OM bound to poorly crystalline Fe and Al (hydr)oxides is more vulnerable to exudate-induced destabilization than OM bound to more crystalline phases, particularly in response to direct, ligand-promoted mechanisms. These findings demonstrate that the stability of MAOM is not just a function of their inherent properties, but also will depend in large parts on the ability of plant roots and microbes to produce exudates capable of triggering suitable mobilization mechanisms. We further employed a well-controlled rhizobox approach, combining advanced microsensor and mass spectrometry techniques, to resolve spatiotemporal variations in the composition and availability of exudates along single growing roots of grasses. Our results show that the composition of functionally relevant exudate compounds varies at extremely short time scales, seemingly shifting from ligands such as aromatic acids around root tips to less reactive metabolites such as amino acids around mature root segments. These results suggest a prevalence of direct MAOM mobilization mechanisms around the root tip, while indirect MAOM mobilization strategies may dominate around more mature root segments. Additionally, we utilized microsensor measurements in rhizoboxes to parameterize a rhizosphere (hydro)biogeochemistry reactive transport model (eSTOMP-ROOTS). The resulting model was used to assess how root exudations affects the stability of MAOM. Model simulations show that diel pulses of root exudation are strong enough to cause oscillations in biogeochemical conditions—particularly in pH, oxygen concentrations, and microbial activity— that repeatedly disrupt MAOM. Finally, we assessed field-scale impacts of root-driven MAOM destabilization over short and long time scales. A combination of in-field incubations and field-based characterizations showed that MAOM may not only be vulnerable to seasonal variations in root activity, but also to root-driven weathering over pedogenic time scales. In sum, results from our Exploratory Award highlight the strong control plant roots exert on MAOM mobilization and, thus, on the potential for carbon and nutrient export from watersheds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Pathways for methane emissions and oxidation that influence the net carbon balance of a subtropical cypress swamp

We evaluated the major pathways for methane emissions from wetlands to the atmosphere at four wetland sites in the Big Cypress National Preserve in southwest Florida. Methane oxidation was estimated based on the d13C-CH4 of surface water, porewater, and bubbles to evaluate mechanisms that limit surface water emissions. Spatially-scaled methane fluxes were then compared to organic carbon burial rates. The pathway with the lowest methane flux rate was diffusion from surface waters (3.50 ± 0.22 mmol m-2 d-1). Microbial activity in the surface water environment and/or shallow oxic sediment layer oxidized 26 ± 3% of the methane delivered from anerobic sediments to the surface waters. The highest rates of diffusion were observed at the site with the lowest extent of oxidation. Ebullition flux rates were 2.2 times greater than diffusion and more variable (7.79 ± 1.37 mmol m-2 d-1). Methane fluxes from non-inundated soils were 1.6 times greater (18.4 ± 5.14 mmol m-2 d-1) than combined surface water fluxes. Methane flux rates from cypress knees (emergent cypress tree root structures) were 3.7 and 2.3 times higher (42.0 ± 6.33 mmol m-2 d-1) than from surface water and soils, respectively. Cypress knee flux rates were highest at the wetland site with the highest porewater methane partial pressure, suggesting that the emergent root structures allow methane produced in anaerobic sediment layers to bypass oxidation in aerobic surface waters or shallow sediments. Scaled across the four wetlands, emissions from surface water diffusion, ebullition, non-inundated soils, and knees contributed to 14 ± 2%, 25 ± 6%, 34 ± 10%, and 26 ± 5% of total methane emissions, respectively. When considering only the three wetlands with cypress knees present, knee emissions contributed to 39 ± 5% of the total scaled methane emissions. Finally, the molar ratio of CH4 emissions to OC burial ranged from 0.03 to 0.14 in the wetland centers indicating that all four wetland sites are net sources of atmospheric warming potential on 20-100 yr timescales, but net sinks over longer time scales (500 yr) with the exception of one wetland site that was a net source even over 500 yr time scales.

Ward, Nicholas D.↗
DOE OSTI2024

Tripartite interactions among free-living, N-fixing bacteria, arbuscular mycorrhizal fungi, and plants: Mutualistic benefits and community response to co-inoculation

Interactions between arbuscular mycorrhizal (AM) fungi and free-living nitrogen fixers (FLNF) occur in the rhizosphere where they can enhance plant nutrient acquisition, impact plant growth, and affect soil processes. Tripartite mutualism commonly occurs between nodule-forming plants, symbiotic diazotrophs, and AM fungi, and can occur between non-nodulating plants, FLNF, and AM fungi. However, information on the extent of, and controls on, tripartite mutualism in non-nodulating plant systems is limited to a small number of crop plants and culturable microbial inoculum, mostly in greenhouse growing conditions. We conducted a systematic literature review to synthesize the current understanding of the responses of plants, AM fungi, and FLNF to co-inoculation, as well as the conditions affecting tripartite mutualism and the magnitude and range of benefits conferred. Our review shows that plants generally benefit from co-inoculation with AM fungi and FLNF taxa, but benefits are highly variable and context dependent, ranging from 94% reduction in plant shoot biomass to 255% increase in total plant biomass. Additionally, the presence of AM fungi can increase abundance of FLNF and the presence of FLNF can increase AM fungal root colonization, but these responses also vary widely. Major factors influencing variation in response to co-inoculation by all organisms include plant phenology/age, soil type and nutrient availability, and partner pairing. There is potential for leveraging these tripartite mutualisms to improve plant productivity and soil microbial function, but successful application is more likely with a thorough understanding of the environmental and mechanistic controls on these relationships and testing of field-scale implementation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

High yield production of 3-hydroxypropionic acid using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Biotechnology↗
DOE OSTI2023

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

Abstract As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how “microbiomes within microbiomes” affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus . Results Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Sparagon, Wesley J. (ORCID:0000000296274174)↗
DOE OSTI2023

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

16S rRNA gene amplicon Illumina sequencing↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q3

Microbiome data is complex, spanning information from microbial genomes within diverse communities, protein and metabolite readouts, and contextual information (metadata) captured from the environments from which these samples were collected. While the variety and scale of microbiome data generation has dramatically expanded over the past twenty years, infrastructure to support data management, sharing, and access has lagged. New ways to improve interoperability across existing resources and advancing community standards are necessary to support how researchers create, use, and reuse data. The National Microbiome Data Collaborative (NMDC) aims to advance a microbiome data sharing network through infrastructure, data standards, and community building.

54 ENVIRONMENTAL SCIENCES↗