The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource
Explore the source record for details and available documents.
Eloe-Fadrosh, Emiley A↗
SEARCH · Engineering Papers
Results for “environmental sampling”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
UCB-GLOBES: An open-access mass spectral database of identified and unidentified atmospheric organic compounds
Chemical characterization of atmospheric organic aerosols using gas chromatography with 70 eV electron ionization mass spectrometry (GC/EI-MS) has been used for decades in advancing molecular marker detection and identification, though primarily through suspect screening and/or targeted analyses. To advance non-targeted analyses of environmental samples, we have catalogued approximately 27 000 mass spectra (MS) of the trimethylsilyl derivatives of semi-volatile organic aerosol (OA) analytes in the open-access University of California Berkeley Goldstein Library of Organic Biogenic Environmental Spectra (UCB-GLOBES). Analytes were observed in ambient samples from the U.S. and the Central Amazon and/or laboratory simulations of secondary OA (SOA) formation. These samples are representative of OA under urban and biomass burning influences as well as SOA derived from biogenic precursors (e.g., isoprene, monoterpenes, sesquiterpenes) and biomass burning intermediates. MS are documented in UCB-GLOBES without regard to known chemical identity, annotated with extensive metadata such as sample source/experimental conditions, any structural information gained from MS analyses, and predicted chemical properties such as average carbon oxidation state and carbon number. UCB-GLOBES MS are compatible for importing into the NIST MS Search program, and we have also provided a Jupyter Notebook for MS visualization and comparisons. We demonstrate the utility of UCB-GLOBES through MS reanalyses of prior analytes observed in ambient data, finding a 20 % reduction in the number of analytes assigned to OA source categories reliant solely on time series correlation and an overall 11 % increase in new MS-based OA source categorization for the Southeast U.S. For 1513 analytes observed previously in the Central Amazon, we found 375 MS matches using UCB-GLOBES vs. 136 MS matches during prior analyses, representing a 14 % gain in newly confirmed or newly categorized OA species. While OA from laboratory oxidation experiments in UCB-GLOBES are highly diverse chemically, on average only 29 % of UCB-GLOBES MS have a mass spectral match to another MS entry in UCB-GLOBES and/or in databases of known compounds (i.e. NIST MS Database, Adams Essential Oil, MANE Flavor and Fragrance Company). This indicates that roughly 70 % of UCB-GLOBES MS are unique thus far, not observed more than once among the laboratory oxidation samples and ambient data in UCB-GLOBES MS. Further, only 18 % can be positively identified using these databases or known authentic standards. This points to a large gap between these laboratory simulations and ambient OA. Overall, the UCB-GLOBES database can be utilized for improving confidence in OA source categorization and/or identification, novel chemical marker discovery, tracking chemical diversity, de novo structure and properties prediction, and improving MS search and matching algorithms. This can ultimately inform future research priorities for the chemical characterization of atmospheric organic samples.
Mass spectrometry↗
Laser Ablation Plasmas and Spectroscopy for Nuclear Applications
The development of measurement methodologies to detect and monitor nuclear-relevant materials remains a consistent and significant interest across the nuclear energy, nonproliferation, safeguards, and forensics communities. Optical spectroscopy of laser-produced plasmas is becoming an increasingly popular diagnostic technique to measure radiological and nuclear materials in the field without sample preparation, where current capabilities encompass the standoff, isotopically resolved and phase-identifiable (e.g., UO and UO[Formula: see text]) detection of elements across the periodic table. These methods rely on the process of laser ablation (LA), where a high-powered pulsed laser is used to excite a sample (solid, liquid, or gas) into a luminous microplasma that rapidly undergoes de-excitation through the emission of electromagnetic radiation, which serves as a spectroscopic fingerprint for that sample. This review focuses on LA plasmas and spectroscopy for nuclear applications, covering topics from the wide-area environmental sampling and atmospheric sensing of radionuclides to recent implementations of multivariate machine learning methods that work to enable the real-time analysis of spectrochemical measurements with an emphasis on fundamental research and development activities over the past two decades. Background on the physical breakdown mechanisms and interactions of matter with nanosecond and ultrafast laser pulses that lead to the generation of laser-produced microplasmas is provided, followed by a description of the transient spatiotemporal plasma conditions that control the behavior of spectroscopic signatures recorded by analytical methods in atomic and molecular spectroscopy. High-temperature chemical and thermodynamic processes governing reactive LA plasmas are also examined alongside investigations into the condensation pathways of the plasma, which are believed to serve as chemical surrogates for fallout particles formed in nuclear fireballs. Laser-supported absorption waves and laser-induced shockwaves that accompany LA plasmas are also discussed, which could provide insights into atmospheric ionization phenomena from strong shocks following nuclear detonations. Furthermore, the standoff detection of trace radioactive aerosols and fission gases is reviewed in the context of monitoring atmospheric radiation plumes and off-gas streams of molten salt reactors. Finally, concluding remarks will present future outlooks on the role of LA plasma spectroscopy in the nuclear community.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Department of Energy Office of Legacy Management Progress on Defense-Related Uranium Mines Program - 18119
The Defense-Related Uranium Mines (DRUM) Program provides the structure and basis for the US Department of Energy Office of Legacy Management (LM) to manage the verification and validation (V and V) of defense-related uranium mines (mines) that provided ore to the Atomic Energy Commission from 1947 to 1970. V and V activities are conducted to fully understand the scope of potential problems posed by these mines by determining their location, reclamation or remediation status, and potential impacts to public safety, human health, and the environment. Land management agencies have limited resources and have generally not conducted comprehensive inventories of abandoned uranium mines, thus adding to the need to undertake this program. LM has entered into memoranda of understanding (MOUs) with the US Bureau of Land Management (BLM) and US Forest Service (USFS) to facilitate a better understanding of the scope of the problem posed by these mines. Currently, LM has executed MOUs with the BLM state offices in Colorado, New Mexico, Utah, and Wyoming and the USFS Rocky Mountain Region, which includes the national forests in Colorado, Wyoming, and South Dakota. This collaborative effort with partner agencies has led LM to develop a V and V Work Plan that describes the numerous activities and types of data to be collected at the mines. V and V activities verify actual mine location, collect coordinates of mining-related features, collect radiological data and soil samples, identify potential physical safety hazards, prioritize mines using a risk-based screening approach, and report the information to partner agencies. The partner agencies may use the reports to assess priorities and determine if any further action is warranted. The DRUM Program goals are to: - Improve data quality and content in the LM national inventory of abandoned uranium mines; - Conduct site-specific reconnaissance at mines for data verification and validation; - Exchange mine information with other federal agencies and state governments to help address mines presenting the greatest risks; - Develop reports for each mine that will contain a risk scoring assessment to help each agency develop priorities. The preliminary risk screening methodology was based on a joint effort between LM and BLM to develop factors that would be based on field observations, field data, and laboratory data using a multiple-lines-of-evidence approach. The multiple-lines-of-evidence assessment allows land managers the opportunity and flexibility to query specific criteria and make rankings based on specific priorities. The risk screening for each mine is based on evaluating the primary hazards of physical safety and risks to human health and several modifying factors that include accessibility and ecological/environmental risks. Gamma radiation scans are performed across the disturbed area of the mine, and soil samples are taken from waste rock piles and drainages, when applicable. This paper presents the results of performing inventory, environmental sampling, and risk ranking along with other accomplishments and lessons learned during the initial year of V and V activities and reporting. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP
Bacteria colonize highly diverse and complex environments, from gastrointestinal tracts to soil and plant surfaces. This colonization process is controlled in part by the intracellular signal cyclic di-GMP, which regulates bacterial motility and biofilm formation. To interrogate cyclic di-GMP signaling networks, a variety of fluorescent biosensors for live cell imaging of cyclic di-GMP have been developed. However, the need for external illumination precludes the use of these tools for imaging bacteria in their natural environments, including in deep tissues of whole organisms and in samples that are highly autofluorescent or photosensitive. The need for genetic encoding also complicates the analysis of clinical isolates and environmental samples. Toward expanding the study of bacterial signaling to these systems, we have developed the first chemiluminescent biosensors for cyclic di-GMP. The biosensor design combines the complementation of split luciferase (CSL) and bioluminescence resonance energy transfer (BRET) approaches. Furthermore, we developed a lysate-based assay for biosensor activity that enabled reliable high-throughput screening of a phylogenetic library of 92 biosensor variants. The screen identified biosensors with very large signal changes (~40- and 90-fold) as well as biosensors with high affinities for cyclic di-GMP ($K_D$ < 50 nM). These chemiluminescent biosensors then were applied to measure cyclic di-GMP levels in $E. coli$. The cellular experiments revealed an unexpected challenge for chemiluminescent imaging in Gram negative bacteria but showed promising application in lysates. Taken together, this work establishes the first chemiluminescent biosensors for studying cyclic di-GMP signaling and provides a foundation for using these biosensors in more complex systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay
Diverse members of the genus Clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This report introduces a multiplex PCR assay for differentiating members of C. botulinum group I, C. sporogenes , and two major subgroups within C. botulinum group II. Coding region sequences unique to each of the four species/subgroups were identified by in silico analyses of thousands of genome assemblies, and PCR primers were designed to amplify each marker. The resulting multiplex PCR assay correctly assigned 41 tested isolates to the appropriate species or subgroup. A separate PCR assay to determine the presence of the ntnh gene (a gene associated with the botulinum neurotoxin gene cluster) was developed and validated. The ntnh gene PCR assay provides information about the presence or absence of the botulinum neurotoxin gene cluster and the type of gene cluster present ( ha positive [ ha + ] or orfX + ). The increased availability of whole-genome sequence data and comparative genomic tools enabled the design of these assays, which provide valuable information for characterizing BoNT-producing clostridia. The PCR assays are rapid, inexpensive tests that can be applied to a variety of sample types to assign isolates to species/subgroups and to detect clostridia with botulinum neurotoxin gene ( bont ) clusters. IMPORTANCE: Diverse clostridia produce the botulinum neurotoxin, one of the most potent known neurotoxins. In this study, a multiplex PCR assay was developed to differentiate clostridia that are most commonly isolated in connection with human botulism cases: C. botulinum group I, C. sporogenes , and two major subgroups within C. botulinum group II. Since BoNT-producing and nontoxigenic isolates can be found in each species, a PCR assay to determine the presence of the ntnh gene, which is a universally present component of bont gene clusters, and to provide information about the type ( ha + or orfX + ) of bont gene cluster present in a sample was also developed. The PCR assays provide simple, rapid, and inexpensive tools for screening uncharacterized isolates from clinical or environmental samples. The information provided by these assays can inform epidemiological studies, aid with identifying mixtures of isolates and unknown isolates in culture collections, and confirm the presence of bacteria of interest.
59 BASIC BIOLOGICAL SCIENCES↗
Fluorescence-Activated Cell Sorting of Live Versus Dead Bacterial Cells and Spores
This innovation is a coupled fluorescence-activated cell sorting (FACS) and fluorescent staining technology for purifying (removing cells from sampling matrices), separating (based on size, density, morphology, and live versus dead), and concentrating cells (spores, prokaryotic, eukaryotic) from an environmental sample.
Bernardini, James N.↗
The Next Generation Safeguards Initiative s High-Purity Uranium-233 Preservation Effort
High-purity 233U serves as a crucial reference material for accurately quantifying and characterizing uranium. The most accurate analytical results which can be obtained only with high-purity 233U certified reference material (CRM) are required when used to confirm compliance with international safeguards obligations and international nonproliferation agreements. The U.S. supply of 233U CRM is almost depleted, and existing domestic stocks of this synthetic isotope are scheduled to be down-blended for disposition with depleted uranium beginning in 2015. Down blending batches of high-purity 233U will permanently eliminate the value of this material as a CRM. Furthermore, no replacement 233U stocks are expected to be produced in the future due to a lack of operating production capability and the high cost of replacing such capability. Therefore, preserving select batches of high-purity 233U is of great value and will assist in retaining current analytical capabilities for uranium-bearing samples. Any organization placing a priority on accurate results of uranium analyses, or on the confirmation of trace uranium in environmental samples, has a vested interest in preserving this material. This paper describes the need for high-purity 233U, the consequences organizations and agencies face if this material is not preserved, and the progress and future plans for preserving select batches of the purest 233U materials from disposition. This work is supported by the Next Generation Safeguards Initiative, Office of Nonproliferation and International Security, National Nuclear Security Administration.
Certified Reference Material↗
Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy
The spatial distribution oftransition metal valence states is of broad interest in the microanalysis ofgeological and environmental samples. An example is rock varnish, a naturalmanganese (Mn)-rich rock coating, whose genesis mechanism remains a subjectof scientific debate. We conducted scanning transmission X-ray microscopywith near-edge X-ray absorption fine-structure spectroscopy (STXM-NEXAFS)measurements of the abundance and spatial distribution of different Mnoxidation states within the nano- to micrometer thick varnish crusts. Suchmicroanalytical measurements of thin and hard rock crusts require samplepreparation with minimal contamination risk. Focused ion beam (FIB) slicingwas used to obtain ~100–1000 nm thin wedge-shaped slices of thesamples for STXM, using standard parameters. Yet, while this preparationis suitable for investigating element distributions and structures in rocksamples, we observed artifactual modifications of the Mn oxidation states atthe surfaces of the FIB slices. Our results imply that the preparationcauses a reduction of Mn 4+ to Mn 2+ . We draw attention tothis issue, since FIB slicing, scanning electron microscopy (SEM) imaging,and other preparation and visualization techniques operating in thekilo-electron-volt range are well-established in geosciences, but researchersare often unaware of the potential for the reduction of Mn and possibly otherelements in the samples.
58 GEOSCIENCES↗
Pahute Mesa Well Development and Testing Analyses for Wells ER-20-7, ER-20-8 #2, and ER-EC-11, Revision 1
This report analyzes the following data collected from ER-20-7, ER-20-8 No.2, and ER-EC-11 during WDT operations: (1) Chemical indicators of well development (Section 2.0); (2) Static hydraulic head (Section 3.0); (3) Radiochemistry and geochemistry (Section 4.0); (4) Drawdown observed at locations distal to the pumping well (Section 5.0); and (5) Drilling water production, flow logs, and temperature logs (Section 6.0). The new data are further considered with respect to existing data as to how they enhance or change interpretations of groundwater flow and transport, and an interim small-scale conceptual model is also developed and compared to Phase I concepts. The purpose of well development is to remove drilling fluids and drilling-associated fines from the formation adjacent to a well so samples reflecting ambient groundwater water quality can be collected, and to restore hydraulic properties near the well bore. Drilling fluids can contaminate environmental samples from the well, resulting in nonrepresentative measurements. Both drilling fluids and preexisting fines in the formation adjacent to the well can impede the flow of water from the formation to the well, creating artifacts in hydraulic response data measured in the well.
54 ENVIRONMENTAL SCIENCES↗
Data Summary Report for the Remedial Investigation of Hanford Site Releases to the Columbia River, Hanford Site, Washington
This data summary report summarizes the investigation results to evaluate the nature and distribution of Hanford Site-related contaminants present in the Columbia River. As detailed in DOE/RL-2008-11, more than 2,000 environmental samples were collected from the Columbia River between 2008 and 2010. These samples consisted of island soil, sediment, surface water, groundwater upwelling (pore water, surface water, and sediment), and fish tissue.
54 ENVIRONMENTAL SCIENCES↗
Ambient Mass Spectrometry Imaging Using Direct Liquid Extraction Techniques
Mass spectrometry imaging (MSI) is a powerful analytical technique that enables label-free spatial localization and identification of molecules in complex samples.1-4 MSI applications range from forensics5 to clinical research6 and from understanding microbial communication7-8 to imaging biomolecules in tissues.1, 9-10 Recently, MSI protocols have been reviewed.11 Ambient ionization techniques enable direct analysis of complex samples under atmospheric pressure without special sample pretreatment.3, 12-16 In fact, in ambient ionization mass spectrometry, sample processing (e.g., extraction, dilution, preconcentration, or desorption) occurs during the analysis.17 This substantially speeds up analysis and eliminates any possible effects of sample preparation on the localization of molecules in the sample.3, 8, 12-14, 18-20 Venter and co-workers have classified ambient ionization techniques into three major categories based on the sample processing steps involved: 1) liquid extraction techniques, in which analyte molecules are removed from the sample and extracted into a solvent prior to ionization; 2) desorption techniques capable of generating free ions directly from substrates; and 3) desorption techniques that produce larger particles subsequently captured by an electrospray plume and ionized.17 This review focuses on localized analysis and ambient imaging of complex samples using a subset of ambient ionization methods broadly defined as “liquid extraction techniques” based on the classification introduced by Venter and co-workers.17 Specifically, we include techniques where analyte molecules are desorbed from solid or liquid samples using charged droplet bombardment, liquid extraction, physisorption, chemisorption, mechanical force, laser ablation, or laser capture microdissection. Analyte extraction is followed by soft ionization that generates ions corresponding to intact species. Some of the key advantages of liquid extraction techniques include the ease of operation, ability to analyze samples in their native environments, speed of analysis, and ability to tune the extraction solvent composition to a problem at hand. For example, solvent composition may be optimized for efficient extraction of different classes of analytes from the sample or for quantification or online derivatization through reactive analysis. In this review, we will: 1) introduce individual liquid extraction techniques capable of localized analysis and imaging, 2) describe approaches for quantitative MSI experiments free of matrix effects, 3) discuss advantages of reactive analysis for MSI experiments, and 4) highlight selected applications (published between 2012 and 2015) that focus on imaging and spatial profiling of molecules in complex biological and environmental samples.
Environmental Molecular Sciences Laboratory↗
Robot deployable air sampling development suite
Many areas exist within the DOE EM complex where it is desired to obtain a better understanding of the environment through the use of sensors. Many of these areas are hazardous and/or inaccessible to humans requiring the development of capabilities and technologies to remotely access these areas for monitoring. Often it is desired to understand the air quality and basic environmental parameters of these inaccessible areas. The focus this LDRD was to identify and procure air and environmental sampling sensors of common interest to DOE facilities such as pH, Nitric Acid Concentration (NOx), humidity, temperature, and air velocity. Additionally, it was desired to procure a robotic platform as a basis developing a remotely deployable air sampling suite.
54 ENVIRONMENTAL SCIENCES↗
Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations
Restoring facility operations after the 2001 Amerithrax attacks took over three months to complete, highlighting the need to reduce remediation time. The most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite: a single cellulose sponge samples multiple coupons; 2) single medium multi-pass composite: a single cellulose sponge is used to sample multiple coupons; and 3) multi-medium post-sample composite: a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155CFU/cm 2 , respectively). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p-value < 0.0001) and coupon material (p-value = 0.0008). Recovery efficiency (RE) was higher overall using the post-sample composite (PSC) method compared to single medium composite from both clean and grime coated materials. RE with the PSC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, painted wall board, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but significantly lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when responding to a Bacillus anthracis contamination event of clean or dirty surfaces.
59 BASIC BIOLOGICAL SCIENCES↗
Trace-level perchlorate analysis of impacted groundwater by elevated gold ellipse dimer nanoantenna surface-enhanced Raman scattering
Perchlorate (ClO 4 - ) contamination has received increased attention the past two decades because of health concerns from its impact on thyroid function coupled with its environmental ubiquity and persistence. In this paper, we demonstrate the detection of ClO 4 - below micromolar (<1 × 10 -6 moles l -1 ) levels using a portable Raman instrument integrated with novel elevated gold (Au) ellipse dimer nanoantenna surface enhanced Raman scattering (SERS) architectures. The ellipse dimer nanoantenna architectures demonstrate improved ClO 4 - detection limits over previously reported SERS substrates while maintaining good reproducibility. The impact of chloride (Cl - ), nitrate (NO 3 - ), and sulfate (SO 4 2- ) interferences on the detection efficiency is systematically evaluated; SO 4 2- is found to exhibit the largest interference effect at low concentrations while at higher ion concentrations the interference effects among ions are similar. Finally and additionally, ClO 4 - concentrations on the order of 1 mg l -1 are determined in groundwaters collected from an US Department of Defense Navy site demonstrating the applicability of these SERS architectures for the rapid, field detection of trace-level ClO 4 - contamination within complex environmental samples.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Importance of Data Management in a Long-term Biological Monitoring Program
The long-term Biological Monitoring and Abatement Program (BMAP) has always needed to collect and retain high-quality data on which to base its assessments of ecological status of streams and their recovery after remediation. Its formal quality assurance, data processing, and data management components all contribute to this need. The Quality Assurance Program comprehensively addresses requirements from various institutions, funders, and regulators, and includes a data management component. Centralized data management began a few years into the program. An existing relational database was adapted and extended to handle biological data. Data modeling enabled the program's database to process, store, and retrieve its data. The data base's main data tables and several key reference tables are described. One of the most important related activities supporting long-term analyses was the establishing of standards for sampling site names, taxonomic identification, flagging, and other components. There are limitations. Some types of program data were not easily accommodated in the central systems, and many possible data-sharing and integration options are not easily accessible to investigators. The implemented relational database supports the transmittal of data to the Oak Ridge Environmental Information System (OREIS) as the permanent repository. From our experience we offer data management advice to other biologically oriented long-term environmental sampling and analysis programs.
54 ENVIRONMENTAL SCIENCES↗
Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples
Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from omic analyses, including the sensitivity and peak capacity extracted from complex biological and environmental sample analyses. Due to these characteristics, IMS-MS is rapidly gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.
Ion mobility spectrometry,, Mass Spectometry, Omic↗
Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.
59 BASIC BIOLOGICAL SCIENCES↗