Engineering Papers⌕ Search

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.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

The Case for the Application of Worldwide Marine Radioactivity Studies In the Search for Undeclared Facilities and Activities

Undeclared nuclear facilities unequivocally remain the most difficult safeguards challenge facing the International Atomic Energy Agency (IAEA). Recent cases of undeclared facilities revealed in Iran and Syria, which are NPT signatory States, show both the difficulty and the seriousness of this threat to nonproliferation. In the case of undeclared nuclear facilities, the most effective deterrent against proliferation is the application of Wide-Area Environmental Sampling (WAES); however, WAES is currently cost-prohibitive. As with any threat, the most effective countering strategy is a multifaceted approach. Some of the approaches applied by the IAEA include: open source analysis, satellite imagery, on-site environmental sampling, complementary access under the Additional Protocol (where in force), traditional safeguards inspections, and information provided by member States. These approaches, naturally, are focused on specific States. Are there other opportunities not currently within the IAEA purview to assess States that may provide another opportunity to detect clandestine facilities? In this paper, the author will make the case that the IAEA Department of Safeguards should explore the area of worldwide marine radioactivity studies as one possible opportunity. One such study was released by the IAEA Marine Environment Laboratory in January 2005. This technical document focused on 90Sr, 137Cs, and 239/240Pu. It is clearly a challenging area because of the many sources of anthropogenic radionuclides in the world’s oceans and seas including: nuclear weapons testing, reprocessing, accidents, waste dumping, and industrial and medical radioisotopes, whose distributions change based on oceanographic, geochemical, and biological processes, and their sources. It is additionally challenging where multiple States share oceans, seas, and rivers. But with the application of modern science, historical sampling to establish baselines, and a focus on the most relevant radionuclides, the potential is there to support this challenging IAEA safeguards mission.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2021

Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture

Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. Here we provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Trace explosive residue detection of HMX and RDX in post-detonation dust from an open-air environment

Explosives are often used in industry, geology, mining, and other applications, but it is not always clear what remains after a detonation or the fate and transport of any residual material. The goal of this study was to determine to what extent intact molecules of high explosive (HE) compounds are detectable and quantifiable from post-detonation dust and particulates in a field experiment with varied topography. We focused on HMX (1,3,5,7-Tetranitro-1,3,5,7-tetrazocane), which is less studied in field detonation literature, as the primary explosive material and RDX (1,3,5-Trinitroperhydro-1,3,5-triazine) as the secondary material. The experiment was conducted at Site 300, Lawrence Livermore National Laboratory’s Experimental Test Site, in California, USA. Two 20.4 kg and one 40.8 kg above ground explosions (primarily comprised of LX-14, an HMX-based polymer-bonded high explosive) were detonated on an open-air firing area on separate days. The complex terrain of the firing area (e.g., buildings, berm, low-height obstacles) was advantageous to study HE deposition in relation to plume dynamics. Three types of samples were collected up to 100 m away from each shot: surface swipes of aluminum plates, surface swipes of fixed objects, and filters from air samples. We used atmospheric flow tube-mass spectrometry (AFT-MS) to quantify picogram levels of molecular residue of HE material in the post-detonation dust. An aliquot of sample extract in methanol (e.g., 1 µL of 0.5 mL) was placed onto a resistive material and then thermally desorbed into the AFT-MS. We successfully detected and quantified both HMX and RDX in many of the samples. Based on mass (pg) detected and solution dilution, we back-calculated the mass collected on the swipe or filter (ng per sample). The aerial distribution of molecular residue was consistent with the path of the plume, which was strongly determined by wind speed and direction at the time of each shot. The quantity of material detected appeared to correlate more with distance from the shot and the wind conditions than with shot size. This study demonstrates that the picogram detection levels of AFT-MS are well-suited for quantification of analytes (e.g., HMX and RDX) in environmental samples.

atmospheric flow tube-mass spectrometry (AFT-MS), ↗
DOE OSTI2014

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

Summary Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non‐canonical amino acid tagging ( BONCAT ), is based on the in vivo incorporation of the non‐canonical amino acid L ‐azidohomoalanine ( AHA ), a surrogate for l ‐methionine, followed by fluorescent labelling of AHA ‐containing cellular proteins by azide‐alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)‐targeted fluorescence in situ hybridization ( FISH ), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT‐FISH to study microbial physiology in situ . A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano‐scale secondary ion mass spectrometry ( 15 NH 3 assimilation) for individual cells within a sediment‐sourced enrichment culture showed concordance between AHA ‐positive cells and 15 N enrichment. BONCAT‐FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single‐cell level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Extraction chromatographic separations of tantalum and tungsten from hafnium and complex matrix constituents

Ta, Hf, and W analyses from complex matrices (including environmental samples) require high purification of these analytes from each other and major/trace matrix constituents, however, current state-of-the-art Ta/Hf/W separations rely on traditional anion exchange approaches that suffer from relatively similar distribution coefficient (Kd) values for these analytes. This work reports assessment of three commercially available extraction chromatographic resins (TEVA, TRU, and UTEVA) for Ta/Hf/W separations. Batch contact studies show differences in Ta/W,Hf Kd values of up to 106, representing an improvement of a factor of 100 and 300 in Ta/Hf and Ta/W Kd values (respectively) over AG1x4 resin. Variations in the Kd values as a function of HCl concentration for TRU resin show that this resin is well suited for Ta/Hf/W separations, with Ta/Hf, Ta/W, and W/Hf Kd value improvements of 10, 200, and 30 (respectively) over AG1x4 resin. Finally, analyses of digested soil samples (NIST 2710a) using TRU resin and tandem TEVA-TRU columns demonstrate the ability to achieve extremely high purification (>99%) of Ta and W from each other and Hf, as well as enabling very high purification of Ta and W from the major and trace elemental constituents present in soils, using a single chromatographic step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

High-resolution phylogenetic microbial community profiling

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

09 BIOMASS FUELS↗
DOE OSTI2023

Investigation of potential polyatomic interferences on uranium isotope ratio measurements for the LS-APGD-Orbitrap MS system

The determination of actinide (e.g., U and Pu) content and isotopics is of importance to the nuclear forensics and safeguards communities. However, in the analysis of environmental samples, such as those collected by the International Atomic Energy Agency, uranium measurements can be complicated by isobaric interferences from polyatomic variants of heavy elements (e.g., Pb). This leads to complex, time-consuming sample manipulations (i.e., separations) before determining isotope ratios. An alternative strategy to sample pretreatment is to use high-resolution mass spectrometric platforms during the analysis to fully resolve the uranium isotopes from potential polyatomic interferences, negating the need for prior chemical separation. The liquid sampling - atmospheric pressure glow discharge (LS-APGD) coupled with an Orbitrap mass spectrometer provides a high-resolution (>70,000 m/Δm at m/z 200) inorganic mass spectrometry platform. Further, as a demonstration of the power of this instrumental platform, and indeed, the high-resolution approach in general, uranium isotope ratios were determined in the presence of elemental impurities (e.g., Pb, Pt, Ta, W) commonly encountered with environmental sample swipe analysis, without any prior treatment. Even at elemental impurity concentrations of 1000–5000× relative to uranium, no interference was observed with the 235 U or 238 U signal. In addition, the 235 U/ 238 U isotope ratio for the samples with the concomitants present are within 2 standard deviations of the values obtained without their addition, indicating that these impurities do not impact the determined uranium isotope ratio. These findings represent a significant first step in leveraging the high resolution of the LS-APGD-Orbitrap-MS to overcome isobaric and molecular interferences instead of relying on chemical separations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
NASA NTRS2009

Rapid Monitoring of Bacteria and Fungi aboard the International Space Station (ISS)

Microorganisms within spacecraft have traditionally been monitored with culture-based techniques. These techniques involve growth of environmental samples (cabin water, air or surfaces) on agar-type media for several days, followed by visualization of resulting colonies or return of samples to Earth for ground-based analysis. Data obtained over the past 4 decades have enhanced our understanding of the microbial ecology within space stations. However, the approach has been limited by the following factors: i) Many microorganisms (estimated > 95%) in the environment cannot grow on conventional growth media; ii) Significant time lags (3-5 days for incubation and up to several months to return samples to ground); iii) Condensation in contact slides hinders colony counting by crew; and iv) Growth of potentially harmful microorganisms, which must then be disposed of safely. This report describes the operation of a new culture-independent technique onboard the ISS for rapid analysis (within minutes) of endotoxin and beta-1, 3-glucan, found in the cell walls of gramnegative bacteria and fungi, respectively. The technique involves analysis of environmental samples with the Limulus Amebocyte Lysate (LAL) assay in a handheld device, known as the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS). LOCADPTS was launched to the ISS in December 2006, and here we present data obtained from Mach 2007 until the present day. These data include a comparative study between LOCADPTS analysis and existing culture-based methods; and an exploratory survey of surface endotoxin and beta-1, 3-glucan throughout the ISS. While a general correlation between LOCAD-PTS and traditional culture-based methods should not be expected, we will suggest new requirements for microbial monitoring based upon culture-independent parameters measured by LOCAD-PTS.

Gunter, D.↗
NASA NTRS1999

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between results obtained with the ChemScan and traditional plate counts of mixed natural bacterial populations in water. The continuing evolution of these methods will be valuable in the rapid and accurate analysis of environmental samples.

Review, Tutorial↗
DOE OSTI2012

Microbial metaproteomics: Identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics - the characterization of the complement of proteins expressed by a microbial community in an environmental sample

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Isotopic Tracking of Hanford 300 Area Derived Uranium in the Columbia River

A portion of the subsurface contamination at the Hanford Site, the former plutonium production facility in Washington State, affects the Columbia River. A component of this contamination, uranium (U), has variable isotopic composition due to nuclear industrial processes carried out at the site. This characteristic makes it possible to use high-precision isotopic measurements of U in environmental samples to identify even trace levels of contaminant U, determine its sources, and estimate discharge rates. Our data on river water samples indicate that as much as 3.2 kg/day can enter the Columbia River from the 300 Area of the Hanford Site, which is only a small fraction of the total load of dissolved natural background U carried by the Columbia River. This very low–level contamination can be discerned, despite further dilution to <1% of natural background U, as far as 350 km downstream from the Hanford Site. These results indicate that isotopic methods can allow the amounts of U contamination from the Hanford Site to be measured accurately enough to ascertain where they are an environmental concern, and where they are insignificant.

Christensen, John N.↗
DOE OSTI2010

Acceptance sampling using judgmental and randomly selected samples

We present a Bayesian model for acceptance sampling where the population consists of two groups, each with different levels of risk of containing unacceptable items. Expert opinion, or judgment, may be required to distinguish between the high and low-risk groups. Hence, high-risk items are likely to be identifed (and sampled) using expert judgment, while the remaining low-risk items are sampled randomly. We focus on the situation where all observed samples must be acceptable. Consequently, the objective of the statistical inference is to quantify the probability that a large percentage of the unsampled items in the population are also acceptable. We demonstrate that traditional (frequentist) acceptance sampling and simpler Bayesian formulations of the problem are essentially special cases of the proposed model. We explore the properties of the model in detail, and discuss the conditions necessary to ensure that required samples sizes are non-decreasing function of the population size. The method is applicable to a variety of acceptance sampling problems, and, in particular, to environmental sampling where the objective is to demonstrate the safety of reoccupying a remediated facility that has been contaminated with a lethal agent.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate‐reducing bacterial lipids in cocultures and methane seeps

Abstract Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro‐organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate‐reducing bacteria ( SRB ) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane‐oxidizing archaea ( ANME ) and sulfate‐reducing Deltaproteobacteria ( SRB ) recovered from deep‐sea methane seeps. Consistent with previously reported trends, we observed a ~80‰ range in hydrogen isotope fractionation (ε lipid–water ) for D. multivorans grown under different carbon assimilation conditions, with more D‐enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of ε lipid – water values (~36‰) across substrates with shifts of up to 61‰ compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA ) showed similar D‐enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME / SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in ε lipid–water values.

Dawson, K. S.↗
DOE OSTI2013

Surface dust wipes are the best predictors of blood leads in young children with elevated blood lead levels

Background: As part of the only national survey of lead in Australian children, which was undertaken in 1996, lead isotopic and lead concentration measurements were obtained from children from 24 dwellings whose blood lead levels were ≥15 µg/dL in an attempt to determine the source(s) of their elevated blood lead. Comparisons were made with data for six children with lower blood lead levels (<10 µg/dL). Methods: Thermal ionisation and isotope dilution mass spectrometry were used to determine high precision lead isotopic ratios ({sup 208}Pb/{sup 206}Pb, {sup 207}Pb/{sup 206}Pb and {sup 206}Pb/{sup 204}Pb) and lead concentrations in blood, dust from floor wipes, soil, drinking water and paint (where available). Evaluation of associations between blood and the environmental samples was based on the analysis of individual cases, and Pearson correlations and multiple regression analyses based on the whole dataset. Results and discussion: The correlations showed an association for isotopic ratios in blood and wipes (r=0.52, 95% CI 0.19–0.74), blood and soil (r=0.33, 95% CI −0.05–0.62), and blood and paint (r=0.56, 95% CI 0.09–0.83). The regression analyses indicated that the only statistically significant relationship for blood isotopic ratios was with dust wipes (B=0.65, 95% CI 0.35–0.95); there were no significant associations for lead concentrations in blood and environmental samples. There is a strong isotopic correlation of soils and house dust (r=0.53, 95% CI 0.20–0.75) indicative of a common source(s) for lead in soil and house dust. In contrast, as with the regression analyses, no such association is present for bulk lead concentrations (r=−0.003, 95% CI −0.37–0.36), the most common approach employed in source investigations. In evaluation of the isotopic results on a case by case basis, the strongest associations were for dust wipes and blood. -- Highlights: • Children with elevated blood lead ≥15 µg/dL compared with a group with <10 µg/dL. • High precision lead isotopic ratios in blood, house dust wipes, soil, water, paint. • Associations for isotopic measures of blood and dust, blood and soil, blood and paint. • Regressions gave significance for isotopic measures of blood/dust and dust/soil.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2008

LOCAD-PTS: Operation of a New System for Microbial Monitoring Aboard the International Space Station (ISS)

Microorganisms within the space stations Salyut, Mir and the International Space Station (ISS), have traditionally been monitored with culture-based techniques. These techniques involve growing environmental samples (cabin water, air or surfaces) on agar-type media for several days, followed by visualization of resulting colonies; and return of samples to Earth for ground-based analysis. This approach has provided a wealth of useful data and enhanced our understanding of the microbial ecology within space stations. However, the approach is also limited by the following: i) More than 95% microorganisms in the environment cannot grow on conventional growth media; ii) Significant time lags occur between onboard sampling and colony visualization (3-5 days) and ground-based analysis (as long as several months); iii) Colonies are often difficult to visualize due to condensation within contact slide media plates; and iv) Techniques involve growth of potentially harmful microorganisms, which must then be disposed of safely. This report describes the operation of a new culture-independent technique onboard the ISS for rapid analysis (within minutes) of endotoxin and -1, 3-glucan, found in the cell walls of gram-negative bacteria and fungi, respectively. This technique involves analysis of environmental samples with the Limulus Amebocyte Lysate (LAL) assay in a handheld device. This handheld device and sampling system is known as the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS). A poster will be presented that describes a comparative study between LOCAD-PTS analysis and existing culture-based methods onboard the ISS; together with an exploratory survey of surface endotoxin throughout the ISS. It is concluded that while a general correlation between LOCAD-PTS and traditional culture-based methods should not necessarily be expected, a combinatorial approach can be adopted where both sets of data are used together to generate a more complete story of the microbial ecology on the ISS.

Maule, J.↗
DOE OSTI2024

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

X-ray absorption spectroscopy study of Mn reference compounds for Mn speciation in terrestrial surface environments

Abstract X-ray absorption spectroscopy (XAS) offers great potential to identify and quantify Mn species in surface environments by means of linear combination fit (LCF), fingerprint, and shell-fit analyses of bulk Mn XAS spectra. However, these approaches are complicated by the lack of a comprehensive and accessible spectrum library. Additionally, molecular-level information on Mn coordination in some potentially important Mn species occurring in soils and sediments is missing. Therefore, we investigated a suite of 32 natural and synthetic Mn reference compounds, including Mn oxide, oxyhydroxide, carbonate, phosphate, and silicate minerals, as well as organic and adsorbed Mn species, by Mn K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy. The ability of XAS to infer the average oxidation state (AOS) of Mn was assessed by comparing XANES-derived AOS with the AOS obtained from redox titrations. All reference compounds were studied for their local (<5 Å) Mn coordination environment using EXAFS shell-fit analysis. Statistical analyses were employed to clarify how well and to what extent individual Mn species (groups) can be distinguished by XAS based on spectral uniqueness. Our results show that LCF analysis of normalized XANES spectra can reliably quantify the Mn AOS within ~0.1 v.u. in the range +2 to +4. These spectra are diagnostic for most Mn species investigated, but unsuitable to identify and quantify members of the manganate and Mn(III)-oxyhydroxide groups. First-derivative XANES fingerprinting allows the unique identification of pyrolusite, ramsdellite, and potentially lithiophorite within the manganate group. However, XANES spectra of individual Mn compounds can vary significantly depending on chemical composition and/or crystallinity, which limits the accuracy of XANES-based speciation analyses. In contrast, EXAFS spectra provide a much better discriminatory power to identify and quantify Mn species. Principal component and cluster analyses of k2-weighted EXAFS spectra of Mn reference compounds implied that EXAFS LCF analysis of environmental samples can identify and quantify at least the following primary Mn species groups: (1) Phyllo- and tectomanganates with large tunnel sizes (2 × 2 and larger; hollandite sensu stricto, romanèchite, todorokite); (2) tectomanganates with small tunnel sizes (2 × 2 and smaller; cryptomelane, pyrolusite, ramsdellite); (3) Mn(III)-dominated species (nesosilicates, oxyhydroxides, organic compounds, spinels); (4) Mn(II) species (carbonate, phosphate, and phyllosilicate minerals, adsorbed and organic species); and (5) manganosite. All Mn compounds, except for members of the manganate group (excluding pyrolusite) and adsorbed Mn(II) species, exhibit unique EXAFS spectra that would allow their identification and quantification in mixtures. Therefore, our results highlight the potential of Mn K-edge EXAFS spectroscopy to assess bulk Mn speciation in soils and sediments. A complete XAS-based speciation analysis of bulk Mn in environmental samples should preferably include the determination of Mn valences following the “Combo” method of Manceau et al. (2012), EXAFS LCF analyses based on principal component and target transformation results, as well as EXAFS shell-fit analyses for the validation of LCF results. For this purpose, all 32 XAS reference spectra are provided in the Online Materials1 for further use by the scientific community.

Geochemistry & Geophysics↗