James J. Moran

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2−4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.

Characterization of Diesel Fuel by Chemical Separation Combined with Capillary Gas Chromatography (GC) Isotope Ratio Mass Spectrometry (IRMS)

The purpose of this study was to perform a preliminary investigation of compound-specific isotope analysis (CSIA) of diesel fuels to evaluate whether the technique could distinguish diesel samples from different sources/locations. The ability to differentiate or correlate diesel samples could be valuable for discovering fuel tax evasion schemes or for environmental forensic studies. Two urea adduction-based techniques were used to isolate the n-alkanes from the fuel. Both carbon isotope ratio (δ(13)C) and hydrogen isotope ratio (δD) values for the n-alkanes were then determined by CSIA in each sample. The samples investigated had δ(13)C values that ranged from -30.1‰ to -26.8‰, whereas δD values ranged from -83‰ to -156‰. Plots of δD versus δ(13)C with sample n-alkane points connected in order of increasing carbon number gave well-separated clusters with characteristic shapes for each sample. Principal components analysis (PCA) with δ(13)C, δD, or combined δ(13)C and δD data was applied to extract the maximum information content. PCA scores plots could clearly differentiate the samples, thereby demonstrating the potential of this approach for distinguishing (e.g., fingerprinting) fuel samples using δ(13)C and δD values.

Laser ablation isotope ratio mass spectrometry for enhanced sensitivity and spatial resolution in stable isotope analysis

Stable isotope analysis permits the tracking of physical, chemical, and biological reactions and source materials at a wide variety of spatial scales. We present a laser ablation isotope ratio mass spectrometry (LA-IRMS) method that enables δ(13)C measurement of solid samples at 50 µm spatial resolution. The method does not require sample pre-treatment to physically separate spatial zones. We use laser ablation of solid samples followed by quantitative combustion of the ablated particulates to convert sample carbon into CO(2). Cryofocusing of the resulting CO(2) coupled with modulation in the carrier flow rate permits coherent peak introduction into an isotope ratio mass spectrometer, with only 65 ng carbon required per measurement. We conclusively demonstrate that the measured CO(2) is produced by combustion of laser-ablated aerosols from the sample surface. We measured δ(13)C for a series of solid compounds using laser ablation and traditional solid sample analysis techniques. Both techniques produced consistent isotopic results but the laser ablation method required over two orders of magnitude less sample. We demonstrated that LA-IRMS sensitivity coupled with its 50 µm spatial resolution could be used to measure δ(13) C values along a length of hair, making multiple sample measurements over distances corresponding to a single days growth. This method will be highly valuable in cases where the δ(13)C analysis of small samples over prescribed spatial distances is required. Suitable applications include forensic analysis of hair samples, investigations of tightly woven microbial systems, and cases of surface analysis where there is a sharp delineation between different components of a sample.

Stable Carbon and Nitrogen Isotope Ratios of Sodium and Potassium Cyanide as a Forensic Signature

Abstract:  Sodium and potassium cyanide are highly toxic, produced in large amounts by the chemical industry, and linked to numerous high‐profile crimes. The U.S. Centers for Disease Control and Prevention has identified cyanide as one of the most probable agents to be used in a chemical terrorism event. We investigated whether stable C and N isotopic content of sodium and potassium cyanide could serve as a forensic signature for sample matching, using a collection of 65 cyanide samples. Upon analysis, a few of the cyanide samples displayed nonhomogeneous isotopic content associated with degradation to a carbonate salt and loss of hydrogen cyanide. Most samples had highly reproducible isotope content. Of the 65 cyanide samples, >95% could be properly matched based on C and N isotope ratios, with a false match rate <3%. These results suggest that stable C and N isotope ratios are a useful forensic signature for matching cyanide samples.

Analysis of carbohydrate and fatty acid marker abundance in ricin toxin preparations for forensic information.

One challenge in the forensic analysis of ricin samples is determining the method and extent of sample preparation. Ricin purification from the source castor seeds is essentially a protein purification through removal of the nonprotein fractions of the seed. Two major, nonprotein constituents in the seed are the castor oil and carbohydrates. We used derivatization of carbohydrate and fatty acid markers followed by identification and quantification using gas chromatography/mass spectrometry (GC/MS) to assess compositional changes in ricin samples purified by different methods. The loss of ricinoleic acid indicated steps for oil removal had occurred, and a large decrease of ricinoleic acid was observed between unextracted mash and solvent extracted and protein precipitate preparations. Changes to the carbohydrate content of the sample were also observed following protein precipitation. The differential loss of arabinose relative to mannose was observed indicating the removal of the major carbohydrate fraction of the seed and enrichment of the protein content. When the data is combined and multivariate principle component analysis is applied, these changes in fatty acid and carbohydrate abundance are discriminating enough to be indicative of the preparation method used for each sample.

Spatially tracking 13C‐labelled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry

Microbial mats are characterized by extensive metabolic interactions, rapidly changing internal geochemical gradients, and prevalent microenvironments within tightly constrained physical structures. We present laser ablation isotope ratio mass spectrometry (LA-IRMS) as a culture-independent, spatially specific technology for tracking the accumulation of (13) C-labelled substrate into heterogeneous microbial mat communities. This study demonstrates the novel LA-IRMS approach by tracking labeled bicarbonate incorporation into a cyanobacteria-dominated microbial mat system. The spatial resolution of 50 μm was sufficient for distinguishing different mat strata and the approach effectively identified regions of greatest label incorporation. Sample preparation for LA-IRMS is straightforward and the spatial selectivity of LA-IRMS minimizes the volume of mat consumed, leaving material for complimentary analyses. We present analysis of DNA extracted from a sample post-ablation and suggest pigments, lipids or other biomarkers could similarly be extracted following ablation. LA-IRMS is well positioned to spatially resolve the accumulation of any (13) C-labelled substrate provided to a mat, making this a versatile tool for studying carbon transfer and interspecies exchanges within the limited spatial confines of such systems.

A capillary absorption spectrometer for stable carbon isotope ratio (13C/12C) analysis in very small samples

A capillary absorption spectrometer (CAS) suitable for IR laser isotope analysis of small CO(2) samples is presented. The system employs a continuous-wave (cw) quantum cascade laser to study nearly adjacent rovibrational transitions of different isotopologues of CO(2) near 2307 cm(-1) (4.34 μm). This initial CAS system can achieve relative isotopic precision of about 10 ppm (13)C, or ∼1 per thousand (per mil in delta notation relative to Vienna Pee Dee Belemnite) with 20-100 picomoles of entrained sample within the hollow waveguide for CO(2) concentrations ∼400-750 ppm. Isotopic analyses of such gas fills in a 1-mm ID hollow waveguide of 0.8 m overall physical path length can be carried out down to ∼2 Torr. Overall (13)C∕(12)C ratios can be calibrated to ∼2 per thousand accuracy with diluted CO(2) standards. A novel, low-cost method to reduce cw-fringing noise resulting from multipath distortions in the hollow waveguide is presented, which allows weak absorbance features to be studied at the few ppm level (peak-to-rms) after 1000 scans are co-added in ∼10 s. The CAS is meant to work directly with converted CO(2) samples from a laser ablation-catalytic combustion micro-sampler to provide (13)C∕(12)C ratios of small biological isolates currently operating with spatial resolutions ∼50 μm.

Trade-offs between microbiome diversity and productivity in a stratified microbial mat

Productivity is a major determinant of ecosystem diversity. Microbial ecosystems are the most diverse on the planet yet very few relationships between diversity and productivity have been reported as compared with macro-ecological studies. Here we evaluated the spatial relationships of productivity and microbiome diversity in a laboratory-cultivated photosynthetic mat. The goal was to determine how spatial diversification of microorganisms drives localized carbon and energy acquisition rates. We measured sub-millimeter depth profiles of net primary productivity and gross oxygenic photosynthesis in the context of the localized microenvironment and community structure, and observed negative correlations between species richness and productivity within the energy-replete, photic zone. Variations between localized community structures were associated with distinct taxa as well as environmental profiles describing a continuum of biological niches. Spatial regions in the photic zone corresponding to high primary productivity and photosynthesis rates had relatively low-species richness and high evenness. Hence, this system exhibited negative species–productivity and species–energy relationships. These negative relationships may be indicative of stratified, light-driven microbial ecosystems that are able to be the most productive with a relatively smaller, even distributions of species that specialize within photic zones.

Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat

Abstract Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms; however, little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity and metabolic gradient measurements. Draft reconstructed genomes of 34 abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence on metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.

Contributions of the [NiFe]- and [FeFe]-hydrogenase to H2 production in Shewanella oneidensis MR-1 as revealed by isotope ratio analysis of evolved H2

Shewanella oneidensis MR-1 encodes both a [NiFe]- and an [FeFe]-hydrogenase. While the output of these proteins has been characterized in mutant strains expressing only one of the enzymes, the contribution of each to H2 synthesis in the wild-type organism is not clear. Here, we use stable isotope analysis of H2 in the culture headspace, along with transcription data and measurements of the concentrations of gases in the headspace, to characterize H2 production in the wild-type strain. After most of the O2 in the headspace had been consumed, H2 was produced and then consumed by the bidirectional [NiFe]-hydrogenase. Once the cultures were completely anaerobic, a new burst of H2 synthesis catalyzed by both enzymes took place. Our data are consistent with the hypothesis that at this point in the culture cycle, a pool of electrons is shunted toward both hydrogenases in the wild-type organisms, but that in the absence of one of the hydrogenases, the flux is redirected to the available enzyme. To our knowledge, this is the first use of natural-abundance stable isotope analysis of a metabolic product to elucidate substrate flux through two alternative enzymes in the same cellular system.