Jan Sunner

Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.

On the mechanism of laser-induced desorption–ionization of organic compounds from etched silicon and carbon surfaces

The laser-induced desorption/ionization of organic compounds from etched carbon and silicon substrate surfaces was investigated. Two different etching procedures were used. Silicon surfaces were etched either by galvanostatic anodization to produce porous silicon or by a hyperthermal (∼5 eV) F-atom beam to produce nonporous silicon. Atomic force microscopy (AFM) images showed that both etching procedures yielded surfaces with sub-micrometer structures. Highly oriented pyrolytic graphite was etched with hyperthermal O atoms. A 337 nm ultraviolet (UV) laser and a 3.28 μm infrared (IR) laser were used for desorption. Analytes were deposited on the substrates either from the liquid or the gas phase. Mass spectra were obtained provided that three conditions were fulfilled. First, sufficient laser light had to be absorbed. When the IR laser was employed, a thin physisorbed solvent layer was required for sufficient laser light absorption to occur. Though the required fluence of IR and UV light differed by a fact...

An activated carbon substrate surface for laser desorption mass spectrometry

A method to obtain laser desorption/ionization mass spectra of organic compounds by depositing sample solutions onto a carbon substrate surface is demonstrated. The substrate consists of a thin layer of activated carbon particles immobilized on an aluminum support. In common with the porous carbon suspension samples used in previous “surface-assisted laser desorption/ionization” (SALDI) work, the mass spectra contain only a few “matrix” background ion peaks, minimizing interference with analyte ion peaks. The presence of glycerol ensured that the ion signals were stable over hundreds of laser shots. In addition, the carbon substrate surface has several advantages over the suspension samples. The use of a very thin layer of carbon significantly improves the sensitivity. Detection limits range from attomoles for crystal violet to femtomoles for bradykinin. Very little sample preparation is required as the analyte solution is simply pipetted onto the substrate surface and glycerol added. When using an alternate sample deposition method, a mass resolution for bradykinin of 1800 is achieved in linear time-of-flight mode. This is close to the resolution limit set by the detector system and above instrument specification for matrix-assisted laser desorption/ionization mass spectra.

IDENTIFICATION OF A LIGAND BINDING SITE IN THE HUMAN NEUTROPHIL FORMYL PEPTIDE RECEPTOR USING A SITE-SPECIFIC FLUORESCENT PHOTOAFFINITY LABEL AND MASS SPECTROMETRY

A novel fluorescent photoaffinity cross-linking probe, formyl-Met-p-benzoyl-l-phenylalanine-Phe-Tyr-Lys-ε-N-fluorescein (fMBpaFYK-fl), was synthesized and used to identify binding site residues in recombinant human phagocyte chemoattractant formyl peptide receptor (FPR). After photoactivation, fluorescein-labeled membranes from Chinese hamster ovary cells were solubilized in octylglucoside and separated by tandem anion exchange and gel filtration chromatography. A single peak of fluorescence was observed in extracts of FPR-expressing cells that was absent in extracts from wild type controls. Photolabeled Chinese hamster ovary membranes were cleaved with CNBr, and the fluorescent fragments were isolated on an antifluorescein immunoaffinity matrix. Matrix-assisted laser desorption ionization mass spectrometry identified a major species with mass = 1754, consistent with the CNBr fragment of fMBpaFYK-fl cross-linked to Val-Arg-Lys-Ala-Hse (an expected CNBr fragment of FPR, residues 83–87). This peptide was further cleaved with trypsin, repurified by antifluorescein immunoaffinity, and subjected to matrix-assisted laser desorption ionization mass spectrometry. A tryptic fragment with mass = 1582 was observed, which is the mass of fMBpaFYK-fl cross-linked to Val-Arg-Lys (FPR residues 83–85), an expected trypsin cleavage product of Val-Arg-Lys-Ala-Hse. Residues 83–85 lie within the putative second transmembrane-spanning region of FPR near the extracellular surface. A 3D model of FPR is presented, which accounts for intramembrane, site-directed mutagenesis results (Miettinen, H. M., Mills, J., Gripentrog, J., Dratz, E. A., Granger, B. L., and Jesaitis, A. J. (1997) J. Immunol.159, 4045–4054) and the photochemical cross-linking data.

Infrared, surface-assisted laser desorption ionization mass spectrometry on frozen aqueous solutions of proteins and peptides using suspensions of organic solids.

Surface-assisted, laser desorption ionization (SALDI) time-of-flight mass spectra of proteins and peptides have been obtained from bulk frozen aqueous solutions by adding solid organic powders to the solutions before freezing. Abundant analyte ions were obtained with a 3.28 µm Nd:YAG/OPO laser. 20 compounds were evaluated as solid additives, and 16 yielded protein mass spectra. Successful solids included compounds like pyrene, aspartic acid, and polystyrene. The best results were obtained with nicotinic acid and indole-2-carboxylic acid, which yielded protein mass spectra anywhere on the sample and with every laser shot. Compared with ultraviolet-matrix-assisted laser desorption ionization on the same instrument, cryo-IR-SALDI had a comparable detection limit (≈1 µM), a lower mass resolution for peptides, and a higher mass resolution for large proteins. Approximately 2500 cryo-IR-SALDI mass spectra were obtained from a single spot on a 0.3-mm-thick frozen sample before the metal surface was reached. About 0.1 nL of frozen solution was desorbed per laser shot. The extent of protein charging varied between the SALDI solids used. With thymine, myoglobin charge states up to MH12+12 were observed. It is tentatively concluded that observed ions are preformed in the frozen sample.

Mechanism of formation of FAB spectra

Abstract Recent experimental and interpretative work by the authors on the mechanism of formation of FAB spectra is reviewed and a physical picture of the desorption ionization event is presented. The collision cascade causes extensive ionization in the matrix and induces a transition from the liquid to a gas-like state. The extensive ion/molecule reactions that occur in this “gas” are governed by gas phase and not liquid phase energetics. As expected for a gas, extensive positive ion/negative ion recombination takes place, and only a small fraction of the ions survives into the vacuum. FAB spectra of diethanolamine (DEA) solutions of various concentrations in glycerol are successfully reproduced with a kinetic model based on high pressure ion/molecule reactions. There is a wide distribution of “residence times” for the ions in the “gas”, and ions with longer residence times have lower internal excitation energies. A model for the desorption process, the Phase Explosion model, that uses classical thermodynamics as a guide to the desorption process offers explanations for most of the experimental observations.

Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces

Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed ‘cookies,’ revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted.

Space-charge-dominated mass spectrometry ion sources: Modeling and sensitivity

The factors determining the sensitivity of space-charge-dominated (SCD) unipolar ion sources, such as electrospray (ESP) and corona atmospheric pressure ionization (API) have been studied theoretically. The most important parameters are the ion density and ion drift time in the vicinity of the sampling orifice. These are obtained by solving a system of differential equations, “the space-charge problem.” For some simple geometries, analytical solutions are known. For a more realistic “needle-in-can” geometry, a solution to the space-charge problem was obtained using a finite-element method. The results illustrate some general characteristics of SCD ion sources. It is shown that for typical operating conditions the minimum voltage required to overcome the space-charge effect in corona API or ESP ion sources constitutes a dominant or significant fraction of total applied voltage. Further, the electric field and the ion density in the region of the ion-sampling orifice as well as the ion residence time in the source are determined mainly by the space charge. Finally, absolute sensitivities of corona API ion sources were calculated by using a geometry-independent treatment of space charge.

Rapid determination of trace nitrophenolic organics in water by combining solid-phase extraction with surface-assisted laser desorption/ionization time-of-flight mass spectrometry

A rapid technique for the screening of trace compounds in water by combining solid-phase extraction (SPE) with activated carbon surface-assisted laser desorption/ionization (SALDI) time-of-flight mass spectrometry is demonstrated. Activated carbon is used both as the sorbent in SPE and as the solid in the SALDI matrix system. This eliminates the need for an SPE elution process. After the analytes have been adsorbed on the surfaces of the activated carbon during SPE extraction, the activated carbon is directly mixed with the SALDI liquid and mass spectrometric analysis is performed. Trace phenolic compounds in water were used to demonstrate the effectiveness of the method. The detection limit for these compounds is in the ppb to ppt range.

Metabolomic and high-throughput sequencing analysis—modern approach for the assessment of biodeterioration of materials from historic buildings

Preservation of cultural heritage is of paramount importance worldwide. Microbial colonization of construction materials, such as wood, brick, mortar, and stone in historic buildings can lead to severe deterioration. The aim of the present study was to give modern insight into the phylogenetic diversity and activated metabolic pathways of microbial communities colonized historic objects located in the former Auschwitz II–Birkenau concentration and extermination camp in Oświecim, Poland. For this purpose we combined molecular, microscopic and chemical methods. Selected specimens were examined using Field Emission Scanning Electron Microscopy (FESEM), metabolomic analysis and high-throughput Illumina sequencing. FESEM imaging revealed the presence of complex microbial communities comprising diatoms, fungi and bacteria, mainly cyanobacteria and actinobacteria, on sample surfaces. Microbial diversity of brick specimens appeared higher than that of the wood and was dominated by algae and cyanobacteria, while wood was mainly colonized by fungi. DNA sequences documented the presence of 15 bacterial phyla representing 99 genera including Halomonas, Halorhodospira, Salinisphaera, Salinibacterium, Rubrobacter, Streptomyces, Arthrobacter and nine fungal classes represented by 113 genera including Cladosporium, Acremonium, Alternaria, Engyodontium, Penicillium, Rhizopus, and Aureobasidium. Most of the identified sequences were characteristic of organisms implicated in deterioration of wood and brick. Metabolomic data indicated the activation of numerous metabolic pathways, including those regulating the production of primary and secondary metabolites, for example, metabolites associated with the production of antibiotics, organic acids and deterioration of organic compounds. The study demonstrated that a combination of electron microscopy imaging with metabolomic and genomic techniques allows to link the phylogenetic information and metabolic profiles of microbial communities and to shed new light on biodeterioration processes.