A Geomimetic Approach to the Formation and Identification of Fossil Sterane Biomarkers in Crude Oil: 18-nor-D-homo-Androstane and 5α,14ß-Androstane.

A diazonium ion derived from 18-aminoandrostane rearranged upon decomposition by a carbonium and a carbenium ion to furnish a mixture of a cyclopropanated compound and two D-homo-androstenes. Hydrogenation of this mixture gave the saturated hydrocarbons, 18-nor-D-homo-androstane and 5α,14ß-androstane, which are both fossil sterane biomarkers in Neoproterozoic crude oil. The so far unknown constitution and configuration as well as the geochemical genesis were established by this experiment. The starting material for this investigation, 18-aminoandrostane, was prepared in twelve steps from androstan-17-one (12.5% overall yield) with a Barton reaction as the key step.

Gammaproteobacteria as a possible source of eicosapentaenoic acid in anoxic intertidal sediments.

Eicosapentaenoic acid (EPA; n-20:5omega3) was found to be a constituent of phospholipids in three mesophilic strains of Gammaproteobacteria, which were isolated from anoxic most probable number series prepared with sediments from an intertidal flat of the German North Sea coast. Their partial 16S rRNA gene sequences identified the isolates as close relatives of Shewanella colwelliana, Vibrio splendidus, and Photobacterium lipolyticum. So far, eicosapentaenoic acid has mainly been reported to occur in eukaryotes and some piezophilic or psychrophilic bacteria. With decreasing temperature, relative contents of EPA (up to 14% of total fatty acids) increased in all strains. Additionally, Shewanella and Vibrio spp. showed a significant increase in monounsaturated fatty acids with lower growth temperature. Analysis of the phospholipid compositions revealed that EPA was present in all three major phospholipid types, namely, phosphatidyl glycerol (PG), cardiolipin and phosphatidyl ethanolamine (PE). However, EPA was enriched in PG and cardiolipin relative to PE. In the tidal flat sediments from which the isolates were obtained, substantial amounts of EPA-containing PG were detected, whereas other typical microeukaryotic phospholipids-being also a possible source of EPA-were abundant at the sediment surface but were present in clearly lower amounts in the anoxic layers beneath 5 cm depth. Therefore, the EPA-containing PG species in the deeper layers in these sediments may indicate the presence of Gammaproteobacteria closely related to the isolates. These bacteria appear to be an important source of EPA in buried, anoxic sediments beneath the layers harboring significant populations of benthic eukaryotes.

Lipid biomarkers, pigments and cyanobacterial diversity of microbial mats across intertidal flats of the arid coast of the Arabian Gulf (Abu Dhabi, UAE).

Variations in morphology, fatty acids, pigments and cyanobacterial community composition were studied in microbial mats across intertidal flats of the arid Arabian Gulf coast. These mats experience combined extreme conditions of salinity, temperature, UV radiation and desiccation depending on their tidal position. Different mat forms were observed depending on the topology of the coast and location. The mats contained 63 fatty acids in different proportions. The increased amounts of unsaturated fatty acids (12-39%) and the trans/cis ratio (0.6-1.6%) of the cyanobacterial fatty acid n-18:1omega9 in the higher tidal mats suggested an adaptation of the mat microorganisms to environmental stress. Chlorophyll a concentrations suggested lower cyanobacterial abundance in the higher than in the lower intertidal mats. Scytonemin concentrations were dependent on the increase in solar irradiation, salinity and desiccation. The mats showed richness in cyanobacterial species, with Microcoleus chthonoplastes and Lyngbya aestuarii morphotypes as the dominant cyanobacteria. Denaturing gradient gel electrophoresis patterns suggested shifts in the cyanobacterial community dependent on drainage efficiency and salinity from lower to higher tidal zones. We conclude that the topology of the coast and the variable extreme environmental conditions across the tidal flat determine the distribution of microbial mats as well as the presence or absence of different microorganisms.

Spore dipicolinic acid contents used for estimating the number of endospores in sediments.

Endospores are heat-resistant bacterial resting stages that can remain viable for long periods of time and may thus accumulate in sediments as a function of sediment age. The number of spores in sediments has only rarely been quantified, because of methodological problems, and consequently little is known about the quantitative contribution of endospores to the total number of prokaryotic cells. We here report on a protocol to determine the number of endospores in sediments and cultures. The method is based on the fluorimetric determination of dipicolinic acid (DPA), a spore core-specific compound, after reaction with terbium chloride. The concentration of DPA in natural samples is converted into endospore numbers using endospore-forming pure cultures as standards. Quenching of the fluorescence by sediment constituents and background fluorescence due to humic substances hampered direct determination of DPA in sediments. To overcome those interferences, DPA was extracted using ethyl acetate prior to fluorimetric measurements of DPA concentrations. The first results indicated that endospore numbers obtained with this method are orders of magnitude higher than numbers obtained by cultivation after pasteurization. In one of the explored sediment cores, endospores accounted for 3% of all stainable prokaryotic cells.

A highly sensitive HPLC method for determination of nanomolar concentrations of dipicolinic acid, a characteristic constituent of bacterial endospores.

A high-performance liquid chromatographic method with indirect fluorescence detection has been developed for quantification of dipicolinic acid, a major constituent of bacterial endospores. After separation on a reversed-phase column, a post-column reagent of sodium acetate at 1 mol l(-1) with 50 micromol l(-1) terbium chloride was added for complexation of dipicolinic acid. Terbium monodipicolinate complexes formed were quantified by measuring the fluorescence emission maximum at 548 nm after excitation with UV light at 270 nm wavelength. Parameters of post-column complexation were optimized to achieve a detection limit of 0.5 nmol DPA l(-1), corresponding to about 10(3) Desulfosporosinus orientis endospores per ml. The method was applied to the analysis of spore contamination in tuna and for estimating the endospore numbers in marine sediments.

Temperature and pressure adaptation of a sulfate reducer from the deep subsurface.

Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.

Phospholipid analysis as a tool to study complex microbial communities in marine sediments.

To complement information on microbial communities in marine sediments that can be obtained using microbiological methods, we developed an analytical procedure to trace microbial lipids in environmental samples. We focused on analyzing intact phospholipids as these membrane constituents are known to be biomarkers for viable cells. Analysis of intact phospholipids from a fractionated and preconcentrated sediment extract was achieved using liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS). The combined analysis of phospholipid types and their fatty acid substituents allowed a differentiation between various groups of microorganisms living in the sediment. For comparison three strains of marine sulfate-reducing bacteria (SRB) were analysed for their lipid content.

Consistent assessment of trace metal contamination in surface sediments and suspended particulate matter: a case study from the Jade Bay in NW Germany.

Recently, within the framework of European directives, the importance of marine monitoring programs has increased. In this study, a dense sampling grid was applied for a detailed assessment of the metal contents of surface sediments and suspended particulate matter from the Jade Bay, one of the tidal basins in the southern North Sea. The local lithogenic background was defined and compared with average shale, a common reference material. Based on the calculated non-lithogenic fraction and a cluster analysis, the metals are distributed in two groups: (i) elements of mainly natural origin (Co, Cr, and a major portion of Cd) and (ii) elements associated with anthropogenic activity (As, Cd, Cu, Ni, Pb, Sn, and Zn). However, even the metals of the second group are enriched by at most a factor of two relative to the local background, suggesting minimal anthropogenic impact. Spatial distribution maps show that the harbor area of Wilhelmshaven may be a particularly important source of metal.

Method validation of a survey of thevetia cardiac glycosides in serum samples.

A sensitive and specific liquid chromatography tandem mass spectrometry (HPLC-ESI(+)-MS/MS) procedure was developed and validated for the identification and quantification of thevetin B and further cardiac glycosides in human serum. The seeds of Yellow Oleander (Thevetia peruviana) contain cardiac glycosides that can cause serious intoxication. A mixture of six thevetia glycosides was extracted from these seeds and characterized. Thevetin B, isolated and efficiently purified from that mixture, is the main component and can be used as evidence. Solid phase extraction (SPE) proved to be an effective sample preparation method. Digoxin-d3 was used as the internal standard. Although ion suppression occurs, the limit of detection (LOD) is 0.27 ng/ml serum for thevetin B. Recovery is higher than 94%, and accuracy and precision were proficient. Method refinement was carried out with regard to developing a general screening method for cardiac glycosides. The assay is linear over the range of 0.5-8 ng/ml serum. Finally, the method was applied to a case of thevetia seed ingestion.

Cardiac glycosides from Yellow Oleander (Thevetia peruviana) seeds.

Thevetia cardiac glycosides can lead to intoxication, thus they are important indicators for forensic and pharmacologic surveys. Six thevetia cardiac glycosides, including two with unknown structures, were isolated from the seeds of the Yellow Oleander (Thevetia peruviana (Pers.) K. Shum., Apocynaceae). LC-ESI⁺-MS(/MS) analysis under high-resolution conditions used as a qualitative survey of the primary glycosides did not lead to fragmentation of the aglycones. Acid hydrolysis of the polar and non-volatile thevetia glycosides under severe conditions yielded the aglycones of the thevetia glycosides and made them amenable to GC-MS analysis. Comparison of mass spectral fragmentation patterns of the aglycones, as well as high-resolution mass spectrometric and NMR data of four of the primary thevetia glycosides including the two unknowns, revealed the structures of the complete set of six thevetia glycosides. The identified compounds are termed thevetin C and acetylthevetin C and differ by an 18,20-oxido-20,22-dihydro functionality from thevetin B and acetylthevetin B, respectively. The absence of an unsaturated lactone ring renders the glycosides cardio-inactive. The procedures developed in this study and the sets of analytical data obtained will be useful for screening and structure assessment of other, particularly polar, cardiac glycosides.

Alkylated phenol series in lacustrine black shales from the Nördlinger Ries, southern Germany.

Several series of alkylated phenols were detected for the first time in the extractable bitumens of organic matter-rich sediments from the Nördlinger Ries (southern Germany). Most abundant and significant constituents comprise those with n-octadecyl, n-eicosanyl, phytanyl, and iso-pentadecyl and anteiso-pentadecyl substituents. The structures of these compounds are suggested from mass spectrometric and retention time data and coinjection with synthetic standards. Diagenetic alteration of phenolic algal lipids is suggested as a possible way to the formation of these compounds in the Nördlinger Ries sediments.

Mycosporine-glutamicol-glucoside: a natural UV-absorbing secondary metabolite of rock-inhabiting microcolonial fungi.

Microcolonial ascomycetes are known to inhabit bare rock surfaces in cold and hot deserts and thus are habitually exposed to high levels of solar radiation. Several of these stress-tolerant fungal isolates, cultivated in the laboratory under daylight illumination, were studied for the presence of effective UV-radiation protection substances. Liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses allowed for efficient separation and structure clarification of two mycosporines. It was demonstrated that both mycosporine-glutamicol-glucoside and mycosporine-glutaminol-glucoside are natural and constitutive secondary metabolites of microcolonial fungi. The function and relation of these substances in the fungal cell are discussed.

Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds.

We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. Phormidium- and Oscillatoria-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the Cytophaga-Flavobacterium-Bacteriodes group, the gamma and beta subclasses of the class Proteobacteria, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark. n-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with Halomicronema. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described Holophaga-Geothrix-Acidobacterium phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential.