Correction of H3+ contributions in hydrogen isotope ratio monitoring mass spectrometry

Protocols for sample preparation and compound-specific stable-isotope analyses (δ2H, δ13C) of fatty acids in biological and environmental samples

Compound-specific stable-isotope analysis (CSIA) of fatty acids is a powerful tool to better understand the trophic transfer of fatty acids and their biochemical fate in and across ecosystems, including tracing animal migration and understanding physiological processes. The non-exchangeable nature of C-H bonds in acyl chains, hydrogen (δ2H) and carbon (δ13C) stable-isotope values of fatty acids (FA) provide independent information about the origins of fatty acids. Several technical obstacles must be overcome to ensure accurate and reproducible measurements of FA-CSIA can be made. This protocol describes the sample preparation process for successful stable-isotope analyses of fatty acids obtained from environmental and biological samples. Numerous techniques for the preanalytical processing of fatty acid samples are available, and these often have minimal impact on δ values. Here, we provide an in-depth guide detailing our well-established laboratory protocols, ranging from the initial sample preparation, lipid extraction, and transmethylation to the instrumental arrangement, data collection, and analysis.•Protocol from obtaining a sample to standardized fatty acid specific δ2H and δ13C values.•Separate GC analysis procedures for C and H are recommended for optimal performance.

Metabolic exchange between pathways for isoprenoid synthesis and implications for biosynthetic hydrogen isotope fractionation

Hydrogen isotope ratios of plant lipids are used for paleoclimate reconstruction, but are influenced by both source water and biosynthetic processes. Measuring ² H : ¹ H ratios of multiple compounds produced by different pathways could allow these effects to be separated, but hydrogen isotope fractionations during isoprenoid biosynthesis remain poorly constrained. To investigate how hydrogen isotope fractionation during isoprenoid biosynthesis is influenced by molecular exchange between the cytosolic and plastidial production pathways, we paired position-specific ¹³ C-pyruvate labeling with hydrogen isotope measurements of lipids in Pachira aquatica saplings. We find that acetogenic compounds primarily incorporated carbon from ¹³ C2-pyruvate, whereas isoprenoids incorporated ¹³ C1- and ¹³ C2-pyruvate equally. This indicates that cytosolic pyruvate is primarily introduced into plastidial isoprenoids via glyceraldehyde 3-phosphate and that plastidial isoprenoid intermediates are incorporated into cytosolic isoprenoids. Probably as a result of the large differences in hydrogen isotope fractionation between plastidial and cytosolic isoprenoid pathways, sterols from P. aquatica are at least 50‰ less ² H-enriched relative to phytol than sterols in other plants. These results provide the first experimental evidence that incorporation of plastidial intermediates reduces ² H : ¹ H ratios of sterols. This suggests that relative offsets between the ² H : ¹ H ratios of sterols and phytol can trace exchange between the two isoprenoid synthesis pathways.

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea

Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post-depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern-day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high-resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.

Carbon and hydrogen isotopic compositions of n-alkanes as a tool in petroleum exploration

Compound-specific isotope analysis (CSIA) of individual organic compounds is a powerful but underutilized tool in petroleum exploration. When integrated with other organic geochemical methodologies it can provide evidence of fluid histories including source, maturity, charge history and reservoir processes that can support field development planning and exploration efforts. The purpose of this chapter is to provide a review of the methodologies used for generating carbon and hydrogen isotope data for mid- and high-molecular-weight n-alkanes.

We discuss the factors that control stable carbon and hydrogen isotope compositions of n-alkanes and related compounds in sedimentary and petroleum systems and review current and future applications of this methodology for petroleum exploration. We discuss basin-specific case studies that demonstrate the usefulness of CSIA either when addressing particular aspects of petroleum exploration (e.g. charge evaluation, source rock–oil correlation, and investigation of maturity and in-reservoir processes) or when this technique is used to corroborate interpretations from integrated petroleum systems analysis, providing unique insights which may not be revealed when using other methods. CSIA of n-alkanes and related n-alkyl structures can provide independent data to strengthen petroleum systems concepts from generation and expulsion of fluids from source rock, to charge history, connectivity, and in-reservoir processes.

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

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.

An enhanced technique for automated determination of 15N signatures of N2, (N2 +N2O) and N2O in gas samples

RATIONALE

An enhanced analytical approach for analyzing gaseous products from (15)N-enriched pools has been developed. This technique can be used to quantify nitrous oxide (N2O) and dinitrogen (N2) fluxes from denitrification. It can also help in distinguishing different N2- and N2O-forming processes, such as denitrification, nitrification, anaerobic ammonium oxidation or co-denitrification.

METHODS

The measurement instrumentation was based on a commercially available automatic preparation system allowing collection and separation of gaseous samples. The sample transfer paths, valves, liquid nitrogen traps, gas chromatography column and open split of the original system were modified. A reduction oven (Cu) was added in order to eliminate oxygen and measure N2O-N as N2. Gases leaving the separation system entered an isotope ratio mass spectrometer where masses (28)N2, (29)N2 and (30)N2 were measured.

RESULTS

The enhanced technique enabled rapid simultaneous measurement of stable isotope ratios (29)N2/(28)N2 and (30)N2/(28)N2 originating from dinitrogen alone (N2) and from the sum of the denitrification products (N2 +N2O) as well as the determination of (15)N enrichment in N2O. The (15)N fraction in the N pool undergoing N2 and N2O production ((15)X(N)) and the contribution of N2 and N2O originating from this pool (d) were determined with satisfactory accuracy of better than 3.3% and 2.9%, respectively.

CONCLUSIONS

The precision and accuracy of this method were comparable with or better than previously reported for similar measurements. The proposed method allows for the analysis of all quantities within one run, thus reducing the measurement and sample preparation time as well as increasing the reliability of the results.

Variation of compound-specific hydrogen isotope ratios under changing temperature program in gas chromatography/thermal conversion/isotope ratio mass spectrometry

RATIONALE

In recent experiments, we found that compound-specific δ(2)H values can vary as a result of changing the gas chromatography temperature program under common pyrolysis conditions. To achieve better precision, it is necessary to examine the details and find a solution to this problem when using gas chromatography/thermal conversion/isotope ratio mass spectrometry (GC-TC-IRMS) for hydrogen isotope analysis.

METHODS

A test was designed to find the possible temperature effect under four different GC temperature ramp rates using n-alkanes (n-C(21), n-C(27), and n-C(31)) and fatty acids (n-C(12), n-C(18), and n-C(24)). The common 'hexane' method was used initially to condition the pyrolysis reactor. Experiments were then carried out using the 'methane condition' method because it was considered to improve pyrolysis efficiency.

RESULTS

Under the 'hexane condition' the measured hydrogen isotope ratios of the n-alkanes and n-fatty acids became more positive with increasing GC temperature ramp rate. The ion current intensity of hydrogen also generally increased. However, when the 'methane condition' method was used, the measured δ(2)H values of the n-alkanes and n-fatty acids showed little change under different GC temperature ramp rates.

CONCLUSIONS

Higher pyrolysis efficiency could reduce the tailing of the H(2) peak and the related isotopic variations at increased GC temperature ramp rates. In addition, too slow a temperature ramp rate could broaden the peak width and thus increase the background effect and possible isotopic fractionations in the split interface; this could also influence the hydrogen isotope values. We therefore suggest that the appropriate temperature ramp rate is an important factor in improving the precision in analyzing compound-specific hydrogen isotopes.

A gas chromatography/pyrolysis/isotope ratio mass spectrometry system for high-precision deltaD measurements of atmospheric methane extracted from ice cores

Air enclosures in polar ice cores represent the only direct paleoatmospheric archive. Analysis of the entrapped air provides clues to the climate system of the past in decadal to centennial resolution. A wealth of information has been gained from measurements of concentrations of greenhouse gases; however, little is known about their isotopic composition. In particular, stable isotopologues (deltaD and delta(13)C) of methane (CH(4)) record valuable information on its global cycle as the different sources exhibit distinct carbon and hydrogen isotopic composition. However, CH(4) isotope analysis is limited by the large sample size required and the demanding analysis as high precision is required. Here we present a highly automated, high-precision online gas chromatography/pyrolysis/isotope ratio monitoring mass spectrometry (GC/P/irmMS) technique for the analysis of deltaD(CH(4)). It includes gas extraction from ice, preconcentration, gas chromatographic separation and pyrolysis of CH(4) from roughly 500 g of ice with CH(4) concentrations as low as 350 ppbv. Ice samples with approximately 40 mL air and only approximately 1 nmol CH(4) can be measured with a precision of 3.4 per thousand. The precision for 65 mL air samples with recent atmospheric concentration is 1.5 per thousand. The CH(4) concentration can be obtained along with isotope data which is crucial for reporting ice core data on matched time scales and enables us to detect flaws in the measurement procedure. Custom-made script-based processing of MS raw and peak data enhance the system's performance with respect to stability, peak size dependency, hence precision and accuracy and last but not least time requirement.

Carbon and hydrogen isotope fractionation of benzene during biodegradation under sulfate-reducing conditions: a laboratory to field site approach

The microbial carbon and hydrogen isotope fractionation of benzene under sulfate-reducing conditions was investigated within systems of increasing complexity: (i) batch laboratory microcosms, (ii) a groundwater-percolated column system, and (iii) an aquifer transect. Recent molecular biological studies indicate that, at least in the laboratory microcosms and the column system, benzene is degraded by similar bacterial communities. Carbon and hydrogen enrichment factors (epsilon(C), epsilon(H)) obtained from laboratory microcosms and from the column study varied significantly although experiments were performed under similar redox and temperature conditions. Thus, enrichment factors for only a single element could not be used to distinguish benzene degradation under sulfate-reducing conditions from other redox conditions. In contrast, using correlation of changes of hydrogen vs. carbon isotope ratios (Lambda = Delta delta(2)H/Delta delta(13)C), similar Lambda-values were derived for the benzene biodegradation under sulfate-reducing conditions in all three experimental systems (Lambda(laboratory microcosms) = 23 +/- 5, Lambda(column) = 28 +/- 3, Lambda(aquifer) = 24 +/- 2), showing the robustness of the two-dimensional compound-specific stable isotope analysis (2D-CSIA) for elucidating distinct biodegradation pathways. Comparing carbon and hydrogen isotope fractionation data from recent studies, an overlap in Lambda-values was observed for benzene biodegradation under sulfate-reducing (Lambda = 23 +/- 5 to Lambda = 29 +/- 3) and methanogenic (Lambda = 28 +/- 1 to Lambda = 39 +/- 5) conditions, indicating a similar initial benzene reaction mechanism for both electron-acceptor conditions.

Identifying source correlation parameters for hydrocarbon wastes using compound-specific isotope analysis

A preliminary evaluation of compound-specific isotope analysis (CSIA) as a novel, alternative method for identifying source correlation compounds in soils contaminated with residual heavy or weathered petroleum wastes is presented. Oil-contaminated soil microcosms were established using soil (sandy-loam, non-carbonaceous cley) amended with ballast-, crude- or No.6 fuel oil. Microcosms were periodically sampled over 256 days and delta(13)C values (which express the ratio of (13)C to (12)C) determined at each time point for five n-alkanes and the isoprenoid norpristane using gas chromatography-isotope ratio mass spectrometry (GC-IRMS). Although some temporal variation was observed, no significant temporal shifts in the delta(13)C values for the five n-alkanes were measured in all three oils. Isoprenoid isotope ratios (delta(13)C) appeared to be least affected by biotransformation, especially in the No.6 fuel oil. The research suggests that the delta(13)C of isoprenoids such as norpristane, may be of use as source correlation parameters.

Isotope-ratio detection for gas chromatography

Instrumentation and methods exist for highly precise analyses of the stable-isotopic composition of organic compounds separated by GC. The general approach combines a conventional GC, a chemical reaction interface, and a specialized isotope-ratio mass spectrometer (IRMS). Most existing GC hardware and methods are amenable to isotope-ratio detection. The interface continuously and quantitatively converts all organic matter, including column bleed, to a common molecular form for isotopic measurement. C and N are analyzed as CO2 and N2, respectively, derived from combustion of analytes. H and O are analyzed as H2 and CO produced by pyrolysis/reduction. IRMS instruments are optimized to provide intense, highly stable ion beams, with extremely high precision realized via a system of differential measurements in which ion currents for all major isotopologs are simultaneously monitored. Calibration to an internationally recognized scale is achieved through comparison of closely spaced sample and standard peaks. Such systems are capable of measuring 13C/12C ratios with a precision approaching 0.1 per thousand (for values reported in the standard delta notation), four orders of magnitude better than that typically achieved by conventional "organic" mass spectrometers. Detection limits to achieve this level of precision are typically < 1 nmol C (roughly 10 ng of a typical hydrocarbon) injected on-column. Achievable precision and detection limits are correspondingly higher for N, O, and H, in that order.

Measurement of pulmonary surfactant disaturated-phosphatidylcholine synthesis in human infants using deuterium incorporation from body water

The aim of the study was to determine surfactant palmitate disaturated-phosphatidylcholine (DSPC-PA) synthesis in vivo in humans by the incorporation of deuterium from total body water into DSPC-PA under steady state condition. We studied three newborns and one infant (body weight (BW) 4.6 +/- 2.9 kg, gestational age 37.5 +/- 2 weeks, age 9 +/- 9 days) and four preterm newborns (BW 1.3 +/- 0.6 kg, gestational age 30.3 +/- 2.5 weeks, postnatal age 8.8 +/- 9.2 h). All infants were mechanically ventilated during the study and the four preterm infants received exogenous surfactant at the start of the study. We administered 0.44 g (2)H(2)O/kg BW as a bolus intravenously, followed by 0.0125 g (2)H(2)O/kg BW every 6 h to maintain deuterium enrichment at plateau over 2 days. Urine samples and tracheal aspirates (TA) were obtained prior to dosing and every 6 h thereafter. Isotopic enrichment curves of DSPC-PA from sequential TA and urine deuterium enrichments were analyzed by Gas Chromatography-Isotope Ratio-Mass Spectrometry (GC-IRMS) and normalized for Vienna Standard Mean Ocean Water. Enrichment data were used to measure DSPC-PA fractional synthesis rate (FSR) from the linear portion of the DSPC-PA enrichment rise over time, relative to plateau enrichment of urine deuterium. Secretion time (ST) was defined as the time lag between the start of the study and the appearance of DSPC-PA deuterium enrichment in TA. Data were given as mean +/- SD. All study infants reached deuterium-steady state in urine. DSPC-PA FSR was 6.5 +/- 2.8%/day (range 2.6-10.2). FSR for infants who did not receive exogenous surfactant was 5.7 +/- 3.5%/day (range 2.6-9.9%/day) and 7.3 +/- 2.1%/day (range 5.1-10.2%/day) in the preterms, whereas DSPC-PA ST was 10 +/- 10 h and 31 +/- 10 h respectively. Surfactant DSPC-PA synthesis can be measured in humans by the incorporation of deuterium from body water. This study is a simpler and less invasive method compared to previously published methods on surfactant kinetics by means of stable isotopes.