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One of the outstanding current problems in both geobiology and environmental microbiology is the quantitative analysis of in situ microbial metabolic activities. Techniques capable of such analysis would have wide application, from quantifying natural rates of biogeochemical cycling to identifying the metabolic activity of uncultured organisms. We describe here a method that represents one step towards that goal, namely the high-precision measurement of ^(13)C in specific populations of microbial cells that are purified by fluorescence-activated cell sorting (FACS). Sorted cells are concentrated on a Teflon membrane filter, and their ^(13)C content is measured by coupling an isotope ratio mass spectrometer (IRMS) with a home-built spooling wire microcombustion (SWiM) apparatus. The combined instrumentation provides measurements of δ^(13)C in whole cells with precision better than 0.2‰ for samples containing as little as 25 ng of carbon. When losses associated with sample handling are taken into account, isotopic analyses require sorting roughly 10^4 eukaryotic or 10^7 bacterial cells per sample. Coupled with ^(13)C-labelled substrate additions, this approach has the potential to directly quantify uptake of metabolites in specific populations of sorted cells. The high precision afforded by SWiM-IRMS also permits useful studies of natural abundance variations in ^(13)C. The approach is equally applicable to specific populations of cells sorted from multicellular organisms.

Microbial sulfate reduction exhibits a normal isotope effect, leaving unreacted sulfate enriched in 34 S and producing sulfide that is depleted in 34 S. However, the magnitude of sulfur isotope fractionation is quite variable. The resulting changes in sulfur isotope abundance have been used to trace microbial sulfate reduction in modern and ancient ecosystems, but the intracellular mechanism(s) underlying the wide range of fractionations remains unclear. Here we report the concentrations and isotopic ratios of sulfur metabolites in the dissimilatory sulfate reduction pathway of Desulfovibrio alaskensis . Intracellular sulfate and APS levels change depending on the growth phase, peaking at the end of exponential phase, while sulfite accumulates in the cell during stationary phase. During exponential growth, intracellular sulfate and APS are strongly enriched in 34 S. The fractionation between internal and external sulfate is up to 49‰, while at the same time that between external sulfate and sulfide is just a few permil. We interpret this pattern to indicate that enzymatic fractionations remain large but the net fractionation between sulfate and sulfide is muted by the closed-system limitation of intracellular sulfate. This ‘reservoir effect’ diminishes upon cessation of exponential phase growth, allowing the expression of larger net sulfur isotope fractionations. Thus, the relative rates of sulfate exchange across the membrane versus intracellular sulfate reduction should govern the overall (net) fractionation that is expressed. A strong reservoir effect due to vigorous sulfate reduction might be responsible for the well-established inverse correlation between sulfur isotope fractionation and the cell-specific rate of sulfate reduction, while at the same time intraspecies differences in sulfate uptake and/or exchange rates could account for the significant scatter in this relationship. Our approach, together with ongoing investigations of the kinetic isotope fractionation by key enzymes in the sulfate reduction pathway, should provide an empirical basis for a quantitative model relating the magnitude of microbial isotope fractionation to their environmental and physiological controls.

Chronic lung infections in cystic fibrosis (CF) could be treated more effectively if the effect of antimicrobials on pathogens in situ were known. Here, we compared changes in the microbial community composition and pathogen growth rates in longitudinal studies of CF patients undergoing intravenous antibiotic administration during pulmonary exacerbations. Microbial community composition was measured by NanoString DNA analysis and growth rates were obtained by incubating CF sputum with heavy water and tracing incorporation of deuterium into two different anteiso fatty acids (a-C15:0 and a-C17:0) using gas chromatography–mass spectrometry (GC/MS). Prior to this study, both lipids were thought to be specific for Staphylococcaceae and hence their isotopic enrichment was interpreted as a growth proxy for S. aureus. Our experiments revealed, however, that Prevotella is also a relevant microbial producer of a-C17:0 fatty acid in some CF patients, thus deuterium incorporation into these lipids is better interpreted as a more general pathogen growth rate proxy. Even accounting for a small non-microbial background source detected in some patient samples, a-C15:0 fatty acid still appear to be a relatively robust proxy for CF pathogens, revealing a median generation time of ~1.5 days, similar to prior observations. Contrary to our expectations, pathogen growth rates remained relatively stable throughout exacerbation treatment. We suggest two best practices for application of stable isotope probing in CF sputum: (1) parallel determination of microbial community composition in CF sputum using culture-independent tools, and (2) analysis of samples with a minimum a-C15:0 concentration of 0.1 weight percent of saturated fatty acids.IMPORTANCEIn chronic lung infections, populations of microbial pathogens change and mature in ways that are often unknown, which makes it challenging to identify appropriate treatment options. A promising tool to better understand the physiology of microorganisms in a patient is stable-isotope probing, which we previously developed to estimate the growth rates of S. aureus in cystic fibrosis (CF) sputum. Here, we tracked microbial communities in a cohort of CF patients and found that anteiso fatty acids can also originate from other sources in CF sputum. This awareness led us to develop an new workflow for the application of stable isotope probing in this context, improving our ability to estimate pathogen generation times in clinical samples.

The carbon isotope ratio (δ^(13)C value) of marine particulates is a potentially useful tracer for elucidating pathways of carbon flow in the marine environment. Different species of phytoplankton vary in fractionation vs. CO_2 by up to 24‰ in laboratory cultures under varying nutrient and growth conditions, a signal that should propagate through the microbial food web. However, such contrasts have been difficult to confirm in field measurements due to analytical limitations. Here, we combine fluorescence-activated cell sorting (FACS) with a specialized micro-combustion interface and isotope-ratio mass spectrometry (SWiM-IRMS) to provide some of the first direct measurements of whole-cell δ^(13)C values for specific phytoplankton populations in the wild. For three samples collected off Scripps Pier in 2010–2011, Synechococcus averages δ^(13)C values of −25.7 ± 2.0‰, Prochlorococcus averages −23.0 ± 1.3, and diatoms average −20.8 ± 1.7‰. Diatoms were ∼3‰ enriched in ^(13)C when measured during a bloom (March 2011) as compared with mid-summer (July 2010). Sorted particles thought to represent living heterotrophic bacteria averaged −25.4 ± 2.5‰, whereas total filterable particles averaged −19.6 ± 1.0‰, indicating a strong similarity to diatom biomass. These variations demonstrate that in situ differences in δ^(13)C among different populations of particles can be exploited to follow carbon flow through successive trophic levels, and throughout organic matter remineralization, sinking, and preservation.

The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile α-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80 %). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the ‘lipid fingerprint’ produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.

© 2017 Elsevier Ltd The isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding petroleum systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here we present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. In general, clumped isotope measurements indicate plausible formation temperatures for abiotic, thermogenic, and microbial methane in many geological environments, which is encouraging for the further development of this measurement as a geothermometer, and as a tracer for the source of natural gas reservoirs and emissions. We also highlight, however, instances where clumped isotope derived temperatures are higher than expected, and discuss possible factors that could distort equilibrium formation temperature signals. In microbial methane from freshwater ecosystems, in particular, clumped isotope values appear to be controlled by kinetic effects, and may ultimately be useful to study methanogen metabolism.

Fatty acids produced by H_2-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H_2. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H_2-consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH- mutant, and MBH- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δD_(water) values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H_2. Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H-) ions, providing no direct mechanism to connect the isotopic composition of H_2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H_2 plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(P)H by reductases with flavin prosthetic groups, which transfer two electrons and acquire H+ (or D+) from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator are nearly identical to those in many photoautotrophic algae and bacteria. We conclude that strong D-depletion is not a diagnostic feature of chemoautotrophy.

Ooids are one of the common constituents of ancient carbonate rocks, yet the role that microbial communities may or may not play in their formation remains unresolved. To search for evidence of microbial activity in modern and Holocene ooids, samples collected from intertidal waters, beaches and outcrops in the Bahamas and in Shark Bay in Western Australia were examined for their contents of lipid biomarkers. Modern samples from Cat and Andros islands in the Bahamas and from Carbla Beach in Hamelin Pool, Western Australia, showed abundant and notably similar distributions of hydrocarbons, fatty acids (FAs) and alcohols. A large fraction of these lipids were bound into the carbonate matrix and only released on acid dissolution, which suggests that these lipids were being incorporated continuously during ooid growth. The distributions of hydrocarbons, and their disparate carbon isotopic signatures, were consistent with mixed input from cyanobacteria together with small and variable amounts of vascular plant leaf wax [C_(27)–C_(35); δ^(13)C −25 to −32‰Vienna Pee Dee Belemnite (VPDB)]. The FAs comprised a complex mixture of C_(12)–C_(18) normal and branched short-chain compounds with the predominant straight-chain components attributable to bacteria and/or cyanobacteria. Branched FA, especially 10-MeC_(16) and 10-MeC_(17), together with the prevalence of elemental sulfur in the extracts, indicate an origin from sulfate-reducing bacteria. The iso- and anteiso-FA were quite variable in their ^(13)C contents suggesting that they come from organisms with diverse physiologies. Hydrogen isotopic compositions provide further insight into this issue. FAs in each sample show disparate δD values consistent with inputs from autotrophs and heterotrophs. The most enigmatic lipid assemblage is an homologous series of long-chain (C_(24)–C_(32)) FA with pronounced even carbon number preference. Typically, such long-chain FA are thought to come from land plant leaf wax, but in this case, their ^(13)C-enriched isotopic signatures compared to co-occurring n-alkanes (e.g., Hamelin Pool TLE FA C_(24)–C_(32); δ^(13)C −20 to −24.2‰ VPDB; TLE n-alkanes δ^(13)C −24.1 to −26.2 −‰VPDB) indicate a microbial origin, possibly sulfate-reducing bacteria. Lastly, we identified homohopanoic acid and bishomohopanol as the primary degradation products of bacterial hopanoids. The distributions of lipids isolated from Holocene oolites from the Rice Bay Formation of Cat Island, Bahamas were very similar to the beach ooids described above and, in total, these modern and fossil biomarker data lead us to hypothesize that ooids are colonized by a defined microbial community and that these microbes possibly mediate calcification.

© 2016 Elsevier Ltd. Methane is a potent greenhouse gas, and there are concerns that its natural emissions from the Arctic could act as a substantial positive feedback to anthropogenic global warming. Determining the sources of methane emissions and the biogeochemical processes controlling them is important for understanding present and future Arctic contributions to atmospheric methane budgets. Here we apply measurements of multiply-substituted isotopologues, or clumped isotopes, of methane as a new tool to identify the origins of ebullitive fluxes in Alaska, Sweden and the Arctic Ocean. When methane forms in isotopic equilibrium, clumped isotope measurements indicate the formation temperature. In some microbial methane, however, non-equilibrium isotope effects, probably related to the kinetics of methanogenesis, lead to low clumped isotope values. We identify four categories of emissions in the studied samples: thermogenic methane, deep subsurface or marine microbial methane formed in isotopic equilibrium, freshwater microbial methane with non-equilibrium clumped isotope values, and mixtures of deep and shallow methane (i.e., combinations of the first three end members). Mixing between deep and shallow methane sources produces a non-linear variation in clumped isotope values with mixing proportion that provides new constraints for the formation environment of the mixing end-members. Analyses of microbial methane emitted from lakes, as well as a methanol-consuming methanogen pure culture, support the hypothesis that non-equilibrium clumped isotope values are controlled, in part, by kinetic isotope effects induced during enzymatic reactions involved in methanogenesis. Our results indicate that these kinetic isotope effects vary widely in microbial methane produced in Arctic lake sediments, with non-equilibrium δ18values spanning a range of more than 5‰.

Hydrogen atoms from water and food are incorporated into biomass during cellular metabolism and biosynthesis, fractionating the isotopes of hydrogen-protium and deuterium-that are recorded in biomolecules. While these fractionations are often relatively constant in plants, large variations in the magnitude of fractionation are observed for many heterotrophic microbes utilizing different central metabolic pathways. The correlation between metabolism and lipid δ(2)H provides a potential basis for reconstructing environmental and ecological parameters, but the calibration dataset has thus far been limited mainly to aerobes. Here we report on the hydrogen isotopic fractionations of lipids produced by nitrate-respiring and sulfate-reducing bacteria. We observe only small differences in fractionation between oxygen- and nitrate-respiring growth conditions, with a typical pattern of variation between substrates that is broadly consistent with previously described trends. In contrast, fractionation by sulfate-reducing bacteria does not vary significantly between different substrates, even when autotrophic and heterotrophic growth conditions are compared. This result is in marked contrast to previously published observations and has significant implications for the interpretation of environmental hydrogen isotope data. We evaluate these trends in light of metabolic gene content of each strain, growth rate, and potential flux and reservoir-size effects of cellular hydrogen, but find no single variable that can account for the differences between nitrate- and sulfate-respiring bacteria. The emerging picture of bacterial hydrogen isotope fractionation is therefore more complex than the simple correspondence between δ(2)H and metabolic pathway previously understood from aerobes. Despite the complexity, the large signals and rich variability of observed lipid δ(2)H suggest much potential as an environmental recorder of metabolism.

Hydrogen-isotopic abundances of lipid biomarkers are emerging as important proxies in the study of ancient environments and ecosystems. A decade ago, pioneering studies made use of new analytical methods and demonstrated that the hydrogen-isotopic composition of individual lipids from aquatic and terrestrial organisms can be related to the composition of their growth (i.e., environmental) water. Subsequently, compound-specific deuterium/hydrogen (D/H) ratios of sedimentary biomarkers have been increasingly used as paleohydrological proxies over a range of geological timescales. Isotopic fractionation observed between hydrogen in environmental water and hydrogen in lipids, however, is sensitive to biochemical, physiological, and environmental influences on the composition of hydrogen available for biosynthesis in cells. Here we review the factors and processes that are known to influence the hydrogen-isotopic compositions of lipids—especially n-alkanes—from photosynthesizing organisms, and we provide a framework for interpreting their D/H ratios from ancient sediments and identify future research opportunities.

Effective treatment for chronic infections is undermined by a significant gap in understanding of the physiological state of pathogens at the site of infection. Chronic pulmonary infections are responsible for the morbidity and mortality of millions of immunocompromised individuals worldwide, yet drugs that are successful in laboratory culture are far less effective against pathogen populations persisting in vivo. Laboratory models, upon which preclinical development of new drugs is based, can only replicate host conditions when we understand the metabolic state of the pathogens and the degree of heterogeneity within the population. In this study, we measured the anabolic activity of the pathogen Staphylococcus aureus directly in the sputum of pediatric patients with cystic fibrosis (CF), by combining the high sensitivity of isotope ratio mass spectrometry with a heavy water labeling approach to capture the full range of in situ growth rates. Our results reveal S. aureus generation times with a median of 2.1 d, with extensive growth rate heterogeneity at the single-cell level. These growth rates are far below the detection limit of previous estimates of CF pathogen growth rates, and the rates are slowest in acutely sick patients undergoing pulmonary exacerbations; nevertheless, they are accessible to experimental replication within laboratory models. Treatment regimens that include specific antibiotics (vancomycin, piperacillin/tazobactam, tobramycin) further appear to correlate with slow growth of S. aureus on average, but follow-up longitudinal studies must be performed to determine whether this effect holds for individual patients.

Marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. We used stable isotope probing (SIP) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the Coal Oil Point seep field located offshore of Santa Barbara, California. After incubating sediment with 13 C-labeled methane, ethane, or propane, we confirmed the incorporation of 13 C into fatty acids and DNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA and particulate methane monooxygenase ( pmoA ) genes in 13 C-DNA revealed groups of microbes not previously thought to contribute to methane, ethane, or propane oxidation. First, 13 C methane was primarily assimilated by Gammaproteobacteria species from the family Methylococcaceae , Gammaproteobacteria related to Methylophaga , and Betaproteobacteria from the family Methylophilaceae . Species of the latter two genera have not been previously shown to oxidize methane and may have been cross-feeding on methanol, but species of both genera were heavily labeled after just 3 days. pmoA sequences were affiliated with species of Methylococcaceae , but most were not closely related to cultured methanotrophs. Second, 13 C ethane was consumed by members of a novel group of Methylococcaceae . Growth with ethane as the major carbon source has not previously been observed in members of the Methylococcaceae ; a highly divergent pmoA -like gene detected in the 13 C-labeled DNA may encode an ethane monooxygenase. Third, 13 C propane was consumed by members of a group of unclassified Gammaproteobacteria species not previously linked to propane oxidation. This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some pmoA -like genes.

The rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of Earth’s history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. Dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-methylbacteriohopanepolyols (2-MeBHPs), lipids thought to be synthesized primarily by cyanobacteria. The discovery that 2-MeBHPs are produced by an anoxygenic phototroph, however, challenged both their taxonomic link with cyanobacteria and their functional link with oxygenic photosynthesis. Here, we identify a radical SAM methylase encoded by the hpnP gene that is required for methylation at the C-2 position in hopanoids. This gene is found in several, but not all, cyanobacteria and also in α -proteobacteria and acidobacteria. Thus, one cannot extrapolate from the presence of 2-methylhopanes alone, in modern environments or ancient sedimentary rocks, to a particular taxonomic group or metabolism. To understand the origin of this gene, we reconstructed the evolutionary history of HpnP. HpnP proteins from cyanobacteria, Methylobacterium species, and other α-proteobacteria form distinct phylogenetic clusters, but the branching order of these clades could not be confidently resolved. Hence,it is unclear whether HpnP, and 2-methylhopanoids, originated first in the cyanobacteria. In summary, existing evidence does not support the use of 2-methylhopanes as biomarkers for oxygenic photosynthesis.

Sedimentary hopanes are pentacyclic triterpenoids that serve as biomarker proxies for bacteria and certain bacterial metabolisms, such as oxygenic photosynthesis and aerobic methanotrophy. Their parent molecules, the bacteriohopanepolyols (BHPs), have been hypothesized to be the bacterial equivalent of sterols. However, the actual function of BHPs in bacterial cells is poorly understood. Here, we report the physiological study of a mutant in Rhodopseudomonas palustris TIE-1 that is unable to produce any hopanoids. The deletion of the gene encoding the squalene-hopene cyclase protein (Shc), which cyclizes squalene to the basic hopene structure, resulted in a strain that no longer produced any polycyclic triterpenoids. This strain was able to grow chemoheterotrophically, photoheterotrophically, and photoautotrophically, demonstrating that hopanoids are not required for growth under normal conditions. A severe growth defect, as well as significant morphological damage, was observed when cells were grown under acidic and alkaline conditions. Although minimal changes in shc transcript expression were observed under certain conditions of pH shock, the total amount of hopanoid production was unaffected; however, the abundance of methylated hopanoids significantly increased. This suggests that hopanoids may play an indirect role in pH homeostasis, with certain hopanoid derivatives being of particular importance.

Large hydrogen-isotopic (D/H) fractionations between lipids and growth water have been observed in most organisms studied to date. These fractionations are generally attributed to isotope effects in the biosynthesis of lipids, and are frequently assumed to be approximately constant for the purpose of reconstructing climatic variables. Here, we report D/H fractionations between lipids and water in 4 cultured members of the phylum Proteobacteria , and show that they can vary by up to 500‰ in a single organism. The variation cannot be attributed to lipid biosynthesis as there is no significant change in these pathways between cultures, nor can it be attributed to changing substrate D/H ratios. More importantly, lipid/water D/H fractionations vary systematically with metabolism: chemoautotrophic growth (approximately −200 to −400‰), photoautotrophic growth (−150 to −250‰), heterotrophic growth on sugars (0 to −150‰), and heterotrophic growth on TCA-cycle precursors and intermediates (−50 to +200‰) all yield different fractionations. We hypothesize that the D/H ratios of lipids are controlled largely by those of NADPH used for biosynthesis, rather than by isotope effects within the lipid biosynthetic pathway itself. Our results suggest that different central metabolic pathways yield NADPH—and indirectly lipids—with characteristic isotopic compositions. If so, lipid δD values could become an important biogeochemical tool for linking lipids to energy metabolism, and would yield information that is highly complementary to that provided by 13 C about pathways of carbon fixation.

We report hydrogen isotopic fractionations between water and fatty acids of the sulfate-reducing bacterium Desulfobacterium autotrophicum. Pure cultures were grown in waters with deuterium (D) contents that were systematically varied near the level of natural abundance (−37‰ ≤ δD ≤ 993‰). H_2 of constant hydrogen isotope (D/H) ratio was supplied to the cultures. The D/H ratios of water, H_2, and specific fatty acids were measured by isotope-ratio mass spectrometry. The results demonstrate that D. autotrophicum catalyzes hydrogen isotopic exchange between water and H_2, and this reaction is conclusively shown to approach isotopic equilibrium. In addition, variation in the D/H ratio of growth water accounts for all variation in the hydrogen isotopic composition of fatty acids. The D/H ratios of fatty acids from cultures grown on H_2/CO_2 are compared with those from a separate set of cultures grown on D-enriched formate, an alternative electron donor. This comparison rules out H_2 as a significant source of fatty acid hydrogen. Grown on either H_2/CO_2 or formate, D. autotrophicum produces fatty acids in which all hydrogen originates from water. For specific fatty acids, biosynthetic fractionation factors are mostly in the range 0.60 ≤ αFA–water ≤ 0.70; the 18:0 fatty acid exhibits a lower fractionation factor of 0.52. The data show that αFA_–water generally increases with length of the carbon chain from C_14 to C_17 among both saturated and unsaturated fatty acids. These results indicate a net fractionation associated with fatty acid biosynthesis in D. autotrophicum that is slightly smaller than in another H_2-consuming bacterium (Sporomusa sp.), but much greater than in most photoautotrophs.

To investigate potential variability in the biosynthetic fractionation of hydrogen isotopes between environmental water and plant lipids, the cord grass Spartina alterniflora was sampled from a single location in a coastal marsh over a period of 16 months. Values of δD for a variety of lipids were measured by gas chromatography/pyrolysis/isotope ratio mass spectrometry. S. alterniflora grows partially submerged in seawater, so it has a virtually unlimited supply of water with nearly unvarying isotopic composition. Temporal changes in the δD values of lipids can thus be interpreted as representing mainly variations in biosynthetic fractionation. Fatty acids, n-alkanes, and phytol extracted from S. alterniflora have nearly constant δD values from ∼October through May, but exhibit marked decreases of up to 40‰ during summer months. These shifts in lipid δD values are interpreted as representing a change in the source of organic substrates, principally acetate, used for their biosynthesis. Lower summertime δD values for lipids are consistent with an increasing reliance on current photosynthate as feedstock for biosynthesis, whereas stored carbohydrate reserves are utilized more extensively during other times of the year. Regardless of the specific mechanism, the data emphasize that overall fractionations between water and plant lipids depend on biological as well as environmental variables, and that the biosynthetic fractionation is not necessarily constant even for a single plant. Because lipids such as fatty acids are present in all cells and turn over on timescales of weeks to months, measurements of δD values in fatty acids may also provide useful constraints for distinguishing biologic versus environmental controls on cellulose δD values in trees.

Hydrogen-isotopic data are often interpreted using mathematical approximations originally intended for other isotopes. One of the most common, apparent in literature over the last several decades, assumes that delta values of reactants and products are separated by a constant fractionation factor: δ_p = δ_r + e_(p/r). Because of the large fractionations that affect hydrogen isotopes, such approximations can lead to substantial errors. Here we review and develop general equations for isotopic mass balances that include the differential fractionation of each component in a mixture and discuss their use in three geochemical applications. For the fractionation of a single component, the reactant and product are related by δ_p = α_(p/r)δ_r + e_(p/r), where α and e refer to the same fractionation. Regression of δ_p on δ_r should give equivalent fractionations based on the intercept and slope, but this has not generally been recognized in studies of D/H fractionation. In a mixture of two components, each of which is fractionated during mixing, there is no unique solution for the three unknown variables (two fractionation factors and the elemental mixing ratio of the two hydrogen sources). The flow of H from CH_4 and H_2O to bacterial lipids in the metabolism of Methylococcus capsulatus provides an example of such a case. Data and conclusions from an earlier study of that system (Sessions et al., 2002) are reexamined here. Several constraints on the variables are available based on plausible ranges for fractionation factors. A possible refinement to current experimental procedures is the measurement of three different isotopes, which would allow unique determination of all variables.

A wealth of genetic sequence information is available publicly and can be used to support investigations in organic geochemistry. Here, we present a new method to separate ribosomal RNA in order to use this rRNA as a “biomarker” for molecular isotopic studies. The primary goal is to obtain pure fractions that reflect selected phylogenetic groups. We demonstrate the ability to separate rRNA of a target organism from RNA representing a mixture of species. In this approach, an oligonucleotide probe containing a poly-d(GGGT) tail is hybridized to RNA in solution. Simultaneously, an aliquot of oligo-dT paramagnetic beads is hybridized to an oligonucleotide made of poly-d(CCCA) with a poly-dA tail. The two solutions are combined and a high-affinity GCAT complex is formed. The magnetic beads are captured and re-suspended in fresh solution. Careful determination of the melting temperatures of all three hybrids permits melting of the captured rRNA while leaving the majority of the oligonucleotides bound to the beads. Authenticity of the captured product is determined by reverse-transcriptase (RT)-PCR on a sub-sample; the remainder is washed, re-suspended in H_2O, and saved for subsequent isotopic analysis.

Hydrogen isotopic compositions of individual lipids from Methylococcus capsulatus, an aerobic, methane-oxidizing bacterium, were analyzed by hydrogen isotope-ratio-monitoring gas chromatography–mass spectrometry (GC-MS). The purposes of the study were to measure isotopic fractionation factors between methane, water, and lipids and to examine the biochemical processes that determine the hydrogen isotopic composition of lipids. M. capsulatus was grown in six replicate cultures in which the δD values of methane and water were varied independently. Measurement of concomitant changes in δD values of lipids allowed estimation of the proportion of hydrogen derived from each source and the isotopic fractionation associated with the utilization of each source. All lipids examined, including fatty acids, sterols, and hopanols, derived 31.4 ± 1.7% of their hydrogen from methane. This was apparently true whether the cultures were harvested during exponential or stationary phase. Examination of the relevant biochemical pathways indicates that no hydrogen is transferred directly (with C-H bonds intact) from methane to lipids. Accordingly, we hypothesize that all methane H is oxidized to H_2O, which then serves as the H source for all biosynthesis, and that a balance between diffusion of oxygen and water across cell membranes controls the concentration of methane-derived H_2O at 31%. Values for α_(l/w), the isotopic fractionation between lipids and water, were 0.95 for fatty acids and 0.85 for isoprenoid lipids. These fractionations are significantly smaller than those measured in higher plants and algae. Values for α_(l/m), the isotopic fractionation between lipids and methane, were 0.94 for fatty acids and 0.79 for isoprenoid lipids. Based on these results, we predict that methanotrophs living in seawater and consuming methane with typical δD values will produce fatty acids with δD between −50 and −170‰, and sterols and hopanols with δD between −150 and −270‰.

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 (e_(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 e_(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 e_(lipid–water) values.

Understanding the coupling of oxygen, carbon, and sulfur cycles in the past is critical for reconstructing the history of biogeochemical cycles, paleoclimatic variations, and oceanic chemistry. The abundance of sulfur isotopes (δ34S) in sulfate from ancient marine carbonates, or carbonate-associated sulfate (CAS), is commonly used, along with other archives (mainly evaporites and barite), to estimate the δ34S of seawater throughout Earth history. Analyses of CAS from hand-picked foraminifera are potentially valuable because this group of organisms is used in numerous paleoceanographic studies. They could provide coupled, high-resolution records of δ13C, δ18O, and δ34S isotopic changes directly linked to orbitally tuned records of climate change through the Cenozoic. Such measurements have not previously been possible due to limitations of sensitivity in conventional IRMS-based techniques. However, the recent development of CAS analysis by multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS) now allows us to work on samples containing just a few nmol of sulfur with accuracy for δ34S values approaching 0.1‰ and, consequently, to analyze hand-picked samples of foraminifera shells. Here we report the results of culture experiments with the planktonic species Orbulina universa, that establish a shell:seawater δ34S calibration for future applications to the fossil record. Our new method uses

Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value

The organization of lipids within biological membranes is poorly understood. Some studies have suggested lipids group into microdomains within cells, but the evidence remains controversial due to non-native imaging techniques. A recently developed NanoSIMS technique indicated that sphingolipids group into microdomains within membranes of human fibroblast cells. We extended this NanoSIMS approach to study the localization of hopanoid lipids in bacterial cells by developing a stable isotope labeling method to directly detect subcellular localization of specific lipids in bacteria with ca. 60 nm resolution. Because of the relatively small size of bacterial cells and the relative abundance of hopanoid lipids in membranes, we employed a primary (2)H-label to maximize our limit of detection. This approach permitted the analysis of multiple stable isotope labels within the same sample, enabling visualization of subcellular lipid microdomains within different cell types using a secondary label to mark the growing end of the cell. Using this technique, we demonstrate subcellular localization of hopanoid lipids within alpha-proteobacterial and cyanobacterial cells. Further, we provide evidence of hopanoid lipid domains in between cells of the filamentous cyanobacterium Nostoc punctiforme. More broadly, our method provides a means to image lipid microdomains in a wide range of cell types and test hypotheses for their functions in membranes.

Rhodopseudomonas palustris TIE-1 is a Gram-negative bacterium that produces structurally diverse hopanoid lipids that are similar to eukaryotic steroids. Its genome encodes several homologues to proteins involved in eukaryotic steroid trafficking. In this study, we explored the possibility that two of these proteins are involved in intracellular hopanoid transport. R. palustris has a sophisticated membrane system comprising outer, cytoplasmic, and inner cytoplasmic membranes. It also divides asymmetrically, producing a mother and swarmer cell. We deleted genes encoding two putative hopanoid transporters that belong to the resistance–nodulation–cell division superfamily. Phenotypic analyses revealed that one of these putative transporters (HpnN) is essential for the movement of hopanoids from the cytoplasmic to the outer membrane, whereas the other (Rpal_4267) plays a minor role. C 30 hopanoids, such as diploptene, are evenly distributed between mother and swarmer cells, whereas hpnN is required for the C 35 hopanoid, bacteriohopanetetrol, to remain localized to the mother cell type. Mutant cells lacking HpnN grow like the WT at 30 °C but slower at 38 °C. Following cell division at 38 °C, the ΔhpnN cells remain connected by their cell wall, forming long filaments. This phenotype may be attributed to hopanoid mislocalization because a double mutant deficient in both hopanoid biosynthesis and transport does not form filaments. However, the lack of hopanoids severely compromises cell growth at higher temperatures more generally. Because hopanoid mutants only manifest a strong phenotype under certain conditions, R. palustris is an attractive model organism in which to study their transport and function.

The extent to which leaf water D-enrichment (transpiration) and soil water D-enrichment (evaporation) affect the D/H ratio of plant leaf waxes remains a contentious issue, with important implications for paleohydrologic reconstructions. In this study we measure δD values of precipitation (δD_p), groundwater (δD_(gw)), plant xylem water (δD_(xw)) and leaf water (δD_(lw)) to understand their impact on the δD values of plant leaf wax n-alkanes (δD_(wax)) in an arid ecosystem. Our survey includes multiple species at four sites across an aridity gradient (80–30% relative humidity) in southern California. We find that many species take up groundwater or precipitation without significant fractionation. D-enriched soil water is a minor source even in species known to perform and utilize waters from hydraulic lift, such as Larrea tridentata (+10‰). Measurements of leaf water isotopic composition demonstrate that transpiration is an important mechanism for D-enrichment of leaf waters (+74 ± 20‰, 1σ), resulting in the smallest net fractionation yet reported between source water and leaf waxes (L. tridentata −41‰; multi-species mean value is −94 ± 21‰, 1σ). We find little change in leaf water D-enrichment or net fractionation across the climatic gradient sampled by our study, suggesting that a net fractionation of ca. −90‰ may be appropriate for paleohydrologic reconstructions in semi-arid to arid environments. Large interspecies offsets in net fractionations (1σ = 21‰) are potentially troublesome, given the observed floristic diversity and the likelihood of species assemblage changes with climate shifts.

The rise of atmospheric O(2) was a milestone in the history of life. Although O(2) itself is not a climate-active gas, its appearance would have removed a methane greenhouse present on the early Earth and potentially led to dramatic cooling. Moreover, by fundamentally altering the biogeochemical cycles of C, N, S and Fe, its rise first in the atmosphere and later in the oceans would also have had important indirect effects on Earth's climate. Here, we summarize major lines of evidence from the geological literature that pertain to when and how O(2) first appeared in significant amounts in the atmosphere. On the early Earth, atmospheric O(2) would initially have been very low, probably10(-5) of the present atmospheric level. Around 2.45 billion years ago, atmospheric O(2) rose suddenly in what is now termed the Great Oxidation Event. While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved. Our goal in this review is to provide a short summary of the current state of the field, and make the case that future progress towards solving the riddle of oxygen will benefit greatly from the involvement of molecular biologists.

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13 C-enriched C 4 grass Spartina alterniflora and 13 C-depleted petroleum to monitor changes in the 13 C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13 C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma - and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13 C content of biomarker lipids.

Sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-MeBHPs). Here, we report the identification of significant quantities of 2-MeBHP in two strains of the anoxygenic phototroph Rhodopseudomonas palustris . Biosynthesis of 2-MeBHP can occur in the absence of O 2 , deriving the C-2 methyl group from methionine. The relative abundance of 2-MeBHP varies considerably with culture conditions, ranging from 13.3% of total bacteriohopanepolyol (BHP) to trace levels of methylation. Analysis of intact BHPs reveals the presence of methylated bacteriohopane-32,33,34,35-tetrol but no detectable methylation of 35-aminobacteriohopane-32,33,34-triol. Our results demonstrate that an anoxygenic photoautotroph is capable of generating 2-MeBHPs and show that the potential origins of sedimentary 2-methylhopanoids are more diverse than previously thought.