1
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Maloney AE, Kopf SH, Zhang Z, McFarlin J, Nelson DB, Masterson AL, Zhang X. Large enrichments in fatty acid 2H/ 1H ratios distinguish respiration from aerobic fermentation in yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2024; 121:e2310771121. [PMID: 38709917 PMCID: PMC11098093 DOI: 10.1073/pnas.2310771121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/21/2024] [Indexed: 05/08/2024] Open
Abstract
Shifts in the hydrogen stable isotopic composition (2H/1H ratio) of lipids relative to water (lipid/water 2H-fractionation) at natural abundances reflect different sources of the central cellular reductant, NADPH, in bacteria. Here, we demonstrate that lipid/water 2H-fractionation (2εfattyacid/water) can also constrain the relative importance of key NADPH pathways in eukaryotes. We used the metabolically flexible yeast Saccharomyces cerevisiae, a microbial model for respiratory and fermentative metabolism in industry and medicine, to investigate 2εfattyacid/water. In chemostats, fatty acids from glycerol-respiring cells were >550‰ 2H-enriched compared to those from cells aerobically fermenting sugars via overflow metabolism, a hallmark feature in cancer. Faster growth decreased 2H/1H ratios, particularly in glycerol-respiring cells by 200‰. Variations in the activities and kinetic isotope effects among NADP+-reducing enzymes indicate cytosolic NADPH supply as the primary control on 2εfattyacid/water. Contributions of cytosolic isocitrate dehydrogenase (cIDH) to NAPDH production drive large 2H-enrichments with substrate metabolism (cIDH is absent during fermentation but contributes up to 20 percent NAPDH during respiration) and slower growth on glycerol (11 percent more NADPH from cIDH). Shifts in NADPH demand associated with cellular lipid abundance explain smaller 2εfattyacid/water variations (<30‰) with growth rate during fermentation. Consistent with these results, tests of murine liver cells had 2H-enriched lipids from slower-growing, healthy respiring cells relative to fast-growing, fermenting hepatocellular carcinoma. Our findings point to the broad potential of lipid 2H/1H ratios as a passive natural tracker of eukaryotic metabolism with applications to distinguish health and disease, complementing studies that rely on complex isotope-tracer addition methods.
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Affiliation(s)
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Zhaoyue Zhang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Chemistry, Princeton University, Princeton, NJ08544
| | - Jamie McFarlin
- Department of Geology and Geophysics, University of Wyoming, LaramieWY82071
| | - Daniel B. Nelson
- Department of Environmental Science— Botany, University of Basel, Basel4056, Switzerland
| | - Andrew L. Masterson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL60208
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ08544
- High Meadow Environmental Institute, Princeton University, Princeton, NJ08544
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2
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Leavitt WD, Waldbauer J, Venceslau SS, Sim MS, Zhang L, Boidi FJ, Plummer S, Diaz JM, Pereira IAC, Bradley AS. Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris. GEOBIOLOGY 2024; 22:e12600. [PMID: 38725144 DOI: 10.1111/gbi.12600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/31/2024] [Accepted: 04/18/2024] [Indexed: 07/12/2024]
Abstract
Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earth's surface. Tracking the activity of sulfate reducing microorganisms over space and time relies on a nuanced understanding of stable sulfur isotope fractionation in the context of the biochemical machinery of the metabolism. Here, we link the magnitude of stable sulfur isotopic fractionation to proteomic and metabolite profiles under different cellular energetic regimes. When energy availability is limited, cell-specific sulfate respiration rates and net sulfur isotope fractionation inversely covary. Beyond net S isotope fractionation values, we also quantified shifts in protein expression, abundances and isotopic composition of intracellular S metabolites, and lipid structures and lipid/water H isotope fractionation values. These coupled approaches reveal which protein abundances shift directly as a function of energy flux, those that vary minimally, and those that may vary independent of energy flux and likely do not contribute to shifts in S-isotope fractionation. By coupling the bulk S-isotope observations with quantitative proteomics, we provide novel constraints for metabolic isotope models. Together, these results lay the foundation for more predictive metabolic fractionation models, alongside interpretations of environmental sulfur and sulfate reducer lipid-H isotope data.
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Affiliation(s)
- William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, South Korea
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Flavia Jaquelina Boidi
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sydney Plummer
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Julia M Diaz
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri, USA
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3
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Silverman SN, Wijker RS, Sessions AL. Biosynthetic and catabolic pathways control amino acid δ 2H values in aerobic heterotrophs. Front Microbiol 2024; 15:1338486. [PMID: 38646628 PMCID: PMC11026604 DOI: 10.3389/fmicb.2024.1338486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/20/2024] [Indexed: 04/23/2024] Open
Abstract
The hydrogen isotope ratios (δ2HAA values) of amino acids in all organisms are substantially fractionated relative to growth water. In addition, they exhibit large variations within microbial biomass, animals, and human tissues, hinting at rich biochemical information encoded in such signals. In lipids, such δ2H variations are thought to primarily reflect NADPH metabolism. Analogous biochemical controls for amino acids remain largely unknown, but must be elucidated to inform the interpretation of these measurements. Here, we measured the δ2H values of amino acids from five aerobic, heterotrophic microbes grown on different carbon substrates, as well as five Escherichia coli mutant organisms with perturbed NADPH metabolisms. We observed similar δ2HAA patterns across all organisms and growth conditions, which-consistent with previous hypotheses-suggests a first-order control by biosynthetic pathways. Moreover, δ2HAA values varied systematically with the catabolic pathways activated for substrate degradation, with variations explainable by the isotopic compositions of important cellular metabolites, including pyruvate and NADPH, during growth on each substrate. As such, amino acid δ2H values may be useful for interrogating organismal physiology and metabolism in the environment, provided we can further elucidate the mechanisms underpinning these signals.
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Affiliation(s)
- Shaelyn N. Silverman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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4
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Smith DA, Nakamoto BJ, Suess MK, Fogel ML. Central Metabolism and Growth Rate Impacts on Hydrogen and Carbon Isotope Fractionation During Amino Acid Synthesis in E. coli. Front Microbiol 2022; 13:840167. [PMID: 35910622 PMCID: PMC9335129 DOI: 10.3389/fmicb.2022.840167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/22/2022] [Indexed: 11/20/2022] Open
Abstract
Compound specific stable isotope analysis (CSIA) of amino acids from bacterial biomass is a newly emerging powerful tool for exploring central carbon metabolism pathways and fluxes. By comparing isotopic values and fractionations relative to water and growth substrate, the impact of variable flow path for metabolites through different central metabolic pathways, perturbations of these paths, and their resultant consequences on intracellular pools and resultant biomass may be elucidated. Here, we explore the effects that central carbon metabolism and growth rate can have on stable hydrogen (δ2H) and carbon (δ13C) compound specific isotopic values of amino acids, and whether diagnostic isotopic fingerprints are revealed by these paired analyses. We measured δ2H and δ13C in amino acids in the wild type Escherichia coli (MG1655) across a range of growth rates in chemostat cultures to address the unknown isotopic consequences as metabolic fluxes are shuffled between catabolic and anabolic metabolisms. Additionally, two E. coli knockout mutants, one with deficiency in glycolysis –pgi (LC1888) and another inhibiting the oxidative pentose phosphate pathway (OPPP) –zwf (LC1889), were grown on glucose and used as a comparison against the wild type E. coli (MG1655) to address the isotopic changes of amino acids produced in these perturbed metabolic pathways. Amino acid δ2H values, which collectively vary in composition by more than 400‰, are altered along with δ13C values demonstrating fundamental shifts in central metabolic pathways and/or fluxes. Within our linear discriminant analysis with a simple model organism to examine potential amino acid fingerprinting, our knockout strains and variable growth rate samples plot across a wider array of organism classification than merely within the boundaries of other bacterial data.
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Affiliation(s)
- Derek A. Smith
- Department of Biology, Case Western Reserve University, Cleveland, OH, United States
- *Correspondence: Derek A. Smith
| | - Bobby James Nakamoto
- Department of Biology, University of New Brunswick Fredericton, Fredericton, NB, Canada
- Department of Earth and Planetary Sciences, EDGE Institute, University of California, Riverside, Riverside, CA, United States
| | - Melanie K. Suess
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Marilyn L. Fogel
- Department of Earth and Planetary Sciences, EDGE Institute, University of California, Riverside, Riverside, CA, United States
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Chen X, Liu X, Jia H, Jin J, Kong W, Huang Y. Inverse hydrogen isotope fractionation indicates heterotrophic microbial production of long-chain n-alkyl lipids in desolate Antarctic ponds. GEOBIOLOGY 2021; 19:394-404. [PMID: 33799312 DOI: 10.1111/gbi.12441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Long-chain (>C25 ) n-alkyl lipids have long been considered biomarkers for higher plant leaf waxes and widely applied for paleoclimate and paleoenvironmental reconstructions. However, recent experimental and lacustrine sediment studies suggest long-chain n-alkanes and n-alkanoic acids can also be produced by aerobic microbes, probably heterotrophic microbes based on carbon isotope data. Here we show that sedimentary long-chain n-alkanes and n-alkanoic acids in two desolate Antarctic ponds where vascular plants are absent in the surroundings display hydrogen isotopic values up to 300 per mil higher than those of lake water. It is the first time that such strongly inverse or reduced hydrogen isotopic fractionation of lipid biomarkers is observed in natural sediment samples. Based on recent extensive experimental data on microbial hydrogen isotopic fractionation, our data can only be explained by the predominant production of long-chain n-alkanes and n-alkanoic acids from heterotrophic micro-organisms. Together with preliminary 16S rRNA gene sequencing data, our results represent the first unambiguous example of predominant heterotrophic microbial production of long-chain n-alkyl waxes in a natural environment.
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Affiliation(s)
- Xin Chen
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaodong Liu
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Hongzeng Jia
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Jing Jin
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Yongsong Huang
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
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6
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Lengger SK, Weber Y, Taylor KWR, Kopf SH, Berstan R, Bull ID, Mayser JP, Leavitt WD, Blewett J, Pearson A, Pancost RD. Determination of the δ 2 H values of high molecular weight lipids by high-temperature gas chromatography coupled to isotope ratio mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8983. [PMID: 33068049 DOI: 10.1002/rcm.8983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The hydrogen isotopic composition of lipids (δ2 Hlipid ) is widely used in food science and as a proxy for past hydrological conditions. Determining the δ2 H values of large, well-preserved triacylglycerides and other microbial lipids, such as glycerol dialkyl glycerol tetraether (GDGT) lipids, is thus of widespread interest but has so far not been possible due to their low volatility which prohibits analysis by traditional gas chromatography/pyrolysis/isotope ratio mass spectrometry (GC/P/IRMS). METHODS We determined the δ2 H values of large, polar molecules and applied high-temperature gas chromatography (HTGC) methods on a modified GC/P/IRMS system. The system used a high-temperature 7-m GC column, and a glass Y-splitter for low thermal mass. Methods were validated using authentic standards of large, functionalised molecules (triacylglycerides, TGs), purified standards of GDGTs. The results were compared with δ2 H values determined by high-temperature elemental analyser/pyrolysis/isotope ratio mass spectrometry (HTEA/P/IRMS), and subsequently applied to the analysis of GDGTs in a sample from a methane seep and a Welsh peat. RESULTS The δ2 H values of TGs agreed within error between HTGC/P/IRMS and HTEA/IRMS, with HTGC/P/IRMS showing larger errors. Archaeal lipid GDGTs with up to three cyclisations could be analysed: the δ2 H values were not significantly different between methods with standard deviations of 5 to 6 ‰. When environmental samples were analysed, the δ2 H values of isoGDGTs were 50 ‰ more negative than those of terrestrial brGDGTs. CONCLUSIONS Our results indicate that the HTGC/P/IRMS method developed here is appropriate to determine the δ2 H values of TGs, GDGTs with up to two cyclisations, and potentially other high molecular weight compounds. The methodology will widen the current analytical window for biomarker and food light stable isotope analyses. Moreover, our initial measurements suggest that bacterial and archaeal GDGT δ2 H values can record environmental and ecological conditions.
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Affiliation(s)
- Sabine K Lengger
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- Biogeochemistry Research Centre, School of Geography, Earth and Environmental Science, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
| | - Yuki Weber
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St, Cambridge, MA, 02138, USA
| | - Kyle W R Taylor
- Elementar UK Ltd, Earl Road, Cheadle Hulme, Stockport, SK8 6PT, UK
| | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - Robert Berstan
- Elementar UK Ltd, Earl Road, Cheadle Hulme, Stockport, SK8 6PT, UK
| | - Ian D Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Jan-Peter Mayser
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - William D Leavitt
- Department of Earth Science, Department of Chemistry, Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jerome Blewett
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St, Cambridge, MA, 02138, USA
| | - Richard D Pancost
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- School of Earth Sciences and Cabot Institute for the Environment, University of Bristol, Queens Road, Bristol, BS8 1RL, UK
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7
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Magnesium magnetic isotope effects in microbiology. Arch Microbiol 2021; 203:1853-1861. [PMID: 33611633 DOI: 10.1007/s00203-021-02219-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/15/2020] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
Two main properties of atomic nuclei-mass and nuclear magnetic moments-are origin of many biological effects. Mass-dependent isotope effects have been studied for a long time. The effect of magnetic isotopes having a magnetic moment and spin was first shown in the early twenty-first century for the magnetic isotope magnesium 25Mg on enzymatic ATP synthesis. This stimulated the search for experimental evidence and theoretical justification of magnetic nuclei influence on biological processes. This review contains the results of scientific research on the magnesium magnetic isotope effects in microbiology. Microorganisms have been found to be sensitive to the presence of nuclear magnetic moment of magnesium isotope 25Mg compared with non-magnetic 24,26Mg isotopes.
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Wu W, Meador TB, Könneke M, Elvert M, Wegener G, Hinrichs KU. Substrate-dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:555-567. [PMID: 32783290 DOI: 10.1111/1758-2229.12876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/23/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Dual stable isotope probing has been used to infer rates of microbial biomass production and modes of carbon fixation. In order to validate this approach for assessing archaeal production, the methanogenic archaeon Methanosarcina barkeri was grown either with H2 , acetate or methanol with D2 O and 13 C-dissolved inorganic carbon (DIC). Our results revealed unexpectedly low D incorporation into lipids, with the net fraction of water-derived hydrogen amounting to 0.357 ± 0.042, 0.226 ± 0.003 and 0.393 ± 0.029 for growth on H2 /CO2 , acetate and methanol respectively. The variability in net water H assimilation into lipids during the growth of M. barkeri on different substrates is possibly attributed to different Gibbs free energy yields, such that higher energy yield promoted the exchange of hydrogen between medium water and lipids. Because NADPH likely serves as the portal for H transfer, increased NADPH production and/or turnover associated with high energy yield may explain the apparent differences in net water H assimilation into lipids. The variable DIC and water H incorporation into M. barkeri lipids imply systematic, metabolic patterns of isotope incorporation and suggest that the ratio of 13 C-DIC versus D2 O assimilation in environmental samples may serve as a proxy for microbial energetics in addition to microbial production and carbon assimilation pathways.
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Affiliation(s)
- Weichao Wu
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Travis B Meador
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
- Biology Centre Czech Academy of Sciences, Soil and Water Research Infrastructure, Ceske Budejovice, CZ-37005, Czechia
- Faculty of Science, Department Ecosystem Biology, University of South Bohemia, Ceske Budejovice, CZ-37005, Czechia
| | - Martin Könneke
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Gunter Wegener
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Centre for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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9
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Letuta UG, Binder AS, Tikhonova TA. Effect of Magnesium Isotopes on Antibiotic Sensitivity of E. coli. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Wijker RS, Sessions AL, Fuhrer T, Phan M. 2H/ 1H variation in microbial lipids is controlled by NADPH metabolism. Proc Natl Acad Sci U S A 2019; 116:12173-12182. [PMID: 31152138 PMCID: PMC6589753 DOI: 10.1073/pnas.1818372116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The hydrogen-isotopic compositions (2H/1H ratios) of lipids in microbial heterotrophs are known to vary enormously, by at least 40% (400‰) relative. This is particularly surprising, given that most C-bound H in their lipids appear to derive from the growth medium water, rather than from organic substrates, implying that the isotopic fractionation between lipids and water is itself highly variable. Changes in the lipid/water fractionation are also strongly correlated with the type of energy metabolism operating in the host. Because lipids are well preserved in the geologic record, there is thus significant potential for using lipid 2H/1H ratios to decipher the metabolism of uncultured microorganisms in both modern and ancient ecosystems. But despite over a decade of research, the precise mechanisms underlying this isotopic variability remain unclear. Differences in the kinetic isotope effects (KIEs) accompanying NADP+ reduction by dehydrogenases and transhydrogenases have been hypothesized as a plausible mechanism. However, this relationship has been difficult to prove because multiple oxidoreductases affect the NADPH pool simultaneously. Here, we cultured five diverse aerobic heterotrophs, plus five Escherichia coli mutants, and used metabolic flux analysis to show that 2H/1H fractionations are highly correlated with fluxes through NADP+-reducing and NADPH-balancing reactions. Mass-balance calculations indicate that the full range of 2H/1H variability in the investigated organisms can be quantitatively explained by varying fluxes, i.e., with constant KIEs for each involved oxidoreductase across all species. This proves that lipid 2H/1H ratios of heterotrophic microbes are quantitatively related to central metabolism and provides a foundation for interpreting 2H/1H ratios of environmental lipids and sedimentary hydrocarbons.
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Affiliation(s)
- Reto S Wijker
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125;
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Michelle Phan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
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11
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Neubauer C, Sessions AL, Booth IR, Bowen BP, Kopf SH, Newman DK, Dalleska NF. Towards measuring growth rates of pathogens during infections by D 2 O-labeling lipidomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2129-2140. [PMID: 30252972 DOI: 10.1002/rcm.8288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/10/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Microbial growth rate is an important physiological parameter that is challenging to measure in situ, partly because microbes grow slowly in many environments. Recently, it has been demonstrated that generation times of S. aureus in cystic fibrosis (CF) infections can be determined by D2 O-labeling of actively synthesized fatty acids. To improve species specificity and allow growth rate monitoring for a greater range of pathogens during the treatment of infections, it is desirable to accurately quantify trace incorporation of deuterium into phospholipids. METHODS Lipid extracts of D2 O-treated E. coli cultures were measured on liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) instruments equipped with time-of-flight (TOF) and orbitrap mass analyzers, and used for comparison with the analysis of fatty acids by isotope-ratio gas chromatography (GC)/MS. We then developed an approach to enable tracking of lipid labeling, by following the transition from stationary into exponential growth in pure cultures. Lastly, we applied D2 O-labeling lipidomics to clinical samples from CF patients with chronic lung infections. RESULTS Lipidomics facilitates deuterium quantification in lipids at levels that are useful for many labeling applications (>0.03 at% D). In the E. coli cultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl-containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific for S. aureus in CF sputum indicates an average generation time of the pathogen on the order of one cell doubling per day. CONCLUSIONS This study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D2 O.
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Affiliation(s)
- Cajetan Neubauer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, CA, 91125, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, CA, 91125, USA
| | - Ian R Booth
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | | | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO, 80309, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, CA, 91125, USA
| | - Nathan F Dalleska
- Environmental Analysis Center, California Institute of Technology, CA, 91125, USA
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12
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Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A. Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments. Int J Syst Evol Microbiol 2018; 68:1652-1658. [DOI: 10.1099/ijsem.0.002723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rachel Chang
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Lina Bird
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Magdalena Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Elizabeth Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Kenneth Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Annette Rowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
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Johnson DB, Beddows PA, Flynn TM, Osburn MR. Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico. GEOBIOLOGY 2018; 16:319-337. [PMID: 29656514 DOI: 10.1111/gbi.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for <3% of total abundance in Laguna Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this microbialite system.
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Affiliation(s)
- D B Johnson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - P A Beddows
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - T M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - M R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
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Campbell BJ, Sessions AL, Fox DN, Paul BG, Qin Q, Kellermann MY, Valentine DL. Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H 2-Oxidizing Cupriavidus necator. Front Microbiol 2017; 8:1886. [PMID: 29085342 PMCID: PMC5649130 DOI: 10.3389/fmicb.2017.01886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 09/14/2017] [Indexed: 11/25/2022] Open
Abstract
Fatty acids produced by H2-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 H2. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H2-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 δDwater 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 H2. 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 H2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H2 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.
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Affiliation(s)
- Brian J Campbell
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Daniel N Fox
- Undergraduate College of Letters and Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Blair G Paul
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Qianhui Qin
- Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Matthias Y Kellermann
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Wilhelmshaven, Germany
| | - David L Valentine
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, United States.,Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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Leavitt WD, Venceslau SS, Pereira IAC, Johnston DT, Bradley AS. Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression. FEMS Microbiol Lett 2016; 363:fnw226. [PMID: 27702753 DOI: 10.1093/femsle/fnw226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study, we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644T, to investigate how these parameters were perturbed by changes in expression of the protein DsrC. DsrC is critical to the final metabolic step in sulfate reduction to sulfide. S and H isotopic fractionation imposed by the wild type was compared to three mutants. Discrimination against 34S in sulfate, as calculated from the residual reactant, did not discernibly differ among all strains. However, a closed-system sulfur isotope distillation model, based on accumulated sulfide, produced inconsistent results in one mutant strain IPFG09. Lipids produced by IPFG09 were also slightly enriched in 2H. These results suggest that DsrC alone does not have a major impact on sulfate-S, though may influence sulfide-S and lipid-H isotopic compositions. While intriguing, a mechanistic explanation requires further study under continuous culture conditions.
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Affiliation(s)
- William D Leavitt
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA .,Department of Earth Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA .,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
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