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Ran X, Li X, Xie X, Lei J, Yang F, Chen D. Effects of Probiotic Enterococcus faecium from Yak on the Intestinal Microflora and Metabolomics of Mice with Salmonella Infection. Probiotics Antimicrob Proteins 2024; 16:1036-1051. [PMID: 37273089 DOI: 10.1007/s12602-023-10102-5] [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] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
Salmonella spp. are pathogenic bacteria that cause diarrhea, abortion, and death in yak and severely harm livestock breeding. Therefore, it is vital to identify a probiotic that effectively antagonizes Salmonella. To the best of our knowledge, few prior studies have investigated the efficacy of Enterococcus faecium against Salmonella. Here, we evaluated the enteroprotective mechanism of E. faecium in a mouse Salmonella infection model using hematoxylin-eosin (H&E) staining, quantitative real-time polymerase chain reaction (Q-PCR) technology, microbial diversity sequencing, and metabonomics. Enterococcus faecium inhibited the proinflammatory cytokines IL-1β, IL-6, TNF-α, and IFN-γ and promoted the anti-inflammatory cytokine IL-10. The Firmicutes/Bacteroidota (F/B) ratio and the abundances of Firmicutes and Akkermansia were significantly higher in the E. faecium than in the Salmonella group. Metabonomics and microbial diversity sequencing disclosed five different metabolites with variable importance in the projection (VIP) > 3 that were characteristic of both the Salmonella and E. faecium groups. Combined omics revealed that Lactobacillus and Bacteroides were negatively and positively correlated, respectively, with cholic acid, while Desulfovibrio was positively correlated with lipids in both the control and Salmonella groups. Desulfovibrio was also positively correlated with lipids in both the Salmonella and E. faecium groups. Enterococcus faecium antagonizes Salmonella by normalizing the abundance of the intestinal microorganisms and modulating their metabolic pathways. Hence, it may efficaciously protect the host intestine against Salmonella infection.
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Affiliation(s)
- Xuan Ran
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Xianhui Li
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Xueer Xie
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Jiangying Lei
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Falong Yang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest University for Nationalities), Ministry of Education, Chengdu, 610041, China
| | - Dechun Chen
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China.
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest University for Nationalities), Ministry of Education, Chengdu, 610041, China.
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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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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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4
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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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5
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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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6
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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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Liang J, Huang H, Wang S. Distribution, Evolution, Catalytic Mechanism, and Physiological Functions of the Flavin-Based Electron-Bifurcating NADH-Dependent Reduced Ferredoxin: NADP + Oxidoreductase. Front Microbiol 2019; 10:373. [PMID: 30881354 PMCID: PMC6405883 DOI: 10.3389/fmicb.2019.00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) is an electron-bifurcating enzyme first discovered in the strict anaerobes Clostridium kluyveri and Moorella thermoacetica. In vivo, Nfn catalyzes the endergonic reduction of NADP+ with NADH coupled to the exergonic reduction of NADP+ with reduced ferredoxin. Most Nfn homologs consist of two subunits, although in certain species Nfn homologs are fused. In contrast to other electron-bifurcating enzymes, Nfn possess a simpler structure. Therefore, Nfn becomes a perfect model to determine the mechanism of flavin-based electron bifurcation, which is a novel energy coupling mode distributed among anaerobic bacteria and archaea. The crystal structures of Nfn from Thermotoga maritima and Pyrococcus furiosus are known, and studies have shown that the FAD molecule of the NfnB (b-FAD) is the site of electron bifurcation, and other cofactors, including a [2Fe2S] cluster, two [4Fe4S] clusters, and the FAD molecule on the NfnA subunit, contribute to electron transfer. Further, the short-lived anionic flavin semiquinone (ASQ) state of b-FAD is essential for electron bifurcation. Nfn homologs are widely distributed among microbes, including bacteria, archaea, and probably eukaryotes, most of which are anaerobes despite that certain species are facultative microbes and even aerobes. Moreover, potential evidence shows that lateral gene transfer may occur in the evolution of this enzyme. Nfn homologs present four different structural patterns, including the well-characterized NfnAB and three different kinds of fused Nfn homologs whose detailed properties have not been characterized. These findings indicate that gene fusion/fission and gene rearrangement may contribute to the evolution of this enzyme. Under physiological conditions, Nfn catalyzes the reduction of NADP+ with NADH and reduced ferredoxin, which is then used in certain NADPH-dependent reactions. Deletion of nfn in several microbes causes low growth and redox unbalance and may influence the distribution of fermentation products. It’s also noteworthy that different Nfn homologs perform different functions according to its circumstance. Physiological functions of Nfn indicate that it can be a potential tool in the metabolic engineering of industrial microorganisms, which can regulate the redox potential in vivo.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Haiyan Huang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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8
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Assimilation and discrimination of hydrogen isotopes in a terrestrial mammal. Oecologia 2018; 188:381-393. [DOI: 10.1007/s00442-018-4221-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
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9
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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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10
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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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11
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Osburn MR, Dawson KS, Fogel ML, Sessions AL. Fractionation of Hydrogen Isotopes by Sulfate- and Nitrate-Reducing Bacteria. Front Microbiol 2016; 7:1166. [PMID: 27531993 PMCID: PMC4969296 DOI: 10.3389/fmicb.2016.01166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
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 δ2H 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 δ2H and metabolic pathway previously understood from aerobes. Despite the complexity, the large signals and rich variability of observed lipid δ2H suggest much potential as an environmental recorder of metabolism.
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Affiliation(s)
- Magdalena R Osburn
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Marilyn L Fogel
- Life and Environmental Sciences, School of Natural Science, University of California at Merced Merced, CA, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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