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            H variation in microbial lipids is controlled by NADPH metabolism

Wijker, Reto S.; Sessions, Alex L.; Fuhrer, Tobias; Phan, Michelle

doi:10.1073/pnas.1818372116

Cited by 39 publications

(94 citation statements)

References 66 publications

(124 reference statements)

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“…The varying fractionation factors for different substrates are consistent with the pattern that chemoautotrophy is generally associated with higher lipid-water hydrogen isotope fractionation than heterotrophy (Zhang et al, 2009a). This supports the notion that central metabolisms affect the archaeal lipid hydrogen isotope composition (Zhang et al, 2009a;Wijker et al, 2019). During growth on deuterated medium (1% D 2 O; equal to a δD of~+ 64,000‰), the δD values of all three archaeal lipids ranged from +600 to +25 600‰ (Supporting information Table S1).…”

Section: Hydrogen Isotopic Composition Of Archaeal Lipids During Growsupporting

confidence: 78%

“…S1). This contrasts the relative contribution of hydrogen sources to bacterial fatty acid biosynthesis (50%, 25%, and 25% for NADPH, substrate, and water respectively; Valentine, 2009;Zhang et al, 2009a;Wijker et al, 2019). The relatively high contribution of hydrogen atoms derived from sources other than water to archaeal methanogen lipids is consistent with >50% of lipid C being derived from the 13 Clabelled methyl groups of methanol or acetate (see Results).…”

Section: Constraints Of Water-derived Hydrogen To Lipid Biosynthesismentioning

confidence: 79%

“…Stable isotopic compositions of microbial lipids provide valuable metabolic and taxonomic information that helps to decipher the role of microorganisms in biogeochemical cycles (Hayes, 1993;Hinrichs et al, 1999;Dawson et al, 2015). The 13 C/ 12 C ratio, expressed as δ 13 C, of microbial biomass is primarily determined by the carbon sources, fixation pathways and physiological conditions (e.g., Hinrichs et al, 1999;Hayes, 2001;Boschker and Middelburg, 2002;Schouten et al, 2004;Londry et al, 2008;Blaser et al, 2015), whereas the ratio of stable hydrogen isotopes (deuterium/protium ratio; D/H; expressed as δD) is determined by the water and substrate-based sources of hydrogen and the interactions of central metabolic pathways (Valentine, 2009;Zhang et al, 2009a;Wijker et al, 2019). The fractionation factors that determine the δD value of lipids versus source water vary systematically with specific metabolisms, showing a decrease in the order: heterotrophic growth on TCA-cycle precursors and intermediates > heterotrophic growth on sugars > photoautotrophy > chemoautotrophy (Valentine et al, 2004a;Sessions and Hayes, 2005;Zhang et al, 2009a).…”

Section: Introductionmentioning

confidence: 99%

“…Lipid-based SIP with D 2 O provides a bulk, quantitative estimate of microbial community production, without altering natural conditions or selecting for certain autotrophic or heterotrophic C metabolisms, via the measurement of D incorporation into lipids via established gas chromatography-isotope ratio mass spectrometry. Water-derived hydrogen incorporation into lipids is essentially mediated by NADPH in the central metabolism (Zhang et al, 2009a;Berry et al, 2015;Wijker et al, 2019), where NADPH gains hydrogen from organic substrates or water-derived hydrogen via diverse metabolic processes such as glycolysis, the oxidative pentose phosphate pathway and the TCA cycle (Zhang et al, 2009a;Spaans et al, 2015;Wijker et al, 2019). Isotope labeling studies of fatty acid biosynthesis in heterotrophic bacteria indicate that NADPH is the most important H source (~50%) and controls the isotope effect during lipid biosynthesis, while the medium water (~25%) is of less importance relative to NADPH (Saito et al, 1980;Valentine, 2009;Zhang et al, 2009a;Osburn et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Despite this, the resulting δD values of lipids are generally well correlated with that of the medium water source (Valentine et al, 2004b;Zhang et al, 2009a;Zhang et al, 2009b;Pagani, 2013a, 2013b), highlighting that water plays an additional indirect role (Zhang et al, 2009a) in determining lipid hydrogen isotopic composition by potential hydrogen exchange between NADPH and water. Due to the difficulty in determining the hydrogen isotopic composition of NADPH, two ultimate H sources (i.e., external water and organic substrates) are assumed to be incorporated into lipids, with the final lipid H isotopic composition determined by isotope effects of metabolic fluxes and the enzymes involved (Sessions and Hayes, 2005;Zhang et al, 2009a;Wijker et al, 2019). Therefore, the fractionation factor between water and lipids (α l/w ) and the net water-derived hydrogen contribution (X w ) have to be considered for hydrogen assimilation during lipid biosynthesis (Sessions and Hayes, 2005;Zhang et al, 2009a;Kopf et al, 2015Kopf et al, , 2016.…”

Section: Introductionmentioning

confidence: 99%

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Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri

Meador

Könneke

et al. 2020

Environ Microbiol Rep

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Summary 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 D2O and 13C‐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 13C‐DIC versus D2O 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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Section: Hydrogen Isotopic Composition Of Archaeal Lipids During Growsupporting

confidence: 78%

Section: Constraints Of Water-derived Hydrogen To Lipid Biosynthesismentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri

Meador

Könneke

et al. 2020

Environ Microbiol Rep

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Archaeal lipid hydrogen isotopes in a marine thaumarchaeon

Leavitt

Kopf

Weber

et al. 2022

Preprint

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The stable hydrogen isotope composition of persistent biomolecules is used as a paleoenvironmental proxy. While much previous work has focused on plant leaf wax-derived n-alkanes, the potential of bacterial and archaeal lipid biomarkers as carriers of H isotope signatures remains underexplored. Here we investigated H isotope distributions in the membrane lipids of the ammonia-oxidizing chemoautotroph Nitrosopumilus maritimus strain SCM1. Hydrogen isotope ratios were measured on the biphytane chains of tetraether membrane lipids extracted from steady-state continuous cultures cultivated at slow, medium, and fast growth rates. In contrast to recent work on bacterial fatty acids, where the direction and magnitude of isotopic fractionation varies widely (ca. 600 energy metabolism, archaeal biphytane data in the present work are relatively invariant. The weighted average 2H/1H fractionation values relative to growth water (2εL/W) only ranged from 272 to 260 a three-fold difference in doubling times (30.8 hr to 92.5 hr), yielding an average growth-rate effect of 0.2 depleted than all heterotrophic archaeal and bacterial lipid H isotope measurements in the literature, and on par with those from other autotrophic archaea, as well as isoproenoid-based lipids in photoautotrophic algae. N. maritimus values of 2εL/W also varied systematically with the number of internal rings (cyclopentyl + cyclohexyl), increasing for each additional ring by 6.4 ± 2.7 an isotope flux-balance model in tandem with a comprehensive analysis of the sources of H in archaeal lipid biosynthesis, we use this observation to estimate the kinetic isotope effects (KIEs) of H incorporation from water; from reducing cofactors such as ferredoxin, and for the transhydrogenation reaction(s) that convert the electron-donor derived NADH into NADPH for anabolic reactions. Consistent with prior studies on bacteria, our results indicate the KIEs of reducing cofactors and transhydrogenation processes in archaea are highly fractionating, while those involving exchange of water protons are less so. When combined with the observation of minimal growth-rate sensitivity, our results suggest biphytanes of autotrophic 3HP/4HB Thaumarchaeota may be offset from source waters by a nearly constant 2εL/W value. Together with the ring effect, this implies that all biphytanes originating from a common source should have a predictable ordering of their isotope ratios with respect to biphytane ring number, allowing precise reconstruction of the original δ2H value of the growth water. Collectively, these patterns indicate archaeal biphytanes have potential as paleo-hydrological proxies, either as a complement or an alternative to leaf wax n-alkanes.

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Determination of the δ²H values of high molecular weight lipids by high‐temperature gas chromatography coupled to isotope ratio mass spectrometry

Lengger

Weber

Taylor³

et al. 2021

Rapid Comm Mass Spectrometry

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Rationale: The hydrogen isotopic composition of lipids (δ 2 Hlipid) is widely used in food science and as a proxy for past hydrological conditions. Determining the δ 2 H values of large, well-preserved triacylglycerides and other uniquely microbial lipids, such as glycerol dialkyl glycerol tetraether (GDGT) lipids, is thus of widespread interest but has so far not been This is a non-peer reviewed manuscript submitted to Rapid Communications in Mass Spectrometry. 2 possible due to their size which prohibits analysis by traditional gas chromatography pyrolysis isotope ratio mass spectrometry (GC-P-IRMS). Methods: We determined the δ 2 H values of large, polar molecules and applied high temperature gas chromatography (GC) methods on a modified GC-P-IRMS system. The methods were validated using authentic standards of large, functionalised molecules (triacylglycerides, TAG), purified reference standards of GDGTs, and compared to δ 2 H values determined by elemental analyser pyrolysis isotope ratio mass spectrometry (EA-P-IRMS); and subsequently applied to the analysis of GDGTs in a sample from a methane seep and a Welsh peat. Results: δ 2 H values of TAGs agreed within error between different between GC-P-IRMS and EA-P-IRMS, with GC-P-IRMS showing 3-5 ‰ precision for 10 ng H injected. Archaeal lipid GDGTs with up to three cyclisations could be analysed: δ 2 H values were not significantly different between methods with standard deviations of 5 to 6 ‰. When environmental samples were analysed, δ 2 H values of isoGDGTs were 50 ‰ more negative than those of terrestrial brGDGTs. Conclusions: Our results indicate that the high temperature GC-P-IRMS (HTGC-P-IRMS) method developed here is appropriate to determine the δ 2 H values of TAGs, GDGT lipids with up to two cyclisations, and potentially other high molecular weight compounds. The methodology will widen the current analytical window for biomarker and alimentary light stable isotope analyses. Moreover, our initial measurements suggest that bacterial and archaeal GDGT δ 2 H values can record environmental and ecological conditions.

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² H/ ¹ H variation in microbial lipids is controlled by NADPH metabolism

Cited by 39 publications

References 66 publications

Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri

Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri

Archaeal lipid hydrogen isotopes in a marine thaumarchaeon

Determination of the δ²H values of high molecular weight lipids by high‐temperature gas chromatography coupled to isotope ratio mass spectrometry

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2 H/ 1 H variation in microbial lipids is controlled by NADPH metabolism

Cited by 39 publications

References 66 publications

Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri

Substrate‐dependent incorporation of carbon and hydrogen for lipid biosynthesis by Methanosarcina barkeri

Archaeal lipid hydrogen isotopes in a marine thaumarchaeon

Determination of the δ2H values of high molecular weight lipids by high‐temperature gas chromatography coupled to isotope ratio mass spectrometry

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Product

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² H/ ¹ H variation in microbial lipids is controlled by NADPH metabolism

Determination of the δ²H values of high molecular weight lipids by high‐temperature gas chromatography coupled to isotope ratio mass spectrometry