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Leavitt, W. D.

Publications and source records attributed to Leavitt, W. D..

12 recordsLinked to original sources

Acetogenic methane-carbon monoxide comproportionation: an exergonic but unobserved microbial metabolism

Microbial metabolism relies on redox reactions that exploit chemical disequilibria. While aerobic carbon oxidation, carbon fixation, and fermentation are well studied, the broader space of anaerobic carbon redox reactions remains underexplored. In this study, carbon comproportionation, or reverse fermentation, reactions are identified as a previously unrecognized and potentially favorable class of microbial carbon redox transformations. Particular attention is given to the reaction between methane (CH4) and carbon monoxide (CO) to form acetate, a reaction that has not previously been evaluated despite the widespread occurrence of CH4 and CO in anoxic systems. Gibbs energies ({Delta}Gr) for this reaction were calculated across broad ranges of temperature, pH, and dissolved CH4 and CO concentrations using measured physicochemical data from a wide variety of environmental systems. We show that acetogenic CH4-CO comproportionation is exergonic in all environments where both substrates were detected. The most favorable energetic conditions occur at high pH, low temperature, and high reactant concentrations, consistent with cool serpentinizing systems. In several settings, the calculated Gibbs energy yields and energy densities overlap or exceed known anaerobic metabolisms involving CH4, CO, and acetate. These results demonstrate that acetogenic CH4-CO comproportionation can support microbial energy conservation in a variety of settings. To determine if this metabolism could have operated on early Earth or Mars, modeled fluid compositions show that this reaction is also exergonic under plausible physicochemical regimes. This work broadens the suite of possible microbial energy metabolisms and provides testable criteria for evaluating carbon-based catabolic reactions on Earth and on other planetary bodies. Plain Language SummaryMicroorganisms obtain energy by catalyzing chemical reactions in their environment. The energy available from a reaction can be quantified using Gibbs energies of reaction ({Delta}Gr). When {Delta}Gr < 0, energy is released that microorganisms can use to build biomass and carry out other activities. In this study, we predicted a new energy-yielding reaction that could potentially support microbial life. In this reaction, methane (CH4) is oxidized using carbon monoxide (CO) to produce acetate. Using thermodynamic calculations and measured geochemical data from natural environments, we show that this reaction can release usable energy under a wide range of conditions, including continental serpentinizing systems, the deep continental and marine subsurface, and geothermal springs. We also predict that this reaction could support life under plausible early Earth conditions and in modeled Martian fluids. Together, these observations identify the reaction of CH4 and CO to form acetate as a potentially viable microbial energy source in anoxic environments on Earth and other planetary bodies.

microbiology↗

The clumped isotope signatures of multiple methanogenesis metabolisms

Methane is a potent greenhouse gas, an important energy source, and a potential biosignature on extraterrestrial planetary bodies. The relative abundances of doubly substituted ("clumped") methane isotopologues (13CH3D and 12CH2D2) offer important information on the sources and sinks of methane. However, the clumped isotope signatures of microbially produced methane from different methanogenic pathways lack a systematic investigation. In this study, we provide a dataset encompassing the relative isotopologue abundances produced by hydrogenotrophic, methylotrophic, acetoclastic, and methoxydotrophic methanogenesis. We find that a statistical "combinatorial effect" generates significant differences in 12CH2D2 compositions between hydrogenotrophic methanogenesis and other pathways. The thermodynamic drive of methanogenic reactions and phylogenetic affiliation may also influence the isotope compositions of methane. Our study provides new experimental constraints on the isotope signatures of different microbial methanogenic pathways, and evidence of the mechanisms responsible for the observed differences. TeaserA novel stable isotope tool to track and differentiate sources of biological methane.

microbiology↗

Lipid hydrogen isotope compositions primarily reflect growth water in the model archaeon Sulfolobus acidocaldarius

The stable hydrogen isotope composition ({delta}2H) of lipid biomarkers can track environmental processes and remain stable over geologically relevant time scales, enabling studies of past climate, hydrology, and ecology. Most research has focused on lipids from the domain Eukarya (e.g., plant waxes, long-chain alkanes), and the potential of prokaryotic lipid biomarkers from the domain Archaea to offer unique insights into environments not captured by eukaryotic lipids remains unclear. Here, we investigate the H-isotope composition of biphytanes in Sulfolobus acidocaldarius, a model thermoacidophile and obligate heterotroph. We conducted a series of experiments that varied temperature, pH, shaking rate, electron acceptor availability, or electron donor flux. From these experiments, we quantified the lipid/water H-isotope fractionation (2{varepsilon}L/W) values for core biphytane chains derived from tetraether lipids. The 2{varepsilon}L/W values are consistently negative (-230 to - 180 {per thousand}) and are relatively invariant across all experiments despite a 20-fold change in doubling times and 2-fold change in lipid cyclization. The magnitude and relative invariance of 2{varepsilon}L/W values are consistent with studies on other heterotrophic archaea and suggests archaeal lipids may be faithful recorders of the {delta}2H composition of growth water. Our study highlights the potential of archaeal lipid {delta}2H as a hydrological proxy, offering new insights into environments where traditional proxies, such as plant-derived lipids, are not available, including extreme environments and extraterrestrial settings. ImportanceReconstructing past climates is crucial for understanding Earths environmental history and its responses to changing conditions. This study examines Sulfolobus acidocaldarius, a thermoacidophilic archaeon that thrives in extreme environments like hot springs. These microorganisms incorporate hydrogen water in the growth environment into membrane lipids, creating hydrogen isotope signatures that can reflect hydroclimate conditions. Our findings show that these hydrogen isotope ratios remain consistent even under varying temperature, pH, oxygen levels, and electron donor fluxes, indicating a stable fractionation between lipids and water. This invariance suggests that S. acidocaldarius lipids could serve as a robust proxy for reconstructing ancient water H-isotope values, especially in extreme environments where traditional proxies, such as plant waxes, are absent. This research has broader implications for planetary-scale reconstructions, including potential applications in studying past climates on other planets, such as Mars, where similar microorganisms may have existed in hydrothermal conditions.

microbiology↗

Environmental controls on crenarchaeol distributions in hydrothermal springs

Thermophilic archaea synthesize cellular membranes composed primarily of isoprenoid glycerol dibiphytanyl glycerol tetraethers (iGDGTs). Cells can adjust the packing of their lipids by increasing the number of cyclopentyl rings during lipid synthesis, thereby decreasing membrane permeability and fluidity to maintain cellular function at high temperature, acidic pH, or nutrient limitation. Archaea of the class Nitrososphaeria synthesize an iGDGT, crenarchaeol, with four cyclopentyl rings and a cyclohexyl ring, the function of which is unknown. Structural modeling suggests the cyclohexyl ring may increase membrane fluidity, potentially optimizing membranes for mesophilic conditions. To begin to investigate this hypothesis, iGDGT composition was quantified in forty-one thermal springs in Yellowstone National Park (YNP), USA, and contextualized within a global thermal spring iGDGT compilation with pH values of 1.1 to 10.1 and temperatures of 16 to 95{degrees}C. pH was the strongest predictor of both crenarchaeol relative abundance and the number of cyclopentyl rings per iGDGT. Crenarchaeol relative abundance exhibited a nonlinear relationship with pH and temperature, with highest relative abundances at pH 7.4 and 46{degrees}C, then decreasing above and below these values. These observations are consistent with the hypothesis that the cyclohexyl ring of crenarchaeol optimizes archaeal cellular membranes for circumneutral and moderate temperature environmental conditions. ImportanceArchaea change the composition of their membrane lipids to alter the fluidity of their membranes to maintain cell homeostasis when confronted with environmental stress. Some archaea of the class Nitrososphaeria produce a lipid, crenarchaeol, with a unique six-membered ring, the effect of which on archaeal membrane dynamics remains unknown. In this study, we identify pH as the most important geochemical variable for archaeal membrane response in Yellowstone National Park thermal springs. In addition, the lipid distributions indicate that crenarchaeol production is highest in circumneutral and mesophilic environments. The YNP results are supported by similar trends across global thermal springs.

microbiology↗

The hydrogen isotope signatures of autotrophy versus heterotrophy recorded in archaeal tetraether lipids

The stable hydrogen isotope composition of archaeal lipids is emerging as a potential paleoenvironmental proxy, adding to the well-established application of plant leaf wax-derived n-alkanes in paleohydrological reconstruction. A handful of studies reported relatively invariant and depleted hydrogen isotope compositions for archaeal lipids despite the range of different organisms and growth conditions explored. However, how modes of metabolism and physiological state (growth phase) affect the hydrogen isotope signatures of archaeal lipids remains poorly understood, limiting our ability to interpret archaeal lipid biomarker records from the environment. Here we conducted water isotope label experiments with a metabolically flexible and well-studied model archaeon Archaeoglobus fulgidus and quantified the hydrogen isotope fractionation between lipids and water in response to different carbon substrates and electron donor-acceptor pairs. The 2H/1H fractionation between lipids and water ({varepsilon}L/W) was overall negative, ranging from -280 to -226 {per thousand}, and overlapped with the ranges observed for other archaea in previous studies. Isotope flux-balance model results suggest that [&ge;]80 % and [&ge;]50 % of lipid-bound H in A. fulgidus cultures directly reflect water isotope compositions (i.e., not via organic substrate or H2) during autotrophy and heterotrophy, respectively. The model results also suggest the final saturation during isoprenoid lipid biosynthesis catalyzed by a flavoenzyme geranylgeranyl reductase likely contributes to the large 2H/1H fractionation observed in this study, consistent with previous isotope flux-balance model results for a different archaeon. Finally, we synthesized available data to compare {varepsilon}L/W patterns across all three domains of life: Bacteria, Archaea and Eukarya. Emerging patterns between archaeal and eukaryotic lipids are consistent with the notion of highly fractionating geranylgeranyl reductase, and the patterns between archaeal and bacterial lipids suggest that the general state of energy limitation may also contribute to large, negative values of {varepsilon}L/W observed in prokaryotic lipids. Altogether, these findings lend further support for the potential of archaeal lipid {varepsilon}L/W as a paleohydrological proxy and provide a broader insight into the 2H/1H fractionation mechanisms potentially shared among prokaryotic and eukaryotic lipid biomarkers.

microbiology↗

The evolution of multiply substituted isotopologues of methane during microbial aerobic oxidation

Aerobic methane oxidation (AeOM) is an important biological sink of methane on Earth. Stable isotopes are critical tools in tracking the sources and sinks of Earths surface methane budget. However, the major factors that influence the two multiply-substituted (clumped) isotope signatures of AeOM, {Delta}13CH3D and {Delta}12CH2D2, are not well known. Here we quantify the influence of kinetics as a function of temperature, and different methane monooxygenase (MMO) enzymes as a function of copper, on the isotopologue concentrations of residual methane by the obligate aerobic methanotroph, Methylococcus capsulatus (Bath). We observe deviations from traditional closed-system distillation (Rayleigh) fractionation during exponential growth at high oxidation rates. We model this as a reservoir effect controlled by the ratio of oxidation rate in the cells to transport rate of methane into the cells, where environmental temperature affects both rates. We also test whether clumped isotope fractionation values vary for the particulate versus soluble MMOs, but the results show minimal differences. We further determine that the back reaction (re-equilibration) of methane with medium water is unlikely. Together, the observations and model demonstrate that at low oxidation-to-transport ratios, the clumped isotope signatures follow canonical Rayleigh fractionation, whereas at high ratios, more positive {Delta}12CH2D2 values result, deviating from simple Rayleigh-like trajectories. This study shows that the methane oxidation-to-transport ratio is a critical influence on clumped isotope signatures of AeOM that should be considered when interpreting the isotopic data of natural methane samples in both open and closed systems.

microbiology↗

Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris

Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earths 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 co-vary. 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.

microbiology↗

Mode of carbon and energy metabolism shifts lipid composition in the thermoacidophile Acidianus

The degree of cyclization, or ring index (RI), in archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids was long thought to reflect homeoviscous adaptation to temperature. However, more recent experiments show that other factors (e.g., pH, growth phase, and energy flux) can also affect membrane composition. The main objective of this study was to investigate the effect of carbon and energy metabolism on membrane cyclization. To do so we cultivated Acidianus sp. DS80, a metabolically flexible and thermoacidophilic archaeon, on different electron donor, acceptor and carbon source combinations (S0/Fe3+/CO2, H2/Fe3+/CO2, H2/S0/CO2, or H2/S0/glucose). We show that differences in energy and carbon metabolism can result in over a full unit of change in RI in the thermoacidophile Acidianus sp. DS80. The patterns in RI correlated with the normalized electron transfer rate between electron donor and acceptor and did not always align with thermodynamic predictions of energy yield. In light of this, we discuss other factors that may affect the kinetics of cellular energy metabolism: electron transfer chain (ETC) efficiency, location of ETC reaction components (cytoplasmic vs. extracellular), and the physical state of electron donors and acceptors (gas vs. solid). Furthermore, assimilation of a more reduced form of carbon during heterotrophy appears to decrease the demand for reducing equivalents during lipid biosynthesis, resulting in lower RI. Together, these results point to the fundamental role of the cellular energy state in dictating GDGT cyclization, with those cells experiencing greater energy limitation synthesizing more cyclized GDGTs. ImportanceSome archaea make unique membrane-spanning lipids with different numbers of five or six membered rings in the core structure that modulate membrane fluidity and permeability. Changes in membrane core lipid composition reflect fundamental adaptation strategies of archaea in response to stress, but multiple environmental and physiological factors may affect the needs for membrane fluidity and permeability. In this study, we tested how Acidianus sp. DS80 changed its core lipid composition when grown with different electron donor/acceptor pairs. We show that changes in energy and carbon metabolisms significantly affected the relative abundance of rings in the core lipids of DS80. These observations highlight the need to better constrain metabolic parameters, in addition to environmental factors, that may influence changes in membrane physiology in Archaea. Such consideration would be particularly important for studying archaeal lipids from habitats that experience frequent environmental fluctuations and/or where metabolically diverse archaea thrive.

microbiology↗

Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflects pH

Many Archaea produce membrane-spanning glycerol dibiphytanyl glycerol tetraether (GDGTs) lipids that serve as unique biomarkers of past environments. These lipids can contain up to eight cyclopentane rings, where an increase in ring cyclization is generally associated with growth in more acidic, higher temperature, or more energy limited conditions. Recently the genes that encode GDGT ring synthases, grsAB, were identified and characterized in model thermoacidophiles Sulfolobus acidocaldarius and Saccharolobus solfataricus. However, the distribution and abundance of grs homologs across environments inhabited by these and related Archaea remains unknown. To address this, we examined the distribution of grs homologs in archaeal and bacterial cultivar genomes, single cell genomes, metagenomes, and metatranscriptomes from thermal springs across the planet, where temperature, pH, and geochemical data take at time of sampling. The relative abundance of grs in these microbial communities exhibits a strong negative correlation with pH, and weak positive correlation with temperature. Genomes and metagenome-assembled genomes (MAGs) from Archaea that encode two or more copies of grs are significantly more widespread in low pH springs. Homologs of grs were detected in MAGs from 12 archaeal classes, with the most well-represented being the Thermoproteia. Homologs of grs were also detected among several classes of uncultured Archaea, including the Korarchaeia, Bathyarchaeia, and Hadarchaeia. Several Nitrososphaeria MAGs had high copy numbers of grs (> 3), and the functional role of these copies cannot yet be explained. Notably, grs genes were also found in MAGs from the bacterial class Acidobacteria. Based on phylogenetic analyses, it is likely that Acidobacteria acquired these genes horizontally from Archaea. Broadly, our results highlight the key role of grs-catalyzed lipid cyclization in the diversification of Archaea in hot and acidic environments.

microbiology↗

Multiple environmental parameters impact core lipid cyclization in Sulfolobus acidocaldarius

Environmental reconstructions based on microbial lipids require understanding the coupling between environmental conditions and membrane physiology. The paleotemperature proxy TEX86 is built on the observation that archaea alter the number of five- and six-membered rings in the hydrophobic core of their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids when growing at different temperatures. However, recent work with these archaea also highlights a role for other factors, such as pH or energy availability in determining the degree of core lipid cyclization. To better understand the role of these variables we cultivated a model Crenarchaeon, Sulfolobus acidocaldarius, over a range in temperature, pH, oxygen flux, or agitation speed, and quantified the changes in growth rate, biomass yield, and core lipid compositions. The average degree of cyclization in core lipids correlated with growth rate under most conditions. When considered alongside other experimental findings from both the thermoacidophilic and mesoneutrophilic archaea, the results suggest the cyclization of archaeal lipids records a universal response to energy availability at the cellular level. Although we isolated the effects of individual parameters, there remains a need for multi-factor experiments (e.g., pH + temperature + redox) to establish a robust framework to interpret biomarker records of environmental change.

microbiology↗

Large hydrogen isotope fractionations distinguish nitrogenase-derived methane from other sources

Nitrogenase is the main source of natural fixed nitrogen for the biosphere. Two forms of this metalloenzyme, the vanadium (V) and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide into the potent greenhouse gas methane. Here we report carbon and hydrogen stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris. The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13CO2/CH4 = 1.051 {+/-} 0.002 for V-nitrogenase and 1.055 {+/-} 0.001 for Fe-only nitrogenase, mean {+/-} SE). In contrast, the hydrogen isotope fractionations (2H2O/CH4 = 2.071 {+/-} 0.014 for V-nitrogenase and 2.078 {+/-} 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2H2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2H, and that 2H2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles. ImportanceAll forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special protein, nitrogenase. Nitrogenase has a wide substrate range, and in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we developed an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a byproduct of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.

microbiology↗

Hydrogen Isotope Composition Of Thermoanaerobacterium saccharolyticum Lipids: Comparing Wild Type To A nfn- Transhydrogenase Mutant

AbstractThe 2H/1H ratio in microbial fatty acids can record information about the energy metabolism of microbes and about the isotopic composition of environmental water. However, the mechanisms involved in the fractionation of hydrogen isotopes between water and lipid are not fully resolved. We provide data aimed at understanding this fractionation in the Gram-positive obligately thermophilic anaerobe, Thermoanaerobacterium saccharolyticum, by comparing a wild-type strain to a deletion mutant in which the nfnAB genes encoding electron-bifurcating transhydrogenase have been removed. The wild-type strain showed faster growth rates and larger overall fractionation [Formula] than the mutant strain [Formula]. The overall trend in growth rate and fractionation, along with the isotopic ordering of individual lipids, is consistent with results reported for the Gram-negative sulfate reducer, Desulfovibrio alaskensis G20.

microbiology↗