Gruen Danielle S.

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Gruen
First Name
Danielle S.
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Now showing 1 - 4 of 4
  • Preprint
    Experimental investigation on the controls of clumped isotopologue and hydrogen isotope ratios in microbial methane
    ( 2018-06-14) Gruen, Danielle S. ; Wang, David T. ; Könneke, Martin ; Topçuoğlu, Begüm D ; Stewart, Lucy C. ; Goldhammer, Tobias ; Holden, James F. ; Hinrichs, Kai-Uwe ; Ono, Shuhei
    The abundance of methane isotopologues with two rare isotopes (e.g., 13CH3D) has been proposed as a tool to estimate the temperature at which methane is formed or thermally equilibrated. It has been shown, however, that microbial methane from surface environments and from laboratory cultures is characterized by low 13CH3D abundance, corresponding to anomalously high apparent 13CH3D equilibrium temperatures. We carried out a series of batch culture experiments to investigate the origin of the non-equilibrium signals in microbial methane by exploring a range of metabolic pathways, growth temperatures, and hydrogen isotope compositions of the media. We found that thermophilic methanogens (Methanocaldococcus jannaschii, Methanothermococcus thermolithotrophicus, and Methanocaldococcus bathoardescens) grown on H2+CO2 at temperatures between 60 and 80°C produced methane with Δ13CH3D values (defined as the deviation from stochastic abundance) of 0.5 to 2.5‰, corresponding to apparent 13CH3D equilibrium temperatures of 200 to 600°C. Mesophilic methanogens (Methanosarcina barkeri and Methanosarcina mazei) grown on H2+CO2, acetate, or methanol produced methane with consistently low Δ13CH3D values, down to -5.2‰. Closed system effects can explain part of the non-equilibrium signals for methane from thermophilic methanogens. Experiments with M. barkeri using D-spiked water or D-labeled acetate (CD3COO-) indicate that 1.6 to 1.9 out of four H atoms in methane originate from water, but Δ13CH3D values of product methane only weakly correlate with the D/H ratio of medium water. Our experimental results demonstrate that low Δ13CH3D values are not specific to the metabolic pathways of methanogenesis, suggesting that they could be produced during enzymatic reactions common in the three methanogenic pathways, such as the reduction of methyl-coenzyme M. Nonetheless C-H bonds inherited from precursor methyl groups may also carry part of non-equilibrium signals.
  • Preprint
    Nonequilibrium clumped isotope signals in microbial methane
    ( 2015-02-09) Wang, David T. ; Gruen, Danielle S. ; Lollar, Barbara Sherwood ; Hinrichs, Kai-Uwe ; Stewart, Lucy C. ; Holden, James F. ; Hristov, Alexander N. ; Pohlman, John W. ; Morrill, Penny L. ; Konneke, Martin ; Delwiche, Kyle B. ; Reeves, Eoghan P. ; Sutcliffe, Chelsea N. ; Ritter, Daniel J. ; Seewald, Jeffrey S. ; McIntosh, Jennifer C. ; Hemond, Harold F. ; Kubo, Michael D. Y. ; Cardace, Dawn ; Hoehler, Tori M. ; Ono, Shuhei
    Methane is a key component in the global carbon cycle with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply-substituted “clumped” isotopologues, e.g., 13CH3D, has recently emerged as a proxy for determining methane-formation temperatures; however, the impact of biological processes on methane’s clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on 13CH3D abundances and results in anomalously elevated formation temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.
  • Article
    Paleozoic diversification of terrestrial chitin-degrading bacterial lineages
    (Springer Nature, 2019-01-28) Gruen, Danielle S. ; Wolfe, Joanna M. ; Fournier, Gregory P.
    Background Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT) can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups that lack fossils. While HGT is common between lineages, only a small subset of HGT events are potentially informative for dating microbial groups. Results Constrained by published fossil-calibrated studies of fungal evolution, molecular clock analyses show that multiple clades of Bacteria likely acquired chitinase homologs via HGT during the very late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades likely diversified ~ 300–500 million years ago, consistent with established timescales of arthropod and plant terrestrialization. Conclusions We conclude that these age estimates are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and ecological expansion of detrital-chitin producing groups. The convergence of multiple lines of evidence demonstrates the utility of HGT-based dating methods in microbial evolution. The pattern of inheritance of chitinase genes in multiple terrestrial bacterial lineages via HGT processes suggests that these genes, and possibly other genes encoding substrate-specific enzymes, can serve as a “standard candle” for dating microbial lineages across the Tree of Life.
  • Thesis
    Biogeochemical and phylogenetic signals of Proterozoic and Phanerozoic microbial metabolisms
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2018-09) Gruen, Danielle S.
    Life is ubiquitous in the environment and an important mediator of Earth’s carbon cycle, but quantifying the contribution of microbial biomass and its metabolic fluxes is difficult, especially in spatially and temporally-remote environments. Microbes leave behind an often scarce, unidentifiable, or nonspecific record on geologic timescales. This thesis develops and employs novel geochemical and genetic approaches to illuminate diagnostic signals of microbial metabolisms. Field studies, laboratory cultures, and computational models explain how methanogens produce unique nonequilibrium methane clumped isotopologue (13CH3D ) signals that do not correspond to growth temperature. Instead, Δ13CH3D values may be driven by enzymatic reactions common to all methanogens, the C-H bond inherited from substrate precursors including acetate and methanol, isotope exchange, or environmental processes such as methane oxidation. The phylogenetic relationship between substrate-specific methyl-corrinoid proteins provides insight into the evolutionary history of methylotrophic methanogenesis. The distribution of corrinoid proteins in methanogens and related bacteria suggests that these substrate-specific proteins evolved via a complex history of horizontal gene transfer (HGT), gene duplication, and loss. Furthermore, this work identifies a previously unrecognized HGT involving chitinases (ChiC/D) distributed between fungi and bacteria (∼650 Ma). This HGT is used to tether fossil-calibrated ages from within fungi to bacterial lineages. Molecular clock analyses show that multiple clades of bacteria likely acquired chitinase homologs via HGT during the late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades diversified ∼400-500 Ma, consistent with established timescales of arthropod and plant terrestrialization. Divergence time estimates for bacterial lineages are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and expansion of detrital-chitin producing groups including arthropods. These chitinases may aid in dating microbial lineages over geologic time and provide insight into an ecological shift from marine to terrestrial systems in the Proterozoic and Phanerozoic eons. Taken together, this thesis may be used to improve assessments of microbial activity in remote environments, and to enhance our understanding of the evolution of Earth’s carbon cycle.