David Thomas Johnston

David Thomas Johnston
Harvard University | Harvard · Department of Earth and Planetary Sciences

PhD

About

143
Publications
28,594
Reads
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7,857
Citations
Additional affiliations
June 2007 - present
Harvard University
Position
  • Professor (Associate)
July 2002 - May 2007
University of Maryland, College Park
Position
  • PhD Student

Publications

Publications (143)
Article
The triple-oxygen isotope (17 O/ 16 O, 18 O/ 16 O) measurement of oxygen-bearing species represents one of the most robust tools to directly trace oxygen cycling in the environment. One particularly consequential application of this isotope system is the analysis of dissolved oxygen (O 2) in aquatic environments to determine gross oxygen production...
Article
The 18O/16O of precipitated silica in natural environments is posited to record the temperature of the ambient environment. Measurements of 17O/16O in silica (SiO2), when paired with 18O/16O, provide an opportunity to further constrain the environmental conditions at the time of mineral precipitation and ripening. On Cenozoic timescales, siliceous...
Article
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Geobiology explores how Earth's system has changed over the course of geologic history and how living organisms on this planet are impacted by or are indeed causing these changes. For decades, geologists, paleontologists, and geochemists have generated data to investigate these topics. Foundational efforts in sedimentary geochemistry utilized sprea...
Article
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The reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolution...
Preprint
Full-text available
The reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolution...
Preprint
Full-text available
The ability of aerobic microorganisms to regulate internal and external concentrations of the reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by microorganisms to degrade superoxide. SOD is not one, but three separate, non-h...
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The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network-sulfate permease and sulfate adenylyl transferase (Sat)-on the sulfur and oxyge...
Article
Changes in the geological sulfur cycle are inferred from the sulfur isotopic composition of marine barite. The structure of the ³⁴ S/ ³² S record from the Mesozoic to present, which includes ∼50- and 100-Ma stepwise increases, has been interpreted as the result of microbial isotope effects or abrupt changes to tectonics and associated pyrite burial...
Article
The tempo and magnitude of ocean oxygenation during the rise of animals in the Ediacaran Period (635 to 539 million years ago, or Ma) is debated. Reconciling this debate is key to understanding what role, if any, oxygen played in the rise of large morphologically complex life on Earth. We reconstruct a portion of Ediacaran ocean oxygenation history...
Article
Throughout most of the sedimentary record, the marine carbon cycle is interpreted as being in isotopic steady state. This is most commonly inferred via isotopic reconstructions, where two export fluxes (organic carbon and carbonate) are offset by a constant isotopic fractionation of ~25 (termed ε o r g - c a r b ). Sedimentary deposits immediat...
Article
Here, we report the draft genome sequence of Dissulfurirhabdus thermomarina SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the phylum Desulfobacterota . Additionally, comparative genomic and phylogenetic analyses contextualize the converg...
Article
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The Ediacaran Period (635 to 541 Ma) marks the global transition to a more productive biosphere, evidenced by increased availability of food and oxidants, the appearance of macroscopic animals, significant populations of eukaryotic phytoplankton, and the onset of massive phosphorite deposition. We propose this entire suite of changes results from a...
Article
The temperature and chemistry of early seawater have both been inferred from the isotopic composition of Precambrian chert (SiO2), a precipitated mineral formed on or within marine sediments. The δ18O of chert shows a robust quasi-linear increase through time - a signal that has been interpreted in a number of conflicting ways. For example, changin...
Article
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Here, we describe the genome of Desulfobacter hydrogenophilus DSM 3380, a bacterium that belongs to the Desulfobacterales . The genome of this strictly anaerobic bacterium capable of sulfate reduction expands our understanding of microbial sulfate reduction in a wide range of environmental conditions.
Article
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Here, we describe the genome of Desulfovibrio sulfodismutans ThAc01, a Desulfobacterota member first isolated from freshwater mud and the first strain reported to be capable of growth via sulfur disproportionation. As such, this genome expands our understanding of the diversity of sulfur-disproportionating microorganisms.
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The majority of anaerobic biogeochemical cycling occurs within marine sediments. To understand these processes, quantifying the distribution of active cells and gross metabolic activity is essential. We present an isotope model rooted in thermodynamics to draw quantitative links between cell-specific sulfate reduction rates and active sedimentary c...
Preprint
Full-text available
Here, we report the draft genome sequence of Dissulfurirhabdus thermomarina SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the Desulfobacterota phylum. Additionally, comparative genomic and phylogenetic analyses contextualize the converge...
Article
Full-text available
Here, we describe the genome of Desulfofundulus thermobenzoicus subsp. thermosyntrophicus DSM 14055, a member of the Clostridiales that is capable of sulfate reduction coupled to the oxidation of propionate, lactate, pyruvate, and H 2 /CO 2 . This genome expands our understanding of microbial sulfate reduction (MSR) in anaerobic methanogenic enviro...
Article
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Here, we describe the genome sequence of Acidianus ambivalens DSM 3772, an archaeon belonging to the Sulfolobales order that was first isolated from continental solfataric fields. This thermoacidophile was sequenced because it utilizes a unique sulfur disproportionation pathway that enables this metabolism under aerobic conditions, in contrast to o...
Article
Atmospheric O2 and CO2 levels inform us of the changes in chemical and biological environments, yet the history of atmospheric compositions, and pO2 in particular, is not well-constrained. The triple oxygen isotope (16,17,18O) composition of marine SO42− has been proposed to directly record the ratio pO2/pCO2 in the contemporaneous atmosphere. To r...
Article
Measurements of triple oxygen isotope ratios in barite horizons within post-Marinoan cap carbonates have provided some of the most compelling evidence that the Marinoan glaciation was a Snowball Earth event. However, the origin of these barite horizons remains unresolved. To constrain the Ba sources, and thus formation mechanisms of these horizons,...
Article
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The sulfur isotope record provides key insight into the history of Earth's redox conditions. A detailed understanding of the metabolisms driving this cycle, and specifically microbial sulfate reduction (MSR), is crucial for accurate paleoenvironmental reconstructions. This includes a precise knowledge of the step-specific sulfur isotope effects dur...
Article
Recent studies targeting the metabolic, physiological, and biochemical controls of sulfur isotope fractionation in microbial systems have drawn linkages between results from culture experiments and the sulfur isotope signatures observed in natural environments. Several of those studies have used newer techniques to explore the minor isotope (³³S an...
Article
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Iron speciation and trace metal proxies are commonly applied together in efforts to identify anoxic settings marked by the presence of free sulfide (euxinia) or dissolved iron (ferruginous) in the water column. Here, we use a literature compilation from modern localities to provide a new empirical evaluation of coupled Fe speciation and Mo concentr...
Article
Ultramafic-hosted hydrothermal systems – characterized by ongoing serpentinization reactions – exert an important influence on the global sulfur cycle. Extensive water-rock interaction causes elemental exchange between seawater and the oceanic lithosphere, effectively removing sulfate from seawater through both abiogenic and biogenic processes. Her...
Article
A global rise in oxygen levels has been proposed to coincide with the Ediacaran to Cambrian radiation of animals, yet the precise timing and nature of this change remains unresolved. One hypothesis is that the ocean/atmosphere system became temporarily well-oxygenated in the earliest Ediacaran, directly following the Marinoan Snowball Earth glaciat...
Article
Euxinic conditions, which are defined by the presence of sulfide in the water column, were common in ancient oceans. However, it is not clear how the presence of sulfide in the water column affects the balance between rates of sulfide oxidation and sulfate reduction, which plays a major role in regulating the net redox state of the ocean-atmosphere...
Article
Full-text available
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,...
Article
A new approach for measuring the triple oxygen isotope composition of sulfate minerals was developed using fluorine gas and an infrared laser to generate O2. A correction for the mass-dependent isotope effect observed during barite fluorination was rigorously calibrated. Analyte gas purification was performed via numerous cryofocus steps and the in...
Article
The last 125Myr capture major changes in the chemical composition of the ocean and associated geochemical and biogeochemical cycling. The sulfur isotopic composition of seawater sulfate, as proxied in marine barite, is one of the more perplexing geochemical records through this interval. Numerous analytical and geochemical modeling approaches have...
Article
Full-text available
The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/3...
Article
Full-text available
Hydrothermal vents are thermally and geochemically dynamic habitats, and the organisms therein are subject to steep gradients in temperature and chemistry. To date, the influence of these environmental dynamics on microbial sulfate reduction has not been well constrained. Here, via multivariate experiments, we evaluate the effects of key environmen...
Article
Full-text available
Microbial sulfate reduction has governed Earth's biogeochemical sulfur cycle for at least 2.5 billion years. However, the enzymatic mechanisms behind this pathway are incompletely understood, particularly for the reduction of sulfite-a key intermediate in the pathway. This critical reaction is performed by DsrAB, a widespread enzyme also involved i...
Article
The causes behind the appearance of abundant macroscopic body and trace fossils at the end of the Neoproterozoic Era remain debated. Iron geochemical data from fossiliferous Ediacaran successions in Newfoundland suggested that the first appearances correlated with an oxygenation event. A similar relationship was claimed to exist in the Mackenzie Mo...
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Bioturbation, the physical and chemical mixing of sediment by burrowing animals, exerts an important control on the character of modern marine sediments and biogeochemical cycling. Here we show that the mixing of sediments on marine shelves remained limited until at least the late Silurian, 120 million years after the Precambrian-Cambrian transitio...
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The latest Neoproterozoic extinction of the Ediacara biota has been variously attributed to catastrophic removal by perturbations to global geochemical cycles, 'biotic replacement' by Cambrian-type ecosystem engineers, and a taphonomic artefact. We perform the first critical test of the 'biotic replacement' hypothesis using combined palaeoecologica...
Conference Paper
Full-text available
Serpentinization of ultramafic rocks has a significant influence on the cycling of elements between the hydrosphere, lithosphere and biosphere. Along mid-ocean ridge spreading centers exposure of mantle rock to seawater allows incorporation of seawater-derived carbon and sulfur storing these elements over millions of years. In contrast, in continen...
Article
Full-text available
Sedimentary rocks deposited across the Proterozoic-Phanerozoic transition record extreme climate fluctuations, a potential rise in atmospheric oxygen or re-organization of the seafloor redox landscape, and the initial diversification of animals. It is widely assumed that the inferred redox change facilitated the observed trends in biodiversity. Est...
Preprint
Full-text available
The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/3...
Article
Full-text available
Studies of microbial sulfate reduction have suggested that the magnitude of sulfur isotope fractionation varies with sulfate concentration. Small apparent sulfur isotope fractionations preserved in Archean rocks have been interpreted as suggesting Archean sulfate concentrations of <200 μm, while larger fractionations thereafter have been interprete...
Article
The stratigraphic record of shallow-water shoreline paleoenvironments is characterized by significant facies heterogeneity and laterally discontinuous stratal geometries. In contrast, we investigate a uniquely extensive and microstratigraphically spatially uniform interval of upper Famennian (Upper Devonian) marginal marine strata in the Rocky Moun...
Article
Full-text available
A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence...
Article
Full-text available
Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulf...
Article
Small shelly fossils are preserved as apatite steinkerns in the Cambrian Series 2-3 Thorntonia Limestone, Australia. Petrological observations indicate that phosphorus delivered to Thorntonia sediment was remobilized before precipitating in microenvironments defined by the matrix-filled interiors of small, mostly conical skeletons. A previous geoch...
Article
A quantitative understanding of sources and sinks of fixed nitrogen in low-oxygen waters is required to explain the role of oxygen-minimum zones (OMZs) in controlling the fixed nitrogen inventory of the global ocean. Apparent imbalances in geochemical nitrogen budgets have spurred numerous studies to measure the contributions of heterotrophic and a...
Article
Full-text available
We present 28 multiple sulfur isotope measurements of seawater sulfate (δ34SSO4δ34SSO4 and Δ33SSO4Δ33SSO4) from the modern ocean over a range of water depths and sites along the eastern margin of the Pacific Ocean. The average measured δ34SSO4δ34SSO4 is 21.24‰ (±0.88‰,2σ±0.88‰,2σ) with a calculated Δ33SSO4Δ33SSO4 of +0.050‰+0.050‰ (±0.014‰,2σ±0.014...
Article
Full-text available
A substantial body of evidence suggests that subsurface water masses in mid-Proterozoic marine basins were commonly anoxic, either euxinic (sulfidic) or ferruginous (free ferrous iron). To further document redox variations during this interval, a multiproxy geochemical and paleobiological investigation was conducted on the approximately 1000-m-thic...
Article
Full-text available
Video abstract: At Mistaken Point, Newfoundland, Canada, rangeomorph "fronds" dominate the earliest (579-565 million years ago) fossil communities of large (0.1 to 2 m height) multicellular benthic eukaryotes. They lived in low-flow environments, fueled by uptake [1-3] of dissolved reactants (osmotrophy). However, prokaryotes are effective osmotro...
Article
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The fossilization of organic remains and shell material by calcium phosphate minerals provides an illuminating, but time-bounded, window into Ediacaran-Cambrian animal evolution. For reasons that remain unknown, phosphatic fossil preservation declined significantly through Cambrian Series 2. Here, we investigate the phosphorus (P) sources for phosp...
Article
A mechanistic understanding of relationships between global glaciation, a putative second rise in atmospheric oxygen, the Shuram carbon isotope excursion, and the appearance of Ediacaran-type fossil impressions and bioturbation is dependent on the construction of accurate geological records through regional stratigraphic correlations. Here we integ...
Article
Late Neoproterozoic (Ediacaran) strata from northwestern Canada provide a thick and rich sedimentological record, preserving intercalated carbonates and shale extending from the ~635million year old Marinoan glacial deposits up through the ~541million year old Precambrian-Cambrian boundary. This region also holds one of the classic localities for t...
Article
The information encoded by the two stable isotope systems in sulfate (δS and δO) has been widely applied to aid reconstructions of both modern and ancient environments. Interpretation of δO records has been complicated by rapid oxygen isotope equilibration between sulfoxyanions and water. Specifically, the apparent relationship that develops betwee...
Conference Paper
Full-text available