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ABSTRACT The microbial recycling of organic matter in marine sediments depends upon electron acceptors that are utilized based on availability and energetic yield. Since sulfate is the most abundant oxidant once oxygen has been depleted, the sulfide produced after sulfate reduction becomes an important electron donor for autotrophic microbes. The ability of sulfide to be re‐oxidized through multiple metabolic pathways and intermediates with variable oxidation states prompts investigation into which species are preferentially utilized and what are the factors that determine the fate of reduced sulfur species. Quantifying these sulfur intermediates in porewaters is a critical first step towards achieving a more complete understanding of the oxidative sulfur cycle, yet this has been accomplished in very few studies, none of which include oligotrophic sedimentary environments in the open ocean. Here we present profiles of porewater sulfur intermediates from sediments underlying oligotrophic regions of the ocean, which encompass about 75% of the ocean's surface and are characterized by low nutrient levels and productivity. Aiming at addressing uncertainties about if and how sulfide produced by the degradation of scarce sedimentary organic matter plays a role in carbon fixation in the sediment, we determine depth profiles of redox‐sensitive metals and sulfate isotope compositions and integrate these datasets with 16S rRNA microbial community composition data and solid‐phase sulfur concentrations. We did not find significant correlations between sulfur species or trace metals and specific sulfur cycling taxa, which suggests that microorganisms in pelagic and oxic sediments may be generalists utilizing flexible metabolisms to oxidize organic matter through different electron acceptors. 

Abstract The radiation of bioturbation during the Ediacaran–Cambrian transition has long been hypothesized to have oxygenated sediments, triggering an expansion of the habitable benthic zone and promoting increased infaunal tiering in early Paleozoic benthic communities. However, the effects of bioturbation on sediment oxygen are underexplored with respect to the importance of biomixing and bioirrigation, two bioturbation processes which can have opposite effects on sediment redox chemistry. We categorized trace fossils from the Ediacaran and Terreneuvian as biomixing or bioirrigation fossils and integrated sedimentological proxies for bioturbation intensity with biogeochemical modeling to simulate oxygen penetration depths through the Ediacaran–Cambrian transition. Ultimately, we find that despite dramatic increases in ichnodiversity in the Terreneuvian, biomixing remains the dominant bioturbation behavior, and in contrast to traditional assumptions, Ediacaran–Cambrian bioturbation was unlikely to have resulted in extensive oxygenation of shallow marine sediments globally. 

Abstract Planktonic calcifying organisms play a key role in regulating ocean carbonate chemistry and atmospheric CO₂. Surprisingly, references to the absolute and relative contribution of these organisms to calcium carbonate production are lacking. Here we report quantification of pelagic calcium carbonate production in the North Pacific, providing new insights on the contribution of the three main planktonic calcifying groups. Our results show that coccolithophores dominate the living calcium carbonate (CaCO₃) standing stock, with coccolithophore calcite comprising ~90% of total CaCO₃production, and pteropods and foraminifera playing a secondary role. We show that pelagic CaCO₃production is higher than the sinking flux of CaCO₃at 150 and 200 m at ocean stations ALOHA and PAPA, implying that a large portion of pelagic calcium carbonate is remineralised within the photic zone; this extensive shallow dissolution explains the apparent discrepancy between previous estimates of CaCO₃production derived from satellite observations/biogeochemical modeling versus estimates from shallow sediment traps. We suggest future changes in the CaCO₃cycle and its impact on atmospheric CO₂will largely depend on how the poorly-understood processes that determine whether CaCO₃is remineralised in the photic zone or exported to depth respond to anthropogenic warming and acidification. 

Abstract. We introduce a time-dependent, one-dimensional model ofearly diagenesis that we term RADI, an acronym accounting for the mainprocesses included in the model: chemical reactions, advection, molecularand bio-diffusion, and bio-irrigation. RADI is targeted for study ofdeep-sea sediments, in particular those containing calcium carbonates(CaCO3). RADI combines CaCO3 dissolution driven by organic matterdegradation with a diffusive boundary layer and integrates state-of-the-artparameterizations of CaCO3 dissolution kinetics in seawater, thusserving as a link between mechanistic surface reaction modeling andglobal-scale biogeochemical models. RADI also includes CaCO3precipitation, providing a continuum between CaCO3 dissolution andprecipitation. RADI integrates components rather than individual chemicalspecies for accessibility and is straightforward to compare againstmeasurements. RADI is the first diagenetic model implemented in Julia, ahigh-performance programming language that is free and open source, and itis also available in MATLAB/GNU Octave. Here, we first describe thescientific background behind RADI and its implementations. Following this, we evaluateits performance in three selected locations and explore other potentialapplications, such as the influence of tides and seasonality on earlydiagenesis in the deep ocean. RADI is a powerful tool to study thetime-transient and steady-state response of the sedimentary system toenvironmental perturbation, such as deep-sea mining, deoxygenation, oracidification events. 

The dissolution of CaCO 3 minerals in the ocean is a fundamental part of the marine alkalinity and carbon cycles. While there have been decades of work aimed at deriving the relationship between dissolution rate and mineral saturation state (a so-called rate law), no real consensus has been reached. There are disagreements between laboratory- and field-based studies and differences in rates for inorganic and biogenic materials. Rates based on measurements on suspended particles do not always agree with rates inferred from measurements made near the sediment–water interface of the actual ocean. By contrast, the freshwater dissolution rate of calcite has been well described by bulk rate measurements from a number of different laboratories, fit by basic kinetic theory, and well studied by atomic force microscopy and vertical scanning interferometry to document the processes at the atomic scale. In this review, we try to better unify our understanding of carbonate dissolution in the ocean via a relatively new, highly sensitive method we have developed combined with a theoretical framework guided by the success of the freshwater studies. We show that empirical curve fits of seawater data as a function of saturation state do not agree, largely because the curvature is itself a function of the thermodynamics. Instead, we show that models that consider both surface energetic theory and the complicated speciation of seawater and calcite surfaces in seawater are able to explain most of the most recent data.This new framework can also explain features of the historical data that have not been previously explained. The existence of a kink in the relationship between rate and saturation state, reflecting a change in dissolution mechanism, may be playing an important role in accelerating CaCO 3 dissolution in key sedimentary environments.