Biogeochemical modeling

Trace elements and isotopes (TEIs) are important tools in studying ocean biogeochemistry. Understanding their modern ocean budgets and using their sedimentary records to reconstruct paleoceanographic conditions require a mechanistic understanding of the diagenesis of TEIs, yet the lack of appropriate modeling tools has limited our ability to perform such research. Here I introduce SedTrace, a modeling framework that can be used to generate reactive-transport code for modeling marine sediment diagenesis and assist model simulation using advanced numerical tools in Julia. SedTrace enables mechanistic TEI modeling by providing flexible tools for pH and speciation modeling, which are essential in studying TEI diagenesis. SedTrace is designed to solve one particular challenge facing users of diagenetic models: existing models are usually case-specific and not easily adaptable for new problems such that the user has to choose between modifying published code and writing their own code, both of which demand strong coding skills. To lower this barrier, SedTrace can generate diagenetic models only requiring the user to supply Excel spreadsheets containing necessary model information. The resulting code is clearly structured and readable, and it is integrated with Julia’s differential equation solving ecosystems, utilizing tools such as automatic differentiation, sparse numerical methods, Newton–Krylov solvers and preconditioners. This allows efficient solution of large systems of stiff diagenetic equations. I demonstrate the capacity of SedTrace using case studies of modeling the diagenesis of pH as well as radiogenic and stable isotopes of TEIs.

Dissolved Rare Earth Elements (REE) and radiogenic neodymium (epsilon(Nd)) isotope composition (ENd) of seawater are widely used geochemical tools in studying marine processes, but their modern ocean budgets are poorly understood. Recent discoveries of large benthic fluxes of REE with unique epsilon(Nd) signatures from marine sediments, particularly in the deep-sea, have led to a “bottom-up” hypothesis, which suggests that early diagenesis below the sediment-water interface (SWI) controls the ocean’s REE and epsilon(Nd) budgets. To investigate such sedimentary processes, we created a reactive-transport model for the biogeochemical cycling of Nd and epsilon(Nd) in marine sediments. Here, we attempt to quantify the roles of authigenesis, marine silicate weathering and reverse weathering in the diagenetic cycling of Nd and epsilon(Nd) at a deep-sea (3000 m) site on the Oregon margin. Our model predicts that, at this site, Nd carried by Fe/Mn oxides into sediments eventually transforms to authigenic Nd-phosphate, during which similar to 9% of the incoming solid Nd flux is released as a dissolved benthic flux back to the overlying bottom water. We also find that the classic reversible scavenging formulation applied to Nd co-cycling with Fe/Mn oxides is inconsistent with the data. Rather, a co-precipitation formulation, assuming Nd is structurally incorporated into Fe/Mn oxides, successfully simulates the data. The model also shows that authigenesis alone cannot explain the pore water and authigenic epsilon(Nd), which are both more radiogenic than bottom water at this site. However, the weathering of volcanic silicates sourced from the local subduction zone can successfully explain epsilon(Nd). We suggest that, because reverse weathering by authigenic clay formation maintains the under-saturation of primary silicates in pore water, marine silicate weathering can proceed. The processes we model likely affect the sedimentary cycling of many other trace elements and isotopes, with much broader implications for the understanding of ocean biogeochemistry. (C) 2022 The Author(s). Published by Elsevier B.V.

The Global Overturning Circulation is linked to climate change on glacial-interglacial and multi-millennial timescales. The understanding of past climate-circulation links remains hindered by apparent conflicts among proxy measures of circulation. Here we reconstruct circulation changes since the Last Glacial Maximum (LGM) based on a global synthesis of authigenic neodymium isotope records (epsilon(Nd)). We propose the bottom-up framework of interpreting seawater and authigenic epsilon(Nd) considering not only conservative watermass mixing, but also the preformed properties and the non-conservative behavior of epsilon(Nd), both subject to sedimentary influences. We extract the major spatial-temporal modes of authigenic epsilon(Nd) using Principal Component Analysis, and make a first-order circulation reconstruction with budget-constrained box model simulations. We show that during the LGM, the source region of North Atlantic overturning shifted southward, which led to more radiogenic preformed epsilon(Nd) of glacial Northern Source Water (NSW). Considering this preformed effect, we infer that glacial deep Atlantic had a similar proportion of NSW as today, although the overall strength of glacial circulation appears reduced from both North Atlantic and Southern Ocean sources, which increased the relative importance of nonconservative behavior of epsilon(Nd) and may have facilitated accumulation of respired carbon in the deep ocean. During the deglaciation, we find that Southern Ocean overturning increased, which offset suppressed North Atlantic overturning and resulted in a net stronger global abyssal circulation. Faster global scale deglacial circulation reduced the relative importance of non-conservative effects, resulting in AtlanticPacific convergence of abyssal epsilon(Nd) signatures. Variations of Southern Ocean overturning likely drove a significant fraction of deglacial changes in atmospheric CO2 and oceanic heat budget. (C) 2020 The Author(s). Published by Elsevier Ltd.

The role of nickel (Ni) in ocean biogeochemical cycles is both under-studied and controversial. Strong correlations between Ni and organic carbon in modern and ancient marine sediments suggest a prominent biogeochemical role over a substantial portion of Earth history. Addition of Ni to culturing and seawater incubation experiments produces strong responses in terms of cell growth, particularly of nitrogen-fixing organisms. But the implied limiting role for phytoplankton growth is inconsistent with observations in the real ocean, specifically that photic zone Ni concentrations never descend to the very low values that characterise other bioactive, and often bio-limiting, metals like iron. These two observations can be reconciled if a large portion of the total dissolved Ni present in open-ocean surface waters is not bio-available on short timescales. Here we present new Ni concentration and stable isotope data from the GEOVIDE transect in the North Atlantic. We interpret these new data in the light of the growing database for Ni stable isotopes in the modern ocean, with implications for the biogeochemical importance of Ni. In the new North Atlantic dataset, the lowest Ni concentrations (1.8-2.6 nmol/L) and highest delta Ni-60 (up to +1.67 parts per thousand) are associated with low nitrate, south of the subarctic front (SAF). By contrast, stations at latitudes north of the SAF, with higher surface nitrate, show very subdued variation in Ni concentrations throughout the entire depth of the water column (3.6 +/- 0.3 nmol/L, mean and 2SD), and no variation in delta Ni-60 beyond the narrow global deep-ocean range (+1.33 +/- 0.13 parts per thousand). These North Atlantic Ni isotope data also show relationships with nitrogen isotope effects, observed in the same samples, that are suggestive of a link between Ni utilisation, isotope fractionation and nitrogen fixation. The global dataset, including the new data presented here, reveals a biogeochemical divide with Ni isotope fractionation only occurring in low latitude surface waters. A simple observationally constrained three-dimensional model of Ni cycling suggests that the creation of this isotopically heavy, Ni-poor, end-member, together with the physical circulation and remineralisation at depth, can explain the global Ni-delta Ni-60 systematics. Taken together, these findings hint at Ni-N co-limitation in the modern ocean. We advocate for more extensive and detailed culturing/incubation studies of this neglected metal in order to elucidate its potentially crucial biogeochemical role. (C) 2022 The Author(s). Published by Elsevier B.V.