dSED: a database tool for modeling sediment early diagenesis (2023)

Oxygenic photosynthesis is arguably the most important biological innovation in Earth's history, facilitating the transition to a habitable planet for complex life. Dating the emergence of oxygenic photosynthesis, however, has proven difficult with estimates spanning a billion years. Sedimentary manganese (Mn) enrichments represent a potentially important line of evidence given the high redox potentials necessary to oxidize Mn in natural environments. However, this view has been challenged by abiotic and anaerobic Mn oxidation pathways that decouple Mn enrichments from oxygenation. With these in mind, we review Mn oxidation pathways and Mn enrichments and evaluate their relation to Earth's oxygenation. We argue that despite possible alternative pathways, shallow oxygenated seawater is a prerequisite for generating and, importantly, preserving significant sedimentary Mn enrichments (and associated geochemical signals). This implies that Mn enrichments indeed track Earth's oxygenation and oxygenic photosynthesis emerged 100s of millions of years prior to irreversible atmospheric oxygenation.

Dissimilatory sulfate reduction (DSR) is a major carbon mineralization pathway in aquatic sediments, soils, and groundwater, which regulates the production of hydrogen sulfide and the mobilization rates of biologically important elements such as phosphorus and mercury. It has been widely assumed that water-column sulfate is the main sulfur source to fuel this reaction in sediments. While this assumption may be justified in high-sulfate environments such as modern seawater, we argue that in low-sulfate environments mineralization of organic sulfur compounds can be an important source of sulfate. Using a reaction-transport model, we investigate the production of sulfate from sulfur-containing organic matter for a range of environments. The results show that in low sulfate environments (<500μM) the in-sediment production of sulfate can support a substantial portion (>50%) of sulfate reduction. In well-oxygenated systems, porewater sulfate profiles often exhibit sub-interface peaks so that sulfate fluxes are directed out of the sediment. Our measurements in Lake Superior, the world’s largest lake, corroborate this conclusion: offshore sediments act as sources rather than sinks of sulfate for the water column, and sediment DSR is supported entirely by the in-sediment production of sulfate. Sulfate reduction rates are correlated to the depth of oxygen penetration and strongly regulated by the supply of reactive organic matter; rate co-regulation by sulfate availability becomes appreciable below 500μM level. The results indicate the need to consider the mineralization of organic sulfur in the biogeochemical cycling in low-sulfate environments, including several of the world’s largest freshwater bodies, deep subsurface, and possibly the sulfate-poor oceans of the Early Earth.

Phosphorus (P) releases from lake sediments are controlled in the long term by P burial into the deep sediment and on shorter time scales by the redox conditions at the sediment–water interface. In Lake Sempach (Switzerland), hypolimnetic oxygen concentration was increased by artificial aeration after two decades of nearly anoxic conditions. Using diagenetic reaction-transport modeling and sediment core analysis, we investigated the effects that this change, as well as variations in the organic carbon loadings, had on the long-term mobility of sediment P. During low-oxygen conditions, the reducible iron pool in the sediment was depleted, resulting in the release of previously accumulated P. The remobilization of iron-bound P affected phosphate effluxes from the sediment on the time scale of the sediment iron cycle (several years). On longer time scales, P effluxes followed the sedimentation fluxes of organic matter. Mass balance calculations indicate that, despite the dominance of internal P loading in Lake Sempach, over the long-term phosphorus content in the water column was controlled by the external P inputs. The results suggest that, whereas short-term decreases in sediment P releases may be achieved by preventing sediment anoxia, long-term solutions should involve reductions in the external P inputs.

Nitrate and sulfate are two major terminal electron acceptors of anaerobic respiration in nearshore sediments. Potential nitrate and sulfate reduction rates (NRR and SRR) were determined on surficial sediments sampled at 14 sites representing a wide range of shallow-water depositional environments. The rates were obtained by supplying undisturbed slices of sediments with nitrate, sulfate or both using a flow-through reactor technique. No external electron donor was added to the sediments. The results indicate that all studied sediments harbored viable and coexisting nitrate- and sulfate-reducing communities, which were able to instantaneously consume the electron acceptors supplied to the reactors. On average, NRR exceeded SRR by about one order of magnitude (309±180nmol ${\text{NO}}_3^{-}$ cm⁻³h⁻¹ versus 37±29nmol${\text{SO}}_4^{2-}$ cm⁻³h⁻¹). The NRR:SRR molar ratio, however, varied significantly from site to site, with values ranging from 1.7 to 59. Nitrite production, indicative of incomplete nitrate reduction, was observed in all studied sediments and, on average, accounted for 45% of NRR (range 3–80%). Production of sulfate under nitrate-reducing conditions was observed in 10 out of 14 of the studied sediments, suggesting a common occurrence of sulfide oxidation coupled to nitrate reduction. Oxidation of sulfide accounted for 0 to 40% of NRR in the nitrate-only experiments. When both electron acceptors were supplied simultaneously, net sulfate consumption decreased on average by 45%. The effect of nitrate on SRR was highly variable, however, ranging from near complete inhibition to a 25% enhancement of SRR. Overall, the results of this study point to the need to critically reassess the model formulations used to represent anaerobic respiration processes and their interactions in early diagenetic models.

Periodic precipitation patterns (Liesegang bands) constitute good manifestations of self-organization in geochemical systems. Examples of periodic pyrite bands have been previously reported in anoxic sediment systems, such as sapropels from the Eastern Mediterranean. In this contribution, we present a model of Liesegang pyrite band formation in anoxic marine sediments. The model is based on early diagenetic reactive-transport processes and incorporates nucleation and growth of pyrite crystallites. The simulation results of pyrite band formation are compatible with the experimental pyritization pattern observed in a sediment analog, as well as the observations in sapropel sediments.

We perform, for the first time, a global sensitivity analysis on a generic diagenetic reaction-transport model (RTM) to elucidate the effects of environmental, thermodynamic, and kinetic factors on the magnitudes of phosphorus release fluxes from aquatic sediments under a range of conditions typically found in lake sediments. Our model includes the processes that describe redox-sensitive phosphorus releases (the so-called classical model) and processes by which phosphorus mobilization is affected by porewater sulfate. On decadal and longer time scales, sediment phosphorus effluxes are primarily determined by: sedimentation flux of reactive organic matter, sedimentation flux of iron oxyhydroxides, concentrations of dissolved oxygen and sulfate at the sediment–water interface, and the rate at which phosphate is immobilized in reduced sediment. We show that the effects of these factors on phosphorus effluxes are interdependent and discuss the mechanisms of such interactions. The dominant pathways by which dissolved sulfate increases phosphorus efflux in iron-rich hypoxic sediments are discussed in detail. In contrast to short-term phosphorus releases, such as described by the classical model, long-term phosphorus retention is controlled by phosphorus removal to deep, reduced, sediment, rather than processes at the sediment–water interface. Hence, the results of short-term laboratory or in-situ studies (such as sediment incubations experiments) cannot be unequivocally extended to long time scales. Our results provide explanations to the reports that lake restoration measures such as restricting phosphorus inputs to a lake or oxygenating the lake's hypolimneon (or both) in the long-term often fail to decrease sediment phosphorus effluxes. The re-deposition of sediment substances after their release into the water column (the feedback often overlooked in sediment RTMs) can critically affect the magnitude and dynamics of phosphorus efflux from sediments. Depending on sediment history, the same set of external (boundary) conditions can generate diagenetic regimes with either high or low phosphorus effluxes (bistability).

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Volume 115, 2013, pp. 22-25

The mineral kulanite BaFe₂Al₂(PO₄)₃(OH)₃, a barium iron aluminum phosphate, has been studied by using a combination of electron microscopy and vibrational spectroscopy. Scanning electron microscopy with EDX shows the mineral is homogenous with no other phases present. The Raman spectrum is dominated by an intense band at 1022cm⁻¹ assigned to the ${\text{PO}}_4^{3-}{\nu }_1$ symmetric stretching mode. Low intensity Raman bands at 1076, 1110, 1146, 1182cm⁻¹ are attributed to the ${\text{PO}}_4^{3-}{\nu }_3$ antisymmetric stretching vibrations. The infrared spectrum shows a complex spectral profile with overlapping bands. Multiple phosphate bending vibrations supports the concept of a reduction in symmetry of the phosphate anion. Raman spectrum at 3211, 3513 and 3533cm⁻¹ are assigned to the stretching vibrations of the OH units. Vibrational spectroscopy enables aspects on the molecular structure of kulanite to be assessed.

Journal of Molecular Structure, Volume 1074, 2014, pp. 429-434

Geochimica et Cosmochimica Acta, Volume 133, 2014, pp. 443-462

Iron isotopes have been extensively used to trace the history of microbial metabolisms and the redox evolution of the oceans. Archean sedimentary rocks display greater variability in iron isotope ratios and more markedly negative values than those deposited in the Proterozoic and Phanerozoic. This increased variability has been linked to changes in either water column iron cycling or the extent of benthic microbial iron reduction through time. We tested these contrasting scenarios through a detailed study of anoxic and ferruginous Lac Pavin (France), which can serve as a modern analogue of the Archean ocean. A depth-profile in the water column of Lac Pavin shows a remarkable increase in dissolved Fe concentration (0.1–1200μM) and δ⁵⁶Fe values (−2.14‰ to +0.31‰) across the oxic–anoxic boundary to the lake bottom. The largest Fe isotope variability is found at the redox boundary and is related to partial oxidation of dissolved ferrous iron, leaving the residual Fe enriched in light isotopes. The analysis of four sediment cores collected along a lateral profile (one in the oxic layer, one at the redox boundary, one in the anoxic zone, and one at the bottom of the lake) indicates that bulk sediments, porewaters, and reactive Fe mostly have δ⁵⁶Fe values near 0.0±0.2‰, similar to detrital iron. In contrast, pyrite δ⁵⁶Fe values in sub-chemocline cores (60, 65, and 92m) are highly variable and show significant deviations from the detrital iron isotope composition (δ⁵⁶Fe_pyrite between −1.51‰ and +0.09‰; average −0.93‰). Importantly, the pyrite δ⁵⁶Fe values mirror the δ⁵⁶Fe of dissolved iron at the redox boundary—where near quantitative sulfate and sulfide drawdown occurs—suggesting limited iron isotope fractionation during iron sulfide formation. This finding has important implications for the Archean environment. Specifically, this work suggests that in a ferruginous system, most of the Fe isotope variability observed in sedimentary pyrites can be tied to water column cycling—foremost to the oxidation of dissolved ferrous iron. This supports previous suggestions that enhanced iron isotope variability in the Archean may record a unique stage in Earth’s history where partial ferrous iron oxidation in upwelling water masses was a common process, probably linked to oxygenic or anoxygenic photosynthesis.

Journal of Hydrodynamics, Ser. B, Volume 26, Issue 6, 2015, pp. 971-979

After the pollutant discharged into the river or lake has been reduced, the release of the contaminant from the sediment to the overlying water may cause the river and lake be contaminated again. On the condition that the overlying water flow does not lead to sediment suspension, numerical researches are carried out for the mechanism of contaminant release through the sediment-overlying water interface. The overlying water flow is calculated as turbulence. The sediment is regarded as isotropic homogeneous porous medium, therefore the seepage field in the porous sediment layer is obtained by solving Darcy's equations. Coupled two dimensional steady flows of the overlying water and the pore water in the sediment are calculated. Based on the flow fields obtained, the unsteady contaminant solute transportation process in the pore water in the sediment and the overlying water is numerically simulated, as the shapes of the sediment-overlying water interface are flat or periodic triangular respectively. Numerical results show that the exchange of the pore water and the overlying water is an important factor which decides the release flux of the contaminant from the sediment to the overlying water. The pressure distribution produced by the overlying water flow along the sediment-overlying water interface, as it is not flat, may induce the seepage of the pore water in the sediment and through the sediment-overlying water interface, which may increase the release flux of the contaminant from the sediment to the overlying water.

Chemical Geology, Volume 497, 2018, pp. 88-99

Radiogenic strontium isotopes (⁸⁷Sr/⁸⁶Sr) have been extensively used as a tool to explore a diversity of Earth system problems, including long-term global weathering rates and global sequence correlation. Strontium isotopes are measured on a range of geological materials (e.g., calcite fossils, barites, limestone micrites), but whole-rock limestones are by far the most abundant of these materials within the geological record for paleo-seawater ⁸⁷Sr/⁸⁶Sr work. Whole-rock limestones, however, have a poor track record of recording primary seawater ⁸⁷Sr/⁸⁶Sr values. Alteration of the limestone during diagenesis and contamination from detrital aluminosilicate phases during carbonate extraction have been consistent problems. Various preparation and quality control methods have been applied to whole-rock ⁸⁷Sr/⁸⁶Sr work, yet there remains no consistent framework used to separate and identify both contamination and alteration simultaneously. The lack of consistent and systematic methods has made it difficult to gauge the accuracy and fidelity of much of the previously generated whole rock limestones ⁸⁷Sr/⁸⁶Sr data, especially for Precambrian sequences. Building on previous work, we explore a sequential leaching method designed to systematically isolate least-altered carbonate phases from detrital aluminosilicate Sr contamination and present several case studies that demonstrate the advantages of this approach. In the first case study, we use the Mid-Carboniferous Bird Spring Formation to empirically validate the accuracy of this sequential leaching method. Comparing least-altered sequentially leached whole-rock ⁸⁷Sr/⁸⁶Sr values with well-preserved calcite brachiopod ⁸⁷Sr/⁸⁶Sr values from the same section, we find near identical values. Following this first case, we studied the Neoproterozoic Dhaiqa Formation and the mid-Proterozoic Jixian Group and Muskwa Assemblage to outline a framework for identifying least-altered leachate fractions in Proterozoic carbonate samples. As a whole, we find that with this method it is possible to better identify whole-rock samples primary or least-altered carbonate fractions, and better account for alteration, providing a means to back-calculate a samples primary and least-altered marine ⁸⁷Sr/⁸⁶Sr value.

Chemical Geology, Volume 362, 2013, pp. 66-73

Post-depositional diagenetic alteration makes the accurate interpretation of key precipitation processes in ancient sediments, such as Precambrian banded iron formations (BIFs), difficult. While microorganisms are proposed as key contributors to BIF deposition, the diagenetic transformation of precursor Fe(III) minerals associated with microbial biomass had not been experimentally tested. We incubated mixtures of ferrihydrite (proxy for biogenic ferric oxyhydroxide minerals) and glucose (proxy for microbial biomass) in gold capsules at 1.2kbar and 170°C. Both wet chemical analysis and mineralogical methods (microscopy, X-ray diffraction and Mössbauer spectroscopy) were used to analyze the reaction products. Under these conditions, ferrihydrite (Fe^III(OH)₃) transforms to hematite (Fe₂^IIIO₃), magnetite (Fe^IIFe₂^IIIO₄), and siderite (Fe^IICO₃). Silica-coated ferrihydrite prepared at conservative Si:Fe ratios (as predicted for the Precambrian oceans) and mixed with glucose yielded hematite and siderite, whereas magnetite could not be identified microscopically. Our results show that electron transfer from organic carbon to Fe(III) minerals during temperature/pressure diagenesis can drive the production of key BIF minerals. Our results also demonstrate that the post-depositional mineralogy of BIF does not directly archive the oceanic or atmospheric conditions present on Earth during their lithification. As a consequence, atmospheric composition regarding concentrations of methane and CO₂ during the time of BIF mineral deposition cannot be directly inferred from BIF mineralogical data alone.