RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave

We introduce a time-dependent, one-dimensional model of early diagenesis that we term RADI, an acronym accounting for the main processes included in the model: chemical Reactions, Advection, molecular and bio-Diffusion, and bio-Irrigation. RADI is targeted for study of deep-sea sediments, in particular those containing calcium carbonates (CaCO3). RADI combines CaCO3 dissolution driven by organic matter degradation with a diffusive boundary layer and integrates state-of-the-art parameterizations of CaCO3 dissolution kinetics in seawater, thus serving as a link between mechanistic surface-reaction modelling and global-scale biogeochemical models. RADI also includes CaCO3 precipitation, providing a continuum between CaCO3 dissolution and precipitation. RADI integrates components rather than individual chemical species for accessibility and is straightforward to compare against measurements. RADI is the first diagenetic model implemented in Julia, a high-performance programming language that is free and open source, and it is also available in MATLAB/GNU Octave. Here, we first describe the scientific background behind RADI and its implementations. Then, we evaluate its performance in three selected locations and explore other potential applications, such as the influence of tides and seasonality on early diagenesis in the deep ocean. RADI is a powerful tool to study the time-transient and steady-state response of the sedimentary system to environmental perturbation, such as deep-sea mining, deoxygenation or acidification events.

The Influence of Cascade Reservoir Construction on Labile Phosphorus in the Sediment of Lancang River

The influence of cascade reservoirs construction on labile phosphorus (P) is an important scientific problem in the Lancang River. The concentration of labile P in cascade deep-water reservoirs were determined, and the influence of cascade reservoirs construction on the DGT-labile P was analyzed. The construction of cascade reservoirs led to significant differences in concentrations of DGT-labile P, which in the upstream of Xiaowan (XW) Reservoir were differences from that in the downstream Nuozhadu (NZD) Reservoir. The P diffusion fluxes in XW Reservoir were − 8.59–250.50 ng·cm− 2·d− 1, and that in NZD Reservoir were 3.82–24.80 ng·cm− 2·d− 1. The P pollution of XW Reservoir was higher, highlighting the importance of controlling P pollution of XW Reservoir. The construction of cascade reservoirs had made the release of DGT-labile P more dependent on the reductive dissolution of Mn oxides. The early diagenesis transformed bio-availability P (BAP) remobilization into DGT-labile P that made the increase of DGT-labile P/BAP with depth. However, the DGT-labile P/BAP of upstream XW Reservoir was 7.8 times larger than that of downstream NZD Reservoir, which indicated that the construction of cascade reservoirs weakened the remobilization of P in sediment.

Model of Early Diagenesis in the Upper Sediment with Adaptable complexity – MEDUSA (v. 2): a time-dependent biogeochemical sediment module for Earth system models, process analysis and teaching

MEDUSA is a time-dependent one-dimensional numerical model of coupled early diagenetic processes in the surface sea-floor sediment. In the vertical, the sediment is subdivided into two different zones. Solids (biogenic, mineral, etc.) raining down from the surface of the ocean are collected by the reactive mixed layer at the top. This is where chemical reactions take place. Solids are transported by bioturbation and advection, and solutes are transported by diffusion and bioirrigation. The classical coupled time-dependent early diagenesis equations (advection–diffusion reaction equations) are used to describe the evolutions of the solid and solute components here. Solids that get transported deeper than the bottom boundary of the reactive mixed layer enter the second zone underneath, where reactions and mixing are neglected. Gradually, as solid material gets transferred here from the overlying reactive layer, it is buried and preserved in a stack of layers that make up a synthetic sediment core. MEDUSA has been extensively modified since its first release from 2007. The composition of the two phases, the processes (chemical reactions) and chemical equilibria between solutes are not fixed any more, but get assembled from a set of XML-based description files that are processed by a code generator to produce the required Fortran code. 1D, 2D and 2D×2D interfaces have been introduced to facilitate the coupling to common grid configurations and material compositions used in biogeochemical models. MEDUSA can also be run in parallel computing environments using the Message Passing Interface (MPI).

Environmental and diagenetic controls on the morphology and calcification of the Ediacaran metazoan Cloudina

Cloudina is a globally distributed Ediacaran metazoan, with a tubular, funnel-in-funnel form built of thin laminae (ca. 1–10 μm). To what degree local environmental controlled morphology, and whether early diagenesis controlled the degree of calcification of Cloudina, is debated. Here we test these hypotheses by considering assemblages from four, coeval localities from the Upper Omkyk Member, Nama Group, Namibia, from inner ramp to mid-ramp reef across the Zaris Subbasin. We show that sinuosity of the Cloudina tube is variable between sites, as is the relative thickness of the tube wall, suggesting these features were environmentally controlled. Walls are thickest in high-energy reef settings, and thinnest in the low-energy, inner ramp. While local diagenesis controls preservation, all diagenetic expressions are consistent with the presence of weakly calcified, organic-rich laminae, and lamina thicknesses are broadly constant. Finally, internal ‘cements’ within Cloudina are found in all sites, and pre-date skeletal breakage, transport, as well as syn-sedimentary botryoidal cement precipitation. Best preservation shows these to be formed by fine, pseudomorphed aragonitic acicular crystals. Sr concentrations and Mg/Ca show no statistically significant differences between internal Cloudina cements and botryoidal cements, but we infer all internal cements to have precipitated when Cloudina was still in-situ and added considerable mechanical strength, but may have formed post-mortem or in abandoned parts of the skeleton.