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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. 

Benthic animals profoundly influence the cycling and storage of carbon and other elements in marine systems, particularly in coastal sediments. Recent climate change has altered the distribution and abundance of many seafloor taxa and modified the vertical exchange of materials between ocean and sediment layers. Here, we examine how climate change could alter animal-mediated biogeochemical cycling in ocean sediments. The fossil record shows repeated major responses from the benthos during mass extinctions and global carbon perturbations, including reduced diversity, dominance of simple trace fossils, decreased burrow size and bioturbation intensity, and nonrandom extinction of trophic groups. The broad dispersal capacity of many extant benthic species facilitates poleward shifts corresponding to their environmental niche as overlying water warms. Evidence suggests that locally persistent populations will likely respond to environmental shifts through either failure to respond or genetic adaptation rather than via phenotypic plasticity. Regional and global ocean models insufficiently integrate changes in benthic biological activity and their feedbacks on sedimentary biogeochemical processes. The emergence of bioturbation, ventilation, and seafloor-habitat maps and progress in our mechanistic understanding of organism–sediment interactions enable incorporation of potential effects of climate change on benthic macrofaunal mediation of elemental cycles into regional and global ocean biogeochemical models. 

Abstract. Cenozoic stable carbon (δ13C) and oxygen (δ18O)isotope ratios of deep-sea foraminiferal calcite co-vary with the 405 kyreccentricity cycle, suggesting a link between orbital forcing, the climatesystem, and the carbon cycle. Variations in δ18O are partlyforced by ice-volume changes that have mostly occurred since the Oligocene.The cyclic δ13C–δ18O co-variation is found inboth ice-free and glaciated climate states, however. Consequently, thereshould be a mechanism that forces the δ13C cyclesindependently of ice dynamics. In search of this mechanism, we simulate theresponse of several key components of the carbon cycle to orbital forcing inthe Long-term Ocean-atmosphere-Sediment CArbon cycle Reservoir model(LOSCAR). We force the model by changing the burial of organic carbon in theocean with various astronomical solutions and noise and study the responseof the main carbon cycle tracers. Consistent with previous work, thesimulations reveal that low-frequency oscillations in the forcing arepreferentially amplified relative to higher frequencies. However, whileoceanic δ13C mainly varies with a 405 kyr period in themodel, the dynamics of dissolved inorganic carbon in the oceans and ofatmospheric CO2 are dominated by the 2.4 Myr cycle of eccentricity.This implies that the total ocean and atmosphere carbon inventory is stronglyinfluenced by carbon cycle variability that exceeds the timescale of the405 kyr period (such as silicate weathering). To test the applicability ofthe model results, we assemble a long (∼22 Myr) δ13C andδ18O composite record spanning the Eocene to Miocene(34–12 Ma) and perform spectral analysis to assess the presence of the2.4 Myr cycle. We find that, while the 2.4 Myr cycle appears to beovershadowed by long-term changes in the composite record, it is present asan amplitude modulator of the 405 and 100 kyr eccentricity cycles.