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Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
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Discussion papers
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.

Model description paper 25 Apr 2019

Model description paper | 25 Apr 2019

Review status
This discussion paper is a preprint. It is a manuscript under review for the journal Geoscientific Model Development (GMD).

A lattice-automaton bioturbation simulator for the coupled physics, chemistry, and biology of marine sediments (eLABS v0.1)

Yoshiki Kanzaki1, Bernard P. Boudreau2, Sandra Kirtland Turner1, and Andy Ridgwell1,3 Yoshiki Kanzaki et al.
  • 1Department of Earth Sciences, Universityof California – Riverside, Riverside, CA 92521, USA
  • 2Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H4R2, Canada
  • 3School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK

Abstract. Seawater-sediment interaction is a crucial factor in the dynamics of carbon and nutrient cycling on a wide range of spatial and temporal scales. This interaction is mediated not just through geochemistry, but also via biology. Infauna vigorously mix sediment particles, enhance porewater-seawater exchange and consequently facilitate chemical reactions. In turn, the ecology and activity of benthic fauna are impacted by their environment, amplifying the sensitivity of seawater-sediment interaction to environmental change. However, numerical representation of the bioturbation of sediment has often been treated simply as an enhanced diffusion of solutes and solids. Whilst reasonably successful in representing the mixing of bulk and predominantly oxic marine sediments, the diffusional approach to bioturbation is limited by lacking an environmental sensitivity. To better capture the mechanics and effects of sediment bioturbation, we summarize and extend a published bioturbation model (acronym: LABS) that adopts a novel lattice automaton method to simulate the behaviors of infauna that drive sediment mixing. In this new model (eLABS), simulated benthic organism behavior is combined with a deterministic calculation of water flow and oxygen and organic matter concentration fields to better reflect the physicochemical evolution of sediment. The predicted burrow geometry and mixing intensity thus attain a dependence on physicochemical sedimentary conditions. Such an interplay between biology, chemistry and physics can be important to mechanistically explain empirical observations of bioturbation and to account for the impact of environmental changes. As an illustrative example, we show how higher organic rain can drive more intense sediment mixing by luring benthic organisms deeper into sediments, while lower ambient dissolved oxygen restricts the oxic habitat depth and hence tends to reduce bulk mixing rates. Finally, our model, with its oxygen and food availability controls, represents a new tool to interpret the geological record of trace fossils, e.g., burrows, as well as to mechanistically explore biological engineering of early marine environments.

Yoshiki Kanzaki et al.
Interactive discussion
Status: final response (author comments only)
Status: final response (author comments only)
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Yoshiki Kanzaki et al.
Yoshiki Kanzaki et al.
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Publications Copernicus
Short summary
This paper provides eLABS, an extension of the lattice-automaton bioturbation simulator LABS. Our new model couples the simulation of benthic animal behavior by LABS with calculations of oxygen and organic matter, as well as of water flow caused by benthic animal automata in a 2D marine-sediment grid. The model can address the mechanisms behind empirical observations of bioturbation by realizing the interactions between physical, chemical and biological aspects of marine sediments.
This paper provides eLABS, an extension of the lattice-automaton bioturbation simulator LABS....