Within the natural sciences, it has long been recognized that biological activity can modify the texture, structure and composition of surface sediments. Darwin (1881) already examined the stirring of soils by burrowing earthworms and made detailed observations on how these organisms affect soil processes. A similar phenomenon can be observed in aquatic sediments, which are inhabited by a diverse biological community, supported by the flux of organic matter and oxygen from the overlying water column. Surface sediments of oceans, estuaries, lakes and rivers are highly active biogeochemical environments and an effective way to generate insight in the complexity of the interactions is by means of so-called general early diagenetic models (e.g. Soetaert et al, 1996; Van Cappellen and Wang, 1996; Boudreau, 1996; Wijsman et al., 2001). The term early diagenesis refers to the combination of physical, chemical and biological processes that occur in the topmost layer of aquatic sediments following deposition (Berner, 1980). As biological activity plays a central role in early diagenesis, a prime concern in these modelling efforts constitutes the incorporation of an adequate formulation for the influence of benthic organisms on the reactive transport processes (Goldberg and Koide, 1962; Schink and Guinasso, 1975; Aller, 1980; Boudreau, 1986 a, b). However, the relation between biology and geochemistry is truly reciprocal, as a detailed understanding of the sediment environment can also provide valuable insight into the living conditions of the organisms. This thesis reviews and extends the current modelling theory of early diagenesis, focusing on a consistent, mechanistic and realistic description of ecological interactions in surface sediments. The thesis takes a highly theoretical start, with a critical assessment of the fundaments underlying the present modelling theory, but ends very pragmatically, with the presentation of a flexible, efficient and adaptable computer simulation environment for early diagenetic processes. As such, this thesis reports on the three key components of the modelling process: (1) the model formulation in chapters [1]-[4], (2) the model solution in chapter [5], and (3) the model implementation in chapter [6]. |
