The field of biogeochemistry deals with the effect of biological organisms on the chemistry of the Earth. Since there are numerous living organisms, all of which affect the chemistry of their environment in multiple ways, biogeochemistry is a large subject area covering many processes. One process that receives a lot of attention is the emission of CO2 by humans and the associated global increase in atmospheric CO2. However, biogeo-chemistry also deals with the effect of other organisms on the global carbon cycle, like the conversion of CO2 to organic carbon by marine phytoplankton. Biogeochemical processes can also be of subglobal scale, like the respiration of O2 by bacteria at the bottom of a lake. Biogeochemistry encompasses all types of chemicals. Nitrification, the conversion of ammonia to nitrate, by bacteria in soils is a biogeochemical process. So is the reduction of sulfate to sulfide by bacteria in groundwater. Also, the chemistry of minor elements is included, like the methylation of mercury by bacteria in sediments. Further, although the field of biogeochemistry traditionally focuses on naturally occurring elements and compounds, it also includes the effect of organisms on the chemistry of manmade chemicals, like the biodegradation of poly-chlorinated biphenyls (PCBs) by bacteria.

Biogeochemical models are abstract and simplified representations of biogeochemical processes. This includes qualitative models in the form of narratives or diagrams that describe how a process works and convey mechanistic information. It also includes quantitative models in the form ofmathematical equations that predict chemical concentrations and fluxes. Quantitative biogeo-chemical models are used as research tools to test hypotheses, and as management tools to evaluate 'what if' scenarios (e.g., nutrient load reduction to prevent eutrophication of lakes). In application, biogeochemical models are typically smaller components of larger models that describe the biogeochemical cycling of elements at various scales ranging from a small volume of soil to the globe. As such, biogeochemical models have to be compatible with other models, including physical models that describe the transport of chemicals in the environment (advection, diffusion, and dispersion) and ecological models that describe population dynamics.

The purpose of this article is to present an overview of biogeochemical modeling. A thorough review of this subject would necessitate covering the effect of every biological organism on the chemistry of all affected compounds, which is beyond the scope of this article. Therefore, this article focuses on how the transformation of chemicals by organisms is modeled in general, with applicable references to actual processes. Microorganisms constitute the bulk of the biomass and they have a higher turnover rate than organisms at higher trophic levels. They are therefore generally considered to be the main drivers of biogeochemistry and this article will focus on them. Also, consistent with the scope of this encyclopedia, the article focuses on naturally occurring substances, rather than manmade ones (e.g., PCB). Often, the effect of organisms on chemistry is indirect (e.g., via the redox potential), but that is, strictly speaking, a chemical problem, and this article therefore focuses on the direct effect of organisms on the chemistry. First, basic modeling approaches are reviewed, including conceptual and descriptive models, mechanistic chemistry- and biology-type models, and empirical models. Then the integration of ecology and biogeochemistry models is discussed, including their role, methods of integrating them, examples of integrated aquatic and terrestrial models, and the past, present, and future of those models. Following that, is a description of one of the grand challenges of biogeochemical modeling, the scaling problem. Then, the transformation of arsenic by phytoplankton is presented as a case study.

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