Recent rates of plant and animal species’ extinctions have spurred ecologists to consider the consequences of biodiversity loss. Beyond the ethical and aesthetic reasons for conserving it, biodiversity supplies economically valuable ecosystem goods and services on which human society depends (Ehrlich and Ehrlich, 1992; Daily, 1997). Although most biodiversity and conservation research has focused on the value and importance of large organisms, the sheer abundance of microorganisms confers on them a principal role in providing ecosystem services, such as water purification and soil fertility. Bacteria and Archaea alone contain most of the total nitrogen (N) and phosphorus (P) and up to half of the carbon (C) stored in living organisms (Whitman et al., 1998), and the metabolic machinery of microorganisms drives a variety of ecosystem processes. Indeed, microbes carry out the bulk of decomposition and catalyze important transformations in the C, N, sulfur, and P cycles.

Despite their importance to the functioning of ecosystems, microorganisms are rarely explicitly considered in individual ecosystem or global process models. In addition to methodological hurdles, a primary reason for this gap is their overwhelming diversity. Estimates of soil microbial diversity range from thousands to a million microbial “species” in a few grams of soil (Torsvik and Øvreås, 2002; Gans et al., 2005), and how this diversity is related to ecosystem processes is generally unknown (Torsvik et al., 2002; Crawford et al., 2005; Azam and Malfatti, 2007). Moreover, it is infeasible to assess and track each microbial taxon in an ecosystem, let alone include even a small fraction of these taxa in ecosystem models.

Because of these obstacles, ecosystem models often “black box” microbiology. In other words, microorganisms are buried within equation structure as kinetic constants and response functions and are “simplified beyond recognition” (Schimel, 2001). As a result, the abundance, diversity, and interactions of microorganisms are often assumed to be unimportant to ecosystem processes, particularly in terrestrial ecosystem models. [A number of ocean ecosystem models include various phytoplankton groups (e.g., Moore et al., 2002; Salihoglu and Hofmann, 2007)].

In contrast to microorganisms, it is generally accepted that plant biodiversity (both richness and composition) affects terrestrial ecosystem processes (Tilman et al., 1997; Hector et al., 1999; Spehn et al., 2005) and influences ecosystem responses to disturbances such as CO₂ and N addition [e.g., Reich et al. (2001)]. Plant community composition is often incorporated into large-scale models through the use of functional groups, which are based on plant traits (Tilman et al., 1997; Reich et al., 2007). Global change models—whether of ecosystems (Haxeltine and Prentice, 1996; Moorcroft et al., 2001), the terrestrial biosphere (Foley et al., 1996), or global climate (Cox et al., 2000; Higgins and Schneider, 2005)—routinely incorporate 5–10 plant functional groups to improve model predictions.