The role of microbiota in soil carbon dynamics is a fitting example of the ‘borderland character’ mentioned in the introduction of this book. For years, the flux community largely followed the unspoken paradigm that ‘everything is everywhere’, which means that there is a universal potential of micro-organisms to decompose all kinds of organic matter, and that soil carbon dynamics, therefore, only depend on soil organic matter quality, soil properties and climate. A key distinction that controls whether the ‘everything is everywhere’ perspective is workable, however, is considering whether environmental conditions are in steady-state or non-steady-state conditions. Under steady-state conditions, microbial influences will be least apparent as they will have acclimatized to the existing physical, chemical or climatic constraints. Under non-steady-state conditions, however, extant microbial populations may reflect past, rather than present, conditions and their behaviour may be paramount and potentially counter-intuitive.
There is evidence that micro-organisms respond sensitively to changing environmental conditions by: (1) adjusting their intra- as well as extracellular enzymatic repertoire and, consequently, their physiological performance; (2) changes in the species composition and (3) growth or reduction of the microbial biomass.
There are several approaches to analyze the response of micro-organisms to changing environmental conditions.
Microbial eco-physiology (Anderson, 1994) focuses on the microbial biomass and its performance. More recent approaches (Lynch et al., 2004; Zak et al., 2006) include community oriented approaches that allow linking metabolic pathways to species composition or, at least, functional groups.
Microbial biochemistry analyses to determine the production and activity of microbial components, in particular enzymes. Since microbiota release a high portion of their enzymes, extracellular enzymes are included here (Sinsabaugh, 1994).