In one of his influential essays on the nature of the biosphere, which subsequently laid the foundation for modern biogeochemistry, Vladimir Vernadsky quoted his geology teacher, Vasily Dokuchayev, in a manner that made clear Dokuchayev’s view that soil is uniquely influenced by the organisms that live within; it lies at the interface between geology and biology. Roots and microorganisms exchange material with the soil and in doing so influence its chemical composition and physical structure. The interactions between the biological and geological components of soil ultimately determine how it interacts with the atmosphere. Soil is the medium through which terrestrial plants gain access to most mineral elements of the geosphere (carbon being the principal exception), and to liquid water from the hydrosphere, both of which exert major controls over the capacity for plants to exchange CO2, H2O, and energy with the atmosphere. Microbial activities in soil carry out the recycling of organic matter, returning carbon to the atmosphere, thus closing the terrestrial carbon cycle. Certain types of bacteria, in symbiotic relations with plant roots, or free-living in soil and water, facilitate the fixation of N2 from the atmosphere. Chemolithotrophic microorganisms in soil oxidize inorganic compounds to generate energy that is subsequently used to drive the autotrophic assimilation of carbon and at the same time produce volatile trace gases (including nitrogen oxides and N2) that are emitted to the atmosphere. Any concentrated consideration of ecosystem-atmosphere exchange must include soil processes in order to fully comprehend the relevant mass and energy fluxes.

We begin this chapter with an introduction to the decomposition of soil organic matter – a principal source of soil respiration and the process responsible for recycling nutrients between dead and living biomass. We then take up the topic of transport mechanisms for the exchange of mass between soils and the atmosphere, once again focusing on the flux of CO2 from soil respiration. Finally, in a series of sections we consider recent observations and models that focus on biological controls over the exchanges of CH4 and NOx between soils and the atmosphere. Cumulatively, these trace gases represent major contributions to the terrestrial carbon and nitrogen budgets, as well as to the reactive photochemistry and energy partitioning that occurs in the atmosphere.