Microorganisms Cycling Soil Nutrients

Microorganisms drive nutrient cycles in soil, and without this key activity, many essential elements would not be available to plants. Conversely, without the input of carbon and energy, primarily from photosynthesis by green plants, soil would consist mainly of mineral particles produced by the weathering of rocks. Residues from plant, animal, and microbial activity provide organic components, making soils fertile and binding together mineral particles into aggregates that, with the associated pore spaces, confer structure to the matrix that supports terrestrial life. In addition to providing a substrate for plants, soil also hosts a complex food web of microorganisms, microfauna,and mesofauna. Soils host large and diverse microbial communities, which comprise an estimated 109 bacterial and archaeal cells per gram belonging to 104–106 operational taxonomic units (OTUs) per gram in temperate soils. Fungal biomass, as estimated from phospholipid fatty acid biomarkers, is often, but not always, <4% of the bacterial biomass. This is even lower when calculated on the basis of protein or RNA biomarkers, with correspondingly fewer OTUs detected (Dassen et al. 2017). As outlined in Chapter 1, the microscale physicochemical variability of soil creates multiple microenvironments that are at the basis of the multitude of niches required to host this high diversity. The soil microbiome is involved in many nutrient transformations, cycling essential elements between abiotic and biotic pools. The spatial separation of microsites enables parallel evolution of multiple lineages in any soil. In general, microbial transformations of nutrients can be divided into those that are undertaken by many diverse organisms (categorized as “broad” processes) and those that are more specific or “narrow,” performed by defined groups of specialists (Schimel and Schaeffer 2012).