The Prokaryotic Biology of Soil

INVITED REVIEW

Abstract

Prokaryotes (‘Bacteria’ and ‘Archaea’) are the most dominant and diverse form of life in soil and are indispensable for soil ecology and Earth system processes. This review addresses and interrelates the breadth of microbial biology in the global context of soil biology primarily for a readership less familiar with (soil) microbiology. First, the basic properties of prokaryotes and their major differences to macro-organisms are introduced. Further, technologies to study soil microbiology such as high-throughput next-generation sequencing and associated computational challenges are addressed. A brief insight into the principles of microbial systematics and taxonomy is provided. Second, the complexity and activity of microbial communities and the principles of their assembly are discussed, with a focus on the spatial distance of a few μm which is the scale at which prokaryotes perceive their environment. The interactions of prokaryotes with plant roots and soil fauna such as earthworms are addressed. Further, the role, resistance and resilience of prokaryotic soil communities in the light of anthropogenic disturbances such as global warming, elevated CO2 and massive nitrogen and phosphorous fertilization is discussed. Finally, current discussions triggered by the above-addressed complexity of microbes in soil on whether microbial ecology needs a theory that is different from that of macroecology are viewed.