Microbial interactions in soil

Abstract

Our view on the diversity and distribution of soil microbiota has expanded and continues to do so, driven by high-throughput sequencing technologies, but comparatively little is known about how these organisms affect each other. Bacteria, archaea, fungi, protists and their respective viruses impact each other through a range of beneficial and deleterious interactions, and thereby the soil ecosystem [1]. Modern microbiology, such as agriculture, has been shaped by the mono-culture paradigm, and the secrets of cellular function have been uncovered using a single culture approach. For decades, microbiologists have been trained to obtain and study “pure cultures”, clonal lineages able to grow rapidly on protein-rich laboratory media. In contrast, most microorganisms occur in soil and aquatic environments, surrounded by a myriad of life forms from bacteria, fungi and protists to insects, occurring at high densities amid sparse nutrient availability [2,3]. Bacteria contribute 70 Gt of the 550 Gt of global carbon biomass, together with 7 Gt from Archaea, 12 from fungi and 4 from protists. The terrestrial microbial biomass is estimated to be composed of 7 Gt carbon of bacteria, 0.5 of archaea, 12 of fungi and 1.6 of protists [4], so bacteria constitute the largest part of microbiota, not only by number, but also by biomass. In contrast, humans, the hosts to the most studied microbial ecosystem, make up only 0.06 Gt of carbon.