Soil Is Still an Unknown Biological System

More than a thousand million cells encompassing bacteria, fungi, archaea, and protists inhabit a handful of soil. The bacterial and fungal biomass can account for 1–2 and 2–5 tha−1 in temperate grassland soils, respectively. Despite this huge microbial biomass, the volume occupied by microorganisms is less than 1% of the available soil volume because most micro-niches are hostile environments. Soil microorganisms and fauna play a crucial role in soil ecosystem services, and functional redundancy is a peculiar characteristic of soil as a biological system. Complex interactions are often mediated by molecular signals that occur between microbes, microbes and plants, and microbes and animals. Several microbial species have been detected in soil using molecular techniques, particularly amplicon sequencing and metagenomics. However, their activities in situ are still poorly known because the use of soil metatranscriptomics and, in particular, soil proteomics is still a technical challenge. A holistic approach with the use of labelled compounds can give quantitative information on nutrient dynamics in the soil-plant system. Despite the remarkable technical progresses and the use of imaginative approaches, there are many knowledge gaps about soil as a biological system. These gaps are discussed from a historic perspective, starting from the seven grand questions proposed by Selman A. Waksman in 1927.