Actually, very little is known about soil microbes, partially because they are so diverse, but also because most soil microbes cannot be cultivated in the laboratory. For the ones that can be grown in a laboratory setting, scientists have used traditional methods such as direction observation, counting and functional assays, including the measurement of specific enzymatic activities. However, soil microbiologists have recently been applying advanced molecular techniques to understand the diversity and function of soil microbes. This exciting field, called soil metagenomics, relies on a cultivation-independent technology that comprises the isolation of soil DNA, its sequencing, and the characterization of the microbial communities present in soil samples. This has allowed many new taxa to be discovered in the rhizosphere – the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Similar approaches are being used to study the human gut microbiome, for example.
Flow diagram showing the main steps in the construction of a metagenomic DNA library from a soil sample. Soil DNA is recovered through separation of cells from soil particles followed by cell lysis and DNA recovery, or through direct lysis of cells contained within soil and recovery of DNA. Recovered soil DNA is fragmented and ligated into the linearized cloning vector of choice which might be a plasmid, cosmid, fosmid or BAC (bacterial artificial chromosome). Following the introduction of the recombinant vectors into a suitable bacterial cloning host, screening strategies can be designed to identify those clones which might contain new and useful genes. Daniel (2005) Nature Reviews Microbiology (https://www.nature.com/articles/nrmicro1160)