Jim Prosser, University of Aberdeen
The diversity of microbial communities in soil was traditionally determined by phenotypic characterisation of organisms cultivated on laboratory media. Diversity estimates were high but it was suspected that they significantly underestimated true values, due to selectivity of laboratory media and cultivation conditions. This was confirmed following the first revolution in characterisation of soil microbial diversity, which was brought about by the use of molecular techniques for cultivation-independent analysis. The standard method for characterising soil microbial communities now involves amplification of small subunit (SSU) rRNA genes or functional genes from extracted DNA or RNA. Amplified sequences are then analysed using fingerprinting techniques or by sequencing, comparison with database sequences and phylogenetic analysis. SSU rRNA gene-based approaches demonstrated considerable diversity, with estimates of up to one million bacterial species per gram soil, and continue (after 15-20 years) to uncover novel microbial groups at an exponential rate.
Soil microbial diversity analysis is now at the beginning of a second revolution, through application of high-throughput sequencing technology. This increases the depth of sequencing possible for single genes, such as SSU rRNA genes. More importantly, it is being used to investigate soil metagenomics, which targets all genes within extracted nucleic acids, and for single-cell genome studies, which potentially enables sequencing of genomes of hundreds of individual cells from soil.
For both ‘traditional’ and new molecular techniques, the challenge is to determine not only diversity, in terms of the phylogenetic groups present, but also the links between phylogenetic diversity and soil ecosystem function, the extent of functional redundancy and responses to environmental change. ‘Omics’ techniques provide enormous potential in addressing these issues, but also present conceptual and intellectual challenges.