COMPLETE SEQUENCING OF THE SOIL METAGENOME: AN ATTAINABLE UTOPIA?
Résumé
Twenty years ago, bacteriology was the science that investigated the physiological, genetic, ecological properties of some (rare) bacteria that could develop on culture media. Some of these micro-organisms, such as Escherichia coli or Bacillus subtilis, have become invaluable models for studying a number of cellular and molecular mechanisms that have fundamental, medical and applied implications far beyond the bacterial world. However, bacteriology was the science of paradoxes with, on one hand, some representatives that are the most studied and best known among all organisms on our planet, and on the other hand, more than 99.9 % of bacterial species inhabiting this same planet were totally unknown because they were unable to develop in vitro. By providing access to most of this ignored bacterial world metagenomics stands now at the vanguard of environmental microbiology. The combination of metagenomics with new high throughput sequencing technologies opens very promising perspectives for an in depth exploration of microbial diversity, determination of the actual number of species and their putative functions, quantification of the diversity and abundance of mobile genetic elements and their involvement in the evolution and adaptation potential of a bacterial community. In this talk, our objectives will be to give an overview of these perspectives including a description of the on-going international project for the complete sequencing of a reference soil metagenome. This will include discussing sampling difficulties and other technical limitations and proposing solutions for recovering, sequencing and analyzing the entire soil metagenome.