In March 2003 J. Craig Venter and coworkers have begun to explore environmental bacteria in a culture-independent manner by isolating DNA from directly the environmental sample, Sargasso Sea and then transforming into large insert clones for sequencing (1). The sequencing revealed the identification of new species. Indeed, molecular approaches have significantly influenced the understanding of the microbial diversity and ecology. In particular, ribosomal RN (rRNA) gene sequence comparisons have provided a revolutionary approach for interpreting microbial evolutionary relationships (2). In a logical extension of this technique extraction of phylogenetically informative genes directly from naturally occurring represents another important development, in microbiology, opening up the natural microbial world to be closer scrutiny (3, 4).
Further advances in genome sequencing have had and still having a great impact on microbial biology providing insights into biochemistry, physiology and diversity. So far the full genome sequencing of many microorganisms, especially marine ones, have been completed and many others are underway. Combining the cultivation –independent gene sequences with the genomic approaches (e.g. whole genome shotgun, -omic technologies) it is now possible to investigate a more comprehensive natural microbial communities. These techniques, first applied to marine plankton to characterize uncultivated marine bacterial and archeal species (5) are now becoming a common method to characterize the community structure. Applications include the genome analysis of uncharacterized taxa (6, 7) expression of novel genes pathways from uncultured environmental microorganisms, elucidation of community-specific metabolism and comparison of different community gene contents.
If from on one hand, we are discovering huge microbial diversity, on the other hand it is increasing concerns about the loss of biodiversity, especially caused by exploitation, pollution and habitat destruction, or indirectly through climate change and related perturbations of ocean biogeochemistry (8-10). The review will explore the development, application of the genomics technologies to the microbial biodiversity (microbial ecology) monitoring. I will first introduce the concept of microbial world, what we know so far and then facing with the molecular biology tools the transforming view of microbial diversity the (metagenomics, ecogenomics). The second section is dedicated to the applicability and to the illustration of examples of –omics technologies to the monitoring of microbial biodiversity either
in sea/ocean or in freshwaters. This part will be introduced by -omics technologies (DNA Microarray, Mass Spectrometry Maldi-TOFF and single cell genome sequencing) and by the availability of public databases.