Ecology entered a new era with growing evidences of the huge impact of microorganisms on all existing ecosystems. Molecular approaches, such as the SSU rRNA gene analysis and environmental genomic approaches, identified an unexpected microbial taxonomic and functional diversity in all kinds 166of habitats. This diversity and the low cultivability suggest functional interactions within microbial communities as well as between microbial communities and plants or animals in dependence of the environmental conditions. These findings shape the groundwork of new revolutionary ecological concepts away from isolated characteristics of organisms to broad holistic*/integrated views. Aiming to capture and to understand the functioning of interacting microbial communities, they must be considered as a whole, in constant evolution and in adaptation to environmental factors. Since there is no all-inclusive approach combining all targeted aspects of analysis, results obtained from particular molecular ecology approaches are still rather tesserae. Nevertheless, combining different approaches fills the mosaic leading to more comprehensive reproductions of in situ community functions.

In this chapter, we highlight the findings and limitations of environmental genomics that paved the way for new holistic* concepts of community assemblages* as well as perspectives. Combined with insights into molecular techniques, the reader should be well fitted to apply and develop adequate research strategies that imply environmental genomic approaches combined with high-throughput sequencing.