Molecular methods for microbial ecology Developments, applications and results

Abstract: Recent developments in DNA sequencing technology allow the study of microbial ecology at unmatched detail. To fully embrace this revolution, an important avenue of research is the development of bioinformatic tools that enable scientists to leverage and manipulate the exceedingly large amounts of data produced. In this thesis, several bioinformatic tools were developed in order to process and analyze metagenomic sequence data. Subsequently, the tools were applied to the study of microbial biogeography and microbial systems biology.A targeted metagenomics pipeline automating quality filtering, joining and taxonomic annotation was developed to assess the diversity of bacteria, archaea and eukaryotes permitting the study of biogeographic patterns in great detail. Next, a second software package which provides annotation based on environmental ontology terms was coded aiming to exploit the cornucopia of information available in public databases. It was applied to resource tracking, paleontology, and biogeography. Indeed, both these tools have already found broad applications in extending our understanding of microbial diversity in inland waters and have contributed to the development of conceptual frameworks for microbial biogeography in lotic systems. The programs were used for analyzing samples from several environments such as alkaline soda lakes and ancient sediment cores. These studies corroborated the view that the dispersal limitations of microbes are more or less non-existant as environmental properties dictating their distribution and that dormant microbes allow the reconstruction of the origin and history of the sampled community.Furthermore, a shotgun metagenomics analysis pipeline for the characterization of total DNA extraction from the environment was put in place. The pipeline included all essential steps from raw sequence processing to functional annotation and reconstruction of prokaryotic genomes. By applying this tool, we were able to reconstruct the biochemical processes in a selection of systems representative of the tens of millions of lakes and ponds of the boreal landscape. This revealed the genomic content of abundant and so far undescribed prokaryotes harboring important functions in these ecosystems. We could show the presence of organisms with the capacity for photoferrotrophy and anaerobic methanotrophy encoded in their genomes, traits not previously detected in these systems. In another study, we showed that microbes respond to alkaline conditions by adjusting their energy acquisition and carbon fixation strategies. To conclude, we demonstrated that the "reverse ecology" approach in which the role of microbes in elemental cycles is assessed by genomic tools is very powerful as we can identify novel pathways and obtain the partitioning of metabolic processes in natural environments.