IS EVERYTHING EVERYWHERE?
Résumé
“Is everything everywhere, but the environment selects” is a concept formulated by Baas Becking in 1934 based on his own studies and strongly influenced by those of his compatriot Beijerink. This fundamental question in microbial ecology remains unanswered in spite of the development of new analytical capacities including those based on total DNA extracted from soil. When considering a microbially diverse environment, such as soil, limitations to a full exploration of bacterial diversity include technical biases (bacteria and DNA extraction, PCR amplification), heterogeneity and complexity of the soil matrix (microniches) and the presence of numerous populations with limited number of cells. Although these minority populations probably play a fundamental role in community functioning, they are rarely detected by conventional techniques and even metagenomic approaches require the production of DNA libraries containing several million clones before DNA from these minority populations would be significantly represented. Our objectives were to develop a new bacterial diversity analytical approach by combining conceptual and methodological improvements in order to increase the level of minority populations in soils, and thus, reduce their detection limit. This was done in part by inoculating sterilized soil samples that had different physico-chemical characteristics with bacterial communities extracted from these soils and analyzing the resulting bacterial structure by highly sensitive techniques, such as 16S rDNA microarrays (phylochips) and pyrosequencing. Results clearly indicate that inoculation of bacterial communities into new environments yield significant changes in the initial community, confirming the fundamental impact of abiotic soil factors in structuring the bacterial populations. In addition, the phylochip analysis revealed previously undetected bacteria, confirming the presence of minority populations and the possibility of increasing their relative abundance under different conditions. This approach improves microbial population detection and addresses the initial question about the actual bacterial diversity level “everywhere”.