[en] The problem of abundant and scarce bacteria is of growing importance in the comprehension of biological ecosystems. More than anything, rare bacteria could be a reservoir of genes and functions designed to help community survival. However functional description of the community remains a challenge, particularly in the sense of rare bacteria.
During the present research, we designed a synthetic 9-species bacterial community, on the basis of a marine community observed in muddy sediments. This community has been grown under simulated marine condition and stressed using zinc 0.5mM. DNA and protein samples have been harvested after 4 and 28 days to assess taxonomical and functional biodiversity of the community using Quantitative- PCR and Mass Spectrometry (data-dependent LC-MS/MS and data-independent SWATH-MS) respectively.
After 28 days, the taxonomical biodiversity pattern (Q-PCR) of the community was really close to the natural sediments with rarer (Cupriavidus metallidurans, Methylibium petroleiphilum, Burkholderia xenovorans...) and more abundant bacteria (mainly Pseudomonas putida, Shewanella baltica). This pattern was modified, as expected, in the presence of zinc. In order to check the activity of rarer bacteria, functional diversity was first assessed using LC-MS/MS. However, the high abundancy of Pseudomonas putida (about 90% of the community) impaired the detection of rare bacteria.
Using SWATH-MS, we have been successful in fishing out rare bacteria proteome inside the synthetic community. SWATH-MS represents a major breakthrough in the field of functional microbiology. It is a promising technique to reach the full functional description of a community, and subsequently the comprehension of biological cycles.
