We seek to harness the power of multi-omic techniques to disentangle the genetic potential of natural microbial communities and link it to observed activities and phenotypes. Our goal is to predict the niche and occurrence of discrete populations in natural systems (e.g., during phytoplankton blooms) and examine the diversity of microbial populations (e.g., in nature or at single-cell level).
Using cutting-edge massive sequence-generating approaches, we survey microbial communities by examining nucleotide information stored in whole-community DNA fragments used to infer taxonomic affiliation and metabolisms. We also use this information to inspect proteomic profiles to understand their active metabolisms. Additionally, we generate nucleotide-based labels to visualize these microbial communities using microscopic identification approaches.
Our current project focuses on natural surface water populations from the North Sea captured in different pore-size fractions. Future projects will involve the exploration of sediments and their potential for organic matter degradation.
The Euryarchaeota of the North Sea
We combined metagenomic and visualization approaches to explore the Euryarchaeota MGIIa and MGIIb populations' temporal distribution in the North Sea. The combination of oligotyping and FISH approaches revealed that MGII cells were mostly free-living and of a small coccoid shape, likely resulting in grazing avoidance. Our metagenomic approach allowed us to recover MAGs that revealed differences in the genome size and GC content between MGIIa and MGIIb. Additionally, we observed highly identical and annually recurrent discrete populations for both families during the winter and summer periods. These findings allowed us to hypothesize that a combination of size and metabolic potential delineates MGII populations' niches. Read more about it in the "behind the paper" blog post.