Omics' and microbial metabolisms
High-throughput sequencing techniques have allowed the recovery of an enormous amount of microbial genomic information from environmental metagenomic samples. I have been involved in several projects that used metagenomic data to reconstruct microbial metabolisms.
As part of the project TRAITS, I analyze the nitrogen cycle in the Arctic Ocean. We used metagenomics and metatranscriptomic samples from March to July to reconstruct the microbial community in samples from the Canadian Arctic. Based on the functional analysis of our data, we see a transition from a community where nitrogen-based chemolithotrophy plays a relevant role during winter, to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom in spring-summer, where different groups specialize in different nitrogen sources. Publications related to this project:
- Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation. mBio (2025)
- Microbial nitrogen guilds in the oceans: from the bathypelagic to the ocean surface. bioXriv.(2024)
I have also participated in different projects to characterize specific microbial groups from the ocean using metagenomics approaches. For instance, I have been part of the first genomic atlas of syntrophic sulfate-reducing bacteria. I also collaborated in studies investigating the metabolism of deep-sea bacterial groups like Sulfurimonas or Woesiales. Besides, I have been involved in a project characterizing a 2-million years old microbial community recovered from permafrost samples. Relevant publications:
- Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. The ISME Journal (2020)
- A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nature Microbiology (2023)
- Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea. PLoS Biology (2023)
- A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland. bioRxiv (2023)