Extreme environments with harsh conditions—e.g., extreme dryness, very low/very high temperatures or pressures, high salinity, or radiation exposure—can harbor interesting organisms that can survive there, called extremophiles. These environments can also mimic the conditions found on other planets. For example, high-altitude lakes in the Andes in South America are thought to have similar conditions to early Mars. This makes the identification of microorganisms that live in these regions interesting for space-related research.

The microorganisms found in these environments can be identified by performing genome sequencing, either analyzing the whole genome or specific gene sequences. Sequencing of the 16S rRNA gene is often used to identify microorganisms, but can sometimes fail for closely related bacterial species.

Proteotyping could be a useful alternative. The term refers to the use of protein markers for the classification and identification of microorganisms (instead of gene sequences). This can be achieved using tandem mass spectrometry (MS/MS). The proteins in the sample are cleaved into smaller peptides using trypsin, which are then separated and sequenced using mass spectrometry. This broader approach can help to tell species apart because it is not limited to a single gene.

Ralf Moeller, German Aerospace Center (DLR), Cologne, Germany, and colleagues have isolated microorganisms from samples stemming from high-altitude Andean lakes in Chile. The team cultivated 66 different microorganisms and used both proteotyping and sequencing of the 16S rRNA genes to identify them. Both approaches identified 63 of the 66 types of microorganisms. In the other samples, the results of the proteotyping indicated the presence of two potentially new types of extremophile bacteria that were not identified by the 16S rRNA sequencing approach. The work indicates that proteotyping can be a valuable tool for characterizing extremophiles and might also be useful in astrobiology.

• Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping,
  Katharina Runzheimer, Clément Lozano, Diana Boy, Jens Boy, Roberto Godoy, Francisco J. Matus, Denise Engel, Bruno Pavletic, Stefan Leuko, Jean Armengaud, Ralf Moeller,
  J. Proteome Res. 2024.
  https://doi.org/10.1021/acs.jproteome.3c00538