Exploring Mars on Earth: Sequencing Microbes in the Atacama Plateau
Featured Image Caption: The Atacama region is known for its harsh climate and undrinkable water.. Lakes in this area are known to have salt concentrations eight times higher than seawater. “Salar de Atacama” by Francesco Mocellin CC-SA 3.0 Deed via Wikimedia commons.
Primary Source Article: Runzheimer, K., Lozano, C., Boy, D., Boy, J., Godoy, R., Matus, F. J., Engel, D., Pavletic, B., Leuko, S., Armengaud, J., & Moeller, R. (2024). Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping. Journal of proteome research, 23(3), 891–904. https://doi.org/10.1021/acs.jproteome.3c00538S
Special thanks to Julia Bebout. Your edits strengthen my writing and I am very lucky to have your support!
On the borders of the Atacama Desert lie the Altiplano, a region in Chile known for its high UV levels, low oxygen level, salty lakes, and dry climate. Only the toughest microbes survive in the Andean lakes. Rare microbes that thrive in this climate are called extremophiles, organisms that can tolerate extreme environments. Extremophiles are important for understanding life on other planets and can lead to discovering enzymes for important industrial applications in medicine and agriculture.
To discover unknown extremophiles in the Andean Sea lakes in Chile, Runzheimer and colleagues compared the suitability of sequencing techniques for the task. The scientists collected water samples from 5 lakes in the Atacama in Chile, then used two sequencing techniques, 16S rRNA sequencing and MS/MS proteotyping, to search for previously unknown species. They also took this opportunity to determine which technique is better at discovering new microorganisms.
Map of the sample locations in Atacama in chile. Image Source: “Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping” by Runzheimer et. al Copyright Runzheimer et. al. Published by American Chemical Society, is licensed under CC By-SA 4.0 Deed
Two Sequence Techniques: Should the Focus be on DNA or Protein to Identify Extremophiles?
16S rRNA sequencing is the traditional DNA based approach for identifying microbial species. The technique involves isolating DNA of an unknown microbe, cutting out a gene of interest, and then running it through a machine and cross checking it against a known database to determine the microbe’s identity. The 16S rRNA gene of interest is responsible for making the subunit of a ribosome, a hamburger shaped machine that makes proteins in cells.
Screening for the 16SrRNA gene helps identify different types of bacteria and archaea because the code is both common and variable enough among these organisms to be able to differentiate between individual species. Think of the sequencing machine as a barcode scanner that can identify different brands of hamburger buns based on the code that is detected. The code would be similar, but different enough to determine what brand of hamburger bun you have.
In contrast, tandem mass (MS/MS) spectrometry proteotyping does not use DNA to determine the identity of a microbe. Proteotyping focuses on isolating proteins and then scans the results against a database of known microbes.
Comparing the two techniques, proteotyping had some advantages. When faced with samples that were unlike others in the existing datasets of known microbes, proteotyping was able to recognize new species and genera that were not recognized by 16S rRNA sequencing.
Mystery Microbes and Future Directions
In the study, the microbes SS13 and SM33 were discovered. Scientists used both sequencing techniques to determine that SS13 shares similarities with sulfur bacteria, gram negative bacteria, and halotolerant bacteria, but belongs into a genus of its own. Proteotyping revealed that its closest relative is Rheinheimera pacifica, a bacterium that is seen in deep waters of the Pacific Ocean. SM33 closely resembles a type of marine bacteria.
Discoveries of extremophiles like these help us to understand the limits of life as we know it. The first step in understanding mystery microbes is to culture, sequence them, and study them over time. Ultimately, proteotyping will go hand in hand with sequencing microbes that are poorly understood. In this study, scientists used these techniques to study extremophiles on Earth. In the future, these techniques could be used to study microbes on Mars and other planets
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