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Inside the Atacama Desert: uncovering the living microbiome of an extreme environment

Authors
/persons/resource/abartho

Bartholomäus,  Alexander
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

/persons/resource/sgender

Genderjahn,  S.
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

/persons/resource/kama

Mangelsdorf,  Kai
3.2 Organic Geochemistry, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

/persons/resource/bschnei

Schneider,  Beate
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

Zamorano,  Pedro
External Organizations;

Kounaves,  Samuel P.
External Organizations;

/persons/resource/dirksm

Schulze-Makuch,  Dirk
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

/persons/resource/dwagner

Wagner,  D.
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

Glass,  Jennifer B.
External Organizations;

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Citation

Bartholomäus, A., Genderjahn, S., Mangelsdorf, K., Schneider, B., Zamorano, P., Kounaves, S. P., Schulze-Makuch, D., Wagner, D. (2024 online): Inside the Atacama Desert: uncovering the living microbiome of an extreme environment. - Applied and Environmental Microbiology.
https://doi.org/10.1128/aem.01443-24


Cite as: https://gfzpublic.gfz-potsdam.de/pubman/item/item_5029076
Abstract
The Atacama Desert in Chile is one of the driest and most inhospitable places on Earth. To analyze the diversity and distribution of microbial communities in such an environment, one of the most important and challenging steps is DNA extraction. Using commercial environmental DNA extraction protocols, a mixture of living, dormant, and dead cells of microorganisms is extracted, but separation of the different DNA pools is almost impossible. To overcome this problem, we applied a novel method on soils across a west–east moisture transect in the Atacama Desert to distinguish between extracellular DNA (eDNA) and intracellular DNA (iDNA) at the cell extraction level. Here, we show that a large number of living and potentially active microorganisms, such as Acidimicrobiia, Geodermatophilaceae, Frankiales, and Burkholderiaceae, occur in the hyperarid areas. We observed viable microorganisms involved as pioneers in initial soil formation processes, such as carbon and nitrogen fixation, as well as mineral-weathering processes. In response to various environmental stressors, microbes coexist as generalists or specialists in the desert soil environment. Our results show that specialists compete in a limited range of niches, while generalists tolerate a wider range of environmental conditions. Use of the DNA separation approach can provide new insights into different roles within viable microbial communities, especially in low-biomass environments where RNA-based analyses often fail.