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Open AccessArticle

Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

1
Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Oberschleissheim, Germany
2
Center of Astronomy & Astrophysics, Technical University Berlin, 10623 Berlin, Germany
3
GFZ German Research Center for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
4
Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775 Stechlin, Germany
5
School of the Environment, Washington State University, Pullman, WA 99164, USA
6
ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
7
Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
*
Author to whom correspondence should be addressed.
Diversity 2019, 11(11), 205; https://doi.org/10.3390/d11110205
Received: 4 October 2019 / Revised: 27 October 2019 / Accepted: 28 October 2019 / Published: 31 October 2019
Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.
Keywords: mobile genetic elements; soil microbiome; soil metagenome; stress response; hyperarid desert mobile genetic elements; soil microbiome; soil metagenome; stress response; hyperarid desert
MDPI and ACS Style

Sáenz, J.S.; Airo, A.; Schulze-Makuch, D.; Schloter, M.; Vestergaard, G. Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert. Diversity 2019, 11, 205.

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