Abstract
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.
Highlights
The old theory “Everything is everywhere, but, the environment selects” has been critically discussed through time [1]
Mobile genetic elements (MGEs) have been vastly studied in environments with high degrees of anthropogenic pollution, including sites with high loads of antibiotics where the mobilization of antibiotic resistance genes has been documented within the respective microbiome [10,11,12]
Mobile genetic elements were enriched at the hyperarid core of the Atacama Desert, while stress response genes were not, which could suggest a more prominent role of MGEs in the microbiome adaptation to desert soils due to the selection of those elements
Summary
The old theory “Everything is everywhere, but, the environment selects” has been critically discussed through time [1]. It can be understood as an argument for environmental conditions being essential to the structuring of microbial communities but bacterial evolution itself. Some studies have indicated that Mobile Genetic Elements (MGEs) are enriched in the microbiomes of extreme environments, which could facilitate an enhanced evolution and adaptation of the microbiome to environmental stressors [5]. MGEs are fragments of DNA with the ability to mobilize themselves within genomes and between bacterial cells, a process referred to as horizontal gene transfer (HGT). MGEs have been vastly studied in environments with high degrees of anthropogenic pollution, including sites with high loads of antibiotics where the mobilization of antibiotic resistance genes has been documented within the respective microbiome [10,11,12]
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