Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert
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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-10-01
|
| Series: | Diversity |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1424-2818/11/11/205 |
| _version_ | 1811278983497515008 |
|---|---|
| author | Johan S. Sáenz Alessandro Airo Dirk Schulze-Makuch Michael Schloter Gisle Vestergaard |
| author_facet | Johan S. Sáenz Alessandro Airo Dirk Schulze-Makuch Michael Schloter Gisle Vestergaard |
| author_sort | Johan S. Sáenz |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T00:46:46Z |
| format | Article |
| id | doaj.art-8615aff56632473f94aa181f941c96d3 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-04-13T00:46:46Z |
| publishDate | 2019-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-8615aff56632473f94aa181f941c96d32022-12-22T03:09:59ZengMDPI AGDiversity1424-28182019-10-01111120510.3390/d11110205d11110205Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama DesertJohan S. Sáenz0Alessandro Airo1Dirk Schulze-Makuch2Michael Schloter3Gisle Vestergaard4Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Oberschleissheim, GermanyCenter of Astronomy & Astrophysics, Technical University Berlin, 10623 Berlin, GermanyCenter of Astronomy & Astrophysics, Technical University Berlin, 10623 Berlin, GermanyComparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Oberschleissheim, GermanyComparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Oberschleissheim, GermanyMobile 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.https://www.mdpi.com/1424-2818/11/11/205mobile genetic elementssoil microbiomesoil metagenomestress responsehyperarid desert |
| spellingShingle | Johan S. Sáenz Alessandro Airo Dirk Schulze-Makuch Michael Schloter Gisle Vestergaard Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert Diversity mobile genetic elements soil microbiome soil metagenome stress response hyperarid desert |
| title | Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert |
| title_full | Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert |
| title_fullStr | Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert |
| title_full_unstemmed | Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert |
| title_short | Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert |
| title_sort | functional traits co occurring with mobile genetic elements in the microbiome of the atacama desert |
| topic | mobile genetic elements soil microbiome soil metagenome stress response hyperarid desert |
| url | https://www.mdpi.com/1424-2818/11/11/205 |
| work_keys_str_mv | AT johanssaenz functionaltraitscooccurringwithmobilegeneticelementsinthemicrobiomeoftheatacamadesert AT alessandroairo functionaltraitscooccurringwithmobilegeneticelementsinthemicrobiomeoftheatacamadesert AT dirkschulzemakuch functionaltraitscooccurringwithmobilegeneticelementsinthemicrobiomeoftheatacamadesert AT michaelschloter functionaltraitscooccurringwithmobilegeneticelementsinthemicrobiomeoftheatacamadesert AT gislevestergaard functionaltraitscooccurringwithmobilegeneticelementsinthemicrobiomeoftheatacamadesert |