A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils
Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human...
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ftunivgent:oai:archive.ugent.be:8558164 2023-06-11T04:06:12+02:00 A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van de Peer, Yves Cowan, Don A Makhalanyane, Thulani P 2018 application/pdf https://biblio.ugent.be/publication/8558164 http://hdl.handle.net/1854/LU-8558164 https://doi.org/10.1186/s40168-018-0424-5 https://biblio.ugent.be/publication/8558164/file/8558169 eng eng https://biblio.ugent.be/publication/8558164 http://hdl.handle.net/1854/LU-8558164 http://dx.doi.org/10.1186/s40168-018-0424-5 https://biblio.ugent.be/publication/8558164/file/8558169 Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) info:eu-repo/semantics/openAccess MICROBIOME ISSN: 2049-2618 Biology and Life Sciences MICROBIAL COMMUNITIES DRUG-RESISTANCE BETA-LACTAMASES ALASKAN SOIL BACTERIA RESISTOME ENVIRONMENT DATABASE TOOL BIOSYNTHESIS Antibiotic resistance genes Soil resistome Antarctica Metagenomics journalArticle info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 2018 ftunivgent https://doi.org/10.1186/s40168-018-0424-5 2023-05-10T22:27:27Z Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments. Article in Journal/Newspaper Antarc* Antarctic Antarctica Ghent University Academic Bibliography Antarctic Mackay ENVELOPE(168.517,168.517,-77.700,-77.700) Mackay Glacier ENVELOPE(162.000,162.000,-76.967,-76.967) Microbiome 6 1 |
institution |
Open Polar |
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Ghent University Academic Bibliography |
op_collection_id |
ftunivgent |
language |
English |
topic |
Biology and Life Sciences MICROBIAL COMMUNITIES DRUG-RESISTANCE BETA-LACTAMASES ALASKAN SOIL BACTERIA RESISTOME ENVIRONMENT DATABASE TOOL BIOSYNTHESIS Antibiotic resistance genes Soil resistome Antarctica Metagenomics |
spellingShingle |
Biology and Life Sciences MICROBIAL COMMUNITIES DRUG-RESISTANCE BETA-LACTAMASES ALASKAN SOIL BACTERIA RESISTOME ENVIRONMENT DATABASE TOOL BIOSYNTHESIS Antibiotic resistance genes Soil resistome Antarctica Metagenomics Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van de Peer, Yves Cowan, Don A Makhalanyane, Thulani P A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils |
topic_facet |
Biology and Life Sciences MICROBIAL COMMUNITIES DRUG-RESISTANCE BETA-LACTAMASES ALASKAN SOIL BACTERIA RESISTOME ENVIRONMENT DATABASE TOOL BIOSYNTHESIS Antibiotic resistance genes Soil resistome Antarctica Metagenomics |
description |
Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments. |
format |
Article in Journal/Newspaper |
author |
Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van de Peer, Yves Cowan, Don A Makhalanyane, Thulani P |
author_facet |
Van Goethem, Marc W Pierneef, Rian Bezuidt, Oliver KI Van de Peer, Yves Cowan, Don A Makhalanyane, Thulani P |
author_sort |
Van Goethem, Marc W |
title |
A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils |
title_short |
A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils |
title_full |
A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils |
title_fullStr |
A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils |
title_full_unstemmed |
A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils |
title_sort |
reservoir of 'historical' antibiotic resistance genes in remote pristine antarctic soils |
publishDate |
2018 |
url |
https://biblio.ugent.be/publication/8558164 http://hdl.handle.net/1854/LU-8558164 https://doi.org/10.1186/s40168-018-0424-5 https://biblio.ugent.be/publication/8558164/file/8558169 |
long_lat |
ENVELOPE(168.517,168.517,-77.700,-77.700) ENVELOPE(162.000,162.000,-76.967,-76.967) |
geographic |
Antarctic Mackay Mackay Glacier |
geographic_facet |
Antarctic Mackay Mackay Glacier |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
MICROBIOME ISSN: 2049-2618 |
op_relation |
https://biblio.ugent.be/publication/8558164 http://hdl.handle.net/1854/LU-8558164 http://dx.doi.org/10.1186/s40168-018-0424-5 https://biblio.ugent.be/publication/8558164/file/8558169 |
op_rights |
Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1186/s40168-018-0424-5 |
container_title |
Microbiome |
container_volume |
6 |
container_issue |
1 |
_version_ |
1768378011987476480 |