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Mobile genetic elements and antibiotic resistance in mine soil amended with organic wastes

Affiliation
NEIKER-Tecnalia, Department of Conservation of Natural Resources, Soil Microbial Ecology Group, Berreaga 1, 48160 Derio, Spain
Garbisu, Carlos;
Affiliation
Instituto BIOFISIKA (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
Garaiyurrebaso, Olatz;
Affiliation
NEIKER-Tecnalia, Department of Conservation of Natural Resources, Soil Microbial Ecology Group, Berreaga 1, 48160 Derio, Spain
Lanzén, Anders;
Affiliation
Instituto BIOFISIKA (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
Álvarez-Rodríguez, Itxaso;
Affiliation
Instituto BIOFISIKA (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
Arana, Lide;
Affiliation
NEIKER-Tecnalia, Department of Conservation of Natural Resources, Soil Microbial Ecology Group, Berreaga 1, 48160 Derio, Spain
Blanco, Fernando;
GND
1058967878
Affiliation
Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Brunswick, Germany
Smalla, Kornelia;
Affiliation
Beuth University of Applied Sciences, Life Sciences and Technology, Department of Microbiology, Seestraße 64, 13347 Berlin, Germany
Grohmann, Elisabeth;
Affiliation
Instituto BIOFISIKA (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
Alkorta, Itziar

Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors. Moreover, exogenous isolation of MGEs from the soil bacterial community was attempted under antibiotic selection pressure by using Escherichia coli as recipient. Seventeen putative transconjugants were identified based on increased antibiotic resistance. Metabolic traits and metal resistance of putative transconjugants were investigated, and whole genome sequencing was carried out for two of them. Most putative transconjugants displayed a multi-resistant phenotype for a broad spectrum of antibiotics. They also displayed changes regarding the ability to metabolise different carbon sources, RNA: DNA ratio, growth rate and biofilm formation. Genome sequencing of putative transconjugants failed to detect genes acquired by horizontal gene transfer, but instead revealed a number of nonsense mutations, including in ubiH, whose inactivation was linked to the observed resistance to aminoglycosides. Our results confirm that mine soils contain MGEs encoding antibiotic resistance. Moreover, they point out the role of spontaneous mutations in achieving low-level antibiotic resistance in a short time, which was associated with a trade-off in the capability to metabolise specific carbon sources.

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License Holder: 2017 Published by Elsevier B.V.

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