Volume 20, Issue 11 p. 4091-4111
Research article

Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation

Vincent Dunon

Vincent Dunon

Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Box 2459, 3001 Heverlee, Belgium

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Karolien Bers

Karolien Bers

Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Box 2459, 3001 Heverlee, Belgium

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Rob Lavigne

Rob Lavigne

Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Heverlee, Belgium

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Eva M. Top

Eva M. Top

Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA

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Dirk Springael

Corresponding Author

Dirk Springael

Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Box 2459, 3001 Heverlee, Belgium

For correspondence. E-mail [email protected]; Tel. ++32 16 3216 04; Fax ++32 16 32 19 97.Search for more papers by this author
First published: 11 September 2018
Citations: 25

Summary

IS1071, an insertion element that primarily flanks organic xenobiotic degradation genes in cultured isolates, is suggested to play a key role in the formation and distribution of bacterial catabolic pathway gene clusters. However, in environmental settings, the identity of the IS1071 genetic cargo and its correspondence to the local selective conditions remain unknown. To respond, we developed a long-range PCR approach amplifying accessory genes between two IS1071 copies from community DNA followed by amplicon sequencing. We applied this method to pesticide-exposed environments, i.e. linuron-treated agricultural soil and on-farm biopurification systems (BPS) treating complex agricultural wastewater, as to non-treated controls. Amplicons were mainly recovered from the pesticide-exposed environments and the BPS matrix showed a higher size diversity compared to the agricultural soil. Retrieved gene functions mirrored the main selection pressure as (i) a large fraction of the BPS amplicons contained a high variety of genes/gene clusters related to the degradation of organics including herbicides present in the wastewater and (ii) in the agricultural soil, recovered genes were associated with linuron degradation. Our metagenomic analysis extends observations from cultured isolates and provides evidence that IS1071 is a carrier of catabolic genes in xenobiotica stressed environments and contributes to community level adaptation towards pesticide biodegradation.