High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments
Creators
- 1. The Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan, Israel, and The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- 2. The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- 3. DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- 4. EscolaSuperiordeBiotecnologia,UniversidadeCatoĺicaPortuguesa,Lisboa,Portugal
- 5. Faculty of Environmental Sciences, Technische Universitaẗ Dresden, Dresden, Germany
- 6. CNRS, Laboratoire de Chimie Physique et Microbiologie pour l′Environnement (LCPME), UMR 7564, Institut Jean Barriol, 15 Avenue du Charmois, 54500 Vandoeuvre-les̀-Nancy, France, and Université de Lorraine, LCPME, UMR7564, 15 Avenue du Charmois, 54500 Vandoeuvre-les̀-Nancy, France
- 7. Institute for Water Quality, Resources and Waste Managment, Technische Universitaẗ Wien, Wien, Austria
- 8. Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- 9. Department of Civil and Environmental Engineering and Nireas, International Water Research Center, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- 10. Department of Civil Engineering, University of Salerno, Salerno, Italy
- 11. Norwegian Institute for Water Research, Oslo, Norway
- 12. School of Science and Technology, Middlesex University, London, U.K.
- 13. The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- 14. The Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan, Israel
Description
Integrons are extensively targeted as a proxy for anthropogenic impact in the environment. We developed a novel high-throughput amplicon sequencing pipeline that enables characterization of thousands of integron gene cassette-associated reads, and applied it to acquire a comprehensive overview of gene cassette composition in effluents from wastewater treatment facilities across Europe. Between 38 100 and 172 995 reads per-sample were generated and functionally characterized by screening against nr, SEED, ARDB and β-lactamase databases. Over 75% of the reads were characterized as hypothetical, but thousands were associated with toxin-antitoxin systems, DNA repair, cell membrane function, detoxification and aminoglycoside and β-lactam resistance. Among the reads characterized as β-lactamases, the carbapenemase blaOXA was dominant in most of the effluents, except for Cyprus and Israel where blaGES was also abundant. Quantitative PCR assessment of blaOXA and blaGES genes in the European effluents revealed similar trends to those displayed in the integron amplicon sequencing pipeline described above, corroborating the robustness of this method and suggesting that these integron-associated genes may be excellent targets for source tracking of effluents in downstream environments. Further application of the above analyses revealed several order-of-magnitude reductions in effluent-associated β-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.
Notes
Files
acs.est.6b03188.pdf
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