Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination

Emilie Lyautey; Chloé Bonnineau; Patrick Billard; Jean-Luc Loizeau; Emmanuel Naffrechoux; Ahmed Tlili; Edward Topp; Benoît J D Ferrari; Stéphane Pesce

doi:10.3389/fmicb.2021.738629

Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination

Front Microbiol. 2021 Oct 18:12:738629. doi: 10.3389/fmicb.2021.738629. eCollection 2021.

Authors

Emilie Lyautey^{1

2}, Chloé Bonnineau¹, Patrick Billard³, Jean-Luc Loizeau⁴, Emmanuel Naffrechoux⁵, Ahmed Tlili⁶, Edward Topp^{7

8}, Benoît J D Ferrari⁹, Stéphane Pesce¹

Affiliations

¹ INRAE UR RiverLy, Villeurbanne, France.
² INRAE, Université Savoie Mont Blanc, CARRTEL, Thonon-les-Bains, France.
³ Université de Lorraine, CNRS, LIEC, Nancy, France.
⁴ Department F.A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva, Switzerland.
⁵ EDYTEM, CNRS, Université Savoie Mont Blanc, Chambéry, France.
⁶ Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
⁷ Agriculture and Agri-Food Canada, London, ON, Canada.
⁸ Department of Biology, University of Western Ontario, London, ON, Canada.
⁹ Swiss Centre for Applied Ecotoxicology (Ecotox Centre), Lausanne, Switzerland.

Abstract

Lake sediments are natural receptors for a wide range of anthropogenic contaminants including organic matter and toxicants such as trace metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls that accumulate over time. This contamination can impact benthic communities, including microorganisms which play a crucial role in biogeochemical cycling and food-webs. The present survey aimed at exploring whether anthropogenic contamination, at a large lake scale, can influence the diversity, structure and functions of microbial communities associated to surface sediment, as well as their genetic potential for resistance to metals and antibiotics. Changes in the characteristics of these communities were assessed in surface sediments collected in Lake Geneva from eight sampling sites in October 2017 and May 2018. These sampling sites were characterized by a large concentration range of metal and organic compound contamination. Variation between the two sampling periods were very limited for all sampling sites and measured microbial parameters. In contrast, spatial variations were observed, with two sites being distinct from each other, and from the other six sites. Benthic communities from the most contaminated sampling site (Vidy Bay, near the city of Lausanne) were characterized by the lowest bacterial and archaeal diversity, a distinct community composition, the highest abundance of antibiotic resistance genes and functional (respiration, denitrification, methanogenesis, phosphatase, and beta-glucosidase) activity levels. The second sampling site which is highly influenced by inputs from the Rhône River, exhibited low levels of diversity, a distinct community composition, high abundance of antibiotic resistance genes and the highest bacterial abundance. Overall, our results suggest that local anthropogenic contamination, including organic matter and toxicants, is a major driver of the diversity and functioning of sediment-microbial communities in Lake Geneva. This highlights the need to consider benthic microbial communities and a suite of complementary ecotoxicological endpoints for more effective environmental risk assessments of contaminants in lake sediments.

Keywords: PAH; PCB; benthic communities; metals; microbial ecotoxicology; organic matter; resistance genes; urban contamination.