Influence of antibiotics and microbial coalescence on sediment microbial communities’ functions and diversity

Gkoni Ioanna¹, Miege Cecile¹, Chapuis Thomas¹, Kergoat Laura¹, Daval Amandine¹, Volat Bernadette¹, Meziti Alexandra², Cournoyer Benoit³, Vasileiadis Sotirios⁴, Pesce Stephane¹

¹INRAE, UR RiverLy, Villeurbanne 69625, France
²Department of Marine Sciences, University of Aegean, University Hill 81100, Mytilene, Greece
³Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, Marcy L’Etoile, 69280, France
⁴University of Thessaly, Department of Biochemistry and Biotechnology, Larissa, Greece

Abstract :
Microbial communities play a central role in ecosystem functioning by driving processes such as nutrient cycling, organic matter degradation, and contaminant transformation. Yet, their stability is increasingly challenged by chemical pollution and physical disturbances that promote microbial coalescence. Among chemicals, antibiotics, which are frequently detected in soil and aquatic ecosystems, can disrupt microbial diversity and biogeochemical cycles enhancing the dissemination of antimicrobial resistance(AMR), while soil intrusion can introduce exogenous microorganisms and/or genetic materials that may destabilize sediment communities. To investigate these combined effects, we conducted a 27-day controlled microcosm experiment using natural river sediments with contrasting organic matter content. Treatments included the presence or absence of antibiotics(sulfamethazine or ofloxacin) and/or soil inputs(with sterilized soil serving as a negative control), thereby simulating chemical and physical disturbances. Specifically, two sediment types were used, exposed to three antibiotic treatments(ofloxacin, sulfamethazine, or no antibiotic) and three soil treatments(sterile soil, non-sterile soil, or no soil). All treatments were performed in triplicates. Heterotrophic microbial activities(enzymatic activities and aerobic respiration)were generally higher in Tillet sediments, which were richer in organic matter, compared to Leysse sediments. Soil addition had stronger effects on enzymatic activities than antibiotics, particularly influencing phosphatase and β-glucosidase responses. Respiratory responses varied depending on sediment type and antibiotic treatment. Sulfamethazine treatment led to microbial adaptation to the mineralization of the antibiotic, but only in Leysse sediments and in the absence of soil. Finally, qPCR analyses revealed increased abundance of AMR gene markers(sul1, dfrA, blaOXA20, and int1) under combined disturbance scenarios, particularly with sulfamethazine and sterile soil treatments. Overall, our findings demonstrate that microbial coalescence and pharmaceutical pollution interact to reshape sediment microbial communities, altering enzymatic functions, respiration, sulfamethazine biodegradation and resistance gene dynamics. These results highlight the ecological risks of multiple stressors and the need for integrated approaches to safeguard biodiversity and ecosystem resilience.

Keywords: pharmaceuticals, antimicrobial resistance, enzymatic activities, respiration, biodegradation