Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils-Case of Sulfamethazine-Degrading Microbacterium sp. C448.

Loren Billet,Pascale Besse-Hoggan,Arnaud Mounier,Stéphane Pesce,Laurianne Paris,Nadine Rouard,Marion Devers-Lamrani,Martin Leremboure,Aymé Spor,Fabrice Martin-Laurent

doi:10.3389/fmicb.2021.643087

Abstract

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Highlights

Antibiotics and their residues deserve specific attention as pollutants of emerging concern
Despite the exposure to SMZ, its abundance remained below the detection limit. This strongly suggests that the microbial communities of the four soils and manure do not initially possess bacteria carrying sadA, some of them were previously exposed to low concentrations of SMZ (Supplementary Table 3). sadA has only appeared in recent literature on sulfonamide-degrading bacteria isolated from environmental compartments after high and long-term exposure to sulfonamide antibiotics, such as bioreactor membranes (Bouju et al, 2012), active sludges (Reis et al, 2014), or manureamended soils (Tappe et al, 2013; Chen et al, 2019)
The sulfonamide-resistant function confers a selective advantage in competitive environments impacted by the biocidal action of SMZ

Summary

Introduction

Antibiotics and their residues deserve specific attention as pollutants of emerging concern. The disposal processes applied to these matrices lack efficiency, and so the discharge of wastewater into aquatic ecosystems or manure spread on soils, a common agricultural practice for nutrient recycling and soil fertilization, contributes to the release of antibiotics into different environmental compartments (Watkinson et al, 2007; Heuer et al, 2011; Ghirardini et al, 2020). By their mode of action and their targets, antibiotics have several ecotoxicological effects on environmental bacteria. Contamination of ecosystems by antibiotics is a major health concern, as these environmental microbial communities constitute reservoirs of resistance that might potentially be transferred to pathogenic bacteria (Perry and Wright, 2013; Zrimec, 2020)

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