Does flooding proliferate metal and antibiotic resistance genes in riverine floodplains?

Global change-driven floods¹ not only reshape or destroy landscapes but may also create hotspots for antimicrobial resistance. During a flooding event, contaminants and nutrients are mobilized, redistributed, and deposited across flooded areas². While antimicrobial substances, i.e. metals and antibiotics, naturally occur in low concentrations in the environment, their levels often increase through anthropogenic activities³. These contaminants contribute to the unprecedented loss in soil health affecting the soils’ microbiome and its ecosystem functions³. As a microbial adaptation, metal (MRGs) and antibiotic resistance genes (ARGs) proliferate in the environment. Microbial resistance may enhance soil resilience, yet the spread and proliferation of ARGs poses a major public health threat, contributing to the failure of medical treatments and millions of deaths annually⁶. ARGs and MRGs are often co-located on the same mobile genetic elements, and are thus co-proliferated together even in the absence of one of the contaminants⁷. By entering rivers through runoff, leaching and discharge⁸ contaminants can be transferred downstream and accumulate in flood-prone areas. Thus, riverine floodplains may likely be co-exposed to metals and antibiotics and function as reservoirs for resistance genes, potentially facilitating their transfer to humans.

To evaluate how resistance acquisition evolves after flooding, a mesocosm study with combined and single metal and antibiotic contamination of a floodplain grassland from the Elbe river was conducted. Environmentally relevant concentrations of metals, antibiotics, their combination, or uncontaminated water were applied in a single flooding event. Contaminant fate in porewater and microbial resistance in soil were traced over seven weeks.              

The added metal load was not detectable in the mobile phase of soil porewater one day after flooding, indicating adsorption to soil particles. Nevertheless, plants responded with a contaminant-dependent increase in the chlorophyll a/b ratio within two weeks after flooding. In addition, flooding induced microbial cell growth, with the magnitude and timing of growth peaks depending on the contamination treatment. The metal treatment induced a rapid increase in 16S rRNA gene copies as well as a slight increase of MRGs after two weeks, whereas antibiotics and the combined treatment resulted in a delayed response followed by a slower decrease in both gene abundances. Metals and antibiotics combined did not amplify but rather attenuated this microbial response. Subsequently, ARGs were correlated with MRG responses. Overall, even though the microbial community responded to the stressors, the magnitude and duration of effects indicate that the active and diverse community of floodplain soils could be able to buffer low contamination events.      
Increasing frequency of extreme weather events and ongoing contaminant accumulation can further challenge the resilience of microbial communities in flood-impacted soils, highlighting their role as flood protection and water filters but also their vulnerability.        

1 IPCC, 2023 
2 Crawford et al., J Hazard Mater, 2022
3 Cycoń et al., Front Microbiol, 2019
4 Lado et al., Geoderma, 2008
5 IPBES, 2018
6 Naghavi et al., Lancet, 2024
7 Imran et al., Chemosphere, 2019
8 Bailey et al., J Soils Sediments, 2015