The global groundwater resistome: core ARGs and their dynamics – an in silico re-analysis of publicly available groundwater metagenomes

Preprint, 2022

Despite the importance of groundwater environments as drinking water resources, there is currently no comprehensive picture of the global levels of antibiotic resistance genes in groundwater. Moreover, the biotic and abiotic factors that might shape the groundwater resistome remain to be explored on a global scale. Herein, we attempted to fill this knowledge gap by in silico re-analysis of publicly available global groundwater metagenomes. We first investigated the occurrence of antibiotic resistance genes (ARGs) to define the core groundwater resistome. We further tested whether the ARG dissemination in the pristine groundwater environments could be explained by natural ecological processes such as competition between fungal and bacterial taxa. Six ARGs encoding resistance to aminoglycosides (aph3'), aph3''), sulfonamides (sul1, sul2), and beta-lactams (blaOXA, blaTEM) occurred in at least 50% of samples at high abundance, thereby constituting the core groundwater resistome. ARG abundances differed significantly between countries and only weakly correlated with bacterial community composition. While only limited effects of anthropogenic impacts could be observed, ecological interactions played a significant role in shaping the abundance patterns of at least a number of the core ARGs. Fungal abundance positively correlated with blaTEM and blaOXA abundance, ARGs that confer resistance to beta-lactams, regularly produced by fungi. However, no direct correlation was determined for the remainder of the core ARGs. Still, using co-occurrence network analysis we identified that the fungal abundance acted as a hub-node that included blaOXA and blaTEM, but also indirectly contributed to the abundance of aminoglycoside ARG aph3'). Hence, interactions between bacteria and fungi including potential antibiotic production can contribute to the dissemination of ARGs in groundwater environments. Consequently, fungal/bacterial SSU ratio could serve as an indicator for the abundance of certain ARGs in the pristine groundwater environments.