Does bacterial predation restrict antibiotic-resistance spread in soils?

Agriculture is an important component in the spread of antibiotic resistance genes (ARGs) and their carrying bacteria (ARB). Organic agriculture is becoming more prominent and along with-it increased use of manure that may contain ARB. However, the soil imposes a strong barrier on the establishment of ARB/ARGs. Here, we postulate that bacterial predation plays an important role in restricting ARB/ARG spread. Bdellovibrio like organisms (BALOs) are obligate predators of gram-negative bacteria, including ARB, and are common in soil. Our aim is to characterize and quantify the BALO-ARB interactions in soil samples from fields receiving manure and compost in large amounts. To do so, we collect samples from organic and conventionally managed fields, extract DNA and perform targeted 16S rRNA gene community sequencing of the total bacterial and of the BALO communities, along with quantitative PCR of the BALOs as compared to total bacteria. The acquired data will provide BALO diversity, their abundance, and fluctuations along the growth season. Further, an ARG array will measure the abundance and distribution of ARGs in the samples. Based on previous studies and isolation on antibiotic-containing media, ARGs will be partially linked to ARBs. In order to reveal specific predator-prey interactions at the individual cell level, we are developing a novel use of epic-PCR, in which predator and prey genes are linked by “hybrid-PCR,” to be sequenced in bulk. These data will provide fine detail on predatory dynamics and their effect on ARBs. First results will be presented.