21The current epidemic of antibiotic resistance has been facilitated by the wide and rapid 22 horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. 23Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse 24 taxa. While the existence conditions of plasmids have been extensively studied in a few model 25 bacterial populations, their fate in complex bacterial communities is poorly understood. Here, 26we coupled plasmid transfer assays with serial growth experiments to investigate the 27 persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived 28 from a sewage treatment plant. The cultivation conditions combined different nutrient and 29 oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. 30Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial 31 growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up 32 to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped 33 plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness 34 benefits were observed in multiple phylotypes of Aeromonas, Pseudomonas and 35Enterobacteriaceae, which resulted in community-level plasmid persistence. We demonstrate, 36 for the first time, that plasmid fitness effects across community members can be estimated in a 37 high-throughput way without prior isolation. By gaining a fitness benefit when carrying 38 plasmids, members within complex microbial communities might have a hitherto unrecognized 39 potential to maintain plasmids for long-term community-wide access. 40 41
Introduction 42Plasmids -extrachromosomal replicons -can support rapid bacterial adaptation by moving 43 genes between phylogenetically diverse bacteria, a process known as horizontal gene transfer 44[1]. This is particularly important in the case of antibiotic resistance, where acquisition of 45 plasmid-borne antibiotic resistance genes (ARGs) can instantly render a strain impervious to 46 antibiotic treatment [2]. The current global antibiotic resistance crisis has been largely 47 attributed to plasmid mediated ARG dissemination [3]. 48
49Strategies to combat the antibiotic resistance epidemic therefore require an understanding of 50 the mechanisms that underlie plasmid fate in microbial communities. Upon entering a 51 microbial community, a plasmid will only persist if its original or secondary hosts 52 (transconjugants) survive. If it persists, it will constitute a long-term reservoir of auxiliary 53 genes for that community. In fact, persistence of IncP-1 plasmids or their derivatives has 54 recently been observed in ex situ communities like anaerobic sludge microcosms [4] and 55 artificial multi-species system [5] over periods longer than 10 days, as well as in murine gut 56 microbiota experiments [6]. However, by simply interpreting plasmid persistence as the 57 frequency of plasmid ...