Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes


The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.

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Fig. 1: Transconjugant density (%) detected by FACS in the initial filter mating samples (0 day) and in the daily samples through 10-day serial growth experiments (1–10 days).
Fig. 2: Diversity and absolute abundance of the dominant phylotypes in samples from initial filter mating and serial growth experiments.
Fig. 3: Persistent genera or phylotypes at the end of the serial growth experiment.
Fig. 4: Richness of permissive phylotypes relative to all recipient phylotypes over time.
Fig. 5: Plasmid effect of permissive phylotypes during the serial growth experiments.


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This work was supported by a Joint Programming Initiative-Antimicrobial Resistance grant (JPI-AMR; DARWIN project #7044-00004B) to BFS; and a fellowship under the H.C. Ørsted Postdoc programme co-funded by the Marie Skłodowska-Curie Actions awarded to LL.

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Li, L., Dechesne, A., Madsen, J.S. et al. Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes. ISME J (2020).

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