4.3 Barriers to plasmids transfer and the core permissive fraction
We observe a high degree of strain specificity for plasmid uptake within genera (figure 4a). Consistent with this, Maher & Taylor found that the uptake of different HI1A plasmids vary highly at the species level (Maher & Taylor, 1993). Likewise, another study also found that the capability of receiving plasmids is highly variable and strain specific, even within a single genus (Li et al., 2018). We speculate that this phenomenon can be attributed to a lack of host encoded defense systems e.g. R/M, CRISPR-Cas systems, etc. Moreover, other barriers to plasmid transfer that could cause strain-specific levels of permissiveness are plasmid incompatibility and plasmid entry exclusion mechanisms (Novick, 1987). Recently, it has been reported that a fundamental function of the diverse plasmid-encoded type IV CRISPR-Cas system is to target and eliminate competing plasmids (Crowley et al., 2019; Pinilla-Redondo et al., 2020).
We identify 40 shared ASVs (supplementary figure 5), which we define as the core permissive fraction. Within the core permissive fraction of our study, we do find ASVs representing the seven families identified in the overall pool of transconjugants: AeromonadaceaeBurkholderiaceaeEnterobacteriaceaeFlavobacteriaceaeMoraxellaceaePseudomonadaceae and Shewanellaceae. The families AeromonadaceaePseudomonadaceae and Shewanellaceae are even found at relative abundances above 3% for both R27 and pB10 (figure 4b). Previous studies have identified Aeromonadaceae ,EnterobacteriaceaeMoraxellaceae and Pseudomonadaceae as part of the core permissive fraction, which extends across diverse environments (Klümper et al., 2015; Li et al., 2018; Musovic et al., 2014; Pinilla-Redondo et al., n.d.). Of special interest are Enterobacteriaceae and Aeromonadaceae , as these two families have been found to represent a large fraction of the core permissive fraction in WWTPs (Li et al., 2018). Suggesting further importance in the core-permissive fraction of these two families is the observation that a enrichment of R27 and pB10 transconjugants resulted in the domination of a single genus of Serratia (Enterobacteriaceae) or Aeromonas (Aeromonadaceae ), respectively (Figure 5b). Thus we also show that members of the core-permissive fraction are fully capable of further carrying and disseminating plasmids. Given the positive impact a plasmid can have under selective conditions, and conversely, the parasitic burden it may represent when it does not grant advantages, it is not unimaginable that some bacterial families have evolved to embrace plasmids, while other families have evolved to categorically reject them. We speculate that a central feature of the core permissive fraction could be a lack of plasmid-targeting host defenses. Altogether, the families AeromonadaceaeEnterobacteriaceaeMoraxellaceaePseudomonadaceae and Shewanellaceae seem to play a central role in the dissemination of ARGs via plasmids and our work suggest that HI1A and P1 plasmids are included in this network of conjugation within the sewage microbiome.