Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes.

As mobile genetic elements, plasmids are central for our understanding of antimicrobial resistance spread in microbial communities. Plasmids can have varying fitness effects on their host bacteria, which will markedly impact their role as antimicrobial resistance vectors. Using a plasmid population model, we first show that beneficial plasmids interact with a higher number of hosts than costly plasmids when embedded in a community with multiple hosts and plasmids. We then analyse the network of a natural host-plasmid wastewater community from a Hi-C metagenomics dataset. As predicted by the model, we find that antimicrobial resistance encoding plasmids, which are likely to have positive fitness effects on their hosts in wastewater, interact with more bacterial taxa than non-antimicrobial resistance plasmids and are disproportionally important for connecting the entire network compared to non- antimicrobial resistance plasmids. This highlights the role of antimicrobials in restructuring host-plasmid networks by increasing the benefits of antimicrobial resistance carrying plasmids, which can have consequences for the spread of antimicrobial resistance genes through microbial networks. Furthermore, that antimicrobial resistance encoding plasmids are associated with a broader range of hosts implies that they will be more robust to turnover of bacterial strains.

Antagonistic Mobile Genetic Elements Can Counteract Each Other's Effects on Microbial Community Composition.

Bacteriophages ("phages") are hypothesized to be key drivers of bacterial population dynamics, driving microbial community composition, but empirical support for this is mixed. One reason why phages may have a less-than-expected impact on community composition is that many different phages and other mobile genetic elements (MGEs) interact with each bacterium. For instance, the same phage may have higher or lower costs to different bacterial strains or species. Assuming that resistance or susceptibility to MGE infection is not consistent across all MGEs, a simple prediction is that the net effect of MGEs on each bacterial taxon may converge with an increasing number of interactions with different MGEs. We formalized this prediction using in silico population dynamics simulations and then carried out experiments using three bacterial species, one generalist conjugative plasmid, and three species-specific phages. While the presence of only phages or only the plasmid altered community structure, these differential effects on community structure canceled out when both were together. The effects of MGEs were largely indirect and could not be explained by simple pairwise bipartite interactions (i.e., between each MGE and each bacterial species). Our results suggest that the effects of MGEs may be overestimated by studies that focus on a single MGE and not on interactions among multiple MGEs. IMPORTANCE While bacteriophages ("phages") are often cited as some of the key drivers of microbial diversity, evidence for this is greatly mixed. We demonstrate, in silico and experimentally, that the impact of phages, an example of a mobile genetic element (MGE), on community structure can diminish with increasing MGE diversity. This is because MGEs can have diverse effects on host fitness, and therefore as diversity increases, their individual effects cancel out, returning communities back to an MGE-free state. In addition, interactions in mixed-species and MGE communities could not be predicted from simple pairwise interactions, highlighting the difficulty in generalizing a MGE's effect from pairwise studies.

Fitness effects of plasmids shape the structure of bacteria-plasmid interaction networks.

Antimicrobial resistance (AMR) genes are often carried on broad host range plasmids, and the spread of AMR within microbial communities will therefore depend on the structure of bacteria­plasmid networks. Empirical and theoretical studies of ecological interaction networks suggest that network structure differs between communities that are predominantly mutualistic versus antagonistic, with the former showing more generalized interactions (i.e., species interact with many others to a similar extent). This suggests that mutualistic bacteria­plasmid networks­where antibiotics are present and plasmids carry AMR genes­will be more generalized than antagonistic interactions, where plasmids do not confer benefits to their hosts. We first develop a simple theory to explain this link: fitness benefits of harboring a mutualistic symbiont promote the spread of the symbiont to other species. We find support for this theory using an experimental bacteria­symbiont (plasmid) community, where the same plasmid can be mutualistic or antagonistic depending on the presence of antibiotics. This short-term and parsimonious mechanism complements a longer-term mechanism (coevolution and stability) explaining the link between mutualistic and antagonistic interactions and network structure.