Interspecific competition can drive the loss of conjugative plasmids from a focal species in a microbial community

Walker‐Sünderhauf, David; Klümper, Uli; Gaze, William; Westra, Edze R.; Houte, Stineke van

doi:10.1101/2022.06.06.494957

Cited by 3 publications

(3 citation statements)

References 33 publications

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“…On the other hand, in more diverse communities it can be harder to encounter a permissive conjugation partner, which reduces transferability due to this dilution effect [63]. Further, competition with other community members might increase the costs of resistance [64] and could ultimately drive the loss of ARG hosting plasmids from the community [65]. This loss process would be expected to be elevated in more diverse communities with better competitors.…”

Section: Discussionmentioning

confidence: 99%

Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?

Klümper

Gionchetta

Catão

et al. 2023

Preprint

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Background: In the environment, microbial communities are constantly exposed to invasion by antimicrobial resistant bacteria (ARB) and their associated antimicrobial resistance genes (ARGs) that were enriched in the anthroposphere. A successful invader has to overcome the biotic resilience of the habitat, which is more difficult with increasing biodiversity. The capacity to exploit resources in a given habitat is enhanced when communities exhibit greater diversity, reducing opportunities for invaders, leading to a lower persistence. In the context of antimicrobial resistance (AMR) dissemination, exogenous ARB reaching a natural community may persist longer if the biodiversity of the autochthonous community is low, increasing the chance of ARGs to transfer to community members. Reciprocally, high microbial diversity could serve as a natural long-term barrier towards invasion by ARB and ARGs. Results: To test this hypothesis, a sampling campaign across seven European countries was carried out to obtain 172 environmental samples from sites with low anthropogenic impact. Samples were collected from contrasting environments: stationary structured forest soils, or dynamic river biofilms and sediments. Microbial diversity and relative abundance of 27 ARGs and 5 mobile genetic element marker genes were determined. In soils, higher diversity, evenness and richness were all significantly negatively correlated with the relative abundance of the majority (>85%) of ARGs. Furthermore, the number of detected ARGs per sample was inversely correlated with diversity. However, no such effects were found for the more dynamic, regularly mixed rivers. Conclusions: In conclusion, we demonstrate that diversity can serve as barrier towards AMR dissemination in the environment. This effect is mainly observed in stationary, structured environments, where long-term, diversity-based resilience against invasion can evolve. Such barrier effects can in the future be exploited to limit the environmental proliferation of AMR.

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Section: Discussionmentioning

confidence: 99%

Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?

Klümper

Gionchetta

Catão

et al. 2023

Preprint

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“…4 ), which may be related to variation in pKJK5::csg fitness costs and maintenance. We previously observed this phenomenon for a closely related plasmid, pKJK5:: gfp PL , the cost of which was associated with plasmid maintenance and varied between different hosts and growth contexts [ 29 ]. This plasmid cost is likely due to constitutive costs of Cas9 and sgRNA expression, which can have different extents in different species [ 30–32 ].…”

Section: Discussionmentioning

confidence: 99%

Removal of AMR plasmids using a mobile, broad host-range CRISPR-Cas9 delivery tool

et al. 2023

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Antimicrobial resistance (AMR) genes are widely disseminated on plasmids. Therefore, interventions aimed at blocking plasmid uptake and transfer may curb the spread of AMR. Previous studies have used CRISPR-Cas-based technology to remove plasmids encoding AMR genes from target bacteria, using either phage- or plasmid-based delivery vehicles that typically have narrow host ranges. To make this technology feasible for removal of AMR plasmids from multiple members of complex microbial communities, an efficient, broad host-range delivery vehicle is needed. We engineered the broad host-range IncP1-plasmid pKJK5 to encode cas9 programmed to target an AMR gene. We demonstrate that the resulting plasmid pKJK5::csg has the ability to block the uptake of AMR plasmids and to remove resident plasmids from Escherichia coli . Furthermore, due to its broad host range, pKJK5::csg successfully blocked AMR plasmid uptake in a range of environmental, pig- and human-associated coliform isolates, as well as in isolates of two species of Pseudomonas . This study firmly establishes pKJK5::csg as a promising broad host-range CRISPR-Cas9 delivery tool for AMR plasmid removal, which has the potential to be applied in complex microbial communities to remove AMR genes from a broad range of bacterial species.

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“…Each colony was grown individually in 1/64 TSB individually as described previously. In addition, marked (ancestor-cp; chloramphenicol resistance [32]) and unmarked ancestral Variovorax sp. were grown.…”

Section: Phage Resistance and Competition Assaymentioning

confidence: 99%

Phage resistance is associated with density increases in the soil bacteriumVariovoraxsp. and results in changes to community structure

Castledine,

Padfield,

Lewis

et al. 2024

Preprint

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Bacteriophages can be important drivers of bacterial densities, and therefore microbial community composition and function. In response to phage infection, bacteria can evolve resistance while phage can reciprocally evolve to increase infectivity. Coevolutionary arms-races between bacteria and phage have been studied in many model systems and in pairs isolated from natural samples. However, how multiple bacteria-phage pairs coevolve simultaneously within a community is poorly understood. Here, we examine how three pairs of coexisting soil bacteria (Ochrobactrumsp.,Pseudomonassp., andVariovoraxsp.) evolve with three species-specific bacteriophages over eight weeks of experimental evolution, both as host-parasite pairs in isolation and as a mixed community. Coevolution was very limited, with two phages going extinct after two weeks andOchrobactrumphage increasing in infectivity without comparable reciprocal increases in bacterial resistance. One surprising finding was thatVariovoraxsp. increased in density following phage extinction, above that of no-phage controls. We examined the mechanisms behind this density increase through common garden experiments, growth curves, supernatant assays, and sequencing. Our results showed that this density increase resulted from genetic changes and was associated with phage resistance. Growth curves demonstrated that phage resistance shifted population growth curves such that density was higher in the death-phase. That resistance to lytic phage can improve host densities has implications for wider ecology and phage therapy where lytic phages are presumed to have negative effects on their hosts.

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Interspecific competition can drive the loss of conjugative plasmids from a focal species in a microbial community

Cited by 3 publications

References 33 publications

Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?

Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?

Removal of AMR plasmids using a mobile, broad host-range CRISPR-Cas9 delivery tool

Phage resistance is associated with density increases in the soil bacteriumVariovoraxsp. and results in changes to community structure

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