Biology subjects

Gionchetta, G.

Publications and source records attributed to Gionchetta, G..

3 recordsLinked to original sources

bioRxiv2026

Microbial community diversity predicts invasion resistance of freshwater biofilms against antibiotic-resistant bacteria

Rivers receive continuous inputs of antibiotic-resistant bacteria (ARB) from wastewater, agriculture, and other anthropogenic sources, yet it remains unclear whether the recipient ecological component and its microbial communities determine whether introduced ARB establish or disappear. Ecological invasion theory predicts that invasion success depends on biodiversity, community stability, and occupation of ecological niche space, but these mechanisms have rarely been evaluated together in natural microbial communities. Here, we challenged river biofilms collected from 20 sites in 12 European rivers across six countries with a model antibiotic-resistant Escherichia coli carrying a conjugative IncP-1 plasmid The invasion assays were carried out under standardized laboratory flume conditions. River biofilms differed markedly in their permissiveness to invasion despite identical invasion conditions. Higher bacterial diversity consistently accelerated invader loss rates, whereas communities containing more abundant and diverse close phylogenetic neighbours of the invader exhibited stronger exclusion during early biofilm establishment. Diversity loss during transition into the experimental system emerged as the strongest explanatory variable of invasion resistance prior to biofilm maturation, whereas Shannon diversity became the dominant predictor in mature communities. Integrating these complementary ecological dimensions substantially improved explanatory prediction of ARB persistence compared with individual predictors alone. Particularly invasion-resistant biofilms also exhibited distinct ecological community composition consistent with mature, structurally complex microbial assemblages. Together, our findings demonstrate that the establishment of ARB in the environment is not stochastic but can be predicted from measurable ecological properties of recipient microbiomes, highlighting microbial biodiversity and community organization as natural barriers to antimicrobial resistance dissemination.

microbiology↗

bioRxiv2023

Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase

BackgroundAntibiotic resistance, which is mediated by environmental reservoirs, poses a threat to human and animal health. Aquatic biofilms impacted by treated wastewater (WW) are known environmental reservoirs for antibiotic resistance, however the specific influence of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited as to whether genes with low sequence similarity to reference ARGs actually encode for functional ARGs, particularly within complex aquatic microbial communities. ResultsTo disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or nonultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in metagenomic abundances in biofilms grown with increasing percentages of nonultrafiltered WW. In contrast, sulfonamide and BEL family beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to nonultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs which exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing low sequence identity with known ARGs. ConclusionsThis discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted metagenomic analysis on the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms.

microbiology↗

bioRxiv2023

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

BackgroundIn 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. ResultsTo 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.

microbiology↗