Luursema, J.-M. | Search bioRxiv

bioRxiv2025

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution

Background and objectivesAntimicrobial resistance is a major global health threat, driven in part by the rapid evolution of resistance in pathogens, which undermines the effectiveness of antimicrobial treatment. In infections, pathogens rarely live in a well-mixed, single species environment. It is an open question how microbial interactions in contrasting environmental structures affect plasmid mediated antibiotic resistance evolution. MethodologyThis study investigates how a spatially structured versus a well-mixed liquid environment, together with microbial interactions, affect antibiotic resistance evolution in uropathogenic Escherichia coli. We conducted a serial transfer experiment under increasing concentrations of trimethoprim-sulfamethoxazole comparing resistance evolution in the well-mixed and spatially structured environments, both in the presence and absence of a polymicrobial community. ResultsOur results revealed that E. coli in community context displayed parallel evolutionary trajectories, leading to higher final antibiotic tolerance, while the spatial structure allowed for prolonged resistance evolution. Copy number variation of the plasmid-borne resistance locus varied significantly across conditions; E. coli evolved in the well-mixed, monoculture conditions, exhibited the greatest increases in copy number, whereas lineages evolved in the presence of the community showed minimal changes relative to the ancestor. Conclusions and implicationsThese findings underscore the complex interplay between the genetic basis of resistance, the environmental structure and microbial ecology in shaping plasmid-mediated antimicrobial resistance evolution. Lay summaryAntibiotic resistance depends on environmental context, microbial interactions, and genetics. This study shows that E. coli evolved resistance differently in mixed versus structured environments, with changes in plasmid-borne resistance gene copy number. Community interactions led to similar evolutionary paths and higher tolerance, while well-mixed, single-species conditions drove larger genetic changes.

microbiology↗

bioRxiv2025

A breath of fresh air: comparative evaluation of passive versus active airborne eDNA sampling strategies

Terrestrial biodiversitys rapid decline demands expansion of high-resolution biomonitoring to support science-based policy. Environmental DNA (eDNA) analysis has proven effective in aquatic systems but remains underexplored for terrestrial habitats, partly due to point-source sampling bias and difficulty in upscaling. Air has emerged as a promising substrate yet most studies use active samplers which tend to be expensive, bulky, and require power. We used a newly developed, inexpensive, reusable, and easy-to-use passive airborne eDNA sampler (Nutshell eDNA sampler) to capture eDNA suspended in air across time (6 to 96 hours) within Rotterdam Zoo, the Netherlands. Its performance was compared to two commonly-used active airborne eDNA samplers for vertebrate diversity detection. In total, 88 species were detected, including 24 zoo residents. The Nutshell eDNA sampler was the most effec-tive at detecting zoo residents, surpassing active samplers in species richness within 48 hours and continuing to accumulate new species beyond 96 hours, including detections of both patchy and singleton signals. It also detected the furthest species signal (515 m). Zoo airborne eDNA further demonstrated a positive correlation to species total biomass, suggest-ing larger vertebrates release proportionately more DNA into the air. Our findings indicate that for long, unsupervised biomonitoring, passive airborne eDNA sampling presents a prom-ising approach for assessing vertebrate communities and putatively reduces detection noise in stochastic air eDNA signals. While deeper investigations into airborne eDNA sampling strategies are needed, passive methods can offer a much needed logistically flexible, low-maintenance approach compared to short-burst collection strategies employed by many ac-tive samplers.

ecology↗