Department Aquatic Ecology

Global health is threatened by the rise of antibiotic resistance. Bacteria of the Mycobacterium tuberculosis complex (Mtbc) are a major contributor to this antibiotic crisis, with about 450,000 new multidrug-resistant tuberculosis (MDR-TB) cases per year. This study investigates resistance evolution by defining the resistance mutant selection window (MSW) for the important MDR-TB treatment drugs moxifloxacin and bedaquiline. We employed a combination of long-term in vitro experiments supplemented with mathematical modeling that combined pharmacodynamics with population genetics. We assessed resistance selection at concentrations below the minimum inhibitory concentration (MIC), the MSW and fitness cost of eight mutant clones with different resistance-associated variants. Both computational and experimental results show that mutant clone populations are selected far below the MIC, leading to a major growth advantage of resistant populations under weak selection pressure. An eighth of the MIC was enough to enrich mutant clone populations in the short term (five bacterial passages or 20 generations), even in mutant clones with a major competitive fitness loss. In fact, gyrA, gyrB and most Rv0678 mutations have virtually no effect on the bacteria's competitive fitness in vitro. This work highlights the risk that ineffective drug delivery and dosing can lead to the emergence of resistance.

Zooplankton-associated microbiomes play an important role for host health, and contribute to ecosystem processes such as nutrient cycling. Yet, few studies have assessed how environmental gradients and biotic interactions, including parasitism and diet, may shape the microbiome composition of wild zooplankton. Here, we analyzed the microbiomes of water fleas from the Daphnia longispina species complex using 16S rRNA gene sequencing and a long-term field dataset spanning six sampling events over 13 years. Sampling coincided with outbreaks of the virulent eukaryotic gut parasite Caullerya mesnili. Additionally, we explored how microbiome structure varied in relation to water parameters, phytoplankton density (i.e., Daphnia diet), and zooplankton density and community structure. Daphnia microbiomes displayed strong temporal variation and comparatively small differences based on host infection status. Microbiome beta diversity correlated with phytoplankton density but not with its community composition, including green algae, protists, and cyanobacteria. Environmental conditions, including temperature, dissolved oxygen, and cyanobacterial abundance—previously found to drive Caullerya epidemics—were also associated with distinct microbiome structures. Importantly, microbiome beta diversity co-varied with infection prevalence, suggesting a link between microbiome shifts, epidemic size, and environmental conditions driving large epidemics. Dominant bacterial taxa correlated with Daphnia density, whereas the phylogenetic composition of rare taxa was associated with total zooplankton density. These findings demonstrate the dynamic nature of Daphnia microbiomes and suggest potential mechanisms by which they may mediate disease dynamics, particularly through associations with diet quantity, temperature, and host population density.

Different organismal functional feeding groups (FFGs) are key components of aquatic food webs and are important for sustaining ecosystem functioning in riverine ecosystems. Their distribution and diversity are tightly associated with the surrounding terrestrial landscape through land-water linkages. Nevertheless, knowledge about the spatial extent and magnitude of these cross-ecosystem linkages within major FFGs still remains unclear. Here, we conducted an airborne imaging spectroscopy campaign and a systematic environmental DNA (eDNA) field sampling of river water in a 740-km² mountainous catchment, combined with light detection and ranging (LiDAR) point clouds, to obtain the spectral and morphological diversity of the terrestrial landscape and the diversity of major FFGs in rivers. We identified the scale of these linkages, ranging from a few hundred meters to more than 10 km, with collectors and filterers, shredders, and small invertebrate predators having local-scale associations, while invertebrate-eating fish, grazers, and scrapers have more landscape-scale associations. Among all major FFGs, shredders, grazers, and scrapers in the streams had the strongest association with surrounding terrestrial vegetation. Our research reveals the reference spatial scales at which major FFGs are linked to the surrounding terrestrial landscape, providing spatially explicit evidence of the cross-ecosystem linkages needed for conservation design and management.