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This study shows that Escherichia coli can be temporarily enriched in zooplankton in natural conditions and that these bacteria can belong to different phylogroups and sequence types including environmental as well as clinical and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically the two isolates were closer to strains isolated from poultry meat than with freshwater E. coli, albeit their genomes were smaller than those from poultry. After isolation and fluorescent protein tagging of strains ED1 and ED157 we show that Daphnia sp. can take up these strains and release them alive again, thus forming a temporary host for E. coli. In a chemostat experiment we show that the association does not prolong the bacterial long-term survival, but that at low abundances it does also not significantly reduce the bacterial numbers. We demonstrate that E. coli does not belong to the core microbiota of Daphnia, suffers from competition by the natural microbiota of Daphnia, but can profit from its carapax to survive in water. All in all, this study suggests that the association of E. coli to Daphnia is only temporary but that the cells are viable therein and this might allow encounters with other bacteria for genetic exchange and potential genomic adaptations to the freshwater environment.ImportanceThe contamination of freshwaters with faecal derived bacteria is of major concern regarding drinking water acquisition and recreational activities. Ecological interactions promoting their persistence are still very scarcely studied. This study, which analyses the survival of E. coli in the presence of zooplankton, is thus of ecological as well as water safety relevance.

The diffusion of antibiotic resistance determinants in different environments, e.g., soil and water, has become a public concern for global health and food safety and many efforts are currently devoted to clarify this complex ecological and evolutionary issue. Horizontal gene transfer (HGT) has an important role in the spread of antibiotic resistance genes (ARGs). However, among the different HGT mechanisms, the capacity of environmental bacteria to acquire naked exogenous DNA by natural competence is still poorly investigated. This study aimed to characterize the ability of the environmental

Increases in water colour (brownification) have been observed in aquatic systems in the Northern Hemisphere, partly caused by increased loading of organic carbon from terrestrial origins. We investigated the effect of increase in water colour on the composition, structure and function of lake plankton communities (bacteria, phytoplankton and zooplankton) conducting a mesocosm experiment in 3 medium-coloured lakes (average absorbance at 420 nm: 0.034 cm(-1)), with different nutrient concentrations and phytoplankton community composition. To simulate an increase in water colour, we added humic substances (HuminFeed) at 3 different concentrations. The additions significantly affected the water colour of the mesocosms, but had no measurable effect on total organic carbon concentration, thus change in light conditions was the main effect of our treatment on the plankton communities. The increase in water colour did not significantly affect the measured functions (productivity, respiration) and biomass of the plankton communities (bacteria, phytoplankton and zooplankton), but led to changes in the relative abundance of some phytoplankton taxa and, to a lesser extent, the bacterial community (differences in relative abundance). The treatments had no significant effect on zooplankton biomass or composition. Our study suggests that increases in water colour favour low-light-adapted phytoplankton species, which in turn also can affect bacterial composition, whereas the change in light climate had no clear impact on the functioning of plankton communities in weakly humic lakes.