Abstract Understanding how changes in the hydrological regime drive parasite loads and dynamics remains a challenging issue in ecological parasitology. Temporal changes in streamflow and rainfall are key hydrological factors that could alter interactions between the parasite and host and affect parasitism levels. However, to investigate the effect of streamflow, rainfall and its mechanisms, it is important to control host traits that can also influence parasitism levels in freshwater systems. Here, we used a cymothoid‐palaemonid prawn model to test the combined effects of streamflow and rainfall accounting for host traits to predict variations in parasite loads in stream ecosystems. We collected the palaemonid prawns monthly for 2 years and measured the variation of rainfall and streamflow (i.e. stream discharge) at the time of prawn sampling. Our best model showed that streamflow can predict parasitism levels in prawns better than host traits. We found a higher prevalence and abundance of parasites in reduced streamflow compared to increased ones. We also found higher ectoparasite loads in females rather than males and occurring in autumn and winter rather than in spring and summer. Our results also showed that ectoparasite loads also suffer an effect of host body size, sex and moult stage, but not host age. Our findings show that reduced streamflow can facilitate host finding that favours parasite transmission in dry seasons and increase parasitism levels in stream systems. Temporal variability in streamflow can have a strong influence on parasite loads and dynamics compared to host traits in stream ecosystems. Identifying how interactions between aquatic invertebrates and parasites respond to variability in the hydrological regime can help to better understand and predict disease outbreaks as habitat reduction and disturbance continue in stream ecosystems.
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