Current natural populations face new interactions because of the re‐emergence of ancient microbes and viruses. These risks come from the re‐emergence of pathogens kept in laboratories or from pathogens that are retained in the permafrost, which become available upon thawing due to climate change. We here focus on the effects of such re‐emergence in natural host populations based on evolutionary theory of virulence and long‐term studies, which investigate host–pathogen adaptations. Pathogens tend to be locally and temporally adapted to their co‐occurring hosts, but when pathogens from a different environment or different time enter the host community, the degree to which a new host–pathogen interaction is a threat will depend on the specific genotypic associations, the time lag between the host and the pathogen, and the interactions with native or recent host and pathogen species. Some insights can be obtained from long‐term studies using a resurrection ecology approach. These long‐term studies based on time‐shift experiments are essential to obtain insight into the mechanisms underlying host–pathogen coevolution at several ecological and temporal scales. As past pathogens and their corresponding host(s) can differ in infectivity and susceptibility, strong reciprocal selective pressures can be induced by the pathogen. These strong selective pressures often result in an escalating arms race, but do not necessarily result in increased infectivity over time. Human health can also be impacted by these resurrected pathogens as the majority of emerging infectious diseases are zoonoses, which are infectious diseases originating from animal populations naturally transmitted to humans. The sanitary risk associated with pathogen emergence from different environments (spatial or temporal) depends on a combination of socioeconomic, environmental, and ecological factors that affect the virulence or the pathogenic potential of microbes and their ability to infect susceptible host populations.

Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.

The increased input of nutrients into biological systems has been shown to result in altered biotic interactions through changes in food availability. The aim of this study was to test for an association between phytoplankton nutrient content and epibiont variables in natural zooplankton populations. Via a field survey, we studied how a gradient in food quantity and quality impacted host population density and epibiont variables in Daphnia pulex. We found a significant decrease in epibiont prevalence and infracommunity richness, which could mainly be attributed to a changing phytoplankton N : P ratio (caused by P-limitation). We performed a lab experiment in which we exposed Daphnia magna to different algal nutrient ratios and the epibionts detected in the field study. P-limitation in the algae affected D. magna performance and resulted in similar trends of food quality effects in the epibiont variables. The experiment, however, also reflected subtle differences between different epibiont species.

Organisms are increasingly facing multiple, potentially interacting stressors in natural populations. The ability of populations coping with combined stressors depends on their tolerance to individual stressors and how stressors interact, which may not be correctly captured in controlled laboratory settings. One largely unexplored reason for this is that the microbial communities in laboratory settings often differ from the natural environment, which could result in different stressor responses and interaction patterns. In this study, we investigated the impact of single and combined exposure to a toxic cyanobacterium and an oomycete-like parasite on the performance of three Daphnia magna genotypes. Daphnia individuals were first sterilized and then experimentally given a natural or a laboratory-derived microbial inoculum. Survival, reproduction and body size were monitored for three weeks and gut microbiomes were sampled and characterized at the end of the experiment. Our study confirmed that natural and laboratory microbial inocula and gut microbiomes are differently structured with natural microbiomes being more diverse than laboratory microbiomes. Our results showed that exposure to the stressors reduced D. magna performance compared to the controlD. magna not exposed to any stressor. An antagonistic interaction between the two biotic stressors was revealed with respect to D. magna survival when Daphnia individuals were exposed to the laboratory microbial inoculum. This effect was consistent across all three genotypes. In Daphnia exposed to a natural microbial inoculum this antagonistic interaction could not be detected and the genotype x exposure interaction was genotype-dependent. Our results indicate that host-stressor interactions depend on the microbial inoculum and that the gut microbiome potentially has a strong role in this, thereby providing a largely unexplored dimension to multiple-stressor research.

The fungal parasite Podosphaera plantaginis employs both sexual and asexual reproduction to increase its chances of infecting the plant Plantago lanceolata.