While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.

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.

Aquatic organisms rely on microbial symbionts for coping with various challenges they encounter during stress and for defending themselves against predators, pathogens and parasites. Microbial symbionts are also often indispensable for the host's development or life cycle completion. Many aquatic ecosystems are currently under pressure due to diverse human activities that have a profound impact on ecosystem functioning. These human activities are also ex pected to alter interactions between aquatic hosts and their associated microbes. This can directly impact the host's health and -given the importance and widespread occurrence of microbial symbiosis in aquatic systems -the ecosystem at large. In this review, we provide an overview of the importance of microbial symbionts for aquatic organisms, and we consider how the beneficial services provided by microbial symbionts can be affected by human activities. The scarcity of available studies that assess the functional consequences of human impacts on aquatic microbial symbioses shows that our knowledge on this topic is currently limited, making it difficult to draw general conclusions and predict future changes in microbial symbiont−host relationships in a changing world. To address this important knowledge gap, we provide an overview of ap proaches that can be used to assess the impact of human disturbances on the functioning of aquatic microbial symbioses.

The depletion of oxygen as a result of increased stratification and decreased oxygen solubility is one of the most significant chemical changes occurring in aquatic ecosystems as a result of global environmental change. Hence, more aquatic organisms will be exposed to hypoxic conditions over time. Deciphering the effects of hypoxia on strong ecological interactors in this ecosystem's food web is critical for predicting how aquatic communities can respond to such an environmental disturbance. Here, (sub-)lethal effects of hypoxia and whether these are genotype specific in Daphnia, a keystone species of freshwater ecosystems, are studied. This is especially relevant upon studying genetic responses with respect to phenotypic switches (G x E interactions) upon environmental stress. Further, we investigated the effect of hypoxia on the Daphnia microbial community to test if the microbiome plays a role in the phenotypic switch and tolerance to hypoxia. For this, two Daphnia genotypes were exposed for two weeks to either hypoxia or normoxia and host performance was monitored together with changes in the host associated and free-living microbial community after this period. We found G x E interactions for some of the tested Daphnia performance traits. The microbial community responded to hypoxia stress with responses in the bacterioplankton and in the Daphnia associated microbial community with respect to species richness and community composition and structure. The latter response was different for the two genotypes suggesting that the microbiome plays an important role in G x E interactions with respect to hypoxia tolerance in Daphnia, but further testing (e.g. through microbiome transplants) is needed to confirm this.

In aquatic environments, interactions between cyanobacteria and their grazers are crucial for ecosystem functioning. Cyanobacteria are photosynthetic prokaryotes, which are able to produce large blooms and associated toxins, some of which are able to suppress grazer fitness. Cyanobacterial blooms are intensified by global warming and eutrophication. In our experiments, the tolerance of Daphnia magna (Straus, 1820), an efficient grazer of toxic cyanobacteria, was studied. We used different D. magna clones sampled from different sediment depths, which corresponded to different time periods of eutrophication. Our results showed that different clones had a different tolerance towards the toxic cyanobacterial species, Microcystis aeruginosa, confirming the presence of genetic variation in D. magna tolerance to cyanobacteria. However, there was not a significant adaptive effect of sediment depth. As expected, in general under controlled, infection-free conditions M. aeruginosa reduced D. magna survival. However, a coincidental, non-intended opportunistic fungal infection in a first experiment allowed us to compare the response of D. magna to M. aeruginosa in infected individuals and non-infected individuals (from a second experiment). In the presence of this opportunistic infection, there was no negative effect of M. aeruginosa in the D. magna clones, suggesting that exposure to the infection provided protection for Daphnia individuals towards Microcystis. Biotic interactions can thus be important in the interpretation of cyanobacterial effects in zooplankton grazers and in finding appropriate solutions to reduce the occurrence of cyanobacterial blooms.

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 control. 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 has potentially a strong role in this, thereby providing an unexplored dimension to multiple-stressor research.

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory settings often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated the impact of single versus simultaneous multiple stressor exposure on Daphnia magna life history traits and whether this tolerance was microbiome-mediated. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows survival in Daphnia was microbiome-mediated as survival was only negatively impacted when Daphnia received a lab microbial community. Daphnia which received a natural microbial community have a broader environmental pool of microbiota to randomnly and selectively take up and showed no negative impact on survival. Simultaneous exposure to both stressors also revealed an antagonistic interaction for survival. Fecundity and body size were negatively impacted by exposure to stress, however, responses were here not microbiome-mediated. In addition, genotype specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.