Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets

Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species

The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.

Species-Specific Effects of Planktonic Bacteria on the Predator-Induced Life-History Defense of Daphnia: Based on Hierarchical Cluster Analysis and Structural Equation Model

Planktonic bacteria are an important part of aquatic ecosystems and interact with zooplankton. However, it is still unclear whether different planktonic bacteria differentially interfere with the responses of zooplankton to their predators. Here, we investigated the effects of different planktonic bacteria, which were isolated and purified from natural lakes, on the anti-predation (Rhodeus ocellatus as the predator) defense responses of Daphnia magna. Our results showed that the effects of planktonic bacteria on the induced life-history defenses of Daphnia were species-specific. Bacteria which increased (e.g., Escherichia coli, Citrobacter braakii) Daphnia body size also promoted the induced defense of body size, whereas bacteria which decreased (e.g., Pseudomonas spp.) Daphnia body size also inhibited the induced defense of body size. In addition, the same bacteria had different effects on induced defense traits. Some bacteria (e.g., E. coli) promoted the induced defense of body size but reduced the induced defense of offspring number, whereas other bacteria (e.g., Aeromonas hydrophila, Aeromonas veronas) weakened the induced defense of body size but had no significant effect on the induced defense of offspring number. Moreover, the differential effects of planktonic bacteria on Daphnia's induced defenses were not related to the bacterial degradation of kairomone. This study illustrated, for the first time, the species-specific effects of planktonic bacteria on predator-induced responses of Daphnia. IMPORTANCE This study is the first to reveal the differential effects of different species of planktonic bacteria on fish kairomone-induced defense traits and energy redistribution in Daphnia. Our results not only help deepen the understanding of Daphnia's inducible defenses in environments containing a variety of bacteria but also provide insights into the energy reallocation involved in anti-predator defenses.

Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome

Host genotype and environment are considered crucial factors in shaping Daphnia gut microbiome composition. Among the environmental factors, diet is an important factor that regulates Daphnia microbiome. Most of the studies only focused on the use of axenic diet and non-sterile medium to investigate their effects on Daphnia microbiome. However, in natural environment, Daphnia diets such as phytoplankton are associated with microbes and could affect Daphnia microbiome composition and fitness, but remain relatively poorly understood compared to that of axenic diet. To test this, we cultured two Daphnia magna genotypes (genotype-1 and genotype-2) in sterile medium and fed with axenic diet. To check the effects of algal diet-associated microbes versus free water-related microbes, Daphnia were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial inoculum, and medium and diet-mixed microbial inoculum. Daphnia were cultured for 3 weeks and their gut microbiome and life history traits were recorded. Results showed that Daphnia inoculated with medium microbial inoculum were dominated by Comamonadaceae in both genotypes. In Daphnia inoculated with mixed inoculum, genotype-1 microbiome was highly changed, whereas genotype-2 microbiome was slightly altered. Daphnia inoculated with diet microbial inoculum has almost the same microbiome in both genotypes. The total number of neonates and body size were significantly reduced in Daphnia inoculated with diet microbial inoculum regardless of genotype compared to all other treatments. Overall, this study shows that the microbiome of Daphnia is flexible and varies with genotype and diet- and medium-associated microbes, but not every bacteria is beneficial to Daphnia, and only symbionts can increase Daphnia performance.

Understanding host-microbiome-environment interactions: Insights from Daphnia as a model organism

Microbes perform a variety of vital functions that are essential for healthy ecosystems, ranging from nutrient recycling, antibiotic production and waste decomposition. In many animals, microbes become an integral part by establishing diverse communities collectively termed as "microbiome/s". Microbiomes defend their hosts against pathogens and provide essential nutrients necessary for their growth and reproduction. The microbiome is a polygenic trait that is dependent on host genotype and environmental variables. However, the alteration of microbiomes by stressful condition and their recovery is still poorly understood. Despite rapid growth in host-associated microbiome studies, very little is known about how they can shape ecological processes. Here, we review current knowledge on the microbiome of Daphnia, its role in fitness, alteration by different stressors, and the ecological and evolutionary aspects of host microbiome interactions. We further discuss how variation in Daphnia physiology, life history traits, and microbiome interactive responses to biotic and abiotic factors could impact patterns of microbial diversity in the total environment, which drives ecosystem function in many freshwater environments. Our literature review provides evidence that microbiome is essential for Daphnia growth, reproduction and tolerance against stressors. Though the core and flexible microbiome of Daphnia is still debatable, it is clear that the Daphnia microbiome is highly dependent on interactions among host genotype, diet and the environment. Different environmental factors alter the microbiome composition and diversity of Daphnia and reduce their fitness. These interactions could have important implications in shaping microbial patterns and their recycling as Daphnia are keystone species in freshwater ecosystem. This review provides a framework for studying these complex relationships to gain a better understanding of the ecological and evolutionary roles of the microbiome.