Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance

Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.

Genomic characterization of selfing in the cyclic parthenogen Daphnia magna

Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding-involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50% in one generation; however, little is known about the empirical variation on a genome level surrounding this figure and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analysed whole genomes of mothers and selfed offspring, observing the predicted 50% heterozygosity reduction on average. We also saw substantial variation around this value and significant differences among mother-offspring pairs. Crossover analysis confirmed the known trend of recombination occurring more often towards the telomeres. This effect was shown, through simulations, to increase the variance of heterozygosity reduction compared to when a uniform distribution of crossovers was used. Similarly, we simulated inbred line production after several generations of selfing and we observed higher variance in achieved homozygosity when we consider a higher recombination rate towards the telomeres. Our empirical and simulation study highlights that the expected mean values of heterozygosity reduction show remarkable variation, which can help understand, for example, differences among inbred individuals.

Elevated temperature and toxic Microcystis reduce Daphnia fitness and modulate gut microbiota

The gut microbiota has been increasingly recognized to regulate host fitness, which in turn is dependent on stability of community structure and composition. Many biotic and abiotic factors have been demonstrated to shape gut microbiota of cladocerans. However, the interactive effects of these variables on cladocerans fitness due to alteration of gut microbiota and their linkage with life history parameters are poorly understood. Here, we investigated the responses of Daphnia magna gut microbiota to the combined effects of toxic Microcystis aeruginosa and high temperature and its associations with fitness. We found that under good food regime, the temperature has no effect on the composition of the gut microbiota, whereas under high proportion of toxic M. aeruginosa and high temperature conditions, D. magna lost their symbionts. High proportion of toxic M. aeruginosa and high temperature had synergistically negative effects on D. magna performance due to altered gut microbiota. The high abundance of symbiotic Comamonadaceae and good food increased D. magna fitness. The present study illustrates that understanding life history strategies in response to multiple stressors related to changes in the gut microbiota diversity and composition requires integrated approaches that incorporate multiple linked traits and tether them to one another.

Changes in the life history traits of Daphnia magna are associated with the gut microbiota composition shaped by diet and antibiotics

The gut microbiota has a crucial role in host physiology and fitness. Host-microbiota relationships can be disrupted by environmental stressors, which further affect host growth and survival. However, the link between host performance and the gut microbiota composition shaped by increasing antibiotic pollution under different food conditions is not clearly understood. In the present study, we used Daphnia magna as a model organism to investigate the interactive effects of diets (Chlorella with or without Microcystis) and antibiotics on its life history traits, gut microbiota alterations, and their relationship. The results showed that poor diet consumption by D. magna at low and high antibiotic concentrations reduced reproduction and survival. Under good diet conditions, the fitness was reduced only at a high antibiotic concentration. Under good diet conditions, high concentration of antibiotics reduced the abundance of Comamonadaceae and increased the abundance of Pseudomonadaceae, whereas under poor diet conditions, both low and high concentrations of antibiotics increased the abundance of Pseudomonadaceae. Performances of life history traits were positively correlated with an increased abundance of Comamonadaceae but were negatively correlated with increased Pseudomonadaceae abundance. The results of this study revealed the interactive effects of diet and antibiotics on D. magna fitness and correlations between bacterial abundance and life history traits, which has important implications for understanding the effects of pollutants on host-microbiota interactions through changes in phenotypes.

The Mercury-Tolerant Microbiota of the Zooplankton Daphnia Aids in Host Survival and Maintains Fecundity under Mercury Stress

Many aquatic organisms can thrive in polluted environments by having the genetic capability to withstand suboptimal conditions. However, the contributions of microbiomes under these stressful environments are poorly understood. We investigated whether a mercury-tolerant microbiota can extend its phenotype to its host by ameliorating host survival and fecundity under mercury-stress. We isolated microbiota members from various clones of Daphnia magna, screened for the mercury-biotransforming merA gene, and determined their mercury tolerance levels. We then introduced the mercury-tolerant microbiota, Pseudomonas-10, to axenic D. magna and quantified its merA gene expression, mercury reduction capability, and measured its impact on host survival and fecundity. The expression of the merA gene was up-regulated in Pseudomonas-10, both in isolation and in host-association with mercury exposure. Pseudomonas-10 is also capable of significantly reducing mercury concentration in the medium. Notably, mercury-exposed daphnids containing only Pseudomonas-10 exhibited higher survival and fecundity than mercury-exposed daphnids supplemented with parental microbiome. Our study showed that zooplankton, such as Daphnia, naturally harbor microbiome members that are eco-responsive and tolerant to mercury exposure and can aid in host survival and maintain host fecundity in a mercury-contaminated environment. This study further demonstrates that under stressful environmental conditions, the fitness of the host can depend on the genotype and the phenotype of its microbiome.

The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean

Host-associated microbiota vary across host individuals and environmental conditions, but the relative importance of their genetic background versus their environment is difficult to disentangle. We sought to experimentally determine the factors shaping the microbiota of the planktonic Crustacean, Daphnia magna. We used clonal lines from a wide geographic distribution, which had been kept under standardized conditions for over 75 generations. Replicate populations were kept for three generations at 20 and 28 °C. The interaction of the host clonal line and environment (i.e., temperature) influenced microbiota community characteristics, including structure, the relative abundance of common microbial species, and the microbial richness and phylogenetic diversity. We did not find any correlation between host-associated microbiota and the geographic origin of the clones or their temperature tolerance. Our results highlight the prominent effects that host clonal lineage and its interaction with the environment has on host-associated microbiota composition.