Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature

Abstract

Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype-or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.

Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae)

“…Reproducibility remains a fundamental, yet elusive element in microbial ecology and microbiome research 52 . Further research should be conducted under independent laboratory conditions to corroborate the results presented herein, as proposed and conducted in human studies and arthropod systems 53 – 55 .…”

The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community

“… 2018 ; 2020 ; Sison-Mangus, Metzger and Ebert 2018 ; Frankel-Bricker et al . 2019 ; Mushegian et al . 2019 ).…”

“…Frankel-Brickel et al . ( 2019 ), on the other hand, report a significant effect of geographical origin but no differences between clonal lineages from a specific location. Sison-Mangus, Metzger and Ebert ( 2018 ) also observed an effect of host genotype (all originating from different geographical locations) and found this to be correlated with the resistance profile of D. magna against the parasitic bacterium Pasteuria ramosa .…”

“… 2018 ; Frankel-Bricker et al . 2019 ). Several of these experiments also included different clonal lineages to simultaneously study the effect of host genotype on community composition.…”

Targeted manipulation of abundant and rare taxa in the Daphnia magna microbiota with antibiotics impacts host fitness differentially

“…To better understand the relationship between specific taxa in the microbiota and host fitness we applied an antibiotic suppression technique in Daphnia magna , a widely used model organism in ecotoxicology 9 , population genomics 10 , and host-parasite dynamics 11 . Daphnia magna ’s microbiome is relatively simple, with only 10-15 amplicon sequence variants (ASVs) constituting >70% of relative abundance 12,13 . In particular, β-proteobacteria, γ-proteobacteria, and Sphingobacteriia are bacterial Classes consistently identified in the Daphnia magna microbiome across environments and genotypes 14,15,16 .…”