Abstract
The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.
Highlights
The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions
Chlamydomonas samples showed reduced relative abundance of Proteobacteria as compared to adult Daphnia and COMBO; COMBO showed higher relative abundance of Actinobacteria; and healthy Daphnia magna were primarily colonized by Proteobacteria and Bacteroidetes
Our 16S rRNA gene level data shows that the Daphnia magna bacterial community is structured differently than the surrounding culture environment and from the microbiome of their food, which agrees with results from earlier studies[9,30]
Summary
The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. The zooplankton Daphnia magna provides a useful model for studying functional relationships between microbes and their hosts. The ability to raise Daphnia magna clonally allows for the use of genetically identical hosts, reducing the impact of genetic variation on the microbiota. Their indiscriminate filter feeding allows for control over food input. (b) Relative abundance of phyla generated from 16S rRNA community profiles in Chlamydomonas reinhardtii, healthy adult Daphnia magna, and the culture media (all n = 4)
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