Assembly and identification of novel viruses in the Daphnia magna microbiota

Viruses can be important and abundant members of host-associated microbiomes, influencing host fitness directly or indirectly through the microbial communities they cohabit hosts with. Bacteriophages can modulate bacterial species diversity and abundance in the microbiome by introducing virulence factors that may enhance bacterial survival. This can impact host fitness by modifying the host-bacteria interactions present in the microbiome. However, our understanding of bacteriophages in some model systems for microbiome research is limited. By characterizing phages in model systems amenable to experimentation, we can gain a better understanding of multispecies interactions across domains within hosts. Here, we describe and profile potential dsDNA viruses computationally identified in the metagenome of the keystone zooplankton Daphnia magna, an important aquatic model organism. Using a combination of three metagenome-based viral identification tools (VIBRANT, VirSorter, and VirFinder), we find one complete, novel viral genome (a Myoviridae), 24 nearly complete viral genomes (primarily Myoviridae and Siphoviridae), and 508 putative viral contigs in total in a coassembly of 6 Daphnia magna metagenomes. We profiled the novel complete dsDNA virus, finding genes necessary for viral replication and genes obtained from its hosts during lysogeny. Finally, we characterized putative bacterial host-virus interactions by predicting CRISPR-spacer regions across Limnohabitans species, a genus shown to be beneficial to Daphnia fitness. Aligning viral sequences to these CRISPR regions, we found that 1 of 2 Daphnia-associated Limnohabitans genomes had CRISPR-spacer matches to viral contigs, indicating potential tritrophic interactions among bacteriophage, their host bacteria, and the host Daphnia magna. This study highlights the potential importance of viruses in the Daphnia magna metagenome, and can serve as the basis for a complete analysis of the Daphnia magna virome to understand the potential impacts of viruses on microbial abundance and evolution, as well as their impact on the fitness of ecologically important organisms.