4.1 RNA virus study description
Dinoflagellate-infecting RNA viruses (dinoRNAVs) are positive-sense,
single-stranded RNA viruses hypothesized to infect the dinoflagellate
symbionts (Family Symbiodiniaceae) that live in the tissues of
reef-building stony corals (Correa et al., 2013; Grupstra et al., 2022;
Veglia et al., 2022). Although dinoRNAVs can be prevalent in coral
colonies (Grupstra et al., 2022; Howe-Kerr et al., 2022; Montalvo-Proaño
et al., 2017; Veglia et al., 2022), it is unclear how dinoRNAVs (or
Symbiodiniaceae infected by dinoRNAVs) are transmitted among colonies.
Recent work has shown that corallivorous (coral-eating) fishes disperse
100s of millions of live Symbiodiniaceae cells across reefscapes in
their feces each day (Grupstra et al., 2021). To assess the extent to
which corallivorous fish feces disperse dinoRNAVs in their feces (as in
Grupstra et al., 2022), we characterized the presence and diversity of
dinoRNAVs in various environmental reservoirs using amplicon sequencing
of the dinoRNAV major capsid protein (mcp ) gene. Given that
dinoRNAV communities can vary across coral species and colonies
(Grupstra et al., 2022; Howe-Kerr, 2022; Montalvo-Proaño et al., 2017)
and that corallivorous fish actively ‘sample’ corals while feeding
(Grupstra et al., 2021), we hypothesized that corallivorous fish feces
are a reservoir of dinoRNAVs and that fish feces-associated dinoRNAV
communities exhibit higher alpha diversity than coral colony-associated
dinoRNAV communities. We generated 19 dinoRNAV mcp amplicon
sequencing libraries from coral colony biopsies (Acroporahyacinthus , n=8; Pocillopora species complex, n=5), as
well as the feces of corallivorous fishes (Chaetodon reticulatus ,
n=4; Chaetodon ornatissimus, n=2). All samples were collected
from reefs off the north shore of Moorea, French Polynesia (South
Pacific). Methods for sampling and sample processing to generate virus
amplicon sequencing libraries are described in Grupstra et al.
(2021,2022) and Howe-Kerr et al. (2022). DinoRNAV mcp amplicon
libraries were processed and analyzed using vAMPirus (see
doi.org/10.5281/zenodo.7574173).