Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin Islands

Monitoring coral cover can describe the ecology of reef degradation, but
rarely can it reveal the proximal mechanisms of change, or achieve its
full potential in informing conservation actions. Describing temporal
variation in Symbiodiniaceae within corals can help address these
limitations, but this is rarely a research priority. Here, we augmented an
ecological time series of the coral reefs of St. John, US Virgin Islands,
by describing the genetic complement of symbiotic algae in common corals.
Seventy-five corals from 9 species were marked and sampled in 2017, and
following hurricanes in September 2017, 41% were sampled in 2018, and 72%
in 2019; 28% could not be found and were assumed to have died.
Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences
(comprising 42 ITS2 type profiles), and symbiont diversity differed among
host species and individuals, but was in most cases preserved within hosts
over 3 yrs that were marked by physical disturbances from major hurricanes
and the onset of stony coral tissue loss disease. While changes in
symbiont communities were slight and stochastic over time within colonies,
variation in the dominant symbionts among colonies was observed for all
host species. Together these results indicate that declining host
abundances could lead to the loss of rare algal lineages that are found in
a low proportion of few coral colonies left on many reefs, especially if
coral declines are symbiont-specific. These findings highlight the
importance of identifying Symbiodiniaceae as part of a time series of
coral communities to support holistic conservation planning. Repeated
sampling of tagged corals is unlikely to be viable for this purpose,
because many Caribbean corals are dying before they can be sampled
multiple times. Instead, random sampling of large numbers of corals may be
more effective in capturing the diversity and temporal dynamics of
Symbiodiniaceae metacommunities in reef corals.