DOI: 10.5061/dryad.02v6wwq95
title: Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin Islands

description: 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.
description: <em>Project design and field sampling</em>
 In the summer of 2017, nine scleractinian species (Table 1) from
 six genera were selected based on their high abundance and ecological
 importance. A total of 75 coral colonies were sampled from 7–10 m depth at
 White Point, East Tektite, and Cabritte Horn [Fig. S1]), where the reefs
 have been monitored since 1992 (Edmunds
 2018). Colonies were haphazardly selected along 40-m transects
 at each monitoring site (Edmunds
 2018) between 27 July and 7 August 2017, and their positions
 were identified using cartesian coordinates. They were selected based on
 ease of location, and size (&gt; 20-cm diameter to support multiple
 samplings), and marked with aluminum tags epoxied to the substratum.
 Following tagging, a tissue biopsy (&lt; 1-cm diameter) was removed
 from the upper surface of each colony using stainless steel clippers.
 Samples were placed in Whirl-Pak bags and processed within 2 hours of
 sampling. We searched for the tagged colonies in 2018
 (13–15 August), 11 months after Hurricanes Irma and Maria, and in 2019
 (24–29 July). Colonies were located using an underwater metal detector
 (Vibraprobe 580, Treasure Products, CA) to find their tags, underwater
 maps, and site photographs. When located, a tissue biopsy was collected
 using the identical procedure established in 2017. Sampling in 2018 was
 limited due to the lingering effects of the hurricanes on island
 infrastructure. Sampling was comprehensive in 2019, and the reefs were
 exhaustively searched for tagged colonies to increase confidence that
 missing colonies were dead rather than not located. These collections were
 completed under permits issued by the Virgin Islands National Park
 (VIIS-2017-SCI-0037, VIIS-2018-SCI-0019, VIIS-2019-SCI-0023) and the
 Government of the Virgin Islands (DFW18088J, DFW19044J).
 <em>DNA extraction and sequencing</em>
 On shore, coral biopsies were individually transferred to
 microcentrifuge tubes filled with 500 µL of 1% sodium dodecyl sulfate DNA
 buffer using sterilized forceps, and heated to 65°C for 1.5h. Samples were
 shipped to the Hawaiʻi Institute of Marine Biology where genomic DNA was
 extracted using an organic extraction protocol (Baker &
 Cunning 2016). Symbiodiniaceae diversity was characterized
 through the amplification and sequencing of the ribosomal Internal
 Transcribed Spacer 2 (ITS2) region (LaJeunesse
 2001; Davies et al. 2022). DNA samples were sent to the
 University of Texas at Austin for library preparation with ʻitsDʻ and
 ʻits2rev2ʻ primers (Stat et al.
 2009) and sequencing on an Illumina MiSeq platform with 2 x 300
 paired-end read chemistry. The paired forward and reverse reads from each
 sample were submitted to SymPortal to resolve ITS2 type profiles based on
 repeated co-occurrence of purported intragenomic variants (Hume et al.
 2019).
description: # Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin
 Islands
 [https://doi.org/10.5061/dryad.02v6wwq95](https://doi.org/10.5061/dryad.02v6wwq95) 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. This data archive contains the raw ITS2 sequencing data for all corals. Processed data and subsequent analyses can be found at [https://github.com/ealenz/STJ_ITS2.](https://github.com/ealenz/STJ_ITS2.) ## Description of the data and file structure Demultiplexed FASTQ sequence files are provided for each coral sample as *.fastq.gz files. Each subdirectory contains two FASTQ files representing the paired end reads for each sample, indicated by "R1" for read 1 and "R2" for read 2 in the filenames. The samples and associated metadata corresponding to each set of FASTQ files is provided in the metadata file: "Lenz_STJ_SymPortal_datasheet.csv".