DOI: 10.5061/dryad.wh70rxwjw
title: Data from: Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes

description: Coral reefs host hundreds of thousands of animal species that are
 increasingly threatened by anthropogenic disturbances. These animals host
 microbial communities at their surface, playing crucial roles for their
 fitness. However the diversity of such microbiomes is mostly described in
 a few coral species, and still poorly defined in other invertebrates and
 vertebrates. Given the diversity of animal microbiomes, and the diversity
 of host species inhabiting coral reefs, the contribution of such
 microbiomes to the total microbial diversity of coral reefs could be
 important, yet potentially vulnerable to the loss of animal species.
 Analysis of the surface microbiome from 74 taxa, including teleost fishes,
 hard and soft corals, crustaceans, echinoderms, bivalves and sponges,
 revealed that more than 90% of their prokaryotic phylogenetic diversity
 was specific and not recovered in surrounding plankton. Estimate of the
 total diversity associated to coral reef animal surface microbiomes
 reached up to 2.5% of current estimates of Earth prokaryotic diversity.
 Therefore, coral reef animal surfaces should be recognized as a hotspot of
 marine microbial diversity. Loss of the most vulnerable reef animals
 expected under present-day scenarios of reef degradation would induce an
 erosion of 28% of the prokaryotic richness, with unknown consequences on
 coral reef ecosystem functioning.
description: Sampling was conducted in November 2015 in
 Mayotte lagoon shallow (depth &lt;10 meters) barrier and fringing
 coral reefs in Western Indian Ocean. We sampled the most abundant taxa
 from each of the main animal groups of the coral reef (teleost fishes,
 <i>Anthozoa</i>, crustaceans, echinoderms, mollusks and
 sponges) within a radius of 50 m around each site. The skin microbiome was
 collected by swabbing the entire untouched side of the body of fish, by
 exposing to air a specimen of corals to collect mucus, or by swabbing
 entirely other types of collected invertebrates. All samples
 were stored on board at -5°C in an electric cooler during the day, then at
 -80°C back to the lab until DNA extraction.For each of 6 days of sampling,
 six 200-mL samples of seawater were collected 50 cm below sea surface (3
 samples) and at 30 cm from the sea bottom (3 samples). Seawater samples
 were stored in a dark cooler (4°C) and filtrated within 6 hours through a
 47 mm 0.2 µm polycarbonate membrane (Whatman, Clifton, USA) and filter was
 frozen at -80°C until DNA extraction. DNA extraction
 was performed using the Maxwell® 16 Bench-top extraction system following
 manufacturer’s instructions, and eluted in 50 µL of elution buffer. The V4
 region of the 16S rDNA gene was amplified using the prokaryotic primers
 modified for Illumina sequencing 515F (5’-C TTT CCC TAC ACG ACG CTC TTC
 CGA TCT - GTG CCA GCM GCC GCG GTA A- 3’) and the modified version of 806R
 by Apprill et al. (5’ – G GAG TTC AGA CGT GTG CTC TTC CGA TCT - GGA CTA
 CNV GGG TWT CTA AT - 3’), with PuRe <i>Taq</i> Ready-To-Go PCR
 Beads. Equimolar amounts of sample DNA amplified from each reef type were
 separately pooled and sequenced in two separated runs by an external
 laboratory (<i>INRA GeT-PlaGE</i> platform, Toulouse, France)
 on an Illumina platform using the 2×250 bp MiSeq chemistry.
 Sequence reads were processed using the
 <i>‘DADA2’</i> R-package version 1.2 (Callahan <i>et
 al.</i> 2016) and R software v3.4.3 Forward reads were
 trimmed at their 5’ extremity to remove forward and reverse primers, then
 trimmed according to a quality score of 2, and filtered to remove reads
 containing more than 2 expected errors, before de-replication and merging
 forward and reverse primers. Chimeras were then removed and remaining
 Amplicon Sequence Variants (ASVs) were taxonomically classified using the
 SILVA database v132 [4], and non-prokaryotic sequences were
 removed.
description: The dataset is a .rData file. To open it, simply open R (https://www.r-project.org/), go to the directory where you stored the file and run the command: setwd("/your/directory/") load("SM3-ps_Chiarello_et_al2020.rData") The data is formatted in format specific from phyloseq R-package, a convenient package for microbiome data analysis. The package must be installed and loaded before before loading the dataset: library(phyloseq) Please visit phyloseq webpage (https://joey711.github.io/phyloseq/) for more information about phyloseq format and installation instructions.