DOI: 10.5061/dryad.kprr4xh82
title: Monitoring mesophotic scleractinian corals using an underwater mini-ROV to sample eDNA

description: Mesophotic coral ecosystems (MCEs) are light-dependent tropical or
 subtropical communities occurring at depths of 30 to 150 m. We recently
 devised a coral-specific environmental DNA (eDNA) barcoding method that
 can identify 36 scleractinian genera in shallow reefs by sampling ~1L of
 surface seawater. If eDNA barcoding is combined with sampling using
 underwater mini-Remote Operated Vehicles (mini-ROVs), it may be possible
 to survey mesophotic corals more easily and broadly. Around the Zamami
 Islands, in Okinawa, Japan, seawater was collected 1–2 m above the bottom
 at six locations 20–80 m below the surface and subjected to coral-specific
 eDNA amplification. Metabarcoding analyses showed that (a) eDNA from ~0.5
 L seawater was sufficient to identify genera and to yield comparative
 ratios of genera at these sites; (b) Acropora dominates shallow reefs and
 upper ridges of slopes, while other genera including Porites, Pocillopora
 and Polyphyllia are more abundant at mesophotic sites; (c) one site showed
 a gradient in which Acropora was replaced by Plesiastrea at increasing
 depths. Although further technical improvements are required, the use of
 eDNA and underwater mini-ROVs may permit monitoring of mesophotic corals
 more broadly and easily.
description: Seawater samples were
 collected at reefs around the Zamami Islands on 9-10 March and 23-25 May
 2022. Mini-ROV used in this study was
 FIFISH V6Plus. On the boat, seawater collected by the sampler was moved to
 1L bottle and filtered promptly through 0.45-μm Sterivex filters (Merck)
 using peristaltic pomp. 1 mL of RNAlater (Qiagen) was added to the
 filtrate to prevent DNA degradation and was maintained at 4℃ before
 transfer to a -20℃ freezer in the laboratory. eDNA in Sterivex filters was
 extracted following the Environmental DNA Sampling and Experiment Manual
 v. 2.1. Extracted eDNA samples were PCR-amplified using primers,
 Scle_12S_Fw (5’-CCAGCMGACGCGGTRANACTTA-3’) and Scle_12S_Rv
 (5’-AAWTTGACGACGGCCATGC-3’), for mitochondrial 12S rRNA genes of
 scleractinian corals. PCR amplification was carried out Tks Gflex DNA
 Polymerase (Takara) under cycling conditions of 1 min at 94°C, followed by
 35 cycles of 10 s at 98°C, 15 s at 60°C and 30 s at 68°C, with an
 extension of 5 min at 68°C in the final cycle. PCR products were extracted
 and cleaned with a FastGene Gel/PCR Extraction Kit (NIPPON Genetics Co.,
 Ltd.). Amplicon sequencing libraries of cleaned PCR products were prepared
 using a KAPA Hyper Prep Kit (NIPPON Genetics) without fragmentation.
 Libraries were multiplexed and 300-bp paired-end reads were sequenced on a
 MiSeq platform (Illumina) using a MiSeq Reagent kit v3 (600
 cycles). 
description: # Monitoring mesophotic scleractinian corals using an underwater mini-ROV
 to sample eDNA
 [https://doi.org/10.5061/dryad.kprr4xh82](https://doi.org/10.5061/dryad.kprr4xh82) Give a brief summary of dataset contents, contextualized in experimental procedures and results. ## Description of the data and file structure Please refer below chart. | ID | Point name | depth | file name | | --- | ---------- | ----- | --------- | | A | Kuba West | SF | Za4-1\_S9\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | Za4-1\_S9\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | Za4-2\_S10\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | Za4-2\_S10\_L001\_R2\_001.fastq.gz | | 　 | 　 | 40m | Za4-3\_S11\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | Za4-3\_S11\_L001\_R2\_001.fastq.gz | | 　 | 　 | 50m | Za4-4\_S12\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | Za4-4\_S12\_L001\_R2\_001.fastq.gz | | B | Kuba Northwest | SF | 2Za5-1\_S18\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-1\_S18\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za5-2\_S19\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-2\_S19\_L001\_R2\_001.fastq.gz | | 　 | 　 | 9m | 2Za5-3\_S20\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-3\_S20\_L001\_R2\_001.fastq.gz | | 　 | 　 | 20m | 2Za5-4\_S21\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-4\_S21\_L001\_R2\_001.fastq.gz | | 　 | 　 | 28m | 2Za5-5\_S1\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-5\_S1\_L001\_R2\_001.fastq.gz | | 　 | 　 | 40m | 2Za5-6\_S2\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-6\_S2\_L001\_R2\_001.fastq.gz | | 　 | 　 | 50m | 2Za5-7\_S3\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za5-7\_S3\_L001\_R2\_001.fastq.gz | | C | Kitahama Beach | SF | 2Za6-1\_S4\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za6-1\_S4\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za6-2\_S5\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za6-2\_S5\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za6-3\_S6\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za6-3\_S6\_L001\_R2\_001.fastq.gz | | D | Kearama West | SF | 2Za13-1\_S17\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za13-1\_S17\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za13-2\_S18\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za13-2\_S18\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za13-3\_S19\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za13-3\_S19\_L001\_R2\_001.fastq.gz | | 　 | 　 | 20m | 2Za13-4\_S20\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za13-4\_S20\_L001\_R2\_001.fastq.gz | | 　 | 　 | 40m | 2Za13-5\_S21\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za13-5\_S21\_L001\_R2\_001.fastq.gz | | E | Shiru East | SF | 2Za7-1\_S12\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za7-1\_S12\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za7-2\_S13\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za7-2\_S13\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za7-3\_S14\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za7-3\_S14\_L001\_R2\_001.fastq.gz | | 　 | 　 | 20m | 2Za7-4\_S15\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za7-4\_S15\_L001\_R2\_001.fastq.gz | | 　 | 　 | 41m | 2Za7-5\_S16\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za7-5\_S16\_L001\_R2\_001.fastq.gz | | 　 | 　 | 50m | 2Za7-6\_S17\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za7-6\_S17\_L001\_R2\_001.fastq.gz | | F | Jijigatama | SF | 2Za11-1\_S6\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za11-1\_S6\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za11-2\_S7\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za11-2\_S7\_L001\_R2\_001.fastq.gz | | 　 | 　 | SF | 2Za11-3\_S8\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za11-3\_S8\_L001\_R2\_001.fastq.gz | | 　 | 　 | 20m | 2Za11-4\_S9\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za11-4\_S9\_L001\_R2\_001.fastq.gz | | 　 | 　 | 41m | 2Za11-5\_S10\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za11-5\_S10\_L001\_R2\_001.fastq.gz | | 　 | 　 | 80m | 2Za11-6\_S11\_L001\_R1\_001.fastq.gz | | 　 | 　 | 　 | 2Za11-6\_S11\_L001\_R2\_001.fastq.gz | <br>