Monitoring mesophotic scleractinian corals using an underwater mini-ROV to sample eDNA
Data files
Sep 14, 2023 version files 18.30 GB
Abstract
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.
README: Monitoring mesophotic scleractinian corals using an underwater mini-ROV to sample eDNA
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 |
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Methods
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).