Jun 01, 2026

1 - SOP for Cnidaria - Anthozoa

DOI
https://dx.doi.org/10.17504/protocols.io.x54v9b8npl3e/v1
1 - SOP for Cnidaria - Anthozoa
  • 1Muséum national d'Histoire naturelle;
  • 2Génoscope
  • ATLASea
Melanie Van Weddingen
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DOI: https://dx.doi.org/10.17504/protocols.io.x54v9b8npl3e/v1
External link: https://www.atlasea.fr/
Protocol Citation: Melanie Van Weddingen, Karine Labadie, Janaina Rigonato, Barbara Poro, Benjamin Girard, Oscar Demonio 2026. 1 - SOP for Cnidaria - Anthozoa. protocols.io https://dx.doi.org/10.17504/protocols.io.x54v9b8npl3e/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 30, 2025
Last Modified: June 01, 2026
Protocol  Integer ID: 236046
Keywords: ATLASea, Genome, marine species, Biology, SOP, Anthozoa, Cnidaria, sop for cnidaria, anthozoa the standard operating procedure, dna extraction, tissue sample, sop, specimen of anthozoa, processing specimen, cnidaria, procedure, atlasea program, standard operating procedure, scope of the atlasea program, anthozoa, metadata, collection metadata, dna
Abstract
The Standard Operating Procedures (SOPs) contain general guidance on processing specimen of Anthozoa (Cnidaria) within the scope of the ATLASea program. The guidance specifically refers to station metadata (or collection metadata), the tissue samples destined for DNA extraction, and to specimen vouchering.
Materials
Lab material :
- Gloves - Dissection tools (tweezers, scalpels, scissors) - Petri dish with different size - Tube rack - Paper towel - Ethanol, Bleach, Filtered sea water, Liquid nitrogen - Wash bottle - Scale - Dewar - Dissection table - Ice pack - Tooth brush Tubes: - CORNING‱ 1.2 ml conical-bottom cryotube, skirted with external thread and natural screw cap [ref Dutscher # 430658] - CORNING‱ 2 ml Cryotube, skirted, external thread with natural screw cap [ref Dutscher # 430659] - 5 ml screw tube sterile (Eppendorf) [ref Dutscher # 934683] - 25 ml screw tube sterile (Eppendorf) [ref Dutscher #934685] - 50 ml Conical Centrifuge Tubes (Greiner) [ref Dutscher #227261] - 1.5 mL Safe-Lock Tubes (Eppendorf) [ref Dutscher #033290] Bags: - Nylon protection net, reusable with drawstring (15x10 cm) [Amazon #https://www.amazon.fr/Anti-Insectes-Protection-Plantes-R%C3%A9utilisables-Anti-Oiseaux/dp/B08XXJMY4C] - Nylon protection net, reusable with drawstring (15x25 cm) [Amazon #https://www.amazon.fr/AMZMUKAUP-Protection-Raisins-R%C3%A9utilisables-Rangement/dp/B09N7PV2LD/ref=sr_1_1_sspa?crid=2VTI1EVYUW654&keywords=sachet+filet+nylon&qid=1690200116&sprefix=sachet+ny%2Caps%2C213&sr=8-1-spons&sp_csd=d2lkZ2V0TmFtZT1zcF9hdGY&psc=1] - Twist attaches [Amazon #Twist Attaches Or, 800 Pcs Métallique Pince pour Fermeture Sachet Alimentaire, Attache Sac pour Paquet de Bonbon, Sachet Plastique, Transparent Cello] - Zip-Seal Bags (grands sachets) 350x250 mm [ref VWR #129-0307] - Zip-Seal Bags (petits sachets) 170x120 mm [ref VWR #129-0297] Scan: - Bluetooth QR & Barcode to PC application to scan labels with your phone and import the code to the Excel sheet via Bluetooth: https://play.google.com/store/apps/details?id=dev.fabik.bluetoothhid - Honeywell Voyager Extreme Performance 1470g-2D [Ref. Fabricant #1470G2D-2USB-1-R] Photography equipment : see section C of 0 – SOP.

Before start


General recommendations for Cnidaria - Anthozoa
For general instructions see 0 – SOP Sampling General Recommendations.
**Please ensure that you hold sampling permits if these are required, please see the ATLASea Statement

Anthozoa is a subphylum of marine invertebrates in the Cnidaria phylum. This subphylum is divided into two classes: Octocorallia (Malacalcyonacea, Scleralcyonacea), Hexacorallia (Actinaria, Anthipatharia, Ceriantharia, Corallimorpharia, Scleractinia, Zoantharia), which form reciprocally monophyletic groups. The classes differ, among other things, in the type of symmetry exhibited by the polyps. Anthozoans include some ecologically very significant species, capable of constructing reefs which support highly diverse ecosystems.

‱ATLASea Team photography
Legends : left to right, top to bottom : Alcyonium palmatum, Primnoidae sp., Chironephthya sp., Antipathella subpinnata, Actinaria sp., Bartholomea annulata, Balanophyllia cf. regia, Pavona decussata, Micrabaciidae sp.
Sampling
After collection (by hand, dredge/trawl, brushing), specimens are maintained in ambient seawater containers. At this step, specimens are identified with:
  • Sampling date
  • Station number allowing to know sampling date, GPS coordinates, sampling method, harvesters, habitat (via a field sheet completed during sampling).
  • Tracking sheet with the name of the taxa (specie, genus, … rank), the taxonomist name, the sex …

Big colonies of Scleractinia must be sampled by hand and only a small piece must be collected so as not to damage the habitat.
After dredging or trawling, soft coral may be in poor condition and must be processed quickly.
Several Anthozoa species are declared as CITES (Convention on International Trade in Endangered Species) and need special permits to be transported.
Photography
Ideally, images should be taken in the highest quality resolution (macro lens recommended).
In cases where no part of the specimen can be conserved as a voucher, the photographs will serve as a voucher. These should therefore include relevant identifying features, when possible. This must be discussed with the taxonomist.
Specimen should be photographed in a glass container with sea water.
Water should be clean and changed between each specimen.

The first picture is the reference photo (see SOP - 0) taken with a ruler, the code identifier (e.g. 1 ATLASea QR code for the batch, 1 MNHN-IK barcode for each specimen) the tracking sheet and the station label with the specimen.
Take a general photo of the specimen.
Sometimes, shaking the coral may allow the tentacles to come out. Do it carefully.
Take closer pictures of the tentacles, patterns and, in the case of colonies, the polyps.
Dissection for Genome Sequencing
  1. Specimens must be sampled and frozen while still alive. For colonial taxa, ensure sampling of an individual colony.
  2. Remove all visible contaminants and epibionts, including any substrate, although gut contents and symbionts will remain (wash and gently brush in FSW). Blot to remove excess seawater and mucus.
  3. Depending on species and conditions, tissue sampled may be the polyps, column tissue or eventually tentacles. Where possible, try to remove polyps from the skeleton.
  4. Dissect :
a. 15 pieces (approx. 300-500 mg each) for flash-freezing in liquid nitrogen. Cut each piece into smaller before putting them in separate tubes (with unique identification labels).
  • If soft tissues:  300 mg /tube
  • If hard tissues (e.g.: polyps with skeleton): 500 -1000 mg /tube
b. 10 pieces (approx. 500 mg each) put in ethanol 98% and stored at -20°C.
5. Weight the tubes and scan the barcode on the log sheet.

‱ATLASea Team photography
Example of Anthozoa morphology and type of tissues.

Voucher samples conservation
Voucher will be stored at MNHN.
See 0 - SOP for general instructions.

Keep the leftover organism, as many hard parts/tissues as possible or another individual from the same population and checked by a taxonomist as belonging to the same species.
Place the barcode MNHN-IK identifier and the station label with the organism in tube/container.
Put 85% ethanol in the tube/container. There must be 10 times the volumes of specimen in alcohol.
Send to the MNHN.