KBay Coral Chipping 2021

Coral Chipping Spreadsheet

Thank you for all for the help and assistance with chipping! Below is a set of instructions on how to chip the coral fragment so that we keep this uniform across so many people helping.

The list of coral fragments is located here. Colony ID is the ID of the coral fragment, which will be written on the whirlpak the coral fragment is in. Species is either Montipora capitata or Porites compressa. Timepoint is the sampling date for that coral fragment.

Please sign up for how many fragments you are able to chip under the column ‘Chipping Tech’ with your name (example below). For example, if I chipped these two fragments, I include my name and the date I chipped the coral. Only fill in the date chipped after you have actually done this, not the date you plan to.

Example of spreadsheet above:

Colony ID	Species	Timepoint	Chip Date	Chipping Tech
3	Montipora capitata	9/16/19	20210309	Emma
4	Montipora capitata	9/16/19	20210309	Emma

Each coral will take ~5 minutes to chip.

Book your time on the organismal bench 1 or 2 on the teamup schedule. Please be mindful of the COVID restrictions we have in lab: 5 people max at a time (total for both sides) and for the Putnam lab: 1 person on molecular side and 1 person on organismal side at a time until midnight the night before (i.e. if Kevin is on molecular bench doing his own thing and Danielle is already on the microscope bench counting away then I have to wait until midnight the night before to take the open organismal bench 2 spot and only if there aren’t already 5 people in at that time). Please come in at your assigned time and change your time slot to reflect how late you stay. If you sign up for 1-4 pm, but only stay until 3 pm then before you leave lab, change your time slot to reflect 3 pm. Other people check this calendar frequently to see when they can come in and arrange their schedules around the lab schedule so we want to be very mindful of taking up lab time and space.

Location of coral fragment whirlpaks

Corals are kept in their sampling date timepoint in individual whirlpaks. These fragments need to be kept at -80C so the larger bag needs to be kept in the freezer, only remove the whirlpak you are clipping one at a time.

Each timepoint is in its own mesh bag labeled with the timepoint and “KBay Bleaching”. Please keep these altogether in the freezer while you are clipping the fragments.

Sept 2019, Oct 2 2019, Oct 16 2019, Oct 30 2019 (all in separate plastic bags within the yellow mesh bag), and Dec 4 2019 (black mesh bag) are in the green freezer across from the hood. Start with these fragments for now.

See images at the bottom of the post.

Chipping the coral fragment

These fragments need to be kept cold at all times so do the following steps swiftly but do not rush.
The coral chipping tool and sterilizing solutions (listed below) will be kept on the organismal benches 1/2 for the weeks we are clipping coral. See bottom of this post for a video example of clipping a coral.

We are waiting on the coral chipping tool to come in so in the meantime, you can use the clippers from the RNA bench.

Wipe down the organismal bench with 70% ethanol and DI water.
Get three dry ice coolers from the green -80C freezer across from the hood. One will hold the foil, clippers, and forceps. Another will hold the fragments ready to be clipped and the labeled tubes. The last one will hold the fragments and tubes that have already been clipped.
Sterilize a piece of foil with (in order): 10% bleach, Type II DI water, and 70% ethanol. Wipe dry. For each solution: add a small amount of that solution to a kimwipe, and wipe the foil side facing up. Place this piece of foil in one of the dry ice containers.
Sterilize the coral chipping tool with (in order): 10% bleach, Type II DI water, and 70% ethanol. Wipe dry. Place these clippers on the piece of foil in dry ice. The clippers need to be cold prior to clipping the fragment to avoid melting the cut site.
Sterilized a set of tweezers as described above. These will be useful if you are having trouble moving the coral fragment or the small clipping.
Grab a set of 10 coral fragments from the freezer and keep them in a dry ice cooler with the lid closed. Neatly label a new 2 mm screw cap tube for each coral you just grabbed with: 1.) colony ID (write this piece of information multiple times on the tube) 2.) Species (“Mcap”, “Pcom”) 3.) Timepoint (write this piece of information multiple times on the tube). See below image for an example. Place the 2 mm screw cap tubes in dry ice to cool the tube itself. Unscrew the cap so that when you clip the coral piece it will be easier to place in the tube immediately.

This is a running timeseries with the same corals sampled multiple times a year. Make sure you have both the colony ID and timepoint written correctly and multiple times on the tube.
Grab 10 corals at a time to avoid opening and closing the freezers so often.

setup

labels

tube in dry ice

uncaptube

Unwrap a whirlpak and slowly move the coral fragment towards the opening of the whirlpak using your hands on the outside of the whirlpak so that you are not touching the coral fragment with your gloves.
While holding the fragment with one hand, take the coral chipping tool with the other hand and chip off ~0.5-1 cm piece of the coral fragment. Immediately place this fragment in a 2 mm screw cap tube.

Try to find a groove or notch or something in the coral to get the clippers around and then squeeze tightly to break off a skeleton chunk. Breaking a chunk is often easiest when the clippers don’t cover the entire width of the fragment, but about half. This creates enough pressure to clip the skeleton.
Please be mindful of how much fragment you are taking. Take no more than 1/2 of the fragment. If you are unsure about the size because the coral feels too small, feel free to ping Emma and save that fragment for another time.
Place both the 2 mm screw cap tube in the appropriate freezer box (see above section for photo) and the coral fragment into the plastic bag that reads ‘clipped corals’ with the appropriate timepoint (i.e. “Kbay clipped corals 9/16/19” is a red mesh bag in the green freezer and “kbay clipped corals sept 19” is a freezer box in the green freezer). Please be mindful that you are placing the fragment and screw cap tube in the correct timepoint’s mesh bag and freezer box.
Repeat these steps for as many fragments as you have time for.
Clean the benchtops and equipment used according to our lab’s COVID protocol.

Send a slack message to Emma with what you were able to get done and update the google spreadsheet with the fragments you chipped. Please do this before you leave lab so that another labmate doesn’t come in after you and chip the same coral.