Download PDF of All Ocean Bitemap Protocols

In order to rigorously quantify how predation pressure varies through space and in association with fish community structure, you will conduct the standardized predation assay (Squidpops) and fish sampling (seine haul and/or video monitoring) in tandem at no fewer than three time points in each of the two habitats (seagrass, unvegetated) over a period of less than 3 weeks (ideally on successive days). Individual protocols for each activity can be found detailed below.


Download PDF of Squidpop Protocol


The basic assay involves attaching standardized pieces of animal food to a plastic stake (“Squidpop”), deploying the stake in a shallow water habitat, retrieving the stake after 24 hours, and scoring whether the food is present or absent. We use food that should be readily available throughout the world and is easy to work with. The simulated animal prey is a piece of dried squid mantle tissue. Dried whole squid is available in many Asian grocery stores as well as online; it is important to get the type of squid in which the squid’s mantle (main part of body) remains whole, resembling a flattened sheet (see materials appendix for sources).


dried squid mantle (about 1.3 cm diameter circle) 25 per deployment
auger hole punch or cork borer (1.3 cm diameter) 1
green fiberglass garden stakes (~50cm) 25 per deployment
fine monofilament fishing line (2-10 lb. or similar) ~5 cm per stake
electrical tape 1 roll
sewing needle 1
scissors 1 pair
data sheets and pencils several
GPS unit (optional) 1
GoPro camera (optional) 1

Getting Prepared:

  • Use auger punch to make 25 round pieces of dried squid mantle, 1.3 cm diameter (OR cut 1 x 1 cm squares).
  • Pierce the squid with a needle threaded with a thin monofilament line. Wrap the line around the piece of squid and then tie a knot to the lead line to secure the squid to the line.
  • Cut the line approximately 5 cm from the piece of squid. Affix line to the stake with tightly wrapped electrical tape. Wrap the free end of the line to the rod leaving approximately 1 cm in length for the tether (see photo).

Note: keep the squid as dry as possible until deployment. The dried squid can become oily or slimy when immersed and may foul the water. We recommend keeping the squidpops in the refrigerator until deployment.

Deploying Squidpops:

  • Deploy the array of squidpops at roughly the same depth in the same type of habitat. This may involve a linear or other arrangement according to the site conditions. The Squidpop rods should be stuck firmly and deeply into the sediment to prevent dislodgement by waves, drifting algae, energetic predators, etc., and spaced approximately 1-2 meters apart. Take care to deploy the rods in such a way that they can be easily relocated after 24 hours.

Note: If using a GoPro to help identify fishes consuming the squid bait, deploy it underwater in such a way that you are able to capture several of the squidpops in the frame. This is not necessary but can be helpful determining what fish species actually consumed the bait. See additional protocols appendix II for more detailed instructions.

  • Record the time of deployment, GPS coordinates (if possible), ambient weather conditions (sunny, partly cloudy, rainy, etc.), and water temperature (see Site Characterization protocol).

Note: If not using GPS, be sure to note your relation to land features that will help you find the Squidpops later and identify your approximate GPS coordinates on Google Earth.                    

Observing and Recording Data:

  • One hour after deployment: Examine the Squidpops in situ and record how many stakes have lost the squid bait. Make sure all 25 squidpops are still in place, and be sure to note how many (if any) stakes have gone missing. Avoid disturbing or removing the stakes, which will be collected the following day. Bait loss is recorded as ‘all or nothing’, that is, to be counted as missing the entire disk of bait must be removed. There are no ‘partial’ counts.

Note: leave all stakes deployed after one hour in place, regardless of whether the squid has been eaten or not. This will keep the number of stakes on-site constant and prevents confusion when collecting after 24 hours.

  • 24 hours after deployment: Recover the stakes as close to 24 hours after deployment as possible. Score in the same way as the one-hour observations. When you record the data make sure you clearly indicate that the number you wrote down is the number gone.

Note: At 24 hours, record whether bait is missing from each of the 25 Squidpops, including those you already accounted for at 1 hour. This is to capture cumulative loss of bait. For example, if 5 pieces were gone at 1 hour, and an additional 10 were gone at 24 hours, you would record 15 pieces of bait missing after 24 hours.


Fish Seine

Download PDF of Fish Seine Protocol


The fish community in the area where Squidpops are deployed will be characterized using a standard seine haul protocol. The Nearshore Seining Survey is based on one developed for a long-term research study on dynamics of fishes and invertebrates at the Smithsonian Environmental Research Center (SERC) on the central Chesapeake Bay. For Bitemap, the standard seine haul provides a method that allows rigorous comparisons of nearshore fish communities across sites, provided the sites are sufficiently shallow (< ~1.5 m) and free of structure to allow a seine to be pulled through. While it may vary among study sites, it is typically easiest to accomplish seines of this type at low tide.


seine net with 0.635cm (1/4 in) stretch mesh, 10m mouth width 1
bins and buckets several
metric rulers 1 per person
metric tape measure 1
small aquarium dip nets 1 per person
transect markers (PVC pole, flag, tape, etc.) 4
weighted float or pole marker 1
data sheet and pencils several
digital camera 1
crab tongs (optional) several
GPS unit (optional) 1

 Getting Prepared:

  • Gather all the necessary supplies listed above.
  • Once in field, partially fill your large and small bins with water and place these on beach where the seine will come in. Fill in data on data sheet including time, date, location, etc.

Note: Do not walk through the water anywhere near the transect you are about to sample. This will disturb the fishes prematurely and alter your capture efficiency.

  • Set your transect markers near the water line 10 meters apart from each other in front of the area where you intend to seine. These will provide guides allowing the seiners to maintain a direct line to the shore with 10 meters between them.

Note: If your site does not abut shoreline, you will have to modify the protocol to standardize the length of your seine haul. We recommend pulling the net no less than 20 m across your site. You will then have to sample the captured fish community from a boat, stable platform, or any other method that allows you to access all the fish in your net while minimizing stress on the animals.


  • With the seine net rolled up, walk it well outside the margins of the transect to a depth of 100 cm, carrying a weighted float or pole marker. Once at this depth, approach the transect border. One person should stop offshore of the closest corner of the transect (keeping a hold of one end of the net), while the other person continues to walk parallel to shore toward the point offshore of the other transect marker. While walking, the net should be unrolled between the two people. At this stage, the two seiners are in position to start, with the seine pulled out parallel to shore, 10 m apart, in 100 cm of water. Use the transect markers on shore as guides to maintain a 10 meter distance between you as you begin.
  • Once in position, drop or secure the transect marker (weighted float or pole) at the beginning starting point of the seine haul. This will allow you to measure the distance from the shore to the start of the transect later.
  • Haul that seine! Both people holding the seine should walk towards their shore markers, staying parallel with each other, 10 m apart, and perpendicular to shore. Keep the poles of the seine net upright or pointed towards shore, not slanting back behind you.

Note: If the net gets snagged on a log, have a person walk outside of the seine net to the point where the net is snagged. Lift the net minimally off of the bottom to un-snag it. Remove the debris from the transect if possible and continue seining.

  • Once the two seine pullers have reached the shore and pulled the first couple of feet of net in, lay the poles down on the beach and begin to pull the net in.

Note: It is very important to keep the seine’s sinker line (the bottom part of the seine), on the bottom. As you’re pulling it in, it is natural to want to lift the line as you pull—but do not lift the seine off the bottom as fish will escape. Keeping the sinker line on the bottom, pull the top (float) and sinker lines in together. This should be done evenly from both sides.

  • Once the sinker line is completely on shore you have formed a ‘netted pouch’ with the seine. Lift up on the sinker line and the float (or top) line at the same time from the ends of the net (if available, have people stationed through out the middle to make sure the net doesn’t drop into the water).
  • Shake fish carefully down the net until you have the whole pile of fish in a single pocket of net. Usually it is easiest for the two seiners to do this by moving toward the center of the seine. Holding the net together (to prevent escape), bring the net out of the water, and transfer the fish into the large bin of water including those individuals that have become entangled in the net.
  • Sort the fish from the large bin into the smaller bins/buckets by species. Keep larger fish separate to prevent predation or injury while in captivity. It is important to minimize the time spent holding and handling the fish, which stresses them. To maximize efficiency, some people should start measuring while others finish sorting.
  • Begin measuring the fishes, starting with the most delicate. Measurement should be of the fish’s total length, from snout to tip of tail. Measure 25 individuals of each species collected, then simply count the rest of that species. For example, if you collected 45 of a particular species, you would measure the lengths of the first 25, then simply note that you caught 20 more individuals of that species. Big animals (larger than 10cm along widest axis) other than bony fishes should be measured using the standard for that type of animal: carapace width for crabs, or length and width of the body for animals like horseshoe crabs, turtles, rays, etc.

Note: For ease of processing and to avoid confusion, try to focus on a single species at a time. One person should serve as ‘recorder’ and write down fish ID, length, and count measured by the fish ‘handlers’.

  • Continue this process until all fish have been measured or counted. When you finish a bucket or bin, pour the water out of the bin through a net to make sure that you haven’t missed any fish.
  • Once all animals have been measured, counted, and released, clean up your site.


Site Characterization 

Download PDF of Site Characterization Protocol


The physical environment is a primary driver of marine community characteristics. Here we present a method for meauring several metrics that are known to have strong influence on animal and plant communities in coastal habitats. While collecting data on all the metrics is ideal, we welcome data collected on any of the metrics listed below according to the protocol.


temperature probe 1
salinity probe/refractometer 1
GPS unit 1

Getting Prepared:

  • Gather all your supplies. If calibration is required for your temperature and/or salinity probe be sure that it has been done.
  • For each place that you take an individual measurement, you will also take a GPS point, either directly from a GPS unit (preferred), or by orienting yourself to landmarks and determining the GPS points on Google Earth (or similar).
  • Haphazardly choose three spots within your site for taking temperature/salinity measurements. They should all be in the subtidal zone (if possible), and at least 10m apart from each other.

Note: Be sure to consult tide predictions for your area so you can ensure that you are sampling in the subtidal zone.


  • Take GPS point (if using GPS on site).
  • Take temperature/salinity measurement according to manufacturers specifications for your particuarr probe. Measurements should be made at least 20cm below the water’s surface.
  • Record data on your data sheet.
  • Repeat at each of the haphazardly selection spots within your site

Note: These measurements should be taken at the time of all Squidpop and seine deployments/recoveries. We recommend taking the measurements before deploying Squidpops and after conducting seine activities to minimize disturbance that might impact the other observations. You will do this protocols at both vegetated and unvegetated sites.


Video Protocol

Download PDF of Video Protocol


To characterize the fish communities and identify common predators, it is possible to use small GoPro cameras in place of, or in tandem with, beach seines. Here we present two video methodologies for using GoPros to this end. This first is a protocol to be used specifically with Squidpops to identify and size predators, the second is a general fish observation protocol to use for characterizing the fish community. Keep in mind these protocols are designed to be done in relatively clear-water conditions where visibility is at least 3 meters.


GoPro Camera affixed to PVC Stake 1
Scale Bar (large enough to be seen by camera, metric units) 1
Prepared Squidpops (for Squidpop observations) 25
Bait Bag (for fish community observations)[squid, plastic mesh, zip ties, post or dowel] 1

Getting Prepared:

  • Attach GoPro to PVC stake at least 0.5m in length (or long enough to clear seagrass canopy if deploying in seagrass habitat).
  • Set GoPro to medium angle setting (to prevent distortion of fish at edges of frame). Make sure all time and date settings on your GoPro are correct.
  • Make bait bag to attract fish (if not deploying with Squidpops). This can be done by cutting up dried squid (see resources list for products) into chunks (~3cm square, use at least one whole squid) and placing into plastic mesh canvas (see resources). Close the mesh like a pouch around the squid pieces and close with zip ties. This is then affixed to the end of a rod or dowel with a similar length to your GoPro PVC stake.

GoPro Video Monitoring:

  • Deploy Squidpops (Squidpop Protocol) or push rod/dowel with bait bag attached into substrate in approximately 1m of water so the bait bag is at approximately 30cm above the substrate, or clear of any seagrass canopy.
  • Push the PVC stake with GoPro into the sediment so that the field of view captures at least one Squidpop (or the bait bag), but preferably multiples at the beginning of your deployment.
  • Begin recording. Note the time on your data sheet
  • Hold your scale bar in the same plane as the Squidpop closest to the GoPro in clear view of the camera for at least 10 seconds. This will allow you to set the scale for measuring fish predators later.
  • Finish deploying Squidpops and let soak for one hour, or leave bait bag in place and return in one hour.
  • Retrieve the camera after you return for your one hour bait count. Note the time. Remove bait bag as necessary.

GoPro Video Analysis:

  • Watch a one hour segment of the video beginning from the moment you removed the scale bar.
  • Using the scale bar as a guide, track the size and identity (to lowest taxonomic resolution possible) of the fish(es) responsible for removing the bait.

Note: A simple, cost-effective way to measure distances in video is to use the scale bar from the beginning of the video to make a grid on a piece of clear plastic that you can then tape over your computer monitor. Remember that lengths measured are only accurate when the fish is in the same plane as the original location of the scale bar, therefore you will only be estimated fish lengths when fish strike at squidpops or interact with bait bags, putting them in roughly the same plane.

Video Analysis Rules – Squidpops

  • Track the strikes, or number of bites taken by all fish (identified to lowest taxonomic level and length measured) that approach and interact with the bait, whether they visibly remove bait or not.
  • If a fish leaves the frame it is considered ‘gone’, and you will still count every fish that enters the frame after, even if it looks identical to a fish you think you’ve already seen and counted. (for example, if a 10cm long parrot fish enters the frame, strikes twice at the bait then leaves the frame, and then 15 seconds later a 10cm long parrot fish enters the frame, strikes once and removes the bait, you would record both occurrences as separate events. See data sheet metadata for more information).
  • Keep track of the identity of all other fishes that enter the camera’s field of view during the one hour viewing period. In other words, if you see a species you haven’t seen before, note it on your datasheet (abundance and measurement are not needed).

Video Analysis Rules – Bait Bag

  • Identify and measure all fish that approach and interact (touch) the bait bag.
  • If a fish leaves the frame it is considered ‘gone’, and you will still count every fish that enters the frame after, even if it looks identical to a fish you think you’ve already seen and counted. (for example, if a 10cm long parrot fish enters the frame, interacts with the bait bag, then leaves the frame, and then 15 seconds later a 10cm long parrot fish enters the frame and interacts with the bait bag, you would record both occurrences as separate events. See data sheet metadata for more information).

Data Submission

  • Submit the results of your video analysis to using spreadsheets provided on the Resources page with the email subject line: BITEMAP GOPRO DATA [your site name]