Investigation into the Cause of the Clam Decline: 2016

Downeast Institute Field Studies – Freeport, Maine

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DEI and local clammers continued investigating the cause of the soft-shell clam decline and exploring ways to protect clams from predators and enhance clam populations. In 2016 we conducted six experiments at 30 different intertidal locations. These included expanding clam recruitment and survival monitoring across all three tidal heights at the same 10 locations as the previous year. We continued comparing the effects of predator protection with sediment buffering on clam and quahog abundance and growth, and also continued testing different methods to protect clams from predators. We piloted the use of clam impoundments, tried using blood worms to deter milky ribbon worms from eating clams, and tested ways to prevent mud snails from fouling protective netting with their eggs.

These experiments discovered high productivity of the intertidal ecosystem and uncovered shellfish recruitment patterns across the entire Harraseeket River. We again found sediment buffering to have no effect on clam survival compared to predator protection.

High levels of predation impacted three experiments at six sites. The clams growing in boxes at Little River, Recompense, and Staples experienced predators such as crabs ripping through the flexible netting to eat the clams. The predator protection we installed with clam impoundments at Winslow Park and Recompense failed to adequately prevent predators from reaching the clams. And predator infiltration thwarted our field test of a novel bioremediation method to reduce milky ribbon worm predation on soft-shell clams.

Attempts to deter mudsnails from fouling clam protective netting yielded no clear
answers. In order to ensure as much confidence in our results as possible, experiments were designed to be statistically valid. The details, experimental design, and results can be found below.

Experiments & Results

#1: Measuring levels of clam recruitment in the Harraseeket River at each tidal height
#2: Examining sediment buffering vs predator protection on clam recruitment and growth
#3: Predator deterrent grow-out boxes
#4: Testing clam pounds to store clams
#5: Bioremediation to stop milky ribbon worm predation
#6: Reducing mud snail eggs on netting

#1: Measuring Recruitment

Measuring Recruitment Across Tidal Heights in the Harraseeket River

Building on our findings from last year we expanded our investigation into how many soft-shell clams were settling onto different areas of the Harraseeket River. Using the same twenty locations as the previous year (10 on each side of the river) we placed 14 recruitment boxes at each site in the high, mid, and low tide areas.

This experiment tested the interactive effects of location, tidal height, and predator deterrent netting on clam recruitment. Settling clams fall into the boxes and are able to survive and grow since the box protects them from most predators. Recruitment boxes allow scientists to understand how many clams and other species are settling onto mudflats.


The experiment used 720 1 x 2 x 6-inch deep recruitment boxes which were protected on the bottom by PetScreen® netting. There were three different size mesh tops for the boxes. One-third of the boxes had PetScreen® tops, one-third has 4.2 mm mesh tops, and one-third had 6.4 mm mesh tops.  We also placed additional 120 boxes without any predator deterrent netting (i.e. wooden frames) onto the mud as controls to verify that the recruitment boxes do not attract clams, rather they are simply static collectors that reflect recruitment that occurs at the particular site.

The 840 boxes were placed at each tidal height (high, mid, and low) at each of the twenty locations, prior to clam spawning season in early May. They were arrayed in two blocks with two replicates of each of box treatments and one replicate per block of the control (unscreened box). There is a total of 42 boxes at each of the 10 sites. The boxes were taken off the mud at the end of the clam growing season in early November 2016.

Sediment core samples were taken upon deployment to determine initial baseline densities and sizes of clams. The contents of each of the 840 boxes, in addition to the controls, were processed through a 1mm mesh sieve to determine the number of clams and other species that settled into them. Recruit growth is determined by measuring a subsample of the clams from each box. Core sediment samples were also taken randomly outside each array of 14 boxes in November to determine how many of the clams that settled onto the flats were able to survive past their first year.


Our results, similar to  2014 and 2015, found that post-settlement mortality, not a limited supply of clam larvae, is responsible for regulating densities of soft-shell clams. This experiment continued to show how productive our intertidal ecosystem continues to be.

Upon analysis of the samples, it was found that the west side of the river, consistent with 2014 and 2015 results, continued to have fewer clam recruits settling than the east side (Wolfe Neck). The average number of clams per box was about 10 (1 clam per sq. ft). We did not find significant differences between treatments in terms of the mesh size for the tops of boxes.  We found over 1,000 green crabs, ranging in size from 5.6 mm-45.6mm.

The east side of the river continued with its pattern of relatively high clam recruitment. There was an average of 74 clams per box (7 clams per sq. ft). The most we found in one box was 1,719, which was found in a box with 1/6 inch aperture netting at site II in the upper tidal height. There were 641 green crabs found ranging from 5.6mm to 40.2 mm. Higher recruitment was found in the boxes with the larger size mesh (1/6 inch and 1/8 of an inch).

Recruits were twice as numerous in netted boxes without crabs that were larger than 20mm on the west side of the river, and 25% more numerous in netted boxes on the east side of the river. At both sites, more than sixty percent of the smallest clams per box were less than a half-inch in size. On both sides of the river that was a great percentage of clams that were able to grow to one and a quarter inches and larger in size. We found one recruit that grew 47 mm on the west side.

The results of these experiments were presented by Dr. Brian Beal at the 2017 Maine Fishermen’s Forum. Learn more about the results by watching the video below.

#2: Sediment Buffering

The Effects of Sediment Buffering for Coastal Acidification vs. Predation on Clam Recruitment and Growth

For the third year in a row we deployed an experiment that looked into the effect of sediment buffering low pH flats on clam recruitment and survival. This year we  did not conduct our large scale experiments with 6.6 ft x 6.6 ft plots.  Instead we expanded the use of plant pots as experimental units.

At two coves with low pH, Little River and Recompense, 12 treatments were laid out inside 6 –inch plant pots 10 times (120 experimental units at each site). We tested each of three sizes of crush clam shells with and without predator netting, as well as oyster shells and granite chips with and without netting.  Finally, we included two control pots in each treatment, which contained no shell or stone, with and without netting.   The treatments were deployed randomly. We measured pH at the sites throughout the experiment.


Results showed that both sites experienced a decrease in pH inside the netted experimental units. So, overall netted units have more acidic sediments.

At the Little River site, neither crushed shell or netting made a statistically significant difference in the survival of soft-shell clams or quahogs.

At Recompence we did find a statistically significant difference in survival of both soft-shell clams and quahogs when adding predator protection. However, adding crushed shells to buffer acidic sediments did not make a difference in increasing clam survival. In general, more clam recruits were found in the netted pots even though the netted pots were more acidic. In spite of the netting creating a chemically harsher environment for the settling clams due to the lowered pH, clams were more abundant in the netted vs. unnetted units. The likely reason for this is that settlement was equal in all plots and units, but recruitment mortality was greater in the unnetted units which were susceptible to predators.

The results from this study were presented at the 2017 Maine Fishermen’s Forum.


Results of this experiment, along with the results from 2014 and 2015, have been accepted for publication in the Journal of Experimental Marine Biology and Ecology with an expected publication date of 2020 or 2021.

Images (click to view slideshow)

#3: Grow-out Boxes

Testing Protective Clam Growing Boxes

Development of the protective box technique grew out of the iterative process of the Freeport Clam Experiments. Clammers initiated this study after learning through previous field trials with DEI that milky ribbon worms were not deterred by protective netting placed on top of the mud flats, nor are they discouraged from entering boxes seeded with cultured soft-shell clam juveniles through the bottom of the box with a 4.2 mm opening. We designed field trials to attempt to discourage these worms from entering boxes.

This experiment examined the effects of small aperture mesh netting on cultured clam survival and growth. This set of experiments used clams that clammers had grown in an upweller the previous year and had been overwintered.

Forty-five protective culture boxes planted with different densities of clams and deployed at Little River, Staples, Recompense coves in the first week of May (before clam settling season). The boxes were 4-ft long x 2.5 ft wide x 6 inches deep and there were 135 boxes total. The bottom of each culture box is a piece of Pet screen attached directly to the box reinforced with a piece (4-ft x 2.5-ft) of 1-inch vinyl-coated trap wire. The top of the boxes had different size mesh. One-third of the boxes had Petscreen® tops; one-third of the boxes had 2.1 mm aperture, and one-third of the boxes had 3.2 mm (1/8 of an inch) aperture tops.

At each site, forty-five boxes were arrayed in a 9 x 5 matrix, with 3-ft between each box in each row and column. The boxes were placed directly on the mudflat surface and were not filled with sediments. All boxes received different densities of overwintered clam seed. One-third of the boxes at each site received 200 clams, one-third received 400 clams, and one-third received 800 clams (these represent densities of 20, 40, or 80 animals per square foot). The total number of clams used in this study was 63,000 clams.

During the course of the summer, it was observed that predators were able to penetrate the boxes, especially those with flexible netting  (3.2 mm and 2.1mm), which was able to be torn apart. Repairs were made throughout the season, especially at Little River and Recompense, to attempt to keep predators out. Upon analysis, at the end of the field season, it was confirmed that many of the clams had been eaten.

Scientists and clammers counted all the planted clams that were alive in the boxes (identifiable because of the hatchery mark). The growth of all the live planted clams were determined by measuring the final length and the hatchery mark.

The boxes also collected recruits and the number of recruits were either counted or measured volumetrically.  All data were recorded on datasheets.

Of the planted clams that did survive, some experienced really phenomenal growth, especially at Little River and Recompense.


The results continued to find high levels of clam mortality in boxes that predators were able to penetrate and provides more evidence that predation is the #1 threat to shellfish populations. The data shows that green crabs have not “gone away” and milky ribbon worm densities remain high.  Combined these predators pose serious impediments to wild and cultured clam populations.

Images (click to view slideshow)

#4: Clam Pounds

Testing Clam Impoundments

Clam impoundments were tested as a possible method of protecting clams from predation and for clammers to store their clams while they wait for a higher market price. At two coves, Recompence and Winslow, we planted 30 wire cages (3-ft x 2-ft x 5-inch deep) lined with different types of netting (PetScreen® or 2.1mm) in an attempt to protect the clams from predators. A half a bushel of legal size clams was added to each impoundment and then the cages were buried in the mud.

On June 12 and June 29, respectively,  5 cages at Winslow and 5 cages at Recompense were dug up to assess the status of the clams inside. It was found that significant numbers of the clams were dead and that predators such as milky ribbon worms and green crabs had been able to infiltrate the protective netting to access the clams.

In August, when the prices of clams were highest, the remaining 50 cages were dug up and the number of clams were counted. Unfortunately, too many of the clams were lost due to predation and lack of oxygen to determine if this was a viable method for storing clams.

We continued this experiment, with a modified design, in 2017.

Images (click to view slideshow)

#5: Bloodworm Bioremediation

Bioremediation to Reduce Milky Ribbon Worms

Research in 2013, 2014, and 2015 found milky ribbon worms to be a major predator of clams in southern Maine. In an effort to research methods to reduce predation on clams, in 2016 and 2017 we tested a novel bioremediation approach to protect clams from predators.

A Canadian study conducted in a laboratory in the late 1990s found that the addition of bloodworms to aquariums with milky ribbon worms substantially decreased clam deaths (Bourque et al., 2001). In 2016 DEI designed a field experiment to test if the initial laboratory experiment could be successfully duplicated in the wild, and in doing so provide a natural method of protecting clams. from this prolific clam predator.

The experiment was deployed at Collins Cove/Yorkies in Freeport at the beginning of May in the mid intertidal.

80 experimental units (EU) were deployed. These  EUs were wooden boxes with dimensions of 4-ft x 2.5-ft x 6-inch deep. One-half (40) of the boxes had a Pet Screen® bottom that effectively exclude milky ribbon worms while the other half had a 4.2 mm flexible netting bottom that does not inhibit worms. To reinforce the bottoms, both types of bottoms were backed by a 4-ft x 2.5-ft piece of vinyl-coated trap wire. The top of each box was covered with a piece of flexible netting with a 1/8th inch (3.2 mm) aperture.

Boxes were filled with ambient sediments from the study site. The ambient sediments were carefully checked for small green crabs and milky ribbon worms before being placed in each box, which contained 400 juvenile clams added (a total of 32,000 clams). As part of the investigation into the cause of the clam decline, clammers grew these juvenile clams in an upweller the previous year and overwintered them using methods invented in the 1990s at DEI. Each box received either 0, 20, 30, or 40 bloodworms (a total of 1,800 bloodworms).

The eighty boxes were sampled in September 2016 by taking five sediment cores (A = 0.02 ft2) from each box. The contents of each core were washed through 1 mm sieves and the number and size of live and dead cultured and wild soft-shell clam seed were measured.

We were unable to determine if bloodworms do stop milky ribbon worm predation on clams due to the presence of predators inside the boxes. We did, however, make two key discoveries. The first was that milky ribbon worms are able to enter boxes with bottom mesh of 4.2mm aperture, making this size netting too large to protect clams from these predators. The second was that green crabs are so pervasive and persist at very small sizes in the intertidal mud. Even though we were careful not to add any visible green crabs to the boxes, their tiny size made them unable to detect and we inadvertently added some to the boxes. Most of the soft-shell clams were recovered dead with undamaged shells (from milky ribbon worms) or crushed/chipped shells (from green crab attack).

We continued this experiment, with a modified design, in 2017.

Bourque, D., Miron, G. & Landry, T. Predation on soft-shell clams (Mya arenaria) by the nemertean Cerebratulus lacteus in Atlantic Canada: implications for control measures. Hydrobiologia 456, 33–44 (2001).
#6: Mud Snails

Investigating How to Reduce Mud Snail Eggs Laid on Netting

In previous experiments, we found that mud snail eggs caused predator nets to became so fouled that clams died beneath them.

This experiment tested an observation made over the course of the experiments that seemed to indicate that snails prefer to lay their eggs on certain materials that are off the mudflat surface. So we devised an experiment to see if snails will lay eggs on nets if the nets remain flush with the mudflat surface.

To do so we deployed 40 12 x 12 predator nets at two mid intertidal sites,  Staples and Collins Coves, where scientists and clammers had observed high densities of mud snails and mud snail eggs.

Twenty of the nets had nine Styrofoam floats to keep the netting above the sediment during tidal inundation. The remaining twenty had no flotation, so these nets would remain flush with the sediment.

Five 6 inch plant pots were planted in each of the 40 plots. The plant pots had 12 cultured clams planted inside them. The nets were then placed over the plant pots, covering the plot, and walked into the mud.

At the end of the field season, the nets were removed and the 5 plant pots under each net (n=200) were taken off the mud and processed through a 1mm mesh sieve. The fate and growth of each of the 12 clams in each pot were recorded and analyzed. A statistical analysis of the clams found that there was no statistical difference in clam survival under the nets that rose off the mudflat surface and the nets that remained flush with the mudflat surface.

Images (click to view slideshow)

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