Investigation into the Cause of the Clam Decline: 2015

Downeast Institute Field Studies – Freeport, Maine

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Building on 2014 investigations into possible remedies to increase clam harvests, DEI scientists continued our collaboration with clammers from the Maine Clammers Association to conduct six different experiments at 31 different intertidal locations in 2015. This work included continuing green crab trapping at the same intertidal and subtidal locations of the Harraseeket River as in 2014. We also continued to work with clammers to raise clams in upwellers, doubling the amount of space in which to do so. We also tested whether sediment buffering or predator exclusion had any impact on clam survival.

Green-crab trapping continued to yield large numbers of crabs but had no effect on clam survival. There was great variability between naturally settling clams between two locations, if clams were protected from predators, and we found that survival of hatchery clams increased 90% when using predator protections. Transferring hatchery upweller technology proved to be very successful.

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: Green Crab Trapping in the Harraseeket River
#2: Understanding Spatial Variation in Clam Growth and Survival with Predator Deterrent Netting in the Harraseeket River
#3: Spatial Variability in Wild Soft-Shell Predator Clam Recruitment in the Harraseeket River
#4: The Effects of Sediment Buffering vs. Clam Protection on Clam Recruitment, Growth, and Survival
#5: Spatial Variability in Clam Grow-Out in Predator Protected Boxes
#6: Raising Clams in an Upweller (Nursery)

#1: Crab Trapping

Systematic Green Crab Trapping in the Harraseeket River

For the third year in a row, DEI scientists and clammers conducted a green crab trapping program to better understand the dynamics of this predator in the Harraseeket River.  As in the 2014 trials (see the first and second progress reports), we divided the river into an Upper and Lower section with two subtidal and three intertidal sites located in each.  Two factors were different this year: 1) we set and fished the five traps at each site every four days and 2) switched bait upon each haul, one time with salted herring (similar to that used by lobstermen) and the next time with crushed adult soft-shell clams (similar to that used in the previous two years.) The first traps were hauled on May 10 and the final haul date was October 29. Over the 24 weeks, clammer field techs conducted 45 green crab fishing trips, hauling 50 traps each time.

As we did last year, upon hauling, crabs from each of the 5 traps in a string were combined and weighed to the nearest 0.1 lb to form a sample. Using a scale, when the crabs in the sample weighed over 2 lbs, a random sample of 2 lbs was taken and the crab carapace width was recorded, as well as the gender. If a sample weighted less than 2 lbs, the entire contents of the sample were measured and sexed.

The sampling design allowed DEI scientists to estimate spatial and temporal variability in green crab abundance, size-frequency distributions, and sex ratios between locations, as well as between intertidal and subtidal sites. In addition, the use of different baits provided some insight on catch rates between locations and sites.


In 2015 we caught 1,137 lbs of green crabs at our established locations. This amount was 38% less than our 2014 total of 1,852 lbs, but the previous year we hauled more traps (60 twice a week and 50 once a week) and conducted more trips (66), although we trapped for two more week in 2015.

Over the course of the green crab trapping season (May 10 to Oct. 29, 2015), the average weight of the captured crabs increased substantially as the water warmed (see Fig. 4 below). Mean crab weight per trap did not rise above 0.2 lbs until early August. After early August, the average weight per trap increased nearly exponentially through late September (Fig 4). This trend of catching more crabs in the warmer summer months is similar to the 2014 results.

Bait Preference

Traps baited with herring produced approximately 10% higher catch rates than those baited with adult clams. However, the effect of bait on catch rates varied significantly across sampling dates (P < 0.0001, see below).


Overall, crabs were approximately 18% more abundant in the Lower vs. Upper Harraseeket. The higher average weight per trap occurred in the Lower Harraseeket on 5 October (1.7 ± 1.04 lbs/trap; n = 5) and on 17 October in the Upper Harraseeket (1.67 ± 1.41 lbs/trap; n = 5).

Crab abundance varied significantly from site-to-site within each site (P < 0.0001). I the lower Harraseeket, crab abundance was highest at two of the intertidal sites (Spar Cove and Staples Cove) and one of the two subtidal sites (adjacent to the Freeport Yacht Club). In the upper Harraseeket, green crab abundance at only one site (subtidal off Collins Cove) averaged less than 0.1 kg/trap (0.2 lbs/trap). No significant difference in mean green crab weight was observed between the other sites.

Sex Ratios

Mean sex ratios varied significantly across dates and locations (P = 0.016; Fig 7), but were, for most dates, male-biased (i.e., above 50% male). Beginning in mid-September, there was a trend towards a 50% ratio in both locations.

Size (Carapace Width and Weight)

Carapace Width: Average green crab carapace width varied significantly (Table 2). Prior to mid-July, when catch per trap was typically low (Fig. 4), there was high variation in average size (Fig. 8). After that period, however, variation in CW decreased between sampling dates at both locations, and a trend emerged as shown below (Fig. 8). Size of the crabs gradually increased from mid-June to early September. For the final 14 sampling dates beginning 3 September, mean CW (± 95% CI) for crabs in the Lower Harraseeket was 45.7 ± 0.8 mm and 51.2 ± 0.7 mm for crabs in the Upper Harraseeket.

The average number of green crabs per pound (Fig. 10) showed similar variability to that observed for mean crab CW. Early in the spring and summer when crabs were small, the number per pound varied between 50-200 animals. The size of crabs increased through at least one molt, and the number per pound leveled off around 3 September. At that time, mean number per pound from traps hauled in the Lower Harraseeket River was 17.1 ± 1.92 crabs/lb (n = 15), whereas the mean number from traps hauled in the Upper Harraseeket River was 12.6 ± 0.9 crabs/lb (n = 15). These two means are significantly different (T = 4.59, df = 28, P < 0.001), suggesting that the average size of crabs was somewhat larger in the Upper vs. Lower portion of the Harraseeket River after 3 September (see Fig. 8). This size difference may relate to warmer temperatures in the upper reaches of the Harraseeket during the summer months.

For more details on the 2015 green crab trapping, please see pages 2-13 in the third progress report.

Images (click to view slideshow)

#2: Netting Clams

Understanding Spatial Variation in Cultured Clam Growth and Survival Under Nets on Both Sides of the Harraseeket River

In 2014, we observed dramatic differences in cultured clam survival, and in wild clam recruitment, from one side of the Harraseeket (near Collins Cove) to the other (directly across the river on the Wolfe Neck shore).  We were curious whether these differences (less than 10% survival in the 40 plots near Collins Cove vs. greater than 90% survival at the site across the river) were a result of some random event, or whether these differences could be attributed to some biological or environmental factor. Beginning in mid-April 2015, we established ten study sites on the east and west side of the Harraseeket River by deploying four plots (14-ft x 22-ft) that were seeded with overwintered hatchery seed at a planting density of 10.5 clams/sq. ft.  Upon deployment, we also took core sediment samples to establish baseline densities of wild clams. In the fall, core samples were taken from each of the 80 nets. Each sample was washed through a sieve, and the number of live and dead clams counted.  All live clams also were measured to estimate growth rates.  Wild soft-shell clam recruits (0-year class individuals) from each core sample also were counted and measured.

Upon analysis of the data, we learned that the trend of low survival on the western side of the river (Collins/Yorkies Cove, South Freeport) with more survival on the eastern side (Wolfe’s Neck, Freeport) continued.

West Side (South Freeport)

Mean percent of live clams was extremely low (70% of the sites yielded no live clams). Overall, only 5.7 ± 5.4% (n = 40) of clams were recovered alive. Although mean percent of live clams was as high as 33.3% (site X –Pettengill), there was no significant spatial variation in survival from site-to-site on the western side of the Harraseeket River. Nearly 75% of clams were either dead with undamaged valves or with chipped or crushed valves. Of those, over 55% of clams recovered in the benthic cores from netted plots were dead with undamaged valves (57.4 ± 9.8%). The size-frequency distribution of clams from this category indicates that most clams added new shell prior to dying, and it is presumed that milky ribbon worms were responsible for most of the clam deaths. Mean SL (shell length) of dead clams with undamaged valves was 26.7 ± 1.1 mm (n = 157). Five core samples (of 80; ca. 6%) contained milky ribbon worms, and, while this density appears to be low, other field trials conducted at sites I and VII (see below) suggest that this predator was a major source of clam mortality in these field plots during the summer and fall of 2015.

East Side (Wolfe’s Neck)

Core samples from each of the ten sites along the east side of the Harraseeket River demonstrated mean rates of live clams between 0 and 55%; however, no clear spatial (i.e., site-to-site) pattern was apparent. Although few nemerteans (Cerebratulus lacteus) and green crabs (Carcinus maenas) were found in the core samples (4 of 80 for each species), many milky ribbon worms were seen in the sediments while sampling and information from other field trials in 2015 indicates that these have become a major predator of clams. Studies have shown that these animals consume their soft-shell clam prey without leaving any damage to the valves (Bourque et al., 2001). Mean SL of clams with undamaged valves was 30.1± 1.8mm (n = 124).

The size-frequency distribution of clams recovered dead with undamaged valves showed that at least 65% were larger than the biggest clam seeded into the plots in April. This suggests that many of the clams had grown prior to dying. 

While milky ribbon worms leave no damage, chipped or crushed clams are typical of damage due to crustaceans such as the green crab, Carcinus maenas, or rock crab, Cancer irroratus. The frequency distribution of clams recovered with chipped or crushed valves demonstrates that crabs preyed on smaller clams than did nemertean worms. Mean SL of crushed clams was 23.6± 1.4mm (n = 58).

Images (click to view slideshow)

#3: Recruitment Variability

Spatial Variability in Soft-Shell Clam Recruitment Along Both Sides of the Harraseeket River

To examine natural recruitment without the potential influence of cultured clam seed, we initiated a study at the same twenty sites in the Harraseeket River that were described in experiment # 2 above.

We deployed a series of six wooden boxes (1-ft x 2-ft x 3-inches deep) that were placed directly on the surface of the mud at each of the ten sites on the east and west side of the Harraseeket River.  Two boxes had Pet screening (1.6 mm aperture) on both top and bottom and initially contained no sediment.  Two boxes had Pet screening on both top and bottom and contained 1,000 ml of play sand.  Two boxes had an extruded polyethylene netting (6.4 mm aperture) on both top and bottom and contained no sediment initially.  We assumed that juvenile clams might wash into the boxes or enter directly through natural larval settlement.

The boxes with Pet screen® excluded large crabs and milky ribbon worms – Cerebratulus lacteus, but the larger mesh boxes did not exclude small crabs or milky ribbon worms from crawling through the netting.  


Conducting this experiment opened up a whole new understanding of the productivity of the intertidal ecosystem. The good news is that clams are still settling onto the mudflats in what seem to be high numbers (1,400 per. sq. ft in some areas). the bad news is that over 99% are being lost to predation before they can reach a harvestable size.

The full results from the experiment were published in the 2018 Journal of Shellfish Research.

Images (click to view slideshow)

#4: Sediment Buffering

The Effects of Sediment Buffering vs. Protection on Clam and Quahog Recruitment, Growth, and Survival

One hypothesis that has been proposed for the recent decline of soft-shell clams along the shores of Casco Bay is that ocean and coastal acidification has resulted in acidic mud and seawater, and these environmental assaults result in the dissolution of clam shells that ultimately leads to widespread mortality.  The Friends of Casco Bay has indicated that acidic mud could wipe out clam harvesting in Casco Bay.  In 2015, a report was released that linked ocean acidification to declining clam numbers.

To follow up on our 2014 examination of the same hypothesis, two study sites (Little River and Winslow Park) were chosen and, in 2015, the same experimental design was used on a small and large scale.  


The results from the 2015 sediment buffering experiments, along with the results of 2014 and 2016 sediment buffering experiments were published in the September/October 2020 Journal of Experimental Marine Biology & Ecology.

The results of the 2015 large-scale experiments:

  • At both sites, adding shell (13 or 26 lbs) to plots did not result in significant enhancement of soft-shell clam recruits compared to plots without shells. 
  • At both sites the plots covered with predator-deterrent netting contained more soft-shell clam recruits (70x at Winslow Park and 20x at Little River) than plots without netting, whether or not shell was added to plots..

The results of the 2015 small-scale experiments were:

  • At the Winslow Park site the numbers of soft-shell clam recruits did not vary significantly over the four substrates. However, significant differences were detected between units with and without predator-deterrent netting.  Approximately four times more recruits were found in netted units.
  • At the Little River site no significant differences were observed in the mean number of clam recruits for any of the treatment variations.

All of the 2014 and 2015 sediment-buffering experiments showed that none of the shell and substrate additions used to buffer acidic sediments resulted in an increase in clam recruits. In 4 of the 6 experiments the addition of predator-deterrent netting increased the number of clams that survived.

Images (click to view slideshow)

#5: Grow-Out Boxes

Spatial Variability in Clam Grow Out in Predator Protected Boxes

Field experiments using juvenile soft-shell clams grown in the Freeport upweller in 2014 and overwintered using techniques discussed in Beal et al. (1995) were initiated by Maine Clammers Association members in 2014.

In the first 2014 experiment, a series of thirty 4-ft x 2-ft wooden boxes were placed directly on the mudflat surface at four coves in Freeport (Celia’s, Across the River, Calls, Staples).   To deter predators, the bottom of each box was lined with a flexible netting (1/6th-inch aperture).  The boxes were filled with ambient sediments and seeded with cultured clam seed at densities of 30, 45, or 60 clams per sq. ft.  After seeding, the tops of the boxes were covered and secured with either 1/4-inch flexible netting or 1/6th-inch flexible netting to deter crabs.  Protective netting on the box top, as well as stocking density, were both varied, resulting in a total of six treatments, each with five replicates.  

In November, two random benthic cores (Area = 0.008107 m²) were taken haphazardly from each box. The contents of each sample were washed through a 1 mm sieve and all live and dead cultured clams, wild clams, and green crabs were enumerated and measured (SL for clams; CW for crabs) to the nearest 0.01 mm using digital calipers. 

These experiments assessed stocking density, type of exclusion netting used on top and bottom of the boxes, and intertidal location.  Results from all the boxes showed us that adding ambient sediments also added predators to the boxes, resulting in very low clam survival. Further details from these experiments can be found in the 3rd and 4th Progress Reports. 

Staples Cove Milky Ribbon Exclusion

Our experiments showed that milky ribbon worms were not deterred by protective netting placed on top of the mud flats, nor are they discouraged completely from entering boxes seeded with cultured soft-shell clam juveniles through the bottom of the box with a 4.2 mm aperture. We designed a field experiment to attempt to discourage milky ribbon worms from entering boxes. The experiment was initiated in mid-May to examine the effects of milky ribbon worms and green crabs on the survival and growth of cultured soft-shell clam juveniles.  A series of 21 boxes were arrayed near the mid-intertidal at Staples Cove, Freeport, Maine.  To discourage milky ribbon worms from entering the boxes, different bottom nets were applied. Seven boxes had a piece of extruded netting (6.4 mm aperture) on the bottom, seven boxes had a piece of flexible netting (4.2 mm aperture), and seven boxes had a piece of PetScreen® (1.6 mm aperture) on the bottom.  Soft-shell clams ranging in size from 6-20 mm SL were scattered onto the surface sediments of each box at a density of 100 individuals/sq. ft. 

After planting, all boxes were covered with a piece of flexible netting (1/6th-inch aperture). 

In November, two core samples were taken from each box, and the contents of each core washed through a 1 mm sieve.  All live and dead clams were counted and measured to estimate survival and growth.

At the end of the experiment the only boxes with clam survivors were the boxes with pet screen bottoms, indicating that PetScreen® is successful in excluding milky ribbon worms and smaller predators while the larger aperture netting (4.2 mm and 6.44 mm ) does not deter milky ribbon worms or small green crabs.  Further results can be found on pages 62-67 of the 3rd Progress Report and on our Milky ribbon worm research page.

Images (click to view slideshow)

#6: Using an Upweller

Raising Clams in an Upweller to Enhance Clam Protection Efforts

In 2014 clammers were successful in growing clams in an upweller.  We began our 2015 field season by overwintering clams off the South Freeport docks using methods that have been used at DEI since the early 1990s.  In late November 2014 clam juveniles previously reared in Freeport’s nursery upweller during 2014 to sizes of 12-20 mm in length were added to 18 in. x 18 in. PetScreen® bags for overwintering at densities of three to five thousand per bag. 

Upon opening the bags in early spring 2015, we determined that approximately 95% of clam juveniles survived the overwintering process. These clams, grown in the upweller by clammers in 2014, were used in some of our six field trials initiated in April and May 2015.

We decided to construct and deploy a second nursery upweller at the South Freeport dock in 2015.  The upweller was deployed in mid-July, doubling the capacity for growing soft-shell clam seed, thus providing great opportunities for continued efforts in 2016.

Images (click to view slideshow)

Final Report:

To see the 3rd progress report for NOAA/NMFS, click here.

To see the 4th progress report for NOAA/NMFS, which covers most of the results of the 2015 projects, click here The Final Report can be downloaded.


Funding for 2015 was provided by: 1) National Marine Fisheries Service (Saltonstall-Kennedy Grant program); 2) University of Maine System (Maine Economic Improvement Fund – Small Campus Initiative); and, 3) The Broad Reach Fund (Maine Community Foundation).

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