Investigation into the Cause of the Clam Decline: 2014

Downeast Institute Field Studies – Freeport, Maine

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Portland Press Herald video.


With lessons learned from the town of Freeport’s 2013 shellfish restoration project, DEI devised a six-pronged research initiative to continue to investigate how to battle the effects of green crab predation on soft-shell clams. Experiments included green crab trapping, predator exclusion, and flat restoration, as well as the relative importance of green crab predation compared to sediment buffering (to counteract ocean acidification) on clam growth and survival.  

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 Exclusionary Fencing and Netting
#2: Green Crab Trapping in the Harraseeket River
#3: Investigating if Clams Settle Gregariously
#4: Sediment Buffering Acidic Clam Flats vs Predator Protection on Clam Recruitment, Growth and Survival
#5: Enhancing Flats with Cultured Seed under Predator Protective Netting and Green Crab Trapping
#6: Raising Clams in Upweller (Nursery)

#1: Crab Fencing

Predator Exclusion Fencing

This study examined the effectiveness of exclusionary fencing in deterring green crab predation on soft-shell clams. Fencing was installed in the intertidal in the 1950s, when seawater temperatures surged and green crabs damaged clam harvests (see gallery for photos of these fences in Bremen and Newburyport).  In 2013 the town of Freeport installed fencing at two coves but did not maintain the structural integrity throughout the clam growing season (May-November). (Intertidal structures are subject to intense pressure from tidal action, so maintenance is strenuous.)  The study was repeated in 2014 with the objective of maintaining the fence throughout the clam growing season, in order to determine if fencing works to deter clams and, thereby, enhance clam populations. To provide more comprehensive information about the relative effectiveness of fencing, it was compared to netting, another predator-deterrent technique.

Specifically, this study was designed to determine how effective fencing and netting are at excluding predators and whether cultured soft-shell clam seed will grow and survive better in fenced plots, under netting, or in plots that are completely accessible to predators. 


The experimental design included a total of twenty-eight 30-ft x 30-ft plots.  Fourteen plots were surrounded by wooden fencing (see photo album), and fourteen plots had no fencing.  A total of 1,680 linear feet of fencing was installed and maintained.  Each of 12 sections of fencing was ten feet long and three feet tall. Due to the intense amount of physical labor involved, we are indebted to the members of the Maine Clammers Association who built, installed, and maintained the fencing throughout the entire six-month field season.

The inside of each of the 28 30-ft by 30-ft plots received four treatments: A = flexible netting (4.2-mm aperture) without cultured clams; B = no netting plus cultured clams planted at 20 per square foot; C = netting with cultured clams planted at 20 per square foot; D = no netting and no clams.

Bottom samples were taken from each subplot within each of the 30-ft x 30-ft plots in November 2014.  Samples were washed through a fine (1-mm) mesh sieve to determine number and sizes of 0-year-class soft-shell clams (2014’s spat), as well as number and size of cultured clams (in subplots B & C).  Further information about the study design can be found in the First Progress Report.


Analysis of the number of clams found in each treatment suggested that fencing alone had no more ability to deter green crabs than netting alone.  Survival and growth rates were similar between fenced and unfenced controls, and netted plots within each fence resulted in higher overall survival than control plots (with no netting) within the fenced areas. This is good news from a practical standpoint because fences are expensive to build and difficult to maintain on flats compared to the installation and maintenance of plastic, flexible predator-deterrent netting.

Images (click to view slideshow)

#2: Green Crab Trapping

Green Crab Trapping

Green crab trapping was tested as a method of removing green crabs to reduce populations, thereby enhancing clam harvests. In 2014, a trapping regime was continued that began in 2013 as a volunteer effort by the town of Freeport’s Shellfish Conservation Commission.  Set points were established within a highly productive clamming area of the Harraseeket River and traps were “fished” for green crabs three times each week throughout the six-month study.  


Systematic green crab trapping in the Harraseeket River commenced in the first week of May. To increase confidence in the results of this experiment, variables were limited by using the same type of trap (the “Acer”) and bait type (crushed clams)  as in 2013.  

Our study was designed to answer the following questions:

1) Do more crabs reside in the Upper vs. Lower Harraseeket River?

2) Do more crabs reside in the subtidal vs. intertidal?

3) When are more crabs caught, after 1, 2, or 4 days of soak time?

4) Is the sex ratio 1:1?

5) Does crab density remain constant over time?

6) Does size frequency of male and female crabs remain constant over time?

Fifty traps were fished in ten locations within the Harraseeket River (see map in the gallery below). Five locations were in the “Upper” portion of the river (above the town dock), and five locations were in the “Lower” portion of the river. These ten locations were a mix of intertidal and subtidal locations. In the Lower river, three locations were intertidal (Spar Cove = A; Staples Cove = B; and Wolfe’s Neck = D) and two were subtidal (Mouth of River = C; Yacht Club = E). In the Upper river, three locations were intertidal (Collins Cove = G; Pettengill = I; Sandy Beach = J) and two were subtidal (the Channel = F; Weston Point = H).

At each of the ten locations, five traps (a string) were set approximately 100-feet apart. 

Traps were baited with crushed soft-shell clams and fished following 1-day, 2-day, and 4-day soaks.  As in 2013, information from each haul of the five traps at each location was pooled and a weight measurement was obtained.  In addition,  subsamples were collected to examine how size frequency and gender vary by location and/or time.  Finally, on the 1-day soak, a subsample of individual crabs was collected to examine their gut contents and learn more about their diet. 


Results indicate that green crab catch rates were relatively low from May 5 to June 30 while seawater temperatures were cool, though increasing soak time to two or four days resulted in more crabs caught during those months. Throughout the river, the average weight of green crabs caught in each trap was less than half a pound until mid July. After that, green crab catches increased in intertidal areas of the Upper Harraseeket, while in the Lower Harraseeket (closest to the mouth of Casco Bay), green crab catches increased faster in subtidal areas than in intertidal areas. Male and female populations of green crabs varied throughout the trapping season in the upper and lower river and across intertidal and subtidal areas. Female green crabs were significantly smaller from May to August, while male green crabs increased significantly in size during those same months. 

This data shows the effect of warming ocean water, as crab densities increased with water temperature through the summer and fall, especially in the intertidal zone. Results indicate that it is not possible to reduce green crab populations locally through trapping in open systems, including rivers. Thus, green crabs should be considered permanent inhabitants of the marine coastal environment.

For more details see the first performance report.

Images (click to view slideshow)

#3: Gregarious Settlement

Adult Clams Used to Enhance Wild Clam Recruitment

Many marine invertebrates settle gregariously near their own kind, especially adults.  This has been shown in barnacles, ascidians (sea squirts), tubeworms, oysters, and other bivalves, but has not been shown definitively in soft-shell clams.

In early May 2014, a manipulative experiment was deployed at two intertidal locations (Spar Cove and Recompence Flat) to determine if planting adult clams could be a way to encourage juvenile clams to settle to the mudflat.  If it is found that adult clams do attract settling juveniles, planting adult clams could be a way to locally enhance clam populations.

The studies were designed to examine the combined effects of adult clams and predator-deterrent netting on the number of juvenile wild clams.

This experiment was conducted in the lower intertidal gradient of the two sites. These same two locations in Freeport, Maine were used for subsequent experiments conducted in 2017 and 2018, when this experiment was repeated.  


At both sites, five replicates of each of six treatments were distributed randomly in 10-ft x 1 0-ft plots within a 6 x 5 matrix (20 ft between rows and columns).  The six treatments were as follows:  1) Plots with no clams; 2) Plots with no clams plus 4.2-mm aperture, flexible netting (to discourage predators); 3) Plots with 1 bushel of live, commercial size clams that were hand-planted throughout the 100-square foot plot; 4) Plots with 1 bushel of commercial size clams plus netting; 5) Plots with 2 bushels of commercial size clams; and 6) Plots with 2 bushels of commercial size clams plus netting.

This experiment also tested the possibility that wild spat are not gregarious, but can be enhanced using netting to deter predators such as green crabs.

In November, samples were taken from each of the 30 plots at both sites to determine whether adult clams attract 0-year-class individuals (spat).  The 2014 results were compromised by high milky ribbon predation, so this experiment was repeated in Freeport in 2017 and 2018.  See this link for more information about all three years of this experiment. See this link for more information.

Images (click to view slideshow)

#4: Sediment Buffering

Sediment Buffering for Coastal Acidification

Coastal and ocean acidification pose significant threats to soft-shell clams and other shellfish.  Carbon and nitrogen inputs to the marine environment result in lower pH of seawater and coastal sediments. Soft-shell clam shells contain calcium carbonate in the mineral forms calcite and aragonite.  Previous short-term experiments found that adding crushed clam shells to the flats enhanced numbers of settling recruits. For example, over a period of 16 days, Green et al. (2009) found that acids produced in the upper few millimeters of coastal sediments in southern Maine result in this region of sediments being the most corrosive to calcium carbonate.  Soft-shell clams settle into the top layers of sediment on intertidal flats.   Then, over a period of thirty-five days Green et al. (2013) performed a sediment-buffering experiment in a small, sheltered intertidal mudflat off Portland Harbor in Portland, Maine.  Intertidal mudflat sediments were buffered with ground clam shells and settlement of soft-shell clams, (Mya arenaria) was measured.  Buffering of sediments increased clam recruitment by just over a factor of two.

In 2014, DEI conducted a sediment buffering experiment in an attempt to see if these results extended to a larger scale, thus allowing for sediment buffering with shell hash to be used as a way to mitigate ocean/coastal acidification. If so, shell hash can be used to buffer acidic sediments and increase clam harvests.


In May 2014, we worked with Mike Doan of Friends of Casco Bay to take sediment pH samples at five intertidal mudflats around Freeport: Winslow Park, Staples Cove, Cove Road, Sandy Beach/Cushing Briggs, and Recompence Flat.  Ten samples were taken at each flat, and the average pH ranged from 7.10 at Staples Cove to 7.8 at Recompence Flat.  To determine whether sediment buffering with crushed clam shells would result in an enhancement of wild soft-shell clam spat, we chose the flat with the lowest sediment pH – Staples Cove.  Of the ten samples taken at that location, pH values ranged from 6.78 to 7.47.  

Beginning on 18 May, we established 30 plots (10 ft x 10 ft,).  Six treatments, each replicated five times, were used:  1) 13 lbs of crushed soft-shell clam shells per plot; 2) 26 lbs of crushed soft-shell clam shells per plot; 3) No shells were added to plots as a control; 4) 13 lbs of crushed soft-shell clam shells plus plastic, flexible netting (4.2 mm aperture); 5) 26 lbs of crushed soft-shell clam shells plus netting; and 6) Control plots with netting. Aged, commercial-sized clam shells from a shell pile in Beals, Maine were used to buffer the sediments. See photo album for pictures of the process.

Benthic core samples were taken from each of the 30 plots in November 2014 to determine whether number of soft-shell clam spat (0-year-class individuals ranging in size from 2-8 mm in length) was related to the shell material used for buffering the sediments, predator protection, a combination of the two factors, or whether numbers of soft-shell clam spat are independent of the treatments.

This study found only significant differences in quahog survival in plots that were protected with netting only (vs. sediment buffering).

Due to the fact that crushed shells (used for buffering, in an attempt to increase wild spat survival) could also provide a spatial refuge from predators, an additional,  “small-scale” experiment was deployed adjacent to  the plots described above, which used granite chips to provide habitat with no buffering.

This study included eight treatments replicated ten times. The treatments were: 1) Control (no netting); 2) Control + Netting; 3) Layer of clam shells on top (no netting); 4) Layer of clam shelsl on top + netting; 5) Limestone (oyster) chips on top (no netting); 6) Limestone (oyster) chips on top + netting; 7) Granite chips on top (no netting); 8) Granite chips on top + netting.


In both studies, there were twice as many soft-shell clam recruits in protected plots as in plots without predator protection (see table below).

The large-scale study found only significant differences in quahog clam survival in plots that were protected with netting only (vs. sediment buffering). Nearly 40x more hard clam (quahog) recruits were observed in plots covered with netting compared to those without nets. Nearly 98% of animals were sampled from netted plots.

In terms of soft-shell clams, the only significant difference between treatments was observed in treatments that were protected with netting.

The results from this research, as well as results from 2015 and 2016 sediment buffering experiments, were published in the September/October 2020 Journal of Experimental Marine Biology & Ecology.

Images (click to view slideshow)

#5: Protecting Flats

Clam Enhancement Using Cultured Seed and Netting

In 2014 an experiment was conducted at two intertidal locations to determine the effects of planting density on growth and survival of cultured soft-shell clam seed under protected netting.  



In late April 2014, experiments were established at two intertidal locations in the Upper Harraseeket River, one in Collins Cove on the south side of the Harraseeket River, and the other directly across the river, about 600 meters away, along the Wolfe Neck shore. 

At both locations, 40 nets (14-ft x 22-ft) were deployed in 10 groups of four nets each.  Clams were seeded underneath the nets in one of two densities, 20 or 40 individuals per square foot. Strings of five green crab traps each were deployed adjacent to five of the groups of nets, and were fished twice a week.

In the schematic of the experiment shown below,” “20” and “40” refer to planting density of clams per square foot. The rectangular objects adjacent to a group of four nets represent the presence of a string of  green crab traps.

After 205 days (on November 8-10, 2014) DEI scientists and clammer partners peeled back the nets at each site and took two benthic core samples from each of the 40 plots (n=80), as well as two similar benthic cores from outside the plots (n=20. Core (mud) samples were washed through a 1-mm mesh sieve and all soft-shell clams were counted and measured. The number of soft-shell recruits found was reported in Beal et al. 2018).


Regarding the success of planting protected clams under netting to enhance clam populations, there was a startling difference in clam survival between the two flats located only 600 meters apart on each side of the river. On the western side of the river at Collins Cove we found less than 10% survival in the 40 plots, while on the eastern side of the river we found more than 90% survival. In addition, the planted clams on the eastern side grew extremely fast, with approximately 26% of cultured clams sampled in the cores attaining final lengths that were greater than 50.8 mm (legal size for harvesting in Maine).

In Collins Cove, a high number of dead clams with crushed or chipped shells indicates that approximately 40% of the clams were preyed on by crustacean predators soon after planting. 

For more detailed results, see pages 18-38 in the July 26, 2015 Progress Report. 

Survival rates of recruits found in the plots and in the unprotected sediments were also examined. Remarkably, soft-shell clam recruits obtained densities of 899 times greater in large-scale predator-protected plots compared to adjacent unprotected plots.

Results of this study were presented at the Maine Fishermen’s Forum on March 5, 2015 in Rockport. Follow this link to that presentation.

Results from this experiment were also published in the Journal of Shellfish Research.  

Images (click to view slideshow)

#6: Using an Upweller

Growing Cultured Clams to Transplantable Sizes Using an Upweller

Cultured clams are expensive, especially if a community purchases transplantable size clams (> 8 mm in shell length).  However, it is possible for a community or individual to purchase smaller, less expensive clams from a hatchery (1-2 mm in length) and to grow them in an upweller nursery.  Because cultured soft-shell clam seed has never been grown in a nursery setting in Freeport, we wanted to see if it was possible.  

For a full description of the upweller construction and results, see the photo album. During the 37-day period between 5 June and 12 July, many clams grew from 1.5 mm to nearly 12-14 mm in length.  Maximum size hatchery clams that can be purchased at DEI are generally 8-12 mm in length.

In 2014, funding for this research came from three sources:  $200,000 from the Maine Economic Improvement Fund (Small Campus Initiative), to be used over two years;  $348,767 from the National Marine Fisheries Service (Saltonstall-Kennedy fund), to be used over two years; and $28,000 from Sea Pact, to be used in one year.

Images (click to view slideshow)

Final Reports:

The first progress report for NOAA/SK (NA14NMF4270033) for the period between July 1 and 31 December 2014 can be downloaded here.

The second progress report for NOAA/SK (NA14NMF4270033) for the period between 1 January and 30 June 2015 can be downloaded here.


Green, M.A., G. Waldbusser, S. Reilly, K. Emerson, and S. O’Donnell. 2009. Death by dissolution: sediment saturation state as a mortality factor for juvenile bivalves. Limnology and Oceanography 54 (4): 1037–47.
Green, M.A., G. Waldbusser, L. Hubazc, E. Cathcart, J. Hall. 2013. Carbonate mineral saturation state as the recruitment cue for settling bivalves in marine muds. Estuaries and Coasts 36:18-27.
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