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The Sound School Inter-District Marine Education Program Newsletter
Habitat Information for Fishers and Fishery Area Managers
Understanding Science Through History
Connecticut’s Coves Do Contain
“A Habitat History”
Winter Flounder Fisher Habitat Concerns in the 1980s
Habitat History Capstone #12
The Poquonock River – Jordan Cove and Holly Pond Cores
Provide Habitat Histories for Potential Capstone Projects
Timothy C. Visel, The Sound School
January 2014
Original Discussion Paper DEP – EPA Long Island Sound Study
Habitat Restoration Committee July 2010
IMEP #15 – Part 1



The prospect that changes in shellfish and finfish populations often have a direct habitat link has been mentioned by fishers for centuries. What fishers provide are their observations as directly connected to the resource abundance later recorded as fishery catch statistics. As such fishers can provide confirmation of Winter flounder success and abundance as important first accounts of habitat change.

The concept of energy and temperature dependent habitat successional clocks was first introduced to the Long Island Sound Study during the period 2006-2008. The distribution of a report that described a series of climate cycles that once favored malaria outbreaks in Connecticut included this information. That report was titled “Climate Change and Public Opinion – A Case History of Salt Marshes and Malaria” and was made available to the DEP/EPA Long Island Sound Study habitat restoration committee in August of 2008. That report discusses how the public opinion and public policy regarding salt marshes was changed by a series of Malaria outbreaks were traced by observations to the saltwater mosquito habitats at the turn of the century (Greenwich, CT). Coastal habitats changed then during The Great Heat 1880-1920 following the much colder 1870s. Habitats would change again in the 1950s and 1960s as climate conditions became colder and stormier. These changes appear to be evident in marine core studies of Connecticut’s estuaries in the early to middle 1990s. During this time a “habitat war” was declared upon mosquito habitats and in an act of desperation orders to fill in all salt ponds in Greenwich, CT.

Winter flounder Fishers Ask Questions about Habitat Change

In the middle 1980s, eastern Connecticut Winter flounder, bay scallop and recreational shell fishers all noted habitat changes in several eastern Connecticut coves, primarily those bisected by the Northeast Amtrak™ corridors. Reports included a transition in habitats from the 1950s and 1960s a colder and storm prevalent period, previously “hard bottoms were now turning soft.” Winter flounder fishers were especially concerned as previous estuarine shell or clam beds were now covered with decaying leaves. Some of the first studies were directed by John Scillieri, Chairperson Waterford Flood and Erosion on Control Board regarding habitat changes in Jordan Cove (Waterford urges Action for Coves, December 3, 1983). It was Mr. Scillieri who also noticed very substantial habitat changes especially the buildup of leaves in coves. Upon returning to Connecticut from the Barnstable Mass Cape Cod Extension Service Mr. Scillieri was one of the first people to raise the alarm bell about restricted circulation and increased organic matter in them. A December 3rd New London Day article titled “Waterford Studies Urge Action on Coves” and refers to a study that actually began in 1980. “The town has an obligation to maintain its coastal resources. The problems experienced are due to various acts by man… therefore, man should intervene in some of these cases to reverse a process he certainly has played a key role in,” said John A. Scillieri Jr., chairman of the Flood and Erosion Control Board. Among the man-made creations affecting the coves are railroad bridges, roads, filled in portions to support building and dams.” Waterford conducted several studies in the 1980s and found like many fishers the upper reaches of coves – those poorly flushed had severe benthic degradation associated with excess organics. In a 1988 report (Whitlatch Zajac, Nov. 1987) reported that the “importance of the benthos to estuarine dynamics, especially in small systems such as the cove {alewife} is well recognized {and one of the factors is} “high organic loading” pg 2. (A Study to Assess Dredging Effects on the Ecology of Alewife Cove, Nov. 1987).

Fishers were not alone in noticing the impact of heavy organic loadings as leaves collected in the “back waters” turned black and rotted in a jelly like substance. Alewife fishers also reported alewife getting “stuck” by leaves and branches across streams. Rotting organic matter in high heat is known to create sulfide blocks – a chemical toxic barrier to returning alewife. As these conditions appeared fist in shallow coves and creeks and a major feature of eastern Connecticut was a shore Amtrak™ railroad line that crossed many productive eastern CT coves. Fishers had long complained about them and the restricted flushing that tended to hold all these leaves back in the shallows. Some two decades after Winter flounder fishers were alarmed about habitat changes from rail crossings. Looking back they had good reason to be concerned. The Conservation Law Foundation in 2000 ranked road and railroad constrictions as primary causes for “allowing invasive freshwater (marsh) species to alter salt marshes, reducing its unique habitat value “Return The Tides project to inventory tidal marsh restrictions Working Waterfront “Inter Island News, March 2000 pg 7).

Study of the BNSF railway causeway of Bellingham in Washington state (Tim Wahl 2008) provides navigational charts denoting navigability on charge area how termed “Mud Bay” explaining that the reduced ecological functions of the basins original, deeper, sandier and gravel state. A trestle was replaced with a earth causeway (as was the habitat history for many eastern Connecticut coves) and crabbing and digging for clams n “Mud Bay” soon declined.

Mr. Benjamin F. Rathbun a long time and well known fishing vessel Captain in the Noank area wrote to me on Feb. 19, 1989 and asked “What about the railroads” their bridges and trestles have done more to degrade and restrict access to state waters than almost all other activity combined.” And now as other studies results become known I would agree with Mr. Rathbun – habitat wise they did.

Most of these negative habitat fisher observations included the build up of “Black Mayonnaise” more properly termed recent Sapropel. Comments included post road and rail causeway construction observations that once had hard sandy and bivalve shell habitats in eastern Connecticut changed, they had transitioned to soft organic layers including many comments from oyster fishers concerning the Poquonnock River in Groton. Other observations from Winter flounder fishers and bay scallopers were very consistent- all reported that hard bottoms had changed during their lifetimes, reversed from hard bottom estuarine shell habitat types to soft deep organic accumulations, mainly consisting of dead sea grasses, leaves and tree limbs. Reports often included bubbles and strong “gas” smells when these deposits were disturbed. The odors are now suspected to hydrogen sulfide. Several contained references to plant material including plant species themselves (mostly eelgrass and sea lettuce) transitioning shellfish and finfish habitats. Fishers often linked these habitat changes to the tidal restrictions of railroad causeways, especially in eastern Connecticut as creating this apparent habitat reversal, but it was also getting “hotter.” Fishers consistently raised questions about tidal restrictions and reducing the flushing ability of tides to remove now accumulating organic debris. This debris to fishers become deeper since their observations from fishing experiences accumulated to site specific fishing locations. Some of the first Winter flounder fisher concerns came from Alewife and Jordan Coves in the town of Waterford.

In response to Winter flounder fishers and bay scallopers, after many requests in the late 1980s and early 1990s, The Office of Long Island Sound Programs (DEP) then funded a study to review sedimentation rates in three eastern Connecticut Coves, looking for transitions of habitat types as described by many eastern Connecticut fishers at the time (late 1980s). This effort produced a report in 1992 CWF-266-R that did not support the role of railroad causeways as the source of this habitat reversal or excess organic matter properly termed Sapropel over hard or “shell bottoms.” However additional core studies in three additional coves, two in the east and one in the west did show historic multiple pronounced soft bottom / sand shell layers as mentioned by fisher observations. In some core samples they contained many distinct shell/sand layers and these were found in different coves (1993). An Army Corps of Engineers, Section 22 report titled Connecticut Wetland Restoration Investigations (May 1994) did not include this important core information, and at least one sample from Quiambaug Cove in Stonington, Connecticut itself did contain multiple shell layers. Additional research was to indicate Connecticut’s coastal coves contained cores exhibiting many distinct shell layers. In fact it was common to find this type of habitat history in core samples.
This information (report date 8/10/94) apparently was not made available to eastern CT resource users or Shellfish Commissions in 1994 but additional core samples from similar coves showed many such layers/habitat reversals detailing multiple pronounced shell layers as historical evidence of profound habitat changes. These habitat changes now appear have a direct climate and energy link. One key core QC #3 taken in Quiambaug Cove itself shows three such shell sand layers.

This habitat history information would have been of interest to eastern Connecticut municipal Shellfish Commissions as it directly influenced shellfish restoration policies at the time. It certainly confirmed some Winter flounder fisher observations as we were perhaps just entering a prolonged period of heat with few strong storms and that core examinations detailed these previous habitat reversals in the past.
One of the first studies to make an energy habitat link to estuarine shell layers in coves occurred with a study of pollution history of Narragansett Bay Sediments (Goldberg et. al August 1976 Estuarine and Coastal Marine Science 1977 5, 549-561 Scripps Institute of Oceanography) funded by EPA National Marine Water Quality Laboratory of Narragansett Rhode Island. Here studies focusing on heavy metal pollution history found a distinct shell layer thought to be represented by a 1954 hurricane event, pg 549. Records from the Rhode Island oyster industry do indicate the 1950s were devastating and excess silt and organic matter covered oyster beds in the upper Narragansett Bay. Three cores were taken in 1974 two outside the Providence River and one from the Pettaquamscutt River. The two cores from the upper Narragansett Bay indicated a deposition rate of 1cm/year and shell layers at 22 centimeters were concluded to be introduced during the 1954 hurricane (pg 551). Researchers were intrigued by the presence of this shell layer and produced a Radiograph of NAR – Cove 7408 – 2813. “Clearly visible shell energy layers are at 15 to 22 cm and below.” The authors also mention other energy events as suggested core/shell interactions involving the Narragansett Bay region in 1944, 1938, and 1893 on pg 551.

Although researchers were correct in identifying the estuarine impacts of energy insufficient habitat information was available as to the impacts of organic deposition in high heat and low oxygen conditions. Temperature and energy have profound impacts upon habitat quality and the species that were sought after for recreation, food and commerce. Habitats in these coves were subject to change first, they were shallow and subject to quicker temperature and energy impacts. It appears from Waterford’s coves with tidal restrictions Sapropel (Black Mayonnaise) appeared years before other areas possibly as soon as 1982.
Habitat quality has a direct bearing upon shellfish restoration programs today. In periods of high heat, bay scallop restoration is risky at best. In periods of cold oyster recruitment is reduced and sets often fail to occur or if they do too late to survive the winter. Habitat reversals as illustrated by core studies would have been very useful to shellfish commissions and Winter flounder fishers at the time and ongoing restoration policies. Although Winter flounder fishers first expressed concerns in 1983 the coastal cove/core results were made public in 2001.

The results of this continued core study from 1993 should be reviewed especially for key markers, for the storm prevalent period of the 1870s, the 1938 Hurricane and very stormy 1950s. This raw data, the work of Dr. Peter Patton of Wesleyan University, and report CWF 310-CWF 266-R should be reviewed immediately as it adds to our baseline long term “habitat history” understandings of Long Island Sound and its fisheries.
A second report for a second grant CWF 310-R 8/26/93 – 8/31/01 an eight year study that reviews vibra cores taken in three additional coves the Poquonnock River in Groton, Jordon Cove in Waterford and Holly Pond of Stamford and Darien. In that study Dr. Patton continued to find layers of estuarine shell sandwiched between those darker layers termed marine humus or more exactly in hot periods Sapropel. It provides an excellent foundation upon which to build a core history comparison to fish and shellfish habitat quality.


Climate Change and Habitat Histories

The reports by Dr. Patton describe the investigations of the sedimentary environments and geomorphic history of three small coastal coves on the Connecticut shoreline of Long Island Sound. It followed the P.C. Patton and C.L. Arnold Study – Post Glacial Stratigraphy and Rates of Sediment Accumulation in Three Eastern Connecticut Coves (Funding from the Long Island Sound Research Fund) and appears as a 1993 Connecticut Sea Grant Publication No Ct-SG-93-03 continued to examine core samples beyond those first reported in 1992. Extensive coring occurred in Holly Pond (Darien), Jordan Cove (Waterford) and the Poquonnock River (Groton) occurred in 1993. Unpublished and published data of this extended study includes:

Core samples taken from Holly Pond, July 13, 1993
Jordan Cove, June 30, 1993 – July 1, 1993
Poquonnock River – June 22, 1992 to July 9, 1992

The concept of a habitat history indexed with climate and energy producing habitat reversals (layers) appears in this later core study; and in cores taken nearly a year before the May 1994 Section 22 Army Corps of Engineers report was published. The Patton study lists many core samples that include layers of organic material sandwiched between those of estuarine shell. This Army Corps study Connecticut – Wetland Restoration Investigation (1994) therefore is missing key core information for the upper basins of the Poquonnock River; the upper basin and middle basin was once the site of historic oyster beds, now bisected by two railroad causeways one abandoned and one still active. The Poquonnock River cores are most valuable as the upper and middle basin contain oyster maps showing both natural and granted shellfish leases. The Poquonnock River cores PR-7 6/2392 and PR-3 6/26/92 clearly illustrate multiple layers of mud between distinct shell layers8. These changes indicate changes in habitat types influenced by climate and energy transitions, including quality changes in historic fisheries9. This information was very significant and important to Winter flounder fishers who consistency asked where have all the flounder gone?

Energy events are most likely recorded in these coves from strong storms, and floods hurricanes and probably the best example of a habitat history related to soft bottom transitions is found in the Holly Pond Core sample taken at 10 a.m. on July 13, 1993. Several other core samples contain similar shell layers.
Dr. Peter Patton data for reports CWF 310-R and CWF 266-R details an extensive series of layers showing oyster and scallop shells in many cores. Core samples should be reexamined (if possible) for species as species identification as species changes can indicate energy and temperature habitat preferences. Western Connecticut cores especially from Greenwich, Connecticut could yield much data as it became a center for bay scallop production in the much colder and storm filled 1870s. Finding bay scallop shells in Greenwich cores is therefore highly significant.

An excellent sample which illustrates the layers of detailing a habitat history are the Holly Pond cores from 1993 presented below,

3. Holly Pond Cove HP#3 7/13/93 10:00 a.m. Water depth 1.68 meters total cove length 816 cm pg 24 cove profile as from Patton document 8/18/01 (unpublished report) as reported as core depth/profiles of 14 distinct sections/layers,
From the Patton Data - Holly Pond Core Sample HP #3
Layer 1 0-25 cm black organic rich mud
Layer 2 25-30 shell layer (no type specified)
Layer 3 30-46 cm black mud
Layer 4 46-50 cm sand with scallop shells
Layer 5 50-150 cm black mud, one large oyster shell at 65 cm
Layer 6 150-153 cm reworked shell debris
Layer 7 153-170 cm black mud, single gravel clast at 161 cm
Layer 8 170-180 cm sand and oyster shell debris
Layer 9 180-545 cm black mud, single pebble clast at 222 cm, fragments of wood at 337 cm, detrital plant fragments at 405 cm
Layer 10 545 -560 cm black mud bound by plant roots (radiocarbon sample)
Layer 11 560-713 cm black to brown mud, wood fragment at 713 cm
Layer 12 713-746 cm brown mud bound with plant roots (radiocarbon sample)
Layer 13 746-800 cm interbedded layers of coarse sand and detrial plant fragments
Layer 14 800-816 cm yellow-brown mud

In fact, many coves found similar habitat history layers and similar to those described in the Holly Pond example above, excerpts include;

“Cores did contain sand layers, mollusk shells and the mud is often bound by the roots of marine grasses, probably Ruppia” pg 6.

And further core evidence of energy profiles – habitat reversals also on gray sand and gravel fascias “The gravel can be weakly cemented with gray mud. Shells of marine mollusks occur within this gravel in several cores and plant fragments of freshwater (marsh plants Scirpus) and or salt marsh plants (s.a hesniflora.s.patex) is interbedded with this unit.”

And also Jordan Cove, Waterford on pg 9 “In three cores, JC-2, 4 and 5 shell debris occurs stratigraphically above this transgressive sand. In cores JC-4 and 5, the shell debris is up to 40 cm thick and is predominantly oyster (ostrea) shells.” Jordan Cove has the thickest core layer of estuarine shell ever documented in Connecticut.

And also Holly Pond (Waterford) on Page 11 “The upper two meters of the core is punctuated with thin layers of sand and shell (fig 15). There are occasional isolated shells, usually oyster shells, and pieces of gravel and wood fragments. Some sections of the mud are bound together by fine roots that may be the remains of submerged aquatic vegetation for example in cove HP.3”

While coastal cove studies were finding pronounced shell layers in the other cove / core results in 1993 program, the Section 22 Army of Corps of Engineers Report (1994) includes the statement on the foreword on page 2 attributed to the DEP Office of Long Island Sound Programs that states:
“The key findings of Dr. Patton’s studies are summarized below: (This was a core study).
“No buried sand or shell deposits were observed and surface sand deposits were only found near the inlets to coves especially at Quiambaug and Munford Coves which lie adjacent to sandy beaches,” Forward page 2, 1994.

In my opinion, this statement does not accurately represent the research and data collected by Dr. Patton. This statement is incorrect as Dr. Patton did find sand and shell layers even in Quiambaug Cove itself (See figure 13 Quiambaug Core QC-03). In core samples taken on the east side of Quiambaug cove it would be hard not to find oyster shell. The site was once and an oyster culture site. A University of Connecticut Sea Grant Shellfish survey in 1987 of Quiambaug Cove (Tim Visel) found a dense oyster shell layer under about 20 to 30 centimeters of loose black organic material (Tim Visel Shellfish Survey Report July 21, 1988, Senator Spellman meeting Quiambaug Firehouse) . It is suspected that this was the remains of oyster bedding aquaculture grow out practices of the last century. This statement in the foreword did not include apparently all the core research completed before May 1994.

The above research findings also appear to be consistent with the survey of the Pattagansett River in 1990 (Auster DeGoursey -Visel et al published NSA abstract 1990 Annual meeting April 1-5, 1990) and to ongoing other core studies themselves (Patton 1993 in progress). The layers of sand gravel and shells indicate distinct habitat reversals, a habitat history, and core studies such as the above area were very important to our understanding about the loss of energy and increased energy habitat reversals over time. Important here would be the indexes of storm events (the Blizzard of 1888- the Portland Gale of 1898 or the Great New England Hurricane of 1938) as key indicator markers in previously collected core samples. The presence of scallop shells in the Holly Pond cores may represent a storm or the 1870s when western Long Island Sound habitats supported a very large Bay Scallop fishery during this colder and storm prevalent period.

Evidence of Changing Habitat Conditions – The Rise of Sapropel

In the 1980s, fishermen in eastern Connecticut felt that energy loss now blocked by railroad causeways) had caused habitat changes that were previous hard or firm. A firm shelly bottom ones containing bivalve shell had become soft or buried by soft plant materials. Winter flounder fishers described site specific “spots” that had changed and fishing then declined (Louis Bayer, personal communication 1987-8. Winter flounder fishers came forward to described fishing conditions during the NAO - a period cold and frequent storms. Mr. Flanklin Rich in 1988 recalled that back in 1961 you could catch a half bushel of flounder in one day at the core (Quiambaug) now you can’t even find one.” (The Day, Nov 10, 1988). In fact many of the cores taken in this extended study showed such historic shell layers under organic deposits. In some cases, cores showed multiple layers of estuarine shell and soft organics. A larger and more comprehensive habitat history review is warranted and a full review of the missing data for the 1993 cores of the Quiambaug Cove required. The core studies were not compared to Sapropel formation according to temperature nor the ability for oxygen reduced sediments to naturally concentrate metal salts and lower pH related to previous EPA research (Takak, Henry Hietal 2003) was known for many years before this study. The sulfur rich organic Sapropel were also acidic and now linked to bacterial necrosis of Winter flounder (fin and tail rot) during this period.

Fin Rot now Linked to Organic Sludge -

The appearance of large Winter flounder with at times large necrotic absences ulcers were brought to me while employed by the University of Connecticut. Between 1983 and 1988 dozens of Winter flounder (some frozen) were submitted for examination. I really did not understand at the time what was happening but some of the flounder had huge ulcers of oozing rotting flesh, and many questions regarding if such winter were still fit to consume. I advised no, not fully understanding the habitat reversal that was in full view – oysters were dying by the millions in the Madison, Clinton region 1985 (MSX) Winter flounder which needed cool water (sufficient oxygen) and clean shelly bottoms now found black sulfur rich material acidic and filled with bacteria reducing organic matter in high heat. A scratch on the flounder tail, it seemed yielded a bacterial infection which wasted away as an open wound. That is what fishers witnessed and reported. Many grotesquely deformed with necrotic lesions were brought to the UCONN Sea Grant Marine Advisory Service at this time.

As high heat drove juvenile flounder from the protection of shallow cores where they needed to be (low oxygen) they faced new predators such as Blue fish. I can recall personally catching some large Bluefish with a whole small Winter flounder in its cavity – my first reaction was what was these 3 to 4 inch long Winter flounder doing in offshore waters? The truth of the matter was the shallow water habitats which offered refuge from such predators had become itself a toxic deadly environment. Sapropel soon covered previous alkaline bottoms – those that still contained estuarine shell, lowering pH and sustaining sulfur reducing bacteria. Sulfide gases (rotten egg smell) were a sign of a complete Winter flounder “habitat failure” for these shallow coves. When the shallow predator free areas failed small Winter flounder died by the millions as they had a century ago during the Great Heat. A Winter flounder fishery “failure” soon followed the habitat failure. Those Winter flounder that could fled these areas. Although fishers were often blamed for the fishery failure (See footnote*) that also was incorrect – fishers were not responsible for the regional declining habitat quality for Winter flounder. Winter flounder prefer colder and clean bay bottoms containing oyster shell and mostly Sapropel free. Fishers were not responsible for the high heat or the huge increase in leaves that enhanced Sapropel formation called black mayonnaise during this period. Colder temperatures and storms that reverse shallow coastal habitats– as signified by shell layers in more coves are beyond the ability of fishers to control – those habitat changes are largely natural. The fishery failure occurred as temperatures exceeded thermal lethal limits in nursery habitats. “Bridge fishing” for Winter flounder held the last viable Winter flounder habitats in eastern CT as tidal restrictions increased water flows clearing organics.

As Connecticut’s climate changed from the cooler and stormier 1950s and 1960s habitat types also changed. The 1950s habitats firm and often shelly became softer and contained luxuriant growths of macro algae such as sea lettuce and eelgrass in the 1980s and fishers reported this change.12 This change was not only in Connecticut but fishers across southern New England were experiencing habitat similar impacts (Jim Turek, NOAA Office Restoration, personal communication 2011).

At first glance the observations of eastern Connecticut Winter flounder fishers where shown to be proved correct but not accurately presented in the Army Corps of Engineers Section 22 report titled “Wetland Investigations.

In Connecticut coves past core research Indicates a “Habitat History” – several reversals of habitat types. This information is helpful to the climate change habitat health debate of modern times. What constitutes natural or cyclic habitat quality loss as compared to causes assigned to human coastal activity? {Capstone project questions}

The significance of these coastal cores, shell layers and habitat observations of fishers in the 1980s were to be discussed in the next newsletter – “The Role of Marine Habitat Succession to Estuarine Species Abundance.”

Anyone interested in a short review of the Climate Pattern (NAO) North Atlantic Oscillation that directly affects habitat and therefore Connecticut’s shell and fin fisheries see The Search for Megalops-The rise of Blue Crabs Special Report #1, January 2014, available from Sue Weber at susan.weber@new-haven.k12.ct.us or can be obtained or accessed on the Adult Education and Outreach directory by accessing the Sound School website: www.soundschool.com/publications%201.html.
Anyone wishing a copy of this article including footnotes, please contact susan.weber@nhboe.net

For information about The Sound School website, publications, and / or alumni contacts, please contact Taylor Samuels at taylor.samuels@new-haven.k12.ct.us

The Sound School is a Regional High School Agriculture Science and Technology Center enrolling students from 23 participating Connecticut communities.

Program reports are available upon request. For more information about New Haven Environmental Monitoring Initiative for IMEP reports, please contact Susan Weber, The Sound School Adult Education and Outreach Program Coordinator, at susan.weber@nhboe.net