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PostPosted: Wed Jul 19, 2017 11:24 am    Post subject: Eels, Eelgrass & The Bay Scallop Fisheries 1880- 2000 #6 Reply with quote

IMEP #61-A Habitat Information for Fishers and Fishery
Area Managers
Understanding Science Through History
(IMEP History Newsletters can be found indexed by date – Title on the BlueCrab.info™ website: Fishing, Eeling and Oystering thread)
The Sound School ISSP – Capstone Series
Do Climate Factors Lead to Habitat Failures?

Vibrio Bacterial Series in Eelgrass/Sapropel
- A Multidiscipline Approach – for Several Capstone Questions

Timothy C. Visel, Coordinator
The Sound School Regional Vocational Aquaculture Center
60 South Water Street
New Haven, CT 06519
Revised for Capstone/SAE Proposals, March 2017
ASTE Standards Aquaculture #6 Natural Resources #6, #7, #9
This is a two part report readers should review IMEP #61- B
available in April 2017

(This report reflects the viewpoint of Tim Visel. On February 8, 2016 and on February 8, 2017 I asked our EPA habitat committee of the Long Island Sound Study to identify sapropel as a district habitat type. No consensus has been reached as to the existence of sapropel. This is not the viewpoint of the EPA Long Island Sound Study.)

Preface – How Eelgrass Got Its Name

Very recently I watched three presentations (Long Island Sound Study, EPA habitat meeting) about the habitat services of eelgrass Zostera marina in New England waters. All three presentations provided much information about mapping and changes in relative percentages of habitat coverages, and the appearance of new eelgrass growths and also areas where eelgrass was declining. I waited to hear information about marine soils, temperature or soil porosity and changes from energy (storms). That aspect of eelgrass habitat quality – the foundation of plant growth in soil was not mentioned. Some areas planted with eelgrass had quickly washed away; others did not hold on for long while others seemed to flourish. Explanations for these differences remained the usual -- human pollution, coastal development, shading from docks/piers, dredging, silt from land and poor watershed management practices. None of them mentioned subtidal soil conditions or the impacts of temperature nor energy (chemical) impacts to these marine soils. I waited, but these important habitat conditions were not mentioned. Upon some later questioning, it became apparent that the name itself was somewhat perplexing: eelgrass, and its presence in shallow water locations and at times dense growths offshore in deeper waters. A year ago, a similar discussion revolved around sand eels –Ammodytes americanus as perhaps the name (sand eels do inhabit eelgrass in deeper areas) eelgrass came from them. However, anyone who has looked at the historic inshore fisheries literature will come to recognize that “eelgrass” got its name from a habitat association to the American eel, Anquilla rostrata in shallow waters subject to a hand held spear fishery in winter. This eel fishery was conducted in shallow water covered at times by ice, over “eelgrass.”

So many habitats are named for the species found in abundance continued from Colonial times to today. Such terms as “Herring Gut,” “Alewife Cove,” “Oyster Pond,” etc. provides clues to the previous fisheries. Some of the historic literature from Cape Cod can be traced to “eel ponds” such as the one behind the “Woods Hole” Oceanographic Institution in Falmouth, Massachusetts. Eel Ponds on the Cape were good places to spear “eels”, even historically the bottoms then could contain eelgrass/Sapropel – what fishers call today “Black Mayonnaise” – a Sapropel with a vegetation cover plant, this is often eelgrass.

A Massachusetts Cape Cod study by Curley, J.R., R.P. Lawton and J.M. Hickey and J.D. Fiske, titled, “A Study of the Marine Resources of the Waquoit Bay- Eel Pond Estuary,” Commonwealth of Massachusetts, Division of Marine Fisheries Monograph Series #9, 40 pages, 1967, provides some important habitat references of eels: The connection of course “Eel Pond” a reference to eel fisheries of long ago. Page 23 gives reference to the name:

“The American eel is the only finfish species harvested commercially in the Waquoit Bay – Eel Pond estuary. Fishing is done through the ice with spears during winter and with eel pots during the warmer months. Fishermen harvested 1,000 pounds, valued at $200 in 1967.”

In areas without eelgrass, the Sapropels can become very hot in summer and drive fish from them. Researchers at the Belle Glade, Florida Peat Experiment Station found that black peat, stripped of its vegetation cover in direct sun could reach 130 degrees F. This heat sink would also influence biochemistry of eelgrass meadows stressing plants and creating very hot areas that held little to no fish (observations of Buttermilk Bay shellfish survey, Cape Cod, Tim Visel 1982). These areas of shallow water – and poorly flushed could see the first buildup of black mayonnaise – that has occurred here at Eel Pond in recent times and linked the buildup to tidal circulation. This is a section from a recent 2000 report regarding Eel Pond of Mattapoisett, A Massachusetts Restoration Project:

“Eel Pond has also been long closed to shellfishing due to elevated fecal coliform levels from various sources. However, few shellfish grow there because the excessive inputs of nitrogen have contributed to large areas of the salt pond having thick layers of fine anoxic mud that has the appearance of black mayonnaise. Shellfish cannot survive in these kinds of habitats.”

So much of the habitat services of “eelgrass” come from its long association to eels and is the foundation of understanding some of the basic biochemical interactions of eelgrass peat in shallow water estuaries. The biochemistry of Sapropel/eelgrass peat has been absent in many eelgrass habitat papers. It is also directly related to how eelgrass it got its name.

Eelgrass and the Great Heat – 1890s Heat Waves and Cold Winters

During the 1880-1920 period in Southern New England, the eel fishery flourished. In cold, after ice formation salt ponds and in shallow rivers, eeling with spears was a productive winter fishery. Although the term spear is used, they were for the most part different from winter flounder spears, which were designed to penetrate flesh, eel spears would pinch eels with a paddle shaped tine or blade rather than a barb, some spears looked like several flattened spoons. These spears were pushed until resistance, and then pushed hard. Eels would form balls or “nests” of eels tightly packed into eelgrass peat, the root tissue itself – creating burrows under the root tissue mass – the spears were not designed to penetrate the eelgrass deeply just the surface top layer which held those eels in sapropel. During winter sapropel seeped sulfides or toxic chemicals into seawater an “odor” that warned potential predators to keep clear. In these little or no oxygen organic deposits were perfect for eels, a soft, juicy, prey species they lacked little protection from hungry predators, except they could live in this sulfide rich “smelly compost” while other species could not. The biology of eels gave them an unusual second advantage – eels can absorb a large percentage of its respiratory oxygen through its skin, not gills. (Why they can live if kept moist so long out of water). This feature called a “cutaneous respiratory pathway” also exists in the bottom tail skin of winter flounder, also giving them an edge in summer heats absorbing oxygen from bottom groundwater as tides ebbed, then allowing groundwater to seep up past sand bars.

Eels coiling or nesting under the surface of edge of eelgrass also benefited from oxygen loss from eelgrass root tissue itself. To keep a layer of oxygen bacteria alive and to protect its root tissue from sulfides/sulfuric acids eelgrass roots “leak” oxygen into the sapropel- a life support function to keep a root shield of oxygen bacteria alive. Thus, eels in the roots benefited even more from an eelgrass/oxygen life support system; they could live/hibernate in eelgrass (peat) meadows. Eels also had a shield mechanism that protected their skin from sulfur and humic acids and the dangerous vibrio bacteria living under eelgrass by the way of producing copious amounts of mucus. [Winter flounder often fell victim to the vibrio bacteria winter fin rot in estuaries during the 1980s from a small scratch or cut – under the tail meat where mucus coverings were thin. In the 1980s as water temperatures increased, sapropel Vibrio bacterial containing deposits also increased. (Donald Rhoads personal communication, Tim Visel, 1982) and was the infection site for Vibrio often described as a flesh wasting “necrotis.” Most of the bacterial shellfish and finfish diseases are now associated with the Vibrio bacteria series, which in heat survive in eelgrass peat that has sealed organic deposits below from oxygen. In time, these deposits become Sapropel. (Researchers are finding Vibrio bacteria living below eelgrass across the globe).

It is the mucus and cutaneous respiratory pathway that allowed eels to live over the winter in eelgrass peat. When eel spear fishers headed out, they sought out the grass that contained eels hibernating – we know this species as Zostera marina or “eelgrass.”

Eel Fisheries

Historically the community with one of the largest New England eel fisheries was Edgartown on Martha’s Vineyard, Massachusetts. The 1887 U.S. Fish Commission report lists Edgartown producing over 60 thousand pounds of eels (no doubt related to its salt ponds) (See Eels, 66,000 lbs. The District of Edgartown, Pg. 258-259). The same report mentions the damage to earthen dikes (most likely for Cranberry bogs) as the eel burrows weakened them requiring thin sheets of tin to protect them “U.S. Commission of Fish & Fisheries, The Geographical Review of the Fisheries, Section II, 1887.” The Fisheries of Plymouth, MA, pg. 222, “Eels were formerly so plenty as to do much damage to the dam, which had to be sheathed with tin in many cases.”

When eel fishers sought them out to spear in winter (almost always requiring a hole cut into the ice), they went to eelgrass in shallow water, sometimes using a stake or float to mark locations but most of the time, just memory. Here at low tides a 14’ or 16’ handle would suffice, a few plunges, the eel spear would be taken out and examined, a few pieces of live eelgrass was a good sign, a black sticky deposit (frequently called black mayonnaise today) that smelled of sulfur were denoted as “dead bottoms” those so sulfide rich they supported little oxygen requiring life – were not. (John Hammond account - Oyster Pond Eel Fishing, Chatham Massachusetts, T. Visel, 1982). These areas were avoided and most likely were sapropel or on the verge of becoming sapropel.

To eliminate cutting holes in areas of deep muck sapropel that had no eels, the “eel grass” growths became the habitat location of first choice for winter eelers and the name stuck. That is why today it is known as “eelgrass.” This grass held eels.

Eelgrass Habitat Succession

Eelgrass, over time, forms a dense mass of root tissue and peat, which then becomes subject to the bacterial “war” between bacteria strains in the soil below. In cold and after storms, eelgrass moves into sandy soils. In time and in the upper reaches of estuaries, it traps organic matter and the elevation of these “meadows” rise over time, building a peat and seals from oxygen, the organic matter below. When disturbed, the strong smell of sulfur is a sign that sulfur sulfate-reducing bacteria are already below and a clear signal to fisheries that these areas “held little life” or was an area that had “dead bottoms.” Shellfishers could determine the edges of dead bottoms quickly by examining the soil, its consistency and odor. These areas did not hold eels or sustained shellfish and thus avoided.

In heat, this eelgrass peat fostered the production of ammonia, and in cold, the production of toxic sulfides. The bottoms that held few fish or shellfish and once disturbed shed sulfides, a kind of poisonous smoke that sent a scent into the water column. Here next to dead bottoms that produced sulfides the first sapropel formed in or near eelgrass and when New England fishers went to spear eels in deep holes or cut a hole in the ice they did so over “eelgrass” and also near black muck called the “dead bottoms.” This is a 1920 account from “The American Angler” – pg. 498 (my insertions in brackets T. Visel), that describes an eeling trip and the habitat conditions associated with this fishery in a magazine article by Will R. McDowell:

“The eels on the close approach of winter had worked their way up the creeks and marshes, and with the making of the first icy nights (usually late October – early November – T. Visel) they had squirmed (usually form a group or ball of eels, T. Visel) and literally buried themselves body and soul in the soft mud bottom. I soon found that eels were not everywhere on the bottom for to simply put one’s spear down and haul them forth. For it seems Mr. eel is particular, if not quite fastidious as to the certain kind of muddy bottom he buries himself in for the winter months. In fact, he does not seem to like soft and deep, black sticky mud (now thought to be toxic sapropel T. Visel). On the contrary he will generally prefer what is known in fishermen parlance as clean, or “live mud bottom.” It seemed this clean or live bottom is to be found near or along the edges of the channel, and while soft mud, its constituted or rather a firm mud, and is apt to have patches or a scattering of eelgrass growing on it. In such eelgrass bottom, where the ebb and flood of tide sweeps over it, the eel delights to bury or bed, and there while in a state of semi hibernation he waxes fat and sleek the winter long while snow and ice deeply out the surface of the waters above him” (The American Angler, Vol. 5, 1920, Pg. 498-500 “We Go’s A-Eelin” Through the Ice for the Slippery One).

In high heat, even the eels avoided sapropel; this is the “dead bottoms” that are mentioned many times in the historical fisheries literature and followed the cycle of eelgrass growths. In time, the habitat successional aspects of eelgrass to gather organic matter in heat helps form sapropel. When that happens, the bottoms become “dead” to fish, shellfish and in time even to eelgrass.

What About the North Atlantic Oscillation and our Fisheries – Climate Prediction Center NOAA
Climate Cycles and Water Quality Research for Capstones
Timothy C. Visel
February 1, 2017 The Sound School
The Concept of Marine Habitat Succession for Vegetation

The presentation of climate cycles and habitat quality change is an historical viewpoint of past changes. A quick review also finds that shallow water habitats have an important role in seafood production, yet so little has been accomplished in terms of habitat succession. Shell fishers and especially blue crabbers see these habitats succeed or change over time and one of the most recorded in habitat history is the bottom consistency and vegetation cover. They often observe these changes of cycles first as they fish in the shallowest of waters those 20 feet deep or less. Change the salinity and temperature, and sea grasses change - periods of no storms followed by constant energy and the bottom itself changes. Periods of drought allow saline waters to flow deeper into estuaries, and heavy rains drive that saltwater wedge out; all of these factors can and do change water quality. Perhaps one of the best historical reviews we have is the Back Bay Currituck Sound Data Report (Bureau of Sport Fisheries and Wildlife, 1958-1964). For nearly a century, duck hunters, fishers, and shellfishers reported on different bottom changes in vegetation, unusual smells, changes in color “purple” or “chocolate” waters, brown waters and brown tides. Many of these observations have a temperature and energy barrier beach/spit (tidal flushing) connection. When barrier spits widen or breach habitats can change very quickly.

Most often, in the most recent habitat literature the explanation for those changes was an unnatural one – pollution, resource overuse or human caused bottom disturbance. Most often historically, the rises and then falls of seafood were not caused by us, but rather by cyclical water quality/climate changes influenced by long-term climate patterns. Today this cyclic pattern is called the North Atlantic Oscillation or “NAO.” I recall many workshops in the late 1970s and 1980s in which small boat fishers would speak of sudden increases and then decreases in fish and shellfish, changes in the bottom and most often changes in the bottom vegetation over time (1960s) from firm shelly sand to soft vegetation cover a black ooze and a marine compost in low oxygen conditions, a form of sapropel (1980s).

The Waquoit Bay – Eel Pond Estuary Monograph series number 9 report (as in many Massachusetts estuarine bulletins had until 1972) has a section on eelgrass (pg 34) and other sub tidal marine vegetation – called “SAV” or submerged aquatic vegetation today. The rise and fall of marine plants also has a climate cycle/succession pattern that had habitat impacts upon shellfish – as found in this report.

Eelgrass (Zostera marina)

“Many flats below mean low water covered with eelgrass, a flowering marine plant. Leaves of this plant are ribbon like and grow to five to eight feet in length. Eelgrass spreads by sending out runners and by seeds which are produced through the pollination of underwater flowers. Eelgrass provides habitat for many forms of marine biota.

In the 1930’s the disappearance of eelgrass, which provided pasturage, protection, and spawning habitat, was disastrous for many marine species, including bay scallops, periwinkles, blue claw crabs, hermit crabs and waterfowl (Yonge, 1949; Hay and Farb, 1966). As eelgrass declined, its stabilizing effect on sands and sediments was lost and many oyster and clam beds in Massachusetts were silted (Hay and Farb, op cit.). The loss of this plant also affected many of man’s other activities. Early Cape Codders used massive amounts of this grass as house insulation, bedding for livestock, sound proofing, mattress and furniture filler, and mulch for gardens (Yonge, 1949; Hay and Farb, 1966.)

Reasons for the decline of eelgrass have not been definitely established. According to Milne and Milne (1951), a parasitic fungus, the slime mold, Labyrinthula sp., became virulent and destroyed populations of eelgrass along the Atlantic coast in 1931. Labyrinthula has since been studied as the possible causative agent of wasting disease. Dawson’s (1966) account of wasting disease states that some biologists claim other fungi and bacteria are the primary casual agents, and Labyrinthula is a secondary invader of weakened plants. Although eelgrass populations are recovering, the problem is still not completely resolved. Labyrinthula is abundant and widespread (Dawson, 1966).

While eelgrass in moderate density is beneficial, an over abundance may be a problem. Excessive growth in Waquoit Bay is hampering the harvesting of shellfish, swimming and boat navigation.”

Cladophora – (and in addition includes reference to this S.A.V. a highly branched green algae).

“Cladophora sp. is a macroscopic branching green algae which grows in saline or brackish waters. It is found attached to the substrate, resting near the bottom or floating on the surface. In Waquoit Bay during the summers of 1967 and 1968, this species was a nuisance, occurring in unsightly mats and producing an unpleasant odor. A soft-shell clam flat at the mouth of the Quashnet River was nearly eliminated because of the density of this species. There is no practical method of controlling this algae at the present time.”

Shellfishers from Connecticut to Cape Cod watched as eelgrass transformed thousands of acres of washed/cultivated marine soils following the Hurricane of 1938, followed by a series of hurricanes in the 1950s, 1960s. In coves and bays eelgrass soon moved into these cultivated marine soils that now held enormous sets of the hard clam Mercenaria – mercenaria. While eelgrass habitat services could help shellfish, its edges slowed water allowing shellfish veligers a chance to set, clean blades held seed bay scallops, and in general stabilized marine soils (which terrestrial grasses do as well) in time gathering organics changed the appearance and chemistry of bay bottoms. For decades shellfishers and shellfish biologists noted this change as eelgrass moved from isolated patches to “carpets” it suffocated hard and soft shell clams, restricted tidal circulation (starving bay scallops) and changed the chemistry of marine soils. In a short time eelgrass moved from a nuisance (eelgrass would fill rakes and tongs) to an enemy that took no prisoners (John Hammond comment to T. Visel Chatham, MA 1982).

Shellfish biologists and shellfish managers could not ignore the consequences of eelgrass meadows and an except from a Massachusetts Study of Westport River in 1963 this period is when eelgrass was dominating inshore habitat types sums up precisely the situation of inshore shellfishers, this is a section of the report.

A Study of the Marine Resources of the Westport River is the seventh in a series of monographs initiated by the Division of Marine Fisheries in 1963. These reports relate the extent and value of the marine resources of the major bays and estuaries in Massachusetts. (page 32).

“The major factor limiting quahog abundance seems to be lack of favorable bottom. During the past decade eelgrass has been rapidly spreading on bottom areas which were formerly productive in quahogs. Quahogs sampled in eelgrass areas have reflected poor growth suggesting that the dense eelgrass interferes with circulation and food supply to the quahog. Soft bottom and dense eelgrass is especially obvious in the west branch of the river.

On September 23, 1966 biologists made a survey of scallops occurring on an extensive shallow eelgrass flat in the west branch of the river. This sampling occurred about one week before the opening of the scallop fishing season. The “eyes” were notably small and not of commercial quality. Because of the small size of the scallops and the density of eelgrass in the area which hampers dredging, fishing during the scallop season was confined to the deeper areas further downstream in the estuary. (page 31)


Below mean low water, eelgrass (Zostera marina) is the most prevalent vascular plant growing in the Westport River. In recent years eelgrass has been rapidly spreading in the Westport River just as it has in other protected bays and estuaries of Southern Massachusetts. In moderate density, eelgrass is beneficial to many forms of marine animals.

Detriment to shellfisheries also occurs when dead eelgrass accumulates in dense mats and smothers beds of shellfish. (page 44).

Because of the increasing growth of eelgrass on shellfish beds, considerable research is presently being conducted to find an effective method of control. To date, no attempted methods have proven themselves completely practical. One town on the south shore of Massachusetts has attempted to cut eelgrass with an underwater mower designed for cutting submerged vegetation. At best, this method is only temporary since the plan stalk is cut off above the substrate surface leaving the stems and roots to produce new growth. Experimentation by various agencies with herbicides is presently being conducted. While certain chemicals such as 2, 4-D have effectively destroyed eelgrass, the toxicity of the chemicals to associated fauna is not clearly known.”

The largest habitat factor not understood at that time (except by the shellfishers) was the impact of the sulfur cycle to these marine soils. As the soil changed to reflect the sulfur cycle they became toxic to sea life that needed oxygen. A lack of soil circulation (soil porosity) and heat could assist the sulfur cycle transition these soils helped by dense growths of eelgrass. By the time sapropel could form under eelgrass as the shellfish had long since died. As sapropel itself changed the biochemistry in heat it now weakened eelgrass that it also perished from fungal and bacterial attach called sulfate reducing bacteria that caused sulfuric acid to kill its roots in a climate cycle that is the foundation of the US Fish and Wildlife Service’s term the “wasting disease.”

Climate Cycles Influence Bacterial Nitrogen Levels
Marine Soils and Bacteria

The scientific community has largely omitted the concept of a living marine compost, instead continuing to use the term sediment or black facies, which broadly interpreted are minerals and grit washed from land into the water. However, included in sediment is organic matter with hard- to-digest sugars bound up in cellulose molecules in dead plant matter. The remains of grass, bark, and leaves swept into estuaries now rots and forms a compost – and in low oxygen/high temperatures – a deadly one to inshore fish and shell fish species. It is alive as much as any terrestrial soil with sulfate reducing bacteria (SRB), which changes the habitat quality in many ways. Although the term sapropel has not been formally or fully accepted by the United States scientific community, it does describe a biological/chemical aspect of living bacterial change. It describes a biological/chemical process largely omitted from many estuary studies, organic matter putrification and a direct connection to the sulfur cycle. In fact, many shellfishers have never heard the term sapropel, or been offered an adequate explanation of these sulfur bacterial groups. Decades and even centuries ago, researchers studied the bacterial growths under terrestrial grass, in fact promoted “harvesting” the soil beneath them as a valuable bacterial growth media for those soils that had few bacteria. Dr. Holmer J. Wheeler (1911), once President of the University of Rhode Island, published agricultural articles on soil inoculation of bacteria to soils to assist plant growth. In these articles he promoted the harvesting of soil rich bacteria under grass as a soil “innoculant.”

Selman Waksman (1940), a microbiologist at Rutgers University, researched the dumping of horse manure on top of peat and monitored the change in bacterial populations. In broad terms, the sulfur bacteria went to battle with the oxygen bacteria, the byproducts of Dr. Selman’s bacteria research we know today as the term antibiotic, and its bacterial weapon streptomycin. His employer Merck released the streptomycin patent to Rutgers University, which funded an entire institute called the Waksman Institute of Microbiology today. Other agriculture researchers, dating all the way back to Thomas Green Clemson, benefactor of Clemson University, wrote about the sulfur cycle and bacterial composting in 1862.

Climate Cycles Determine Habitat Succession – Disease Presence

Now, as more research becomes available (mostly from overseas), we are learning more about marine sapropel and the sulfur cycle. I was first made aware of the disease association of it from Edward Wong of the Environmental Protection Agency (1979-81). He arranged for me to participate in an early 1980s shellfish survey of Mumford Cove, Groton, CT. It is a small cove in a restricted tidal exchange area that was subject to a sewer outfall, and as the temperature increased, the sulfur smells in summer became strong, a sign of sulfate reduction by sulfur bacteria. Sulfate reduction is a slow organic reduction process and in heat, poor tidal flushing low dissolved oxygen organics tend to build up on the bottom. Any organics, sewage sludge, manure and leaves accumulate and rotted in “leaky dam” effect. Organic debris in these areas tended to settle out. Coastal dams suffer from being at the end of a large organic natural “pipe” a stream, brook or river delivering an organic paste of fall leaves and forest organics to them. Mumford Cove in 1980 was filled with black mayonnaise (black facies or black mumie – and called numerous other terms), which in heat (low oxygen conditions) forms a sapropel while emitting sulfides. This is the sulfide smells in late August reported by cove residents. Some core studies were done then in the cove in the center of this black sticky organic compost and researchers found viable red tide cysts up to two meters below the surface. How did these red tide cysts end up deep in these sapropel accumulations and how could they be sealed from oxygen and still be classified as alive? To answer these habitat questions, we may need to rely on the peat researchers of the last century to provide accurate answers to the eelgrass habitat services of eelgrass, a form of subtidal peat and its life cycle, past climate cycles of heat and cold, energy storms, and the lack of energy or “quiet periods” that fully describes bacterial responses and the build up of organic matter on the bottom. (Note – Mumford Cove continues to have a ban on hydraulic harvesting. “In order to prevent the re-suspension of cysts of HAB causing organisms*.” When I asked Dr. Wong about these cysts he mentioned that climate conditions long ago left cysts deep in this material.

State of Connecticut Department of Agriculture – Bureau of Aquaculture and Laboratory Protocol for Hazardous Algal Blooms/Marine Biotoxin Events State of Connecticut Department of Agriculture Bureau of Aquaculture effective date 2/23/11.

Some natural tidal barriers such as barrier spits act as manmade tidal restrictions; they tend to both speed up and slow habitat transitions. This fact makes inshore shallow areas that heat up and cold down faster, ideal candidates for estuarine habitat succession study, a combined interdisciplinary approach of “Ocean Science,” such as the one proposed for eelgrass peat which often forms over sapropel. More recent research has identified eelgrass peat as areas of Vibrio bacteria growths, some of which are pathogenic and include the lobster shell disease Vibrio, chitinolytic species the Vibrio anguillarum found in winter flounder fin rot, Vibrio vulnificus species that impacts the shellfish industry and most recently habitat refugia for the human pathogens Vibrio cholera. It is now thought the cholera oyster outbreaks in the 1920s were the result of sapropel build ups during the very hot 1890s. This was also a period of immense eelgrass growth and habitat coverage. Researchers in more southern climates are identifying dozens of Vibrio strains beneath submerged aquatic vegetation – termed SAV.

Students interested in this research project or in any of the Capstone questions 1 to 5 should contact Tim Visel in the Aquaculture office.

Student investigations of a multi disciplinary approach involving the fields of Soil Science, Natural Science, Fisheries Biology, Fisheries History, Marine Biology, Plant Science and Meteorology to determine the natural cycles of eelgrass Zostera marina abundance and relationship to the bay scallop Argopecten irradians in New England.

Capstone Questions – five primary research areas -

Geology, Meteorology, Soil Science, Botany and Marine Pathology. Students interested in participating in this study or Capstone questions 1 to 5 please see Tim Visel in the Aquaculture Office.

1) Complete descriptions of marine eelgrass peat – (Botany)
Tidal – Salt Marsh Peat – bacterial Processes heat/cold
Subtidal – Eelgrass Peat bacterial processes heat/cold
Florida Peat Experiment Station Research – Belle Grade Florida (1925)

2) Climate Impacts Upon the Bay Scallop Fishery (energy and temperature) Meteorology, Eelgrass habitat services – energy and temperature parameters
Marine soils – succession – energy and temperature parameters
The Northeast Atlantic Oscillation – NOAA Climate Prediction Center

3) Sapropel – Acid Sulfate Soil – (Soil Science)
Three layers – mapping and identification, humic, (fibric) sapric and formic layers
Sapropel Diseases, MSX – Littorina in blood fluke outbreaks, Red Tide, HAB Cysts
Sulfuric Acid activation historic accounts of Sapropel (mussel mud) fertilizer use, sulfide formation

4) Soil Bacteria – Selmon Waksman Rutgers Experiment Station (Marine Pathology)
Vibrio impacts in heat – antibiotics – relationships between organic matter and bacterial richness.
SRB Sulfate reducing bacteria and ammonia generation.
Eelgrass reservoirs for Vibrio bacteria – lobster shell disease and winter flounder fin rot Vibrio in the Indian River Lagoon (also Tampa Bay Florida). Shellfish industry concerns regarding Vibrio.

5) Coastal Processes – Barrier Spit and Inlet openings - Geology
The Niantic “Bar” Weselyan University Core Studies of Connecticut in the 1990’s.
Has core studies in Connecticut and southern Rhode Island left a habitat history – Hurricane varves layers and coastal energy pathway (Rhode Island Study).

To more fully understand the edge of the sea we need to look at all the sciences that impact it. For far too long we have failed to combine the disciplines in a holistic view of coastal processes. Instead much of the natural resources focus the past century has revolved around our interactions, first as utilization, then exploitation, conservation and now protection. Regulatory protection often minimizes natural conditions while maximizes human impacts. It often gives a false security that regulations alone can stop marine habitat succession – it cannot do so – my view Tim Visel.

Belding’s Comments on Eelgrass Habitat Impacts to Shellfish

Dr. David Belding provides an important look at the habitat services of eelgrass at times positive, small patches to provide current modification/setting of veligers and places of attachment. This is usually the first stage of eelgrass growths, patches with edges. It is the edge that provides similar reef surfaces in cold oxygen rich waters – the bright clean and green eelgrass. However in time dense growths of eelgrass became negative, it smothers clam and oysters, and slow currents restricting currents carrying food for bay scallops. At the end of a warm period then coastal storm energy declines and temperatures rise its services can turn negative as it did at the turn of century at the time Dr. Belding was conducting his studies, and his report on the scallop fisheries (1920) contains these negative observations in Massachusetts a century ago.

Dr. David Belding comments about eelgrass (when eelgrass was at its habitat dominance in 1910 – 1915) Bay Scallops – The Scallop Fishery of Massachusetts 1920.

“As shown by the channel versus eelgrass (shallow water) scallop, the greater growth occurs in the deep waters; but as has been stated, this is essentially due to better circulation in the channel pg 92. “By a comparison between growth on clear sand bottom and in thick eelgrass, where other conditions were approximately the same, the scallops on the clear bottom show a greater rapidity of growth than those within the grass” pg 91. “Eelgrass versus channel scallops (depths up to 60 feet) in observing the catch from the scallop beds, it was recorded that the larger scallops always came from the deep water or channel, while the smaller were taken in the eelgrass or shallow water” pg 89. “Scallops can arbitrarily be separated into two classes (1). The channel or deep water scallops, found in water or eelgrass variety, from low water mark to 15 feet. The natural barrier to the distribution of the scallop is the exposed nature of the coast, as this mollusk cannot live in rough waters” pg 13.

Shallow flats covered with thick eelgrass are usually the most productive of heavy ‘sets” although the exposed nature of these flats during the winter often causes a severe mortality among the young scallops.” Pg 51.

New beds (scallops) seem to spring up when the eelgrass is rolled away, but the scallops probably have been there always, or have been carried a short distance by either, wind or tide” pg 63.

Eelgrass from its abundance proves the most common place of attachment, but is often detrimental to growth by shutting of the circulation of water – in comparing the growth of small scallops in eelgrass and outside, the eelgrass scallops show a slower growth” pg 84.

The third office of the current is purely sanitary one. It sweeps away the decaying vegetable matter so destructive to scallops situated in eelgrass (and all other poisonous debris) which would otherwise kill the scallops by contamination or at all events would check their growth pg 88.

The shallow water scallops are much smaller, usually proportionately thicker, and have not the large “eye” and fine appearance (Clean shells T. Visel) of the channel scallops, which are preferred by the bay scallops “ pg 89. This difference held true to such an extent that the scallop fishermen could tell by the appearance of the scallop from what section of the bed it came from, pg 89.

“While the adult scallop is little affected by the native of the soil, the young scallop would soon perish in soft mud were it not attached to eelgrass” pg 91.

In the case of the large channel scallop, the soil is either sand, gravel, hard mud shells but with little eelgrass” pg 91.

The soil indirectly affects the growth of the scallop by the production of eelgrass, which is found in more or less abundance on the scallop beds – pg 92.

This ability of eelgrass to stop or slow water currents is frequently mentioned in the fisheries history and as a result scallops growing poorly in it, having low meat weights or not growing at all. When eelgrass moved beyond isolated patches in sandy soils but formed extensive meadows eelgrass in heat it became deadly.

The simple fact was in upper reaches of bays and coves habitats had succeeded from those bay scallops preferred the lack of storms and the build-up of eelgrass/sapropel (peat) was however noticed by local shellfishers. Corraline red algae have been found to contain scallop setting and spawning chemical compounds now associated with corraline species worldwide (Maerl rhodoliths), and eelgrass is being reported to favor blue crab and green crab megalops sets, green crabs thrive in eelgrass and eats small bay scallops. In waters with sufficient oxygen eelgrass is an extremely important blue crab megalops habitat as well.

Historical reports of the bay scallop fishery rarely compared long term marine habitat succession processes. But in actual fact these shallow warm areas contained less nitrate/algae but as temperature warms – contains “brown” algal species which were not nutritious for shellfish. Ammonia now purged from eelgrass below, its “plant” cover from sulfate reducing bacteria that now began to dominate the bacterial spectrum in the organic matter. The organics below the eelgrass peat rotted in the lack of oxygen called putrification. Homer Jay Wheeler once University of Rhode Island President (1912) wrote about this process in 1911.

Dr. Wheeler (Agriculture Experiment Station of The University of Rhode Island) as other agricultural researchers at the turn of the century had discovered that those soils stabilized by grass covering humus (humic layers) was rich in bacteria as compared to bare ground (low humus) or those soils burned by forest fires termed carbon or forest soils. Farmers for centuries had burned fields to release carbon for increased plant growth. These fires for grasslands and meadows stimulated plants’ next growing season. Soil inoculation, as described by Wheeler [Proceedings of the Farmers Institute – Rhode Island, State Board of Agriculture, March 1-2, 1911, Pg. 10], was the stripping of plant cover to harvest the soil below rich in nitrogen-fixing oxygen bacteria needed for the transfer of nitrogen to plant root tissue, which could increase crop harvest value (Wheeler, 1911, pg.10). {My comments in brackets T. Visel}.

“This is not only of importance on account of possibly influencing the actual yield, but also on account of the fact that a well inoculated soil is likely to produce alfalfa containing a higher percentage of nitrogen than a soil in which the specific organism [Bacteria, T. Visel] renders possible the assimilation of atmospheric nitrogen is absent [Forest/burned soils, T. Visel] or but sparingly present [Sandy, low humus-containing soils, T. Visel].” Dr. Wheeler describes the process further as alfalfa root nodules were rich in bacteria surrounding them. “For the purpose of inoculating soils for the culture of alfalfa, one may employ a soil where alfalfa plants, bearing root nodules, are growing, or one where similar plants of the tall white garden clover, (Mellelotus alba) are to be found. From 200-500 pounds of such soil are required to inoculate an acre of land and the larger amount is of course preferable.”

Dr. Wheeler also describes the impact upon ultraviolet light sterilization (killing off of bacteria) that the plant cover shields the bacteria living in the soil bacteria matter (1911 Report, Pg. 10-11) [Ultraviolet light is the basis of residential pool sterilizers, today, T. Visel]. “In doing this, one should remember that direct exposure to the sunlight (Ultraviolet light, T. Visel) will greatly injur or even over time destroy these organisms (Bacteria, T. Visel) if the soil used for inoculation is left on the surface on this account, this should preferably be done on a dull day, and in any case, the harrow should follow immediately after the person who disturbing the soil [Inoculate with bacteria, T. Visel] with care being taken to sow it only over a strip that the harrow will cover.”

What researchers of the 1950s and 1960s did not review was the impact of eelgrass peat, the very thick growths of eelgrass that gathered organics (mostly oak leaves) and in warmer temperatures that become sapropel. The study of terrestrial peat by Selman Waksman (1945) conducted by the New Jersey Experiment Station had identified the role of bacteria sealed from oxygen (or in the case of eelgrass peat, warmer temperatures with less dissolved oxygen T. Visel)) and the study of low moor peat bogs – wet bogs had identified transitioning bacteria as deeper deposits were effetely sealed from water column oxygen. According to Waksman (1945): {My comments in brackets T. Visel}.

“In low moor peat bogs, the numbers of aerobic bacteria diminished gradually with depth, whereas the numbers of anaerobic bacteria increase” … The activities of the anaerobic bacteria in the lower layers [sealed from oxygen, T. Visel} result in the production of cellulose [plant organics T.Visel} of various gases rich in methane and hydrogen in sulfur-containing bogs [sulfate is not limiting in estuarine waters T. Visel} hydrogen sulfide is another characteristic product of decomposition … Furthermore, the lack of nitrifying bacteria prevents the oxidation of the ammonia to nitrate.”

(This describes in fact the interruption of the ammonia to nitrate pathway, the basis of biological filter systems in the Aquaria and Aquaculture industries).

As water temperatures rose from the 1980s into the 1990s, eelgrass peat could, in high temperatures, form sapropel (acid sulfate soil), create sulfides and have increasing ammonia discharges in reality now releasing several poisons, sulfide, aluminum, and ammonia, into the water column all from the biochemistry of sulfate-reducing bacteria (SRB). It is natural for sulfate reducing bacteria to do this as part of their sulfur cycle respiratory pathway – the increased of sulfur compounds in the water nearby residents could now smell as hydrogen sulfide gas. It was known during this time not to park your car under Niantic street lamps on foggy nights a form of sulfuric acid drip could ruin a car finish, (Bob Porter, personal communication – Tim Visel 1980s). Along with the build up of Black Mayonnaise (Sapropel) the incidence of swimmers itch (once unknown) suddenly increased during not summers in the Niantic River (see Appendix A).

Observations of sulfide toxicity also include yellowing or browning of salt marsh plants, prevalence of molds and fungus. High sulfides below eelgrass have been shown to produce very similar toxic impacts in Tampa Bay, Florida studies (Sediment and Vegetation as Reservoirs of Vibrio vulnificus in the Tampa Bay Estuary and Gulf of Mexico by Chase, Young, and Harwood in the Journal of Applied and Environmental Microbiology, April, 2015).

Sapropel formation, in shallow waters that obtains oak leaves, forms a waxy, sticky deposit as sulfate-reducing bacteria cannot break down oak leaf wax, which dominates leaf fall in several coastal communities. In time this Sapropel accumulated the wax and becomes the “sticky bottoms,” on historic nautical charts or in observations of habitats.

The Chemistry of Marine Soils Can Change –

Key to both eels and bay scallops was the biochemical nature of the soil itself, eelgrass fosters acid bottoms by minimizing contact with alkaline sea water as a buffer – eels had evolved specific biological features that allowed it to live below eelgrass and eelers had discovered the chemistry of oxygen “live bottoms” versus the chemistry of sulfur “dead bottoms” long ago. Bay scallops could set in eelgrass but preferred the alkaline soils of live Mearl. The chemistry of marine soils is largely beyond our control but understanding this chemistry is key to understanding habitat quality. Eel fishers were in fact selecting areas that had better soil chemistry they just did not realize it. It is the marine soil chemistry and the study of sapropel bacteria that largely determines habitat quality and important fish and shellfish “healthy” habitats.

The Increase of Sapropels Long Island Sound 1980s
NOAA Estuary of the Month Seminar Series #3
Long Island Sound: Issues Resources, Status and Management

These proceedings are from a seminar on the status and management of living resources in Long Island Sound. The seminar, sponsored jointly by the National Oceanic and Atmospheric Administration’s (NOAA) Estuarine Programs Office and the U.S. Environmental Protection Agency’s (EPA) Office of Marine and Estuarine Protection, was held in the main auditorium of the U.S. Department of Commerce on May 10, 1985 – published January 1987 NOAA/EPO-87-03

Program Abstract –

This report contains papers presented at a seminar on Long Island Sound held on May 10, 1985 with the objective to bring to the public attention the important research and management issues in the Sound. The 10 papers address the natural, biological, chemical, geological, and physical processes that characterize Long Island Sound; the status of the Sound’s living marine resources; the effects of humankind on the Sound environment and living resources; and management problems.

The Benthic Ecosystem
D. Rhoads
Department of Geology and Geophysics
Yale University

“I have a difficult task, as all the speakers do, because we’re trying to summarize years of data and experience. In my case, some 20 years, and I hope to do it in 20 minutes or less.

With the build-up of reactive organic matter in the sediment and a lack of pore water oxygen, hydrogen sulfide, ammonia, and methane gas may be generated and enter the overlying water column. These reduced compounds, along with the reactive organic matter, may deplete water in contact with the bottom of its oxygen.

Underlying the dysaerobic and anaerobic water one typically finds organic-rich black (i.e., sulfidic) muds that are termed sapropels. These are rich in iron mono-sulfides. The physical properties of these muds are distinctive and the best description that I have heard of them is that they are like a “black mayonnaise.”

(Response to question)-

Dr. Rhoads: Yes. One reason I mentioned the importance of the sapropels –these black iron monosulfite muds on the bottom—was the direct point that Peter raised. The system is so dynamic that to measure the change from year to year in dissolved oxygen as measured in the water column would take more money than we have. It’s not practical at all.

Given that kind of variability, what you need is a low-pass filter and an integrator, and that’s the sediment. I suggest that a very sensitive index of the waxing and waning of this condition would be the map of where the sapropels terminate, whatever isobath that might be. Follow the edge of those sapropels. If they’re encroaching upwards into shallow water, it’s getting worse. If they’re receding, it’s getting better.”

The Great Stink of 1858 Vibrio Cholera and the Thames River London England
The Rise of Sapropel linked to the Vibrio Cholera and the “Miasma” Theory of Disease
“The Ocean, Atmosphere, and Life”

Being the Second Series of a Descriptive History of the Life of the Globe

By Elisee Reclus, Author of “The Earth,” Etc.

New York: Harper & Brothers, Publishers, Franklin Square, 1873
(reference to the lower Thames River London England)

“At the ebb of the tide, when the current of the river, with its slow and dark stream, flows on toward the sea, beds of semi-liquid mud filled with putrifying rubbish are gradually laid bare, emitting into the air their nauseous exhalations: inspired by a sentiment of instinctive disgust, one is almost surprised to see the blue sky and clouds reflected in these beds of moist filth. At the flow of the tide, when the body of water, being arrested in its progress, gradually rises and ascends the Thames, the islands of mud cease to be visible, but most of the unclean rubbish which has been borne down by the ebb is again carried up by the flow of the tide; a kind of to-and-fro motion is constantly shifting these impurities up and down stream under the eyes and noses of the inhabitants.*”

Long Island Duck Farm History and
Ecosystem Restoration Opportunities
Suffolk County, Long Island, New York
February 2009
US Army Corps of Engineers
New York District
Suffolk County, NY

“The increase and decomposition of organic matter, derived directly from the duck waste as well as the increase in algal biomass, contributed to anaerobic benthic conditions impacting flora, such as submerged aquatic vegetation; and fauna, such as benthic invertebrates and foraminifera.

Dense algal blooms prevented light penetration to the benthos, causing plant decay and
additional organic deposits (O’Connor 1972). These organic rich sediments, often several feet deep, became soupy, black, clayey silt that had a rich odor of hydrogen sulfide, so potent that homeowners adjacent to Moriches and Great South Bays complained that the paint on their homes was being discolored (Nichols 1964; O’Connor 1972). Ecological degradation that was associated with the accumulation of nutrients throughout the estuarine bays continued throughout the history of the duck industry, and was heightened when the Moriches Inlet was temporarily closed (Nichols 1964; Lively et al. 1983) in the early 1950s.”

February 2009 4 Long Island Duck Farm History
and Report Ecosystem Restoration Opportunities




Nelson Marshall

Narragansett Marine Laboratory, University of Rhode Island, Kingston, Rhode Island

“The disappearance of the eelgrass, Zostera martina, with the epidemic of the early 1930s permitted better circulation near the river bottom. Apparently this was advantageous to the bay scallop, which thereafter became the predominant sessile grazer with a production calculated at 2.2g C/m2/yr. Anchorage previously offered by eelgrass for the early setting stages of scallops was subsequently available through the abundance of small branching algae.
In an earlier paper (Marshall 1947), I attempted to show that the local scallop population had been sparse and had suddenly increased to an abundance which supported a new fishery after the eelgrass disappeared. Doubts raised from the recollections of others as to from when the fishery developed prompted me to check the accounts of the early fishery in the archives of the New London Day, Write-ups of the fall of 1934 and to early 1935 emphasized the developing fishery. Consistent with these accounts and the dates thereof is the legislation of 1935 establishing the Waterford-East Lyme Escallop Commission. Thus the association in time between the development of the scallop fishery and the disappearance of eelgrass in the early 1930s is well documented. Well over half the take was in the first two months, October and November of the six-month season. The take was primarily from the shallows downriver.

Scallops are abundant elsewhere in the estuary and do well in the deeper water though restrictions against the towing of gear has made it difficult to fish much beyond the shallows.

In natural setting the scallops attached in quantities to most anything, including the frayed manila rope which had not worked effectively for the counts. It was evident that the small branching algae, observed to be very abundant throughout, the river, were heavily laden with attached scallops. In this connection it is noteworthy that fishermen of the Niantic River refer to such algae as scallop grass.”
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