EC #20 - Sulfate Metabolism and Bacterial Disease

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Environment/Conservation #20
In High Heat Salt Marshes Sink From Sulfate Bacteria
Sulfate Metabolism Linked to Vibrio Disease
Nitrogen/Bacteria Series
"The Agency of Nitrogen Releasing Bacteria"
Sapropel, The Composting of Organic Matter in the Absence of Oxygen – Known For A Century
High Temperature Sapropel Linked to Formation of "Oil"
August 2020
Viewpoint of Tim Visel, no other agency or organization
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A note from Tim Visel

In most blue crab studies, explanations of the rise and then fall of blue crab populations have largely centered on our actions.  Did we catch too much, did we pollute the water, have we altered ecosystem dynamics by harvesting prey species?  It seems in the last century a type of extreme conservation has melded with environmental protection to form a consensus (I contend at times seriously flawed) that we alone can determine the fate of all seafood populations. By doing so, we have given nature a free pass when it came to habitat conditions, both good and bad.  Perhaps no better example of this human bias is exhibited by submerged grasses and the blue crab.  During the last three decades, the association of submerged grasses to blue crab megalops has been reported as positive numerous times. At times, this habitat association or link is correct; at other times, it is a deadly habitat.  It is a perfect example of monoculture habitat succession, often following an event, a storm or flood that carries organic matter into shallow estuaries where blue crabs live.

This organic input event (tropical storms) is magnified by higher temperatures and low energy.  Nature has, in many respects, in this example dumped a huge compost pile on top of pre-existing habitats.  Eelgrass may or may not survive but any thick growths tend to slow water and cause greater organic buildups.  In heat, these organic deposits change the chemistry of estuarine bottoms.  Once was described as a "live bottom" can become overtime "dead."  In heat they can kill blue crab larvae.

In this dead bottom, bacteria can also change the pH (by shedding ammonia), become sulfide-rich, a plant and animal toxin, reduce elemental oxygen (deadly to oxygen requiring organisms), and when re-exposed to oxygen release heavy metals.  All of these chemistry factors can be associated with dense eelgrass meadows that in heat undergo a different "peat chemistry" over time.  Now in the most recent submerged vegetation studies, the chemistry of the sulfur cycle is being included and the diseases in which they contain - finally.  Certain organisms (diseases) wait, in fact, for the sulfur cycle to happen – an ammonia rich alkaline environment that most fishers rarely see because they are very poor fishing locations.  Fishers do not see them out because they produce few fish.  That is why it is, at times, so disturbing to watch once productive fish habitats over time change into ones that are not – and we often seek explanations as to why the change?  Some are human caused, the flow of warm street water from paved surfaces, dams and the loss of trees and plant ground cover are three large human caused explanations.  But they are only of part of more complex and often localized habitat change.  In shallow water heat is transferred faster and in cold they cool off quicker.  Any severe climate conditions are often experienced in the shallow habitats first.

While other changes seem to be natural cycles, the relationship between prey and predator forage, the natural cycles of energy and temperature or the occurrence habitat capacity diseases.  The occurrences of drought or low rainfall especially influence the returns of alewife, shad and salmon.  The extended hot period of the 1890s was especially hard on brook trout and led to the establishment of the US Fish Commission trout hatcheries.  We tend to look at human causes for population shifts without giving nature a review.  In the 1940s the US Fish and Wildlife Service seemed to be ready to break with the well established tenet of reproductive capacity for the blue crab, instead focusing upon fresh water flows that both killed pre megalops stages and drove blue crabs to move to more saline areas.  Low fresh water flows showed the ability of crabs to move up rivers and expand habitat coverage.  Blue crabs in heavy rains formed schools that moved to better salt water habitats – from Commercial Fisheries Review in Chesapeake Bay in 1958.  Vol 20, No 6 The Blue Crab and its fishery is found this statement,

"Some schools (Blue Crabs) are especially noticed because the crabs are unusually large and because often are heavily fouled with ribbed mussels (Hay 1905, Van Engel, unpublished data). 

Van Engel also provides a glimpse into the sulfur cycle and the formation of sapropel from the same study is found statement on page of this 1958 study.  Poor meat quality is found in the shellfish industry often described as poor or thin meats, watery meats or "waterbellies."  The lobster industry noticed that lobsters caught near sewage had shells that were pitted or missing shell portions termed shell disease.  The presence of Vibrio bacteria that are termed chitinolytic destroy the shell is one of the prime indicators that the sulfur cycle, others include poor meat quality and bad or rotten egg pungent smells, and this statement contains all three, pg 15 "crab dredgers report that in winter in the vicinity of Cape Henry crabs are often a strong odor, have shells deeply pitted, and produce a very small quantity of very inferior meat, the catches of this kind are quickly dumped overboard."

The return of the sulfur cycle harms all sea life that we call seafood.  We may find that one of the most important indicators of the return of the sulfur cycle is the winter habitat of the blue crab.  My view - Tim Visel.

I respond to all emails at [email protected] 

I wasn't surprised when I read some of the first New York reports regarding harmful algal blooms (HABs) and they found higher cyst (think of seed) densities in marine sapropels in the upper reaches of harbors or coves, the carbon residues of bacteria digestion of plant matter – a marine compost.  I recall very well being surrounded at one New York Fishermen's Forum by skiff fishermen, who once small otter trawled in several New York bays as they described precisely the habitat succession process that eliminated winter flounder and the bay scallop.  It was the presence of this loose, sticky deposit covering "flounder bottoms" that turned white and when disturbed smelled bad (sulfur bacteria that live in sulfide rich habitats), like sulfur.  Others described a sweet smell, perhaps the whiff of ammonia compounds, a powerful toxin to sea life and once influenced by heat and tidal flushing again with a direct bacterial connection.  The climate had given a death blow to some shallow habitats, in periods of low energy and heat, inlets or barrier spits tended to heal, thus reducing tidal exchange and, in many cases, poorly flushed with increasing "residence time," the time from origination to removal.  In basic terms, it is the amount of time a certain substance stays around before it is lost to the system. As the climate warmed, inlets closed, reducing flushing and trapped substances – residence time could be increased. It is here that organic matter is held in high heat and becomes a compost for bacteria.

Most reports on residence time suggest it is almost impossible to assure complete removal and it is assumed that tidal action keeps substances longer in bays with long narrow connections to the sea.  A hot, energy-poor period would have naturally higher residence times and this appears to be true for ammonia.  Ammonia generation in hot periods from bacteria would tend to slosh back and forth for days, each tidal cycle bringing in more ammonia to mix with ammonia generated from bacterial processes a natural ammonia "pump." This feature is often not included in residence time but the "bucket replacement" method that discounts tides bringing back any substances that exited.  This influences tidal time, i.e. the exit of bay or cove waters that is out of sync with tidal action, a restricted sill feature or narrow inlet will not allow full discharge before it meets the incoming tide again and pushes back waters trying to exit.  This is further complicated by cycles of low rainfall drought as entering "new" fresh water is measurably reduced.  This also described as a "tide lag" and reduction in inlet size or lower rainfall would impact tidal time.  Sometimes in bays or coves, the waters would slosh back and forth for many tides influencing ammonia (nitrogen) levels.  It is in these coves that HAB cysts are often found.  Intense blooms of HABs after occur when ammonia levels are very high.  This happened in eastern New York Long Island with "brown tides' in the 1980's.

The Sulfur Cycle and Disease

Some organisms need the sulfur cycle to exist, and bacteria change the peat chemistry even further.  Now an association to parasites comes in as photosynthesis is replaced by disease and parasites; some impact us as well.  It is in these times that eelgrass blades turn black and break (personal observations Buttermilk Bay Cape Cod 1981-1982).  In the heated pools over sapropel, a transition away from oxygen gives rise to opportunistic diseases and parasites not found or rarely found in colder oxygen sufficient environments.  Commonly found in these environments are Vibrio bacterial diseases and parasites including the blood fluke released by the mud snail.  The association of winter flounder fin rot (also a Vibrio) is attributed to these same sulfur organic deposits often termed sapropels.  It is the buildup of sapropel (fishers term "black mayonnaise") that is so damaging to marine life.  It is also termed fine grain sediment, a poor term because it refers only to the size of particles largely deposited by way of geological processes (erosion) but fails to include composting processes of subtidal peat chemistry.  It is also termed for a nitrogen chemical balance of sink or source termed benthic flux but often this excludes the chemical foundation of sapropel as the beginning of "oil" from bacterial processes.  This transaction tends to consume peat plant and root tissue turning it into an ooze.  In areas of hot water pools the sulfur cycle burns holes in salt marsh peat.

In 1920, George Nichols of the famous Torrey Botanical Society wrote about Connecticut salt marsh vegetation in the last years of the Great Heat, 1880-1920.  It is during this time of killer heat waves and ice famines (lakes and ponds were so warm that ice, an important commercial product, could not form); it is also the time that sulfate-reducing bacteria consumed salt marshes from below turning peat into loose sapropel.  Salt marshes with bacterial sulfate metabolism would now sink.  Some sinking was gradual while others reported the creation of pannes, deep depressions or slumps that filled with water.  Salt marshes in heat will sink from bacterial digestion and purge ammonia and hydrogen sulfide, both toxic compounds to fish and shellfish.  Salt marshes in heat are reduced to sapropel, a loose thin organic ooze, and linked to the deadly and disease causing Vibrio bacteria.  The rise of Vibrio bacteria is now linked to high heat and sapropel formation.  When this happens, it allows sulfuric acid formation and the release of toxic aluminum (DEP Office of Long Island Sound Program (1994), Section 22 Planning Grant, Foreword – Lost Lake Great Harbor Marsh in Guilford reviews this process).  In heat, the action of sulfate-reducing bacteria converts marsh peat to sapropel, creating "rotting" depressions.  Page 531, Nichols, "The Vegetation of Connecticut" contains the following statement:

"These salt meadow pools and rotten spots (technically termed "pannes") the origin of which will be described later, may lack vegetation entirely so far as the higher plants are concerned."

One explanation, page 545, describes the absence of oxygen and bacterial decay.  Dead grasses or wrack when it covers salt marsh plants, removing access to air and super heating the surface peat as it now begins to sink.  Nichols quotes Harshberger (1916), Johnson and York (1915) in the following section:

"Smother out the existing plant cover.  Sebsequently he maintains (Harshberger) rapid decay sets in, affecting not only the aerial plants organs but the underground parts as well, and eventually a depression of some depth may thus arise."

These are the salt pannes of today.  As sulfate reduction cause peat to be converted to sapropel and as the woody tissues loses its structure and volume, (composting) salt marshes then burn into the sulfur cycle and sink.  This bacterial composting is very similar to a huge pile of fall leaves and a small pile of compost in spring. Coastal residents are the ones who notice this salt marsh sinking most often by a change of plants and then pools of water.  These pools can become very hot in August with high ammonia and sulfides killing vegetation.  These areas once held the green salt marsh grass, Spartina patens, turn to red as glasswort Salicornia virginica now fills in a high salinity tolerant plant that often rings these pools, giving the green salt marshes patches of "red" or brown in long periods of heat.  It is the heat and low oxygen that brings Vibrio bacteria close to the marsh surface.  When that happens, the good habitat services of salt marshes in "cold" become toxic in "heat."  Marsh vegetation may turn yellow a sign of sulfide poisoning.  The cycle of sapropel has been known for over a century.  A 1909 issue of Mining Science, pg. 562, describes the final bacterial compost process:

"This organic mud is called "sapropel" and the various stages in the formation of bituminous matter are traced to the sapropel, which means putrid mud.  One has only to observe the abundant algae growth of the sea on the coast of the Ionian Isles to understand how beds of marine weed are constantly being buried by sediment and extending their growth through and over it, thus providing a growth of sapropel capable of producing petroleum.  Time and great pressure may have produced the same effect on organic remains in the earth's crust that high temperatures have in the laboratory without the invention of volcanic or metamorphic heat of which there is no evidence in the principal oil fields.

Chemical evidence shows that if marine organisms are the source of petroleum, their nitrogenous parts are eliminated prior to the formation of the oil through the agency of bacteria, which in the death of an animal or plant attack the cellulose of the latter and the nitrogen tissues of the former, but leave the fatty matter from both untouched.  After the elimination of the nitrogenous element, the process of transformation of fats into oils proceeds slowly at low temperatures, acting for a very long period.  Dr. Engel enumerates the various stages occurring in the formation of petroleum from organic matter.  Thus:

1)   Putrification or fermentation by which albumen and celluloid are eliminated.  Fatty matter and waxes from albumen remain.

2)   Occurs partly during first stage saponification of the glycerides and products of free fatty acids from action of water or ferments.

3)   CO2 eliminated from acids and esters, water from alcohols, oxyacide etc. leaving hydrocarbon.

4)   Formation of liquid hydrocarbons and violent reactions, with cracking into light or gaseous products – formation of proto-petroleum.

With moderate temperatures and pressures oil of an intermediate grade is formed, in areas of either producing "light oil," the various hydrocarbons are formed; Thus,

Methane – direct product from bitumen, that is the fats of Stage 1, heavy hydrocarbons Stage 2.

Olefines – directly formed by splitting up of saturated hydro-chain carbons of the paraffin series (these are also the waxy esters of oak leaves – T. Visel).

Napthenes – from decomposition of aromatic acids under heat and pressure.

Lubricants – formed directly from the original fats at low temperatures.

Benzines – from decomposition of fats at high temperature"

This 1906 excerpt from Mining Science helps explain why in the beginning of this bacterial "attack" the parrafins of oak leaf wax gives black "mayonnaise" its "greasy" feel.  Many no or low oxygen bacterial strains cannot digest them and they tend to accumulate.  It is from the oil (glycogen) and wax from bacterial reduction that over time concentrates.  In the presence of oxygen, sapropel purges nitrate, without oxygen, ammonia.  This is why in small bays or coves or below the thermocline of large water bodies, pH rises with the ammonia levels ions (the pH of ammonia is 13).  The pH can become so high it may cause ions of carbonate to form a layer.  Once sapropel is re-exposed to oxygen in the presence of iron, it will "flash" sulfuric acid, driving pH to the other extreme, now very low.  This low pH can now release metals chelated by bacteria and create toxic aluminum conditions.  Because our area is rich in iron, it is home to iron-reducing bacteria that thrive in the absence of oxygen Fe3+.  As such, these deposits tend to concentrate mono iron sulfide FeS and are usually black.  These sapropels can then become super hot, like the heat on black asphalt and burn into the sulfur cycle - the hot August smells of sulfur coming off the salt marshes a century ago referred to as "rotting eggs."  Coastal residents often report these hot August night odors.  A few years ago in the Old Saybrook Oyster River area residents (2011-2012) closed their windows because the smell of sulfur was so strong on hot calm nights (personal communications, Tim Visel).

But this substance sapropel has been long associated with organic rot.  Only one has to look to Maine's rivers loaded with bark and sawdust from lumber operations of the previous century when it was not a desired mulch but dumped into flowing water.  Heavy organic loads after heavy rains swept this sawdust and wood mill waste into the estuaries here in high heat (1880 to 1920) (See E/C Bacterial/Nitrogen post #1 "What About Sapropel and the Conowingo Dam?" posted September 29, 2014, The Blue Crab ForumTM, Environmental & Conservation Thread); it putrified and turned into sapropel.  Sapropel then covered oyster beds, killing them. This state of Maine Sea and Shore Fisheries Report (1912) on page 520 contains the following statement:

Sea & Shore Fisheries – Oysters pgs. 520-21 (thirty second report of the Commissioner of Sea and Shore Fisheries for the Two Years ending November 30, 1912 – James Donahue, Commissioner).  The search for suitable oyster habitats.

"Examination of other sections, particularly at or near the mouth of rivers – such locations being best adapted to the growth of oysters on account of the amount of fresh water that comes down the river and mixes with the salt – showed where there was not so much trouble from marine growth on the bottoms.  They were almost invariably found to be covered with a thick coating of black, soft mud, evidently the result of sawdust and mill waste that came down the rivers and settled and rotted on the bottom, making a soft mud on which it would be impossible to plant oysters successfully!"

The section from the December 16, 1909 edition of Mining Science 1909 and one hundred years later just as appropriate as today.  Yet, some might question why sapropel is missing from marsh study and is not a top study area in better understanding the salt marsh ecology we so often try to "preserve."  What happens in heat is very different than cold, and salt marsh ecology holds a narrow margin of life.  In heat, it sinks; in cold, it can build.  That is how Louisana loses so much salt marsh each year; the flow of organic matter changes, and in heat, bacteria consume it in the process emitting H2S (sulfide) which kills salt marsh plants as the marsh is "eaten" from below.

The presence of hydrogen sulfide a byproduct of the bacterial reduction of sulfate (a compound containing oxygen, which is non-limiting in salt water) can decrease or eliminate marine rooted vegetation such as eelgrass.  In a 2016 Ocean Sciences meeting, Chesley Ekelem of Harvard investigated the pore water sulfide levels of high levels of sawdust upon eelgrass.  This paper accurately portrays the situation of human caused organic matter impairing or destroying estuarine habitats but what about when nature does that as well? 

Effects of Wood Pollution on Pore – Water Sulfide Levels and Eelgrass Germination

Consider the fish kill report of the Atchafalaya Basin Keeper following Hurricane Gustau in September 2008.  Here after heavy rains washed millions of tons of organic matter (tree leaves) into the watershed.  This was described as a "green fertilizer" and in a few days generated black water and a large fish kill.

Leaves over time rot and form a waxy paste producing black water from bacterial action upon organic matter.  This is the peat chemistry that can form "black water."

This is the same sapropel that forms in high heat low energy cycles in any estuary where oxygen is limiting and organic matter is deposited (mostly natural).  This material impacts shellfishers and blue crabbers most directly as it covers habitat, but its description of acid, dead or rotten egg bottoms is found many times in the historical fisheries literature and even today.  The following is an excerpt from an article titled "What Are Clams' Economic Impact On Greenwich?" in the Greenwich Times, June 25, 2016:  My comments (T. Visel).

"The Sound (Long Island Sound – T. Visel) is affected by runoff from the mainland, but also garbage and litter that settles at the bottom, decomposing into an anaerobic muck. Stilwagon's crew calls that muck "black mayonnaise" because it is so black and greasy you have to use soap and water to get it off your hands."

A century ago, a similar response regarding the same putrification of organic matter in heat (some poorly flushed areas with human sewage) was recorded in The New London Day newspaper article titled "Long Island Sound – Remarkable Revelations – A Bottom of Putrefied Things," March 21, 1890:

"An old mattress which fell to pieces when brought to the surface (cotton batting) and gave out such a foul smell that is was impossible to remain in its vicinity, and it had to be dropped back into the water as no one could have remained on deck...The water splattered from the dredge coming off this foul matter, discolored paints wherever it stuck" signifying acid conditions.

Sapropel has been recorded up and down the Atlantic coast but its most studied location is perhaps the duck manure deposits of Long Island, New York.  This is evidenced in the following 2009 report.

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

... which contains this statement:

"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."

Source: February 2009
Long Island Duck Farm History and Ecosystem Restoration Opportunities

The impacts of excess organic matter, wood pulp wastes, cotton and millage refuse, sawdust and leaves have all contributed to the sulfide rotten egg smells in heat.  Maine has an extensive habitat history of when it was common to dump tree bark and pulp trimmings into streams with much different temperature impacts to stream and river life.  It was Kolkwitz and Marson with the Saprobic System 1909, who detailed the foundation of the first water quality index of this organic matter, termed the organic wellness system or more commonly known as the "Saprobien System."  Any organic matter forest duff, leaves, twigs, blossoms and dead grasses all can contribute to organic richness that, when bacteria consume it, utilize oxygen as an electron transfer process and fix nitrogen in the process.  It is the nitrogen locked up in the organic tissues that, by way of several bacterial pathways, which gets "recycled" into new mobile forms, nitrate, nitrite and ammonium, which the latter is largely formed with sulfate reducers.

When it is hot and little energy (flushing), the residence time of any nitrogen compound in coastal bays and coves increases.  As bacterial nitrogen (and any non-natural sources, such as human sewage) levels increase in it as estuarine waters now favors the bacterial strains that live without oxygen and use sulfate as an electron source, breaking sulfate to obtain the oxygen held by sulfur.  Sulfur now binds with hydrogen forming hydrogen sulfide or H2S, a deadly toxin to sea life and plants.  That is why the cycles of eelgrass abundance are determined by marine soil pore capacity and the absence of high pore water sulfide.

Marine soils that once held good soil pores, able to move water and purge bacterial byproducts become sulfide-rich when organics fill these soil voids or soils are simply blanketed by organic matter.  Soft shell clammers perhaps have the most experience with marine soil sulfides, the surface of a clam flat appears brown, an oxic layer that shows oxygen is present, but digging deep into the flat substrate, the soil changes to a black, sometimes bluish hue, is sticky and can emit the smell of sulfur.  This is a toxic soil for most shellfish and only a few species of worms that are extremely "sulfide tolerant" can live. Most clam flats with high sulfide levels contain dead clams below and limited surface sets.  It is also toxic to eelgrass, Zostera marina.  That is why periods of low energy and high heat (less oxygen) are bad for eelgrass as it dies from sulfide attacking its roots which weakens the plant, making it vulnerable to other diseases, especially fungus.  It is natural to have eelgrass cycles of abundance.  It is also natural in heat that salt marshes will sink.  In heat, seawater naturally contains less elemental oxygen.  Those oxygen-requiring bacteria die off and are replaced by bacteria that can use sulfate - in seawater, a non-limiting oxygen source.  In times of heat, it is the sulfate bacteria that "win".  (See EC #7 Salt Marshes – A Climate Change Bacterial Battlefield Blue Crab Forum™ posted September 10, 2015).   

In 2016, Chesley Ekelem of Harvard University detailed the impact of wood waste on marine sediments (soils) and the bacterial reduction of sulfate.  Following is an excerpt from the 2016 Ocean Sciences Meeting:

Effects of Wood Pollution on Pore-Water Sulfide Levels and Eelgrass Germination Chesley Ekelem, Harvard University, Cambridge, MA, United States

"Historically, sawmills released wood waste onto coastal shorelines throughout the Pacific Northwest of the USA, enriching marine sediments with organic material. The increase in organic carbon boosts the bacterial reduction of sulfate and results in the production of a toxic metabolite, hydrogen sulfide. Hydrogen sulfide is a phytotoxin and can decrease the growth and survival of eelgrass. ... Higher concentrations of sawdust led to higher levels of pore-water hydrogen sulfide and drastically slower eelgrass germination rates. Treatments with greater than 10% wood enrichment developed free sulfide concentrations of 0.815 (± 0.427) mm after 118 days, suggesting sediments with greater than 10% wood pollution may have threateningly high pore-water hydrogen sulfide levels."

When pore water holds large amounts of hydrogen sulfide, another type of bacteria emerge.  These strains do not need oxygen but obtain energy by oxidizing hydrogen sulfide in the presence of nitrate.  When oxygen (O2) levels drop, this bacteria can utilize nitrate as a secondary electron acceptor.  It oxidizes hydrogen sulfide and can produce a thick white mat of Beggiatoa bacteria.  A century ago, as these sulfide mats covered the bottom, fishers termed it as dead bottoms, correctly observing that these habitats supported little life.  A century ago, the last great heat (See IMEP #61-A, 61-B) fishers seeking eels noticed that eelgrass was still a live bottom and marked them for winter ice fishing as the grass that holds eels or "eelgrass."  This is how eelgrass got its name.

For more habitat history reports and salt marsh habitat histories, see the IMEP series posted on The Blue Crab ForumTM
The Rise and Fall of Lobsters – Duck Hunters and Farmers - Had Climate
Practice Change Signals
The Great Heat 1880 to 1920 with the most severe hot weather occurring between 1895 to 1912, was the time of the shore cottages and lake hotels catering to those who could afford to escape the "hot terms" that caused so much hardship in cities.  However, this period of "great heats" or waves also changed how duck hunters hunted ducks. The winters had frozen marshes and ponds and ducks often congregated in the remaining "open water," making for the best shooting, but those habitat areas often meant sometimes walking miles to hunt by those areas. In time, hunting clubs built camps near productive submerged grass habitats so that affluent duck hunters could be closer to the ducks (also with cabins came catered food-- some others even had private chef's "feasts" – which did not equate with hunting success.)
For most duck hunters, warm winters meant soft marshes and open water everywhere, and harder to find best areas to shoot. Walking across the marshes was also dangerous in knee boots (in the fishing community, termed "dead men shoes,") as they would immobilize the ankle and in soft marsh muds acted more like a plumbers helper than a device to keep your feet dry in cold weather.  The inability to point your toes down or flex the heel up meant your rubber boot held suction that was hard to break, and to pull on it meant more weight on the other boot, causing it to perhaps sink as well.  To pull on a stuck boot meant a free hand, and that usually held a game bag and a shotgun.
Lifting a foot-- now off balance-- usually resulted in a fall, which then resulted in wet feet, boots or no boots at all. That is why hunters preferred shoes even in the winter because you could use them on frozen marshes. However, what if the marshes did not freeze, as Southern New England suffered tremendous heat waves in the summer (1900s) and "ice famines" in warm winters?  Hunters often came home with cold, wet shoes.  New England's waters were so warm, that in 1899 an ice famine hit Southern New England, but the icehouses in Maine made fortunes. Ice was important to food cooling, it was also important to duck hunters. (The ice famine of 1899 would spur the creation of commercial ice machines in 1900.)  Some ice made duck hunting better in the remaining open water, deeper areas that still had food (submerged plants) held more ducks.
Most likely one of the best illustrations of how we change practices or procedures besides the wrap around Victorian front porch was L.L. Beans' invention of the Maine hunting shoe boot™. As accounts portray an avid duck hunter who at the end of the Great Heat 1880 to 1920, grew weary of wet, cold soaked shoes, and set out to create the hunting boot™, a shoe base waterproof lower and a flexible boot top leather upper.
This hunting shoe/boot™ could flex the ankle like a shoe, yet had waterproof leathers that if quickly pulled up when stuck, kept your feet dry so you could continue to hunt.  In a few years, their use quickly became a hunting accessory for many duck hunters.
Having grown up along the salt marshes by the Hammonasset River and Tom's Creek in Madison, CT with my brother Raymond, many "lost boots" in soft mud usually quickly ended our marsh trips. In short time, we learned that boots (we called them Wellington's) in marshes were a great liability, not a benefit. What made hunting conditions even worse in these mild 1900's winters is that hot summers before them had caused the marshes to soften and sink, at times leaving a grass covered root mass on the surface, but below a pool of deep, loose sapropel (organic ooze) to an unsuspecting step. This bacterial process that produces sulfides, caused "black water" to form in many marshes and the term is still found today, a reminder of what happens when marshes get hot, and decay, the sulfide smells of sulfur, the low tide smell of hot summer shore nights.  The boot of the ocean – water and the shoe of the land were combined into something that was perfect for crossing these "wetlands" in search of ducks.
Warm Water Marshes And Salt Hay Crops – The Agriculture Community
It was not only Maine's duck hunters that changed practices, but also the salt hay farmers in Southern New England abandoned salt hay crops. The marshes became so soft they could not hitch cutters to horse teams, as the horses would now sink into the marsh itself, as the winters were warm. Guilford's (CT) remaining salt hay producers (mostly mulch for tomatoes) developed "hay shoes" – larger horseshoes that looked like a snow shoe so horses could walk across the soft marshes.  Even in these hot times, hay shoes could not keep horse teams from sinking and this crop was then "let go".  A rare set of those hay shoes are on display in the Durham Farm Agriculture History Exhibit Hall on the Durham Agriculture Fairgrounds in Durham, CT.  Researchers at the New Haven Agricultural Experiment Station wrote that farmers were missing a valuable crop; they just could not harvest it.  The 1870s salt marshes were very firm, therefore easy to cut.  That was not the same in the 1890's.
The marshes of the 1870s were very different, then great cold waves (30 degrees below zero for days at a time) devastated Connecticut's apple orchards nearly eliminating all of its valley apple orchards at the time.  We have the accounts from The CT Board of Agriculture for the 1870s that give us a brief view of the terrible cold, to 36oF below 0oF – In Cheshire, CT, this is the account of what we know from the past century.  The cold was good for lobsters but not the blue crab.  When lobsters died in heat (1898), blue crabs then surged.  I have talked to many people about this, the first response is a series of questions (I think that is from the fact that 1898, and 1998 lobster die offs were reported in the research and fisheries management literature but the increase of blue crabs was generally not) that it was perhaps a coincidence (I don't think so – my view) and that it did not indicate a pattern and if other species have indicated similar rises and falls of seafood (they have).  However, most people have never heard of the North Atlantic Oscillation the NAO a climate pattern in the North Atlantic (also called the Icelandic low) known for over 1000 years and possibly far before that about colder and stormier sections of the North Atlantic.   Many times, we just do not have sufficient or complete habitat histories in today's fisheries literature. It just doesn't exist. The loss of our fisheries institutional memory is a huge deterrent to fully understanding the cycles of seafood. That is why John Hammond remarked, "If I wanted to learn about climate cycles just follow the fish" – Mr. Hammond was referring to Chatham, as a leading New England producer of the soft shell clam in the (1890s) a period of "heat" and sixty years later, a leading producer in "cold" for the bay scallop.  The clues to the fish were climate cycles- A New England Oscillation, we know today as the NAO.
The winter of 1872-1873 by Philo S. Beers of Cheshire CT – CT Board of Agriculture – following the loss of Connecticut Orchards from cold winters, Mr. Beers writes:
"The cause of such a calamity is not in doubt. The winters of 1872-3 was the coldest on record, and the mercury sank to a lower point, according to the records kept in New Haven, than for the last one hundred years. The mercury at my house indicated, on the coldest morning, 22° below zero. No trees were killed either in the nursery or orchard; a very few in the nursery were affected by the cold, showing it in the discoloration of the wood in pruning, but not enough to affect the growth, the following summer.
One-half mile north, and fifty feet lower in a hollow, the same morning, and the same hour, the mercury indicated 30° below 0°. There I had another orchard of apple trees, and many limbs were killed entirely, both on grafted and natural trees; they have not, and never will, recover from the effects of that cold morning. In the north and south parts of this town, in the valleys, the mercury sank to 36° below 0°, at this time, and it was in these places that some whole orchards were killed, others on a little higher ground suffered less, part of the trees being killed, and others started with a little life and have since blighted and died. Apple, pear, peach and quince trees suffered the same fate. I visited many parts of this state in the meantime, and find in all the valleys more or less loss, according to the depression of those valleys; but little loss has been sustained on high ground in a portion of the state."
This communication of Mr. Beers, giving his experience and observation, coincides with that of close observers all over our state. Communication from P.S. Beers – The writer of this communication, Philo S. Beers, of Cheshire, died in January 1875. This is probably his last article on fruit culture" (CT Board of Agriculture, 1875 Report).  This habitat lesson to Connecticut farmers left a lasting impression.  From then on, apple tree orchards would be planted on hilltops – a practice that continues today.
This same time is when Greenwich CT, a western Connecticut community with its coves and indented coastline, small skiffs would catch 100 bushels a day of bay scallops. It is thought that this cold period nitrate from the nearby city (New York City) enriched the water that green algae grew dense enough to feed these dense scallop populations that in cold "held" more nitrate than heat, which in heat naturally held more ammonia.  Early winter snowfalls blanketed Connecticut in 1840 (six inches on October 25th – 26th) and continued to damage mulberry trees planted in a warmer period.  But the cold created ideal conditions for the bay scallop.  In 1841, a November 17th report on page 41 of Before And After 1776: A Comprehensive Chronology of the Town of Greenwich printed in 1978 by the Historical Society of the Town of Greenwich contains this account:

"Within the last two months, more than 20,000 bushels of scallops have been taken out of Greenwich Cove, and they still continue to be plenty that a single person can gather from six to eight bushels at a time."

By 1900, bay scallops were gone, and Greenwich was battling mosquito disease.   

The opposite occurs in heat, bacteria populations change to those that can live in low or no oxygen.  Instead of nitrate, these bacteria allow ammonia levels to climb and release sulfides.  This directly impacts soil chemistry and can be seen by a shift or change in species.  Soils, that with energy, have pore spaces to move chemical compounds, close up and become stagnant.  In heat or low oxygen conditions, soils become acidic and sulfide-rich.  Species can change because the soil chemistry changes – this occurs with clams.

Many times this transition was marked by an increase in an acid pH tolerant clam Macoma balthica known also to be very sulfide tolerant.  I often use the terrestrial habitat succession of lawn monocultures to illustrate this change.  Taking away the lawn mower does not preserve the lawn.  In fact, once "energy" (mowing) is stopped, habitats succeed and the "lawn" is soon gone.  Reports of long ago buried huge oysters exposed during dredging projects have been recorded by Harold Castner (1950) in the book titled The Story of Ancient Pemaquid in Maine.  They were buried by layers of organic compost and accessible only after energy (dredging) removed the layers of compost.

Shell Middens and Species Habitats – A Potential Climate Record 

For decades, attention has been focused upon salt marshes and shallow waters as being important to near shore fisheries, from the "bay scallop" to blue crabs and to winter flounder.  Oysters are also a shallow water near shore fishery as well extending up into brackish waters including major rivers.  In times of drought or extended cold rivers provide a habitat refuge, a stable climate period.  It is the change from warm to cold or from much energy to less a "quiet" aspect of estuarine shore life that governs what species does well.  Long periods of heat and limited energy has in shore waters obtaining huge sets of mya the soft shell clam, but in cold and energy sets of quahog (hard shell clams) mercenaria increase.  Quick changes to cold and storms bring in bay scallops from offshore into bays – and in reach of inshore skiff fishers.  Blue mussels in cold temperatures also invade rivers as well.  The organic compost sapropel harvested from rivers and bays in winter for terrestrial fields was called in many localities "mussel mud."  The blue mussel sets blanket the bottom so much so they suffocated clams and oysters.  In times of heat however such blue mussel sets are rare.   

A long period of cold blue mussels (extremely sensitive to sulfide) in cooler oxygen rich waters could set and form nearly impenetrable mussel reefs and trap organic waste.  Below a thick mass of blue mussels a mud is often found and mussels a century ago a shellfish of low market value were dug up and spread on farm fields "mussel mud."  In heat sulfide bottom waters are extremely toxic to blue mussels – it is the transitions from very warm to cold that bring back mussel growths and sets.  In 2007 the Long Island Sound sustained an immense blue mussel set (noticed on lobster traps) but within two years of very warm temperatures most of this bottom set west of New Haven had perished.  My son Willard was lobstering at this time and his lobster traps were covered by tens of thousands of small blue mussels.  In all the years I had lobstered in the same area had never seen such a blue mussel set.  It was cooler in the 1960's and 1970's.

Warm temperatures are great for oysters (and blue crabs) and during these periods expand habitat coverage to low energy bars and reefs offshore.  Bay scallops find cold alkaline bay bottoms welcoming and in times of great energy.  It is difficult to imagine that the best bay scallop year in Connecticut's most recent fisheries history is the 1950's – period of cold and tremendous storm damage.  While the remaining oyster companies had hundreds of acres of seed oysters destroyed (burial) by storms bay scalloping now soared.

Quahogs set into shallow water after the New England Hurricane of 1938 and later storms reinforced those sets so that by the late 1950s quahog clam landings increased as some species have a temperature preference and energy habitat succession as well. 

Large long oysters for example signify a stable soft bottom, colder and sufficient oxygen.  A hot environment would quickly bury such oysters, as organics would tend to accumulate and force oyster reefs upward.  Paul Galtsoff in his 1964 bulletin illustrates this in a section of oyster reef with each generation setting upon the next -long tapered shells indication rapid burial.  Oysters that are rounder and cupped signify a hard bottom environment and opportunistic setting.  Bay scallops themselves indicate temperature and perhaps life history.  Large bay scallop shells with no growth ring (a raised ridge along the shell) indicates excellent growth conditions – cool following storms.  A scallop shell with a raised ring indicates the second summer – and those bay scallops with a second growth ring (have seen several example shells in Niantic with two very clear raised growth rings on very large shells) a scallop that has perhaps reached biological maturity only because of extreme cold.  The relationship of bay scallop seed is significant as it illustrates a cooling for inshore waters.  A habitat history for bay scallop might be illustrated by a small appearance of small scallop seed, for a period of years, replaced by larger scallops later.  (Native Americans had no notion of "nubs" those scallops that obtain a large size without a raised growth ring – excellent growing conditions can produce a shell of harvestable size without one).  Extreme cold is thought to provide a genetic clock or clue for living beyond the first spawning period – living several months beyond spawning – gaining adductor muscle meat weight but perishing just a few months before the opportunity to spawn again.  This extended life competing with small scallops for space and food without any biological benefit has perplexed biologists for over a century but turn the temperature down and perhaps the scallops now fully hibernate and do not expend energy allowing them to live a few months longer – to a second spawn.  The bay scallop might have lived long ago with much shorter "summers."  That is how several bay scallops from the Niantic River - Bay described it to me those second ring scallops were in deeper water and found during the coldest winters.

Native American shell middens may provide important clues to this bay scallop mystery.  Here in deep shell middens free from commercial bias could record the changes in shell morphology size, thickness and age rings could provide important clues to climate conditions.

While Mr. Hammond was watching habitat succession in Oyster Pond River, Chatham, Mr. McNeil of Clinton, CT was trying to keep it from ruining his last crops.  In the 1950's and 1960's leaves blanketed his lower Hammonasset Oyster beds – after coastal storms and blamed the closing of the barrier inlet locally called the Dardanelles for it (1951).  This was his statement from a Hartford current article in 1987,

"George T. McNeil, an oysterman in Connecticut for more than 61 years, said he has been nothing like it before.  "I started to notice it a couple of weeks ago."  McNeil said "and now its all over the place."  McNeil who cultivates the last oyster bed in the inner harbor said he was afraid the growth could hurt the bed.  He explained that when oysters spawn, the spator juvenile oysters must settle a clean shell to survive.  McNeil said he has noticed the growth (Exteromorpha - Tim Visel).   

Covering the oyster shells in the bed and could think of no way to remove the growth without disrupting the oyster bed.  Jack P. Andrews, owner of J and J Lobster on Commerce Street said lobstermen and recreational boaters have had boat motoy clogged by the slimy green growth.  Andrews said he grow up by Clinton Harbor and had never seen or heard of anything like this.  He said a possible reason for these types of abnormal plant blooms in the harbor could be the closing in the 1930s of harbor inlet called straits of Dardanelle fishermen and residents said that when the inlet was closed, the flushing action of the tides was disrupted between harbor and Long Island Sound allowing decaying organic materials to build up in the harbor." 

What was happening was habitat succession. 
   

Appendix #1

Ellerslie Reserve Benthic Studies Faunal
Survey of Ellerslie Reserve in 1962
Fisheries Research Board of Canada Annual Report (1965) – B-9

Fisheries Research Board of Canada Biological Station
St. Andrews N.B.
Annual Report and Investigators Summaries 1965
J. L. Hart, Director, Biological Station, St. Andrews N.B.
Page 1 – Work on oyster environment and eelgrass control made good progress – Assistant Director S. C. Medcoff
Summary Report Oyster and Clams B-1 to B-13

BENTHIC STUDIES

Faunal Survey of Ellerslie Reserve

   This survey was started in 1962 with the intention of gaining a better knowledge of benthic conditions in the Ellerslie Reserve, and to provide a basis for future development and management work.  The survey has proceeded through several stages including general subtidal benthic surveys, intertidal benthic surveys, general sedimentary surveys and a survey of the flora and fauna of the shore area covered by extreme high tides.  The analysis of the data from these surveys is not yet complete.

   Although core of the bottom have shown that the area was once mainly oyster bed, there is now relatively little true oyster bed left.  Most of the area is now soft mud harbouring a fauna characterized by the bivalve, Yoldia limatula... At present, sedimentary conditions favour a transition from oyster bed to mussel bed and then to Yoldia or other less productive communities.  There is thus a reduction in the benthic productivity of the estuary.  Since most commercially harvested estuarine species are part of the benthos, this change is a direct loss to man.  However, estuarine areas are essentially highly productive and proper utilization and management could restore favourable conditions...

   The series of stations established in 1963 to study long-term changes at selected sites in Ellerslie Reserve were sampled in May, July and November 1965.  Conditions at most of the stations appear to be reasonably stable; one station on the Sand Bed however, has shown a steadily diminishing biomass.  The Sand Bed used to be in transition to a different fauna...

   Macoma balthica, a mud-living bivalve, typical of low salinity areas, settled heavily in mud and sand at all stations except the deepest one (R8).  Individuals grew larger in mud than in sand, reaching a mean length of 8.1mm by late October.

   Yoldia limatula, the bivalve typical of the deeper, muddy parts of the reserve, settled almost exclusively in mud at six of the eight stations.

   Cumingia tellinoides, a bivalve typical of good oyster bed, settled sparsely, being abundant only in the shell tray on the Totten Bed.

   In summary, these studies appear to show that the biotic environment in the Ellerslie Reserve favours the spread of fauna associated with mud and to a lesser extent sand.  These species appear able to colonize small areas of suitable substrata set in an unsuitable area, whereas the reverse is not true of the shell bed fauna.  The reasons for this are not understood but the future trend is clear."

The report also noted increasingly dense populations of the "false quahaug" Pitar – pg B-12 – heavy concentration of Pitar were found with an escalator harvester – in shallow water (10 to 15 feet deep).

Appendix #2

The Pitar Beds of Narragansett Bay – 1980's The Decline of Shallow Quahogs

In Rhode Island as the clams matured from heavy quahaug sets in the 1950's and 1960's soon found dense concentrations of Pitar – Pitar marihuana - thought to be more tolerant of acids – sulfide containing soils than the true quahaug valuable for food, Mercenaria mercenaria.  What was happening was marine habitat succession as the climate warmed this favored bacterial strains that did not need oxygen but sulfate.  Colder water favored the oxygen bacteria, the bacteria that helped salt marsh plants grow – when the climate became hot which favored the oxygen the bacterial strains that could use sulfate – these bacteria consumed the marsh peat for energy they literally ate the marsh and below the oxic zone turned the rooting peat into a jelly sapropel.  In Europe this process is called gyttja – from the decaying of peat – and described as black and has a gel like consistency.  In Europe this liquid has been found at depths about 10 meters – far from oxygen requiring bacteria. It has been studied for over a century and core marsh studies (a process of taking cores of the marshes and subtidal areas) show periods of large habitat transition, termed habitat reversals, on Cape Cod by a retired oyster culturist in Chatham, Massachusetts. 

This happened with the increased abundance of an unmarketable bitter tasting "pitar clam."  The appearance of "Pitar" in quahog beds was a bad sign to Rhode Island Bullrakers (communications to Tim Visel at the Wickford Fisheries School 1975 to 1981) they are only slowed quahog harvesting they seemed to be taking over "the bottom" becoming denser and more numerous – starting in the shallow waters first – requiring longer bullrake handles (Dave Ward communication to T. Visel).  The Deep Water Beds were still productive but many have given up fishing the shallows – Pitars were so numerous attempts were made to kill them.  Comments and trips on quahog trips showed me that pitars were living in softer – muddy bottoms – same bullrake hauls had live pitars in areas where small quahogs had died – the shell hash made a particular sound when washing – a bad sign that was different than the metal clink sound of live clams against metal bars.  These areas were declining in terms to "productive" or commercial value and bullrakers soon no longer "fished" them.     

These are the shallow soils the ones that blue crab also spend winters knowing the sulfide tolerance of Pitar may lead to important habitat succession of our clam marine soils and also those for the blue crab.  My view - Tim Visel.