IMEP @133 - Part 1 Salt Ponds, Coves and Tidal River Choking

[BlueChip]

IMEP #133 - Part 1
Salt Ponds, Coves and Tidal River Choking
Tidal Choking Destroys Coastal Habitats 1880 – 2000
"Understanding Science Through History"
Viewpoint of Tim Visel – no other agency or organization
March 2019
Thank you, The Blue Crab ForumTM for supporting these Habitat History posts
Tim Visel retired from The Sound School June 30, 2022
This is a delayed report – June, 2023

A Note from Tim Visel

I started working for Charles Beebe while in high school.  Mr. Beebe ran a small marina at the Route 1 bridge between the towns of Guilford and Madison, Connecticut.  I would help with various tasks, painting, fiberglass boat repair, salting fish, sorting oak lath (for lobster pots) and other activities of commercial fishing and outboard motor repair.  I had never "caught" a tree.  This morning, when I arrived, I could see that things were not "okay."  A large tree had come down the East River in March (there was still some skim ice on the East River).  The tide was going out and other floating branches were seen on the opposite shore.  I recall "Charlie" saying something to the effect of the need to remove a large tree before it chokes the river.  That was the first time I heard the term, or that a river could be "choked."  The truth of the matter was the East River (the boundary between the towns of Madison and Guilford, CT) had already been choked by a rail causeway in 1891 and a trolley line between 1905 and 1910.  Mr. Beebe was especially concerned that the tree would move downstream below the Route 1 bridge and get stuck in the abandoned trolley line trestle pilings and block completely the existing channel.  Here, Mr. Beebe predicted this tree could trap other limbs and trees moving downstream.  That would block navigation to his marina.

Fifty years ago, I did not realize how important this choking aspect could be.  Trees could also trap leaves and block or slow tidal exchanges.  The larger "choking" happened when dams or causeways altered the natural flows and, in time, changed the habitat below the water – out of sight.  Over many years, trapped organics and transitions to fresh water habitats occurred both as a natural event (such as from storms) and man-made structures, such as rail and road causeways or dams built in the coastal zone.  In a cold climate, this growing compost is slowed as bacteria consumed this organic food in the presence of dissolved elemental oxygen.  This is a rapid composting process and organic residues flushed out by venturi currents under thick river ice (comments by George McNeil to Tim Visel, 1980's).  Clear, cold water allowed oyster fishers to see these black leaves or other areas scoured by "ice currents," leaving black oyster shell flushed (cleaned) of organic matter when winter ice thawed.  When ice did not form (warmer winters), a loose marine compost could accumulate over the winter.  Coastal areas with long or narrow connections to the sea are most susceptible to choking if partially blocked or restricted.  Nature could block small inlets and we could also with culverts.

A History of Tidal Restrictions

As identified in the alewife fisheries of coastal New England, this tidal choking had a direct climate connection.  In times of heat, storms had a history of closing tidal alewife runs.  Storm surge sand often would block alewife runs and coastal landowners (early farmers were also at times fishers) would unblock them, returning tidal flows to prevent sulfide containing black water, which would kill fish and shellfish trapped in high heat.  In times of heat, this choking would greatly impact the negative outcomes of marine composting, producing a sulfide-rich sapropel.  Coastal residents frequently term this compost "black mayonnaise."  This compost purged sulfides and in the historical fisheries literature the smell of "rotten eggs."  As water temperatures rose and oxygen bacteria died off, the use of sulfate by bacteria that wasted sulfides increased this toxic compound that kills oxygen-requiring organisms.  The areas that showed the first increase of sapropels were those tidally choked and held huge deposits of organic matter.  In heat, these organic deposits would rot in low oxygen conditions.  This marine composting would fill shallow waters with so much sulfide – its smell would be associated with fish and shellfish kills for over a century.

Charles Beebe of Madison, CT told me that oystermen then, those who tonged oysters, would watch a tree undercut from river banks and fall into the East River.  To prevent the loss of navigation and damage to oyster beds by the gathering of leaves, Mr. Beebe described a tree harpoon, a sharp blade strong enough to withstand an oxen pull (team) and metal ring to drag this obstruction from the river (similar to horse hitching rings).  Chains were also used at times.  This impact was confirmed by Frank Dolan of Guilford after so many trees were cut during the construction of Route 95, which then had trees ending up in the river.  Mr. Dolan claimed that oysters once lived above the current Route 1 bridge but are now buried on the bottom.  I learned this during the removal of a large tree from the bend just below Beebe Marine; it had blocked more than half of the river.  With a metal grapple hook, which Mr. Beebe had sharpened on a grinding wheel in his shop so as to dig into the tree, my part of this project was to row the Brockway skiff over the branch and drop the grapple hook.  After several drops, I was able to get the hook around a large limb and an incoming tide was able to get a chain around the trunk.  A local tow truck winched the tree onto the bank (Madison side) where in two hours it was cut up with chain saws and hauled away at low tide.  I think that is how it was done before with tow trucks and wire rope.  It was for me (around 1972) a lesson about what one tree could do.

Natural Choking

When a tree got lodged in (the Branford) river in 1985, it made the local newspapers by 1988.  It had come down the Branford River after Hurricane Gloria in 1985.  It partially blocked the Branford River and started to gather leaves.  In hot weather, this tree started to smell (See Appendix #1).   This tree had become a hazard to navigation and, from reports in local news media, emitted hydrogen sulfide, the smell of rotten eggs (See Appendix #3).

While trees could choke rivers and narrow channels and largely natural, one factor could be there was just more leaves.  In 1910, only about 25% of Connecticut's acreage could be considered forested.  By 2010, it would be about 70%.  Fields once cleared for agriculture transitioned to low canopy understory then to a maturing oak-hickory forest.  With more trees came more leaves and the paving of streets meant local bays would obtain more leaves than during the last two centuries. 

The research community did examine tidal choking in the late 1970's and early 1980's.  Howarth and Teal 1979 in a paper titled "Sulfate Reduction in a New England Salt Marsh," Limnology and Oceanography, Vol. 24, No. 6, pgs. 999-1013, mentions tidal choking, the holding of terrestrial plant matter held in estuaries.  Estuary Comparisons, Victor S. Kenney 2013, mentions a report by B. C. Welsh, R. B. Whitlatch and W. F. Bohlen that "lateral imports of terrestrial litter (mostly oak leaves, T. Visel) are known only for Connecticut estuaries and all quantification was done in Alewife Cove" (Welsh and Whitlatch, 1980).  Alewife Cove in eastern Connecticut has been studied for tidal restrictions for decades. Composting processes, however, remain poorly represented in the fisheries habitat literature.

But research in this area (composting) was controversial and linked to nutrient "outwelling" and changes in nitrogen towards ammonia in low oxygen conditions.  Researchers even noted returning to some coves only to see the remains of leaves from the previous fall and estimated they could be 3 to 5 years old.  If you fished in shallow water in early spring, you could see the fall leaves because the waters were clear. Large amounts of leaves happened after heavy rains, including ice and snow "melts." 

While lobstering in the 1960's and 1970's, trees also came down Connecticut's rivers each spring after snow melts.

While tree leaves collected in Tom's Creek each fall, they never seemed to build up – we saw more trees than leaves on beaches each spring.  The leaves were "hung up" in the areas of restricted flushing along the shore as in Fence Creek west of Tom's Creek.

Growing up next to the Hammonasset River and commercial fishing with my brother Raymond, we often saw large trees each spring on the beaches and along Hammonasset Beach.  These trees mostly came down the Connecticut River during spring floods, some years more than others, but each spring "free firewood" came to the mouth of Tom's Creek.  Small trees, especially oak, could be hand cut on the beach and added to our firewood for the winter.  These were the trees that floated, not realizing for many years that trees could sink and change river flows for decades.  We became familiar with this while seed oystering in the Hammonasset River, hitting these submerged trees with metal seed oyster dredges was a constant danger. 

A small pipe or culvert could also change the tidal characteristics but act as a man-made choking point.  This would hold back leaves on the bottom, an unseen flow of organics making its way to the Sound.  Here, over time, a marine compost would build up, burying previous coastal habitats, thus destroying them (See A Review Of Fisheries Histories For Natural Oyster Populations In Tidal Rivers, January 12, 2008, 68 pages).  The increase in leaves would be the most noticeable in habitats "choked" by restrictions, such as causeways too narrow for ebb flows or culverts too small to handle heavy rain events.  Coastal dams could block energy while holding "legacy sediments."  Marine plants could also be held in waters as well.  Researchers, who looked at open, high energy systems, would report high oil, glycogen-rich deposits – those from oil-rich algae – meaning deposits (organic carbon did not originate locally or being "far away" or allochthonous.  Researchers, who looked at closed or tidally "choked" systems, found larger deposits of terrestrial leaves (See Appendix #8: Zobell, 1938) or those from "nearby" or autochthonous.  These deposits would show greater wax (ester) contents from terrestrial leaves, especially oak leaves.  This is the sticky bottoms reported north of eastern Connecticut railroad causeways in eastern CT, starting with Jordan Cove in Waterford around 1980.

One of the signs of a growing marine compost was a burial of shellfish habitats.  This was often reported in areas still open to shellfishing in the 1970's but later by winter flounder fishers in the 1980's.  I had also noticed this marine compost increase immediately after the shellfish closure of Tom's Creek in 1973.  By 1974, many of the oysters were being buried in a loose, sulfur-smelling ooze.  The climate had moderated in 1965.  Long Island Sound had frozen over as far as the eye could see in 1965 (personal observation, Tim Visel).  But into the 1970's, the climate moderated and winters became less severe and sometimes considered "mild."  Warmer seawater is less dense and storm severity reduced, causing sand to block tidal exchange in some coves. The Alewife fisheries have many accounts of runs being blocked by sand bars after coastal storms. 

The closure of long connections to the sea became known after the 1880 to 1920 period.  It was at this time that coastal property once of little value (mosquitoes and lack of protection from wind) became valuable for a growing summer trade of those seeking relief of heat and disease of cities.  A storm blocking a creek or salt pond in periods of warm weather often led to stagnation in the early 1900's.  Efforts were made to unblock them quickly as these stagnated and now brackish habitats supported large mosquito populations (See The Mosquito Plague of the Connecticut Coast Region and How to Control It, CT Agriculture Experiment Station, New Haven, CT, Bulletin #173, July, 1912). This is the time that "shore" communities grew quickly as people sought to escape these brutal killing heat waves.  One such community was Groton Long Point and its Mumford Cove area of Groton, CT.  It is the brutal heat waves of the 1890's that led to the creation of this summer community, not unlike many "shore" villages during this same time along New England's coast.  From the 1971 publication "Groton Long Point – Fifty Years And Then Some" published by the Groton Long Point Association, July 3,1971 (114 pgs.) is found this segment:

"In regard to the development of the Point as a summer place, the New London Day, September 3, 1894, indicates that Mr. Armstrong, Mr. Newcomb, Mr. Perry, and Mr. Sherman had bought "300 acres of land" and a farm house from Chauncey Abbey."

Once this sale was completed, by 1895 the farm was divided into "lots" and marketed to those wishing to come to the shore for cooling summer breezes.  Although many may not realize that these shore communities developed for the activities that we associate with them today – boating, swimming or fishing, the primary reason then was to escape killer heat waves and disease outbreaks of inland or central cities.  Summers at the shore (for those who could afford to do so) were to avoid the diseases of hot summers in population centers.  The following account is found on page 24 from Groton Long Point of Gladys Griswold, who details this aspect found in many "summer camps" quickly built on the coasts and islands of New England:

   Gladys Griswold-
"My father, Charles Wheeler, was Professor of Engineering at Connecticut Agricultural College – now the University of Connecticut.  His experience in sewage disposal and water supply problems made him most far-sighted.  One reason he selected Groton Long Point for our summer home that it was far from the city "contamination."  Today, we call it pollution.  So he bought land on East Shore Avenue in 1914 and built "Orient" in 1923.  The fourth generation is now enjoying it."

(For those interested, the Charles A. Wheeler papers are part of the archives Special Collections University of Connecticut, 405 Babbidge Road, Unit 1205 – a short biography reads "Mr. Charles A. Wheeler was a member of the 1888 graduating class of the Storrs Agricultural School.  In 1897, he returned to his alma mater, now Storrs Agriculture College, as an instructor in Mathematics, as well as those associated with being the College Engineer 1915-1930.")
   
Part of the Mumford Cove Groton Long Point shore was a barrier spit and coastal lagoon.  As more people moved to this community, the environmental and climate history reports increase.  In a way these summer residents became the first "citizen scientists" as they kept records of beach barrier spit movements and the increase of sapropel (muck) in the lagoon.  As storms (energy level increased) became stronger, the loss of property (sea level rise) and tidal choking (the need to dredge) is now reported by those impacted by this change – the summer community itself.  Much of the environmental history is now in records of Mumford Cove shore changes.  The example of a cove impacted by a rail causeway and road culvert and one in which we have fisheries records is Quiambaug Cove in Stonington, CT.  This cove is located east of Mumford Cove and is bisected by two man-made choking causeways – the Amtrak rail causeway at its mouth and a road causeway at Route 1.  The records of fish catches and oyster culture reflect how tidal choking is reflected in core studies.  A restricted tidal opening changes the salinity profiles and warming water enhances bacterial sulfate metabolism.   Tidal choking is mentioned in a publication titled "The Ecology of New England Tidal Flats – A Community Profile" by Robert B. Whitlatch (US Fish & Wildlife Service, Whitlatch, 1982, 125 pgs.) describes the sulfide dead line as the boundary between and position of the oxygenated and black anoxic zone as the "redox potential discontinuity" or redox zone.  I prefer what John Hammond (Cape Cod) described as the sulfide dead line, the line or depth in which bacterial use of sulfate emits toxic sulfide.  This line is almost nearly absent in sandy, well oxygenated soils, but in high organic areas, the oxygenation/nitrate line is just below the surface.  It also explains the grey sands and grey stains cast into the water after a severe storm.  Page 7 of The Ecology of New England Tidal Flats contains the following segment:

"In muddy sediments, two or three distinctly colored zones commonly exist.  The uppermost is light brown, extending 1 to 5mm below the sediment surface.  This is the zone of oxygenated sediment.  Below this thin layer is a black zone where oxygen is absent and the sediments smell of hydrogen sulfide (rotten egg gas).  The black color is due primarily to the presence of iron sulfides.  In some muddy sediments, a third grey-colored zone may exist below the black zone due to the presence of iron pyrite."

And further, on page 8 is found the following:

"Despite the lack of oxygen, black reducing sediments contain a variety of small organisms, such as bacteria and nematodes."

Nematodes have adapted to living in this sulfide-rich mud.  When the sulfide line moves to the surface, this habitat favors these marine worms.  This is perhaps why a soft shell clam flat gains more organic matter – the sulfide dead line moves up and the milky ribbon worm becomes more abundant.  This habitat edge may reduce the number of sand worms, Nereis virens, that prefer more sand than monosulfide-rich sapropel.

Other cores show the impact of storms as layers of sand or those of sand mixed with bivalve shell as sudden severe remains of storms.  A tremendous amount of research is coming online as to the impacts of tidal choking first documented by Kaare Munster Strom in 1938 with his studies of Norwegian fjords having a natural underwater dam or sill (See IMEP #59-B, posted August 6, 2015, The Blue Crab ForumTM). 

Kaare Munster Strom's research at the University Geological Museum, Oslo, Norway (March 4, 1938) was titled "Land-locked Waters and The Deposition of Black Muds" and describes the sulfide deadline in fjords that were tidal choked by a natural sill or lip.  Words that describe residence time or flushing were, at that time, referenced as stagnation and ventilation.  This is the rotten egg smell mentioned during fish and shellfish kills during late August.  From Strom as reported in "Recent Marine Sediments" – Parker D. Trask, editor 1939, reprinted in 1955, National Research Council, Library of Congress #67-26966.

Pg. 356 –
"When the bottom waters of a basin become stagnant for a sufficiently long time, the results of oxidation processes entirely preponderate over the feeble photosynthesis by plants, which is possible in the deep.  The waters thus become depleted of oxygen and hydrogen sulphide, which commences to form in the mud even when the waters themselves still contain oxygen, will gradually dissolve into the waters.  The deep waters eventually contain great quantities of hydrogen sulphide, which gradually diminish towards the surface until a limit is reached where there is an equilibrium between hydrogen sulphide and oxygen, the quantities of both gases being nought (zero, T. Visel).  The bottom sediments and the waters containing hydrogen sulphide become sterile with regard to animal and plant life (except for a few bacteria) and the constant rain of dead plankton organisms and other organic detritus from the surface waters forms a blackish (pyritic) mud, which covers all the deep bottom." 

This choke point reduced tidal exchange and documents some of the same organic sulfide levels in the Narrow River in Rhode Island.  The name of Narrow River explains in part the habitat history of this coastal lagoon and upper estuary lagoons.  The Narrow River has some of the highest sulfide levels (Pettaquamscutt lakes) recorded in New England (See Gaines and Pilson 1972 – Anoxic Water in the Pettaquamscutt River, Limnology and Oceanography, Vol. 17, Issue 1).

Core studies of coastal coves and lagoons provide a climate-influenced habitat history.  This habitat change can be checked with research reports (Mumford and Quiambaug Cove both have extensive core studies) and referenced to the presence of historical finfish and shellfish (both coves have shellfish and finfish records) populations.

Tidal choking also has been shown to change plant species (subtidal) as well.  Duck hunters and the efforts of the US Fish & Wildlife add to the changes in marine soils after storm events.  We are fortunate to have the United States Fish & Wildlife Service report titled "Back Bay – Currituck Sound Data Report (1965)" conducted in the mid-1960's.  The overall concern was established by several duck hunting clubs, which sought answers to waterfowl population changes and overwintering in the Back Bay Currituck Sound complex.

This report is unusual as it reflected upon coastal conditions going back to the 1860's.  The report centers upon dramatic changes in subtidal grass populations, known as duck or waterfowl grass – today referred to as forage grass, the food of many species of waterfowl.  The study sought to respond to these concerns and focused upon storm frequency and intensity that open or closed barrier beach inlets.  This changed the salinity and noted that freshwater submerged plants died back while allowing more saline grasses, such as eelgrass, to grow.  Here, the report connects storm activity to salinity change and changes in vegetation over time.  The report also mentions changes to bottom firmness (thought to be from retention of organic matter) and species change.  Some areas had submerged vegetation die out completely and raised the issue of soil change, especially that of clay.  Major changes in barrier spit openings are highlighted throughout the report, including the March 7, 1962 storm, which broke open barrier beaches.

[Note: Tidal choking (restrictions) has been recognized as one of the most important areas in need of research and mitigation.  In 2020, the EPA issued a national report (85 pgs.) titled "Tidal Restrictions Synthesis Review – An Analysis of US Tidal Restrictions  and Opportunities for Their Avoidance and Removal – EPA–842-R-20001, December 2020.  It is an excellent report covering aspects of shellfish, finfish, plant species and wildlife such as waterfowl.  Unfortunately, with 37 coastal coves and marshes crossed by the Northeast Corridor Amtrak rail causeways in eastern Connecticut, it appears, did not contribute any references.  Many features of this problem of tidal choking can be found in IMEP #117: A Review of The Dowd's Creek Habitat Restoration Project 1986-1989, posted June 23, 2022, The Blue Crab ForumTM Fishing, Eeling and Oystering thread.  Restoring tidal flows has been found to reverse sulfide-toxic buildups and allow more oxygen-dependent species to survive.]

Tidal Choking, Climate Cycles and Near Shore Fisheries

For shellfish, this soil storm cultivation pattern clearly exists.  This is shown by sudden heavy sets of softshell clams following storm events and cultivation of estuarine submerged soils by winter or summer storms.  Because these habitats can change quickly, the biological response is a shorter life cycle.  Clammers often find two clam bottoms – one surface and one buried by storms containing dense clams all dead.  A period of less energy has soils change to suffocate surface sets.  Here, silts and clays cover beds, killing them.  The Maine Department of Sea and Shore Fisheries, revised to January 1950, The Story of the Maine Clam, Robert L. Dow et al., pg. 10, has this segment:

"Loose shifting soils often bury clams so deeply that they are unable to survive.  "Clam graveyards" beneath silt have been noted along our coast as far back as 1913 when a Department fish culturist then reported that, "There has been a radical change in conditions of clam flats in the past decade or two where conditions were favorable.  The flats are now covered with soft mud from two to four inches deep." (1913)

Because we tend to believe that productive flats are always possible – soil texture and type have complicated our complete understanding of the softshell clam.  In once high energy areas, it is natural that soil aging (clay buildup) also diminishes clam density.  The question of soil cultivation has appeared in reports for over a century.  Cultivation (digging) can extend soil qualities but cannot stop soil aging.  This is a comment from a report of J.R. Stevensen upon observations and Experiments on Mollusks in Essex County during 1906.  Public Document Annual Report of the Commissioners on Fisheries and Game, 1906, State of Massachusetts:

"Many clammers on Plum Island Sound when asked to the value of frequent digging of the clam flats unanimously declare in favor of it – "this constant digging keeps the soil in a wholesome healthy condition."
And also –

"but I do maintain that the clams where seeded should be "cultivated" and frequently cultivated, especially if set in soil comprised largely of clay or mud."
And the portrayal of overfishing (although that can certainly happen) shellfish as the only reason for a resource decline continues this bias. We may be able to finally end this bias with the close examination of bivalve sets in marine soils after huge cultivation events such as the hurricane example illustrated in Waterfowl Tomorrow United States Dept of the Interior Bureau of Sport Fisheries and Wildlife – Fish and Wildlife Services United States 1965 GPO provided by the examination of nature's "tidal choking" of Back Bay and Currituck Sound along the coasts of Virginia and North Carolina.  This review of the impact of hurricanes and coastal storms is so important to the complete understanding of barrier spit influence upon subtidal marine plants.  We need to review the complete habitat history of eelgrass and coastal storms apart from conservation protection environmental policy, which has tainted so much of the eelgrass literature to date (post 1972) it is of little habitat research value for soil understanding (my view).

Chemical Soil Profiles and Tannin/Residue Signatures in Tidally Choked Embayments

The lack of energy (can be accentuated by breakwater or culvert construction) can turn once moderate successive marine soils into active successive soils.  Some of the first radio carbon (14) studies occurred on salt marshes in Barnstable Massachusetts (Redfield, Rubin 1962).  The analysis of depth age and "identification of organic remains enables direct comparison between the vertical zonation of the living plant (s) at the surface and the depth of its organic remains in the soil profile" – Ecology of Salt Marshes and Sand Dunes, pg. 86, Ranwell, 1972 contains this statement: "Such core studies also provides direct evidence of successional relationships that have occurred in the past and that are likely to be occurring at the present time."

It may be that submerged aquatic vegetation has evolved to carry site specific relationships based upon changes in environmental factors, energy, temperature and salinity but also to include soil characteristics as well including nitrogen, pH and charge (CEC).  Ranwell (1972) also includes a discussion about changes in blooms and makes note of explosive macro algal growths in English salt marshes considered a nuisance or fouling algae – giving evidence of perhaps successional change, on page 203 is found this statement: 

"One of the most noticeable changes in southern English salt marshes over the past 20 years (1952 to 1972 T. Visel) is the extensive growths of green algae (Enteromorpha and Ulva species) which have developed around the seaward edges of salt marshes." 

In times of excessive heat, shallow waters often reported blooms of Ulva – lying in or near sapropel deposits.  This is a quote from Nichols 1920 Torrey Bulletin - The Vegetation of Connecticut pg. 525 with earlier very similar observations:

"At ordinary low tides these tidal flats of the lower littoral present a surface of soft, blue black ill smelling mud and area in which, except for local colonies of eelgrass or salt marsh grass (Spartina glabra) seed plants and attached algae are practically are absent" (suspected to be sapropel- T. Visel).

And Nichols further states (my comments, T. Visel):

"At certain seasons these muddy flats may be destitute of visible vegetation of any description; (ammonium generation suspected T. Visel) but at others the bare mud at low tide is littered with loose sheets of Ulva, and tangles of Enteromorpha, which my cover the ground so thickly that; when viewed from a distance, the surface appears verdant green" (pg. 525 Nichols, The Vegetation of Connecticut Bulletin of the Torrey Botanical Club, Vol. 47, 1920). 

The condition of dense Ulva mats is associated with sapropel deposits (ill-smelling mud) is likely to be sulfide – rotten egg smell mentioned so many times in the historical fisheries literature.  These blooms over them are suspected of shedding ammonia a nutrient for sea lettuce – also reported to grow so dense as to suffocate oysters in the last century.  The New England farm community had already described in heat and soaked terrestrial composts leaked ammonia dissolved in water.  It was described as a "sweet" odor coming from manure piles.  As ammonia was washed away, it reduced the nitrogen benefit to many plants that preferred nitrate.

Heat also impacts submerged plants, such as eelgrass, which prefers cooler water nitrates.  Nature does not waste habitat space so as temperature rises and resulting bacterial reactions, nitrogen tends to accumulate as ammonia and not nitrate.  In heat and deep sapropel (marine) composts, oxygen is limiting and, therefore, ammonium tends to increase and in the process favor plants that can utilize (think prefer) ammonium.  This, in heat, results in thick blooms of macroalgae, and in our area, eelgrass dies back to be replaced by thick matts of sea lettuce, Ulva.  Areas with restricted tidal exchange or with natural retainment – a cove with a small opening may have Ulva matts several inches deep.  This occurs in heat as the composting bacterial process now favors ammonia.  This was noticed in Connecticut during a hot climate period 1880 to 1920 (See Nichols, 1920).  This has happened again in Connecticut after 2010.  Dense matts of Ulva and similar reported species have happened in many states (See Removal of Sea Lettuce, Ulva Species, in Estuaries To Improve Environments, Clyde Mackenzie, Jr., Marine Fisheries Review 67(4), 2005), especially during late summer.

The blue crab may be impacted as well by dense sea lettuce mats as they have been shown to shed low weight molecules toxic to crab larvae (Detrimental Effects of Ulva lactuca, Exudates and Low Oxygen on Estuarine Crab Larvae.  Journal of Experimental Marine Biology and Ecology 1985 – Ulva lactuca was cultured for 24 days.  "No crabs survived the molt into megalops) molecules that were toxic to zoeae crabs species in estuaries." 

It is the presence or absence of bacteria that is a successional attribute of temperature and energy.  More importantly colder water is clear, has less algae and allows ultraviolent light to kill surface bacteria – bacteria now live in the soil itself and bacterial action measured by soil characteristics.   These are the marine soils close to land that has enough organic matter to sustain bacterial life in shallow water.  More recently, researchers looked at UV light levels to minimize bacteria in seawater (or freshwater with most domestic recreational pool filters are now equipped with a UV unit) I had seen some of the first stand- alone shellfish bacterial purification systems (called depuration) at Harbor Branch Institute in 1974 for oysters while attending oceanography classes at the Florida Institute of Technology.  Here, homemade UV units were placed after sand filters to maximize bacterial killing power.  Years later while attending the University of Rhode Island Aquaculture program at East farm we would make them for fresh water systems holding trout and salmon. 

This is why nearly all environmental organizations have reported the water filtering capacity of shellfish, fastest growth – shallow water and clear shallow water improves UV light control of bacteria in effect shellfish are in effect are natural filters and presence connected to water clarity or absence conversely to turbidity.  If the waters are cloudy or turbid, UV light cannot penetrate as deep.  A loose compost with clay and organic matter can build rapidly in warm, low energy periods.  This compost building process is helped by the presence of tannin and leaf residues.  During storms, fines (many times beneath eelgrass) are dislodged and add to turbidity.

And one of the easiest ways to measure the impact upon organic matter feeding bacteria is to examine its tannin signature – the tannin compounds found in vegetation washed from land.

Tannin is termed nature's flocculant or better coagulant and is often used to treat water as a filtering process.

Tannin is persistent is the estuarine habitats delivered during rains into rivers and streams.  It is a natural flocculant; it binds bacteria and minute organic matter together and during heavy rains, rivers and streams appear brown.  These are often termed chocolate waters after heavy rains/floods associated with tropical storms.  A heavy spring rain in New England can have a brown tint – the remains of the previous fall leaf drop.  Oak leaves are very high in tannin, which is a weak acid.  Oak leaves, themselves, are acidic with a pH around 4.6.

The signature is that organic matter leaves that behind, and its characteristic identification or "signature" is measurable.  Tannin has unique chemical properties as a chemical binding agent and gave rise to its name associated with a household astringent cleansing compound marketed under the term Witch Hazel™, and extract of the plant H. virginiana, naturally high in tannin.  Composting organics can show high tannin levels.

Another important research area for estuarine soils is its affinity potential to exchange soil ions.  Ions reflect movement of water and oxygen into them influencing what bacterial strains become dominate - in cold the nitrogen/nitrate pathway and in heat the nitrogen/ammonium pathway.  It is the flow of ions that bacterial actions allows terrestrial plants to utilize nitrate, it is the sulfate reducing bacteria that stops it.  That is why turf management soil science spends so much time on "root health" of oxygen bacteria and "root rot" in sulfide rich water logged or "poorly drained soils" that cause a sulfide root failure.  In salt ponds and coves, this can be a sulfide deadline, the depth at which oxygen life forms are low or even become absent.

In the marine environment, you could say that marine soils by their existence constitutes the definition of poorly drained but retain many of the features of soil health.  Healthy marine soils are able to exchange ions because their soil pores (space) allow them to do so, when soil pores fill with organic debris a type of soil compaction forms (and why athletic fields must in time be aerated by mechanical means) from the weight of the water the ability to move changed ions decline as such soils filled with organics tend to have a negative charge.  A similar feature exists in terrestrial soils over time the soils pores collapse impacting root tissue health. (Connecticut State Park officials would rope off sand dunes for the same reason, human foot traffic would collapse dune grass soil structure reducing the plants ability to move ions (nutrients) across its root tissue.)  Capillary action of new bacterial growth stimulates healthy root tissue and partially explains the old practice of spreading sand on cranberry bogs to increase yields – same basic soil/root response. 

The Study of Peat/Sapropel Formation Is Key to Understanding Coastal Habitats

As soon as salt marshes were ditched and drained, they could sink. This also occurred in the Northern maritimes with salt hay production for agriculture farmers noticed they slumped peat and marsh levels sank as these soils were re exposed to oxygen.  They started to "burn" not as the rapid oxidation of combustion but oxidation nonetheless (That is why terrestrial composts also generate heat). Some of the first detailed reports regarding this came from Florida you can even see pictures of sapropel collected from Florida almost a century ago). Page 690 of the experiment station record C. W. Okey, The subsidence of muck and peat soils in southern Louisiana and Florida (1917).  Proceedings of the American Society of Civil Engineers, Vol. 43, 1917, Issue #7, pg. 1499 -1522 reports on the subsidence of drained muck and peat lands are reported with "first hand observations made in Louisiana and Florida" as shown below:

"It is clearly evident that in planning drainage improvements, improvement for areas of deep muck lands some provisions should be made for the gradual, but certain decrease in elevation of the surface." (1917)

This removal of water caused the peat to lose mass and when dried, they sank.  Once stabilized peat soils can be extremely productive but the exposure of peat soils to oxygen would cause elevations to sink from composting processes but in the marine environment in heat many marshes would now collapse. The heat deep within the peat would decrease decompose as gas (mostly methane) pockets built up below the surface and then escaped into the atmosphere. Sea level rise has dramatic consequences as dissolved sulfate now allows sulfate bacteria to consume greater quantities of peat and saltmarsh.  Peat bogs once drained now would sink.  This is now occurring along the Louisiana coast as sinking saltmarshes estimated to be many acres per day. 

New England farmers would harvest sapropel for fields and put a top dressing of marine sapropel on saltmarshes to keep up with subsidence.  Drained areas for salt hay agriculture, once tidal action was restored and not so treated (called thin layer deposit today), could over time become a lake.  As water carries yet more sulfate into marsh surfaces, this feeds sulfate reducing bacteria. In this process, high levels of sulfide from sulfate metabolism may reach toxic levels in peat (lack of oxygen), killing surface vegetation on them (See E. S. Yuhas, 1984, The Importance of Oxygen Diffusion Rates and Chemical Oxygen Demands in Influencing Vascular Plant Zonation on the Salt Marsh).  This process can kill Spartina patens while submerged aquatic vegetation (See Appendix #7), such as eelgrass, also dies from the toxic sulfide levels.  This is the shallow water cycle of eelgrass sapropel in New England (See IMEP #68-A, posted December, 12, 2018, The Blue Crab Forum™).  Salt marshes undergoing this process often see an explosion of glasswort, giving it a red color.  Coastal residents, who live along marshes, have reported this and an excellent photograph of this condition is on the internet.  It is of Madison, CT. 

Tidal choking and high heat sulfate metabolism can change all of these habitat conditions, resulting in habitat succession and massive transitions of marine life.  This needs to be a part of marine habitat conditions – my view, Tim Visel.

Appendix #1
Branford Review, Wednesday, August 10, 1988
60th Year – Number 42
Branford, Connecticut
National Guard Comes to Rescue

THE CONNECTICUT NATIONAL GUARD made a visit to Branford on Saturday to remove a tree downed during Hurricane Gloria almost three years ago. Residents complained that the tree caused debris to collect since it crossed the Branford River, behind Riverside Drive. In the photo below, Branford Fire Lt. Ron Mullen watches from the Branford fire rescue boat as Sgt. Bill Keen, left, of the Branford Fired Department and National Guard Staff Sgts. Joseph Lucia and Gerald Wright attempt to remove the tree. In the photo at left, Wright is hard at work with a chain saw.

Appendix #2
The Hartford Courant, Thursday, April 30, 1987
TOWN BRIEFS
River becoming hostile to shellfish

EAST LYME – The Pattagansett River is becoming useless for the cultivation of shellfish because of "black mayonnaise," a marine resource specialist said Wednesday.

Timothy C. Visel, of the University of Connecticut's marine extension service, said recent efforts to reintroduce oysters in the river are failing because of the build-up in the river of decayed leaves, sticks, logs and other organic materials that break down and form a gelatinous substance that he calls black mayonnaise.

Visel said the substance depletes the river's oxygen, raises the acidity of the water and prevents shellfish beds from being properly seated on the river's bottom.

Visel said he suspects the substance builds up in the river because of a railroad embankment that interferes with the tidal surge into the river.  He said the narrowed waterway no longer allows the tidal surge to perform its natural cleaning function in the river.

Appendix #3
New Haven Register, Friday, August 5, 1986
Engineers to remove fallen tree from river
Huge oak tree snares debris floating in water
By Catherine Sullivan
Register Staff

BRANFORD – Since Hurricane Gloria, residents on Riverside Drive have watched debris and even dead fish pile up on a fallen oak tree that stretches across the Branford River.

"It's a huge oak and it's practically across the whole river," said Marie Wall, a Riverside Drive resident.  The tree is lodged in a section of the river near her property.  "There's just enough room for the boats to go by," Wall said.

Saturday, the local unit of the Connecticut Army National Guard and the fire department plan to remove the tree.
"The tree has caused so much debris and grass to block up, it's actually giving off an odor," Fire Chief Peter Mullen said.
Mullen said the area will become passable again for boaters.  And it will appease the neighbors, who have been complaining to town officials since the oak made its grand fall.

"The first year, we had fish heads out there and everything," Wall said.  At first, Mullen said Branford Company C, 242nd Engineer Battalion, was going to try to get a helicopter, so the tree could be air-lifted out of the river.  But a National Guard spokesman said that idea was dropped for safety reasons.
Instead, the National Guard will send several engineers to chop up the tree.  The tree will be removed between 8:30 and 9:00 a.m.  The National Guard will use the event as a training exercise, Mullen said.  Spectators are not encouraged in the immediate area, Mullen said.  Marie Wall hopes to catch a glimpse of the tree being removed.  Otherwise, she lamented, "I am going to miss the whole show." 

Appendix #4
Oyster Bed and Spatfall Survey of Rivers in Madison, Connecticut
1986
Prepared for: The Madison Shellfish Commission
Jeffrey Internship Program

Bradford H. Burnham, Intern/Program Assistant
Connecticut College
Dr. Paul Fell, Advisor

Joseph Lennon
Middletown Vocational Agricultural Program
Patricia Jepson, Animal Science Teacher

Timothy C. Visel
University of Connecticut
Sea Grant Marine Advisory Program
Avery Point Campus, Groton, CT


Present Conditions That May Retard Salt Water Intrusion

Natural seasonal events make all rivers the recipients of tremendous amounts of unconsolidated organic matter.  Spring rains and melting snows wash all types of dead trees, logs, waste wood, branches and miscellany into the East River as in other rivers.  Any restriction in flow may restrict these trees and logs' passage to the salt marshes and beaches for eventual decay.  This accumulation of trees can disrupt current and river flow patterns.
   In addition, bridges may prevent tides to "surge" upriver thus reducing salinities over a tide cycle.  Bridges may also destroy or disrupt saltwater wedges entering an estuary and cancause scouring and deposition if water velocities increase at the bridge and slow downstream.  With this situation in mind, three conditions are present in the East River:

1)   Scouring is occurring downstream of the railroad bridge and may disrupt the incoming salt wedge.  Note in 1984, the town of Madison removed an abandoned automobile from below the railroad bridge.  Possibly two or three more autos are still there.

2)   The old trolley trestle piles catch trees and logs each spring, causing a log jam of debris that restricts flow.

3)   An accumulation of oyster shells presently exists between the railroad bridge and the Route 1 bridge.

Recommendations:
1)   Remove trolley pilings.

These old junk piles catch trees and etc., creating a gridlock of junk, trapping additional logs, etc.  They should be removed at once.
2)   Map depths of river from Route 95 to Cedar Island (Guilford).

Oyster shells can be washed, roll or tumble along the bottom during high water velocities and drop when the flow slows.  Mapping the depths could provide information on the extent of the scouring and deposition.

3)   Take salinity measurements. If the salt water wedge is destroyed when it reaches the railroad bridge, that could have a tremendous effect upon upstream oyster restoration efforts.

4)   Use a drag line to remove any autos or wreckage below the railroad bridge.

There may be quantities of unwanted scrap metal that were dumped during a period of resource neglect/misuse.


Appendix #5

THE WILLIAMS COLLEGE – MYSTIC SEAPORT
PROGRAM IN
AMERICAN MARITIME STUDIES
___________________________________________________
MYSTIC, CONNECTICUT 06355   ˖    TELEPHONE 203 572-XXXX


                                 21 April 1987
Mr. Brad Burnham
Box 61
Connecticut College
New London, CT 06320

Dear Brad:

I am very glad to tell you that our admissions committee has accepted your application to the Williams-Mystic Program for the fall semester of 1987-88.  This acceptance is of course conditional on your continued good standing at Connecticut.  Please send us a copy of your transcript at the end of this spring semester.

We have a very fine group of students coming this fall, and we very much hope that you will be joining us!  Please note the changes in our schedule: the fall semester begins on Tuesday, 1 September and finishes on Thursday, 17 December.  We look forward to your participation in the program and will be in touch with further details when we have heard back from you. 

With best wishes for a good spring semester at Connecticut,

                        Sincerely yours,

                        Benjamin W. Labaree

                        Benjamin W. Labaree, Director


Appendix #6
Silt Is a Major Killer of Young Oysters
Commercial Fisheries Review June 1969
Bureau of Commercial Fisheries
US Fish and Wildlife Service


   BCF Milford (Conn.) Biological Laboratories SCUBA examination of local oyster beds in early spring shows that many beds accumulate a sufficient layer of silt during the winter to bury many young oysters.  On May 1, for example, on one bed of 1966-generation oysters, many oysters, mostly doubles and singles, were buried under as much as a half-inch of bottom material.  Most were still alive; only 3.6% had died because of smothering.

   Another bed with a heavy population of 1968 seed oysters also had accumulated a heavy layer of silt.  By May 1, 14.9% of the spat already had been killed; by May 16, however, mortality on this lot had increased to 33.1%, probably due primarily to smothering by silt – but also partly due to predation by rock crabs.

   On other beds, indicated mortalities due to suffocation by silt range as high as 40 to 50%, or higher.  Much of this mortality can be avoided by transplanting the oysters to beds free of silt during March, or early April, while the oysters still are essentially dormant.


Appendix #7
The Importance of Oxygen Diffusion Rates and Chemical Oxygen Demands in
Influencing Vascular Plant Zonation Patterns on the Salt Marsh
By Eric S. Yuhas
Selected Investigations on New England Salt Marshes
Project Oceanology – Pfizer
Marine Research Program
1983


Abstract
This study was designed to investigate the importance of oxygen diffusion rates and chemical oxygen demands in influencing the zonation of vascular salt marsh plants. Oxygen diffusion rates and chemical oxygen demands were examined in the Spartina alterniflora, short and tall form, Spartina patens, and Juncus gerardi zones of a salt marsh in the lower Poquonnock River estuary on Groton, Connecticut. Oxygen diffusion rates were found to be significantly higher in the tall Spartina alterniflora zone than in all the other zones. Chemical oxygen demand was found to be higher in the tall Spartina alterniflora zone, but in this zone, the chemical oxygen demand was found to be a lesser percent of the available oxygen than in all the other zones. The zonation of the height forms of Spartina alterniflora was found to be influenced by oxygen diffusion rates, and available oxygen, which is affected by chemical oxygen demand. The zonation of Spartina patens and Juncus gerardi was found not to be influenced by oxygen diffusion rates, chemical oxygen demand, or available oxygen.


Appendix #8
Recent Marine Sediments

A Symposium

Edited by
PARKER D. TRASK
U.S. GEOLOGICAL SURVEY, WASHINGTON, D.C.

PUBLISHED BY
THE AMERICAN ASSOCIATION OF PETROLEUM GEOLOGISTS TULSA, OKALAHOMA, U.S.A.
___________________

LONDON, THOMAS MURBY & CO., I, FLEET LANE, E.C. 4
1939

OCCURRENCE AND ACTIVITY OF BACTERIA
IN MARINE SEDIMENTS

CLAUDE E. ZoBELL
Scripps Institution of Oceanography, University of California, La Jolla, California

ABSTRACT

Aerobic as well as anaerobic bacteria are found in marine bottom deposits. They are most abundant in the topmost few centimeters of sediment below which both types of bacteria decrease in number with depth. A statistical treatment of the data on their vertical distribution suggests that aerobes are active to a depth of only 5-10 centimeters whereas anaerobes are active to depths of 40-60 centimeters below which they seem to be slowly dying off. However, microbiological processes may continue at considerably greater depths owing to the activity of the bacterial enzymes that accumulate in the sediments. The organic content is the chief factor which influences the number and kinds of bacteria found in sediments.

Bacteria lower the oxidation-reduction (O/R) potential of the sediments. Vertical sections reveal that the reducing intensity of the sediments increases with depth but the muds have the greatest reducing capacity near the surface. Three different types of oxygen absorption by the reduced muds are described, namely, chemical, enzymatic, and respiratory.

Bacteria that decompose or transform proteins, lipins, cellulose, starch, chitin and other organic complexes occur in marine sediments. These bacteria tend to reduce the organic matter content of the sediments to a state of composition more closely resembling petroleum although methane is the only hydrocarbon known to be produced by the bacteria. The precipitation or solution of calcium carbonate as well as certain other minerals is influenced by microbiological processes that affect the hydrogen-ion concentration. Other bacterial processes influence the sulphur cycle and the state of iron in the sediments. The possible role of bacteria in the genesis of petroleum is discussed.

DECOMPOSITION CAUSED BY BACTERIA

Various physiological or biochemical types of bacteria have been demonstrated in the sediments that are capable of attacking most kinds of organic matter present in the sea. The rate and end-products of decomposition of the organic matter depend upon environmental conditions and the types of bacteria that are present. Waksman and Carey (49) have shown that diatoms, Fucus, alginic acid, copepods and other marine materials are utilized by bacteria with the rapid consumption of oxygen and the production of carbon dioxide and ammonia. More resistant fractions of marine plants and animals such as lignins hemicellulose-protein complexes may be only partially decomposed to give rise to marine humus (50).

Approximately one-fourth of the bacteria isolated from marine sediments are actively proteolytic (18,56) as indicated by their ability to attack proteinaceous materials and in so doing liberate ammonia, hydrogen sulphide and carbon dioxide. Presumably the topmost layer of sediment is the zone of greatest proteolytic activity below which there is a gradual, but not very appreciable, decrease in the nitrogen content of the sediments (30). According to Trask (45) amino acids and simple proteins constitute a very minor part of the organic-matter content. Hecht (23) reports that most simple proteins are completely decomposed even under anaerobic conditions and are not converted into adipocere. He records that about 90 percent of the nitrogen content sediments is due to chitin. Chitinoclastic bacteria are widely distributed (57) throughout the sea but chitin is only slowly attacked by bacteria even in the presence of oxygen and it may be more resistant under anaerobic conditions.

Most simple carbohydrates are readily decomposed (54) by the bacteria that occur in bottom sediments. Under aerobic conditions the end-products of the fermentation of carbohydrates are chiefly carbon dioxide and water. In the absence of oxygen, carbohydrates may be attacked and thus yield organic acids, methane, carbon dioxide, hydrogen and other products. Buswell and Boruff (9) noted the production of acetic, butyric and lactic acids, alcohol, methane, hydrogen, and carbon dioxide from the bacterial fermentation of cellulose under anaerobic conditions. Several types of cellulose-decomposing bacteria (48,49,51) have been isolated from bottom deposits but very little is known concerning their metabolism. The fact (45, 46) that less than 1 percent of the total organic-matter content of recent sediments is carbohydrate, whereas ancient sediments contain none, is indicative of the vulnerability of this class of compounds to bacterial attack. However, much remains to be done to ascertain the end-products of the reactions.

Perhaps bacteria have a greater influence than any other form of life on the hydrogen-ion concentration and O/R potential of sediments; properties that in turn tend to modify both the chemical composition and physical characteristics of the sediments. They may deplete the oxygen as noted above, they may liberate nitrogen from nitrites or nitrates and they may produce carbon dioxide, carbon monoxide and methane in appreciable amounts.