EC #27 Sapropel Habits and Fisheries -An Alewife Cove History

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EC #27
Sapropel Habitats and Fisheries – An Alewife Cove History
Environment/Conservation Nitrogen/Bacteria Series
The Layers or Boundaries of Sapropel, Humic, Sapric, and Formic Horizons
A Capstone Research Proposal – October 2020
Viewpoint of Tim Visel, No other Agency or Organization
View the Nitrogen/Bacteria Series on The Blue Crab ForumTM
Thank you, The Blue Crab ForumTM for supporting these Nitrogen/Bacteria Posts
June 2021 – This is a Delayed Report
Revised to June 2022
Tim Visel Retired from The Sound School June 30th 2022

A Note from Tim Visel

One of the reasons that composting chemistry is not found in many salt marsh studies is perhaps the byproduct of sulfate metabolism – the bacterial use of sulfate that produces sulfur in the presence of hydrogen ions, forming H2S or deadly hydrogen sulfide.  Hydrogen sulfide is toxic to many organisms and is a known plant toxin.  The compound is chemically active and forms metal sulfides – therefore it is natural that sapropel deposits contain heavy metal ions.  Sulfate reducing bacteria naturally complex metal ions so completely it is sometimes used as a heavy metal spill cleanup media in Europe.  In 2001-2003 the EPA once used sulfate reducing bacteria to precipitate metal ions from acid mine water wastes – in this case cow manure and straw were the source of the sulfate reducing bacteria or SRB.  In 2003, Takak at EPA conducted tests to see how much of any heavy metal ion present would become complexed by the presence of SRB. His study published in 2003 is presented in Appendix #3.  Percent Recovery of Metals from Mine water using Sulfate Reducing Bacteria (Takak, et al. 2003 - Biodegradation).

In the mining literature, SRBs are often referred to as the metal "ore builders" as to their role in complexing heavy metal ions by the presence of sulfide.
The ability of bacteria to complex metal sulfides has been controversial because many times the presence of heavy metal ions has been used in halting or slowing coastal work such as dredging.  This process often takes a metal analysis of the dredge sample – without any (it seems) explanation that it is unnatural in heat and during low oxygen periods not to have metal sulfides present.  Since dredging often is done close to shore it is apt to have high organic matter content sealed from oxygen and therefore contains more SRB bacteria.  The older the sapropel the more time it has to chelate metals, and the resulting higher the metal counts.  Since the chelation of metal ions is a natural process and one indication of low oxygen and high organics – not necessarily human pollution, it is often a poor pollution indicator (my view Tim Visel).  Although such tests are used to slow or block dredging (Clean Water Act) this natural metal binding is often portrayed as dangerous human caused pollutants and toxic to sea life. 

This is where soil scientists can help end this bias by explaining that such sapropel formation is natural at times, (often termed black mayonnaise) and indications of metal sulfides is something that nature also produces and not just man.  In Europe such high metal sapropels are being looked at replacing important metals from agriculture soils leached by acid rain.  In this way lost soils metals needed for plants are recycled by the application of non-toxic sapropels.

More and more research is looking into black mayonnaise (sapropel) impacts to coastal habitats especially after heavy rains – floods.  Flowing water has moved millions of tons of leaf material and other woody tissue into estuaries and in heat, the recipe for sapropel formation.  But sapropel itself has three layers largely defined until recently by the types of bacteria living in it.   (See Deep-Sea Bacteria Zobell and Marita, Scripps Oceanographic Bulletin #926 in 1959).

Sapropel (1) Marine Humus Compost – Humic or Fibric Layer

This organic deposit consists largely of marine and terrestrial plant material.  It is exposed to oxygen and has an oxygen redox layer as bacteria have access to oxygen and nitrate as potential electron acceptors.  The bacterial spectrum can be described as aerobic or "oxygen sustaining."  Bacteria in this layer cannot easily digest wax which tends to collect and become sticky or greasy to the touch.  Shrimp, lobsters and crabs can burrow into this compost deeply enabling oxygen (nitrate) to penetrate into this compost and termed "bioturbation."  Complex cellulose structures or fibers are recognizable.  This deposit has a low pH especially of subject to acidic oak leaf falls and sealed from tidal exchanges such as those deposits below subtidal vegetation.
Sapropel (2) Putrefaction of Humus, The Sapric Layer

This layer is where oxygen or nitrate becomes deficient – in heat bacteria that can utilize ferric iron and sulfate now dominate the bacterial spectrum.  Here is found some of the most dangerous gram negative Vibrio bacteria family included those associated with lobster shell disease and fin necrotic rot "fin rot" in winter flounder.  These bacteria can utilize sulfate as an electron acceptor.  It is the sulfate reducing bacteria that causes the sulfuric acid washes when exposed to oxygen or when used as soil nourishment on land.  It often has a blue/black "shiny" appearance which dries to a grayish/white powder.  In the historic literature the pungent smell of sulfide rotten eggs is frequently mentioned.  This is the layer most often termed black mayonnaise by fishers as it undergoes putrefaction (reduction) without oxygen. The name sapropel comes from the Greek contraction of words sapros and pelos – the putrefaction of mud. This layer from ammonia production at times contains lethal high pH saprophytes which has survived as a term in the current literature.  The saprophyte is life that lives off the dead.   This is the layer that assists the sulfur cycle and is responsible for ammonia, metal chelating, and aluminum toxicity.
Sapropel (3) and Disease-Causing Vibrio Bacteria and Sulfide Fish Kills The Formic Layer (also methanoic acid layer).

As bacterial reduction continues and all secondary electron acceptors are depleted (no oxygen nitrate sulfate or ferric ion) here a bacterial family uses molecules from plant synthesized carbon chains for chemical energy and concentrate carbon chain fragments in organic layers by bacteria called methanogens.  Some methanogens can utilize CO2 as an oxygen acceptor in this process.  Elemental oxygen is O2 toxic to most methanogens.  It is the methanogens that produce methane gas a powerful greenhouse gas or what is commonly termed natural gas.  Methane odorless is highly toxic (natural gas contains an agent that is sensitive as a "smell") to us.  An incident occurred in Cameron (1986) in which over 1,700 people perished from Lake Nyo's gas release that included sulfide smells. 

This toxic organic layer is also being promoted as "Blue Carbon" deposit able to concentrate carbon.  This layer from the ability to purge formic acid usually has a low pH.  Cleaning anerobic aquaculture filters can be very dangerous without proper air circulation.  Sulfide gas can be released and kill humans.  In 2002 the University of Maine suffered a tragic sulfide accident at a Franklin Aquaculture facility.  We need to include the bacterial sulfur cycle in estuarine study – my view, Tim Visel.

Marine Composts and Fish
Once sapropel was stabilized and reached higher into the water column, it could be invaded by plants – Submerged Aquatic Vegetation (SAV) mostly eelgrass – and when it reaches tidal levels Spartina alterniflora or Spartina patens the salt marsh cord grass (See EC #17-B posted on April 12, 2019).  When root tissue grows into sapropel becomes peat and in the historic literature the terms peat and sapropel are often used together.  Salt marshes are sapropel deposits which reached the surface and now sustains plants –it is difficult to imagine salt marshes as huge marine compost piles but that is what they are.  Further conflicts arose as to what type of dead plant material composes sapropel, the remains of marine plankton or the vegetation of grasses or trees of the land.  The process and even the bacterial boundary layers were well known by the 1930's.  Most of the coastal literature during this period is when salt marshes were often described as "peat."  In one of the best descriptions of the role of bacteria and the reduction of organic matter can be found in "An Introduction to Botany" by Arthur W. Haupt Associate Professor of Botany University of California at Los Angeles (First Edition 1938) – McGraw - Hill Book Company, Inc In the Environmental Relations section – The Decay of Organic Matter pg 154 to page 156 – (1938) contains this statement,

"The decomposition of dead organic matter involves a complicated series of changes, there being usually a large number of intermediate products formed, such as various alcohols, organic acids, etc.  Ordinarily there is a succession of various kinds of decay producing organisms, chiefly bacteria, each carrying the process a little farther, until finally only a few relatively simple substances are left.  All these organisms gain their subsistence from the great amount of potential energy contained in the dead material, but none except the last ones exhaust it.  The ultimate products of decompositions are mainly water (H20), carbon dioxide (CO2), ammonia (NH3), methane (CH4) hydrogen sulfide (H2S), free hydrogen, and free nitrogen.  The water and carbon dioxide may be used again by green plants in photosynthesis.  Certain bacteria can obtain energy from the other substances by being able to oxidize them and in doing this form products directly utilizable by green plants.  Ammonia is converted to nitrites and then to nitrates by the nitrifying bacteria.  Nitrates also are formed directly from free nitrogen by the nitrogen-fixing bacteria.  Other kinds of bacteria oxidize methane, hydrogen sulfide, and free hydrogen.  Besides the bacteria of decay, many other kinds of saprophytes are found among the fungi, examples being yeasts, molds, mushrooms, and many others.  These plants live on humus, rotting logs, dead animals, etc."

Sapropel as a term/name was "dropped" from the literature in the middle 1970s as nitrogen was looked at for speeding eutrophication of estuaries.  The first instruments for testing nitrogen levels relied on those compounds dissolved in water, and not those locked up in organic matter.  This is sometimes referred to as "old nitrogen."  At first researchers could not measure it and controversy still existed with salt marsh researchers well into the 1980s (John Teal – Scott Nixon – The "Outwelling" Controversy") about have much productivity (organic) algal material stayed in salt marshes and how much "outwelled" detritus into areas outside the marshes.  Another conflict came up as well what organic matter reduction pathways to include as well – the cold, oxygen sufficient nitrate or the warm, oxygen deficient sulfate ammonia pathway.  Organic matter was going to be reduced the question was it by what pathway or by what bacterial series?  In many nitrogen studies, the nitrogen released by bacteria in sapropel was not counted at all.  To further complicate the issue sulfate reducers of sapropel – could shed sulfuric acids unlocking sulfide, phosphates, aluminum and metals into the water once again exposed to oxygen.  Deposits of dead algae could become "greasy" from high lipid oil content. 

In time these deposits could produce paraffin hydrocarbons and under pressure a nitrogen/sulfur solid termed kerogen.  The high wax (paraffin) content separates it from petroleum and it is today called oil bearing shale – derived form dead algae and bacteria.  This substance in low oxygen conditions emits a smell and stains the hands – this is a 2016 segment from a hard shell clam operation in Greenwich Connecticut, Greenwich Times, "What Are Clams Economic Impact On Greenwich," by Peregrine Frissel June 25, 2016,

"Stilwagen's crew calls that muck "black mayonnaise" because it's so black and greasy you have to use soap and water to get it off your hands."   
This is why a bias exists in the salt marsh literature – as much of it excludes the impact of temperature or energy into carbon, nitrogen or sulfur "fluxes" from them.  Most salt marsh research was done during a growing environmental movement against human pollution, in a cooler climate period and later transitioned into environmental protection.  The impacts of large amounts of organic matter would be eclipsed by human population and their pollution being classified as "not" natural.  But organic matter delivered into marshes in times of heat and low energy was a natural pollutant as the nitrogen criteria today now describes.  It could at times overwhelm oxygen bacteria that were basically composters of the shallow sea marine soils.  During extreme heat, bacterial reduction salt marshes emitted sulfides, sulfuric acid, at times toxic levels of aluminum.  Salt marshes, in times of extended heat now became sulfur killing fields and in many places the site of fish kills.  Sapropel was formed a more dangerous material hosting pathogens itself (Vibrio).  In heat sulfate reducing bacteria could cause sulfides levels so high as to kill eelgrass and even salt marsh plants – the suspected cause of recent salt marsh dieback outbreaks of the last two decades.  (This sulfide connection is frequently referred to as the smell of rotting eggs).

In February (2016), I asked resource agencies here in Connecticut to recognize sapropel as a distinct habitat type – capable of high heat ammonia discharges that are toxic to sea life.  As you can imagine it would mean nearly rewriting the last half century of salt marsh ecology – one in "cold" temperatures and now one for the "heat."  (However, with the global warming discussions it is now a necessity to include such revisions we cannot ignore the formation of these heated sapropels T. Visel).  Sapropel, however, is an important link to inshore fisheries and shellfish – oysters for example stop filter feeding in heat from toxic sulfide discharges – the blue crab jubilees in the historical literature are also part of this sapropel sulfide discharge.  I do find it somewhat ironic that many agencies that comment about the negative impacts of sea level rise (more sulfate) and global warming (less oxygen) yet remain quiet about this growing sapropel danger? 

In many areas, the term "black mayonnaise" has become the term of choice as many estuarine reports continue to mislabel it as fine grain sediments.  It is not the mineral sediments of geology but plant organic matter of biology – largely governed by temperature that helps bacteria form sapropel.  That is why fishers could have an important role in describing habitat histories as part of environmental histories that looked beyond human pollution (significant in its own right) events but includes cycles of fish catches and climate features of temperature and energy.  It is the fishers that experience these two bacterial pathways and comment upon them.  The concept of salt marshes and the deadly sulfur cycle in them is often hard to understand after decades of omission (my view, T. Visel).  Many chemistry textbooks give little or no attention to the marine sulfur cycle although may have large sections on global warming.  I see that now slowly changing fortunately (my view, T. Visel).

So understandably the recognition of sapropel continues to be slow or subject to endless misleading terms.  The lower Susquehanna River Watershed Assessment Report was released in March 2016, it mentioned volatile organic solids as "organics which are living or previously living solids" (page 89), but fell short of describing the full impacts of black mayonnaise (sapropel) formation to habitats below the Conowingo Dam, largely as the result of storm events delivering huge organic loads to those estuarine areas below.  I have little doubt that leaves have been held back by the Conowingo dam as many reports mention declining depths over time (forest duff dead leaves manure yard wastes, etc). This usually happen following rain-storm events. (See Sapropel and Climate Change, The Sound School Adult Education Directory January, 2013).  These events overwhelm nitrate and oxygen composting (reducing) bacteria to those that can utilize sulfate with very significant habitat and biological impacts to fish and shellfish habitats that then occur sometimes for years, perhaps decades.  This impact was reviewed in the first nitrogen/bacteria series on the Blue Crab ForumTM Environmental/Conservation index posted Sept 29, 2014 "What About Sapropel And The Conowingo Dam?

From time to time I still read accounts from Chesapeake Bay blue crabbers that some blue crab habitats have yet to recover from Hurricane Agnes (1972).  Sapropel that had oxygen when it is covered by leaves seals any oxygen exchanges below are now reduced by bacteria that do not require it.  This turns into the sapric layer and if buried leaves a layer of organic matter described as black mold.  (Harold Castner, 1954) in the historic literature but likely describes sapric to formic process below water – on terrestrial soils that black layer is frequently described as a "top soil."  A half century ago it was termed a vegetable mold.

History can, for example, help us rediscover some of our habitat histories. At one time New England and Canadian Maritime coastal farmers harvested near surface sapropel deposits for soil enrichment to nourish depleted terrestrial soils from an estimated 1,000 mussel mud machines (Drawing Lines In The Ice – Mussel Mud Digging in the Southern Gulf of Saint Lawrence by Joshua D. MacFadyen, 2013).  But farmers soon learned of its high sulfur content and its ability once re-exposed to air (oxygen) to generate a sulfuric acid pulse.  Once mitigated with calcium (oyster shell), it was valuable soil conditioner coastal farmers boasted about increased crop yields in agricultural reports for over two centuries.

John Hammond once grew huge tomatoes in Sapropel mixed with oyster shell in buckets from the Oyster Pond River in Chatham, Mass.  Mr. Hammond on Cape Cod was a retired oyster planter in Chatham Mass.  He had noticed the increase of "humus" covering hard bottom habitats on Cape Cod while culturing oysters.  The deeper and more oxygen limited the sapropel deposits, however, the greater amount of sulfuric acid was generated. This is a comment from a farmer in my town of Essex, CT who used sapropel (marine mud) a century ago and its impacts to local crops (1879).  The Connecticut and Oyster River in Old Saybrook were local "marine mud" fertilizer sources.  At times, the organics trapped behind millpond dams was tried with disastrous results.  These mill pond contained deep deposits of leaves rotting without oxygen and the odor is from the sulfides.  These smells were often very strong of sulfur and mentioned many times just prior to a fish kill.

An 1879 CT Board of Agriculture has this report – regarding direct (no pH modification) of Sapropel application to a farm as reported by the Connecticut Agricultural Experiment Station.

"Mr. Stevens of Essex, CT remarks – Our mill ponds, a few miles back from the river, contain a rich black mud, quite deep and with a very strong smell.  It has been tried on various crops, but kills everything – after being hauled and dried it turns from black to white, and puckers the mouth like alum."  (Alum is aluminum sulfate – T. Visel).

And then what happens to habitats when sapropel forms in shallow estuarine habitats today?  That is happening now in the Indian River Lagoon in Florida.  Organic matter from many sources animal, human, plant has accumulated and formed a sapropel.  Once formed it will forever alter the chemical characteristics of the waters above.  An article titled "Legislature Funds Muck Removal in Central Lagoon" (Indian River Florida), describes a "black mayonnaise" as a growing habitat health threat to the Indian River Lagoon – the article is dated February 15, 2014 in the Vero News by Steven Thomas and contains the following segment:

"A world-renowned expert on sedimentary, Trefry, a professor of marine and environmental chemistry at Florida Institute of Technology tells the committee there has been an incredible expansion of muck since he came to the area in the 1980s due to fertilizer and other causes.  "It is like a cancer that has been spreading," Trefry said, "besides clouding the water column and continually releasing nutrients that feed algae blooms much accumulates toxins and contains bacteria that deplete oxygen levels in the lagoon.  It smothers all life forms other than bacteria – whenever the muck is, all habitable life is gone." 
And the soil conditions that made those sulfuric acid impacts so noticeable are also mentioned by Mark H. Stolt and Martin C. Rabenhorst (2010) in report on Subaqueous Soils and mentions many of the features of sapropel.  (Several soil scientists have recently started to term nearshore "sediments" as acid sulfate soils recognizing the sulfur bacteria processes in them that make them so).

They also describe the work of Dr. George Demas (1998) who called for the mapping and classification of subaqueous marine soils – a major departure of the previous label of just sediment. In a review of the progress a 2010 report contained this segment (page 5).
•   "These subaqueous soil materials here also referenced to as sedimentary peat, copiogeneus earth, limnic materials.
•   Subaqueous layers that contain various amount of more or less unrecognizable organic debris that are enriched in sulfides were termed sapropel.
•   Most of these sulfides are Fe (iron) monosulfides or pyrite in the solid form or hydrogen sulfide gas as recognized by the rotten eggs smell – colors are typically black that changed to gray upon drying."

This last description is almost the same as Stevens (Essex, CT) above made over a century ago.  It seems to me that the work on subtidal soils that Dr. George Demas started in 1998 has been continued by only by a few soil scientists – they have been doing the heavy lifting in describing salt marsh acid sulfate soils to the public (my view); we need to see some biologists and ecologists involved in sapropel study as well, my view. The habitat impacts of sulfate reduction and the formation of sapropel has been noticeably absent representing these fields and no longer should be (my view).  This is especially important because in a warming climate bacterial processes shift to utilizing sulfate dissolved in sea water.  Just a few degrees can shift entire habitats to sulfate metabolism.  Some of these warm water bacteria are pathogenic as well.

And the country providing the clearest explanations of sulfate reduction is, in my opinion, is Australia Dept of Agriculture Water and the Environment.  Several fact sheets describe the formation of blackwater and describe blackwater events.
The Blackwater fact sheet has this description:

"Blackwater can be natural feature of lowland river systems and occurs during flooding when organic matter is washed into waterways and consumed by bacteria leading to a sudden depletion of dissolved oxygen in water. The black appearance of the water is due to the release of dissolved carbon compounds including tannins as the organic matter decays, similar to the process of adding water to the leaves."

And the second fact sheet, "About Acid Sulfate Soils?" (brackets [  ] indicate my comments T. Visel).
"Acid sulfate soil is the common name for soil that contains metal sulfides. In an undisturbed and water logged state [i.e. such as accumulations behind dam or tidal restriction, T. Visel] or exposed to oxygen acid sulfate soils undergo a chemical reaction known as oxidation; oxidation produces sulfuric acid which has led to these being called acid sulfate soils – Acid sulfate soils are formed by bacterial activit
y in water logged conditions when there is no or little available oxygen."
"Naturally occurring bacteria convert sulfate from seawater, ground water or surface water into sulfide. This sulfide reacts with metals especially iron in the soil sediment or water column, to produce metal sulfides. In order to convert the sulfate into sulfide, the bacteria also need a source of energy provided by organic material such as decaying vegetation."

For over a century, researchers have known about two distinct bacterial reduction pathways – the oxygen – nitrate pathway and the sulfate ammonia pathway; The controversy between scientists would divide those who wanted to include both and those who chose to promote the oxygen – nitrate pathway leading to charges of perhaps improper science research bias while glossing over or "forgetting" the sulfate bacterial processes.

And a redefinition of the ecology of the "low salt marsh" would include sulfate reduction (and a source of sulfide salt meadow "browning") and the high salt marsh ecology which would favor drained peat and oxygen.  Within four years two complete salt marsh studies would be published by the same funding agency the U.S Fish and Wildlife Service – one titled The Ecology of New England High Salt Marshes (Nixon, 1982) and other titled The Ecology of Regularly Flooded Salt Marshes of New England (Teal, 1986).  Each of them focused upon a different pathway, Nixon focused on oxygen and Teal included sulfate.
In the discussion of what role salt mashes had in supporting the food chain as a source of plant food, dead plant material that "outwelled" from salt marshes to feed fish (sulfate sufficient) or that of a giant filter absorbing organic matter recycling it in place (oxygen sufficient).  Lost in the debate (which still continues today) is what happens when the high marsh ecology becomes that of the low marsh (in extreme heat) the conversion of saltmarsh peat into sapropel pools with all its negative habitat consequences.  (These are termed pannes today on salt marshes).  Impacts included vibrio bacteria to ammonia supporting Harmful Algal Blooms.  Even here these HABs have left a history lesson for us as well buried in sapropel with high ammonia the cysts and spores that lie dormant waiting for sapropel to unleash them – with an acid reaction again.  In times of heat and drought acid soils increase – in cold and rain organic matter is added to the compost pile.

This buildup or decline depends upon they type of bacteria and sulfate metabolism by products which we can measure and obtain data.  This has a chemical explanation as Dr. Robert Whitlatch describes in The Ecology of New England Tidal Flats A Community Profile Biological Services Program, March 1982, pg. 7 has this description by depth and thus the removal from elemental oxygen.
"In muddy sediments, two or three distinctly colored zones commonly exist.  The upper most is light-brown, extending 1 to 5 mm 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 gray-colored zone may exist below the black zone due to the presence of iron pyrite."   

Dr. Robert Whitlatch was also one of the first researchers highlight "tidal choking" a scenario in which the inlet or tidal exchange is restricted and traps organic matter in a cove or salt pond.
Salt Marshes and the Sulfur Cycle

Most of the salt marsh studies that examine cores have reviewed changes in vegetation from the melting of the glaciers until today.  Cores of New England salt marshes that showed surface vegetation at depths below the current sea levels were often explained as the result of three factors:
1.   Sea level rise—the melting of the huge ice that covered temperate areas has raised sea levels submerging coastlines for thousands of years (submergence).

2.   The earth's crust on which salt marshes developed is sinking (called subsidence).
3.   Or a combination of both submergence and subsidence.

Largely excluded from salt marsh habitat histories is a fourth mechanism, a chemical one induced by heat—the digestion and purging of substances as a composting process involving bacterial reduction that consumes the salt marsh peat.  In times of heat, the salt marshes were consumed and sank.  This happens in heat and a reduction of organic matter as during a drought.  Salt marshes became very soft and at times slowly sink below the high tide level.  This allows more sulfate dissolved in seawater to flood them, providing sulfate reducing bacteria fresh sources of oxygen locked in this sulfate compound (Organic matter that once flowed onto marshes could be retained by dams – the so called "Nile River Effect").
Teal (1986) also includes the most complete descriptions of the Sulfur Cycle in a salt marsh—one that although penned over three decades ago, stands up today.  The fact that it is mentioned at all is noteworthy.  This sulfate metabolism absence is complicating climate change global warming discussions along our coast.  A warming climate will "push" the organic reduction process towards the deadly Sulfur Cycle—a segment of a very important climate change discussion that is missing in many estuarine studies (my view) and helps unfortunately to explain the bias surrounding sapropel study and or its recognition.  (See appendix 2 – Bo Barker Jorgensen).

While Teal (1986) described the Sulfur Cycle in his 1986 Fish and Wildlife paper, Nixon (1982) largely omitted the Sulfur Cycle, other than including how organic matter could be oxidized in a much faster oxygen reduction bacterial pathway mentioning the research from 1976 (Valiela, et al.)  This is why the surface organic material is quickly "mobilized" recycled from the reduction processes of oxygen bacteria that thrive and from Valiela, et al. (1976) this segment is found in the Nixon 1982 study."  We did not expect the marked decay in dead matter... since we supposed that decomposition in anoxic sediments would be slow.  However, dead parts still attached to the living plant would be supplied with oxygen from the plants air spaces.... So that aerobic oxidation could occur." 

This would cause in heat sections of salt marsh to give way or sink.
Some of these same features were talked about by George Nichols a century ago in his series on the Vegetation of Connecticut Torrey bulletin titled,
"The Vegetation of Connecticut VII The Associations of Depositing Areas Along The Sea Coast" by George E. Nichols (1920).
The heat that Nichols reported (1920) had high toxic sulfide levels – the byproduct of sulfate reduction or the eating of organic tissue by strains of sulfur reducing bacteria – the source of the marsh stinks so often reported during this 1880-1920 period.  This situation often perplexed shore botanists and Nichols on Pg. 531 makes a very accurate observation of the impact high sulfate/sulfide levels can do – leaving the marsh surface lower and absent of living vegetation -   (my comments, T. Visel):

"These salt meadow pools are "rotten spots" (most likely sapropelic – T. Visel) (technically termed pannes) the origin of which will be described later, may lack vegetation entirely.  So far as the higher plants are concerned and, while the alkaline grass is frequently present (the surface bacteria exposed to air can release ammonia, driving pH to extreme basic levels – a high pH at the surface that decreases with depth – T. Visel) the salt meadow grass and the black grass are almost invariable absent."

The pannes (Nixon, 1982) of the 1960's and 1970's did not resemble the chemical features of salt marshes in the 1880 to 1920 period along New England's coast.  Here in the heat, one finds reference to sapropel in the creeks and sulfate digestion slumping salt marshes to form large pannes as many had healed in the colder 1950's and 1960's.  Researchers noticed as did farmers that few organisms could survive in sulfide rich sapropel on land soils or over marine soil - The Sulfur Cycle, kept plant life diminished until oxygen reduced sulfuric acid and rains moderated the lowest pH values (Bivalve shell was recommended as well to moderate acidity as early as 1879).

While Teal gives a good discussion of the sulfur cycle covering much of the bacterial sulfate reduction processes and on page 9 which describes sulfide toxicity when many salt marsh researchers of that time period did not.  This is a huge issue when waters are warmed.
Pg. 9 Teal –
Biological Report 85 & 7.4, June 1986 – The Ecology Regularly Flooded Salt Marshes Of New England – A Community Profile by John M. Teal Woods Hole Oceanographic Institution has this quote on page 9:

"Conditions in the marsh sediments are greatly influenced by the abundance of sulfate in seawater.  Under anoxic conditions, there are some bacteria that use sulfate as an electron acceptor, decompose organic matter, and produce sulfide.  The resulting sulfide is primarily responsible for the degree of reduction in marsh sediments.  Sulfide is highly toxic to most organisms, so those that inhabit marsh sediments must either deal with it or avoid contact with it.  Metals, especially iron, are also abundant in marsh sediments, and much of the sulfide produced is bound up as metal sulfides" (King 1983; Howarth and Giblin 1983).   

Pg. 47 – Teal also mentions the toxic impacts of leaves and organic matter:
"There is additional accumulation of heavy metals in dead leaves and fresh detritus formed from marsh plants as they begin to decompose (Breteler, et al., 1981a).  Detritus may be enriched to potentially toxic levels by uptake of metals in the more oxidized surface layers of marsh sediments or by metals associated with surface organic layers, just as the detritus is about to enter the food chain.  If the amounts of metals are small, they will have no effect, but in larger concentrations, the marsh products may reach toxic levels."

The increase of methyl mercury in the recent salt marsh browning is a sign of this Sulfur Cycle impacts.  This transition is seen by the color of the salt marsh itself.  A 1950's and 1960's oxygen dominant marsh has been transitioning to the Sulfur Cycle with the slumping (better term digesting) of salt marsh peat, the formation of hot sulfide rich pools and a transition of plant species to the red glasswort.  The green salt marshes in some areas now appear "brown" with sulfide toxicity of Spartina patens and the appearance of glasswort, contain red patches as it is a marine salt marsh plant able to withstand high levels of salt and sulfide.  I have heard some shell fishers comment that the salt marshes do not look healthy; some areas appear to be sinking and pools have formed where healthy, thick strands of cord grass once existed.  In the deeper pools, a blue/black sticky muck has now formed with grey to white streaks —the bacterial beginning of sapropel.  The winter largely stops the process, but when summer heat arrives the oxygen levels lower and these pools can get deeper over time.  The reduction of salt marsh peat can go unnoticed, although marsh levels can subside and at times collapse.  This is caused by the sudden release of bacterial produced gas.

Salt hay operations in New England often had tide gates placed at marsh creeks.  In a process of reduced tidal exchange marshes could be "dried" (drained is a better term) and salt haying could be made easier.  If organic matter (hay) was removed faster than what accumulated salt marsh (peat) levels over time would "drop."  In high heat oxygen could accelerate subsidence and marshes "sink" below tides to be slowly digested by bacteria and a pond may replace the marsh.  Cores of such ponds often show peat below and in time no recognizable plant tissue remains, just a dark humus layer.  To replace the loss of organic matter farmers would just scoop out sapropel (termed "dressing" in the farm literature) and apply it to reinvigorate salt marsh monocultures.         

We see the result of oxygen composts in our terrestrial "top soils" as well the black humus of thousands of years of decomposed organic matter grasses, tree leaves and tree tissue, bark, blooms, nuts, etc.  It is the "top soil" that has the good oxygen sufficient bacteria that helps plants grow (and is a valuable land scape foundation for lawns/shrubs) fix nitrogenous compounds and move them into root tissue.  Terrestrial soils low in organic matter were termed poor or "impoverished" by the colonial New England farmers.  Although nitrogen could have been limiting it was also a factor of soil bacteria the living microbes in the top soil also needed "food" that made it a "valuable agricultural soil."  Nature washes organic material into valleys or drowned river mouths and some of the best "fertile" soils were those that occasionally flooded.  It was the valleys that contained the deepest top soils, the hill sides were subject to erosion and on sandy soils the rains tended to wash nutrients quickly below levels of plant roots.  Such soils were often termed "leached" for most nutrients drained from the quickly from the surface. 

Salt marshes are in many ways the composts that collected along the shore (although some ecologists recoil at the term compost – that is the foundation of salt marshes, when roots grew into these organic composts they were then termed "peat") this happens in freshwater systems as well and soils termed peat can be made some of the richest of agricultural soils – when exposed to oxygen.  Colonial Connecticut history is rich with accounts of dewatering salt marshes to "help" hay harvests and drained the peat became firmer and more suitable for agriculture.

The history of the Everglades sugar industry was developed in the Florida Peat Experiment Station established in 1923.  Once peat was drained and re-exposed to oxygen, sulfur levels dropped enabling some plants with high sulfur tolerance to grow – sugar cane Saccharum in the south and cordgrass Spartina patens in the north.  That is why New England farmers were anxious to improve soil yields and looked to organic matter as enriching soils.  Stable manure, bird guano, fish scrap, and sapropel were all utilized to improve New England's soils.  New England soils were still often described as "thin." Just as the Native Americans before use noticed that soils deficient in bacteria produced less plants/grain – used fish as a fertilizer.  Bacteria no doubt fed on the fish decomposing it and making plants able to utilize what nitrogen was available.  Soils that contain little bacteria in organic matter shed nitrogen because soils did not hold ions, therefore the plants could not mobilize it.  To slow this loss clay was often mixed into sandy surface soils to retain moisture and slow nutrient loses – this type of soil was frequently termed excessively drained soils.  Organic matter was often added as a top dressing not so much to feed the plants but to nourish the bacteria that in turn helped plants grow.           

Some factors about climate change are that colder and warmer periods (climate changes) have occurred before and left a habitat history in chemical/organic deposits in different parts of the planet.  Most climate change soil or sapropel research has not occurred in the temperate zone from the impacts of ice/glaciers has been very recent.  Our warm-up in New England is very recent about 10,000 years ago and many Connecticut hillsides have been shaped by thick glaciers.  Connecticut also has a dinosaur park with footprints estimated to be made 200 million years ago.  The concept of large changes in climate is not new just our role in creating or enhancing it is.  Most climate research has occurred in the Mediterranean and Black Seas as coastal habitats have been more stable than ours.  This provides a long-term view of subtidal habitats – as compared to our coasts heavy indented with bays sounds, lagoons and river mouths.  Some of the concern is that climate change research has focused upon "cultural pollution" our role in changes of chemical and biological induced climate change.  Bacteria may have left us a chemical history in these organic layers of long ago – that could provide a unique view of colder and warmer organic matter reduction and how dangerous a warming climate is to oxygen life.

One of the ways we can examine climate change is its influence on how we lived.  In the 1890s most houses were not insulated in New England it was warm along the coast and in 1899 New England had an "ice famine" it was so warm then ponds did not freeze, and the entire ice industry "failed" which led to "ice panic" as ice prices soared.  But houses built then often had a porch – the air conditioning of the present time for "hot terms."  But then it turned colder in New England and insulating your home or apartment was no longer looked at as a new industry or additional expense soon developed to make homes more livable in heat and cold.  Insulation now became a "necessary" item.  In the 1890s eelgrass peat flourished and the first paper backed home insulation was made from it and was called "Cabots Quilt." Eelgrass grew thick in the 1890's and became a well-accepted insulating material. The Niantic River, for example, is noted for its large eelgrass harvests in Connecticut.  The heat and cold and its impact upon organic peat deposits is also mirrored by the rise and fall of oxygen in sea water and its impacts. 

When the Florida Everglades peat bogs were drained and converted into Acid Sulfate Soils – oxygen rapidly allowed bacteria to take over from "drowned peat" bacteria which had produced metal sulfides.  An entire New England industry would be recognized from this sulfur cycle process and iron bacteria as the chelation of soil iron is termed "bog iron."  Madison, CT for example had "bloomeries" bog iron furnaces that produced crude but serviceable "bog iron" from marsh metal deposits.  Now buried peat in heat burned (rapid oxidation) chemically and at times physically dry (they actual caught on fire).  In these areas the organic matter gain was quickly offset and large areas of drained peat began to "sink" or subside – efforts were soon made to drain the peat only to reoxide (oxygen) the first 20 or 30 so inches and not to over drain as rapid oxidation/consumption by bacteria would consume the peat faster that collection of surface organic matter.  In areas of deep drainage canals peat surfaces (edges) would collapse. 

Europe had long used dried peat as a fuel and at times considered even here in the United States.  The largest use of peat today is the primary ingredient in potting soil.  Much of the historic peat research comes from southern regions.

The Florida Peat Experiment Station established in 1923 soon recorded what happens when peat was drained and conditioned into agriculture soils.  The distinct layers that govern pH and chemical characteristics are found in the literature but were overshadowed by draining canals and drought.  Vast areas of the Everglades peat during dry periods caught on fire and burned for weeks.  Drought had a natural oxidation consequence as oxygen sufficient bacteria consumed peat in cracks but drainage canals made this situation worse – described then as shrinkage. During droughts water was no longer a foe to be drained away but now was needed for "peat" to control the bacteria consumption of the peat itself.  The Florida State Horticultural Society manuscript titled Florida Peat Investigations, Vol. 41, April 10, 11, and 12, 1928 by R. V. Allison of the Everglades Agricultural Experiment Station, Belle Glade Florida mentions this problem in 1928 if the peat was wet, it could not sustain production agriculture but once exposed to oxygen peat was subject to rapid oxidation (fires) and chemical oxidation by bacterial composting – the peat surface was too dry and would sink.

This is a section of R. V. Allison's 1928 paper during a meeting of the regarding then some three million acres of Florida's "peat lands" concentrated in the Everglades (my comments, T. Visel):

"The peat land of the Everglades as a result of the protracted period of drought is completely broken up by a through ramification of enormous cracks and the consequent additional exposure of the mass to natural oxidation (exposure to oxygen T. Visel) and shrinkage must necessarily be tremendous. These remarks pertaining to the rapid dissipation (bacterial reduction, T. Visel) of the actual soil material itself under such conditions of exposure are offered only as suggestive of the great desirability of more fully investigating soil water movements under these conditions in order that we may be able to handle the water in such a way to afford a maximum amount of protecting to the mass (peat lands, T. Visel) of the material at all times."

In just a few years of study, agricultural peat researchers learned to control bacterial reduction of peat by water and limiting oxygen from the air.  The bacterial process over time would leave a chemical signature in the peat changing its pH a plant production potential.  As peat cores were examined characteristics were noted, and on page 59 introduces new three profiles, with the bottom "black peat" residues of under growth stems and roots.  Allison also mentions the chemistry of oxidation both combustion (burning) and chemical bacterial reduction.  These peat soils could be at times enormous heat sinks and matches my observations in Buttermilk Bay on Cape Cod in the early 1980's.  There on Cape Cod when sapropel first covered the shallow bottom waters of eelgrass peat actually became "hot" well over 100oF, Allison (1928) mentions that surface peat soil at midday at the Experiment Station (Belle Grade Florida) could reach as high as 142oF (pg. 62).  Plants that live in peat would need to survive huge changes in temperature but existence in peat would at times also be dominated by the return of the sulfur cycle, especially in those peat deposits that in oxygen poor conditions sulfur bacteria has ample supplies of sulfate – the coastal salt marshes with flushes of sea water containing huge amounts of dissolved sulfate.  (When I attended the Florida Institute of Technology for oceanography study in 1973, I would wake to the smell of sulfur from huge peat fires just west of the Jensen Beach Campus).

These "peat" plants would need to be sulfide tolerant and contain the ability to keep its oxygen bacteria alive – a natural bacterial filter (shield) that allowed roots to utilize nitrate surrounded roots termed the rhizosphere.
The plants that live in sapropel share many of the terrestrial plant defense mechanisms for sulfide by the ability to move oxygen to its vulnerable root tissue.  Eelgrass is especially suited for living in both worlds – for a while.  While it thrives in oxygen environments it can for a time survive in increasing sulfides –much of this from the bacterial action of sulfate reducing bacteria in low oxygen conditions.  Some of the pioneer research on this submerged aquatic vegetation and the impacts of sulfide upon it was conducted in Tampa Bay – on a submerged aquatic plant Thalassia testudinum commonly called today turtle grass.

Carlson et al (1994) details the implications of sulfide toxicity impacts to submerged vegetation – Bulletin of Marine Science 54 (3) pg. 733-746 (1994) Florida waters titled "Relationship of Sediment in Sulfide to Mortality of Thalassia testudinum in Florida Bay, Florida" on page 739  is found this section (my comments, T. Visel):
"Stable Sulfur – Isotope analyses of Spartina alterniflora (Carlson and Forest, 1982) and other seagrass and mangrove species (Fry, et al., 1982) indicate that pore water sulfide may be incorporated by plants growing in anaerobic sediments (marine soils T. Visel) presumably when the capacity of the plant to maintain an aerobic environment in its below ground tissue (roots, T. Visel) is exceeded.  The prevalence of gas conducting tissue (aerenchyma) in roots and rhizomes of flood – tolerant and submerged aquatic plant species suggest that tissue is a primary defense against sulfide toxicity."     
And further,

"Aerenchyma provides a path for photosynthetically produced oxygen to move from leaves to roots and rhizomes (Armstrong, 1979) and Thalassia shoots, roots and rhizomes have large lacunar spaces (Tom Linson, 1969) Thursby (1984) has shown that photosynthetically produced oxygen diffuses from the roots of Ruppia maritima and oxidizes then surrounding sediments (marine soils T. Visel) and Penhale and Wetzel (1983) found that aerenchyma volume was greater and root respiration rates were lower for Zostera marina (Eel grass) in intensely reducing sediments (marine soil, T. Visel) than in more oxidized sediments (marine soils, T. Visel) Smith, et al. (1988) found that photosynthetic oxygen production and shoot to root transport was generally sufficient to maintain aerobic conditions in Zostera roots and rhizomes during the day but anaerobic conditions occurred in roots and rhizomes at night." 
This would make eelgrass roots vulnerable to any low oxygen soil conditions and fungal rotting.  In the years following the 1920s this would be known as the eelgrass wasting disease.     

In a habitat transition process from submerged eelgrass sapropel to salt marsh peat it needed a plant that could survive the sulfides of sub surface sapropel but could move oxygen to its roots in a mechanism critical to eelgrass – as often in the historical literature the description of a blue black ill smelling mud that supports little to no plant life (Nichols, 1920) Spartina alterniflora appears to be that plant in northern areas perhaps duplicating the role of mangrove trees in southern marshes.  Sapropel at the end of habitat succession can only support plants that can protect its rhizome bacterial shield from sulfide so it can continue to obtain nitrates from this oxygen reduced soil.  Tides can supplement low oxygen but it is the ability of Alterniflora to move oxygen from the air into a specialized plant organs called the aerenchyma.  In peat environments plants ability to protect its root systems with oxygen largely determines when and where it can live in the coastal zone that is often termed zonation.  Eelgrass is very prone to natural cycles because it is on the front line of climate changes.  If it turns hot chemical and biological (bacterial) oxygen demand the soil turns sulfide rich toxic to eelgrass.  It is a war so to speak between oxygen and sulfur bacteria and plant life represents causalities that we can watch/or monitor. 

There is very little that we can do to change the outcome of this habitat war and why some eelgrass restoration efforts did not succeed when eelgrass was planted into sapropel.  The effort to restore seawater to salt marshes – in times of cold oxygen sufficient to salt marsh plant life but in times of heat peat becomes chemically unstable when tidal marine waters sustain sulfate metabolism or the sulfur cycle.  Sapropel can reach the surface as the sulfur reducing bacteria now utilize sulfate as an oxygen source from enhanced water flows.  To salt marsh researchers previously firm peat now turns softer or mushy.  To utilize oxygen locked in the sulfate molecule, sulfate-reducing bacteria can break apart sulfate and combine it with hydrogen ion to form the toxic hydrogen sulfide molecule H2S – only plants able to withstand the chemical changes in sulfide and the presence of salt can now survive.  It is the smell of sulfides that denotes this process has started – and the stronger the sulfide smell the greater the damage to oxygen requiring sea life.  (This is described as the smell of rotten eggs in the historical fisheries records).

Spartina alterniflora offers us a chance to study this process as it lives under the water but has access to oxygen in the air part of the tide cycle.  It will outlive the subtidal eelgrass because of submerged in hot oxygen depleted seawater rich in sulfate will slowly die.  When that occurs, blue crab megalops lose this habitat as it now becomes toxic and kills blue crab larvae almost on contact.       
The Rise of Sapropel Dominated Habitats in Areas of Reduced Flushing and Tidal Exchange
By the mid-1970's, strong storms often moved sand waves into the mouths of inlets blocking them.  In southern Rhode Island salt ponds, sand waves (think of storm driven sand bars) were observed to form and move into breachways.  These sand waves restricted circulation exiting them, trapping organics.  This is an old cycle illustrated in the alewife fishery and the unblocking of inlets before blackwater could form.  This event is frequently associated with strong sulfide smells termed "rotten eggs," a common observation of the coasts long before they became summer villages – many of which were built to escape summer heat waves.

Sand waves in or near inlets tended to act as breakwaters and they were a natural feature that sometimes became a dune line or "Bar" such as the feature at the mouth of the Niantic River, the Clinton Cedar Island or Sandy Point in New Haven Harbor.
In long periods of heat and few storms, these bars tended to move inland; in cold and ice, they broke and lobes of new sand deposited by new breaches or cuts.

In Connecticut, these waves were cut by ebb tides (termed ebb tide channels) water flowing out at low tide.  The amount of water ebbing was key to keeping good flows and circulation.  In large flow rivers, such as the Connecticut, these sand bars were offshore the mouth and sometimes were a series of them.  In Connecticut's navigation reports, these bars are often listed as navigation barriers or hazards.

In areas with barrier beaches, a sudden western shift of sand can block coves and salt ponds, especially if they have long connections to the sea.  This allows organics to be trapped in the upper cove or bay.  Tidal flow constrictions also in the form of the rail and road crossing often concentrate incoming flows and push sands north of constriction as the ebb flow is most always weaker, especially in coves where sudden ebb tide runoff acts to move sands back.  A dam or freshwater diversion reduces the ebb flow, and sand waves often move into and then block exit channels.  To restore flows, this often required oxen teams and scoops to cut into the barrier and restore flows.  Today, these storm-driven bars are removed by dredging. Causeways that restrict the flows are seen as "reverse deltas."  They act as man-made sand waves and are easier to observe/find in survey work.  In a survey of Alewife Cove in 1987, Waterford – New London, CT these conditions were observed to move far into the cove (See IMEP #15, 2014, Winter Flounder Fisher Habitat Concerns in the 1980's).
But my research in the 1980's concerned the buildup of sapropel – the organic composts held in coves and salt ponds – the black mayonnaise linked to sulfur smells and the suffocation of shellfish.  In 1985 and 1986, my research was in Alewife Cove between the towns of Waterford and the City of New London.  I was asked to survey the area for fin and shellfish habitat by John Scillieri, then Chairman of the Town of Waterford Flood and Erosion Control Committee.  Alewife Cove became a key study area for this marine compost referred to as silt in research papers at this time.  An important survey occurred in Alewife Cove between 1975 and 1976 and provides a critical look at Alewife Cove conditions as a baseline reference.  This paper was given to me by Dr. Barbara Welsh of the University of Connecticut Department of Marine Sciences after a meeting about my Alewife cove shellfish surveys.  In one of my shellfish surveys under about three feet of sand (some street sand had washed in also), I found dead hardshell clams, quahogs – obviously buried by the sand after storms (north of Peninsular Avenue).  Another location had about five feet of ooze, requiring a small gasoline water pump to sample.  Finding the sapropel was much easier, still basin waters held it and a ten-foot pipe easily penetrated this compost.  This material is so water-filled that it is easy to move if currents (flow) are present. 

My study was more toward the acid conditions and the absence of shellfish sets observed in central Connecticut and on Cape Cod.  Shellfish shells were often found below this organic compost but hard clams were buried by sand mud mixture.  In the upper basins, I did find deep layers of sapropel.  Alewife Cove shared many of the barrier spit interactions of Goshen Cove immediately to the west.  Coves with barrier spit beaches have a long history of blockages and were unblocked to preserve the alewife fisheries of which Alewife Cove is named.  My research interest was the trapping of organics behind tidal restrictions and loss of winter flounder habitat.  I observed this happening on Cape Cod.  In time, coastal fishers would term it black mayonnaise.  When these coves and bays blocked in heat soon produced sulfur smells.  Much of this may have been the result of sapropel formation.   When this happened, these habitats no longer supported winter flounder.

After many years Alewife Cove is being looked at again as a potential case study, a sand wave once again has moved into and blocked a substantial exit flow.  In 1985 to 1987 Alewife Cove was dredged to remove this storm driven sand, the upper sections still have large accumulations of sapropel (observations of T. Visel while employed by the University of Connecticut Sea Grant program).  A new study seeks to map and log the sulfide levels of these upper organic deposits – the information from such estuary may help understand layers and buried shellfish populations under it, and the impacts of sapropel sulfide/ammonia to fish over it.  We may need to look to the Cape Cod Community Dredge Program and study how coves and salt ponds are kept open to tidal changes.  These flows tend to keep water temperatures lower and help prevent sulfate metabolism in hot stagnant waters.
Alewife Cove as the name implies once was an important alewife habitat and mentioned in US Fish Commission reports as supporting oyster culture (1887) and locating those lost oyster beds may be an excellent "time stamp" for these composting processes. 
Finding and recording the location of these century ago oysters areas might be the logical first step in helping us understand the sapropel formation in similar coves along the coast – my view, Tim Visel. 

Appendix #1
The Effects of Reduced Wetlands and Storage Basins on the Stability of a Small Connecticut Estuary
By: Barbara L. Welsh, Janet P. Herring and Luana M. Reed
Marine Sciences Institute
The University of Connecticut, Groton, CT 1978
Estuarine Interactions, Pgs. 381-401

Pgs. 391-393: (my comments, T. Visel)
"In addition to the salinity gradients, prevailing pH values in the pore waters were extremely low for marine sediments (Baas Becking, et al., 1960).  During the summer months, a number of measurements dropped below the limits of the carbonate system (4.0) and may have resulted from the leaching of organic acids or iron from the large amounts of allochthonous material present (twigs and oak leaf fragments – T. Visel).  Dissolved materials in the surface water and the groundwater intrusions could also contribute to low pH.  Iron commonly exceeds .3 ppm in local streams, especially during low-flow conditions, and it is even more prevalent in groundwater (Thomas, et al., 1968).  The decaying vegetation in the newly formed swamp upstream should certainly constitute a local source.  By December, however, pH had returned to normal (5.7 – 7.2).

Taken together, the low and variable values for salinity (more prevalent in winter) and pH (more prevalent in summer) within the upper 10 cm of sediment would impose irregular, multiple stresses for infauna, which might reasonably be considered more lethal than either factor alone.  Hence, the sediments could not provide the homogenous sanctuary for infauna described in Sanders, et al. (1965).

At the lower pH values, even the microbial community would be limited to such forms as thio and iron bacteria" (Baas Becking, et al., 1960)."
(These conditions would support in high heat the acid formation of sapropel.  This material would have very few organisms of regular oxygen life but species highly tolerant of hydrogen sulfides, T. Visel).

Appendix #2
In Times of Heat Scallops Decline from Sulfide
The Sulfur Cycle of a Coastal Marine Sediment
Bo Barker Jorgensen, Sept 1977
Limnology and Oceanography Pg. 814-832

"Due to the activity of heterotrophic organisms, reducing conditions are maintained in most coastal sediments below a thin, oxidized surface layer.  This stratification provides the basis of a transformation of inorganic sulfur compounds through a cyclic series of redox processes.  In the anoxic sediment, sulfate is reduced to sulfide by the respiratory metabolism of sulfate reducing bacteria.  Much of this sulfide is trapped in the sediment by precipitation with metal ions, but some may remain dissolved in the pore water and reach the oxic and photic surface layers of the sediment. Here it is oxidized back to sulfate via intermediate oxidation steps, partly by a spontaneous chemical reaction, and partly by catalysis by chemoautotrophic or photoautotrophic sulfur bacteria.  These processes have a strong influence on the chemical environment in the sediment.  They mediate a significant part of the energy flow in detritus food chains connected to anaerobic decomposition (reported here), and the balance between oxygen and sulfide is an important factor for the distribution of benthic organisms (Fenchel, 1969).  In the early diagenesis of anoxic sediments, the transformations of inorganic sulfur also play a dominating role (Goldhaber and Kaplan, 1974)."

Appendix #3
Framework for Metals Risk Assessment, Section 3-20
Takak, EPA 2003 – 120/Ra>001 March 2007

"Reduced soils can form sulfide, and sulfide forms low solubility compounds with most of the metals of concern in soils, including Pb, Zn, Cd, Cu and Ni" and further,

"Upon oxidation of the soil, sulfide is quickly oxidized, and the metals are returned to more normal equilibrium reaction of aerobic soils."
But in the marine environment, soils are not classified so these reactions are not included in tests, or models and often grouped as man-made contaminants.
They are frequently not measured, page 70 of a report EPA QAPP for Boston