EC #19-A The Chemistry of The Sulfur Cycle And Habitat Change

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EC #19-A   The Chemistry of The Sulfur Cycle And Habitat Change
Sea Water Sulfide Levels Just As Important As Oxygen
View all Nitrogen and Bacteria Posts on the Blue Crab Forum™
Tim Visel, The Sound School, New Haven, CT  06519
EPA Uses Sulfate-Reducing Bacteria to Bind Metals
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June 2020
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A Note From Tim Visel

Readers should review Blue Crab forum™ Environmental/Conservation thread 17A and 17B which was posted on April 12, 2019 and 18 A and B posted on October 20, 2020 on the Blue Crab Forum™ and provides an introduction into the rise and fall of sulfides in marine soil.  This paper introduces the habitat characteristics of when sulfides seep from marine composts and at times marine soils and then into the water column.  These composts in heat and low oxygen conditions can form a sapropel.

The information presented here is perhaps not new to many small boat fishers – those that have fished the shallows in the early morning and perhaps smelled sulfur gases and why blue crab shallow water habitat observations are so important today – they point directly to the rise and fall of sulfides.  Here shallow water observations provide the first signs of sapropel formation, the black stain upon shellfish, the so called "sulfide deadline" in salt ponds.

Small boat fishers a century ago faced intense heat and when that happened gave rise to the terms "live" and "dead" bottoms, especially in the eel spear fisheries (see IMEP 61-A, 61-B posted on the Blue Crab Forum™ posted on March and April 2017).  The smell of sulfides has long distinguished the "good" and "bad" bottoms or habitats or the putrid smell of bacterial action in the absence of oxygen.  Iron sulfides tend to be black and one characteristic that occurs in our fisheries history is the term "black water."  These black waters are the result of bacterial reduction decay in hot low oxygen waters but also in cold – a sulfide sulfuric acid release in winter called the dead line.  Both sulfide events can kill fish and "dead" the habitats in which fish and shellfish live. 

It is the presence of sulfide that causes oysters to stop feeding and starve, it is the sulfides that causes soft shell clams to pop out of marine soils, it is the sulfides that causes the rotten egg odor almost always present just before a large fish kill and the toxic chemical source for blue crab jubilees.  A missing element however is the absence of sulfide measurements in most estuarine studies.  Sulfide measurements are key to understanding habitat quality in shallow waters but we focus upon oxygen and ignore mostly the rise and fall of sulfide – we need to include sulfide measurements as well.


Understanding the shallow water sulfur cycle (largely ignored in most fishery management discussions about nursery habitats) is the key to understanding great fluctuations in blue crab populations (and other shellfish species) after a very hot summer (the Blue Crab Jubilee) or after a bitter cold long winter (the Blue Crab Winter Kill) and the role that sulfide has in both of them – my view, Tim Visel).

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The Sulfur Cycle

Most blue crabbers over time have experienced this estuarine sulfur cycle in the shallow iron sulfide rich composts – the sticky black and sulfide rich composts in many areas called black mayonnaise but more properly termed a young sapropel – an organic ooze the result of bacterial action in low or no oxygen waters.

A half century ago the study of the remains of bacteria digestion caught the attention of plant scientists.  Often termed "the agency of bacteria" the correct term for this process then was called (Saprophytism), and plants without chlorophyll living off dead organic matter were called Saprophytes.  And sapropel the by-product of this process from these bacteria was well known by the 1920s.  These researchers strived to explain this process to the public in terms that could be understood.  Much of this organic matter breakdown in low flow streams in heat, which would become the basis of organic matter wellness or the Saprobien System (Kolkwitz and Marsson, 1909).


In a book titled "An Introduction to Botany" by Arthur W. Haupt (1938) reprinted in 1946 by McCraw – Hill Books London describes this process as the agency of saprophytes while others termed it the agency of bacteria – the process produced the same result – the breakdown of plant tissue into primary organic compounds.

And below an excerpt from –

An Introduction To Botany By Arthur W. Haupt, Associate Professor of Botany,
University of California at Los Angeles First 1938 – Second Edition New York London - McGraw-Hill Book Company, Inc – 1946

"Saprophytism – Plants are related in their life habits not only to the physical factors of their environment, but to other organisms as well. Each kind of living thing has reciprocal relations with other kinds – none can live unto itself. The limitless ways in which plants interact with one another and with animals constitute such a vast subject, however, that here attention can be given to only a few of its many aspects. The phenomena of saprophytism and parasitism are of considerable biological interest in that they illustrate some of the ways in which plants are adapted to their living environment.

Saprophytes are plants without chlorophyll that absorb their food directly from dead organic matter. Their supply of carbon comes not from the carbon dioxide of the air, as does that of green plants, but from organic compounds occurring in dead plants and animals or in organic waste products. In the course of obtaining food for themselves, saprophytes gradually break down complex organic substances into simpler ones and so are the direct cause of decay. The decomposition of all dead organic matter takes place entirely through the agency of saprophytes, which thereby obtain material and energy necessary to their own metabolism."
Decay of Organic Matter – 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 acid, etc. Ordinarily there is a succession of various kinds of decay-producing organism, chiefly bacteria, each carrying the process of little farther, until finally one 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 decomposition are mainly water (H2O), carbon dioxide (CO2), ammonia (NH3), methane (CH4), hydrogen sulphide (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 nitrite and then to nitrates free nitrogen by the nitrogen-fixing bacteria. Other kinds of bacteria oxidize methane, hydrogen sulphide, and free hydrogen. Besides the bacteria of decay, many other kinds of saprophytes are found among the fungi, example being yeasts, molds, mushrooms, and many others. These plants live on humus, rotting logs, dead animals, etc."
Although we have focused on the amount of elemental oxygen shallow waters can hold we have largely ignored the other "oxygen sources" those compounds that have oxygen in a compound form such as sulfate, nitrate, acetate, and phosphate.  There are bacteria that use these compounds for oxygen and when oxygen in its elemental state 02 declines they can switch to other oxygen sources.  Sulfate for example is the largest source of "oxygen" in sea water and often described as "non-limiting" that is bacteria that utilize sulfate as a oxygen source will never run out but has dire consequences to the oxygen requiring life that need element 02. 

That is why summer coastal residents often report sulfur smells late at night – in August as seawater loses its plant life oxygen source – at night plankton cannot complete photosynthesis and the purging of oxygen from it in heat ceases.  Bacterial processes now draw against dissolved 02 in sea water and the "oxygen minimum" occurs at around 4am – a time when blue crabbers using flashlights to scrape blue crabs off of docks lines and poles.  When that occurs oxygen is usually at minimum and sulfide at maximum.  The problem is of course we only measure the oxygen, and not the sulfide.  (At recent EPA Long Island Sound workshop several attendees also asked about sulfide measurements – T. Visel).  The largest chemical signature of high sulfide during a fish kill event is the report of rotten egg smells.  It causes the blue crabs to rise off the bottom at night and if sulfides increase (low oxygen) blue crabs can even leave the water itself – the summer blue crab jubilee.  The winter kill by sulfide is harder to see, nature has a way with recycling nutrients even low pH sapropel can dissolve shells.  One of the indicators of a sulfide skill is black stains on shells.  The winter kill is reflected in declines of catches and is found in the historical literature for many hibernating species.  This is especially true for species that chose to hibernate in this marine compost that is governed by temperature and bacteria.  These species include eels, blue crabs and terrapins. 

Introduction

This paper is in part a response to so many crabber requests after the 2017-2018 winter kill (The Search for Megalops Series).  The run up of blue crabs in Southern CT was hard to miss – although I did until 2009.  I was already suspicious that a massive habitat reversal was possible in 2005, and in 2006 presented a paper at the International Shellfish Restoration Conference in South Carolina detailing some NOAA – Sea Grant shellfish restoration projects which had failed linking them to habitat health conditions.  In 2007, I proposed a habitat monitoring program Project Finfish followed by a paper about the Malaria outbreak in Greenwich, CT in the early 1900's (Climate Change and Public Opinion – The Mosquito Habitat War Claims Connecticut Marshes – available on the Blue Crab Forum™ Eeling, Oystering and Fishing thread posted on May 29, 2014).  Project Shellfish was proposed soon after and sought investigating the increased oyster spat falls across the Connecticut coastline.  The heat was returning to New England in the 1980's and within strong oyster sets, and now an increase in the blue crab.

By 2009, I was following the Northeast Atlantic Oscillation (NAO) that was first mentioned to me by a retired oyster farmer on Cape Cod – John Hammond almost three decades earlier.  When the NAO turned sharply negative in 2010 to levels not seen since the 1950s I was convinced that the blue crab explosion in southern New England could end suddenly just as some oral histories predicted it could or did some time ago while attending the University of Rhode Island.  Those conversations were with John Healy posted on July 27, 2015 titled Narragansett Bay Deep Water Bay Scallop Habitats of the 1870's.  Mr. Healy detailed the transition of deep water scallop habitats of cold to the decline in heat – the 1890's.  This habitat reversal of Bay Scallop is reflected in the Rhode Island fishery statistics.

But just how does a habitat reversal happen and how will it affect blue crabs were some of the dozens of questions that have come in since the start of the megalops series – started by precisely those same questions including where does our blue crab megalops come from?  Crabbers in CT were very disappointed with the 2018 Blue Crab season and this concern carried into 2019.  I just can't be certain if it will be disappointing again.  Another cold winter and cool spring for the winter 2019 or 2020 could bring another disappointing blue crab season in New England.

I wish I could have more certain what the future of southern New England blue crabs will bring but cannot.  Two things I can say is the answers to these questions most likely can be found in historical habitat observations, the other is we need to include habitat chemistry especially sulfide measurements in today's resource management discussions.  All the aspects of the 1880 and 1920 events Mr. Hammond predicted would happen again (See IMEP #45 posted on February 5, 2015 on the Blue Crab Forum™).

We need to include marine soil chemistry and it impact of hot weather composts that heat it.  This is the habitat chemistry of the blue crab that rarely appears in recent blue crab studies – my view Tim Visel.

The Absence of Climate Cycles?  A blind spot for environmental policy?

The rises and then fall of many fish and shellfish species is clearly evident in southern New England.  Sadly the concept of having a chemistry based habitat history is conflicted by public policy agendas that seem to dominate so much of the present day media that it can only get hotter.  The cycle of blue crabs appears to be a long one in southern New England and one that has likely happened here before – from the height in landings (1912) to the recent blue crab explosion of "2010" was nearly a century in length.  The next few years could help answer these habitat questions and perhaps and many others.  To do this we need to include all the "science" and not just sections of it, we have hot cycles and colder ones as well.  Blue crabs may have an important roll in understanding these cycles.

With the climate and energy information (hurricanes and storms) available today (records) it is possible to reconstruct how blue crabs lost a habitat battle, going from incredible abundance at the turn of the century 1900's in southern New England to one of scarcity in the 1960s – one common denominator was colder winters and more powerful storms following a long "hot term" years of brutal summer heat.  We seem to be experiencing that now in southern New England a long hot period by a series of cold storm filled negative NAO winters.  Although this paper focuses upon winter kill blue crabbers might be interested in the habitat change observations reported a century ago.  Southern New England might be the best region in which to study how cold and hot periods alter blue crab populations - My view, Tim Visel.

Capstone ISSP Series – How Does Cold Water Kill Blue Crabs?
The Sound School – January 2020

Introduction

With the Chesapeake Bay winter dredge survey release in the spring of 2019 and having had some good news for southern crabbers with small crab increases – a good sign for future catches. But also news about the "winter kill" and the death of over 25% to 40% of the Bays blue crab population – from the winter before?  This below report is from 2018 and a much different report for blue crab abundance.

"The long cold winter appears to be one cause of low abundance low water temperatures resulted in one of the worst cold kill events since 1990 – causing the death of an estimated 28 percent of the adult crabs in Maryland" (Source, Maryland Dept of Natural Resources) but how does cold water kill blue crabs?  It is natural to have large mortalities over the winter and can soil sulfide chemistry help understand this winter loss?

That science explanation is a complex one – all relating to sapropel a marine compost a topic I have written about several times this past year.  It involves a struggle between oxygen and sulfur chemistry involving several research fields.  Crab mortalities have been associated with disease, predators, our fishing, storm events but the largest source of mortality is most likely natural and related to habitat changes in marine soil chemistry.  Cold water and storm energy need not only to be included but connected to habitat types and how they impact the blue crab.  Significant habitat indicators have been linked to bacterial infections, such as Vibrio parahaemolyticus - and also primarily shell disease bacteria possibly mentioned by Van Engel in foul smelly bottoms – the presence of chitinoclastic Vibrio bacteria – better known as shell disease.  Shellfish resting or adjacent to sapropel may become stained black, salt ponds often have a sulfide deadline if bottom waters become sulfide rich.

Sapropel supports many of the most hazardous bacterial strains traced back to the first organic sludge (Dump) deposits off New York City.  Here Rhode Island lobster fishers reported catching lobsters with shell disease in 1978.  Bacterial outbreaks in winter are quite rare – they often occur in high heat opposite the climate mortality winter kill.  Predation is usually slower in winter and the habitat type selected might even have a defense mechanisms rarely considered, a natural biocide, a natural poison.  A low oxygen/ammonia event is also frequently listed as a major source of blue crab mortality but winter kills occurs when sea water is cold and therefore seasonally at the highest oxygen saturation levels (mixing occurs).  Ammonia is highest in summer not winter and largely the result of bacteria soil processes.

If ice forms so thick it can freeze bottoms (shellfish for example at low tide) it is a possible source or explanation but the winter dredge surveys does not examine these very shallow waters but only areas five feet deep or more.  The presence of dead yet stained black adult blue crabs could provide important habitat data.  Sea water sheet ice in saline areas rarely gets this thick.  The 1960 to 1965 was an extremely cold period for New England – Long Island Sound waters were at times very clear (less plankton) but the recent Blue Crab explosion occurred in a period that is related to the very hot conditions and high plankton levels.  The water was often "cloudy."  So how does winter kill crabs – that is related to the sapropel – sulfur cycle and why crabs sometimes smell bad and are often stained black.  It is an explanation that involves chemistry, bacteria and natural poisons and why at times fishers sometimes complain of acids eating away their metal crab traps (sulfuric acid).  It is a story of habitat conflict that has been ongoing since the start of time itself.  The battle between oxygen and sulfur chemistry that occurs out of sight with the most primitive life forms, the bacteria on bay bottoms.   

For many fishers (and members of the general public for that matter) this oxygen/sulfur conflict had not been on the public policy radar – at times the habitats promoted for so long as "good" can at times become not so good at all.  This aspect includes a look at long term environmental climate patterns which govern cycles in so many coastal fish and shellfish populations.  So how does winter kill Blue Crabs I offer this chemical explanation we need to look at many aspects of the chemical compounds we call hydrogen sulfide, as a respiratory block and the science we use to measure its impacts.

How Does Winter Kill Crabs?

When one hears of winter kill, you think of snow ice and freezing (the past few winters it's not a stretch) or a blizzard.  But just how does winter kill blue crabs – taking into account they hibernate in dormant in areas that rarely get contact ice – not so for shellfish an extremely low tides which can freeze in very cold weather (1945 to 1965 New England, for example).  Several factors came into habitat quality, soil pore size, grain sizes pH and oxygen redox depths (Megalops Report Oct 7, 2014).  Compounding this issue is a much reduced cold water metabolism crabs – semi hibernation living off stored food for months until spring. So if they don't freeze outright or starve how does cold water kill?  That is the ability of sulfide to block oxygen exchange itself, its chemistry of replacing or harming oxygen transport in blood.  Sulfide toxicity is a type of respiratory failure; it kills quietly and out of sight.

One factor that influences sulfide formation could be bottom type – and not just the "bottom" but what type and where.  With the basic known blue crab biological parameters – male crabs seek out the lower salinity, lower energy headwaters the same areas with heavy organic loading.  Females tend to be in deeper higher salinity areas also prone to higher energy (storms) and where organic deposits are typically less – males might be subject to a greater winter kill from sulfide because of where they tend to hibernate – the upper reaches of bays and coves that have the lowest flushing, lower salinity and the greatest terrestrial organic deposits.  These areas tend to be shallow and therefore "less buffered" for temperature.  This may help explain differences in ratios of crabs why some years females appear higher (population) than others when males dominate.  It is these organic deposits that might hold the key to winter sulfide concentrations that might enhance blue crab mortality – they make a natural poison – hydrogen sulfide. 

There is a tendency not to include the toxic impacts of bay bottoms because it is in opposition to environmental policy of non disturbance and that all estuarine habitats are very valuable and therefore very "good."  But this is not always the case and rarely discussed as some bottoms are toxic to crabs.  We fail to study these marine soils subjected to temperature extremes.  Most often the more recent blue crab studies mention low oxygen as a concern but in winter cold waters contains more oxygen and dead zones retreat back to the deeper more poorly "mixed" or flushed areas.  One report "The Roles of Anoxia, Hydrogen Sulfide and Storm Events Of Fish Kills Of Dead End Canals of Delaware Inland Bays (George W. Luther III – June 2004, Estuaries Vol. 27, #3, 550-560) mentions the same areas that had hydrogen sulfide formation in heat were also shallow and poorly flushed.  The impact upon Blue Crabs from hydrogen sulfide was very noticeable in them, in fact a constant problem in canals.  On page 558 of the Luther 2004 study has this statement:
"We observed that Blue Crabs (Callinectes sapidius) in Torquay Canal were on pilings above the water air interface to breathe 02 from air since 02 was not detectable and sulfide was detectable."     
The report more importantly also mentions the bias for sulfide (H2S) study in low oxygen conditions.
"Most studies concerning anoxia only document the loss or disappearance of 02 and do not document the presence or extent of H2S in the water column."

The presence or absence of sulfide might be a key factor in blue crab survival and how cold water can kill blue crabs.  But the situation raised by Luther is correct very little study has been done on the sulfide chemistry aspect of "dead bottoms."

Canals have long been associated with "dead" or poorly flushed waters.  Canals need not be very long to slow or trap waters and in the heat of summer be the site of spectacular fish kills.  In New England these fish kills usually happen in late August when water temperatures are warm and contain less oxygen.  When thousands of fish die (this can be in the millions for schooling forage fish – such as menhaden) they provide food for sulfate reducing bacteria and lead to a sulfide event.  Sulfide from the fish kill builds and can kill shellfish on the bottom and give off the odor of rotting eggs.  Shellfish can be killed on the bottom (frequently have black shells) as this water becomes sulfide rich and dead – sulfide levels on the bottom become a silent killer of shellfish.  When storms mix the bottom dead water it diffuses the sulfide levels – and water quality improves.  The term "dead water" itself denotes a lack of mixing between layers of salt and fresh water was first described in Norwegian fjords (See Strom, 1938 Recent Marine Soils, IMEP #59-B).  They can be at times subject to sapropel formation first just as poorly flushed estuarine areas.  If not dredged they can fill with sapropel and then subject to sulfide smells.  When a cold and energy filled period ends it is these poorly flushed areas that often show the fastest habitat change.  Winter flounder fishers noticed this in CT landward of undersize railroad causeways that allowed waters to flow but not flush out organic deposits (Jordan Cove Waterford, CT 1981). 

A creek with a road pipe too small for flow or an old canal or just bays and coves with long connections to the sea can show the first chemical signs of these sulfide containing organic deposits. As waters warm and organic matter deposition increases we can see that accumulation as smelly "muck."  What we don't often see is the conflict over which bacteria types get to consume it nor the chemistry that changes these habitats.  We often do not measure the sulfide levels but focus upon low dissolved oxygen.  However, the low oxygen starts the rise of sulfide.  On Cape Cod, John Hammond described this as an underwater forest fire – driving those organisms that can to flee out and those like shellfish to perish of sulfide continued to rise (See IMEP #44 posted January 2015 and EC #15 posted April 4, 2018).  That sulfide is the underwater smoke of a sulfur cycle "fire" that consumes organic matter and lowers oxygen which increases the sulfide levels.  This kills more fish which then adds more organic fuel in which to produce more sulfide – the sulfur cycle "burn." 
Organics on the bottom is the fuel for this sulfide gas smoke but the damage on the bottom is evidenced by dead organisms.  Canals can even make organic deposition rates increase and perhaps the starting point of sulfide events.  Slower water and little capacity to clear captured organics adds to the "fuel."  They can under the correct conditions allow flows of organic waste (mostly leaf laden waters) into estuarine areas – from sulfate limited waters into those where sulfate is not limiting.  When organic digestion products are exposed to oxygen (floods) products of the bacterial processes produces sulfuric acid.  In some areas canal lock gates were badly corroded by such natural acids in the coastal zone.  Abandoned canals often contain sapropel organic deposits, still undergoing digestion in low oxygen environments.  Trees or organic matter are slowly digested by these bacteria in freshwater (very slowly) an entire industry has developed around reclaiming old – logs sunk in river bottoms.  Once recovered the timber is still quite usable even if it has been submerged for a century ago or more in oxygen poor waters (See The Red River Great Wood Raft for an interesting review (long term) of this process).     

Cold water organic matter digestion is also slow in the estuarine environment but the presence of secondary oxygen source sulfate (is not limiting in sea water) can supply the needed oxygen in a compound form.  In heat organic matter is reduced in low oxygen conditions (sulfurization) which can release sulfides as iron pyrite forms.  When iron deoxidizes exposed to organic waters it can release sulfuric acid.  These sulfuric acid washes occur after these putrified organic deposits are disturbed quickly (floods usually) ripped up and iron rich sulfide deposits washed downstream.  The sulfide is in them leaves a black stain on metal surfaces, the acids "eat" metals away.  Blue crabbers mention that metal blue crabs were eaten away – often after these deposits are moved by flood waters. 

In soil tests of freshwater sapropel, researchers found out how rapid soil tests need to be done on sapropel samples, as metals chelated under oxygen free conditions were released as pH levels quickly dropped.  "The source of this extractable Fe (iron) that accumulates under anoxic conditions in the fine particle size fraction of most lake sediments.  As this sediment Fe (iron) is released during weathering under acid conditions, high levels of extractable Fe (iron) are maintained even under oxidizing conditions where ferrous Fe (iron) ferrous iron (II) tends to be converted to the loss soluble ferric form FET3 iron (III) of iron.  The sensitivity of extractable Fe to pH was as great as for aluminum" Connecticut Agriculture Experiment Station Bulletin (1980) #789 – Bantam Lake Sediments Physical and Chemical Properties Relevant to Dredging and Spoils Disposal by W.A. Norvell (The release of aluminum would be implicated in young of the year striped bass die offs in Chesapeake Bay in the 1980s).

In deep areas, these organic deposits can accumulate undergoing sulfur digestion – bacterial break down for decades in navigation channels such deposits are dredged and brought to the surface, once that happens and re-exposed to air (oxygen) they become acidic as sulfuric acid is formed in them. The Army Corps of Engineers (ACE) and the United States Geology Service (USGS) have began to investigate into what is termed sapropel or "Acid Sulfate Soil" in which soil iron oxides and free sulfates undergo rapid conversion in anaerobic saline environments" from page 9 of a report titled "Beneficial Reuse of Dredged Material in Upland Environments Nicholas Wes, Haus Virginia Polytech Institute 2011 – Also states "after excavating and exposure to an aerobic environment the sulfides are "re oxidized" creating acid sulfate conditions if insufficient carbonates exist to neutralize the acidity generated."  The largest sources of the carbonates in seawater in the shallow blue crab habitats would be oyster shell and the seawater itself. 

The report continued, and comments on air/oxygen exposure; "Once dredged and deposited on land – this soil then "ripened" as very similar to Dutch polder processes."  The deposits dried, cracked and crumbled into smaller sub units.  A case history is also presented of utilizing dredge material from a bridge replacement (Woodrow Wilson Bridge) on the Potomac River near Washington DC.  Between the years 2000 to 2005 nearly a half million cubic yards of clean freshwater dredge material (once it breaks the surface it is now termed Acidic Sulfate Soil) was allowed to dry "ripen" and crumble.  In 2001 areas were planted with winter wheat and corn in 2002 only after a single year of dewatering "wheat and corn yields surpassed the country average and have continued to do so almost every year" pg. 14.  Such organic deposits that "sink" or collect nitrogen is a very good fertilizer, as it's a compost.  But this report mirrors almost precisely New England Agriculture Experiment Stations (1890's) advice to New England farmers a century ago – who long used it as soil nourishment.  In the 1880's marine mud (Harbor Mud) or mussel mud when exposed to air develops a "hurtful acidity" and if not allowed to freeze and fallow first "would kill all crops."  Specially designed scoops then dug these deposits out for fertilizer use on land but deposits behind mill dams were found to be deepest and the most acidic (and toxic) (See CT Rivers Lead Sapropel Production 1850 to 1885, IMEP #26, posted Sept 29, 2014) and described them as blue – black and greasy.  These deposits were avoided and mentioned in Experiment Station reports (CT).  Page 49 of The 1879 New Haven Experiment Station Report contains this section –

"Unlike stable manure and ordinary composts, the mud (marine) contains considerable amounts of sulfuric acid."
Also, Mr. Stevens of Essex also remarks "Our mill ponds a few miles back from the river, contains a rich, black mud, quite deep and with a very strong smell.  It has been tried on various crops but kills everything."
For nearly 50 years New England Agricultural Experiment Stations tested "marine mud" (Sapropel) fertilizers and found high sulfur levels and wondered why.  Others had better luck and that involved oyster clam and mussel shell sapropel mixtures. Josh MacFadyen (Canadian Environmental and Digital History) reports that by 1871 Prince Edward Island contained 1,400 mussel mud machines and once applied to fields increased food (agricultural) products, for a period up to 15 years per application."  In the teens oyster farmers lobbied for protection from the as even though it is called mussel mud its most frequently contained many oyster shells important to oyster habitats.  The presence of oyster shells it is thought offset the sulfuric acid impacts on land – just as they do in estuaries.  The term mussel mud makes it plausible that the first compost harvest was under mussel beds was during colder times and the name just stuck.

Acidic Sulfate Soil – A Marine Compost – that purges chemical compounds.

The use of marine compost a terrestrial soil was well established by the 1850's – even much before.  George Washington even used creek Potomac muck for his soil studies, see letter from George Washington, Arthur Donaldson Oct 16, 1785.  The Agriculture of Maine forty fifth annual report (1864) has this advice to farms "when first taken out mussel mud is adhesive and somewhat like blue clay and must be frozen before it can be spread on land."  Some of the most desirable mussel mud was dug up near oyster bars and contained oyster shell (also a recommendation a century ago was to till in oyster shells for best results to offset acidity) – A 1913 description of acid soil (mussel mud) harvesting in Canada includes complaints from oyster fishers about the loss of oyster shell (For a more detailed description, see IMEP newsletter #26 "Connecticut Rivers Lead Sapropel Production 1850 to 1885," The Blue Crab Forum™ posted September, 2014 Fishing, Eeling and Oystering thread).  In the Carolinas, it is frequently called "plough mud" or "pluff" an old term when it was used as a soil nourishment (See IMEP #66-A Seafood, Saltponds and Fish Kills of the 1890's, posted November, 2018).  Deep buried deposits without bivalve shell usually purged sulfuric acid for several months when spread on land.

Oyster shell, organic deposits and eelgrass are habitats all associated with the blue crab.  Of these three habitats organic deposits and eelgrass can assist sulfate reduction while oyster shell can reduce or buffer the acids from it.  It is the shallow habitats and those that are heavily filled with organic matter that may influence winter kills.  It is these areas in which at times the sulfur reducing bacteria "win" and overwhelm the bacteria that need oxygen like us.  We have some clues from the historical literature – bad smelling crabs and crabs with bacterial shell disease coming from foul bottoms, Van Engel (1973) mentions a problem with sulfide toxicity in a report about sea water holding systems for the rock crab which during the much cooler 1960's became at times prevalent at the mouth of the Chesapeake Bay.  Regarding the need to keep water flowing and mixed, in these rock crab holding systems Van Engel comments:

"Any dead spots or layering (water) will cause stagnation which leads to low oxygen gases such as hydrogen sulfide."
Layering is known to happen in cold under ice sealed from atmospheric oxygen and assists sulfide formation.  It is called a thermocline.  Sediment sampling under ice would be an important part of this habitat discussion.  We really don't know that much about sulfide toxicity – most of the information comes from the Netherlands such as those studies conducted by H. Thede, "Comparative Studies On The Influence Of Oxygen Deficiency And Hydrogen Sulfide On Marine Bottom Invertebrates," (Thede, Netherlands Journal of Sea Research, Vol. 7 (1973), 244-252) that resistance to sulfide toxicity in general for many species is higher at low water temperatures and lower pH levels.  This could explain why blue crabs pick these bottoms that can produce such toxics in the winter and why they leave these same waters during summer "jubilees."  It is also perhaps why eelgrass dies off in high heat from these same sulfides.  Some of the biological parameters of organisms that live in these habitats do provide us some chemistry clues.  Chief among them is the ability to slow respiration rates when waters warm and oxygen levels drop.  Many crabbers have noticed this ability in shallow waters, on an ebb tide on hot days crabbing will slow and everything seems to slow down.  Crabs remain motionless unless disturbed, in very hot water (observations of shallow waters 2009-2011, Tim Visel).  When the tide changes, crabbing often improves.

In fact, blue crabs are often observed being dormant or motionless at slack tides in high heat.  I was able to observe this myself in Tom's Creek (Madison, CT) while still in high school as part of a Yale University Study.  It involved monitoring over a complete tidal cycle (2 days) oxygen levels and it was very hot.  Our small skiff was used by a Yale graduate student and by mid tide – you could easily see bottom crabs become motionless and small winter flounder stayed quite still.  The change of tide was a different story – here mummichogs by the hundreds, rode the incoming tidal wave and once the change of tide occurred everything seemed to leap up at once (including blue crabs) and begin to move – it was that sudden and that was twice a day.  Blue crabbers often experienced this effect in CT River at low tide on hot days crabbing often becomes very slow or just stops – but a few minutes after the tide turns crabbing improves.  Moving water seems always to be the better crabbing times.  (Other studies looked at gut cavity analysis found that few crabs had food contents on the flood and nearly all of them on the ebb).  It could be said that on hot summer days anoxic conditions occurred daily and organisms adapted their behavior to low oxygen and high sulfide conditions.  It seems that oxygen aerobic life clings to this shallow habitat with a tight grip – very cold or very hot extremes cause these habitats to "fail" to become unsuitable very quickly.  A type of chemistry habitat battle occurs between those organisms who need oxygen and those who do quite well without it.  This conflict is mostly unseen unless it is extreme – the hot weather jubilee and the cold water winter kill – we can see that and sometimes measure it.  The battle between oxygen and sulfur has been going on since oxygen life evolved and the foot soldiers of this chemistry battle are bacteria species – not us.
Low Oxygen Conditions in Cycles
The term anoxia had been used so much lately most coastal fishers know it and likely experienced it as well.  Low levels of oxygen can be deadly to marine life and to us.  We are squarely in the "anti anoxic" camp and bet on the demise of anoxia – as compared for the return of sulfur.  That is much of the foundation of current nitrogen abatement program as a way to increase oxygen levels in coastal waters by reducing organic matter from plant life.  It is part of the regulatory policy in many states to reduce human produced nitrogen compounds.  But temperature has an important role in organic matter sulfate metabolism – the purging of ammonia.  This ammonia is such a high pH it can cause calcium to precipitate.  In cores of estuarine areas it leaves a layer of vaterite and calcium carbonate forms of calcite and aragonite.

Early studies first identified previous oceanic, anoxic events (not good for the marine life we value) by the use of sediment cores and the discussion of geological time (Schlanger OAE, 1976).  Several recent core studies of CT estuaries have found in a more time boundary and  how geological time is preserved in them – by distinct bivalve shell layers in the cores themselves.  The substance linking habitat "reversals" is the prevalence of hydrogen sulfide and absence of bivalve shell.  Some recent observations in Rhode Island Narrow River have mentioned "purple waters" and some of the bacteria strains that reduce organic matter by sulfur are indeed purple.  The Narrow River has been found to contain sulfide levels ten times those found in the Black Sea (Gaines 1975, Orr and Gaines, 1974 – Observations On The Rate of Sulfate Reduction and Organic Matter Oxidation in the Bottom Waters of an Estuarine Basin of the Upper Pattagansett River Rhode Island, 791-812).  Shallow narrow bodies of waters with long connections to sea are some of the first battlegrounds between oxygen and sulfur.  These sulfur shifts now thought to be climate induced are often mentioned as layers in sediment core studies.

The oxygen/sulfur battles have been recorded in the Narrow River – In the 1999 Narrow River Special Area Management Plan – Chapter 3, pg. 69 has this statement (from The Narrow River, Rhode Island SAMP prepared for the Rhode Island Coastal Resources Management Council, April 12, 1999 Ernst. Miquel and Willis.  Part C "As consequence of this strong stratification that impedes mixing bottom waters become anoxic or devoid of oxygen.  Analysis of sediment cores show anoxic bottom waters in the upper basins occurred prior to significant human inhabitation of the area" (Gaines 1990).  It is the record left in organic matter that provides clues to anoxic conditions.

This climate factor is being experienced in the reservoir created by the construction of the Conowingo Dam.  Periodic heavy release of organic matter has impacted habitats below the dam but as in the Narrow River system – a much smaller system than the Susquehanna River, The Narrow River study mentions the sapropel formation – and crabs that lives in it,

"What were once clean gravels and sand that supported good setting surfaces for shellfish, become covered with black organic mud as bottoms sediments become more organic, the benthic organism composition will shift from desirable to less describe food species with a consequent impact on the fish and crabs that rely on those species for sustenance (Bagge 1969, Dearson and Rosenberg 1978 Sorda 1995).  As organic matter increases in the bottom sediments, nutrient flux (this term is used commonly to describe bacteria generated nitrate or ammonia – T. Visel) from the sediments will increase add more nitrogen to the overlying waters which will stimulate more aquatic plant growth and exacerbate the already problematic nutrient badly situation (Lee and Olsen 1985 Nowicki and Nixon 1985).

Note –
A better source for bacteria nitrogen generation and resulting sulfide release explanations see Gaines A.G. 1975 papers on the Geomorphology, Hydrography and Geochemistry of the Pettaquamscutt River Estuary Ph.D. – Thesis University Rhode Island.

Many studies tend to minimize the impacts of sapropel – sulfide – ammonia generation from bacteria in organic matter because research parameters did not include them (a human bias that surprisingly ignores climate cycles).  A major EPA study of inputs of nitrogen (Latimer and Charpentier 2010) titled Pg. 129 J. S. Latimer and Charpentier/Estuarine Coastland and Shell Science 89 (2010) pg. 129 notes this exclusion "Internal nitrogen regeneration from sediments and the water column is not considered in this paper, however it is taken into account by the ELM.  The sediment has been described by others to be a net sink, except during summer periods where it may be a net source (Howes et al., 2003) in either case it is not "new" nitrogen, therefore, it was not included." 

Therefore, bacterial generation of nitrogen long considered in soil science and bacterial aquaculture filter systems was not included although soil bacterial releases of nitrogen is long a feature of growing terrestrial crops.  For systems with restricted flushing and therefore higher nitrogen residence times ambient tests would measure the tidal sloshing of nitrogen back and forth many times of bacteria nitrogen – therefore it is possible (more than likely) that a large percentage of nitrogen was assigned to human inputs but actually was from bacterial nitrogen.  This was made worse with areas with restricted flushing).  The scientific community has not qualified what is a "new" or "old" nitrogen as these forms share identical chemistry configurations.   
Climate cycles could therefore greatly influence nitrogen levels as bacteria are temperature sensitive (why we cool food, etc.) and in heat generate enormous amounts of nitrogen outside of many nitrogen models.  Such nitrogen models need to be recalibrated – others may need to be abandoned completely so that all nitrogen sources are included – my view.

Bacteria ammonia is an indicator that oxygen is declining or absent.  It is a much slower process in winter as lower temperatures slow bacterial growth.  As sulfide seeps out from organic composts, it accumulates in the soil (or loose compost) and then purges into the water column.  Crabs at low temperatures cannot move and as sulfide blocks oxygen transport, blue crabs slowly suffocate buried in place.  In spring, such crabs are often surrounded by the mud snail consuming pieces of dead flesh (observations of blue crabs in the Oyster River, Old Saybrook, CT, Spring 2016).

The habitats that blue crabs choose to overwinter in could, with soil science sampling, determine if and when sulfide levels that are toxic happen.  The same holds true for ammonia – we need to include all nitrogen sources for our estuaries, including ammonia from sulfate reducing bacteria – my view, Tim Visel.



Appendix #1
Sulfide as an Environmental Factor and Toxicant: Tolerance and Adaptations in Aquatic Organisms
Abstract:

This review brings together a large number of independent and seemingly unrelated studies in various disciplines under four major topics: (1) sulfide as an environmental factor in aquatic habitats; (2) sulfide as a toxicant; (3) sulfide tolerance of aquatic organisms; and (4) adaptations limiting sulfide toxicity. Sulfide is widely distributed in the aquatic environment, but has been largely overlooked as an environmental factor for aquatic organisms. Sulfide at nanomoiar to millimolar concentrations adversely affects cytochrome c oxidase, various other enzymes, oxygen transport proteins, cellular structures, and consequently the physiological functions of organisms. These toxic effects are well documented in the biomedical literature, and also occur in the aquatic organisms that have been studied. Sulfide tolerance varies widely among protozoans, sediment meiofauna, polychaetas, bivalves, crustaceans, marine and freshwater fishes, and aquatic plants, often in correlation with the relative sulfide levels in the respective habitats. Aquatic organisms have evolved various adaptations against sulfide toxicity, possibly several acting in concert. Most animals are able to avoid and escape from sulfide, but cannot exclude sulfide from the body. No sulfide-resistant cytochrome c oxidase has been demonstrated, and most animals are capable of some degree of anaerobic metabolism. Various invertebrates have entered into symbiotic associations with sulfide-oxidizing bacteria. Some of these invertebrates immobilize and transport sulfide by means of sulfide-binding proteins or persulfides in the blood.

Citation:

Bagarinao, T. (1992). Sulfide as an environmental factor and toxicant: tolerance and adaptations in aquatic organisms. Aquatic Toxicology, 24(1-2), 21-62.

Appendix #2

Oxidation of sulfide by Spartina alterniflora roots Abstract—Root tips from the marsh grass Spartina alterniflora, collected from areas of high and low pore-water sulfide, exhibited a substantial capacity to catalyze sulfide oxidation, as determined by closed-chamber respirometry. A large proportion of this catalysis was apparently nonenzymatic and was higher in roots of plants from the high-sulfide versus the low-sulfide site. Activity exhibiting characteristics of enzymatic sulfide oxidation was significantly higher in plants from the low-sulfide site. Results from elemental analysis of root tissue were consistent with the theory that metals play a role in nonenzymatic catalysis. These results indicate that estuarine plants may detoxify environmental sulfide via sulfide oxidation. Hydrogen sulfide is a common metabolic poison that is abundant in marine-reducing environments. Sulfide (H2S, HS2, and S22) blocks aerobic respiration by inhibition of mitochondrial cytochrome c oxidase (Nicholls 1975; Wilson and Erecinska 1978) and spontaneously oxidizes in the presence of dissolved oxygen, thereby reducing oxygen availability. Despite this, many aerobic marine organisms can survive chronic sulfide exposure. The mechanisms that enable these organisms to avoid sulfide toxicity are beginning to be characterized. Most of the work in this area has involved marine invertebrates, many of which are symbiotic with sulfur-oxidizing chemoautotrophic bacteria (reviewed in Somero et al., 1989; Childress and Fisher, 1992). Although plants are found in many of the same environments as the invertebrates that exhibit mechanisms of sulfide detoxification (e.g., salt marshes, eel-grass beds, and mangrove swamps), no studies have investigated the sulfide-detoxification mechanisms of marine plants.
S. alterniflora may detoxify sulfide in ways similar to those exhibited by marine invertebrates. An important feature of the lifestyle of invertebrates that tolerate sulfidic environments is that they bridge oxic and anoxic environments. For example, invertebrates at deep-sea hydrothermal vents inhabit areas where sulfide-laden water mixes with oxygenated water. Sediment-dwelling invertebrates aerate their environment by pumping oxygenated waters into their burrows. Another strategy, exhibited by some symbiotic clams, is to live partially in aerated seawater and to extend part of the body into sulfide-rich sediments or fissures. The presence of oxygen allows sulfide to be oxidized to less toxic species, such as thiosulfate, sulfite, sulfate, and elemental sulfur. Although sulfide is spontaneously oxidized by oxygen, invertebrates have a variety of means of catalyzing sulfide oxidation in order to gain greater protective benefit and, in some cases, in order to allow sulfide oxidation to be coupled to the production of cellular energy. Mechanisms that enhance the rate of sulfide detoxification but that do not result in energy gain are sulfide oxidases and catalysis by heavy metals (reviewed in Somero et al., 1989). Mechanisms that can result in energetic gain are sulfide oxidation by bacteria symbionts (Cavanaugh et al. 1981; Felbeck et al. 1981) or mitochondrial sulfide oxidation (e.g., Powell and Somero, 1986; Lee et al., 1996; Vo¨lkel and Grieshaber, 1997). Like sulfide-tolerant marine invertebrates, S. alterniflora bridge oxic and anoxic environments. In S. alterniflora and other aquatic plants, a well-developed aerenchyma system facilitates the transport of oxygen from the atmosphere to the roots, where oxidation of sulfide potentially reduces its toxicity (Teal and Kanwisher, 1966; Hwang and Morris, 1991; Arenovski and Howes, 1992; Armstrong et al., 1994; Howes and Teal, 1994). Thus, sulfide oxidation may be a mechanism that allows S. alterniflora to tolerate sulfide. It is not known whether S. alterniflora actively facilitate oxidation. This plant-mediated oxidation could be catalyzed by sulfide oxidases, metals, mitochondria, or hitherto uncharacterized mechanisms. In the present study, we measured the potential for sulfide oxidation in roots of S. alterniflora and then determined whether this capacity is catalyzed by known mechanisms.
Citation:

Limnol. Oceanogr., 44(4), 1999, 1155–1159 q 1999, by the American Society of Limnology and Oceanography, Inc.


APPENDIX #3

Mine Waste Technology Program. In Situ Source Control Of Acid Generation Using Sulfate-Reducing Bacteria
Description:
This report summarizes the results of the Mine Waste Technology Program (MWTP) Activity III, Project 3, In Situ Source Control of Acid Generation Using Sulfate-Reducing Bacteria, funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by EPA and the U.S. Department of Energy (DOE). This project addressed EPA's technical issue of Mobile Toxic Constituents – Water through a field demonstration of a water treatment technology based on the use of sulfate-reducing bacteria (SRB) at a remote inactive underground mine. This project was undertaken to demonstrate the effectiveness of SRB technology to treat metal-laden water flowing through and from an abandoned mine. The Lilly/Orphan Boy Mine, located in the Elliston mining district of Montana near the capital city of Helena, was selected as the site for the field demonstration. The Lilly/Orphan Boy Mine, active in the first part of the 20th century, was a relatively small mine that produced lead ore, which was shipped to a smelter in Helena. After active mining ceased in the 1950s, the mine workings subsequently flooded with groundwater and this eventually resulted in acid rock drainage (ARD) discharging from the mine portal. Under the MWTP, MSE Technology Applications, Inc. (MSE) demonstrated an innovative, in situ biological technology to treat and control ARD emanating from the Lilly/Orphan Boy Mine. Cables were installed to suspend platforms 30 feet below the static water level in the mineshaft that was open to the surface. Organic matter, primarily cow manure and straw, was placed on the platforms in the shaft, forcing the ARD coming from the mineshaft to pass through the organic matter before exiting the mine through the portal. Dissolved metals were removed from the ARD entering the in situ bioreactor, and the water subsequently flowed out of the mine through the downgradient portal. Because the SRB technology also caused the shaft water pH to rise and the oxidation reduction potential to drop, the amount of acid leaving the mine was substantially decreased. The bioreactor was activated in August 1994, and the water was analyzed for more than a decade (through July 2005). In general, the water has seen a considerable reduction in dissolved metals concentrations, and the discharge pH has been increased from a historic level of near 3 to a more neutral pH close to 6.

Citation:
Nordwick, S. Mine Waste Technology Program. In Situ Source Control Of Acid Generation Using Sulfate-Reducing Bacteria. U.S. Environmental Protection Agency, Washington, DC, EPA/600/R-08/096 (NTIS PB2009-102096), 2008.

Appendix #4
FINAL REPORT—SULFATE-REDUCING BACTERIA REACTIVE WALL DEMONSTRATION
MINE WASTE TECHNOLOGY PROGRAM
ACTIVITY III, PROJECT 12
IAG NO: DW89938870-01-1

Executive Summary
This document is a final report on the performance of sulfate-reducing bacteria (SRB) bioreactors that were constructed and operated for Mine Waste Technology Program (MWTP) Activity III, Project 12, Sulfate-Reducing Bacteria Reactive Wall Demonstration. The MWTP is funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by the EPA and the U.S. Department of Energy (DOE) through an Interagency Agreement (IAG) and under DOE contract number DE-AC22- 96EW96405.

The organic matter, an electron donor and carbon source for the SRB, was provided as an 80% to 20% by volume mixture of cow manure and cut straw. The cut straw was added to provide secondary porosity to the mix and to prevent settling of the medium. TerraCellTM material, commonly used in landscaping for slope stabilization and made of high density polyethylene, was used to form a cellular containment system (CCS)1 to house the organic matter.

Overall, the project documented that SRB technology, as applied in this demonstration, is effective in removing Zn, Cu, and Cd by precipitating them as sulfides. Removal mechanisms for Fe, Al, Mn, and As were overshadowed by a dramatic change of the quality of the influent AMD (Acid Mine Drainage). The results of the project have also allowed the formulation of an important recommendation regarding the design and construction of SRB bioreactors.



A D V E R T I S E M E N T