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« on: April 23, 2023, 04:23:30 PM »

EC #24 - Soil Cyanides Linked to Shell Coloration in Oysters and Clams
The Nitrogen/Bacteria Series on The Blue Crab Forum™

Marine Soils and Sulfur Reducing Bacteria – Natural Soil Cultivation
Viewpoint of Tim Visel, no other agency or organization – August 2020
This is a delayed report - Revised to January 2023

(Tim Visel retired from The Sound School June 30, 2022)

Thank you, The Blue Crab ForumTM, for supporting these Nitrogen/Bacteria posts – over 100,000 views to date

Bivalve Shells May Have A Role in Coastal Paleontology

A Note From Tim Visel

This paper was started in 2019 and was not focusing on quahogs growing in high organic soils or sticky muds.  Frequently, these quahogs had a brilliant blue shell coloration on the inside area adjacent to the incurrent and excurrent siphons.  This intense blue coloration is linked to the low oxygen high organic soils that, themselves, often have a blue coloration.  This coloration is associated with the formation of ferric cyanide, an iron salt.  This compound is well known to artists as the Prussian Blue paint pigment.  However, after 2012, reports have come in, indicating that clams set in sandy soils have little or no blue coloration.
In low oxygen conditions, cyanides are produced by iron-reducing bacteria and could be the source of brilliant blue coloration on the inside of quahog shells.  It is also linked to a similar coloration on some subtidal oysters, which often exhibit (although to a much lesser extent) a blue or purple shell band.  This connection came as a result of observations of oyster shells pumped with dredged material at the west end of Hammonasset Beach as a beach nourishment project.  Here, millions of oyster shells were dredged from the Housatonic River, an estuary with one of the largest natural oyster beds in North America and deposited on Hammonasset State Beach.  In gathering samples of black shell for an April 2022 dredge material talk (See IMEP #112 posted June 8, 2022, The Blue Crab ForumTM), I noticed a high percentage of these dredged Housatonic River shells had a brilliant band of blue, almost purple coloration.  These shells were mixed with a sapropel itself with a strong sulfide smell during this project.  Local news media also reported on these smells. 

Steve Joseph, Senior Aquaculture Science Teacher at The Sound School, brought in samples of Branford, CT quahogs he caught in soft sulfide muds.  These shells had brilliant deep blue coloration – and quickly compared them to some Rhode Island salt pond quahogs caught by my son Willard, which had no coloration.  These clams were caught in almost a pure sandy soil and almost free of organic matter, called “honey sand” in the Rhode Island shellfish literature. 

A quick check of my shell sample catalog confirmed those clams caught in light brown sandy soils showed almost no or very light staining (blue coloration) while those harvested in “sticky” sulfide muds were larger in size and had the brilliant blue coloration.  In some very old quahog samples, the blue coloration could be a natural “tag” for the type of soil in which these clams once grew.  The deep blue stain is often found in old adult clam beds with few stains on small clams.  This could be the result of low oxygen anaerobic metabolism, a survival mechanism described by Michael A. Rice – The Northern Quahog, The Biology of Mercenaria mercenaria 1992, pgs. 21-22:

“There is evidence that even in adequately high oxygen concentrations, the various anaerobic biochemical systems of Mercenaria mercenaria are actively producing metabolic energy.”

The presence of deep blue coloration on interior quahog shells may represent oxidation of a naturally toxic cyanide or dying marine soil cyanides, including iron sulfide, a natural toxic substance, and in winter, associated with the sulfide deadline of high sulfate bacterial metabolism.  Quahogs with little or no coloration should be indexed for low organic matter content in marine soils.

Quahogs living in sandy soils may naturally represent little to no shell staining.  Oxidation of iron ferrocyanide (salts) produces Prussian Blue.  Cyanide is naturally produced by soil bacteria in high organics and found in salt marsh peat.  Toxic concentrations of cyanide were documented in the pore waters of a salt marsh in 2012.  High organic loading (natural and man-made) is correlated to a natural toxic soil and is found in the fisheries literature as “dead bottoms.”  Further studies on quahogs living in “new” or recently cultivated marine soils may show much less blue coloration.  The connection to organic loading can be found in NOAA Technical Memorandums – NOS ORCA 80 – “Biological Effects of Toxic Contaminants in Sediments from Long Island Sound and Environs,” Silver Spring, MD, August 1994.

One of the things that concerned John C, Hammond, a retired Chatham, Massachusetts oyster planter was that instead of looking at the habitats of marine soils, researchers had started to give up on the bottom. He had obtained a copy of Luther Blount’s off bottom Rhode Island study of oysters which showed oysters grew faster off the bottom. That was not always the case. He had participated in some raft culture experiments in Oyster Pond River in the 1960’s, but oysters in the mud died over the winter.  Ice damaged and then destroyed the oyster culture rafts.

Other researchers had come to the same conclusion that deep salt ponds, not the shallows had the most promise for off bottom culture (See Oyster Pond Corporation).  Here oysters suspended off the bottom survived and grew quickly; his oysters --at the end of his oystering career --died for no apparent reason on the bottom.

Still of great concern was that something was killing his oysters and he did not know what it was; he suspected it was part of the sulfur cycle, as these bottoms were the ones that give up a sulfur odor—signaling the buildup of sulfides (See Oysterman article Appendix #2).  In the early 1980’s, Mr. Hammond was studying the culture of rice and impacts of soil sulfides.  We term that today under the category of bacterial sulfate metabolism. 

The early 1990’s hot weather on the Cape had caused a change on bottom habitats.  Most shellfishers noted that once “hard bottoms” now had become “soft.”  He was not alone about detecting a “soft bottom.”  Sulfate reducing bacteria associated with high heat and low oxygen do not break down waxes or wax esters.  They allow waxes to accumulate, forming a “plant signature” in these marine composts.  This is the “sticky bottom” that grabs a crab net pole or oar stuck in it.  Shellfishers on Cape Cod frequently noted that once firm bottoms, which were good clam bottoms, had turned soft filled with dead clams (comments to T. Visel, 1981-1983).  Inlets on Cape Cod were beginning to close and become stagnant or poorly flushed.  Those salt ponds had a deepening deposit of organic matter, an ooze or soft bottom.  In April 1999, Sandra Macfarlane wrote a report for my old employer The Barnstable County’s Cape Cod Cooperative Extension Service titled “Bay Scallops in Massachusetts Waters: A Review of the Fishery and Prospects for Future Enhancement and Aquaculture,” 27 pages.  On page 16, Macfarlane notes that a survey contained components now associated with warming waters, soil conditions, increased algal blooms and tidal choking – closing of inlets.  From page 16 is found the following:

“Many respondents reported a change in sediment from hard to soft (48%) but few reported a change from soft to hard (4%).  Respondents also noticed increased phytoplankton blooms (44%) and an increase in motor boat activity (87%) with a concomitant increase in boat size (61%).  Inlet dynamics have changed according to a number of respondents where 57% is a result of natural occurrence, 22% from dredged channels and 9% from jetties, seawalls or other structures.”

The transition from “hard” to “soft” bottoms would be noticed in southern New England just not on Cape Cod.  This is now linked to the climate pattern today known as The North Atlantic Oscillation or NAO.

Marine Soils and Sulfur Reducing Bacteria

For over a century, Chatham oyster planters at one time according to Mr. Hammond numbered around 20.  The remains of a half-dozen oyster floats were still in the marshes across from the oyster shops in various stages of decay; in January of 1983.  Chatham oyster planters once had purchased seed oysters from Rhode Island and Connecticut to plant for one season or two in the Oyster Pond River --something had changed in the bottom and was killing oysters.  In 1964, Paul Galtsoff issued his bulletin on oysters and Mr. Hammond mentions the work of Clyde MacKenzie, who gave me my first tour of the Milford lab in 1969 and a copy of Paul Galtsoff’s The American or Eastern Oyster, 1964.  On page 93 is pictured a Hammonasset oyster, Mr. Hammond purchased as 2-year-old “bedding stock” from George McNeil of Clinton, CT.

But in the early 1970s, Mr. Hammond’s oysters would perish with little or no signs of predation; they sunk and they would, in spring, appear as “box shells” oyster shells still paired, but with dead or had rancid meats inside. These meats were often accompanied by intense sulfur smells. Mr. Hammond was looking at the marine sulfur cycle and the rise of a loose organic compost he called humus.  He was also studying the culture of rice in hot climates, also subjected at times to hydrogen sulfide.

Researchers knew then that oxygen requiring bacteria could draw down oxygen levels in seawater then in the colder 1960s and 1970s, in lakes under ice. This had been the source of many sulfide winter fish kills, but the bottom had also changed for oyster culture. One of the studies Mr. Hammond gave me was a study of Chatham, Mass. itself: The Oyster Pond. It mentions a dredging project in which a sand wave had encroached on the Oyster Pond River channel used for small boats (a frequent condition at the mouth of many Cape Cod salt ponds) and these sand waves could bury organic composts, sealing them from oxygen requiring bacteria, in effect killing them.  That would create “two bottoms” one much older than the other.  The sand wave also reduced tidal exchange according to Mr. Hammond.

Things that happened with sulfate (sulfur) bacteria – organic composting pathways early on in salt marsh studies could be explained by the formation of a marine compost – sapropel:

1. Large temperature change, cooler water drives bacteria populations to oxygen reducers consumes sapropel, reverses it with heat tends to favor sulfate bacteria a much slower composting pathway; (composts become deeper and jelly like).

2. Increase energy flushing by dredging spit openings that remove sapropel from man-made or natural barrier spit openings increasing the ability of oxygen bacteria to live -

3. Stop all inputs of organics, increase oxygen to offset any inputs hold sapropel to a few inches by dredging.  (This had a history on Cape Cod for alewife fisheries).  This is well known by pond and lake associations as autumn leaf falls accumulate into sapropel.

4. Perhaps cultivate soils and increase clams, oysters natural filters, this process similar to storms mixes oxygen into marine soils.  (Mr. Hammond introduced me to the work of David Belding whose culture experiments asked the same soil cultivation questions in 1920).  These soil cultivation experiments were well underway by a shellfishermen’s group BSSA, the Bourne Sandwich Shellfish Association and Cooperative Extension specialist Karl Rask of the University of Massachusetts (See Appendix #2).

Items 2, 3, and 4 involve work or mechanical energy.  It is our energy or work that can alter bacterial populations; we do this with terrestrial soils by draining them of water or opening soils to air -- that action alone can tip the balance in favor of oxygen bacteria by opening soil pore space. We can also supercharge bacterial action by adding compost called “suspended solids” the organic residues of plants. This is the food of bacteria that releases plant nutrients into the land soils enabling the next generation of plant life to grow. It is an old practice and the foundation of growing food from farm soils.  While it is a practice to add compost to terrestrial soils the opposite is true for marine soils.  When they obtain excess compost, they can in heat become toxic and purge toxic sulfides.  One of the early wastewater treatment concerns was the oxygen deficit condition caused by human organic matter called suspended solids.  The bacterial action on suspended solids would draw on any oxygen dissolved in water.  This was the basis of the Saprobien System or “organic wellness” index created by Kolkwitz and Marsson a century ago.

As more and more information comes in about Desulfovibrio bacteria series, we might finally have some habitat answers to questions asked by shellfishers for centuries: is it good to work the bottom (marine soil) and how does that influence clam sets?

The Desulfovibrio series are described as gram negative sulfate reducing bacteria. They can live in oxygen environments but just barely survive they don't thrive until it gets hot in organic matter that collects on bay and cove bottoms.  In high heat and little energy -- they now thrive in these organics described as sticky mud, but more properly termed a sapropel. We can look for bottom cultivation events in nature (storms) and review the catch statistics that follow. In cooler and energy filled periods, quahogs do better in times of heat organics and little bottom disturbance they do not. The great sets appear a decade or so after hurricanes. I believe the Portland Gale (1898) was the bottom cultivation event for the great Nantucket quahog bed discovered in 1913. Although no explanation of the size or sudden appearance of this clam population is given in the historical literature, I believe, as Mr. Hammond did, that this huge quahog bed was connected to soil changes from these gales.  They cultivated the soils removed organics and most likely destroyed any sulfate reducing bacteria. 

They could have reduced predatory worm species as well.  Mr. Hammond strongly felt this storm created the habitat conditions for this clam bed by improving soil conditions for a clam set.  This included the reduction in predator worms, which at times could destroy a set (softshell clams, John Hammond observation).

Most of the habitat changes and now diseases are being linked to the Desulfovibrio bacteria series were first described in 1936.
[Some readers might be interested in learning more about these habitats damaging and disease associated bacteria a series of short reports can be seen on previous posts to The Blue Crab forum™ Environment and Conservation thread. Blue crabbers experiences with these dangerous Vibrio marine bacteria can also be found on the northeast crabbing resources thread at the same website. These vibrios can cause human disease, the most infamous perhaps being cholera or its scientific name Vibrio cholerae.]

In my meetings with Mr. Hammond, he frequently used the terms soil and humus for his underwater lands only later is when I came to realize his knowledge of agriculture soils.  He felt they deserved the same level of attention that “land soils” obtained.

In a review of the literature there is pronounced absence of marine soil study as it relates to chemical habitat succession. It is the concept that marine soils can be subject to soil characteristics such as compost, soil pH, soil pore sizes and ion capacity (CEC) that seems to be largely absent. The combination of soil cultivation and organic matter long the basis of terrestrial agriculture is almost unknown in the marine field. I know that there is not that much because my reference searches often reveal my own works-- not that helpful for expanding a larger reference pool, and I hesitate to leave just fisheries history catches as a primary focus. Instead, I have looked to early works on peat soils those conducted by soil scientists in Florida and also work conducted by the Bureau of Soils and Reclamation especially those termed forest soils in the 1930’s, 1940’s and 1950’s.  (After severe forest fires, these soils purged bacterial methane.)
I believe the absence of soil work in subtidal areas is from the fact that recent environment policies greatly discouraged any bottom disturbance, certainly nature itself at times greatly violates this man-made non-disturbance policy as this is how disturbance (cultivation) is injected into sub-tidal soils.  We can also observe changes from the removal of energy as flushing and inlet closure or stagnation, a frequent historical comment regarding herring inshore fisheries along the coast.

Perhaps because bottom disturbance has so overwhelmed today's coastal policy it has left an enormous research void, the chemistry of marine soils and the impacts of temperature and energy (cultivation) upon them.  This is a concern as it removes a knowledge base directly connected to the dangers of warming estuarine areas and what happens when they cool.

When I started looking at the chemistry of shallow water habitats since the 1980’s after meeting John Hammond I was amazed at how little existed for marine topic areas. Saltmarshes had extensive research literature most of which detailed how important they are for fisheries but very little about their chemistry as a whole or their responses to climate change. Most of the helpful habitat information has come from terrestrial peat bog research or those areas that once were wet but converted over to agricultural lands such as the Florida Everglades or in northern more temperate regions cranberry bogs.  Peat soils that are drained or flooded have chemical characteristics that are often defined by bacteria that live in them, those that exist in oxygen and those that do not.  Plants that thrive in peat saltmarsh Spartina pattens and the Everglades sugar cane, tropical rice paddies or cooler cranberries all can tolerate higher degrees of the sulfur cycle and these plants more tolerant to toxic sulfides. 

It is in heat and low oxygen that the sulfur cycle returns.  I suspect now that is the reason that John “Clint” Hammond, the retired oyster farmer I met with on Cape Cod years ago, urged me to learn more about the sulfur cycle and was looking at the culture of rice at the time.  He was also looking at the habitat expansion of eelgrass meadows over shellfish beds which was transforming marine humus into subtidal peat by eelgrass (See IMEP newsletter #30 posted October 9, 2014 on The Blue Crab Forum™).  In high heat, he noticed that even eelgrass blades became weak and roots broke, releasing the plants from the bottom.

Rice culture has an interesting life cycle as two other plants sugar cane and cranberry we culture them in these productive soils. All share that characteristic to tolerate submersion and water and in general have higher tolerances to sulfides and the sulfur cycle. That is because they live at the edge of the sulfur and low oxygen environments.  When these plants turn yellow and struggle with fungal infections such as the eelgrass wasting disease of the 1930’s, it is at that this time the sulfur cycle is gaining strength and killing organisms that need oxygen. In high heat the sulfur cycle with sulfur reducing bacteria can turn salt marshes into nature’s sulfide killing fields.  Eelgrass meadows can do the same collecting organic matter in time helping the sulfur cycle win that is why Danish researchers commented on the “eelgrass death rings” as even submerged grasses can be subject to the deadly sulfur cycle often observed in terrestrial turf and in deserts.

I think that is why so many fishers were surprised to learn about the negative side of eelgrass and organic matter in times of heat, it helps the sulfide blue crab “jubilees” and can purge toxic nitrogen substances killing larval forms of finfish and shellfish.  Early researchers were aware of these toxic terrestrial impacts and Northern Agriculture Experiment Stations reported on the use of marine mud fertilizers a century ago.  Florida established a Peat Experiment Station in 1921 near Belle Glade and studied the ability of sugar cane to grow in high sulfur soils.  This facility is now called the Everglades, Research and Education Center.

Indian River Lagoon – Jensen Beach Florida – Some Personal Observations

I had an opportunity to study oceanography at the SOMET Jensen Beach campus of the Florida Institute of Technology on the Indian River.  This campus, located on the “river” side of the Indian River Lagoon is no longer open.  Part of this facility is now Children’s Museum of the Treasure Coast, but its campus pier remains close to the “Tiki Hut” restaurant where my father and brother would join me for a dinner.  I spent many hours fishing for red snapper just beyond the paddle ball court and taking outboard and machine mechanics in the Ralph S. Evinrude Building on the campus.  Many longtime Jensen Beach residents most likely recall Frances Langford’s Outrigger resort, which was on the southern edge of the now closed FIT Jensen Beach Campus, which happened in 1986. 

Some aspects of the Indian River Lagoon in 1974 seemed familiar to me such as oysters and some blue crabs and a good shore fishing for red snappers, which I could often catch off the campus pier.  Some were not.  I was familiar with barrier spits and lagoons from years of lobstering and oystering out of Clinton harbor, which had a barrier spit and river opening. That was nothing like the size of this system, the barrier beach went on for miles  - “Indian lagoon” resembled a long narrow salt pond. 

The Belle Glade Agriculture Research Station was just west of Jensen Beach Florida FIT Campus, and my first introduction to the sulfur cycle was the smell of Florida Everglades “muck fires.”  The sulfur smell was the result of peat chemistry but all I knew was the morning sky had orange glow and of course the sulfur smoke.  I was so alarmed by this sulfur smoke, and I asked some Florida residents if we needed to leave.  I was assured that the smell of sulfur was natural seasonal event and from burning peat.  Mud Lake (Florida) was the site of some of the first research studies into sapropel, the organic compost of sulfur bacteria.  Herman Gunter G. M. Ponton – Florida Geological Survey – Bulletin #30 Peat Deposits of Florida Their Development and Uses – notes on the Geology And Occurrence Of Some Diatomaceous Earth Deposits of Florida 23rd to 24th Annual Report 1930-1932 Ponton conducted studies of sapropel in Mud Lake northeast of Ocala in 1931. (Today, this substance is frequently called “black mayonnaise.”)

Research of subtidal sapropel before it becomes a peat was under way in Florida nearly a century ago and indicated a direct climate link, most peat deposits occurred during a period of climate cold, and slowed or stopped in heat.  Page 76 of the Florida Geological Survey 23rd -24th Annual Report (See Diatoms of the Florida Peat Deposits by G. Dallas Hanna) contains this section.

Sample No. IX-29 Home Deposit, Tavares With Key Out Organisms Indicated, my comments (T. Visel).

“The assemblage found in such as might reasonably be expected to occupy a body (Bay Cove or Sound – T. Visel) of somewhat stagnant water in a warm climate.

Several of the top most samples (read core sections T. Visel) of the peat were examined with great care to ascertain if any of the typical cold water forms could be found alive, but in case was this true.  All of the frustules (diatom cell walls) which were critically studied were empty.  It seems however, that since the peat comes practically to the surface of the bottom some investigators have been led to believe that accumulation is still going on.  I am inclined to doubt this surely the bottom material is in a state of more or less unrest constantly (storm bottom disturbance, T. Visel) due to wind and waves, moving and burrowing animals, etc. (termed bioturbation today, T. Visel) but in view of the mass of information which tends to show accumulation of peat at the present time only in cold climate, it seems reasonable to assume that no additions are being made to the Florida deposits at present.”

Today, researchers recognize that such organic deposits hold spores and cysts (See Appendix #1) and New York researchers confirmed such HAB cyst presence in 2015 (See Tang & Gobler, Journal of Phycology, January 19, 2015).

Marine Soil Composting

Most gardeners are familiar with or use of compost as a humus “top dressing” or folded into garden soils.  The partially decomposed organic plant matter is collected and utilized after bacterial action.  From time to time, the compost pile is turned to introduce oxygen and keep nitrate formation high.  If the compost is wet or soaked, the bacterial process slows and starts to show more ammonia, a much less valuable nitrogen component.  If the compost dried to a powder, the bacteria that need some moisture begin to die off and can then burn.  This can happen to forests naturally as the amount of leaves, limbs and branches become very dry and this causes a forest fire.  I was introduced to compost – peat burning in Florida and later in Ireland as peat stoves. 

Nature has provided bacteria that recycles plant tissue into plant nutrients – some bacteria thrive in cool, oxygen-rich conditions; some thrive in heat and do not require oxygen.  Seawater conditions introduce a substance dissolved in it that some bacteria can use or “mobilize” – sulfate.  Sulfate is a chemical compound consisting of one sulfur atom surrounded by four oxygen atoms.  Bacteria can slice off the oxygen from the sulfur, leaving sulfur to react with hydrogen ions, forming H2S or hydrogen sulfide.  That is the product that is mentioned during fish kills, the often reported “smell of rotten eggs.”  Other products include ferric cyanide, hydrogen cyanide, iron sulfide and various metal sulfides.  It is the marine compost signature that contains metals from the action of sulfate-reducing bacteria.  It also introduces the impact of nature’s turning of the compost piles by storms (hurricanes) or floods.  In cores of salt marshes, we can observe layers, iron-enriched by sulfate bacteria, interspersed with “brown” oxygen-rich layers.  This has left us a habitat history in core samples of once subtidal marshes.  Cores may include sandy and bivalve shell layers, pointing to significant habitat shifts in storm energy.  Surface peat – composts in which plants cover – like terrestrial grasses, can be very thin or deep in areas that had wet or flooded conditions.  We observe these deep accumulations in “peat bogs.”  Peat is harvested today as a natural renewable soil nourishment.  Its familiar commercial name is “potting soil.”  One could consider (but few researchers do) salt marshes a marine compost pile that can be, at times, dominated by sulfate, not oxygen bacteria – and this happens and builds in long periods of heat.  This is the danger of climate change, what was once was a “good” habitat for fish in heat turns deadly.

This introduces the same growth of New England salt marshes that deposits have a direct link to cold that would naturally increase the habitat for oxygen reducing bacteria, while greatly slowing those bacteria that use sulfate as an oxygen source.  Healthy salt marsh plants would tend to collect organics and silt – from storm or flood waters.  This acted as a fertilizer and in the literature is termed the Nile River effect.  With seawater, sulfate would be introduced as well.  Peat soils were acidic but layers containing bivalve shell were less acid.  Hill and Shearin,1970, Tidal Marshes of Connecticut and Rhode Island, Bulletin #709 of The Connecticut Agricultural Experiment Station, New Haven, CT – on page 9 is found this section:

“In the estuarine marshes along the major rivers, the sediments are more acid, with pH ranging from 4.3 to 6.6.  The acid pH corresponds to that in freshwater marshes.  The greater hydrogen ion concentration comes from organic acids produced by decaying plants in an environment deficient in oxygen.  In the deep coastal Great Island Marsh at the mouth of the Connecticut River, the pH is also acid.  It ranges from 5.0 to 5.6.  Here, seawater is often displaced or mixed with freshwater, and the sediments are as acid as in estuarine marshes even though we shall see that they are salty. 

In the Clinton Marsh, below 36 inches, pH exceeds 7.5 in places.  Beneath the organic layers alkaline shells are abundant in the silt and clay (Bloom and Ellis, 1969) and the dissolving of carbonate in the shells raises pH.”

Shell may also provide a more suitable pH modifier for eelgrass and mangroves.  Perhaps much information could be obtained from fisheries especially blue crabs they are very responsive to habitat conditions and blue crabbers fish the shallows.

Since Cape Cod 1980’s and for several decades later, I've heard about value of cultivating marine soils loosening hardpacked soils with hydraulics breaking up sand in mud soils 4 to 12 inches deep from the shellfish industry.  This includes observations from the hand raking fisheries as well.  Small pump jet clam fisheries years ago on Cape Cod termed the Yarmouth wand or Barnstable jet clamming. These hydraulic accounts nearly always describe the positive soil cultivation aspects increasing pore water circulation allowing these subtidal soils to again “breathe.”  Such hydraulic cultivation often brought shell pieces (shell hash) to the surface to sweeten these soils exactly the same process of adding agricultural terrestrial soil time for pH moderation. Coastal storms could accomplish the same over much greater areas and in deeper waters, washing away clay particles. (Clay particles tend to have a high CEC.)

I think we need to add another aspect of cultivating benefits the adding of oxygen to marine soils and by doing so changing the bacterial composition in them.  Upon review of the negative impacts of sulfate reducing bacteria (sulfate metabolism) complexing heavy metals discharging toxic sulfides and holding disease agents in a marine compost.  The injection of oxygen containing seawater, by way of hydraulic manifolds or jets not only cultivated these marine soils but injected seawater containing oxygen, creating a habitat lethal to some sulfate-reducing bacterial strains similar to turning terrestrial composts.  Injecting oxygen allows the oxygen bacteria to return (nitrate pathway) and sulfate bacteria (ammonia pathway) to lessen.  Elevating oxygen is a better environment for the “good” oxygen reducing bacteria, which are far more efficient at breaking down organic matter or the “short organic cycle” versus the sulphate (sulfate) reducers who are for less efficient, the “slow organic cycle” that produce toxic sulfide.  In heat, the use of sulfate as an oxygen source ensures sulfate-reducing bacteria will never face an oxygen shortage. They have plenty full (non-limiting) supplies of sulfate waiting for them dissolved in salt water. 
So, I am now considering that in times of cold and storms, sapropel organic deposits are removed by direct soil cultivation and most likely reduce the sulfate-reducing bacteria.  This has the ability to change marine soil pH and facilitate clam sets.  It is these sulfate reducing bacteria that are the source of sulfides and once these are exposed to oxygen create and almost instantaneous sulfide-sulfuric acid wash. Sapropel once was harvested for terrestrial soil nourishment to support agriculture.  This compost of carbon, nitrogen and organic matter to feed the good oxygen requiring terrestrial soil bacteria that plants need.  Once it was harvested, farmers soon noticed a hurtful acidity as the sulfuric acid content quickly increased.  Agricultural experiment stations (New Haven included) soon issued warnings and advice to “cut in” oyster shell to buffer this acid.  Agricultural experiment stations in Maine and farmers in the Canadian Maritimes also used lobster shell.  This sulfide sulfuric acid wash can occur after a strong storm as well almost like the smoke of a forest fire signaling massive habitat change by natural conditions.  It is after these massive storms (hurricanes) that by waves current and tidal surges that reopen closed soil pores and wash organics sapropel compost from them.  The evidence of sulfide staining is sometimes observed by coastal residents as storm waters may have a grey coloration.  Such cultivated marine soils often sustain tremendous sets in “new sands.”  This opens long stagnant soils to oxygen.
Now I think we need to include changes in marine soil bacteria as well, hydraulic jetting these soils can increase habitat quality for clams but also change the bacterial spectrum.  Terrestrial farmers and home gardeners recognize this as a “smelly” ammonia compost.  Land composts that are wet in high heat can also go over to anaerobic reducing bacteria.  The lack of air (oxygen) had caused them to thrive in low oxygen conditions.  Home gardeners frequently turn the compost to introduce air (oxygen) into the organic mix.  They reduced the formation of ammonia by introducing oxygen for oxygen-requiring bacteria, which increases levels of nitrate, an important plant nutrient and far less toxic to fish than ammonia. 

Storms I suspect also alter the bacterial strains in the soils perhaps reversing from sulfur (sulfate) strains to those who thrive in oxygen.  This does take time as marine bioturbation helps keep oxygen in soil pores (like earth worms in terrestrial composts).  It is the sulfur strains that are so deadly such as Desulfovibrio and sulfate reducers that produced sulfides and increased ammonia. Several shellfish researchers from the turn of the century, notably Dr. David Belding (Mass) commented on these organic acids interfering with clam growth and sets.  He suggested deep plowing to turn these wet organic filled soils. Some of the first increases of organic matter occur when these subtidal soils stabilized that is a natural process but is greatly speeded by the growth of the submerged aquatic vegetation such as eelgrass. By its very nature eelgrass helps end marine soils capacity for shellfish sets by slowing waters and trapping organics.  In time, accumulating organics set up conditions for the habitat damaging sulfate-reducing bacteria.   Eelgrass meadows tend to rise as they trap these organics and the sulfate reducing bacteria begin to generate sulfides beneath them. This is a natural process and in high heat and low energy (few storms to thin (thatch) organic deposits in eelgrass meadows) sulfide levels build up to levels which in time is toxic to other marine life, but now to eelgrass itself.

Researchers in the 1980’s, first documented this sulfide toxicity in what appears to be forming sapropel deposits in Old Tampa Bay, termed the Tampa Bay Effect in the 1970’s.  Estuarine areas that had a constructed tidal restriction (such as railroad crossings) collected organic matter.  Strong storms in the fall likely wiped out most of these high heat Vibrios, which coincides with the drop in seawater temperature.  Storms also rob these sulfate reducing bacteria of food washing away organic matter keeping the surface to 18 inches below in sulfate bacteria. Any beach walker who finds cobblestones and turns them over will see the blackened result of sulfide bacterial action sealed from the oxygen above and can give off a hint of sulfur more like a matchstick smell rather than the stronger sapropel deposits behind dams or tidal restrictions especially railroad crossings. These deposits can be several feet deep and in sharp smell of sulfide “rotten eggs” can be at times “breathtaking.”  Although Connecticut Environmental officials once dismissed coastal resident concerns about railroad crossings with continued sea level rise these restrictions keeps warmer water from existing only to warm even faster.  This aspect now favors the growth of Vibrio bacteria.  Sapropel deposits grow the fastest behind such tidal restrictions, which now function as more like a dam as widths do not widen with increased flow. They now act to warm water.

This organic matter trapped behind coastal dams or held in deep deposits behind tidal railroad and road bridges restrictions are the perfect places for sulfate using bacteria.  Deep deposits of sapropel, mostly from dead leaves, now rot supplied with sulfate by tidal action.  Here these bacteria grow and in time overwhelmed coastal habitats. These deep sapropel deposits end the fish and shellfish populations near them. These soils and sulfur reducing bacteria can change the habitat diversity and types of species living in them.  They often contain little if any submerged vegetation.  In the historical fisheries literature, they are referred to as the “dead bottoms.”  Coastal residents, on hot August days, experience this bacterial change by the intensity and duration of sulfide smells.

Sapropel Formation Is Not “New”

The rise of sapropel was also reported by researchers looking at coastal vegetation a century ago, and we have an excellent description from The Torrey Botanical Society – and research George E. Nichols in the 1920 publication titled “The Vegetation of Connecticut VII, The Associations of Depositing Areas Along the Seacoast.”

Under Section C Muddy Bottoms and Shores, pg. 525, is found the following:

“At ordinary low tides, these tidal flats of the lower littoral present a surface of soft blue-black, ill smelling mud – an area in which, except for bed colonies of eelgrass or salt marsh grass (Spartina glabra) seed plants and attached algae are practically absent.”
And further, Nichols implicates “heat” as the reason for an absence of plant life:

“The failure of the eelgrass to flourish on tidal flats is probably associated with its inability to withstand the dessication and extreme temperatures to which plants growing here are frequently subjected at low tide.”

The shellfish industry had also taken notice of organic buildups as they could observe oyster bed burial and the loss of oysters (See Appendix #3: E. P. Churchill, Jr., The Oyster and the Oyster Industry of the Atlantic and Gulf Coasts, 1920) that “During warm weather, this organic deposit is likely to undergo rapid decomposition, the toxic products of which sicken and kill the oysters.”

The description of soft, blue-black and ill smelling all point to the organic ooze termed a black mayonnaise a century later (See “Black Mayonnaise in Wellfleet Harbor: What is it and Where does it come from?” Mittermayr et al., September 2020, Center for Coastal Studies).

The Wellfleet paper – Black Mayonnaise in Wellfleet Harbor describes accumulations, at times reaching 8 to 12 feet deep.  Page 13 of the report has this segment (some core samples indicated more than 20% organic matter) – my comments, T. Visel:

“At first glance at the measured sulfur isotope signatures suggest sedimentary sources including pyrite and sapropel.  Pyrite is generally considered to be the end product of sulfur diagenesis (sulfur diagenesis refers to biological processes after deposition – composting, T.Visel) in anoxic marine sediment (Hoefs, 2004) and sapropel describes anaerobic sediments that are rich in organic matter.”

Its buildup can suffocate benthic shellfish.

That's why John C Hammond was studying the sulfur cycle and reviewed rice cultivation when we would meet in the early 1980’s.  The products of sulfate reduction in sapropel is just as severe for fish to shellfish.  This is recorded in habitat histories in salt ponds of Rhode Island eastern Long Island New York and those on Cape Cod for alewife.  Here, local fishers observed what happens when coastal tidal circulation is reduced by closing inlets as those bays and ponds warmed.  Sulfate reducers generated more sulfides, which complexed iron into iron sulfide which turned lakes and then waters black with fish kills.  An example of winter flounder fish kill in 1917 here is found in the fisheries history.  The New York Copeia March 19, 1918 #25 has an account by J. T. Nichols:
“They sometimes perish by the thousands in very hot spells of summer weather if they are trapped in shallow enclosed bays as happened in Moriches Bay Long Island New York in 1917 between July 29th and August 4th when the air became extremely hot.” (This is from his 1918 article.)

“About August 1, 1917, there was an unusually heavy mortality of Pseudopleuronectes americanus (winter of flounder) in Moriches Bay, Long Island New York.  This is a broad almost tideless bay but much of it is very shallow (extensive flats having but a few inches of water) and it is decidedly brackish.  Pseudopleuronectes is one of the few marine fishes found in the bay in numbers.  An exceptional number of dead of this species were noticed July 28, and on August 4 it was estimated that thousand dead were seen.  They averaged about 8 or 9 inches in total length.  This high mortality was probably correlated with a period of usually hot weather which that section had just experienced.”

We today recognize that these shallow flats, with iron sulfide black coloration can become super hot with seawater temperatures ready over 100f in bright sun.  Diver observations in Great South Bay reported that winter flounder became inactive at 23oC 74oF and temperatures measured 50 to 60 mm below the sand measures 2oC to 3oC, 3 to 4 degrees cooler than the surface and buried themselves.  Olla et al., 1969 (See Olla, BL, R. Wicklund and S. Wilk 1969, Behavior of Winter Flounder In A Natural Habitat, American Fish Society).

The Sapelo Island National Estuaries Reserve has a great description of what temperatures can do to intertidal mud flats – this is an except from Intertidal Mud Flats by Margaret Olsen.  It describes the presence of hydrogen sulfide.

“Intertidal mud flats are located along the edges of the salt marsh.  This harsh habitat is covered by water at flood (high) tide and exposed to the scouring sun at ebb (low) tide.  Slack tide is the brief period between flood tide and ebb tide during which the water is not flowing in or out but is still.  Only the upper layers of this muddy substrate contain oxygen.  The deeper layers contain decaying organism matter that gives of a hydrogen sulfide gas that causes a rotten egg smell.”

When water is retained in an estuary in heat, this allows oxygen levels to drop.  This is very noticeable in eastern Connecticut in coves bisected by the railroad.  At the end of the “great heat,” the period in New England of very hot summers 1880-1920, coastal residents noticed the buildup of sapropel, an organic marine compost in coves that “smelled bad.”  Coastal families that fished (sometimes going back before the railroad crossings) recalled how productive they once were – firm and shelly bottoms.  I spoke with members of the Manwaring, Wilcox and Rathbun families, whom all provided a glimpse of how productive these coves were.  Unfortunately, inshore fisheries had declined and so the numbers of commercial docks.  In 1989, a proposal was made to tax all docks and Benjamin F. Rathbun wrote to me on February 19, 1989 this response:

“While I will be the first to admit that we are a vanishing species, there are, however, still a number of Connecticut commercial fishermen whose families have been using their own small wharfs for three and four generations, and who, in no way could be considered to be one of the aforementioned “Fat Cats” (to pay for docks, T. Visel).  Be that as it may, the proposal itself is so vaguely stated that a number of questions come immediately to mind, as follows –
What about the railroads, their bridges and trestles have done more to degrade and restrict access to state waters than almost all other activity combined.”
These railroad causeways had disrupted the ability to rid themselves (usually during rain and storm events) of organic matter, which over time built up behind them, covering previous shell and sandy bottoms.  While these railroad crossings did allow for some tidal exchange, they largely blocked energy from them.  In extreme cases, organic matter built up and caused more retention.

Retaining water that is hot helps the formation of sulfides a plant toxin.  At 32oF, oxygen solubility is high at 14.6 mg/liter at 93oF it is only 7.7 mg liter.  Bacterial digestion can remove what little oxygen remains.  High organic laden waters frequently have levels approaching 1 or 2 mL of oxygen per liter – too low to support fish life.  Under these conditions, bacteria can take what little oxygen remains.

Storms, I suspect, now also alter the bacterial strains in the soils, perhaps reversing from sulfur strains to these who thrive in oxygen.  It is the sulfur and low oxygen strains that are so deadly to marine organisms (Desulfovibrio series) that produce sulfides and ammonia.  Several shellfish researchers from the town of the century (notably Dr. David Belding) commented on these organic acids can interfere with clam growth and sets and suggested deep ploughing to turn these wet organic filled soils.  Some of the first increases of organic matter occurs when these subtidal soils stabilize that is a natural process but is greatly speeded by the succession of the submerged aquatic vegetation – such as eelgrass.  By its very nature, eelgrass helps end marine soils’ capacity for shellfish sets by slowing waters and trapping organics and in time setting up conditions for the habitat damaging sulfate reducing bacteria.  In time eelgrass meadows rise as they trap these organics and the sulfate-reducing bacteria begin to generate sulfides beneath them. 

This is a natural process and in high heat and low energy (storms to thin organic deposits in eelgrass meadows) sulfide levels build up to levels which in time is toxic to other marine life but now to eelgrass itself.  Researchers in the 1980’s first documented this sulfide toxicity in what appears to be forming sapropel deposits in old Tampa Bay – termed the Tampa Bay Effect (1970’s) of estuarine areas that had or contained tidal restrictions.  Organic matter tends to collect behind such restrictions, railroad and road causeways in the 1980’s as reported by winter flounder fishers in eastern CT (See IMEP #15-A, #15B posted on The Blue Crab ForumTM).

The rise of sapropel (marine humis) favors these sulfur-reducing bacteria, but in seasons they change as well.  In the summer, low oxygen in the shallows favors them – this is often the source of the rotten egg smells in late August arising from waters with poor flushing (mentioned as stagnation in the historical literature) or restricted circulation.  Some of these bacteria now include the potentially dangerous Vibrio series.  In winter with colder seawater, these vibrios die back to low levels.

Florida Sapropel Research In Marion County

By the 1920’s, the study of sapropel was well underway in Florida and the Peat Experiment Station to study peat soils was especially important to understanding the chemistry of peat.  Several plant science researchers contributed to the understanding of peat soils and sapropel before it emerged as marsh, including Florida and New Jersey, Florida Mud Lake In The Big Scrub about 23 miles of Ocala image number GE 1313A on 1931 August 181931 GM Ponton and DS Wallace in a small boat – getting sample of Sapropel) soon would lead the country in the study of peat and sapropel, they had many thousands of acres of peat marsh soils; the Everglades of Florida or the Meadowlands of New Jersey.  You see many of the mosquito control programs emerge from these states as these marshes also supported at times large amounts of biting insects. Peat soils once drained could become very productive for certain crops.  This was the research field of R.V. Allison of the Everglades Experiment Station at Belleglade Florida in the 1920’s and 1930’s.  (In 1921, the Florida legislature authorized the creation of the Everglades Experiment Station on lands near Belleglade (See University of Florida “History” – Everglades Research and Education Center).

Water -soaked soils- glucose metabolism was slow deeper peat was oxygen reduced and organic material reduced by the slower (less efficient) bacterial species the sulfur reducing and then the methogens bacterial strains that stripped off the last nourishing compounds leaving only carbon.  Methane a carbon atom surrounded by four hydrogens CH4.  It is the methogens that waste methane – (marsh gas) from deep within peak deposits.  Peat soils, to make them suitable for agriculture, were ditched and drained following the pattern of soil capture long practiced in the Netherlands.

Missing Iron Sulfide – Cyanide Chemistry

One of the items I consistently find in marine studies of inshore waters is the absence of bacteria created toxins specifically iron sulfide and ferric cyanide both natural bacterial/chemical component of low oxygen composts.  The following is a segment of a University of Massachusetts Center for Agriculture, Food and the Environment fact sheet on odor control from livestock manure and its capture:
“Hydrogen sulfide is a strong smelling gas associated with manure.  Hydrogen sulfide also stick

s to iron.  If you pass manure odors through a filter made of iron filings, hydrogen sulfide will stay with the iron and not escape to the surroundings.”
   “Manure is food to bacteria, and bacteria give off odors as they digest manure.”

This is the usual chemistry in a low sulfur high iron compost, but marine composts are high in both sulfur and iron and largely absent references to ferrocyanide, chemistry and the formation of ferric ferrocyanide.  The oxidation of ferrous ferrocyanide salt produces a deep blue coloration termed Prussian Blue.  This chemistry in high organic soils may answer why in the historical records sapropel appears to have a blue tint, especially when removing deep deposits.

Bivalve Shell Blue Coloration

The intense blue coloration on shells may indicate low oxygen soils.  Deep blue quahog interior shell may just indicate an enriched organic soil.  Organic matter such as natural leaf fall or human-induced sawdust and wood pulp, including sewage suspended solids, can influence sulfate metabolism by creating low oxygen conditions.  The transfer from oxygen bacteria to sulfate bacteria is accompanied by a drop of nitrate and an increase of iron sulfides. This creates a black sapropel and was a concern as this deposit grew under the first fish net pen operations.  This is frequently termed as excess “organic loading” – terrestrial gardeners can use the term “deepening compost” and often turn compost piles to introduce oxygen-sustaining oxygen-requiring bacteria.  A June 2002 paper (thesis) by Jon Chamberlain from cooperative research between the Fisheries Research Laboratory in Aberdeen (which I visited in 1989) and the Dunstaffnage Marine Laboratory Oban – titled “Modelling the Environmental Impacts of Suspended Mussel (Mytilus edulis L.) farming explains this chemical change in marine soils on pgs. 6-7, my comments in (   ) Tim Visel.

“As redox conditions decrease (a lowering of oxygen, T. Visel), microbiological activity in the sediment (soil, T. Visel) switches from aerobic oxidation, producing carbon dioxide and water to anaerobic bacterial degradation (this is called anaerobic digestion or just “AD” today, T. Visel) of organic matter using nitrate and sulphate as oxygen sources leading to the formation of compounds such as methane, hydrogen sulphide and ammonia.”
And further:

“The characteristic black colour of these reduced sediments (marine compost, T. Visel) arises from the formation of iron sulphides through the reaction of hydrogen sulphide (released during sulphate reduction) with labile (easily broken down) iron (Jorgensen, 1982; Morris, 1983).  The processes of nitrification and denitrification by which bacteria oxidise ammonia to nitrite and nitrate, and reduce nitrate to nitrogen gas, respectively, become inhibited as nitrate levels increase and may cease to function as a mechanism for removal of organic nitrogen (Kaspar et al., 1988).”

And then explains the drop in nitrate:

“However, the general absence of nitrate in the sulphate reduction zone of marine sediments suggests that nitrate can be fully utilised (bacterial consumption of nitrate as a reserve oxygen source, T. Visel).  This process, the development of biogeochemical zones in marine sediments, is found in other areas of organic enrichment, such as sediment surrounding pulp effluents (Pearson and Resenberg, 1978) and sewage sludge dumping grounds (Pearson, 1987).  It is often reported along with the development of mats of distinctive white sulfide oxidising bacterial communities (Beggiatoa sp.) (This is frequently found in stagnant pools of water on New England salt marshes, T. Visel).  In extreme cases (low turbulence and high organic input), the water overlying the sediment (soil or compost, T. Visel) may also become anoxic (T. Sutsumi and Lakuchi, 1983).

This toxic condition is now associated with anaerobic bacteria release of methane gas and hydrogen sulfide. (The use of nitrate by oxygen bacteria is often termed “nitrate buffer.”)

Bivalve Shell and Paleontology – A Historic Habitat Connection

We might have a natural paleontological marker for these enriched organic soils low in oxygen.  Some strains of bacteria naturally produce cyanides and in low or no oxygen conditions provide the chemistry for the deep blue coloration of interior quahog shells. These shells can persist for thousands of years on coves (See Holocene Evolution of Boston Inner Harbor, Massachusetts, Rosen, Brenninkmeyer and Maybury, Journal of Coastal Research, Vol. 9, No. 2, 1993).  Researchers have found intact bivalve shells estimated to be 3,570 to 3,090 years ago.  Cores of the Back Bay section of the city of Boston were “interpreted as channel deposits based on numerous channel-bottom shell-lag layers.”

Some bivalve shells may provide evidence of climate conditions by the remains of shell stains or color.

On the inside of a quahog shell, these are the blue-purple colorations and signify a high organic matter soil, which at times, purges cyanides that complex in the thinner shells. Sandy soils or those that contain less than 10% organic matter have interior shells that show much less blue or no color at all.  This absence is also marked by a low soil CEC and faster growth and calcium shell chemistry.  This same effect is also found in shallow water oysters only observed on the outside of the shell, a streak or single band of purple coloration.  If a shallow water oyster is moved to deeper, more alkaline bottoms, this purple-blue coloration stops.  (The basis of Prussian Blue, a powerful paint pigment, is ferric cyanide an iron salt.)  After sulfate-requiring bacteria run short of oxygen in a compound sulfate form, they die off and give rise to a bacterial strain that lives off the remaining energy left in protein plant tissue bonds, and produce the gas consisting of one carbon atom surrounded by four hydrogen atoms or CH4.  This is the most dangerous “greenhouse gas” – it naturally makes the earth warmer.  This is the action of the bacterial group known as the methanogens.

The chemistry of peat soils in oxygen is very different than those surrounded by sulfate.  This compost under water is being consumed by different strains of bacteria, ones that produce chemicals not associated with land composts, namely sulfides, which chelate metal ions, acid composts rich in sulfides and at times sulfuric acid, an increase of ammonia in heat and the creation of cyanide salts.  Some cyanide salts created by bacterial action occur under ice or during extreme heat.  A key factor is a large organic matter component, around 30% organic matter, 30% clays and 30% mineral sands or rock flour.  This is usually termed a mud or soft bottom and the home of the hard shell clam Mercenaria mercenaria. 

Methane Under Ice

One of the ways that I can tell a sandy soil low in organic matter and one rich in organic matter is the color of Prussian Blue on the shell.  These blue-purple markings are believed to be a chemical reaction in the organic matter that produces natural cyanides.  Methane is a natural product in the last step of converting long carbon chain molecules by bacteria.  Methane can even accumulate under ice, and methane bubbles trapped in ice is one of the ways we can study this process.  This study is underway as this methane was produced by ancient plant matter when the polar regions were filled with vegetation millions of years ago.  The bacteria responsible for methane release exist in no-oxygen conditions and can build up under ice in the winter.  In 2019, researchers were actually able to punch holes in ice and ignite the methane trapped below the ice.  We know this gas as “natural gas” but an earlier name was “fossil gas” recognizing its ancient origins from decaying plants of long ago.  This soil chemistry may provide answers to questions about the blue staining of bivalve shells.  Some recent reports from Cape Cod appear to confirm this possibility. Quahogs in sandy soils have been reported to have no or very little blue staining.

Appendix #1

Tampa Bay, Indian River and Lake Studies Lead
Nation about Sapropel-Nitrogen-Ammonia Connections
Sapropel/Submerged Aquatic Vegetation Contain Bacterial Processes Related to Climate Cycles

In the 1950’s and 1960’s, the effects of a changed water cycle in the Everglades had caused researchers to concentrate on Florida peat studies – an area that is often “hot” according to our New England standards.  New England during this period was in a cold climate cycle with subzero temperatures that froze over bays and salt ponds. Here in the fisheries literature you can see the results, of this New England cold strong hurricanes, thick ice and shorter growing seasons.  Seed companies faced with a shorter growing season developed the “number of days till harvest” label seeking an advantage for marketing.  Seed packets sold today have the same reference as the growing season time.

But in the 1950’s and 1960’s if you were interested in the sulfur cycle or sapropel, you needed to be in Florida.  Most of the direct references to sapropel or subtidal peat – either in the formation of coal or using such wet peat for agriculture Florida was the place to be.  In fact, Florida hosted the first agricultural Peat Experiment Station in Belle Glade opening in 1923.

To fully understand sapropel you needed to look at bacteria and the formation of coal.  It is the sulfur reducing bacteria (SRB) that utilize sulfate as an oxygen source and in the process seeped hydrogen sulfide into this ooze and later fossilized is coal seams.  That is how sulfur was introduced into coal by bacteria.  To have this happen it needs to be “hot” and oxygen bacteria not present or at least then a small part of the bacterial population.  This is why coal was formed long ago when the earth was hot and sulfur was a dominant atmosphere constituent.  In fact the discussion about global warming is largely the possible return of sulfur to the loss of oxygen requiring life.  Putting sulfides into the air hurts oxygen life – it is as simple or complicated as that.  Researchers here found that coal has residual antibacterial features thought to be from Vibrio species that thrive in heat, but fire can destroy them. 
That is one of the interesting aspects of the blue crab, it is so to speak as it can carry vibrio bacteria, with little effect (it seems), while vibrio bacteria is a pathogen to many organisms (including us) the blue crab lives in an environment that fosters sulfur bacteria but has adapted to its presence.  Some research has indicated that some species have the ability to immobilize vibrio – not kill it but to make it “sticky” by changing bonding locations as to make them ineffective.  It was described to me as grease on a door knob- the door is still there but the knob has no grip and therefore cannot “be opened.” 

To understand the chemistry of sapropel the explanation of this bacterial battle needs to be included.  The area of study that allows us to study this bacterial battle is the soils and peats in cold or hot periods, and Florida presents a longer growing  season for sulfur because its climate is warmer (New England has vibrio perhaps in only the hottest of times).  In cold and in oxygen containing waters sulfate reducing bacteria loose to oxygen bacteria that are energy efficient.  In heat, sulfate-reducing bacteria (SRB) set the habitat conditions that extend into acid conditions and sulfuric acid soils that can be part of seafood disease and parasites.  Sapropel is now considered a bank of spores and cysts that are possibly released in rapid sulfuric acid (part of the sapropel – sulfur cycle) release that activate disease hosts even perhaps the dreaded oyster disease MSX.  There appears to be a correlation between storms and disease perhaps related to release of sapropel spores and cysts – the creation of acid bottoms that could activate these spores and cysts.

The connection to organic matter, heat and acid release of breaking outer shells is associated with cryptosporidium parasites that can cause human disease from thin walled oocysts.  The spores of thick wall oocysts are released from intestinal tracks into water, which is neutral to alkaline.  The breaking of the cyst wall from digestion is termed excystation.  Crytosporidium disease is frequently linked to contaminated water.  It is interesting to note that the parasite cryptosporidium and the dreaded oyster disease MSX or Haplosporidium nelsoni both form spores found in organic matter.  In fact, the intestines of marine worms are found to contain MSX spores and could be a potential source of activated cysts (excystation) or be activated in spontaneous low pH events, such as a storm in very hot weather.  A third parasite Glugea stephani that infects winter flounder is also described as a microsporida that thrives in hot seawater.  Similar to pollen grains in deep peat cores, these cysts may provide important clues to how dangerous high heat low-oxygen pathogens can be.  Such cysts such as the northern red tide lay dormant until released (many feel connected to storm events) as shown by an EPA Mumford Core study in 1981.  Here cysts several meters below the “current” surface were sampled and were still biologically active (See IMEP #97


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