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PostPosted: Fri Apr 27, 2018 3:35 pm    Post subject: EC #15 - Blue Crabs and Marine Soil Habitats Reply with quote

Blue Crabs and Marine Soil Habitat Histories
Environment And Conservation #15 Eelgrass Peat/Sapropel Linked to Finfish and Shellfish Diseases – Parasites – Harmful Algal
Blooms (HABS)
A Possible Chemical Habitat Quality/Nitrogen
Bacteria Index for Blue Crabs
Tim Visel
October 2017 – The Sound School
- Eelgrass Meadows A Possible Source of Vibrio Pools – Update March 2018
View all EC Reports on the Blue Crab Forum™ &
CT Fish Talk ™ Salt Water Reports

The views expressed here do not reflect the Citizens Advisory Committee or Habitat Stewardship Working Group of the EPA Long Island Sound Study. On February 16, 2016, and February 8, 2017, I have asked Connecticut resource management agencies to recognize Sapropel as a distinct subtidal habitat type. This is the viewpoint of Tim Visel.

Environmental and Conservation Thread #13 Blue Crabs, Salt Marshes and Habitat Succession was posted on July 13, 2016, and should provide an introduction to this habitat history concept. It has been one of the most viewed posts to date.

A Note from Tim Visel

Addendum – March 2018
I would like to thank The Blue Crab Forum ™again for posting these bacterial / nitrogen series on the Environment/Conservation thread. The first one was about the Conowingo Dam trapping large amounts of organic matter (September 2014) and negative aspects of bacterial habitat change from it. This research coincided with records about climate cycles, temperature, rainfall and the organic matter associated with the bacterial processes of sulfate reducing bacteria (SRB). In 2014, my research was focusing upon fish and shellfish disease in heat in or near organic deposits. These are termed sapropels, but sometimes referred to as a “black mayonnaise” when the bacteria reduction of organic matter is without oxygen and results in sulfide discharges from them in heat – the blue crab jubilees. Most submerged aquatic vegetation (SAV) studies then were not looking at bacterial change in submerged peat soils –under a vegetation cover or growth, long a research area of terrestrial soil research but not prominent in subtidal marine studies.
A large part of this sapropel process involves a bacterial type that is heat related – the Vibrio’s, or those other strains that use sulfate as an oxygen source (not elemental oxygen) which is not limiting in seawater. Sulfur reducing bacteria is a pathogen to seafood but also at times to us. While terrestrial farm and agriculture researchers had long ago discovered that grasses could bind organic matter in a compost and could contain rich bacteria growths beneath them, (P. E. Brown 1918- Iowa State University – Agronomy Section Soil Bacteriology and Homer J. Wheeler, Rhode Island Experiment Station, Rhode Island State College Bulletin 152 (1913) ; until recently, similar efforts in estuary research were few or non-existent. Many turn of the century studies looked at bacteria growing in or under grasses as an inoculation media or for ammonia generation (sealed compost) however, this knowledge did not present itself in current estuarine study.
Vibrio is a bacteria that is part of the sulfur cycle; in heat, which was on the rise generally in the 1980s (Duncanson and Saad 1989) Connecticut and the eastern seaboard had seen very hot temperatures 2006 to 2011, and a dangerous rise in Vibrio bacteria soon followed. It takes two to four years for research papers to go through the peer review process, another year or so for proofreading and journal publication. It has taken 4 or 5 years beyond the very hot 2010-2011 year to review them. Now those papers are coming on line and the submerged grass (eelgrass) sapropel’s SAV connection is being reported currently as significant to Vibrio populations impacting seafood in shallow waters, and the list is getting longer world-wide.

Seahorse disease Vibrio zosterae
Winter flounder fin rot Vibrio anguillorum
Lobster shell disease Vibrio beneckea
Fish diseases (general) Vibrio alginolyticus
Black band coral disease Vibrio shiloi
Human pathogen (shellfish) Vibrio parahaemolyticus
*Human pathogen (water/seafood) Vibrio vulnificus
Cholera reservoir (pathogen) Vibrio cholerae

*This is the Vibrio that has been so devastating to blue crabbers – some posts on the Blue Crab Forum™.
In addition, the Florida Institute of Technology (FIT) is now educating the public on organic matter bacterial discharges that can be huge source of ammonia. This is something that the New England Agricultural Experiment stations knew over a century ago- a warm or hot marine mud was capable of shedding ammonia in low or no oxygen conditions – a sapropel.

From reviews of the eelgrass and SAV literature, the first sapropels are formed beneath dense root peat with high sulfides (in heat), a signal of low oxygen – not unlike turf management science of terrestrial grass sulfide/ root rot studies. In cold oxygenated sea water, thin organic layers with submerged aquatic vegetation has very positive habitat services to many species, but in heat (warming climate) these habitat types can turn deadly discharging toxins ammonia/sulfide and help form Vibrio reservoirs (T. Visel). Researchers are also finding cysts and spores that cause bacteria thrives in organic matter and heat- harmful algal blooms (HABS) in deep sapropel layers.
I respond to all emails.

1. Soil Inoculation by P.B. Brown – Iowa State University Agriculture Experiment Station 1913
“Soil inoculation is the introduction of certain desirable bacteria into the soil. As a practice, it is very old, having been followed many years before its beneficial influence was understood. In reclaiming infertile land, the addition of fertile soil was often found helpful, especially for such crops as clover. The practice did not become general, however, until some thirty years ago when the reason for the soil-enriching properties or legumes was discovered.”
At that time it was demonstrated that when clovers, vetches, alfalfa, cowpeas and all other legumes are associated with certain bacteria, these crops have the power of taking nitrogen from the air for their growth.

2. Dr. Homer J. Wheeler in 1913 (Rhode Island Experiment Station) printed an extensive bulletin on Manures and fertilizers in 1913 – in which on page 33, mentions the bacterial processes sealed from air – (oxygen).
“The storage of manure (organic matter, Tim Visel) requiring exclusion of air (oxygen, Tim Visel) conditions are created favorable to certain anaerobic bacteria, which may reduce sulfate to sulfide. This in turn readily reacts with carbonic acid to form calcium carbonate with simultaneous liberation of hydrogen sulfide.”

3. WHOI-89-35
Shellfish Closures in Massachusetts: Status and Options
Edited by Alan W. White and Lee Anne Campbell
Woods Hole Oceanographic Institution Woods Hole, Massachusetts 02543
September 1989
Technical Report

Robert A. Duncanson Water Quality Laboratory Town of Chatham Chatham, MA 02633
Dale L. Saad Town of Barnstable Health Department Hyannis, MA 02601 (1989)

The use of bacterial species as indicators of the sanitary quality of water had its origins in the early part of this century. The indicator concept was begun as a protective measure for potable water supplies in response to widespread outbreaks of waterborne diseases such as typhoid and cholera. The use of bacterial indicators in the shellfish arena began in the 1920s following several outbreaks of typhoid linked to oysters. Since the introduction of bacterial standards for both shellfish growing waters and market samples, the incidence of shellfish-borne disease has declined. The question thus becomes, why should consideration be given to a change in the indicator system that appears to have been working adequately for over 60 years?

The answer to the question posed above is multifaceted. Although the incidence of classical shellfish-borne diseases (typhoid and cholera) have declined, there are increasing numbers of disease outbreaks attributed to shellfish.
This would indicate that the pathogenic agents involved in these more recent outbreaks are not the classical pathogens which the original indicator system was meant to warn of. Indeed, in many recent outbreaks other bacteria, such as Aeromonas hydrophila, Vibrio parahemolyticus and V. vulnificus, have been the cause.

In 1885, The Maine Agriculture Experiment Station issues a caution on page 35 in a section titled, “Harbor Mud” as producing ammonia –
“This station (Maine Experiment Station) was sent a sample by Fred Atwood of Winterport (Maine), the barrel of mud was received several weeks before sampled and when it was opened it emitted a strong odor of ammonia.”
[The Maine Fertilizer Control and Agriculture Experiment Station 1885-6, Augusta Sprague and Son, Printers to the State 1886].

A Possible Chemical Habitat / Bacteria / Nitrogen Quality Index for Blue Crabs
Marine Soil Chemistry

To perhaps to more fully understand blue crab populations and characterize its habitat parameters, we need to know first more about the soil in which it lives. It is the blue crab that could provide important information about climate cycles, the impacts of heat and cold over long periods. Short term I see large fluctuations in habitat compression and expansion therefore blue crab catches can fluctuate greatly. Debates occurred between fishery area managers occurred in the 1930’s and 1940’s over climate influence or reproductive capacity of the blue crab. This was quite evident in the lobster fishery die off at the turn of century in the late 1890s. (See IMEP #62 The Lobster Convention of 1903 Blue Crab Forum™ posted April 6, 2017 on the fishing eeling oystering thread). At a 1947 U.S.Fish and Wildlife Service program, conference researchers had come to largely a climate conclusion versus reproduction for changes in blue crab abundance the following is a segment from the conference report (1947):

“The Blue Crab of Chesapeake Bay exhibits wide variations in abundance that cause large losses to the industry. Restrictions on the catching of adult egg bearing crabs did not remedy this condition. Research has just discovered that those variations in abundance are caused by changes in the survival of young crabs rather than by the number of eggs spawned.”

Longer term we need to look at core samples of deep sapropel/peat salt marsh and eelgrass meadows. Those marine organic habitats also have left a climate energy/biochemical record that could provide clues as to the temperature chemical/biological impacts similar to land habitats, such as the sulfide deaths of marsh dieback we see in wetlands today. Habitats change and many wetlands have the remains of trees that long ago perished from chemical sulfide soil changes that destroyed its roots. To understand marine soils we may need to look at terrestrial soil changes as well. Our marine soils have both oxygen bacteria that oxidizes organic matter with sufficient oxygen, and if oxygen is limiting, then reduction of organic matter by way of sulfate-reducing bacteria which becomes part of the marine sulfur cycle. As in terrestrial soils marine soils have both oxygen and sulfur bacteria that rely on different growing conditions. These conditions impact directly and influence habitat health of marine tidal plants and the seafood that lives near them. One of the areas in most need of research is the bacterial growths below marine grasses. That chemistry is a unique feature of the blue crabs because they live in or near at times, sapropel.

Unfortunately, our information on marine soil chemistry is very limited and has been slowed by environmental policy (my view). Several New England states have yet to identify marine sapropel as a distinct habitat type perhaps for its negative habitat policy consequences to eelgrass, my view. We have unfortunately, with eelgrass a situation policy wise, which now resembles the “Waldsterben Controversy” (forest dieback) that occurred in Germany in the late 1970s and early 1980s but only for us perhaps, its eelgrass. In the 1970’s as a dieback occurred in German forests, researchers reported it and numerous studies undertaken only to find out the dieback was not entirely human caused but a part of a long natural cycle. A long term view was needed to properly evaluate a forest observed dieback but apparently was superseded by the rush to obtain grant funds (my view) and is still the source of much environmental controversy in Germany today (Von Storch H, 2012 Sustainable Climate Science). The sensational media attention and reports did greatly alarm Europeans and a crisis soon generated dozens of studies and significant research grants.

In a recent review in the late 1970s and early 1980s, German forests did suffer a “dieback” and then opportunistic fungal and parasite diseases damaged trees there. After the first dieback reports a sort of environmental panic set in. Germany had of course over time recognized the value of forests and the wood products from them -part of its culture and necessary to many organisms that were themselves dependent upon them. A public media sensation happened and concern had soon included Waldsterben indexes, reports and supporting grants to Universities. The media reports surrounding the illness of German forests greatly alarmed the public during this period and in time influenced public opinion and funding.

In the decades that followed Germans were confronted by the overselling and dramatization of this dieback that ceased in the late 1990s – Hans Von Storch mentions in 2004 (Sustainable Climate Science 2012) one observer commenting on the forest dieback issue stated “The damage for the scientists is enormous – nobody believes them any longer.”

We have it seems a similar situation with eelgrass Zostera marina (SAV) on the east coast which is subject to habitat, expansion and constriction from largely natural cycles. We also have a complicating factor as to the avoidance of marine soil habitat succession and during hot and energy poor cycles as the buildup of a marine compost called sapropel found below dense eelgrass peat and other submerged aquatic vegetation termed SAV when marine soil pore water exchange of oxygen is blocked. It is this last point that is so problematic, the marine compost beneath submerged aquatic vegetation can generate some very negative high heat habitat consequences (such as sulfide and ammonia generation) for seafood including blue crabs and for decades that it has been ignored or glossed over in the recent estuarine literature for nitrogen policies – my view. More and more research now indicates that eelgrass ability to hold organic matter provides an organic matter reservoir (culture media) for bacterial diseases, Vibrio’s HAB cysts and parasites. With discussions about a warming planet the damage to seafood from the sulfur cycle, it should lead off any eelgrass report. In cold water, bacteria generate nitrate, a form of nitrogen that algae needs, in hot water, a different type of bacteria produce ammonia. To better understand habitat quality, we need to look at both – my view (T. Visel).

Marine soils should be classified and sapropel with eelgrass (SAV) peat mapped – any further exclusion of the sulfur cycle or sulfate bacterial growths in shallow waters or temperature/energy records and we risk a United States Waldsterben – my view. Blue crabs could provide us a unique species to study its tolerance of sapropel and the bacteria that live in it, including Vibrio at times and we should take advantage of it- my view.

I respond to all emails at tim.visel@new-haven.k12.ct.us

Marine Peat Soils

Many salt marsh ecologists were unprepared for the 1982-2012 hot climate cycle, which saw Long Island Sound water temperatures rise in response to this increasing heat. In high heat, salt marsh surfaces were bathed in sulfate, an important oxygen source for sulfur reducing bacteria commonly abbreviated as “SRB.” Sulfate reduction – (bacterial respiration) “consumes” organic matter when oxygen is limited and can cause collapse of salt marsh surfaces from sulfate digestion below. Sulfate reduction has a temperature element; the hotter it is the better the chance for sulfur/sulfate reducing bacteria to flourish. In long periods of heat, salt marshes can virtually disappear, reduced to sapropel.

At the turn of the century, a famous botanist George E. Nichols described the salt marsh collapses at the end of the great heat – an extremely hot period (“hot term”) in New England’s coastal history, approximately 1880-1920. His description is quite accurate today a century later. The end product of sulfur reduction was often a barren expanse of sterile mud flat. “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 local colonies of eelgrass or salt marsh grass (Spartina glaba), (alterniflora) seed plants and attached algae are practically absent. At certain seasons these muddy flats may be destitute of visible vegetation of any description; but at others the bare mud at low tide is littered with loose sheets of Ulva and tangles of Enteromorpha, which may cover the ground so thickly that, when viewed from a distance, the surface appears verdant green. The failure of the eelgrass to flourish on tidal flats is probably associated with its inability to withstand the desiccation and extreme temperatures to which plants growing here are frequently subjected at low tide.”

That is an excellent description of sapropel – still valid today.

It is extreme temperatures that Nichols refers to an exceptionally “hot” period for New England even up into the Northern Maritimes. (Many New England shore villages and lakeside communities were built as the result of these 1890s killer heat waves). The heat (extreme temperatures) was horrific for city residents and NPR has an excellent segment titled “The Heat Wave of 1896 And The Rise of Roosevelt” – August 2010 that provides vivid details to the hardship city residents faced. At the same time people rushed to the shore for cool waters and breezes – a habitat reversal occurred, helping blue crabs, oysters and soft shell clams but harmful to lobsters, bay scallops and the hard shell clam or quahog.

In the 1990’s, however, the very hot summers would again return altering bacterial respiration or pathways as bacteria that thrived in high heat low oxygen organic deposits soon dominated bacterial reduction. Their population is measured by their products – very acidic sulfide containing metal discharges that can be high in very toxic aluminum levels. In time our creeks and tidal flats contained the same blue-black ill smelling mud (called black mayonnaise by fishers), described by Nichols more properly termed sapropel today. We have a Connecticut example and warning that was written as far back as 1994 as part of a Section 22 Planning Grant Public Law 93-251 titled Wetlands Restoration Investigation – Leetes Island Salt Marsh Guilford, CT {March 1994 U.S. Army Corps of Engineers – New England Division} of what sulfate digestion could do to our salt marshes, these bacteria could consume them in high heat and in doing so kill fish and have long term toxic impacts of ammonia generation.

Case study 1 – Lost Lake Guilford, CT – Sulfate Reduction – Sulfides

The foreword (pg 1) prepared by the Connecticut Department of Environmental Protection – Office of Long Island Sound Programs (today known as CT DEEP) for the Leetes Island Salt Marsh Lost Lake Report – describes acid sulphate soils case study (1) in Guilford, CT. (Author unknown – not delineated).

A 1994 publication for a Section 22 planning grant assistance to states – Water Resources Development Act of 1974 PL93-251 authorized the Army Corps of Engineers to cooperate with the states in preparation of plans for the development, utilization and conservation of water and related land resources. Section 319 of the Water Resource Act of 1990 Public Law 101-640 authorized the Army Corps to collect from non federal entities (commonly referred today as non government organizations or NGO) fees for the purpose of recovering fifty percent of Section 22 program costs. The non federal match for these projects came by the CT DEP Long Island Sound Clean Up Fund. The purpose of Leetes Island salt marsh study was to investigate the restoration of tidal flow to this marsh now bisected by a railroad and road causeways. From the report is this section below,

“A case in point is the Lost Lake-Great Harbor marsh complex in Guilford. This marsh had been drained by tide gates until a hurricane in the early 1950s removed the tide gate. The surface elevations of this marsh had subsided so much that two thirds of the wetland would no longer support vegetation because of overly wet soils and prolonged flooding. Forty years later, Lost Lake (a misnomer since this was a marsh) still supports no salt marsh vegetation.

Draining causes chemical changes in the soil, which causes the marsh to become a non-point source of water pollution. Specifically, pyrite is unstable when exposed to oxygen. Through a series of chemical reactions, pyrite is converted to sulfuric acid, which in turn, causes a drastic decrease in soil and creek water pH. Levels as low as 3 to 4 are not uncommon in drained salt marshes. These altered soils are called acid sulfate soils. Under such low pH values, the aluminum associated with natural clays in mobilized and this metal is toxic to aquatic organisms at very low concentrations. Where dissolved oxygen levels have been monitored in drained salt marshes, low dissolved oxygen levels, known as hypoxia, have been observed during the summer months especially following rain storms. It appears that the leachate removes oxygen from the water. Fish kills have been observed in some of these wetlands.”

Very few salt marshes studies looked at the increase of sulfate reduction as a condition of restricted tidal flows (or long term drought) subjecting organic deposits (peat) from oxygen in the air – but the same chemical reaction occurs when subjected to warm or hot seawater flooding and sulfate, as an oxygen source which in not “limiting” as a function of bacterial respiration – bacteria breathing sulfur instead of oxygen, we know that today as “marsh die back.” The condition of high heat and low oxygen with sufficient sulfate – sulfur-reducing bacteria (SRB)now consumes the marsh peat sending high amounts of sulfides that, at times, gives rise to the term “the smell of rotten eggs” associated with the Blue Crab Jubilees and Black Water fish kills (sulfuric acid, toxic aluminum and ammonia). That can cause the plants roots to rot or dissolve in the lower marsh, with organic matter blocked bacterial digestion can lower marsh elevations. These marshes over time “sink” before organic material reaches them to replace bacterial respiration. Salt hay operations on such meadows would cause marshes to sink faster and to maintain elevations and salt hay crops would require a sapropel “top dressing” or organic matter spread over them.

In the Northern Maritimes, at one time over 1,000 mussel mud harvesting machines were scooping out sapropel for terrestrial soil nourishment. (See IMEP #26 Connecticut Rivers lead sapropel production 1850-1885, The Blue Crab Forum™ Sept 2014). New England Experiment Stations tested marine mud and provided chemical and nitrogen analysis to farmers. In 2013, Acadiensis Press, New Brunswick included a section titled “Drawing Lines in the Ice: Regulating Mussel Mud Digging in the Southern Gulf of St. Lawrence” from the book “Land and Sea.” Environmental History I Atlantic Canada by Claire Campbell and Robert Summer by Murray. The section regarding sapropel and humus harvesting (mussel mud) was written by Joshua D. MacFadden (pg. 99 – 119) and detailed the operation of mussel mud machines, humus and sapropel harvesting for agriculture in the Gulf of St. Lawrence.

Farmers harvested this sapropel before it became peat, and contained enough oxygen to perhaps keep Vibrio and sulfate-reducing bacteria to low populations. Once applied on land and quickly worked into fields, the organic matter now fed terrestrial soil bacteria, provided a good carbon source for plants, and replaced metal salts leached by rainfall. Ultraviolet light killed surface bacteria Deeper deposits, however, presented problems. Here, the sulfur-reducing bacteria yielded deposits rich in sulfide and sapropel exposed to oxygen presents a flash of sulfuric acid (acid sulfate soils). To counteract this impact, they would allow sulfuric acids to leach away with salt residues and of mostly fresh water (low salinity) sapropel cut in oyster shell/lime to offset this low pH impact. In more northern areas, even lobster shell was used to neutralize this chemical reaction (This is the same chemical reaction in seawater for the thinning of mooring chain or the eating away of metal blue crab traps). Once pH treated, agriculture operations thrived.

Early Shellfish Researchers Identified Habitat Succession

This is the first report on marine bacteria and its direct impacts upon habitat quality and succession. The next reports will focus upon sulfide toxicity to benthic species, or “how sapropel kills.” One of the things I have learned in this your-year series is how very little we know about marine bacteria, marine soils and its seafood impact. I include myself in this category and realize just how much we don’t know. Dr. George W. Field however knew about the impact a century ago (See RI Blue Crab Capital November 2, 2015 Special Report #3 Newsletter– The Search for Megalops) – he wrote about it and no doubt influenced the work of David Belding in Massachusetts who Dr. Belding reported to Dr. W. Field while conducting his Massachusetts shellfish research in the early 1900’s. It was Pt. Judith Pond (Rhode Island) that had a fish kill event in 1895 – leading to the establishment of his marine research station on its western shore which Dr. Field directed in 1896.

Although Dr. Field’s earlier research targeted first coastal energy; the opening of a breach inlet that had been closed (inlets during The Great Heat (1880-1920) period such as barrier beach inlets tended to heal or close). He also looked at organic matter from Saugatuck River which suffocated oysters. Here is the first salt pond accounts of black water death as in high heat these areas succumbed to bacterial respiration as sulfides increased these fish kill events; residents on the Cape Cod and Islands have similar habitat histories and would reopen such closed inlets immediately especially for saving then valuable herring “runs.” Dr. Field urged that a permanent breakaway be made which had closed up to allow minor tidal exchanges to increase to Great Salt Pond known as PT Judith Pond today - no doubt that was a popular position of small boat fishers; those who would watch and smell this “stagnation” as it occured during this “hot term.” The result of which killed seafood species and with them a source of livelihood also perished. (IMEP #11 Historic Climate Impacts to Fisheries February 28, 2014 on the Blue Crab Forum™ eeling/oysters/shellfishing thread). The increased energy we recognize today as “flushing” letting the black water sulfides out and letting ocean waters “in.” (This is still a monthly occurrence for Mecox Bay on Long Island New York.”) As more saline waters flowed in a change occurred, and with greater flushing came saltwater habitats and saltwater shellfish predators as well. In Green Pond on Cape Cod when tidal restoration was restored, Sapropel appeared to “melt away” as bacteria now had oxygen to consume it. (Observations - T. Visel Cape Cod, MA).

The heat during this period (1890’s) would cause habitat failures all along the New England coast as inlets closed naturally with less storm intensity. Dr. Field was investigating changes in the plankton community in addition to bottom habitat observations. As we know, from brown harmful algal blooms (HABs) of more recent times, this would have happened as well then in response to heat as they thrive in ammonia habitats. To further the study of plankton, he commissioned a device termed, the planktonokit — a huge centrifuge that he was using in the study of Cyanaphceae, a type of blue green algae we know as cyanobacteria. In the heat during this period these blue-green algae could have dominated in areas with high ammonia. They are also at times themselves toxic. This device (see Proximity to Sea Coast: G.W. Field and the Marine Laboratory at Point Judith Pond, Rhode Island, 1896-1900 by C. Leah Devlin, Ph.D and P.J. Capelotti, Ph.D. Journal of the History of Biology 29-251-265, 1996) could obtain speeds of 4,000 revolutions per minute enabling biologists to study “more successfully these lowly forms which lie close to the basis of life,” bacteria. It was the first such use of this type, developed around 1899 (The University of Rhode Island has Dr. Field’s bulletins online.)

Dr. Field (according to Devlin and Capelotti in their 1996 review of this lab, which is a great account of this effort) had come to review “coastal energy” long witnessed by coastal fishers. What could happen to small coves and ponds cut off from cleansing tides and cooler ocean waters which naturally held more oxygen? Fishers since the first early colonial records have reopened such inlets that have been closed by storms and moving sandbars. These barrier beach inlets and spits move and in times of heat (usually with lower coastal energy during the period from 1880-1920, especially 1890 to 1910) they tended to “heal” or close. Here are some of the first accounts of black water (sulfide) deaths as in high heat these shallow, hot habitats succumbed to bacterial respiration as sulfides increased to create these fish kill events. One of the most spectacular and certainly has left some accounts in local newspapers (more cities and towns are putting past reports on line) was the winter flounder black water fish kill of August 1917 in Long Island New York Moriches Bay. It was a combination of factors, heat, low flushing and organics from land and us – the factors first described in the Saprobien System (1909). Fishers have long known the dangers of sulfate organic reduction – releasing toxic sulfides – they smelled it and H.W. Harvey of the Marine Biological Station Plymouth, England was one the first researchers to make a direct bacteria organic matter – sulfide – sulfate reduction link. Writing in a January 1938 paper titled “Biological Oceanography” and republished by the National Research Council, Washington, D.C.- US Geological Survey in 1955. Parker D. Trask editor in 1955 – Library of Congress catalog card number 67-26966 – Recent Marine Sediments from Harvey (1938) is found this section which describes the formation of sapropel – acid sulfate soils. (Note: In the 1930’s, the sulfur spelling was slightly different – T. Visel).

“One may assume that much of the soluble organic matter which dissolves into the water when plants and animals die or are killed is utilized and built up into the bodies of bacteria, and it follows that organic detritus consists, to some extent, of dead bacteria. Close to the bottom and in the surface layer of bottom deposits, bacteria are numerous. They bring out changes in the organic detritus, converting it to “marine humus,” which is in its nature similar to humus formed on land. With age, that is, with continued bacterial attack, this marine humus undergoes further change; the ratio of carbon to nitrogen, in the organic matter in muds tends to increase with increasing depth, that is, with increasing age, of the deposit. At a variable distance below the surface of marine deposits containing organic matter, conditions may become anaerobic and bacteria utilize sulphates as a source of oxygen, setting free hydrogen sulphide. The material becomes blackened with iron sulphide. A black layer is commonly found some inches below the surface of a sandy beach where this has occurred, and where subsequent oxidation of the iron sulphide sets free sulphur.”

The “free” sulfur is what people smell, hydrogen sulfide and when fish detect it they flee from it as game running from a forest fire, they swim as though their lives depended upon it, and, in fact it often does. Sulfide is the “smoke” so to speak of rapid habitat change and for oxygen requiring life forms a very strong signal to flee. If fish cannot swim out of sulfide waters they quickly die. The sulfides come from high temperature bacterial reductions of those that need sulfate not oxygen to reduce organic matter. The interaction and speed of bacteria to influence the nitrogen cycle – the short faster “cold” nitrate cycle or the longer (slower) ammonia generation was to catch Dr. Field’s attention. Many biologists looked at salt marshes as important source of “cold” nitrogen (nitrate) to grow algal species for shellfish. But in high temperatures “hot” ammonia fuels the toxic harmful blooms – the HABs. (This is why today terrestrial composters on land mix in oxygen “turn over the compost pile”). Bacteria can also alter the presence of disease especially in times of heat – they themselves are often pathogens themselves. We know these as the Vibrio bacteria and several researchers are pointing to submerged aquatic vegation including eelgrass as forming the first Vibrio pools. In fact more and more research is indicating that as terrestrial grass supported rich bacterial growths so does eelgrass peat. These bacterial growths change with temperature and alter the habitat quality for inshore fish and shellfish species. It is no different that Selmon Waksmans research at Rutgers University in the 1940s on terrestrial peat.

It is the bacterial pathway long or short depending upon temperature that Dr. Rhoads attempted to explain in the NOAA EPA workshop about Long Island Sound held in Washington, D.C. during the May 10, 1985 conference proceedings published on in the 1987 NOAA-EPA Long Island Sound Seminars, Baltelle Contract# EG8-03-3319.

Here is an excerpt from Dr. Rhoads’ presentation:

“An Estuary Of The Month Seminar US Dept of Commerce Main Auditorium Washington, D.C. May 10, 1985 sponsored by NOAA Estuarine Programs Office and the Environmental Protection Programs Agency EPA – Battelle contract #68-03-3319 to EPA January 15, 1986 Proceedings published January 1987 NOAA Estuary Seminar Series. No. 3 (note many of their Washington DC seminar participants later became part of the Long Island Sound Study committee membership by 1988 - Tim Visel.)

Dr. Rhoads of Yale responds following a question from Dr. Schubel of the Marine Sciences Research Center State University of New York.

Dr. Rhoads responds, “Yes, one reason I mentioned the importance of the Sapropel – these black iron monosulfite muds on the bottom was the direct point that Peter raised (Dr. P.K. Weyl) the system is so dynamic that to measure the change from year to year in dissolved oxygen as measured in the water column would take more money than we have.

It’s not practical at all given that kind of variability. What you need is a low pass filter an integrator and that’s the sediment. I suggest that a very sensitive index of the waxing and waning of this condition would be the map of where the Sapropels terminate whatever isobaths that might be follow the edge of those Sapropels. If they are encroaching upwards into shallow water, it’s getting worse. If they’re receding its getting better.”

This should have been the first mapping effort for Long Island Sound – something that fishers brought to the scientific community dozens of times in the 1980s the increase on bay bottoms of black mayonnaise. It is in this marine compost that dangerous bacteria live, the ones who use sulfate as an oxygen source. It is also the home of the blue crab – and the study of Vibrios and its seafood impact.

People recognize the reactive capacity of bacterial strains in oxygen, they spoil food, they can cause disease and are saprophytes in a way living off the dead. But they also help form compost on land. Some bacteria are “good” can be found in our gut cavities and help us digest our foods, others cause much hardship during very hot periods cause disease (EC #6 Pure Oysters And Clean Milk for Cities - The Blue Crab Forum™). While some bacteria needs elemental “pure” oxygen, others do quite well without it accessing oxygen locked up in nitrogen compounds, nitrite, nitrate and then sulfur compounds the most abundant oxygen source in sea water being sulfate. The bacteria that utilize sulfate as an oxygen source will “win” the bacteria battle in a warming planet. When that happens, we lose our seafood.

Warm seawater naturally contains less oxygen in an elemental form – cold water contains more until oxygen saturation occurs but as waters warm oxygen-requiring bacteria can utilize nitrate and nitrite for some time and in very hot water the bacteria which uses sulfate. That is why, when we removed nitrate and nitrite in hot weather; we also removed a potential oxygen supply as well – an oxygen source for the good bacteria. (EC #10 When It Came To Fish And Shellfish Did We Take Out The Wrong Nitrogen? The Blue Crab Forum™ posted December 17, 2015).

Many papers are now reporting on “nitrate buffering” a chemical safety valve for elemental oxygen bacteria in times of heat. Wastewater treatment plant operators have known how important nitrate was to helping keep bacterial filters “alive” for decades. The return of the sulfate requiring bacteria is the end for most oxygen requiring life forms – the age of sulfur that proceeded oxygen. In this battle, the natural bacterial filters change from oxygen bacteria to those who need sulfate. In this process, the “good” habitats now become bad (See: EC #7 Salt Marshes A Bacterial Battlefield - The Blue Crab Forum™ Sept 29, 2015). Climate has a heavy hand in determining whether oxygen or sulfur will rule – a cold climate increases oxygen saturation, a warm or hot climate does not. When it gets hot, the sulfur bacteria or sulfate requiring bacteria return with all their deadly consequences. They contain the Vibrio strains that consume shells of lobsters and blue crabs, cause necrotic flesh wasting (winter flounder) or pathogens themselves even to us - the most infamous strain of the Desulfo Vibrio/bacteria was, of course, Cholera.

What does this bacteria battle look like – blue crabbers fishing in the most shallow waters most likely experience this change the most in fact it even has a name a Blue Crab Jubilee – as sulfide is the smoke of this habitat changing marine forest fire. The sulfur cycle “burns out” those needing nitrate which can be formed by bacteria both terrestrial and marine habitats – some are termed “good” in cold water releasing nitrates for algal species and in terrestrial soils. Habitats now “succeed” and with this SRB species ammonia levels surge. The increase in nitrogen compounds can be linked to bacteria in closed system filters (see EC #8 Natural Nitrogen Bacteria Filter Systems) or in open systems land and sea. The botanists in the 1940s had clearly identified the beneficial aspects of oxygen/nitrate requiring bacteria (pg 162). In a book titled, “An Introduction to Botany by Arthur Haupt University of California, Los Angeles, McCraw-Hill Books New York 1946, details the importance of the “good” “nitrifying bacteria,” on pg 162, over 70 years ago.

“As previously pointed out, nitrates are formed in the soil both by the action of the nitrifying bacteria upon ammonia, and by the nitrogen fixing forms, which convert free nitrogen to nitrate.”

Sapropel black mayonnaise is linked to dangerous bacteria – culture media for HAB cysts and fish and shellfish parasites. Florida has the most Vibrio research projects currently underway, as it has impacted the Indian River Community. Studies being conducted by the Florida Institute of Technology have linked black mayonnaise to the production of ammonia.
I urge all blue crabbers to review these studies and dredging projects to remove sapropel. In the future, it might be possible to index sapropel by way of bacterial species, and in doing so, determine blue crab habitat quality.

Appendix (1)

Arthur, Michael A. Graduate School of Oceanography, University of Rhode Island, Kingston, Rhode Island.

Updated 2014

“A term possessing genetic implications, originally defined as an aquatic sediment rich in organic matter that formed under reducing conditions (lack of dissolved oxygen in the water column) in a stagnant water body. This contrasts with the term gyttja, which is also a sediment high in organic carbon content but which formed under inferred oxygenated conditions in the water column down to the sediment-water interface (thus benthic organisms may be present). Such inferences about water-column dissolved-oxygen contents are not always easy to make for ancient environments. Therefore, the term sapropel or sapropelic mud has been used loosely to describe any discrete black or dark-colored sedimentary layers (>1 cm or 0.4 in. thick) that contain greater than 2 wt % organic carbon.

Sapropels may be finely laminated (varved) or homogeneous, and may less commonly exhibit structures indicating reworking or deposition of the sediment by currents. Sapropels largely contain amorphous (sapropelic) organic matter derived from planktonic organisms (such as planktonic or benthic algae in lakes or plankton in marine settings). Such organic matter possesses a large hydrogen-to-carbon ratio; therefore, sapropelic sequences are potential petroleum-forming deposits. The enhanced preservation of amorphous organic matter in sapropels may indicate conditions of exceptionally great surface-water productivity, extremely low bottom-water dissolved-oxygen contents, or both.

Some sapropels may, however, contain substantial amounts of organic matter derived from land plants.”

Appendix (2)

The Sulfur in Sapropel and Fossilized Coal
Henry Potonie – Botanist and Paleobotanist
- 1907 -

The sulfur compounds in coal had long interested geologists but it was an interest in plants that guided Potonie’s research in the formation of coal or “Kohle” then koll” or now coal of today.

Saprokolls became the intermediate substance between plant life buried without oxygen and its fossilized rock consisting of hydrogen, sulfur, oxygen and nitrogen. This is an abstract of a 1907 paper on the origin of coal written by Henry Potonie.

Potonie, H., On the Origin of Coal. (Rep Brit. Assoc. York (1906) p. 748-749. 1907).

“Three kinds of coal, bright coal, dull coal, and strata coal are distinguished, all connected by transitional stages. If we include the recent combustible biolithes, which have certain characteristics of coal, there are also three classes, first the peat, secondly the sapropel and saprokoll, and thirdly the strata peat.

“Sapropel is formed from the excrements and bodies of completely aquatic animals and from plants, which have lived in stagnant water, and do not decay completely. Sapropel is a slime or mud, and becomes Saprokoll, a gelatinous substance, when sub fossilized. The Saprokoll of Tertiary rocks may be gelatinous, but that of the older rocks is very hard

“The strata peat is formed in places which are periodically under water. This produces sapropel, which is again covered with peat when the water disappears. Coal corresponding to strata peat is very common. The chemistry of bright coal is very different from that of dull coal. Whitby jet is wood transformed into sapropelit to the sapropelits belong also the bituminious limestones and clays which eventually becomes jet.” (Jet coal or very black coal – T. Visel).

“As generally peat is terrestrial and sapropel aquatic, both being autochthonous, (formed in its present position – location T. Visel) so the bright coal and the dull coal have the same genesis.”

*(Unfortunately many Connecticut homeowners have learned about the Saprokell of rocks termed “pyrrhotite” when exposed to air or water (oxygen) forms a sulfuric acid and damages concrete (the material of foundations in homes). Cannel coal is a fossil Sapropel. Genuine coal is fossil peat. The under clays of the coal measures correspond to the soils with roots, rootlets and rhizomes, found under modern peat seams.”

Appendix (3)

Climate Cycles Influence Bacterial Nitrogen Levels
Marine Soils and Bacteria

The scientific community has largely omitted the concept of a living marine compost, instead continuing to use the term sediment or black facies, which broadly interpreted are minerals and grit washed from land into the water. However, included in sediment is organic matter with hard- to-digest sugars bound up in cellulose molecules in dead plant matter. The remains of grass, bark, and leaves swept into estuaries now rots and forms a compost – and in low oxygen/high temperatures – a deadly one to inshore fish and shell fish species. It is alive as much as any terrestrial soil with sulfate reducing bacteria (SRB), which changes the habitat quality in many ways. Although the term sapropel has not been formally or fully accepted by the United States scientific community, it does describe a biological/chemical aspect of living bacterial change. It describes a biological/chemical process largely omitted from many estuary studies, organic matter putrification and a direct connection to the sulfur cycle. In fact, many shellfishers have never heard the term sapropel, or been offered an adequate explanation of these sulfur bacterial groups. (My view.) Decades and even centuries ago, researchers studied the bacterial growths under terrestrial grass, in fact promoted “harvesting” the soil beneath them as a valuable bacterial growth media for those soils that had few bacteria. Dr. Homer J. Wheeler (1911), once President of the University of Rhode Island, published agricultural articles on soil inoculation of bacteria to soils to assist plant growth. In these articles, he promoted the harvesting of soil rich bacteria under grass as a soil “inoculant.”

Dr. Wheeler (Agriculture Experiment Station of The University of Rhode Island) as other agricultural researchers at the turn of the century had discovered that those soils stabilized by grass covering humus (humic layers) was rich in bacteria as compared to bare ground (low humus) or those soils burned by forest fires termed then carbon or forest soils. Farmers for centuries had burned fields to release carbon for increased plant growth. These fires for grasslands and meadows stimulated plants’ next growing season. Soil inoculation, as described by Wheeler [Proceedings of the Farmers Institute – Rhode Island, State Board of Agriculture, March 1-2, 1911, Pg. 10], was the stripping of plant cover to harvest the soil below rich in nitrogen-fixing oxygen bacteria needed for the transfer of nitrogen to plant root tissue, which could increase crop harvest value (Wheeler, 1911, pg.10). {My comments in brackets T. Visel}.

“This is not only of importance on account of possibly influencing the actual yield, but also on account of the fact that a well inoculated soil is likely to produce alfalfa containing a higher percentage of nitrogen than a soil in which the specific organism [Bacteria, T. Visel] renders possible the assimilation of atmospheric nitrogen is absent [Forest/burned soils, T. Visel] or but sparingly present [Sandy, low humus-containing soils, T. Visel].” Dr. Wheeler describes the process further as alfalfa root nodules were rich in bacteria surrounding them. “For the purpose of inoculating soils for the culture of alfalfa, one may employ a soil where alfalfa plants, bearing root nodules, are growing, or one where similar plants of the tall white garden clover, (Mellelotus alba) are to be found. From 200-500 pounds of such soil are required to inoculate an acre of land and the larger amount is of course preferable.”

Dr. Wheeler also describes the impact upon ultraviolet light sterilization (killing off of bacteria) that the plant cover shields the bacteria living in the soil bacteria matter (1911 Report, Pg. 10-11) [Ultraviolet light is the basis of residential pool sterilizers, today, T. Visel]. “In doing this, one should remember that direct exposure to the sunlight (Ultraviolet light, T. Visel) will greatly injure or even over time destroy these organisms (Bacteria, T. Visel) if the soil used for inoculation is left on the surface on this account, this should preferably be done on a dull day, and in any case, the harrow should follow immediately after the person who disturbing the soil [Inoculate with bacteria, T. Visel] with care being taken to sow it only over a strip that the harrow will cover.”

What researchers of the 1950s and 1960s did not review was the impact of eelgrass peat, the very thick growths of eelgrass that gathered organics (mostly oak leaves) and in warmer temperatures that become sapropel. The study of terrestrial peat by Selman Waksman (1945) conducted by the New Jersey Experiment Station had identified the role of bacteria sealed from oxygen (or in the case of eelgrass peat, warmer temperatures with less dissolved oxygen T. Visel)) and the study of low moor peat bogs – wet bogs had identified transitioning bacteria as deeper deposits were effectively sealed from water column oxygen. According to Waksman (1945): {My comments in brackets, T. Visel}.

“In low moor peat bogs, the numbers of aerobic bacteria diminished gradually with depth, whereas the numbers of anaerobic bacteria increase” … The activities of the anaerobic bacteria in the lower layers [sealed from oxygen, T. Visel} result in the production of cellulose [plant organics T.Visel} of various gases rich in methane and hydrogen in sulfur-containing bogs [sulfate is not limiting in estuarine waters T. Visel} hydrogen sulfide is another characteristic product of decomposition … Furthermore, the lack of nitrifying bacteria prevents the oxidation of the ammonia to nitrate.”

(This describes in fact the interruption of the ammonia to nitrate pathway, the basis of biological filter systems in the Aquaria and Aquaculture industries today).

Appendix (4)

Lower Flushing Rates and The Bay Scallop
Thick Eelgrass Starved “Bay Scallops”

In one of the most frequent associations regarding the impact of flushing to a specific shellfish species in the historical literature is with the Bay Scallop. Here fishers and fishery area managers both agree, thick eelgrass could slow currents bringing exchanges of food algae to the Bay Scallop. In areas of dense eelgrass a reduced flushing (tidal flow) produced Bay Scallops with smaller “eyes” – the adduct or muscle cut from the scallop as so many pounds of meat to bushel measure. Here in the eelgrass slow currents subject to reduced flushing is mentioned in 1905 in Massachusetts.

A tidal restriction could reduce “food” (algae) for an entire system. In this case tannins from leaves (brown waters) could flocculate dead algae, and further reduced tidal exchange as eelgrass meadows would rise cutting off water circulation gathering dead organics. The impact of a restricted flushing and rising eelgrass meadows speeded up habitat succession, under eelgrass meadows was frequently buried shellfish, as sapropel formed commonly called (black mayonnaise).

This excerpt mentions this impact directly “eelgrass” cuts off the current and prevents circulation of water. In the years after this publication Dr. David Belding shellfish research a decade later was more direct, “as we have seen eelgrass is fatal to a clam bed.”

Commonwealth of Massachusetts
Report of the Commissioners on Fisheries and Game
Public Document No. 25 Pg. 57
Year Ending 1905 Boston, Massachusetts
Wright and Potter Co. State Printers

VIII Why is a sand bottom or channel scallop larger than an eelgrass scallop?

“Scallopers know from experience that you can find larger and better scallops in the deep channel or on sand bottom than in the shallow water among eelgrass.

These are scallops of the same age, only the former has grown more rapidly than the later. The increased growth of the channel scallop is due to its more advantageous location. The difference in growth is due to the current. The same is true with the clam and quahog; those situated in the current grow most rapidly. Every shellfish needs circulation of water for growth, eelgrass cuts off the current and prevents circulation of water. The growth of the scallop depends upon the amount of food it can produce. This microscopic food is found rather eventually distributed throughout the water. Currents bring more food. As more food is brought to the scallop in the channel by the free circulation of the water, the growth there is naturally more rapid.”

Powder Hole Chatham Shellfish Experiments Monomay, 1904, pg. 30 search Chatham, MA eelgrass impacts to shellfish.

Appendix (5)

Dr. David L. Belding, Massachusetts Research On the Growth of Soft Shell Clams – 1930.
Eelgrass “Eelgrass as we have seen is fatal to a good clam bed. Many productive beds would be quickly spoiled by eelgrass if it were not for constant digging. The grass raises the surface of the bed above the normal level by bringing in silt, which smothers the clams. The reclamation of such flats can be accomplished by destroying the grass and allowing the water to carry away the accumulated muddy deposits. At Newburyport, an eelgrass flat with a surface layer of soft mud was converted into a productive hard flat by digging. A strong current removed the loosened material, and a new flat about one foot lower than the original was formed. A coating of algae often helps to protect the flat from too much shifting and the mud surface furnishes abundant food forms. Eelgrass helps to hold the mud firmly, but as it also catches silt, it forms a layer of soft mud which is apt to smother the small clams. It occasionally happens that parts of a flat, which seem similar in every respect exhibit extreme differences in the way they harbor or repel that clam set. It is almost as though an invisible line had been drawn beyond which clams did not grow. Hydrogen sulfide and other organic compounds in the soil may account in part for this condition.”
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