EC #25 - Eelgrass Bacteria, Subtidal Peat and Disease Cysts

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BlueChip

EC #25 - Eelgrass Bacteria, Subtidal Peat and Disease Cysts
High Temperature Submerged Aquatic Vegetation Linked to Shellfish and Fish Diseases
The Use of Soil Bacterial Inoculants
Bacteria Concentrations Higher in Grass Monocultures
Eelgrass and Vibrio Bacterial Pools in Peat
Reference the work of Selman Waksman & Holmer Wheeler, The Rutgers And Rhode Island Agriculture Experiment Stations
February 2022
Viewpoint of Tim Visel – no other agency or organization
This is a delayed report, March 2023
Thank you, The Blue Crab ForumTM for posting these Bacteria and Nitrogen reports
(Tim Visel retired from The Sound School in June 2022)


Introduction

Since the start of the bacteria and nitrogen newsletter series, I had hoped to bring forward a sense of natural history to the inshore fish and shellfish discussions – more than what I experienced but also what information that was shared with me.  Between 1978 and 1990, I estimate about 3 thousand inshore shellfishers participated in my workshops, fisheries forums, and adult education programs across New England.  I was fortunate to be able to hold them and today recall meetings that went well into the a.m. hours, discussing fishing gear, changes in habitats and on-the-water fishing experiences.  For many, I learned more from the participants than perhaps I helped them but that is how I feel.  When I had a small trawl workshop with 10 to 15 participants, I looked at hundreds of years of fishing experience and history in the room.

I caught the end of a different time, my mentors of George McNeil, Frank Dolan, Larry Malloy, Steve Jones, Ken Holloway, Ronald Paffrath, Charles Beebe, J. Milton Jeffrey, Sally Richards, J. R. Nelson, Elmer Edwards, John Healy, Luther Blount, Hillard Bloom, Alfred, Peter and Jeff Wilcox, John Scillieri, Mervin Roberts, Michael Bevans, Robert Porter, Lloyd Bayreuther, Ben Rathbun, John Wadsworth, Ron Ribb and of course, John Hammond, and many others too many to mention here, who all took the time to talk about their experiences and history.  I guess the difference was I was also willing to listen – many, unfortunately, were not – my view. 

I don't have the time to go into the social aspects but early workshops had participants much older than me, and for many, I was just a kid (I was) but one that valued the fisheries history very much, which was a surprise to many workshop participants.  They were anxious to have anyone listen and hear them out.  I did and gained a life-long appreciation of what they were willing to share – their knowledge of habitats and fisheries changes that could fill volumes.

When I started, I had 50 papers on inshore fisheries in mind and close to triple that now, but the ones I feel most significant are the ones about John Hammond on Cape Cod and George McNeil for Connecticut.  Of all, Mr. Hammond felt that knowing your fisheries history was so critical and realized the difficulty of that task, knowing that full well the cycles he studied were longer than our lifespans.

To him, it was the papers and habitat description manuscripts that could survive and help for taking sadly all that oral history and fishing knowledge when a life ended – sad but true.  He felt in the 1980's we were experiencing many of the climate conditions a century ago.  He had an extensive collection of shellfish reports, many of which gave me a head start in understanding the cycles of fish and shellfish and how biology and climate intersect in regards to seafood.  I found out recently you could listen to my mentor, "Clint" Hammond, on the Cape as part of the oral history archives of the Chatham Historical Society.

He never saw the change in the weather patterns he so much predicted.  The heat he described would continue to 2011, two decades after his passing, but change it did.  The North Atlantic Oscillation would turn negative in 2011-2012, ending a period that started in 1971 and in 1991, he was only able to witness only about half of it.  I would see the rest, including another die-off of Long Island Sound lobsters exactly one century apart.

The NAO

In 2011, I felt coastal residents should be worried.  The negative NAO changed our storm tracks, producing a deep bulge in the US resembling a horseshoe shape, letting cold air flow far south and opening the door to an increased number of stronger coastal storms just as Mr. Hammond predicted.  Concurrently, the westerlies weakened many storm tracks closer to us.  Most of our environmental officials had never heard of the North Atlantic Oscillation (NAO) a decade ago nor felt a warning was necessary (no information about  it on CT Climate website).   Mr. Hammond's history lesson, I believe, has a public policy edge as well and not knowing our habitat history, we made some very expensive mistakes, one of which now appears to be nitrogen and bacteria in a warming climate.

More and more, I see the NAO today mentioned in regards to fisheries, cycles of habitat quality that resulted in cycles of finfish and shellfish populations (that is a good sign), but inshore fishers knew this decades ago – they watched it happen.  Fish and shellfish came and went as a natural event many call cycles, Mr. Hammond called them clocks – but relationships with species including predators remained the same.

Weather, catches and habitat quality were all things Mr. Hammond knew so well and, therefore, he gained much respect on the Cape and amongst his shellfish peers. 

We could do much more, I feel, in understanding our fisheries history that is presently available.  If we do, we have people like John Hammond who shared his knowledge to thank – my view.

The bacteria and nitrogen newsletters reach into that very serious problem, one that includes what I term "public policy research" that is "scientific papers," which appear to answer public policy questions.  As we learn more about nitrogen and eelgrass, I feel these concerns will be validated and perhaps the need of an historical balance included in environmental impact statements of the 1970's.  We need to balance environmental history with our impacts.  In no way should this perspective be seen to reduce pollution concerns nor minimize the dangers of a warming planet.  In fact, a warming planet is a real concern and shallow waters often show the first negative warming impacts.  That is why shallow water observations are so important; they give a faster response or a faster "habitat clock."   We need, however, a longer view free of funding grants.  We most likely have two of the most grant influenced topics in shallow water of eelgrass and nitrogen.  Both seem to become important environmental indicators but both largely influenced by the NAO – climate.  [For a terrific explanation of the NAO, see North Carolina State Climate Office, November 21, 2014 – From Top to Bottom, Global Conditions May Shape Winter's Polar Jet Stream by Bradley McLamb.  It describes the Icelandic low and Bermuda High and is one of the best NAO references I have found – T. Visel]

Climate would greatly impact inshore habitats and dramatically change bacterial-nitrogen pathways in shallow waters.  Heat and hot seawater also impact how much oxygen seawater can hold and influence seawater chemistry.  These changes occur over relatively long-time scales and do not match observations of short-term reports.  This is evidenced by a continuous observation report process or records over a long period of time.  For example, eelgrass does best in cool, high energy marine soils – in heat, sulfate bacterial metabolism (hot compost) harms it.  It responds to soil conditions not unlike its terrestrial grass relatives, the grasses of lawns and athletic fields.

The Bacteria of Marine Soils

The selection of eelgrass as an important habitat type was based upon habitat services that are untenable in a warming composting environment or habitat.  Much of the good habitat services of eelgrass is dependent upon high amounts of oxygen – oxygen needed by bacteria that break down amino carbon chains releasing nitrate.  This was seen to be a seasonal – cold water (think high dissolved oxygen) cycle – transitioning to ammonia as waters warmed and held less elemental oxygen (See Vaccaro segment from Congressional testimony as Appendix #2).  This change to ammonia was long recognized in the farm community as wet "sweet" composts of high alkalinity.  The change between nitrate or ammonia could be considered a natural switch – with seawater temperature and dissolved oxygen.  In warm cycles (climate warming), the switch is now "stuck" in the position of ammonia – a toxic compound.  In times of heat, it is natural to see ammonia levels in shallow water increase.  This signals a bacterial change in marine composting and a declining habitat quality for eelgrass.

In fact, the use of eelgrass as a positive sign of healthy inshore habitats is not possible near so much carbon (compost) from plant tissue in low oxygen.  It is the heat that, in fact, ends eelgrass monocultures, they foster ammonia and nitrate explosions (purging) as bacteria race to consume organic matter carbon chains held in its roots after storms.  In heat, eelgrass can hold disease-causing bacteria and fosters fungal growths – also a sign of what warming can do to it, which thrives in cooler waters with more storms.  It is, in many ways, a holder of marine composts that as oxygen declines, the amount of sulfide increases when seawater warms.  This is a natural process that slowly kills eelgrass plants

Eelgrass collects organic matter, which is food for many bacterial strains and algal species that benefit from composting nitrogen releases.  We may need to rely on the studies of terrestrial peat to better understand the climate implications of eelgrass peat.  Much of the high heat impacts of eelgrass peat is missing from the current literature.  This is evidenced by the lack of detail around the "sulfide deadline" in marine soil and seawater over it.  So much bacteria is under eelgrass that it is similar to terrestrial grass.  A century ago, organic matter under terrestrial grass was used as a soil bacterial inoculant.  Bacteria concentrates beneath grass monocultures and, in heat, favor the formation of sulfide below eelgrass and Vibrio pools in peat underneath it, impacting the nitrogen cycle. 

Selman Waksman of the Rutgers New Jersey Agriculture Experiment Station and Dr. Holmer Jay Wheeler of the Rhode Island Experiment Station both studied bacteria under grass.  Dr. Wheeler is known for his work in bacterial fixation of nitrogen and Dr. Waksman for his study of "bacterial wars" and the discovery of antibiotics (Both were soil researchers.)

Research from many parts of the world, especially those about peat deposits from southern mangrove estuaries, are showing that they hold reservoirs of Vibrio bacteria.  The warmer the peat, the more likely it is a reservoir for bacteria, such as Vibrio to live.  The use of this compost (contains living organisms termed sapropel), which contains sulfur-reducing bacteria (SRB) as an inoculant, is found overseas for heavy metal cleanup.  Its affinity for metal ions is so strong that it acts as a heavy metal absorbent.  I wrote about bacterial wars in Environment/Conservation post #7 titled "Salt Marshes: A Climate Change Bacterial Battlefied," regarding the change of bacterial populations in high temperatures of peat (salt marsh/meadows/bogs).  In heat, eelgrass dies off as a result of compost fungus (slime mold), similar to terrestrial grasses.  A chief indicator of grass monoculture failure is the destruction of its root rhizosphere by fungus.  Root tissue can, for a short time, kill small amounts of fungus by creating natural fungicides, termed "root exudates."  You can even purchase products that utilize natural fungus pathogens that can kill root fungal strains including Fusarium – linked to salt marsh diebacks (See New Species of Fusarium Associated With Dieback of Spartina Alterniflora in Atlantic Salt Marshes, Wade H. Elmer and Robert E. Marra, Myrologia, Vol. 103 (2011), Issue 4, pgs. 806-819).

Eelgrass meadows (subtidal peat) are known to contain huge amounts of bacteria, and some of the dangerous Vibrio strains.  A century ago, plant scientists and agricultural researchers also noticed that bacterial levels rose the fastest under dense grass meadows.  In well-oxygenated organic matter soils, these bacterial cultures helped plants grow (nitrate), forming a beneficial bacterial coating that assisted the transfer of nitrogen ions across the root tissue termed the rhizosphere shield.  In soils low in organic matter (the food for this beneficial bacteria), it could take years for this bacteria to reach certain densities to be able to help plants grow.  These soils could be excessively drained (porous), subject to erosion and loss of surface humis, or naturally low in organic matter (for example, heavy agricultural use, forest fires or ice cover (cold temperatures)).  It could take years for organic matter to increase bacteria in these soils needed to help plants grow.  These low or wet organic agricultural soils were often termed impoverished or "poor" growing soils.  Much has been written about the need to add carbon and maintain "soil bacterial health," but that is linked to the carbon "locked up" in organic matter and the action of soil (compost) bacteria.

However, lush green grass was an indication that bacterial levels were high and plants now able to use nitrogen more efficiently.  This soil under grass monoculture became valuable for not only plant growth but also as a quick start of bacterial supply, a soil "inoculant" for bacteria in oxygen that forms nitrate.  Farmers noticed (as so did agricultural researchers) that bacterial levels under grass were so high it could be dug up and used in soils that needed this plant bacteria.  In 1911, Holmer Wheeler of the Rhode Island Experiment Station describes this transplant/infusion process as follows:

Dr. Wheeler's paper on Soil Inoculation was part of the Official Proceedings of The Farmers Institute, Rhode Island State Board of Agriculture, March 12, 1911, pg. 10 has this segment by Dr. Wheeler – my comments (   ) 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 that a soil in which the specific organism (bacteria, T. Visel) renders possible the assimilation of atmospheric nitrogen is absent (forest fire/burned soils, T. Visel) or but sparingly present (sandy, low humus–containing soils, T. Visel).  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 (Melilotus alba) are to be found.  From 200 to 500 pounds (or about 6 bushels, T.Visel) of such soil are required to inoculate an acre of land and the larger amount is, of course, preferable."

Dr. Wheeler also advises this process be done on a cloudy day as ultraviolet light would kill these bacteria.  Pg. 11 of his 1911 report contains this warning – my comments (   ) T. Visel"

"In doing this, one should remember that direct exposure to the sunlight 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 be done on a dull day, and, in my case, the harrow should follow immediately after the person who disturbing the soil with care being taken to sow it only over a strip that the harrow will cover."

(The recent increased interest in compost bacteria and carbon cycles Dr. Wheeler's 1913 textbook on Manures and Fertilizers first published by The Macmillan Company, New York to be reprinted in 2015, it is now again available from several sources.)

In 1911, Holmer Jay Wheeler was head of the Rhode Island Agriculture Experiment Station, housed in today's University of Rhode Island "quad" in Taft Hall and Lippitt Hall.  The beginnings of the University of Rhode Island was the 1892 (second Morrill "land grant") sales of public lands to support Agriculture, Military and Mechanical Arts and was first called the Agriculture Experiment Station to Rhode Island College of Agriculture and Mechanic Arts in 1892.  Wheeler, from the description found on the University of Rhode Island website was a no nonsense administrator, who like many Agricultural Experiment Stations, was committed to ending fertilizer fraud in the marketplace. 

But Dr. Wheeler (who assumed for a brief period President of the entire University in 1920) was also credited with promoting the concept of work study on the Experiment Station farm, allowing students to work earning money while attending classes to offset tuition costs.  (In 1978, I was able to gain from this work study concept working for the same Experiment Station and Dr. Andreas Holmsen at the University of Rhode Island.)

In 1910, he was most likely asked by the Rhode Island Board of Agriculture to submit a research paper of interest or respond to concerns/questions from the Rhode Island Agricultural community that describes the knowledge that below certain grasses dense bacterial populations existed that could be used to inoculate other soils.  This inoculation method still exists in marine aquaculture systems, the transfer of oyster shell or samples of marine mud themselves to jump start biological filters – it is much the same process a century later.

It was the presence of hundreds of strains of bacteria in soils containing high amounts of organic matter that was the basis of Dr. Selman Waksman's research into soil bacteria pure cultures, those bacterial strains that were specific to certain plants and certain biochemical conditions in the soil itself.  Since peat is largely composed of organic matter, it contained a rich assortment of often competing "warring" bacteria strains – that is under circumstances, they fought biochemical "wars" beneath the peat surface.  Some bacterial strains were beneficial to use, those that helped plants grow to produce food, fiber and forestry products and those that were not – disease causing toxic or pathogenic – harmful bacterial strains (HBS).  Some plants seemed to have specific strains and grass monocultures, the "good ones."  P.E. Brown, in a 1906 article titled "Soil Inoculation," describes the process of soil bacteria, assisting the growth of root tissue and then plant growth.

Agricultural Experiment Station (1906)
Iowa State College of Agriculture and Mechanic Arts
Soil Inoculation by P.E. Brown

"At that time it was demonstrated that when clovers, vetches, alfalfa,
cowpens and all other legumes are associated with certain bacteria,
these crops have the power of taking nitrogen from the air for their
growth. It was demonstrated further that if the bacteria were introduced
into soil deficient in nitrogen, legumes would grow satisfactorily
on that soil and actually increase the amount of nitrogen in it. They
not only take enough nitrogen from the air for their own growth,
but store a surplus in the cell. Without the presence of the bacteria,
however, the legumes do not thrive and they are not able to secure
their supply of nitrogen from the air.

It was also demonstrated that not only must the necessary bacteria
be present In the soil for this important work of the legumes, but they
must enter the roots of the plants and form swellings or nodules there.
Through this means, a state of mutual helpfulness is set up, called
symbiosis. The plant supplies the bacteria with certain food materials
and in return the bacteria draw nitrogen from the air and furnish it
directly to the plant.

Later investigations led to the discovery that the nodules on any
legume contain only one kind of bacteria; they are therefore called
"pure cultures." The organisms which grow thus with all legumes
have since been found to belong to the same species, and have been
named Bacillus radicicola. They include, however, well defined strains
or varieties, each especially adapted to grow with certain legumes,
and it is more or less difficult if not impossible for them to adapt
themselves to certain other legumes. Such adaptation apparently
does occur through long periods of time, but farm practice demands
immediate results and hence the proper species of bacteria must be
present in the soil if inoculation is to occur."

It was the competition between bacterial strains that have, in a way, battled each other, which led Dr. Waksman in his studies at Rutgers University to become associated with the Woods Hole Oceanographic Institution. Coastal salt marshes were also huge peat deposits along the edge of the sea.  The mechanism that guided how the bacteria waged war against each was termed antibodies – substances that bacteria created to kill other bacteria or protect themselves from other bacteria attacks.  Dr. Waksman's research on soil organisms in peat would lead to the identification of more than two dozen antibiotics.  His most famous discovery was streptomycin in 1942, arriving in time to save countless lives during World War II.  Dr. Waksman's research on the bacteria of peat resulted in several hundred papers, numerous books and entire lines of antibiotic research (the mycins).  His work with Merck (1938) eventually caused that company to release its rights to streptomycin to Rutgers University.  Royalties from that release led to the Rutgers Department of Soils, and Institute of Microbiology renamed in 1974 as the Waksman Institute of Microbiology at Rutgers University.  Dr. Waksman's research into the bacteria strains in peat was known throughout the world.  This is a 1942 excerpt from Dr. Waksman's research on peat:

"In a peat profile, one may find dark, well-decomposed layers, indicating a period of low water level or drought.  The occurrence of several such layers indicates that similar conditions have occurred at different times during the peat formation.  The occurrence of a layer of poorly decomposed fibrous plant residues points to a period of prolonged precipitation and to a rise in water level." (Pg. 13 – The Peats of New Jersey and Their Utilization by Selman A. Waksman, The New Jersey Agricultural Experiment Station, 1942)

Peat in High Heat Becomes a Bacteria Battlefield

Is should be no surprise that peat, even subtidal as those organic rich soils in heat under grass monoculture (such as eelgrass monocultures) bacteria would wage war under them.  It is the same bacterial conflict that Dr. Waksman studied how bacteria fought each other.  He investigated how some populations rose and fell and what substances organic acids and enzymes they created – the rise of sticky bacterial films organic substances that did not kill rival bacteria but coated them in sticky molecules that inactivated them.  In other words, a substance that glued them together in clumps, making them biologically inactive (his experiments included placing stable manure over peat and monitoring the change in bacteria sealed from oxygen).  The chemistry of terrestrial peat would change in heat and conditions that favored some bacterial species over others - on the surface lived bacteria that needed oxygen (air), but ones that fixed nitrate good for plants or those in the absence of oxygen shed ammonia.  The high heat ammonia shedding had been known by researchers at Agriculture Experiment Stations a century ago by way of the direct harvest of marine sapropel – organic matter that was subject to bacterial reduction in the absence of oxygen – the terrestrial "smelly" compost that purges ammonia in heat.  Much of this research is recorded in Agriculture Experiment Station report for Connecticut (See IMEP #86-B: Oyster Fisheries/Farmers Struggle Over Harbor Mud 1820 to 1920, posted May 20, 2021, The Blue Crab ForumTM).

Composts sealed from oxygen in high heat have been known to produce ammonia for over a century.  One of the byproducts of this bacterial conflict was the production of sulfides, a plant toxicant.  Sulfate formation in peat deposits has also been known for over a century.

Peat deposits in sulfate waters add a new dimension – the advent of gram negative Vibrios – long dominated by oxygen requiring bacteria.  Vibrios win in times of high heat and low oxygen.  That is why Vibrios thrive in summer and die off each fall as cooler waters replace oxygen from the seasonal minimum, around the third week of August, the climatic period of maximum soil heating.  Most fishers observe this bacterial war without realizing it, but the biochemical residues, the battlefield "smoke" is sulfur, the source of the Blue Crab Jubilees. It is the shallow, most warm waters that foster the highest ammonia-lowest oxygen so that the appearance of Vibrios in the water columns is related to algal blooms.  In heat, organic matter from the soil/water interface teems with Vibrio (and also why waders, blue crabbers and swimmers are most at risk), dispersing into the water column and hitching a ride on algae – its food or opportunity to expand its population.

And some of the first references of eelgrass forming a peat with bacterial processes came from New York over a century ago.

Following is an excerpt found in the Documents of The Senate of the State of New York 1902.  It is found in the 55th Annual Report New York State Museum – Report of the Director and State Geologist, 1901, Vol. 21, No. 38, Albany, New York, J. B. Lyon Company State Printers,

r 78 -

"Marine Marsh Soils – These form a special type, which is found to some extent along the seashore.  They are formed by the accumulation of fine mud in sheltered or quiet waters along the coast.  On this mud flat, there springs up a growth of eelgrass which serves to entangle more mud and organic remains, thus raising the general level of the flat and on this raised surface land grasses and plants spread out forming a marine marsh."   

(See IMEP #60, posted February 7, 2017, The Blue Crab ForumTM)

Chemical nature of organic matter or humus in soils, peat bogs and composts (Waksman, 1935).  The Peats of New Jersey and Their Utilization Bulletin #55-Part A (Waksman, 1942).

Pg. 34:

"In the aquatic types of peats, the plant remains accumulate below the level of the water.  The residues comprise structureless, soft fragments of plants, outer roots of cellular organisms, diatoms, algal filaments, any varying proportions of silt, laid down by wind and current.  These peats may be further subdivided into three groups, macerated peat (mud sapropel gyttja) consisting of spores, pollen grains, fragments of leaves and aquatic material."

Pg. 37 (1):

"Peats have often been characterized by their botanical composition and by their physical properties (1) Deposition of peat.  It is important to determine whether the particular peat or layer of peat was formed in place or whether it was brought in by water and other agencies to the place where it is found.  In the first case, so called allochtonous peats, sedimentary formations or guttja. (4) The nature of the decomposition processes.  An insufficient recognition of these processes has resulted in a rather complex terminology.  In terms of Von Post's concept, anaerobic decomposition in the bog or the so called process of putrefication and fermentation, gives sapropel products."

Pg. 46 has this segment:

"The lake deposits have been described by Potonie as sapropel.  A marked distinction was recognized between this type of material and ordinary peat or soil humus.  The former is produced from aquatic plants in which the predominate role was ascribed to algae.  Such deposits are rich in fat and protein.  Humus, however, is formed from land or bog plants, in which carbohydrates and lignins play a predominate role."

Waksman also terms eelgrass as a type of peat in his co-authored study with Margaret Hotchkiss on The Oxidation Of Organic Matter In Marine Sediments By Bacteria and on pg. 26 of Peats of New Jersey.

The "cloudy" waters of a bloom also absorb the killing aspects of ultraviolet light, toxic to bacteria.  They thrive away from light in low oxygen and high organic deposits – those typically found below grass monocultures or in peat.

Peat and soil researchers of the last century documented these "soil bacteria" and that grass monocultures supported bacteria beneath them.  It should be no surprise when researchers (mostly Denmark and Italy) started noticing that sea grass formed bacterial pools or inoculants (this rich bacterial content is often termed activated sludge in waste water treatment) in the 1990's and 2000's as temperatures warmed.

Dr. Paul Galtsoff in his 1964 U.S. Fish and Wildlife Bulletin #64 The American Oyster was aware of sulfide toxicity from bacterial reduction (See York River study "Ecological and Physiological Studies of The Effect of Sulfate Pulp Mill Wastes on Oysters in the York River, Virginia," Fishery Bulletin #43, Vol. 51, USGPO 1947) and mentions the works of peat researchers Waksman and Hotchkiss decades before.  Cape Cod oyster growers had noticed a sulfur (sulfide) deadline on chains and blackened oysters (rotting meats) in areas that smelled strongly of match sticks – sulfur (John C. Hammond personal communication to T. Visel, referencing Raft Off Bottom Oyster Culture Project conducted by William Shaw).  Following is a quote from Dr. Galtoff's 1964 U.S. Fish and Wildlife Bulletin, pg. 413-414, which mentions this study and was assisted by John Hammond:

"Organic material constitutes a major portion of marine muds.  The physical properties of a sediment may be of lesser importance to oyster ecology than the complex biochemical changes associated with the bacterial decomposition of its organic components that result in the formation of carbon dioxide, ammonia, phosphates, sulfates, and various organic acids.  In the case of anaerobic oxidation, methane and hydrogen sulfide are formed (Waksman, 1942; Waksman & Hotchkiss, 1937).  The effects of these products of decomposition on bottom than for those which are kept above the bottom on trays or are suspended from rafts and floats (Shaw, 1962).

It was these series of off bottom culture (raft) experiments (Shaw, 1962) that led Mr. Hammond to focus upon the buildup of marine humus, what I called black mayonnaise, but it is more properly termed a sapropel.  He linked the buildup of it to sulfides and disease.  The issue of site-specific climate induced resistance to subtidal peat pathogens includes opportunistic parasite infections.  Certain climate factors would cause bacterial strains to dominate in one area while remaining subclinical or dormant as to host/parasitic relationships in others. 

We must recognize the impacts of this bacterial spectrum when we drink from different water supplies.  During years of bacterial challenge, we become desensitized to "background" bacterial species in tap water.  While traveling south and even in other countries, tap water can produce sickness, and visitors from southern areas exposed to our bacterial strains here having much the same impact.

For shellfish, lobsters and blue crabs, it is often the bacterial strains you know, i.e., in the habitat you live.  Dramatic shifts in climate can cause periodic outbreaks of disease – lower salinity, water temperature and nitrogen compounds being the most indicative – in heat, the increase in ammonia.  Massive climate changes also change the resident bacteria and are the reason why, as waters warm, Vibrio prevalence increases.

Host bacteria may mobilize antibodies to fight unknown or unchallenged bacteria in the host itself.  In other words, some of these bacterial strains fought each other to dominate the bacterial spectrum (The very old adage "Nature despises a vacuum").  It was this bacterial battle that Waksman reviewed deep within peat layers, the survivors and refugees from bacterial battles thousands of years ago.  It was the battle between bacteria that led Waksman to biological bullets and drugs we call antibiotics, and many antibacterial agents we have today are from the work of Selman Waksman.

Just as terrestrial researchers examined peat, other agriculture researchers focus in upon the bacterial/nitrogen cycle.  Four years after Waksman reports on peat bacteria, Arthur van Haupt, Associate Professor of Botany at the University of California, Los Angeles in 1946, published "An Introduction to Botany" (McGraw-Hill Books, New York-London).  On page 266, Haupt provides an excellent summation of what bacteria could do depending upon oxygen.  With oxygen, the bacterial nitrate when oxygen is limited more ammonia.  Arthur W. Haupt (1946) in An Introduction to Botany describes these composting nitrogen pathways on pg. 266:

"Nitrifying bacteria also live in the soil and like those just mentioned form nitrates, but in a different way.  The decomposition of organic matter by the bacteria of decay yields ammonia."

And the role of bacteria in the nitrogen cycle and the relationship to plants is critical to composting and peat vegetation.


Eelgrass as a Peat Builder Under Water

For decades, I had heard accounts from Connecticut oyster growers (F. Dolan, G. McNeil, J. R. Nelson, H. Bloom, J. Hammond) about the dangers of leaves.  Although most grew oysters in offshore waters, it was the river "seed beds" that produced the most consistent sets and natural growers harvested seed from these natural river beds for growers.  In the 1940's and 1950's, heavy rains and floods carried tremendous amounts of leaves downstream into the slower moving estuaries.  George McNeil's accounts were the most dramatic; he noticed blackened leaves sometimes measured in feet suffocating oysters.  If the waters were warm enough for oysters to "pump," they were quickly killed and called "stools."  The historical literature contains a direct reference to this type of impact in the East River between Guilford and Madison:

"As not enough set is caught upon the stools, a thousand bushels or so of seed oysters are annually raked from the natural beds in the vicinity of East River or bought from dealers in Stony Creek" (pg. 59, The Oyster Industry by Ernest Ingersoll, 1881, Washington, DC, GPO).

And into the lower estuaries, eelgrass now grew into cleaned washed estuarine soils, constant wave and wind driven surges reached up into estuaries and removed nature's compost, now into the late 1970's, the energy dropped and temperatures now rose.  A restored tree canopy meant a greater amount of leaves.  Aside from sewage pollution control measures, nearly all small boat fishers mentioned an increase in leaf matter or "chaf" on the bottom (Cape Cod shellfishers termed it oatmeal) in bays and coves after a fall leaf burning ban.  On Cape Cod, Joe DiCarlo, then head of herring run clearing and restoration, claimed that leaves dumped in streams had seriously impaired the long Cape Cod alewife runs.  Leaves at one time collected so deeply on Hamburg Cove, CT that nearby residents appealed to Congress for dredging assistance.  Hamburg Cove had transitioned from cleared dairy fields to woods, and leaf material would collect in these areas forming a sticky black bottom (from a conversation regarding Daniels Fish Trap Company located on Hamburg Cove – T. Visel).

Each rain or storm runoff from ice and snow, countless particles of leaves flowed downstream to be trapped in eelgrass meadows, feeding them and rose as the meadow transitions into a subtidal peat.  At first, the aggressive peat building plant tendency of eelgrass perhaps went unnoticed.  Peat plant builders live on the surface of peat – shallow root systems at first spread by aggressive stolons that radiate out in a linear pattern gathering loose organics in this process.  Shellfishers on Cape Cod in the 1940's noticed after the 1938 hurricane (John Farington, personal communication Tim Visel, 1980's) that eelgrass soon appeared as isolated plants or patches.  (It was thought that pieces of eelgrass with viable root tissue or seed pods were distributed in the energy/waves from the storm itself.)  In time, these patches grew together reducing the "clear bottom" and eventually blanketing the bottom.  It was at this time that inshore shellfishers noticed the aggressive habitat expansion characteristics.  In this process, it suffocated shellfish and transitioned habitat types.  The negative consequences of rapid eelgrass growths were mentioned numerous times in the shellfish literature.  These negative impacts were listed as reducing water exchange (Poquonnock River 1880's), replacing in other submerged plants (forage for waterfowl) reduced oxygen levels, direct suffocation (acts to collect sediments) and the presence of heated bottoms.  In many areas in shallow water, eelgrass would intensify solar heating.  In heat, the composting aspect of organic deposits would allow slime molds and fungus to grow underneath eelgrass.  A slime mold called Labyrinthula would be termed the wasting disease.  Much could have been learned by just a one-word change by substituting eelgrass composting for eelgrass wasting – my view, T. Visel.

When eelgrass growth subsided and circulation improved, as colder seawater contains more oxygen bacteria that once depended upon sulfate also reversed and was replaced by the much more efficient (faster) oxygen composting bacteria.  It is at this time, according to John Hammond, that sapropel seemed to melt away.  The example of a heavy snowfall was Mr. Hammond's example but coves or salt ponds once blocked once reopened as this low oxygen compost slowly disappeared.  It just didn't vanish but nourished the bacteria that consumed it, breaking it down to carbon chain fractions, each one harder to digest.  Cooler temperatures also improved bay scallop habitats, which in the following decades contained stronger and stronger storms – energy.  What composting bacteria could not consume storm tidal surges, waves and currents moved out to feeding grazers in the food chains especially shrimps in waters with higher oxygen levels.  I can recall some hydraulic clam experiments in sapropel in Buttermilk Bay, Cape Cod.  When the demonstration ended, shrimp by the thousands came into the test area and started to feed.  Below dying eelgrass roots, we hit "black sand," a frequent comment by shellfishers and that bottom held many dead quahog clams, remains of a much cooler energy-filled habitat period of long ago. 

I have hit this older bottom at the mouth of Clinton Harbor – Hammonasset River, which was very thick peat, about three feet, which with a pair of clam tongs breaking into a sandy soil contained very old dead softshell clam shells and a much more energized marine soil.  Nelson Marshall, who directed much of his research on inshore habitats, especially that of the bay scallop, wrote how the Niantic River bay scallop fishery grew at the end of eelgrass/sapropel cycle.  Eelgrass had dominated inshore habitats in the late 1900's (peak monoculture 1905-1915), but by the late 1920's, it started to die off.  He noticed as bay scallopers that followed that dense accumulation of eelgrass were damaging to shellfish populations.  Eelgrass by 1930 had reached the end of its "habitat clock."  As New England winters grew colder, ice cover allowed sulfides to build in the peat it once helped create, then died from it.  Sulfide is a plant toxicant – it kills and weakens plants so that they pick up fungal and mold infections.  As weakened eelgrass plants wasted away, bays and coves had increased tidal circulation, more energy waves, currents, scoured out sapropel and recultivated marine soils once buried by compost.  A cultivated soil with high amounts of sand is what allows eelgrass to flourish in shallow waters.

This pattern seems to be repeated a century ago.  When eelgrass was thick and dominant, it declined when a compost slime mold killed it.  In the colder and stormy 1950's, eelgrass regained its habitat coverage.  So did the bay scallop that does well in cold as its algal food needs nitrate to grow.

In this climate cycle, more energy and colder seawater not only scoured out eelgrass/sapropel but also allowed oxygen bacteria to "win."  Gone were the Vibrio cholera outbreaks of the 1850's that so plagued the oyster industry in high heat (it is unfortunate that heat, which helps the oyster sets, also favors Vibrio bacteria strains and why benthic monitoring programs, especially monitoring under sea grass/eelgrass meadows (monocultures) are much needed now – my view). [The 1915 to 1925 typhoid outbreaks threatened the existence of the entire oyster industry and led to the adoption of the National Shellfish Sanitation Program in 1925, following an outbreak of typhoid traced to New York oysters.]

For over a century, agricultural researchers wrote and issued papers about bacteria in peat and bacteria under grass monocultures but little of this research it seems made it into this century.  Almost none of this bacterial research is mentioned today in regards to eelgrass habitat services - the use of cold water bacteria criteria in times of warming (heat) for the same subtidal peat – eelgrass deposits. 

We need to review the impact of eelgrass upon bacterial growth, including Vibrio species, in warm water – my view, Tim Visel.

Appendix #1

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

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

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

Saturday, the local unit of the Connecticut Army National Guard and the fire department plan to remove the tree.

"The tree has caused so much debris and grass to block up, it's actually giving off an odor," Fire Chief Peter Mullen said.

Mullen said the area will become passable again for boaters.  And it will appease the neighbors, who have been complaining to town officials since the oak made its grand fall.

"The first year, we had fish heads out there and everything," Wall said.  At first, Mullen said Branford Company C, 242nd Engineer Battalion, was going to try to get a helicopter, so the tree could be air-lifted out of the river.  But a National Guard spokesman said that idea was dropped for safety reasons.

Instead, the National Guard will send several engineers to chop up the tree.  The tree will be removed between 8:30 and 9:00 a.m.  The National Guard will use the event as a training exercise, Mullen said.  Spectators are not encouraged in the immediate area, Mullen said.  Marie Wall hopes to catch a glimpse of the tree being removed.  Otherwise, she lamented, "I am going to miss the whole show." 

Re-keyed by Angela Lomanto for the Sound School


Appendix #2

The Impact of Organic Matter upon Blue Crab and Fisheries Habitat Quality
Ralph Vaccaro – Woods Hole Oceanographic Testimony 1981
The Mapping of Coastal Sapropels for Marine Chemistry
Timothy C. Visel
The Sound School, New Haven, CT

Ralph Vaccaro of Woods Hole Oceanographic Institution in 1981 gave a detailed explanation of the impacts of organic sludge to marine environments in Congressional testimony during a May 1981 hearing before a subcommittee of the then House Merchant Marine Fisheries Committee on Ocean Dumping – it is during this testimony Congress learned of the double impact of organic sludge – mostly sewage sludge, including the suffocation of the bottom and then the negative bio chemical impacts of glucose digestion in it (composting) to benthic organisms.  (See IMEP The Blue Crab Forum™ #15 part II, April 2nd 2014 – Fishing, Eeling and Oystering thread) Ralph Vaccaro – testimony (1981).

"The negative impacts from indiscriminate sludge release in near shore coastal waters include the accumulations of excessive concentrations of inorganic and organic nutrients (which diminish the quality of the local bio chemical tension) and unfavorable species diversity.  In extreme eases anoxic conditions develop, resulting in odiferous and toxic hydrogen sulfide evolutions.  Such conditions usually signify extensive damage to the benthic biota."
Ralph Vaccaro, Senior Scientist, Biology Dept. – Woods Hole Oceanographic Institution (1981) Testimony before Congress.

Did the members of Congress fully understand the scientific concepts and terms of the testimony?  That is left as an open question, but I have rewritten the testimony in a way I feel could be easier to understand (my view, T. Visel) in terms of blue crab habitat quality and our role in it.

My testimony if presented on the same topic area the impact of organic matter deposits in cove and bay bottoms.

Timothy C. Visel

The habitat destruction from placing organic composts (sludge) in the shallow fish/shellfish nursery areas can cause significant habitat damages far beyond suffocation.  The organic composts—natural or man-made—purge nutrients in chemical or biochemical forms (plant/animal matter).  In time, as the compost (sludge) is consumed by bacteria, it can emit nitrogen compounds (especially ammonia in high heat) that overwhelm the elemental oxygen bacterial reduction pathway and open the sulfur bacterial reduction process to the formation of H2S hydrogen sulfide.  This can result in fish and shellfish die offs, especially in shallow waters as sulfides create toxic conditions to many oxygen-dependent species.  In time, only the ones most tolerant of sulfide can live, such as primitive worms.  Eventually, sulfur rich compost called Sapropel begins to form.  In high heat, Sapropel conditions may release hydrogen sulfide into the air and water and create a sulfur smell similar to that of rotten eggs.  If occurring long enough, such Sulfur/Sapropel conditions can kill most oxygen-dependent life forms, leaving a black/blue greasy wax deposit, devoid of most life forms on the bottom.  - T. Visel

That testimony, in my view, is more understandable.

Water Chemistry of Shallow Waters

In many Long Island Sound studies, the analytical aspect of oxygen saturation was described as anoxic if below 3milligrams/liter of seawater.  That is to be the minimal survival level for oxygen requiring organisms.  The increase of anoxic waters and the release of sulfides and ammonia have a temperature/bacteria link.  This is most severe for western Long Island Sound as described by three conditions.

1.   Flushing—and or turnover with warm surface waters cause a thermal thermocline barrier to mixing.  Bottom waters may become oxygen depleted and deadly (sulfide rich);
2.   It is a shallow body of water that tends to warm faster and causes and increase in bacteria populations that use sulfate as an oxygen source (temperature sensitive);
3.   Has large inputs of organic matter which can form Sapropel—it is organic reduction that can release sulfides and ammonia in times of low oxygen (high heat organic composting).
It is a combination of the above which led to the July-August sulfide event that impacted western Ct blue crabbers in 2011.  Waters then were almost hot, and heavy rains turned the waters brown and dead crabs were reported.  (See Megalops Report #12: Western Crabbers Alarmed at Dead Crabs Following Intense Heat and Street Water Runoff Event, posted August, 2, 2011 on The Blue Crab ForumTM, Northeast Crabbing Resources).  Dead crabs were collected by Norwalk Maritime and sent for disease examination (reports and communications from Joe Schnierlein, T. Visel).

Reports indicated that blue crabbing success fell dramatically after this rain and did not recover.  In the following years, a careful review of this rainfall event leads me to suspect hot organic matter fed into the sulfur cycle—or we had a blue crab jubilee but I did not recognize it as it occurred in open areas.  (See The Western Connecticut Habitat Failure for Blue Crabs, August 2011, posted September 30, 2014 on The Blue Crab ForumTM, Fishing, Eeling and Oystering thread).  By August, crabs (schools) were reported moving east at night along the Connecticut shoreline.

In time, during a review of the extended warm period (1972-2012), blue crabs increased into warm waters, but in the extreme heat, moved out of the western part of Long Island Sound to central and eastern rivers.  These movements appeared as "ocean waves," bringing rusty and yellow face crabs to the east where they remain today in much smaller numbers.  An important link in blue crab habitat quality may in fact be the presence of organic matter close to shore and the biochemical bacterial processes in them.

This is what winter flounder fishers also noticed in the 1970's. Sandy shelly bottoms transitioned into eelgrass patches followed by softer and softer bottoms.  Sapropel without eelgrass is described as a greasy jelly-like substance. That is from undigested leaf wax (primarily from oak trees) left by sulfur reducing bacteria.

In a 2003 report (Cuomo et al., 2003) prepared for the United States Environmental Protection Agency and The New England and Interstate Water Pollution Control Commission, the importance of the benthic oxygen pathway on page 4 is found this section – my comments (   ) T. Visel:

"The sediments consume oxygen via bacterial degradation of organic matter.  This last point is extremely important for sediments that are high in organics, such as those of western Long Island Sound, such sediments, in contact with oxygen via aerobic (oxygen requiring, T. Visel) bacterial decomposition of organic matter.  This sediment oxygen demand can become quite large if bottom water oxygen renewal is limited by either water temperature or the existence of a stratified water column, which prevents vertical mixing ultimately, setting the stage for the onset of hypoxic and perhaps even anoxic bottom (within 2cm of the sediment water interface) waters."

This is how oxygen rich marine humus (nitrate) becomes Sapropel 1 in hot weather.  In longer periods this humus (compost) becomes the deadly Sapropel 2, the sulfides.  In extreme heat, the absence of oxygen leads to sulfur reduction using those bacteria that utilize sulfate as an oxygen source.  It is here that the sulfur cycle intersects the nitrogen cycle and produces large amounts of ammonia—toxic to marine life—all of which is dependent upon organic matter.  Once all sulfate is exhausted, the most deadly bacteria, the methanogens, breaks down carbon molecules and releases methane gas—Sapropel 3.

The final result of carbon stripping (leaving elemental carbon to concentrate) is often described at the mouth of rivers in times of little "mixing" or flushing toxic to sea and shore life- the dead bottoms (zones).

Bay coves and salt ponds are the first to have sapropel buildups- often described by shore residents as "black mayonnaise." Here reduced tidal energy increases "residence time" that is the time it takes organic matter to be digested and leave the system. This feature leads to multiple bottoms described by Clint (John) Hammond on the Cape; Chatham Mass. Increased residence time can be from reduced tidal exchange, eelgrass growth, storm sand deposits and current changes. This is related to climate cycles, warm and low energy periods inlets tend to heal or close, cold and high energy periods inlets tend to widen. This process greatly determines "residence time" of nitrogen compounds especially ammonia. In times of great residence, sapropel tends to build, as flushing (less residence time) tends to hold sapropel from developing.  Fishers then notice changes in the bottom. In heat, areas now sustain blooms of microalgae that need ammonia, not nitrate.  These changes we can measure by mapping the Sapropel as first proposed in 1985 during a conference in Washington DC. This is on excerpt from Dr. Donald Rhoads one of the conference attendees' talk on The Benthic Ecosystem.  On page 7, this condition is described as part of the Long Island Sound Conference:

Dr. Rhoads: "Yes.  One reason I mentioned the importance of the sapropels – these black iron, monosulfide muds on the bottom – was the direct point that Peter raised.  The system is so dynamic that to measure the change from the year-to-year in dissolved oxygen as measured in the water column would take more than we have.  It's not practical at all.  Given that kind of variability, what you need is a low-pass filter and 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 isobath that might be.  Follow the edge of those sapropels.  If they're encroaching upwards into shallow water, it's getting worse.  If they're receding, it's getting better."

Taken from:

NOAA Estuary-of-the-Month Seminar Series No. 3. Long Island Sound: Issues, Resources, Status and Management, 1987, Gibson, V. R.; Connor, M. S.

The above report contains papers presented at a seminar on Long Island Sound held on May 10, 1985 with the objective to bring to the public attention the important research and management issues in the Long Island Sound.



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