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« on: June 21, 2022, 01:34:40 PM »

Environment/Conservation #23
Sapropel and Submerged Aquatic Vegetation Contain Bacterial Processes
The Bacteria – Nitrogen Series
Viewpoint of Tim Visel, no other agency or organization
Thank you, The Blue Crab ForumTM, for supporting these Nitrogen Bacteria posts
This is a delayed report
Tim Visel – The Sound School


Is it pollution or is it nature?  That is a question that has been increasingly asked as we entered a hot period in New England, which started in 1972.  The estuarine literature from 1972 contains a climate bias as it references studies from the 1950’s and 1960’s, (a usual practice) a time of much cooler temperatures and with much higher seawater oxygen saturation.  While most current studies have concentrated on what we put into the water, there is very little about what nature contributes as a “natural” pollution.  Both concepts need a seat at the seafood habitat table (my view).  It is a bias that most estuarine research contains; we look to previous studies to help explain present conditions, usually about a decline in seafood, and lack the primer as how to assess those changes.  What happens during cold can be far different in heat, and even, at times, just natural. 

For all of the climate change discussions in current studies, none perhaps has the occurrence of fish kills left the public thinking it is human- caused, most if not all of the time.  But that belief has (in my view) built a propensity to blame all negative habitat features on “us,” realizing that we can contribute to negative habitat impacts and can destroy habitats.  However, our acts need to be measured against what “nature” can do as well, that aspect is often “missing” from current estuarine research (i.e., the tendency to assign all seafood decline blame to our actions).  It never used to be that way.  Researchers 50 years ago tended to include nature in habitat change. 

Researchers in the 1960’s and the 1970’s used to include that review – that at times, nature can be destructive as part of natural cycles, at least this was briefly mentioned.  H.B.N. Hynes in The Biology of Polluted Waters (1971), University of Toronto Press was careful to raise this point, that sometimes what may seem very bad (i.e., red tides) can be part of the natural system.  On page 66, he explains this process and clearly raises this issue, especially in waters that have little energy or flow, described as “reaches” “slow water” and our tendency to blame human involvement for chemical changes. 

In a way, current papers that fail to mention natural cycles or environmental conditions many times give nature a “free pass” for habitat loss or change leading to seafood loss, especially fish kills.  Most of the historic large fish kills have a natural environmental sudden shift foundation – very few attributed to pollution events except for oil spills.

We tend to blame “us” for most seafood losses and this includes dredging.  Dredging is a type of estuarine energy, man-made energy, but the natural removal of earth is called erosion.  The opposite of erosion is also called deposition, both influenced by energy, a bias for excess salt marsh peat in cold, wet periods and the reverse of that, the removal of peat in heat/prolonged heat – seen today as a general policy of minimum disturbance as good (deposition) and estuarine disturbance as “bad” or erosion. 

However, this non-disturbance policy is not bounded by science for fish and shellfish habitat quality.  Instead, it is often guided by perception.  Nowhere is this perception more evident than the discussion about dredging – when many times dredging can lead to habitat improvements especially when it removes sapropel, a natural low-oxygen marine compost.  This organic compost in hot conditions is a tremendous source of ammonia, a plant (nitrogen) nutrient.  Removing it as a source of ammonia helps keep waters clear, light is a natural bacteria sterilizer (UV).  Colder temperatures slow bacterial growth and reduce nitrogen formation from ammonia to nitrate, a much less toxic form of nitrogen in coastal waters.

Tim Visel –

Capstone Questions:

1)   Does clear water allow ultraviolet light to kill bacteria that has a temperature link and benefit for the blue crab?

The presence of shellfish has an enormous filtering capacity.  Cold water bacterial nitrate was, at times, thought to be limiting in the Long Island Sound in colder periods (1950’s).  In some texts, baymen report that bay scallops would move away (mostly at night) when they ran out of food.  In extreme cold, nitrate levels from bacterial processes would decline, resulting in a nitrate shortage to support algal strains that the bay scallop could consume.  Colder, clear waters have lower bacterial counts, warm waters with dense blooms usually test higher for bacteria.

The warm water tests may show nitrate bacteria now enter the water column only in winter.  Cold water, clear water may allow ultraviolet light to reduce bacterial populations and reduce bacterial concentrations that produce ammonia.

2)   When it comes to nature’s bacterial filter systems, can we observe habitat changes in relation to heat?

The best example here, perhaps, is nature’s filter failure in high heat following high organic loading after a hurricane when massive amounts of organic matter overwhelm and change filter capacity.  Hurricane Agnes (1972) is often reported to have created negative, long lasting blue crab habitat impacts to Chesapeake Bay.  Organic matter in high heat can produce sulfuric acids and release aluminum into shallow waters, killing fish as well.  They are also associated with higher levels of ammonia and the presence of fouling macro algae matts, adding to oxygen loss. 

This appears to have happened to young of the year striped bass habitats in the Chesapeake Bay after Agnes.  Some of the first striper reports on a sudden drop in young of the year striped bass nursery habitats (critical for future recruitment of striped bass into the fishery in the years to come) happens after a storm.  Some water test reports of this event mention curious spikes of aluminum, a signal of a sapropel-sulfuric acid event.  Sapropel, rich in sulfides when suddenly exposed to oxygen in seawater such as following a severe storm, can cause a sulfuric acid flash or explosion, resulting in a severe drop in pH.  When this occurs (usually a sulfuric acid release), this very low pH, sometimes reported to be as low as three (3), dissolves the clay particles attachment to aluminum, releasing it to the surrounding water where it can impact (kill) fish.  The movement of rushing flood waters can move sapropel that has composted for decades downstream, covering submerged aquatic vegetation slowly killing it.  In heat, both“new”or green organic matter seals deposits below, creating a low oxygen organic deposit we know as sapropel.  It is the sulfate reducing bacteria, SRBs, that can chelate heavy metals, such as aluminum.  Aluminum in only minute amounts can kill fish.

3)   Does the cycle of sapropel formation provide important habitat indicators for the rise and fall of seafood species?  Can it be a relationship between cold water bacteria nitrate and warm water bacteria ammonia?

The level of ammonia in water could be the bacterial “tipping point” for killing eelgrass.  Most descriptions of wetlands describe the natural filter process of salt marsh as one that removes organic matter from the water.  Although not the same function of “sediment trap” in a filter, the eelgrass relationship is similar.  The purification aspect of wetland filters for organic matter has been made available to the public, but the flushing rates or residence time (particles) in different temperatures has been often overlooked for ecosystem habitat quality now recognized as “filter” feeders (i.e., several species of shellfish).  Eelgrass is, at times, a subtidal peat forming process.  In the importance of Wetlands: Natural Filters from Wetlands 4-H Project Manual (1976), Florida Cooperative Extension Service “Purification Plant” (pg. 5) mentions this natural filter capacity:

“The grasses and trees that grow in wetland areas trap solid particles that are in the water.  Bacteria and other microorganisms that live on the roots of grasses and trees eat and digest the organic wastes that are brought into the wetlands.  Tidal action and/or river water carries the cleansed water toward the ocean.  As the water flows nearer the ocean, the tides act as a flushing mechanism, pumping the clean water out into the sea and recovering more river water containing silt and organic wastes.  Many wetland areas act as a “purification plant.”

How does temperature and oxygen impact these purification processes and can they be replicated in a laboratory setting? 

This may involve a simulated marsh habitat and gradually sealing it from oxygen but allowing sulfate to enter as seawater, also at higher temperatures.  This is the filter reversal described by Dick Harris in 1987 – the ability of tidal flats to provide positive ecological services, a valuable nitrate, but in heat the opposite impact, as this bacterial filter process spews out ammonia instead of nitrate, and if hot enough, even more toxin, the deadly sulfides.

In oxygen sufficient waters, this marine compost fulfills a very important filter system function for shallow water habitat (EC #8 Natural Nitrogen Bacteria Filter Systems, 10/20/2015) and Richard Harris writes in article titled More Development of Norwalk Harbor – A Muddy Issue (The Norwalk Hour Monday, Oct. 26, 1987) three decades ago about the value of these composting habitats to function as natural bacterial filter systems, a section is reprinted here.

“This natural system (mud flats) is valuable in providing treatment to sewage wasters oxygenated mud flats provide a substrate for very important aerobic (oxygen loving) bacteria.  Some of these bacteria decompose (oxidize) organic matter or sewage wastes in a process very similar to secondary treatment.   Others (bacteria) oxidize ammonia to progressively less toxic products – nitrite and finally nitrate.  This latter process is very important because a key problem in sewage treatment plants is the inability of most facilities to deal with nutrients in any fashion.  The first form nitrogen to be released upon the decay of organic matter is ammonia, which is very toxic as little as .1ppm (parts per million) is lethal to some marine organism (for example a range of .4 to 2.3 parts per million will cause death to many crustaceans (blue crabs) helped by the large surface areas, mud flats begin the nitrification process.  This natural ability to process some of the sewage in the harbor has been totally overlooked and has yet to be quantified.”
And further (when the natural system is overwhelmed) blooms of algae described as a “Mass of plant cells dies off sinks to the bottom, consumes much of the available oxygen in the decay process and helps form the reducing – black mayonnaise – like blanket for the bottom.  Again, any natural mechanism that exists to help take up excessive sewage derived nutrients from the water ways should be evaluated and quantified, this has yet to be done” (Harris, 1987).

4)   Can we feed sulfate-reducing bacteria and starve oxygen bacteria?  Will this impact the relationship between nitrate and ammonia?

Most closed systems (biological bacteria)/filters supplement oxygen or provide aeration.  Water movement and oxygen are key components of the bacterial nitrogen removal aspect of converting ammonia to less toxic nitrogen compounds.  But what if the energy (movement of water) was turned off and temperature now increased?  What would happen to the “positive” denitrifying bacteria that allow this process to happen, and those bacteria (sulfate-reducing bacteria) that thrive in heat and little oxygen but utilize nitrate and sulfate?  Some species of bacteria oxidize sulfide to less toxic substances.  How would they respond to low oxygen saturation?

Closed system filters are designed to lower ammonia, not increase it.  They depend on sufficient levels of oxygen.  How or what factors are needed or to be considered for large outputs of ammonia and to make nitrate scarce or nonexistent in controlled laboratory experiments?

Nature and Fishkills

H.B.N. Hynes (1971) talks on the impacts of storm water carrying organics into low flush-low energy rivers and the foundation of the Saprobien System.  On page 158, he states:

“This state of affairs was, however, more marked in the English-speaking countries than it was elsewhere and serious study of the biological aspects of pollution was begun in Germany at an early date (Liebmann, 1951).  The results were first codified by Kolkwitz and Marsson (1908, 1909), who developed their now well-known “Saprobien System” for the assessment of organic pollution.  But perhaps well-known is too strong an epithet to use, because although it is widely used on the continent, it is rarely even mentioned by American or English authors.”

The foundation of the Saprobien System is the dumping of manure (sewage), sawdust, paper pulp and cotton mill wastes, all dumped by human activity (all natural substances) and the energy (flow or flushing) needed for a natural stream or river to recover or become “well” again.  In the absence of oxygen, this organic matter “putrifies,” producing sulfides toxic to fish and shellfish.  But these organic pollution events can happen without our help; nature also sheds vast amounts of cellulose by way of trees, grasses and forest duff.  The event below is characteristic of natural events and details many of the factors mentioned in the 1898 upper Narrangansett Bay (Rhode Island) fishkill.  Hynes (1971) mentions these natural events and what happens when we slow or impound water, especially after a heavy rain that can “carry” heavy organic loads (my comments, T. VIsel):

“The limited reach (river stream) becomes filled with water at flood-time, and this water is often more polluted than usual, because at times of heavy rainfall many sewage works are unable to handle the extra run-off from roads and roof drains and so pass quite untreated sewage out through “storm overflows.”  Normally this has little effect, because the discharge is at a time of high water and maximum dilution.  However, if the water is then compounded (Behind a Dam, for example – T. Visel) and left to stagnate, it rapidly putrifies (sapropel formation – T. Visel).  Because of the absence of flow (reservoir residence time) and turbulence (little mixing energy – T. Visel), its rate of oxygen uptake is low (reduced aeration capacity or strong thermoclines – T. Visel) and the water becomes totally de-oxygenated, anaerobic bacteria then take over and reduce firstly nitrates to ammonia and then sulphates to sulphides. (Sulfide will be the fish kill of black water – T. Visel).  Thus, a mass of water is formed (similar to those lakes with peat bottoms such as Lake Okeechobee in Florida – T. Visel), which is not only de-oxygenated but which contains poisons (high ammonia-high sulfides and cyanobacteria – T. Visel) and have a heavy oxygen debt (organic cellulose material – T. Visel) and when a sudden flood (or release from heavy rain – T. Visel), such as a summer thunderstorm, occurs, it is suddenly pushed into the river (or exit canal – T. Visel) and passes downstream as a more or less discrete “plug” (can be visual carrying wood debris or black water – T. Visel).  The sudden death of thousands of fishes, particularly in hot summer weather, can often be attributed to this or some other cause, and it may appear as if there has been a “spill” or some other failure at a treatment plant when, in fact, everything is functioning normally.”

Hynes further comments on the de-oxygenation of organic matter and in low oxygen conditions, produce ammonia and sulfides – “for instance, Pruthi (1927) and many later workers have demonstrated that toxicity (fish kills – T. Visel) is produced by septic (anaerobic) decay (bacterial reduction – T. Visel), and this is now known to be caused by ammonia and sulphides.”

The Compost Called Sapropel

These are the residues of subtidal marine composts – organic matter in many forms that feeds immense bacterial populations.  Florida is now reporting on the ammonia generation from these subtidal marine composts called black mayonnaise (See Internet video clip titled “John Trefry Running Amuck Our Six Decade Legacy To The Indian River Lagoon,” 5/11/16).  In addition, studies are underway for impacts of organic debris from the Conowingo Dam in the upper reaches of Chesapeake Bay.  This introduces “flushing” and related residence time, not the same, but influences each other.  Residence time is how long a particle or compound may stay in a system, hence “its residence.”  Flushing refers to exchanges of water as inlets closed (trapping organic matter), the residence time of it increases, staying in place to “rot.”  These “held” marine organic composts impact fish and shellfish habitats for years, perhaps generations.  The size of the water bodies is far larger than what Richard Kolkwitz or Maximilian Marsson developed in their saprobic biological indicator index in the early 1900’s for organic loads in rivers.  Their research, however, is applicable to larger bays, coves and sounds with different energy pathways – not the flow and current velocity of streams and rivers, but the energy systems of coastal storms and hurricanes.  Moving water has energy.  It mixes surface and bottom water and over rocks or trees helps aerate it.  This was the foundation of the Saprobien index.  In time, stream energy would provide enough oxygen to reduce organic matter into elements and move them to the sea. 

Streams (mountain) that have rapid elevation drops have clean gravel and sand habitats, frequent spills over rocks that creates bubbles and introduces oxygen.   Flat land streams contain much less energy, which results in fewer chances for rapid water movement and, therefore, much less chance for oxygen penetration.  For decades, it was public policy to reduce stream energy, to bury streams in pipes or eliminate them, but these canals had much less energy and sapropel easily forms in these slow-moving water bodies.  Abandoned canals in New England still have the remains of organics, which collected in them and serve as a reminder of how organics build up without energy.  We also notice when stream energy increases and rips the decayed organics up and sends it downstream in a flood.  It is a natural process to clear organics and organisms respond to a different habitat.  The Saprobien System is the foundation of all modern bioindicator indexes and was designed around temperature and energy – flushing or inlet water exchanges.  (Many projects are underway in the United States to restore stream energy – T. Visel).  The formation of sapropels has direct negative impacts upon estuarine marine soils and it may be from natural leaf litter.  New England’s forests have largely recovered from extensive agriculture cutting of the past three centuries.  For instance, Connecticut is now one of the most heavily forested states in the United States – 60% forested (Connecticut’s Forest Action Plan, 2010 – Revised to 2015 Helene Hochholzer, Connecticut Forest Planner). With these mature growth trees come leaves from the 1840’s when only about 25% of Connecticut was forested leaves, now negatively influencing coastal bogs and sounds.  Hynes (1971) discusses the negative impacts of leaves on upstream Trout brooks on page 1 in Chapter 1 of “The History of Water Pollution” a half-century ago:

“Even “natural” streams may show the characteristic signs of pollution.  In densely wooden regions, the autumn leaf fall may add so much organic matter to water that fish are asphyxiated.  Schneller (1955) has investigated this effect in an American stream, and the reader will be familiar with the fetid appearance of many woodland streams and pools in this country, Canada.  In such places, the water is murky and smells foul when disturbed, and the decaying leaves near the surface are covered white, a white coat of sewage fungus … There is little doubt, however, that they have occurred in some places in every age since the invasion of the land surface by plants.”

It is the bacteria of earth that reverses the process of photosynthesis, reducing the sugars and proteins that plants created back into original elements.  Here, the iron and sulfur reducers break and remake chemical compounds.  The largest components include iron (and why black mayonnaise is black and sulfur – why such material emits the smell of rotten eggs, hydrogen sulfide) along the Connecticut shore. 

The chemistry of peat involves two elements in oxygen (or without oxygen) held in pores of it – spaces in which iron and sulfur can react.  Oxygen is the key element here and relates to its valence configuration; that is oxygen needs two electrons to complete its outer valent orbit, and with oxygen, it is often a taking rather than sharing electrons.  It is the bully on the lunchtime schoolyard.  The combination of oxygen with hydrogen atoms (it needs two electrons) gives water, H2O, a relatively stable compound.  Most often we see this unequal sharing changing the chemistry of iron.  We see it as a brown to red rust, as iron carries oxygen in our bloodstream.  Blood rich in oxygen is red, oxygen-poor blood is blue.  Sulfides bind to heme proteins (hemoglobin) in human blood and cause it to carry less oxygen. 

Iron is oxidized in the presence of oxygen, but so is sulfur and sulfate, SO4.  A compound dissolved in seawater as a source of oxygen for those organisms that lived before the earth had a large atmospheric oxygen content.  The chemistry of peat involves all three, iron, sulfur and oxygen, governed by the bacteria, trying to reduce it back to elements from cellulose, in this case root tissue, the product of photosynthesis.  It is primarily bacteria (several types) that reduce plant tissue back to elements and why we seek to protect wood of homes from this bacterial feast.  The navigation shipping interests feared oxygen bacteria much more than saltwater bacteria.  In fact, in the early oyster records, old wood trunnel oyster vessels were sunk (no engines, wires, etc.) to pickle the wood with salt to kill fresh water bacteria viewed as much more dangerous than salt bacteria (Frank Dolan, personal communication, 1980’s – T. Visel).  It is the faster “fresh water” oxygen bacteria that consumed wood ships so fast, sinking wood hulls in seawater would kill them.  That is also why many old wood hulls were in good shape below the water line and topsides rotted out so quickly.  This is why to preserve the cellulose in wood it was salted, and why ice on wood fishing vessels (from using salt) soon caused rot in fish pens.
So much of our fisheries habitat quality and quantity is determined by bacteria and the presence of toxic sulfide.  Much of that often depended upon the depth of organic matter in warm energy-poor habitats.  That was one of my 1974 lessons in oceanography and the Jensen Beach FIT campus, described as the Tampa Bay effect.  Here, transportation crossings had disrupted tides and currents, causing organic matter to accumulate over time (This is often referred to as restricted flushing).

It would be a decade later that I would mention my oceanography year along the Indian River Jensen Beach Florida to John “Clint” Hammond, a retired oyster grower in Chatham Mass.  He was curious as Jensen Beach / Stuart Florida was at the edge of the Everglades and asked if I learned about the sulfur cycle?  As I recall my responses at the time did not instill confidence as he would lecture me (in a polite way of course) that working for Cooperative Extension Service – the University of Massachusetts I should learn it, as it related to marine soils as well as those soils on dry land.  It was a concept Mr. Hammond would mention many times but I did not have that much knowledge then about the sulfur cycle although Mr. Hammond assured me I could see it every day – the salt marsh.  Mr. Hammond’s agriculture experience would be mentioned as simply knowing your soil, how it feels, does it smell, is it sticky or gritty things that I did not relate to wet environments – just on land.  I knew something about soils, I was in a 4-H club in the middle 1960s, raised chickens, cared for a pony, and we had a large garden, but what Mr. Hammond talked about was sulfur and submerged soils – humus and habitat changes.  A recent article came on the internet recently, Science Friday – “use your senses to make sense of your soil” by Daniel Petershmidt brought me back to Mr. Hammond’s meetings 40 years ago, the sulfide cycle and marine humus, layers of organic paste on bay bottoms more properly termed Sapropel.  Mr. Hammond was concerned (mild emphasis) that the sulfur cycle was not a huge issue for estuarine study and to remedy my educational lapse he provided a section about it to me – I still have it.  So much of our inshore fisheries habitat is dependent upon the sulfur cycle and my lack of knowledge of it was, I suppose, a disappointment. 

Sapropel And The Sulfur Cycle

Estuarine studies of the late 1970s did not often include glucose metabolism by sulfate bacteria in heat.  The processes of sulfate reduction, ammonia generation, secondary oxygen acceptors, and sulfide formation were not mentioned.  When presenting evidence of habitat change (fishery or catches), frequently only human factors were associated with negative values or conditions, if some seafood resources did decline it was suggested that coastal development or pollution was the fault.  This is perhaps the beginning of the funding effect that has so much impacted coastal study.  This is what caused a division in salt marsh research (Teal/Nixon) and coastal salt pond assessments decades ago.  In two similar but in some ways competing papers on salt marsh ecology, one researcher Nixon (1982) would talk about the “high marsh” oxygen dominated pathway while Teal, at the same period, focused on the low marsh sulfate dominated pathway in 1986 (Nixon reviewed the high marsh ecology, March, 1982).  And in somewhat competing papers exchanged viewpoints that later threatened to overshadow many research documents with the “funds” that came with viewpoints or positions that may influence the “science.”  This is an excerpt from Teal in his 1986 publication titled “The Ecology of Regularly Flooded Salt Marshes of New England: A Community Profile” (John M. Teal, Senior Scientist, Woods Hole Oceanographic Institution, Woods Hole, MA 02453 – Performed for the National Coastal Ecosystems Team, Division of Biological Services, Fish and Wildlife Service, U.S. Department of the Interior, Washington, DC 20240: Biological Report 85 (7.4), June, 1986). 

“In the past twenty years, a good deal has been learned about the way salt marshes function, but there is still a vigorous controversy about the role of marshes as supporters of production in the waters associated with them.  Nixon (1980), in a detailed review of the questions surrounding marsh export in its various possible forms, pointed out the uncertainty of much of the data and the limit of our understanding of the interactions between marshes and coastal waters.  Note his comment on the inadvisability of trading “our credibility for political advantage.”  It is all too easiest for a scientist, believing he has achieved a new way of understanding some natural phenomenon, to promote his idea for some management purpose.  This has certainly happened in relation to salt marshes.  Both the need for, and the lack of need for, the preservation of marshes have been supported on the basis of incomplete understanding.

There are occasions when it is necessary to act on the basis of less-than-complete information.  Scientists should do their best to make the results of their efforts available to those who make decisions.  If scientists do not, managers will, as they must, make decisions based on whatever information they have.  Unfortunately, those decisions may be based only on politics or outdated knowledge.  Scientists should make the best information available.  They should remain skeptical about their own conclusions.  They should be willing to test their ideas repeatedly when the opportunity arises.  They should not go to the most conservative extreme and never be willing to give an opinion about the wisdom of some proposed action.”

The differences included phrases that included human disturbance.  Scott W. Nixon (1982) in his report titled “The Ecology of New England High Salt Marshes: A Community Profile” speaks to these differences (See Graduate School of Oceanography, University of Rhode Island, Kingston, RI 02881, Prepared for the National Coastal Ecosystems Team, U.S. Fish and Wildlife Service, 1010 Gause Boulevard, Slidell, Louisiana, 70458, U.S. Department of the Interior, Washington, DC, 20240, FWS/OBS-81/55, March 1982):

“The focus of this profile is primarily on the high marsh in New England rather than the low, creekbank or regularly flooded areas which have received most of the attention in the ecological literature.  All of the marsh is intertidal, and it must be understood and managed as a geomorphological  and ecological unit.  I hope it will be useful to those working in coastal planning, management, and research to bring together much of the information that has been developed on this less frequently discussed, but important area of the marsh.

While the high marsh is commonly thought of as lying between mean high water and spring high water, the profile drawn here has not always followed such strict, and somewhat arbitrary limits.  Similarly, the major emphasis is on the Spartina patens-Distichlis spicata community, but in several cases I have included information from the stunted S. alterniflora zone.  The development of marshes and the zonation of different species, especially plant, receive more attention in this profile than do animal populations or community metabolism.  This largely reflects the relative abundance of information rather than my own biases.  I can only hope that the gaps which are so evident in this profile might stimulate future work in these areas.”
(S.W. Nixon, Kingston, RI, June 1980)

The 1980’s would mark the beginning of a funding issue at many universities, the use of graduate students to teach college courses, freeing tenured track professors the time to obtain grants.  I was at the University of Rhode Island during this time and participated in many faculty meetings and discussions.  Grant research was a feature of university existence and the phrase “publish or perish” is well known in the academic fields.  In the 1980’s, this aspect became connected to grants – the funding of research that brought dollars into the university – as public funds declined, grant dollars were sought to fill a void.  That is what John Teal mentioned repeating Scott Nixon “trading our credibility for political advantage” was, I believe, a process that we call today “the funding effect.”  The pressure to obtain grants (from any source) became so intense it was joked that “publish or perish” became “grants or gone,” a reference to newly hired staff needing to obtain grants that helped fund a university position.  This, I believe, folded into research dollars (grants) into the environmental concerns and public policy research initiatives.  Many of these initiatives were species specific and linked to human causes, mostly pollution.  This is now evident in the research around the value of eelgrass after 1982 – my view, Tim Visel.

(See Recent and Historical Changes in Abundance Eelgrass J. Costa).  It was in the early 1980’s that pollution ecology grants went into influencing public opinion or agenda-based objectives.  Arthur Gaines and other benthic researchers with some Cape Cod softshell clam fishers tried to address natural fluctuations in estuaries - habitat changes were all not human caused (I participated in several shellfish surveys on Cape Cod).  Marine soil cultivation using hydraulic rakes was introduced to mitigate sulfide as a climate cycle natural process – the lack of flushing and poor Mya softshell clam sets.  The cultivation and release of sulfides was in direct opposition to non-disturbance policies, which had focused upon dredging policies.

New England Salt Pond Data Book WHO1-90-21 mentions of this situation on Cape Cod then, a condition of salt ponds, which could become sealed or had long connections to the sea that reduced tidal flushing.  In times or reduced flushing and heat, hydrogen sulfide levels increased.

On April 21, 1988, a special symposium on salt ponds and lagoons at a NEERS conference brought to light different viewpoints and Dr. Gaines provides a rare caution in estuarine salt pond changes to the symposium attendees in a paper titled “Value Judgment and Science in Coastal Management The Case of Anoxia – pg. 17 regarding human impacts “A study of the sediments in the basins of the Narrow River (Rhode Island) suggests that bottom waters have been anoxic for over a thousand years – long before significant human impacts could have been present.” 

Hydrogen sulfide was a key factor in habitat quality (hydrogen sulfide is a toxin in the marine environment) and part of the sulfur cycle Mr. Hammond mentioned to me several years before.  This was the cycle of heat and drought or cold and more storms.  In times of heat or poor flushing, it was natural for bays and coves to show more ammonia.  In areas of deposition of organic matter, it was natural to show more sulfides, a plant toxin.

In 2008, I again thought about the Mangroves and toxicity of sulfide to plant tissue, here was a plant that could exist in both – air (oxygen) and water (sulfate) a plant between the hydrogen sulfide of sulfate and the sulfuric acid digested of drained salt marshes which introduced oxygen to terrestrial peat.  The battle between oxygen and sulfur could be measured in sulfides/sulfuric acids as plants adapted to them or not over time.  Attention turned to a plant who could survive air/oxygen and water/sulfur a plant in the middle and for us that plant I could see every day – that was Spartina alterniflora in the salt marshes that John Hammond pointed to across from his oyster shop in 1982.  The sulfur cycle was indeed visible you just needed to know what to look for (See IMEP Series #40 to #45 on the Blue Crab Forum™).

About four years ago I started to look for examples of plants that could tolerate high sulfides.  Eelgrass was killed or weakened by sulfuric acid from sapropel, this subtidal peat and salt marsh cord grass living on exposed peat could collapse or subsurface suffer from sulfide browning in oxygen.  We did not have Mangrove trees, but we do have Alterniflora, a plant that lived in the middle and is tolerant of sulfides.  I used to look at every day growing up along the shore in Madison, CT and not even think of it adapting to the sulfur cycle, but it did. 

Climate Change and Marine Soil Study

One of the climate signals of sapropel formation is ammonia levels so high that it accelerates calcium carbonate deposition, forming a carbonate layer, a transitional marker for anoxic conditions from temperature. A “proxy” signal for climate cycles, core studies in coastal coves and lagoons may show these markers noting temperature shifts 10,000 years ago.  The cause of this carbonate layer is very high ammonia levels in bottom waters long thought to be the result of bacterial action in the soil itself.  Shallow warm coves and lagoons give these ammonia signals in high heat when oxygen levels drop.  When that occurs, ammonia levels soar and carbonate ions (levels) disappear.  These biochemistry factors have been associated with shallow waters.  The Indian River lagoon has been the site of previous marine soil study such as the paper referenced below.  This paper, authored in 1987, helps explain the significance of habitat loss in a warming scenario and the sulfur cycle.

Environmental Chemistry Vol. 50, #2, 1987, Pg. 99 to 110
The Geochemistry of Interstitial Water for a Sediment Core from the Indian River
Lagoon, Florida - 1987
Deyu Gu, Nenad Iricanin and John H. Trefry
Department of Oceanography and Ocean Engineering
Florida Institute of Technology
Melbourne, Florida 32901


“Chemical results for interstitial water from organic rich sediments in the Indian River lagoon, Florida show a classic picture of biogeochemical reactions in anoxic environments.  Interstitial nitrate was depleted throughout the sediment column and complete sulfate reduction was observed at a depth of less than 9cm below and seawater – sediment interface.  Interstitial water chlorinity decreased sharply with depth suggests subsurface occurrence or intrusion of groundwater.  Ammonia phosphate and silica concentrations were high, showing significant nutrient regeneration.  Dissolved sulfide levels were also high and playing a primary role in controlling interstitial water metal concentrations.”

This study (1987) reviews redox potential (Eh) of sediment cores of the Indian River lagoon and the transition of bacterial processes that proceeded from elemental oxygen to nitrate/nitrite species to those that utilized sulfate reduction, a process later commonly associated with the term “benthic flux.”

“Nitrate and nitrite concentrations (in cove pore water – Tim Visel) were below detection limits (less than .2 um) throughout the sediment column at our Indian River location.  This depletion indicates that bacterial decay of organic matter was being carried out under suboxic or anoxic conditions and that decomposition reactor had already shifted to equations 3b or 4 inches the surficial sediments.  This condition results from high organic matter inputs to the sediments.”

This reviews what waste water system operators long knew that in times of heat, nitrite and nitrate become filter bacteria secondary (some say emergency) sources of oxygen for bacterial filter processes of larger tidal systems such as tidal mud flats, which reverse in heat and tend to exhibit sulfate metabolism or “nitrate buffering,” a term that the USGS reviewed in a scientific investigation publication in 2016 #5033 titled “Quantify Benthic Nitrogen Fluxes in Puget Sound, Washington” – A review of available data and contains this statement:
“Open water (pelagic) and bottom water (benthic) processes of organic matter and nitrogen cycling are inherently coupled in marine environments. Particulate matter, which can result internally from primary production or externally from terrestrial process (that is, runoff), is transported to bottom sediment surfaces from settling within the water column. During the transport of particulate matter to marine bottoms, several processes can take place to break down material into various forms of nitrogen (N). This N takes many forms, both organic and inorganic and becomes available for uptake by marine biota. Particulate matter that is not decomposed in the water column will ultimately settle out onto the sediment surface where it can decompose further or be permanently buried. In deep waters, settling times are longer resulting in more time for particulate matter decomposition before reaching the sediment surface (Boynton and Kemp, 2009; Bronk and Steinberg, 2009).

The opposite is true in shallow embayments and estuaries where particulate matter deposition is greater and therefore plays a potentially larger role in nutrient and oxygen dynamics. As particulate matter breaks down on the sediment surface, the forms of N regenerated can undergo a wide variety of transformation processes (fig. 1). Three primary microbial processes influence the type and amount of regenerated N: ammonification, nitrification, and denitrification: (1) ammonification produces ammonium (NH4+) from the breakdown of organic matter and provides a direct link from organic matter deposition to N regeneration from the sediments; (2) nitrification converts NH4+ to nitrate (NO3-) under aerobic conditions; and (3) denitrification converts NO3- to nitrogen gas (N2) under low oxygen conditions in the presence of organic carbon. These three processes can cause concentration gradients between the overlying water and sediment resulting in exchanges between two compartments (fig. 1). This exchange of N across the sediment-water interface is referred to as a benthic flux, which can operate in two directions with a release of N into the bottom water (positive flux) or the removal of N from the bottom water (negative flux).

Environmental factors, such as temperature, can influence flux rates. A detailed description of N cycling in marine sediments is available from Joye and Anderson (2009).  Understanding benthic fluxes is important for understanding the fate of materials that settle to the seafloor and the role these fluxes they have on the chemical composition and biogeochemical cycles of marine waters (Klump and Martens, 1981; Berelson and others, 1987; Tengberg and others, 1995). Organic and inorganic forms of N can be regenerated during the breakdown of particulate organic matter. However, most studies have focused on inorganic N (NH4+ and NO3-) fluxes because these forms are tightly coupled to primary productivity, which in turn, can alter water column oxygen concentrations and provide energy sources to high trophic levels. The source of N species to overlying waters from benthic fluxes can be comparable, or exceed, other external sources to a water body (Kuwabara and others, 2009a, 2009b).  In Puget Sound, Washington, ignoring or underrepresenting benthic flux as a source of N to marine waters can result in ineffective management actions and can lead to chronic water quality problems in sensitive areas.”
The summary again mentions the importance of including the microbial processes of sulfate bacteria and its relationship to nitrogen-ammonia.  The final bacterial process the bacterial depletion of dissolved pore water sulfate (Sulfate is non-limiting in estuarine waters).  Long Island Sound has a habitat history of similar benthic processes and the nitrogen cycle in marine soils – a formation of humus/sapropel.  This compost forms in heat after heavy organic loadings usually associated with tropical rains.
In oxygen sufficient waters this marine compost fulfills a very important filter system function for shallow water habitat (EC #8 Natural Nitrogen Bacteria Filter Systems 10/20/2015) and Richard Harris writes an article titled “More Development of Norwalk Harbor – A Muddy Issue” (The Norwalk Hour Monday, Oct 26, 1987) three decades ago about the value of these composting habitats to function as natural bacterial filter systems, a section is reprinted here – the same year as the Florida Institute of Technology paper.

“This natural system (mud flats) is valuable in providing treatment to sewage wasters oxygenated mud flats provide a substrate for very important aerobic (oxygen loving) bacteria.  Some of these bacteria decompose (oxidize) organic matter or sewage wastes in a process very similar to secondary treatment.  Others (bacteria) oxidize ammonia to progressively less toxic products – nitrite and finally nitrate.  This latter process is very important because a key problem in sewage treatment plants is the inability of most facilities to deal with nutrients in any fashion.  The first form nitrogen to be released upon the decay of organic matter is ammonia, which is very toxic as little as .1ppm (parts per million) is lethal to some marine organisms (for example a range of .4 to 2.3 parts per million will cause death to many crustaceans (blue crabs) helped by the large surface areas, mud flats begin the nitrification process.  This natural ability to process some of the sewage in the harbor has been totally overlooked and has yet to be quantified.”

“And further (when the natural systems are overwhelmed) blooms of algae described as a “mass of plant cells dies off sinks to the bottom, consumes much of the available oxygen in the decay process and helps form the reducing – black mayonnaise – like blanket for the bottom.  Again any natural mechanism that exists to help take up excessive sewage derived nutrients from the water ways should be evaluated and quantified, this has yet to be done (1987).”
This is the same year that in Florida, Gu et al.,1987 reported on the Indian River lagoon:

“Decreases in interstitial water sulfate concentrations are a good indicator of reducing conditions in estuarine sediments.  The production of hydrogen sulfide during sulfate reduction is one of the more noxious (odor causing - Tim Visel) and obvious results of organic matter decomposition as mentioned in the Florida study.  At our study site, pore water sulfate concentrations decreased from 10.6mm at the top core to essentially zero below 9cm.”

But this process also results in the generation of toxic sulfides and the source trace metal sulfides and leads to the formation of black water just prior to or during fish kills.  Again, from Gu et al., 1987, “Sulfate reduction leads to sulfide production, interstitial sulfide concentrations at our study site increase from undetectable levels in the top centimeter to 1.7mm at 13cm.  The sulfide produced is highly reactive and thus is not a reliable indicator of the extent of sulfate reduction.  Sulfide can diffuse from the sediment column as H2S (hydrogen sulfide) and contribute to the odor so commonly complained about along the Indian River, or it can precipitate in the sediments with metal ions, especially iron (this is an accurate representation of so many sulfide fish or shellfish kills that contain references to rotten egg smells or the presence of black water). 
In July 2016, a black water release from Lake Okeechobee Florida caused numerous fish kills and was highlighted in the national new media for several days (Harbor Branch Video: Blackwater Discharge Into St. Lucie River). 

And lastly, temperature-driven bacterial processes greatly influence the nitrogen cycle.  As represented by compounds that contain oxygen, nitrite and nitrate help sustain oxygen bacteria rather than sulfate-reducing bacteria noted as SRB in the scientific literature.  When SRB populations increase the oxidation bacterial pathway of nitrite/nitrate (nutrients that help sustain nutritious algal blooms for shellfish), die off or collapses opening a new nitrogen “pathway” to producing ammonia, a compound toxic to fish and shellfish.
When this occurs, the positive aspect of nature’s bacterial filter reverses instead of consuming toxic ammonia for less toxic nitrite and nitrate.  It now produces ammonia (termed ammonia purging in the literature), especially in areas that obtain organic matter such as leaves, grass residues and forest “duff” in sounds and bays that hold heat.

This paper reviews that nitrogen aspect as well, from Gu et al., 1987 (this report even mentions Long Island Sound):

“Under reducing conditions, nitrogen is regenerated as nitrogen gas and ammonia.  At our study site, dissolved ammonia concentrations were found to increase from 1.1mm at 15cm to 5.3mm at 39cm (depth of core study measurements – Tim Visel) with an average of 3.4 plus or minus 1.7mm.  Dissolved ammonia gradients were largest in the top 12cm where sulfate reduction was most active.  Below 12cm, complete sulfate reduction had occurred with a concurrent decrease in the ammonia gradient.  Ammonia concentrations for our Indian River study site are comparable with those measured for the highly reducing sediments of Chesapeake Bay and the Long Island Sound.”


Brown Tide Cysts Linked To New York Bay Flushing
Sapropel Linked to Shellfish and Finfish Diseases and Parasites

It is becoming evident that organics provide habitats for many organisms that have temperature and energy triggers. These are increasing found to be harmful to seafood and US.  These diseases parasites are now associated in soft ammonia rich organic deposits.  The slower the currents or deeper the organic deposits the apparent higher number of diseases and parasites. Influence of nutrients and climate on the dynamics and toxicity of Alexandrium fund dense blooms in a New York estuary – Theresa Hattenrath 2009 found that cysts concentrations (cysts cubic) centimeter in Northport Huntington Bay in 2008 were over 700 cysts (poorly flushed) while at the Bay Mouth only 0 to 10 cysts pg. 35 (where flushing rates are better).  Cyst densities were much less.

And Hattenrath Lehman et al in a recent survey in 2016 of Shinnecock Bay that cyst surveys of Old Fort and Pond had over 500 cysts in just one cubic centimeter (of C. Polykakoides).

Old Fort Pond is an indented portion of Shinnecock Bay Long Island and could be described as a low energy high organic area that most likely contains an oxygen poor organic layer.  Researchers found that high heat and tidal circulation (flushing) has the ability to hold cysts – a potential seed stock for future blooms.  (Old Fort Pond South Hampton New York Dredging, January 5 minutes regular meeting of the Board of Trustees of the free holders and commonalty of the Town of South Hampton, New York).

Poorly flushed areas nay hold future seed banks for “toxic blooms.”

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

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

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

To fully understand sapropel you needed to look at bacteria and the formation of coal.  It is the sulfur reducing bacteria (SRB) that utilize sulfate as an oxygen source and in the process seeped hydrogen sulfide into this ooze and later fossilized is coal seams.  That is how sulfur was introduced into coal by bacteria.  To have this happen it needs to be “hot” and oxygen bacteria not present or at least then a small part of the bacterial population.  This is why coal was formed long ago when the earth was hot and sulfur was a dominant atmosphere constituent.  In fact, the discussion about global warming is largely the possible return of sulfur to the loss of oxygen requiring life.  Putting sulfides into the air hurts oxygen life – it is as simple or complicated as that.

That is one of the interesting aspects of the blue crab, it is so to speak as it can carry vibrio bacteria, with little effect (it seems), while vibrio bacteria is a pathogen to many organisms (including us) the blue crab lives in an environment that fosters sulfur bacteria but has adapted to its presence.  Some research has indicated that some species have the ability to immobilize vibrio – not kill it but to make it “sticky” by changing bonding locations as to make them ineffective.  It was described to me as grease on a door knob- the door is still there but the knob has no grip and therefore cannot “be opened.”  To understand the chemistry of sapropel the explanation of this bacterial battle needs to be included.  The area of study that allows us to study this bacterial battle is the soils and peats in cold or hot periods, and Florida presents a longer grow, season for sulfur because its climate is warmer (New England has vibrio perhaps in only the hottest of times).  In cold and in oxygen containing waters sulfate reducing bacteria loose to oxygen bacteria that are energy efficient.  In heat sulfate reducing bacteria (SRO) set the habitat conditions that extend into acid conditions and sulfuric acid soils that can be part of seafood disease and parasites.  Sapropel is now considered a bank of spores and cysts that are possibly released in rapid sulfuric acids (part of the sapropel – sulfur cycle) that activate disease hosts even perhaps the dreaded oyster disease MSX.  There appears to be a correlation between storms and disease perhaps related to release of sapropel spores and cysts – the creation of acid bottoms that could activate these spores and cysts.

Our Bacterial Wars – The Bacteria of Treacy
Adapted from One Girl’s Mishap Led to the Creation of the Antibiotic Bacitracin
We will most likely never know what caused Margaret Treacy to pick up her bike one May morning of 1943.  We do know that bicycle ride would forever change the field of bacteriology.  It would give an entire generation of bacteriologists a chance to view this bacterial habitat war that has gone on out of sight in terrestrial and marine soils for time beyond our comprehension.  The battle of bacteria since oxygen became part of earth’s atmosphere and gives as a viewpoint to the bacteria of longs ago.

This account begins with a bike ride that few could argue changed the medical and our world by Margaret Treacy.  Ice still important at this time to keep cool food to prevent bacteria spoilage (refrigerators were in short supply as metal a crucial war material was allocated to “primary” uses) and her bike ride ended by the ice truck hitting her so hard it shattered her leg.

We will never know what caused Margaret Treacy to have this accident one May morning of 1943.  That bike ride would forever change our knowledge of a bacterial war sight unseen by us but not beyond those who closely examined it.  Some, no doubt, have neither heard nor read this story before… that this bike ride would result in a serious leg injury recorded by the hospital and Babina Johnson, a bacteriologist, would take smears of the wound and find that Bacillus subtilis, a soil bacteria, was killing off other bacteria when viewed under a microscope and had produced an antibiotic substance.  Five years after being hit by an ice truck, the “Bacteria of Treacy” would become known as Bacitracin.

It was by many accounts the bike ride that changed the bacterial study world, and for a brief instant pulled back the shades of this bacterial war for millions to see and benefit.  This conflict occurred on the culture smear itself – two different strains of bacteria were killing each other and observed by bacteriologist Johnson and further researched for antibodies.  The “Bacteria of Treacy” we recognize today as Bacitracin the antibiotic is in some form in almost every American household. 

A great write up of this account is found in Smithsonian, June 2017, by Peter Andrey Smith – and speaks to how much we need to learn about the bacteria of soil – that includes our marine soils as well.  We may find more drugs deep inside deep layers of sapropel – my view, Tim. Visel.



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