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Author Topic: Search for Megalops - Report #6 - (Late Fall) February 2018 - Tim Visel  (Read 212 times)
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« on: February 12, 2018, 02:07:53 PM »

The Search for Megalops
“You Do Not Need To Be A Scientist to Report”
Crabs in Waves Exit Connecticut River
Megalops Report #6 - November 30, 2017
A Late Fall Report 
(Delayed Report)
View all Megalops, Environment Conservation and Habitat History Posts on the Blue Crab ForumTM
Tim Visel, The Sound School, New Haven, CT 06519

•   Blue Crab Waves in the Connecticut River
•   Maine Confirms Temperature Drop
•   An Interesting Catch
•   UCONN Announces the “Weiss Key” for Megalops
•   Questions About Dredging
•   The Blue Crab Morning Sulfide Events
•   Black Mayonnaise and the Blue Crab

A Note From Tim Visel

A very warm fall has allowed some great crabbing into October and it continues to be very mild.  The blue crab population has declined in Connecticut and confined by reports on the Blue Crab ForumTM and other state surveys.  The warming temperatures of the late 1990’s was great for the blue crab megalops; it was also great for the mosquito.  The outbreak of the West Nile virus in 1994 was about a century ago since the 1894 Malaria in Greenwich started a mosquito war against them that included filling in salt ponds and salt marshes as a health department directive.  It might be hard for some to realize this, but in 1895 Connecticut declared salt marshes a public health hazard and towns and cities (such as New Haven) formed civic committees to organize funding and fill them in.  It was a public policy and a “civic duty” to do so in this heat and dreaded disease period (See IMEP #16: Mosquito War Claims Connecticut Marshes 1901-1915, posted May 29, 2014, Blue Crab ForumTM) (See David Casagrande account titled The Full Circle! A Historical Context for Urban Salt Marsh Restoration).

As megalops larvae filled plankton net tows in the 1990’s I was perplexed by so many have different stages or species. Was this a lobster, a blue crab megalops, or rock or spider crab?  And we have many crab species here: fiddler, green, purple marsh, oyster an invasive “shore crab,” lady crab, rock, etc.  This made it impossible to identify them.  In August 2017, the University of Connecticut announced that Dr. Weiss had completed his key to larvae of common decapod crustaceans and the notice is printed later in the newsletter.

This guide will help any student, researcher, or megalops reporter who wants to try to see this stage to do so.  It is a great reference and one that held back development of classroom curricula, but no longer (See Megalops Report #1 January 2012, posted February 28, 2012 for a description of sampling equipment).  Teachers in many classrooms now have a guide to bring the blue crab/lobster megalops lessons into the classroom with a modest microscope.  It is a remarkable achievement that we allow a much more detailed look at climate cycles by looking at the megalops - my view, Tim Visel.

Blue Crab Waves in the Connecticut River

By the time Megalops Report #5 was posted, the waves of blue crabs leaving the CT River turned into a flood on October 8th, 9th and 10th, I noticed catches increasing 6 to 8 crabs per hour, but the early fall was so warm I thought it a bit soon.  On October 7th, I had a great talk with CT Crabby Crabber so I thought about dragging those handlines out; a few hours later I did.  The migration lasted 5 days, peaking on Monday, October 10th during the rains.  I was able to catch 55, mostly rusty and yellow face crabs.  The crabs were hungry and the cut mix of menhaden and mackeral (leftover blue fish bait) was irresistible in the VexarTM bait bags.  It was easy to see how effective they were; the crabs would not let go!  I felt bad for those with the chicken bait on the dock, so I gave about 20 crabs away at the dock, including three doubles and one triple as compared to just one with chicken.  I use handlines mostly.  So it is only when crabs hang on is the VexarTM effective, but the migration was very short.  The following weekend I invited Sound School staff and students to the Essex Town Dock for some “excellent crabbing” and could not catch one crab!  CT Crabby Crabber was with me and saved the day with a female crab so I could demonstrate my bander to my guests (a bit embarrassing for me not to be able to catch one crab, especially a few days before I was giving them away).  On October 15th, I obtained reports of blue crabs massing at Griswold Point, and a day later massing along the South Cove Old Saybrook causeway. 

But that is how the last season was at times – if the crabs were there and hungry, a good catch can be made.  But many times, crabbers were telling me this year was no comparison to years past and I agree; it was not as good.  Many reports just asked “Where are the crabs?”

We needed to see a good fall megalops set and it just did not happen.  I was optimistic but the cool waters most likely slowed development.  A megalops set could have happened but went unnoticed.  The cool waters, however, were great for the fish, and the difference quite noticeable.  Cooler waters hold more oxygen and menhaden could live in the very shallow water – much to the surprise to those who witnessed fish kills the summer before (See Brown Waters Menhaden Fish Kills and Blue Crabs, posted October 6, 2016, Blue Crab ForumTM New England Crabbing Resources).

That did not occur this year.  Waters were cool and oxygen-rich, temperatures were by my records 7 degrees cooler at Essex in the spring (June) and the increase in peanut bunker throughout Long Island Sound is another sign that our waters are cooling.  Later in summer, waters did warm but were not “hot” as they were six or seven years ago.

Maine Confirms Temperature Drop

The Working Waterfront (December 2017) in an article confirmed a 1oF inshore drop, small but a drop nonetheless.  The wind and storm pattern has changed and the NAO going into measured pulses that appear to be the source of three warm falls and cool springs.  For Long Island Sound, its shallow basin warms and cools faster; it is the carry over from the previous summer as a gradual trend in water temperatures.  We can see this impact when crabs are out and feeding in May.

While in 2016, the crabs did not appear at all (Connecticut River Blue Crab Fishing Fails, posted September 1, 2015, Blue Crab ForumTM New England Crabbing Resources).

An Interesting Catch

I was enjoying some very good crabbing (I release all the females despite the terrible statistics around egg survival rates; I figure it can’t hurt).  I check the abdomens and release them so I was more than a bit surprised packing up six crab packages (banded claws of course) to give away and I noticed the crab had red claws – perplexed because I check carefully, but the crab had a male abdomen, yet female claws.  I brought it in for Christi Dimon, our fish production staff of The Sound School’s seawater system, but it did not live long.  We estimated temperature shock but sent pictures to Matthew Ogburn at the Smithsonian Environmental Research Center.

Then I noticed I was not alone.  At least two other crabbers posted on the Blue Crab ForumTM the same thing - blue crabs with a male body and red-tipped female claws.  Perhaps some other CT River crabbers notice the same thing?  Anyway, some checking revealed that these blue crabs have been caught before, but many years ago and years apart.  But three such crabs caught within a few days of each other, I am stumped.  Perhaps someone knows more about these crabs?

UCONN Announces the “Weiss Key” for Megalops

I can recall Paula Daddio, a teacher here at The Sound School, reviewing her new teaching assignment of Aquaculture Science course in 1998 and told me she just needed one thing, the Weiss Key.  This was a textbook written by Dr. Howard Weiss, who started the high school program Project Oceanology, which continues today at the University of Connecticut Avery Point campus.  This key to Marine Animals of Southern New England and New York, published in 1995 with 344 pages and hundreds of diagrams, continues to be the backbone of Aquaculture Science today at The Sound School.  It is an incredible resource and every few months, I pull out my copy to check.  Paula Daddio and I still have our copies.

That is why when I learned a few years back Dr. Weiss (known as Mickey to many) and started a guide to crustacean megalops we would soon have an instrument to help assess species/temperature change in Long Island Sound.  One of the things I learned by studying this stage is that they look alike, and sometimes, a mosquito megalops is hard to distinguish from a lobster megalops as being of course in the insect family (This is why the use of insecticides continues to be a concern to lobster fishers – I myself was exposed to insecticide mortality of several crab species on Cape Cod and strongly suspected years ago at Tom’s Creek in Madison, CT) (See Blue Crab ForumTM Report, December 2010, Pesticides and Blue Crabs).

“Keys to the Larvae of Common Decapod Crustaceans in Long Island Sound,” is a 48-page guide to the early life stages of lobsters, crabs and shrimp, was published this spring by Connecticut Sea Grant and Project Oceanology.  Written by Howard “Mickey” Weiss, Project O founder and senior scientist, it includes black-and-white drawings identifying the main parts of the anatomies of various decapods, as well as color photos of more than a dozen species.

To purchase a print copy for $8 plus shipping, contact Andrea Kelly at: [email protected].  Please reference the title and publication number CTSC-17-09.

Questions About Dredging

Megalops Report #5 was out within a few days of the North Cove Old Saybrook dredging announcement.  Earlier in the fall, Sound School teacher, Kirk Kehrley, and I experienced a great blue fish day at Hammonassett Beach; we each caught 8 blue fish.  We also watched the barge/pump approach the West Beach section of Hammonassett Beach.  I had heard that the Housatonic River needed to be dredged from the hurricanes pushing a sand bar wave into it.  This happened in many areas.  In warm areas with few storms, sand bars and barrier spits grow.  In cold storms, they do not.  The shift in storm/temperature over times seals coves and rivers.  I had many pictures sent to me of a breach into Goshen Salt Pond that had been sealed all summer.  Once breached the sand bar open and water flowed out and with it thousands of blue crabs.

The question has been raised about the impact of dredging on marine life and contrary to what has been published, more of our Connecticut dredging projects are removing Sapropel, the black sulfide-rich jelly termed “black mayonnaise.”  This material, in heat, sheds tremendous amounts of ammonia toxic to sea life.  It is actually good to remove Sapropel from low energy shallow water.  The sand from the Housatonic River is mixed with Sapropel – organic compost rich in iron sulfide and therefore black.  In a few weeks it will bleach, but a year later the sulfide stain remains (handling black mayonnaise will stain your hands) and it will appear to be a light gray.  The project was needed and earlier suggestions of a submerged granite reef (mid 1980’s) was not done, and eventually the beach would become two beaches, threatening to re-open Dowds Inlet/Creek, cutting the beach in half towards Webster Point.

Removing this deposit can, at times, improve fishing.  A complete review of this material is found in the appendix.

The Blue Crab Morning Sulfide Events

Many crabbers decided to crab at night and very early in the morning during the oxygen minimum.  On hot nights in marinas and dredged channels, oxygen levels can bottom out on the bottom.  If these areas are dredged, they form a natural “compost trap” for sticks, leaves, bark and grass clippings that settle and rot.  It is a natural marine compost that complexes with iron to form the black ferrous sulfides, and iron carried by water helps form the black color of deep marsh peats or surface deposits termed “black mayonnaise.”  Pyrrhotite, for example, is the product of a sulfate-reducing bacteria and the group termed desulfovibrio bacteria.  The Blue Crab Jubilees to our south are extreme sulfide/bacteria events; the lack of oxygen at the bottom fuels sulfate reducers that fill the waters with hydrogen sulfide and the smell of sulfide rotten egg odors.  In time, the water chemistry changes to sulfide/ammonia.  Fish flee and blue crabs walk from the water (easy catching, thus the term “Jubilee”), but it is not a great long-term seafood event.  Fish that cannot swim out die and contribute to “black water” as any remaining oxygen is used up.  Black waters are toxic (no oxygen) and can cause fish kills as it flows or drifts to other areas, giving an expansion in this fish kill event.  But on intercoastal waterways or dredged channels, jubilees happen on a much smaller scale, out of sight to all except the nighttime blue crabbers.  The tendency in early morning for blue crabs is to “leave” the bottom, advance to salt marsh grass or cling to poles/pilings.  They do that to leave the bottom as the scent of sulfide occurs at low oxygen concentrations just before dawn.

At the turn of the century, torch lighting blue crabs in Noank was a popular activity in the 1890’s. Its coves in heat (especially after 1896) emitted the late night marsh stinks of sulfides, which made for great blue crabbing, but it is toxic to larval stages.  The other response is for blue crabs not to move, making low tide “scapping” (no bait, just a net) an effective harvest technique.  But today those torches or lanterns are replaced with powerful flashlights or “eyeball” headlights.

It is these late night low-oxygen events that allow sulfides to build in poorly flushed areas “dead spots” (no current).  Algae, that in sunlight helped replenish oxygen, sink to the bottom bacteria that do not need oxygen or those that scavenge other oxygen compounds all contribute to low oxygen condition and sulfide “smells.”  Blue crabs contend with this change by just moving to the surface where there is a little higher oxygen level, and wishing to preserve metabolism, just cling onto something.  In 2011, this occurred in Westbrook, CT and each pole at a local marina had dozens of crabs on each piling (boaters who came in late at night from striper fishing often report blue crabs even clinging to dock lines).  And when it comes to sulfide, ammonia also produced in high heat, it is so toxic that just a little can be deadly.

“In a 1987 article titled “More Development of Norwalk Harbor: A Muddy Issue” by Richard Harris (Norwalk Hour, October 26, 1987) states that ammonia is extremely toxic that at only .4 to2.3 part of ammonia per million will cause death to many crustaceans (blue crabs).”

Black Mayonnaise and the Blue Crab

Florida Acts to Limit Sapropel Buildups – Florida Institute of Technology Video Release

As it is known throughout the country, black mayonnaise in heat is a real seafood killer.  Not only does it suffocate marine soils that once held clams and oysters, it can foster some of the most dangerous seafood foes, the Harmful Algal Bloom cysts of red tides (also brown tides), parasites and blood flukes.  And what has caused harm to us and our seafood here in New England and other areas the deadly sulfides and bacteria Vibrios.  Sapropel dominated in heat by sulfur reducers and in cold humus by oxygen requiring bacteria has two habitat profiles, in cold and oxygen, the good and in heat and sulfate, the bad – the Blue Crab Sulfide Jubilee.  It has the ability to measure chemical climate change and provides us with what happens when the sulfur cycle returns.  And it is not a pretty picture and is the reason why some states have begun to remove it and reuse this putrefied compost – the byproduct of sulfur bacteria and the generation of sulfides and ammonia.  Researchers in Connecticut suggested mapping Sapropels in 1985.  One of the factors associated with Sapropel (high heat sulfur composts) is that it has never been identified as a habitat type subject to temperature as its terrestrial relative organic “compost” has.  But agriculture researchers determined decades ago that sealed compost removed from oxygen leaked ammonia and that aerated compost exposed to oxygen yields nitrate.  But that knowledge did not make it into the marine field or into much of our science knowledge of inshore fish and shellfish habitats as sulfate reduction and sulfide root rot.  But Florida (much led by my old Oceanography school, The Florida Institute of Technology) is trying to educate the public about it.  It is an educational challenge in its own right.  Sapropel has some 30+ different terms and never has been clearly explained to the fishing public (my view – Tim Visel).

That is changing, thankfully and Dr. John Trefry is putting that message out for all fishers to see in a video clip titled “Running Amuck Our Six Decade Legacy to the Indian River Lagoon.”  It is a must see – my view for fishers in all of our coastal regions – as it clearly details the ammonia-nitrogen discharges from it.  Sapropel is not new however to New England farmers.  For centuries, they harvested it for soil and salt marsh nourishment and as so soon learned the sulfur cycle connection in it.  Removed from oxygen, it formed a blue-black jelly like substance, rich in metals and some carbon/nitrogen residues; it was used as a soil conditioner.  It was soon learned about a sulfuric acid wash after land application, and farmers cut in oyster shells and, in Maine, lobster shells to neutralize this sulfuric acid reaction (If fishers want to see this reaction as well, please view the video clip titled “Violent Soil”).

This is a quote from a manuscript about hay fields and “flats’ mud” titled “Fish and Men in the Maine Islands” by W.H. Bishop (1880)
Reprinted from Harpers New Monthly Magazine by L. Berliawsky Books Camden, ME

“The Island farmer appeared to have certain advantages over him of the mainland farmer in one way … When the wind was to the eastward, the fog generated out to sea where the gulf stream touches the polar current (The Labrador counter current – T. Visel) making down from Baffin Bay … the steam of the water as he called it melted the snow and mitigated the severity of his winters.  His ground froze up about the first of December, and thawed out for cultivation about the first of May.  The principal crop as in the state of Maine in general way hay.  The Deer Island farmer thought it would be worth double all the others (crops Tim) put together … He put in his hands a top dressing of the refuse from the lobster factories, and also flats’ mud, which he found excellent.”

It is the sulfuric acid wash after Sapropel is mixed after strong storms or a hurricane for released and breaking apart Harmful Algal Bloom cysts red tides buried deep in it. 

The Florida Institute of Technology video clip is approximately 30 minutes long and well worth the view.

It is now thought that many diseases and parasites exist in Sapropel protected by an alkaline pH, much of that from the ammonia levels.  A storm in warm weather can aerate Sapropel and create a sulfuric acid flash, a period of low pH experienced on peat bogs that may “uncoat” or destroy the cyst protective coating, exposing it to warm water and sunlight seeding a HAB bloom.  Research in the state of New York has shown higher cyst counts in Sapropel (organic deposits) in low energy poorly flushed areas (See Studies of Northport Huntington Bay, Objective #4, Chris Cobler, EPA R/CMB-37 NYCT 2011).  And even here in Connecticut with some Mumford Cove Studies, which contain very deep deposits of Sapropel (termed Black Facies) that held red tide cysts. (A red tide cyst warning is still in place for Mumford Cove).  It has been know for decades that the mud snail vectored the blood fluke (worm parasite) in muck deposits termed clammers or swimmer’s itch.  It is now becoming known that deep organic deposits with a vegetative crust holds some of the dangerous Vibrio bacteria series, and at times, blue crabs in contact with Sapropel are known to have Vibrios, which are destroyed by high heat cooking.  Although members of the public have concerns about dredging, it is in fact a way to reduce Sapropel and lessen the chance of this deposit becoming a culture media for disease. (Interested fishers should look at New York Studies, which point to large numbers of cysts in poorly flushed areas).

The hibernation of the blue crab in winter is a good example of how cold and oxygen change this substance by the bacteria that lives in it.  The cold allows crabs to overwinter before the heat of summer and chances of a sulfide kill, they leave it.

That is why, after dredging, flushing is increased, cooler water has more oxygen and reduces the chances of sulfide buildup (any sulfide is quickly dispersed by tides).  It also helps explain the after dredging fishing can improve as sulfur-reducing bacteria dies off.  In fresh water dredging projects, many noted impacts to fish are positive.  The fish and habitats monitored, however, in the marine waters post-dredging monitoring is rare.  We should take advantage of the blue crab life cycle and monitor the chemistry of bottoms in which it spends so much time. 

Knowing more about the chemistry of hibernation habitats is key to understanding the blue crab population changes from temperature and energy – my view, Tim Visel.


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.

“John Trefry FIT Sediments in the Indian River 1987”

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

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. 

“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 get to be quantified.”

“And further (when the natural system 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:

“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.”

Finally, researchers in the 1980’s debated the importance of benthic flux, which differed in hot or cold conditions, and in time, decided to count it out (It was difficult to measure “hard” organic nitrogen locked up in leaves) or at times gave it a zero value.  Many recent nitrogen studies minimize benthic flux and do not recognize the formation of humus or Sapropel in very hot conditions.  Even today, there is conflict between carbon transport in or out of estuaries with those that carbon transport is in from dead algae – or out deposits from land nearby and give rise over the past century if the terms autochthonous denoting “close by” or inhabitant of a place allochthonous meaning sources from outside the area. 

This is an abstract from a paper looking at the movement of carbon in and out of estuaries (Connecticut) in 1987.
In the 1980’s, winter flounder and bay scallop fishers were the first to notice the buildup of Sapropel (humus) called black mayonnaise in the coves and bays of Waterford, CT, namely Alewife Cor, Jordon Cove and the lagoon portion of the Niantic River between East Lyme and Waterford.

“Relationship Between Physical Characteristics and Organic Carbon Sources as a Basis for Comparing Estuaries in Southern New England” B.L. Welsh, R.B. Whitlatch and W.F. Bohlen, Department of Marine Sciences, University of Connecticut Avery Point, Groton, CT – See Estuary Comparisons Victor S. Kenney, 2013, pg. 53.

“Lateral imports of terrestrial litter are known only for the Connecticut estuaries and all quantification was done in Alewife Cove (Welsh and Whitlatch, 1980)” (If an environmental fisheries history (a frequent Capstone proposal) had been done, it would have indicated that 100 years previous it had oyster culture and before then, sustained a large alewife run – T. Visel).

The two bacterial pathways, one in oxygen and one with sulfate, would cause conflict in the research community, resulting in two “counter” papers about salt marsh ecology – that of the “high marsh” focused upon the oxygen-nitrate pathway versus that of the “low marsh” focused upon sulfate bacterial processes that generated ammonia.  Both viewpoints resulted in research bias claims (See The Ecology of Regularly Flooded Salt Marshes of New England, Teal, 1986).  Here in the high marsh peat soils were exposed to oxygen however in the submerged soils – oxygen shortfalls opened the sulfate pathway to ammonia.

“With respect to contributions to production by autochthonous carbon (present position or nearby) Nixon (1980) received a broad range of research dealing with the net exchanges of carbon between tidal marshes, estuaries, and coastal waters, and showed results from study to study were highly conflicting.”

These imports were only 2% to 3% autochthonous (nearby) productivity, but they may exert a disproportionately influence on the inner basins of these estuaries where they become trapped and decompose slowly (restricted flushing, Tim Visel).  Whitlatch, unpublished, has determined that oak (presumed to be oak leaves, Tim Visel) comprises the bulk of the imports (Welsh and Whitlatch, 1980) and requires 3 to 5 years to decompose, which is about 33% longer than in adjacent areas.  About 50% of the bottom debris was material from previous years.  There does not appear to be a high BOD associated with the leaf debris (P. Herry, University of Connecticut, unpublished) probably because of its slow decomposting rate” (true for cool water oxygen-rich waters – T. Visel).

This is the “flux” described by the bacterial pathways, which in a cooler period, oxygen-nitrate pathway dominated.  Others urged estuarine researchers to look at outwelling and consider high temperature sulfate metabolism (Teal and Haworth, Limnology and Oceanography 1979, Vol. 24, Number 6) that could generate ammonium but the oxygen viewpoint held out, the authors continue below:

“As noted in the introduction, the quantification of tidal fluxes (nitrogen pathway of oxygen or sulfate – T. Visel) is a controversial issue (Nixon, 1980).  There are indicators, however, that the tidal impact of particulates (duff and leaves – T. Visel) could be substantial for southern New England estuaries.”  The asymmetries have been modeled as a phenomenon called tidal choking, which is characteristic of basins with small, constricted inlets (Glenn et al, 1971).

These characteristics occur to different degrees in Bissel Flax Pond (Woodwell et al, 1977), Jorden Cove (Welsh, 1978) and the Niantic River (Kollmeyer, 1972).”

In time in heat and less energy, fewer strong storms, the sulfate-ammonia pathway of bacterial reduction would become more than a “flux” but purge millions of tons of nitrogen as ammonia into coastal waters as many recent nitrogen reports mentioned benthic flux as minimal or nonexistent.

In a 1979 article (referenced above Limnology and Oceanography 1979, Vol. 24, Number 6, pg. 999-113), Robert W. Haworth and John M. Teal provide a caution to underestimating the impact of sulfate reducing bacteria.

“The major forms of anoxic respiration are denitrification, (oxygen bacterial nitrate – T. Visel) sulfate reduction (sulfate bacterial ammonia – T. Visel) and methanogenesis (bacterial chemical reducers – they require no oxygen at all, T. Visel) and produce methane as a byproduct gas.  Denitrification in the great Sippewissett Marsh accounts for only 12 grams of carbon per meter per year (Kaplan et al, 1979) and our preliminary measurements suggest that the export to the marsh is small.  Recent studies have shown the importance of sulfate reduction to the metabolism of benthic communities.”

In the decades that followed, the cautions of Haworth and Teal largely went unnoticed or were ignored by estuarine researchers as New England’s waters warmed and oxygen naturally became “limiting.” When that occurred, sulfate reduction would dominate the bacterial spectrum, creating a surge in ammonia that was frequently assigned to human inputs.  In fact in some major nitrogen reports, benthic flux was not even considered, creating opportunities for many student research projects relating to sulfate metabolism.  Many current nitrogen reports fail to include sulfate-reducing bacterial processes even though they were detailed by researchers, including George Wilton Field, a century before.

In a period of heat and low energy, the amount of leaves entering estuaries by heavy rains would overwhelm bacterial processes and flood estuaries with ammonia.  “Tidal choking” would hold these deposits in warm oxygen poor waters, and by doing so, helps to form Sapropel.  This is the rise of soft bottoms (black mayonnaise) noticed by so many winter flounder fishers and a signal for massive habitat change for numerous fish and shellfish species.  The first signal of high sulfide formation from Sapropel processes is sulfide rot failure of submerged aquatic plants, especially eelgrass Zostera marina.

Before the eelgrass die off (a largely natural sulfide cycle), it held organic matter and resulted in a “tidal choking” process as it reduced tidal flushing.  Eelgrass grew so dense as to reduce tidal flushing to such a point that explosives were used to remove it in an effort to restore tidal circulation.  It had also allowed thick ice to form in areas known to retain hard bottom bay scallop seeds, and as eelgrass increased lessened bottom depths, bay scallops disappeared.  The holding of organic matter and “tidal choking” is also illustrated by the Indian River Lagoon, similar to the Niantic River extended residence time of tidal exchange of 27 days.

From Ludwig NOAA National Marine Fisheries Service, Milford, CT:


Michael Ludwig
Environmental Assessment Division
National Marine Fisheries Service
National Oceanic and Atmospheric Administration
U.S. Department of Commerce - Milford, CT 06460

“During the 1930’s, eelgrass (Zostera marina) was subjected to a wasting disease that caused extensive dieoffs of this rooted marine vegetation.  The thallus structures of eelgrass had been found to be a primary location of bay scallop (Argopectens irradians) larval setting prior to their establishment on the bottom within these vegetated areas.  It was, therefore, expected that as the eelgrass beds died out bay scallop populations would decrease.  This expectation was realized along the coastline with the possible single exception of the Niantic Estuary.  Located in Connecticut’s eastern-most New London County, Niantic Estuary is almost entirely land-locked, is relatively shallow, and has minimal freshwater input.  Nutrients are supplied to the area primarily from upland runoff and a tidal prism that cycles approximately 51 percent of the estuary’s low water volume.  However, the residence time for a water particle from the northern area of the estuary is approximately 27 days.  This is quite long for the small size of the water body, but the restrictive opening and resulting poor flushing characteristics of the outer bay area cause such a drawn out exchange.  The reduction in plant biomass induced by the eelgrass disease allowed, within the area, and a more thorough flushing and creation of a tidal gyre in the upper reaches.  The gyre appears to have acted as a passive maintenance system for larval bay scallops while providing a more thorough mixing of waters in this upper estuary region.  Marshall’s 1960 discussion of this situation describes the scallops as setting on red algae in the absence of eelgrass within the estuary.  Apparently the algae served as a suitable substitute for the destroyed eelgrass.  As eelgrass reestablished itself along the coastline it also revegetated the estuary and had, by the early 1960’s, extensively reduced the tidally-generated gyre’s persistence and mixing capabilities.  During this same period bay scallop production suffered a serious decline.  Compounding the reduction in numbers of juveniles the area experienced a series of concurrently occurring harsh winters which had caused the almost complete exclusion of bay scallops from the area.”

At times in the late 1960’s, eelgrass would grow so densely as to suffocate clams and trap organics that could cause sulfides to build in the organic matter below.  Eelgrass, at times, could cause bay scallops to “starve” and result in low weight meats.

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

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

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

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

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

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

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

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

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

All blue crab observations and habitat reports are very important, thank you for any reports. I respond to all emails at [email protected]

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« Reply #1 on: February 18, 2018, 08:14:04 AM »

You're over analyzing all this  . Just go crabbing and enjoy yourself.


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