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Author Topic: Natural Nitrogen Bacteria Filter Systems- Tim Visel Oct 30-2015  (Read 3354 times)
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« on: October 30, 2015, 09:29:22 AM »

Natural Nitrogen Bacteria Filter Systems -
Blue Crab Forum™ Environment and Conservation #8

Tim Visel, The Sound School*
60 South Water St, New Haven, CT   06519
January 2013
October 2014
Revised October 2015
Capstone Questions –

•   Are Natural Filter Systems for Ammonia Now Linked to Bacteria?
•   Should we have another look at Organic Nitrogen Sources for Fisheries Habitat Quality? (The Blue Crab Jubilee Factor)
•   When it Comes to Nitrogen – Which Bacterial Reduction Pathway is best for Finfish or Shellfish?

ASTE Performance Standards – Aquaculture #4, 5, 6
ISSP Capstone Bacteria Experiment
FFA Non Experimental Research SAE - Part A
Natures Natural Nitrogen Bacteria Filters

Note from Tim Visel October 2015
This paper was started in 2012 and is the third seafood/nitrogen caution in two years.  Since that time more information has come in about nitrate as a secondary source of oxygen in waters containing organic matter.  This oxygen source was important in buffering or preventing sulfur reducing bacteria (SRB) from overwhelming those bacteria strains that need oxygen as indications now point to sulfur reducing bacteria as being very deadly to larval forms – shellfish eggs and fish larval species.  Warm organic matter is now linked to increasing antibiotic infections in crabbers, swimmers and shore residents.  Some of the most antibiotic resistant strains are linked to these shallow warm waters, organic matter cultures them much the same as a bacterial lab Petri dish – The Blue Crab Forum™ science thread has a post labeled marine bacteria and a series of fisher comments about these bacteria.  The research community has been slow to address this issue (my view) although lobster and winter flounder studies have mentioned them as flounder flesh eating or lobster shell wasting disease but very little information has been made available to fishers although bacteria in water has long been utilized in closing bathing beaches for swimming.  Bacteria is also the framework for the shellfish industry but very little has been written on these dangerous bacteria strains – fishers it seems are on their own when it comes to this situation (my view).  Blue crabbers and recreational shellfishers are perhaps the groups that experience these bacterial strains the most in sulfide rich Sapropel deposits.

The high heat with reduced oxygen levels and the role of nitrate as an “emergency” supply of oxygen for the “good bacteria” is now being recognized.  Nitrate has long been recognized as an oxygen source to keep waste water bacteria treatment filters “alive” and functioning.  When oxygen is short or absent nitrate it is a “life line” for filter bacteria and a consequence of its removal now subject to bacteria reduction by SRB with the presence of sulfate.  Sulfate in seawater is not short or “limiting” and is a ample oxygen source for sulfur reducing bacteria – available oxygen can be scarce or non existant and sulfur reducing bacteria – use sulfate as part of the sulfur cycle with its deadly impacts to oxygen requiring life forms.  There can be no “available” oxygen and sulfur reducing bacteria will be quite fine as they slowly consume organic deposits with sulfate as an secondary “oxygen” source.  They have plenty of sulfate, I have been told that the sulfur cycle isn’t covered that much anymore which is surprising considering all the concern about sulfur compounds in a warming global climate.  The sulfur cycle in shallow water has huge consequences for fishers worldwide.

Much of the nitrogen cycle over laps the sulfur cycle in areas that obtain organic matter from land.  These are often described as important fish and shellfish “nursery habitats.”  In shallow seas, coves and bays the sulfur cycle is most likely more important – as shallow seas warm the quickest (including coves and bays) then tend to have lower oxygen levels and suffer periodic sulfur benthic events – such as blue crab jubilees in more southern regions.  I will always be thankful for an excellent tour and discussion of mobile bay and its blue crabs provided by Joe Schwartz in 1990.  Blue crabbers in shallow waters of Mobile Bay have experienced this sulfur cycle Jubilee event many times.  A major interstate that crosses Mobile Bay Route 10 is called the “Jubilee Highway”.  That is why.

More information is coming to light that nitrates and to some extent nitrite support natural bacterial strains that counter the most damaging impacts of sulfur reducing bacterial products, toxic sulfides and ammonia – and as time goes on methane.  Fisheries experience these discharges in shallow areas, they are important feeding and nursery grounds for many shellfish and finfish species.  They (fishers) have long warned us (public) about them – blue crab jubilees (almost always in hot weather low energy conditions accompanied by the smell of sulfur) or black water deaths – extreme sulfate reduction (fish kills) after the closure of barrier inlets.  Such sulfide events have been known to react with houses (paint) staining them black.  Coastal residents are not strangers to the sulfur cycle – fish kills are very familiar to the sulfur cycle products fish kills on hot nights are frequently accompanied by the match stick or rotten egg sulfur smells.  Some of the most documented cases of sulfur discharges have come from eastern Long Island New York with the Duck Farm industry there and made worse by heat and a lack of energy (tidal flushing).  This 2009 US Army Corps of Engineers report clearly describes these Sapropel deposit impacts.

Long Island Duck Farm History and
Ecosystem Restoration Opportunities
Suffolk County, Long Island, New York

February 2009

US Army Corps of Engineers
 New York District

 Suffolk County, NY

“The increase and decomposition of organic matter, derived directly from the duck waste as well as the increase in algal biomass, contributed to anaerobic benthic conditions impacting flora, such as submerged aquatic vegetation; and fauna, such as benthic invertebrates and foraminifera.

Dense algal blooms prevented light penetration to the benthos, causing plant decay and
additional organic deposits (O’Connor 1972). These organic rich sediments, often several feet deep, became soupy, black, clayey silt that had a rich odor of hydrogen sulfide, so potent that homeowners adjacent to Moriches and Great South Bays complained that the paint on their homes was being discolored (Nichols 1964; O’Connor 1972). Ecological degradation that was associated with the accumulation of nutrients throughout the estuarine bays continued throughout the history of the duck industry, and was heightened when the Moriches Inlet was temporarily closed (Nichols 1964; Lively et al. 1983) in the early 1950s.”

Often short in duration sulfide kills are extremely deadly to fish and shellfish eggs.  Fishers frequently report the sulfide kill or dead line in salt ponds, or the build up of Sapropel over previously hard bottoms.  All of these factors are related and connected by bacteria, the unseen force in marine life abundance.
Sulfur and sulfate reducing bacteria should have a key role in warming (cycles) along the coast – until this point they have been neglected (my view).

Introduction to ISSP – Capstone Proposal – Two Nitrogen Pathways

We have two very different bacterial respiration pathways or processes.

The “short” nitrogen cycle occurs in cooler water – bacterial respiration (these bacteria “breath” oxygen) reduces organic matter and aqueous nitrogen in a process called denitrification which simply means into nitrogen gas because it is not in a “ready” form or available for plant nutritional purposes.  The long nitrogen cycle (or I sometimes call this the Sapropel/ammonia cycle) is an oxygen limited pathway and nearly always found in hot situations (cycles) which has a much different type of bacteria.  Sulfur reducing bacteria are ones that purges ammonia (nitrogen) now instead of changing nitrogen compounds into a plant “unusable form” it fixes nitrogen and produces toxic ammonia, the nutrient that feeds brown algae blooms.  (That is why in the recent hot period of Long Island Sound the “browns” often dominated shallow waters).  As Long Island Sound waters warmed from the 1960s a colder water then supported the algae termed “greens” – those that needed nitrate as a nitrogen source – reversed with brown species.

Chlorella algal blooms in Long Island Sound for example were noted to be immense by shellfish researchers working at the US Fish and Wildlife Service Lab Milford, CT (today the NOAA Milford Aquaculture lab) in the 1950s.  (There was so much green algae in Long Island Sound National Geographic Magazine covered it in 1957). The short cycle was so efficient researchers in the 1950s felt that Long Island Sound was in fact at times nitrate limited – and even the wastewater treatment plants were looked as providing key nitrogen levels amounts (A viewpoint certainly not shared in recent times).  The 1950s and 1960s are now recognized as being a negative NAO climate pattern colder and containing many more powerful storms.  But what made the short cycle so rapid and efficient was the presence of oxygen.  This occurs on land as well, it is recognized that it takes a century or more to produce an inch of organic rich “topsoil.”  This is the result of a oxygen sufficient bacterial reduction (organic matter) pathway quickly recycling organic matter back into plant material.  It is so “efficient” it takes centuries to accumulate.  The long nitrogen cycle, the Sapropel/ammonia cycle is not efficient it is very slow, organics can build rapidly and purge toxic substances for decades.  Productive fishing spots become “foul” and often reported in the historical fisheries literature.

People who garden and compost experience those bacteria cycles as well and why the long “sulfur” bacteria pathway is discouraged on land as these bacteria breathe sulfur, they require it and it even on land produce toxic substances.  To prevent the “long cycle” in these terrestrial composts they are simply “turned” introducing oxygen for those bacteria species that need it.  Nature turns the marine composts as well by Hurricanes and Northeasters.  Farmers experienced the sulfuric acids that came from exposing this long cycle compost to air in oxygen it developed a “hurtful acidity” offset by lobster shell waste in northern maritime's and oyster and clam shell in the south (Southern New England).  When it was introduced to oxygen it purged sulfuric acid and without shell mixtures it “killed all crops” on land applications {detailed accounts exist from Essex CT from local producers of Sapropel from North Cove Essex (IMEP #26) Connecticut Rivers lead Sapropel Production 1850-1885).

The trouble with recent nitrogen TMDL is that nitrogen reduction programs targeted the short cycle – not taking into consideration it appears warming waters that would naturally contain less oxygen and forgot (my view) about the long Sapropel/Ammonia cycle with sulfur reducing bacteria often termed today as “benthic flux.”  But in times of great heat and tremendous organic input (mostly tree leaves) the long cycle would soon dominate the nitrogen near coastal profile. 

Shellfish surveys in Niantic Bay CT with Robert Porter, T. Visel 1985-87 found huge areas of decayed oak leaves in the upper lobes of the Niantic River in 1985-87 (see appendix #3).  As short cycle bacteria died off and were replaced by those that breathed sulfur as ammonia levels now soared supporting browns or “harmful” algal blooms.  In areas that were poorly flushed, such as salt ponds coves and harbors ammonia purging from this warm marine compost (often with an eelgrass crust) increased (properly termed now as Sapropel) and nitrogen levels were concentrated as tides sloshed these ammonia compounds in and out for days at a time (called residence time or occasionally the flush out time).  In other words some ammonia concentrations were perhaps counted over and over again and identified as agricultural or human source nitrogen – when it was from sulfur reducing bacteria composting organic matter into Sapropel?  We just don’t know if that occurred because many studies forgot the impact of Connecticut’s restored forest canopy as a nitrogen or phosphate source from organic deposits.  It was often not included in nitrogen studies – organic matter trapped behind dams or restricted causeways railroad and bridges were not included or “under represented” in the field of work pertaining to nitrogen studies that proceeded many TMDL determinations.

For students wishing to conduct a SAE – FFA non experimental research in this area we have three excellent case histories regarding organic mater sulfate reduction now available on the internet from three states, they include:

Long Island Sound CT – NY   Did Sapropel and ammonia generation get
The Duck Sludge Account    underestimated during recent warming 1982-2012 Eastern New York coves and coastal bays included.  Can reports be identified that detailed this leaf or manure compost – see the Duck Sludge – Meeting House Creek Study – New York

Guilford “Lost” Lake – (CT)   An example of sulfate reduction that has reduced a former salt marsh to organic constituents including ammonia and is now open water - Is Lost Lake a Nutrient Polluter in high heat?  Where did the salt marsh go?  (Leetes Salt Marsh system)     
Wellfleet Herring River – (MASS)   Did sulfate reduction produce sulfide and aluminum levels so strong it killed alewife trying to return for spawning?  Where SRB (sulfur reducing bacteria) responsible for sulfide or aluminum alewife blocks?  For example Connecticut has recently installed many fish ways before construction were streams cleaned of leaves or brush – were sulfide and aluminum levels determined?  In high heat were they monitored?

Capstone question –

After reviewing the literature available for these three case histories did we take out
the wrong nitrogen when it came to shellfish and finfish habitats?  (Students that
want to look at this for ISSP credit review the bacteria Nitrogen reports Blue Crab Forum
Environment and Conservation thread 1 to 7).

SAE – FFA Non experimental research forms are available in the Aquaculture Office
ISSP proposals from are available from The Sound School ISSP Coordinator in Student
Services.  One half credit (January 15, 2016 deadline) full credit March 2016 for the 2016-
2017 school year.
Environment and Conservation – The Blue Crab Forum™ - Bacteria Nitrogen Series
I want to thank the Blue Crab Forum for allowing me to post in a new thread – Environment and Conservation and also Connecticut Fish Talk for reposting these reports. This is my eighth report about bacteria and nitrogen cycles.  Coastal habitats once praised for valuable habitat services are impacted by bacteria and at times become nature’s killing fields, eliminating critical nursery and spawning grounds for many inshore fish and shellfish species. Coastal fishers often observe these events, mats of bottom bacteria, chocolate or purple waters, brown tides, blue crab jubilees or just fish kills. Beyond these public events bacteria and nitrogen change the habitat qualities that we recognize today as “good” onto something that is “bad” for inshore fish and shellfishing.  Out of sight and rarely discussed, these conflicting bacteria strains have important implications for estuarine health and seafood production worldwide.

   #8 Natural Nitrogen Bacteria Filter Systems 10/20/2015
   #7 Salt Marshes a Climate Bacterial Battlefield 9/10/2015
   #6 Bacteria Disease and Warm Water Concerns 7/23/2015
   #5 Nitrogen, Inshore Habitats and Climate Change 1/12/2015
#4 Black Mayonnaise Impacts to Blue Crabs and Oysters 1972 to Present 10/16/2014
#3 A Caution Regarding Black Mayonnaise Habitats 10/2/2014
#2 Black Mayonnaise, Leaves and Blue Crab Habitats 9/30/2014
#1 What About Sapropel and the Conowingo Dam? 9/29/14

Fishers should follow this bacterial conflict as more and more information comes in regarding habitat quality and important recreational fisheries such as striped bass, winter flounder and blue crabs or lobster habitats are subject to bacterial impacts. It is also important that shallow water fishers be aware that sulfur bacteria contain a series of antibiotic resistant strains first identified in Contaminate Effects On Biota of the New York Bight by Joel, O’Connor, NOAA (1976).  Soft organics with bacteria do pose risks to fishers and bathers – coastal bacteria benthic monitoring programs are needed.

I respond to all emails at [email protected]
Tim Visel

Nitrate Reduction Removed a Key Sulfate Reduction Buffer for Toxic Sulfides – Did We Target the Wrong Nitrogen Compounds for Removal?

As more information is available from overseas (mostly Denmark), the removal of nitrite and nitrate in high heat facilitated the production of second source ammonia, in other words, it made low oxygen impacts only worse. In the marine environment during high heat, sulfur sediment reducers (bacteria) turn to nitrate when oxygen compounds are lowered (this is called limiting). Removing nitrate will allow sulfur-reducing bacteria to quickly access sulfate (electronic affinity), which is not limiting in the marine environment. Therefore nitrate reduction is now linked to increases in deadly sulfide/sediment formation.  Sediments with high leaf (organic) content purge sulfides in winter and shed ammonia compounds in summer, which is now linked to the toxic brown algal blooms termed Harmful Algae Blooms (HABs).  Apparently the availability of nitrate has long been a factor in aerobic digestion in wastewater treatment facilities.  “Aerobic processes are those which occur only in the presence of oxygen; anoxic processes occur then there is minimal oxygen but sufficient nitrate-nitrogen for biological respiration; and anaerobic processes occur when there is no oxygen or nitrate present.”  Source draft Alternatives Screening Analysis Report, Town of Barnstable Mass, Stearns & Wheeler 4-5.  Wastewater treatment operators are today familiar with nitrates as a “buffering capacity” of preventing sulfate reduction that could kill oxygen requiring bacterial filters.  Nitrite is now seen as important to a group of bacteria that utilized it to reduce ammonium.  This type of bacteria is called anammox bacteria other bacteria converts nitrate.  Blue crab shedding systems (often closed recirculating systems) built to facilitate soft shell crab production have long known about the good “filter bacteria” that grows on oyster shell (see Environment Conservation thread Blue Crab Forum™ report Bacteria and Nitrogen #6).  Just as in these blue crab shedding systems it takes time for natural bacteria filters to “build up” the same thing happens in our bays and coves.  We just can’t see it, but it happens.

Eelgrass and the Clean Water Act – Other Estuary Programs

In an attempt (it appears) to strengthen regulatory authority under the Clean Water Act, many state and federal agencies promoted eelgrass as a habitat quality indicator organism and linked excess nitrogen as a factor in seafood population dynamics with it.  As human caused degradation to the environment had much more of a regulatory “standing” lessening human nitrogen inputs became a key estuary health policy for eelgrass and seafood.  A widening investigation of the policies and procedures utilized in determining nitrogen TMDL has been found to be insufficient, (Great Bay New Hampshire nitrogen eelgrass report for example) and as it largely excluded non-human or “nonpoint” services and TMDL allowances perhaps compromised (Indian River Lagoon Program in Florida). Nonpoint source primary and secondary source nitrogen was omitted or minimized when in fact it had a huge role and warnings to that fact were first issued in the 1980s. We may never see the expected results from current nitrogen TMDL in fish and shellfish landings. This was confirmed in a GAO report issued last December (2013) and comments from overseas limit expectations of increases of shellfish and finfish because of the multiple stressors upon them – the combination of high heat and low energy favors for example Sapropel formation.  When that happens our human nitrogen feeds the good bacteria for natures natural filter systems – leading to a research question did we remove the wrong nitrogen oxygen compounds and may made a high heat//low oxygen condition only worse.  The answer to that question is now associated with multiple “stressors” and its just not a sole response from nitrogen.

GAO-14-80 Dec 2013 Report to Congressional Requesters

“The water resource experts reported that about half of the TMDLs they reviewed do not contain key features helping to ensure that implementations can be done, which leads to TMDLs that may do little to actually improve water quality,” pg 41 GAO-14-80 EPAs TMDL program.
“TMDLs without certain key features may be unlikely to help water bodies attain water quality standards and may potentially waste states limited resources” ibid – pg 64.

Temperature and habitat energy levels have a least if not more influence upon fish and shellfish abundance than nitrogen.  Early (NOAA Estuary of the month, Seminar Series #3, January 1987) Long Island Sound researchers did raise Sapropel monitoring questions and the negative habitat implications of it and into this very hot period organic matter accumulated and rotted in shallows.

The ability of bacterial “filter” systems to remove ammonia and nitrate to lower soil sulfides (Tampa Bay SAV studies) raises similar questions that waste water treatment operators asked.  The issue of our continued concentration on the oxygen/nitrate pathway instead of the sulfate/ammonia pathway for nitrogen was the focus of two previous nitrogen cautions (1) over time there appears to be little correlation between nitrogen and fisheries – a much larger driver is warm water – (Climate Change) (2) a focus upon aqueous nitrogen removal and an absence to organic matter impacts – especially a “phosphate flush” from leaf fall (Sapropel).  A third concern now and one that is certain to raise public policy questions – did we target and remove the wrong nitrogen compounds in high heat?

Since the 2012 nitrogen caution I have had some time to focus in on that, the third item high heat and organic deposition and from what I have able to determine in times of heat nitrite and nitrate are helpful to maintaining bacterial filter nitrogen stripping of ammonia capacity and the compound that is most damaging to seafood is in fact ammonia.  We may have reduced nitrogen but also nitrogen at the same time as nitrate and nitrate that are also secondary sources of oxygen as well.  We have two indications to look at, plankton assemblages and bacterial reduction in organic deposits for measures of this impact.
A colder Long Island Sound in the 1950s and 1960s for example supported immense green algal blooms that were important to bay scallops and quahogs.  Chlorella became so prevalent then it gained national headlines and needed nitrate from wastewater systems were then termed “good” replacing it was thought lost nitrogen services from filled salt marshes.  Long Island Sound in this cold period was thought by some researchers to be even nitrogen limited.  Chlorella is a nutritious algae – one that helped shellfish.  The sulfate /ammonia pathway was diminished then it was cold and strong storms removed Sapropel deposits the cold helped oxygen levels remain saturated. 

When Long Island Sound waters warmed brown algae that needed high amounts of ammonia thrived – nowhere nearly as nutritious as Chlorella – over 42% protein and 40% lipid – starch a high energy and nutrient filled food.  The Browns (Aureoceccus) that need ammonia are very low in protein (anophagefferens) that is why shellfish starved while bathed in browns – it was that poor a food.  The brown algal blooms are associated with sulfide/ammonia near organic matter deposits – salt marshes or Sapropel.  There is much literature about these organic deposits dating back to the Long Island Duck farm industry.  The browns are most apt at nitrogen “scavenging” including ammonia.  In times of high heat they just dominate waters with high ammonia levels.  Many Connecticut residents may recall looking at Long Island Sound which had a brown tinge along the coast in the 1980s.

Nitrogen pathways have changed and some of the first published reports mention a shift from denitrification to nitrogen fixation as our waters warmed came from our neighboring State of Rhode Island.  This shift from oxygen/nitrate to sulfate/ammonia takes place in organic matter putrefying without oxygen – Sapropel (leaves).  Some of the first warnings about this were raised nearly a decade ago (Fulweiler – Nixon, Journal Hydrobiologia V 629 #1 pages 147 to 156).  Some bacterial filter systems need nitrate and nitrate as an oxygen source, from Fulweiler - Nixon.

“The recent climate – induced oligotrophication of the Bay (Narragansett) will be further exacerbated by forth coming nitrogen reductions due to tertiary sewage treatment” – {tertiary treatment removes additional nitrogen.}   

And Nixon et al 1996 – linked nitrogen and phosphorus sinks to residence time, Brian et al 2004 explored nitrogen and phosphorus retention as burial in sediments.  The paper was “North Sea Source or Sink for Nitrogen and Phosphorus to the Atlantic Ocean.”  In Biochemistry Vol 68 – pages 277-296 (2004).  In the middle 1990s the role of Anammox bacterial in removing ammonia from coastal waters become known – this bacteria needs nitrite in the absence of oxygen to accomplish ammonia stripping (Hu et al Biochemistry Transactions 2011 Vol 6 1811-1816) in a more recent study.

Another paper titled “Environmental Controls of Anammox and Dentrification in Southern New England Estuarine and Shelf Sediments” Limnology Oceanographer Vol 59 2014 – 851 – 860 looked at autotrophic oxidation of ammonium by Anammox bacteria – and mention “Rates and relative importance of each process may be related to the availability of nitrate, or nitrite as well as organic matter” on pg 851.
In a 2007 article titled “How Climate Change is Choking Marine Ecosystems – Why Warmer Weather Means Bad News for The Estuarine Nitrogen Cycle” (August 3rd 2007 fact sheet).  Robinson Fulweiler describes similar research findings in 2005 – (Narragansett Bay) {brackets indicate my insertions T. Visel}.
“In 2005, we learned that the rate of denitrification {oxygen/nitrate pathway} had decreased substantially since it was first measured here in the 1970s.  The cleaning process {Nitrogen stripping to nitrogen gas} that is so vital for maintaining the estuary had slowed.  We continued to sample through 2006 and we discovered a remarkable change.  Instead of producing nitrogen gas through denitrification, the sediments began to do the opposite.  That is, they were instead fixing nitrogen.  During the nitrogen fixation bacteria in the sediment take nitrogen gas and turn it into a biological usable form of nitrogen {for example nitrate or ammonium}.  This is a major shift from the estuary acting as a nitrogen “filter or sink” to acting as a nitrogen “source.””

During this period Southern New England experienced some very hot summers progressing to warmer water temperatures. The same heat was also causing the loss of bacterial filters at wastewater treatment plants.  Some plants had procedures that utilized nitrate as a oxygen source to maintain filter systems.

When you consider that wastewater treatment plant operators knew this and used nitrate to keep bacterial filter systems alive questions arise as to why the exclusion of the sulfate/ammonium pathway?  Did we with the nitrogen reduction programs actually remove beneficial buffering nitrogen compounds containing oxygen instead of focusing upon the sulfur/sapropel ammonia purging in very warm weather?  It looks now like we did.

With a climate change scenario conditions in Long Island Sound the organic sulfate/ammonium discharges may overwhelm any or all of our nitrogen reduction efforts.  In fact with climate change we may find that we removed beneficial oxygen with nitrogen needed by filter sustaining bacteria and those needed for nitrogen ammonia removal by natures bacterial filter systems? 

Climate change has dramatic consequences for our salt marshes as well - the past warm period 1982-2012 has shown as what the future may bring – the salt marshes so valued for so long will turn against the seafood we value (and why LISS started the nitrogen reduction program) and overwhelm ecosystems with ammonia and aluminum.  That is already occurring in some salt marsh systems during heat and drought.
We should without any further delay include the Sapropel (sulfate) ammonia pathway in nitrogen discussions (my view).  Donald Rhoads of Yale (who I used to car pool with on Cape Cod) felt that mapping the Sapropels was what we should do first.  In my view that would be an excellent first step – mapping these Sapropels.  In times of heat and low energy Sapropels greatly increased sapropel habitat coverage.  In order to map them we first need to acknowledge that they do exist - my view. 

Always welcome suggestions, comments.  I respond to all emails at [email protected]
To understand the impact of organic matter to shellfish populations I have included an appendix part of a 2006 paper that looked at several habitat restoration projects while employed by the University of Connecticut Sea Grant program.  Off all the areas studied Clinton Harbor and Niantic River appeared to have the most leaf fall impacts.  At times the upper portion of Niantic River had several feet of oak leaves – especially the section was which bounded by mature growth oak trees.  Today that section is known as Oswegatchie Hills.  Even one large tree can trap sufficient organic matter to start Sapropel formation.  After Hurricane Gloria tremendous amounts of organic matter was washed into estuaries and in one case blocking (reduction of energy) a section of the Branford River.  By August 5th 1986 the odor was strong (most likely hydrogen sulfide) and a New Haven Register article August 5th 1986 contains this quote “The Tree has caused so much debris and grass to block it up, it’s actually giving off an odor” according to the Fire Chief Peter Mullen that is in appendix #2. 

North International Conference on Shellfish Restoration
November 18, 2006 South Carolina –USA

Timothy C. Visel
Coordinator, The Sound School Regional Vocational Aquaculture Center
60 South Water Street New Haven, CT 06519

A series of CT Sea Grant/Extension shellfish restoration programs for hard clam (Mercenaria mercenerica), soft clam (Mya arenaria), oyster (Crassostrea virginica), and bay scallop (Arogopectin irradians) were coordinated with local municipal shellfish commissions in the 1980’s. Potential candidates for projects were identified by local environmental fisheries history, shellfish maps, natural beds and local shellfish surveys. Several restoration projects were undertaken with federal, state and local agency assistance. Results were highly site-specific; some yielded almost immediate positive results, and some were complete failures.
Estuarine health concerns as communicated by small boat inshore fishermen during initial site investigations correlated with project success.  Local environmental fisheries reviews were often anecdotal so whenever possible, fishing statistics and US Fish Commission reports were consulted. Methods to restore shellfish populations included spawner areas, reseeding, re- shelling, re-cultivating, shell base restoration and spat collection.  This paper reviews shellfish restoration projects in CT from 1979 to 1989 for the following river systems:   

East, Neck, Hammonassett, Oyster, Pattagansett, Poquonock and Niantic.  These projects are reviewed in terms of “estuarine quality” which included water quality, siltation, sedimentation, tidal obstruction or barriers and upland watershed alterations.

Predictions/suggestions by the local residents and resource user groups were often confirmed; therefore, their importance and contribution should not be overlooked. Environmental fishery history reviews can be an important tool in understanding the declines in shellfish production from near shore areas. As much information as possible should be obtained before attempting shellfish restoration programs. In this way, scarce shellfish restoration resources can be maximized.

Podium Comments
Timothy C. Visel
November 18, 2006

Ninth International Conference on Shellfish Restoration

First of all, I would like to thank Richard DeVoe and Dorothy Leonard for the correspondence and their assistance.  I have wanted to attend for many years, and they have always been supportive of my efforts.  In the past, the conferences I attended I learned more and the opportunity to share ideas and exchange information was a large part of my Sea Grant Marine Resource Restoration Partnerships.  I’m from Connecticut and we have had our share of monumental problems related to shellfish culture.  Connecticut has a long history of environmental degradation, unfortunately which continues today.   So the presentation will cover what I term environmental fisheries history and the importance of knowing it.  So much of our coastal environmental habitats have been degraded that what is present today is not indicative of Connecticut’s natural ecology.  I picked 6 shellfish projects that illustrate different problems and will explain my exposure to habitat changes or histories for each, some thing that could have saved a lot of clams, oysters and scallops.  I’m not doing shellfish restoration any longer, so what I’m presenting are some University of Connecticut Sea Grant projects from 1978 to 1990.

I submitted the presentation abstract with six projects and later I found out I had 18 minutes, so observations and some data are in a paper I brought with me. Copies are back on the publications table.
One final thought– sometimes the habitat you see today is the last type of habitat you want to use or protect.

I would be pleased to answer any questions after the presentation.

Thank you.


Paper Presentation 9th International Shellfish Restoration Conference – November 18, 2006
“Connecticut Shellfish Restoration Projects Linked to Estuarine Health.”   11:30 Plenary Concurrent Session E “Small Scale Approaches to Shellfish Restoration”
9th International Conference on Shellfish Restoration November 15-19, 2006
Charleston, South Carolina, USA
Niantic Bay Quahog Enhancement Project
Niantic Bay (River) Waterford, East Lyme Shellfish Commission Hard Clam Aquaculture Experiment 1984-86
The Waterford/East Lyme Shellfish Commission was established by act of the Connecticut General Assembly (CGS-26-287) to cooperatively manage shellfish resources in Niantic Bay (River) which lies between both communities.   SGMAS was contacted to help with a hard clam culture project already underway.
Project History

In 1984, approximately 5,000 5mm to 8mm quahog (Mercenaria mercenaria) clam seed were purchased from Culture Clam on Cape Cod (Robert Porter, personal communication, 1984).  They were planted in a 3’x8’x12” deep “bedding box” which was then covered with a protective metal mesh covering.  When these clams reached littleneck size (and large enough to withstand natural predators), they were to be planted in areas of Niantic Bay in order to increase natural setting.  Niantic Bay once contained deep water hard shell clam beds that were obtained by tongs, especially in Keeney Cove or the easterly spur of Upper   Niantic Bay.  After several months, 50% of the clams had died and living clams showed no or poor growth.  Investigations into why such a large mortality and poor growth had occurred were then initiated.                                                                    
Field Observations
The bedding or culture box was located on the south side of Smith Cove part of the upper Niantic Bay/Niantic River System. It had good tidal exchange and was exposed an hour between outgoing and incoming tides.  Residents recalled that clamming and oystering were popular summer time activities in the Cove many years ago.  Upon investigation, it was apparent the bottom was soft for about 3 inches until a firmer substrate/sand pebble

mixture could be found.  A tremendous amount of maple/oak leaves were around and on top of the culture box. Upon removing the protective metal mesh cover, the surviving clams all had shell erosion, resembling acid/shell erosion and their shells appeared a chalky white.  Low bottom pH (acid bottom) was suspected for the poor growth.   

It was discouraging to the Commission because growth measurements indicated that clams had actually gotten smaller. Following some culture techniques I learned in Cape Cod and Connecticut and detailed by Mackenzie (1970-1983), the substrate in the cutting box was replaced with a 50% clean sand, 25% clean gravel, 25% ocean quahog clam shell mix available in Rhode Island as a driveway cover.  The gravel and sand was purchased locally at a building center.

After the surviving clams (about 2,500) were replaced in the new substrate in May, rapid summer growth was observed until late fall. That fall a strong Northeast storm deposited a thick blanket of leaves over the culture box.  Upon removing the leaves, it was discovered that a thick blanket of “black mayonnaise” had covered the clams and nearly all of them

had perished.  “Black mayonnaise” is a term used in Connecticut to describe a rich, soft, black gelatin-like organic ooze found on many of our bay and cove bottoms.   As part of an estuarine history, Nelson Marshall also was investigating the Niantic Bay ecosystem (personal communication, T. Visel 1993).

Fisheries Environmental Review

A fishery history/habitat environmental review was initiated, and it was discovered that the hard shell clams beds had “disappeared in the 1940s,” when a bullraking fishery had stopped just before World War II (Brian Sullivan, personal communication, 1985).  It was located on the Waterford side  of the Bay in the “deep water” around Keeney Cove.  Investigations of the Keeney Cove area revealed that soft, deep, organic sediments had settled over much of the cove bottom.  In an attempt to calculate the depth, a 10-pipe section got stuck and had to be manually dug out of the bottom.  It was estimated that over 8 feet of organic debris had settled over the area.  Any productive hard shell clam beds had long been suffocated.  The area was undergoing intense euthophication; some euthophic events dated back to the 1920’s.
In conversations with commercial bay scallopers and retired quahog fishermen, all recounted that the bottom environment north of the railroad causeway had become softer and was “choked with weeds.”   (The weed was eelgrass).  It was learned that in the 1960’s, studies were conducted with dynamite to try to dislodge dense eelgrass beds that had caused navigation problems, and it was believed this had caused the Upper River to stagnate (John Wadsworth, personal communication, 1986).  The historical review revealed symptoms to be consistent with enhanced vegetation growth responses to nutrient enrichment.  Much of the marine habitats in Niantic Bay River (above railroad causeway)

had eutrophied (Public Hearing, Comments T. Visel, DEP Regulatory Review, July 9, 1986).

Comments from fishermen indicated that a once very productive “flounder ground” also had disappeared in the 1920’s.  Several fisherman blamed manure dumping at the time for the loss.  A “large hook” tub trawl flounder fishery existed after a much larger fyke net flounder fishery ended around 1900.  Storm water runoff exacerbated the condition bringing large quantities of leaves, sticks and other organic debris.  Additional information indicated that much of Niantic Bay’s original circulation pattern had been altered by the construction of the railroad which effectively cut Niantic Bay into two separate sections (Olive Chendali, personal communication, 1985), the northern or river section (north of the railroad) and the southern or outer harbor (south of the railroad causeway).

Previous to the construction of the hardened railroad rail bed, Niantic Bay had three barrier beach inlets that periodically opened and closed dependent upon storm events (John Wadsworth, personal communication, 1986).  The ecology of Niantic Bay had been substantially altered by the construction of the railroad causeway reducing flushing and wave action in the Upper Bay.

Consequently, areas that were periodically flushed of organics by waves and tides now had become areas of deposition.

Recently, the Connecticut Department of Environmental Protection and municipal officials presented a very detailed Watershed Management Plan for Niantic Bay (August 2006).  At public hearings, the efforts to restore finfish and shellfish populations by controlling run off to Niantic Bay was favorably received by local residents.  Presently, Niantic Bay upper bay and river is designated a Connecticut water body not meeting water quality standards for aquatic life support (DEP Submission.303 (d) of the Federal Clean Water Act, April 28, 2004.

New Haven Register, Friday, August 5, 1986

Engineers to remove fallen tree from river
Huge oak tree snares debris floating in water
By Catherine Sullivan, Register Staff

BRANFORD –Since hurricane Gloria, residents on Riverside Drive have watched debris and eve dead fish pile up on a fallen oak tree that stretches across the Branford River.
“It’s a huge oak tree and it’s practically across the whole river,” said Marie Wall, a Riverside Drive resident. The tree is lodged in a section of the river near her property. “There’s just enough room for the boats to go by,” Wall said.

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

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

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

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

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

Reprint permission as per Kevin Corrado, October 15, 2014 - Author Catherine Sullivan, New Haven Register August 5, 1986.

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« Reply #1 on: October 30, 2015, 09:52:33 AM »

another good read


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« Reply #2 on: October 30, 2015, 10:40:03 AM »

Very interesting read.  I take it that you have at least a Masters degree in marine biology.

Let me introduce myself.  My screen name is Capt. Ron.  I live near New Orleans, La. and have been a commercial fisherman in Lake Pontchartrain for over 30 years.  Raised on the lakes and bayous in the area I've seen many changes to the landscape of south Louisiana.  Hurricanes, costal erosion and man made interventions have deteriorated our coast, estuaries and our way of life.  I will contact you by email to discuss what has and is happening to our area.

Once again thanks for the information,


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