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Author Topic: EC #28 Nitrogen Models and Climate Cycles  (Read 4671 times)
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BlueChip
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« on: March 22, 2024, 02:40:28 PM »

EC #28
Estuarine Nitrogen Models and Climate Cycles
Bacterial Ammonia from Sapropel Deposits Needs to be Included
The EC Nitrogen and Bacteria Series - July 2020
Viewpoint of Tim Visel, No Other Agency or Organization
This is a delayed report
Thank you, The Blue Crab Forum™ for supporting these Newsletters
Revised to January 2023
Tim Visel has retired from The Sound School June 30, 2022


No other issue has defined Long Island Sound’s fisheries in the 1980’s and 1990’s that human nitrogen inputs.  While it is true that nitrogen levels from human sewage has increased most of that nitrogen is mobile and contains compound of nitrogen with oxygen as nitrite or nitrate.  When I first joined the Long Island Sound Study (1980’s), it was the nonpoint source nitrogen that was of interest to me.  I already had seen what a deepening organic paste (from runoff) could do to shellfish populations on Cape Cod and Connecticut.  It could destroy them.  It was on my trips back to CT from Cape Cod with Dr. Donald Rhoads of Yale, who first gave me the chemical name for black mayonnaise, Sapropel, a monosulfide organic-rich mud (1981).  This research would eventually direct me to the impacts of climate and what just a few degrees of temperature could do to shellfish habitats.

I first met Dr. Donald Rhoads in 1978 as part of a dredging DAMOS project in New Haven Harbor based at Emerson’s Boatyard, then on Cape Cod and later again our paths crossed at The Sound School.  Much of my interest in this marine compost is because of his research into the habitat successional properties of it.  His comments about sapropel during a 1985 Long Island Sound Conference can be found in many IMEP habitat history newsletters.  I rejoined the Long Island Sound EPA study August 1, 2006 to try to bring a historical viewpoint of climate cycles to living marine resources, fish and shellfish.  This was evident in the landing fish statistics and my research effort for lobsters that dates back to the late 1970’s and early 1980’s.

The nitrogen abatement programs have reduced human nitrogen inputs, but they do not take into account climate cycles – most notably the NAO – The North Atlantic Oscillation.  We may never see this nitrogen reduction alone connected to abundant fish and shellfish.  It is the humus with oxygen and sapropel (mono sulfide mud) with sulfate that generates most of the shallow water nitrogen in Long Island Sound and this nitrogen is locked into plant tissue released by bacteria not us.  It is collected in shallow waters where warm temperatures lowers oxygen and helps sulfate requiring bacteria grow.  These are the same habitats we call nursery areas or more recently essential habitats.  We most likely caused more impact by releasing suspended solids – organic matter - my view, T. Visel.

Early in the recent Long Island Sound’s study’s history – nitrogen was looked at as causing hypoxia – long periods of oxygen depleted waters and a Management Plan dated Oct 29, 1990 contained these elements as policy*
1)   Long Island Sound will have a no net increase nitrogen policy.
2)   The baseline data year for nitrogen loadings is 1990 (or within this period, T. Visel).
3)   Facilities covered under this policy include point source discharges to the Long Island Sound.

* October 29, 1990 memo to LISS Management Committee Susan Beede, Cynthia Pringham and Mark Tedesco, EPA.
The concern about these issues was climate and that vegetation debris (leaves grass clippings forest duff) also contained nitrogen bound up in plant tissue.  So did suspended solids in human sewage.  It is these plant residues that end up collecting in estuaries especially, in times of low energy and high heat, the buildup of monosulfidic muds – the sapropels.  This source of nitrogen was not included as it was from bacterial composting (called diageneis) and therefore not directly connected to human nitrogen inputs. 

While we have met TMDL nitrogen reductions our fisheries are largely governed by temperature and energy related to the NAO (See NOAA publication – Mackenzie and Tarnowski Large Shifts In Commercial Landings Of Estuarine and Bay Bivalve Mollusks in Northeastern United States after 1980 and Assessment Of The Causes - 2018).  Much of the nitrogen problem is from bacterial release by way of plant tissue reduction – a marine compost that sheds nitrogen (huge amounts) from waste wood, grass clippings, forest duff, organic leaf flour from streets, manure and yes sewage solids (human) from waste water treatment plants.  A reduction of nitrite and nitrate actually removes oxygen from Long Island Sound – and possibly quickens a transition to sulfate reduction which causes ammonia levels to soar.  This ammonia often leads to HAB algal blooms in heat poorly flushed bays and coves that use ammonia as their primary nitrogen nutrient source.  In cold waters, bacterial populations release nitrite less toxic and nitrate nutrients for the “good algae,” the strains that feed shellfish such as the bay scallop.

Our nitrogen reduction programs were identified in a period of very warm temperatures – nitrogen levels naturally rose in hot oxygen depleted waters.  So did hydrogen sulfide now that it has turned colder oxygen saturation rates are higher and bacterial strains are changing again.  (See EC #7: Salt Marsh A Climate Change Battlefield, posted September 29, 2015, The Blue Crab ForumTM).  The seafood connection to nitrogen levels was always weak (it is important to note that in some of the worst Long Island Sound hypoxia years blue crab populations soared in Long Island Sound reaching a population maximum in 2011-2012.)  The heat up to a point favors the diversity and abundance at the edge of the sapropels – even a warming Long Island Sound itself at first benefited lobster populations up to a point.  This prevailing wind from the south tended to keep lobster megalops in the shallows.  This warm water can be highly productive and Donald Rhoads mentions this point directly during the 1985 Long Island Sound workshop held on May 10, 1985 held in Washington, DC titled “The Benthic Ecosystem” pg. 47, NOAA Estuary of the Month Series #3 and meeting minutes printed in 1987 by NOAA, Conner Gibson editor 164 pages Technical Report, 1988, 12.

The salt marsh role and processes associated with nitrogen bound up in terrestrial plant tissue never was fully addressed in the 1970’s and early 1980’s because colder seawater made it less noticeable. The high salt marsh was exposed to oxygen and oxygen reducing bacteria quickly consumed any organic matter and generally why in time fall leaves soon “disappear” on lawns.  We don’t wait for natural bacteria to break down the leaves so we rake them, or we chop them up into bite sized pieces and often then “compost” them.  This makes bacterial reduction faster if oxygen is readily available, so composters from time to time turn over this compost to introduce oxygen. (Composters soon notice that heat is also generated by this bacterial action).

The compost process releases plant tissues by bacterial action who utilizes the sugars captured by photosynthesis.  We don’t call it by its organic cycle “the food dish for bacteria” but that is what it is.  The process (which is multi step of leftovers for many types of bacteria) is controlled by the amount of oxygen present and to speed it up (on also to modify compost temperature) we add energy – we “turn” the compost pile.  Nature provides the energy to recycle natures compost – on land floods and fire, and in the water, storm waves and currents.  With respect to vegetation I frequently use lawn care as a terrestrial example, raking fallen leaves (often described in marine habitats as a rain of organic debris or “marine snow”) and cropping (cutting) a grass mono culture.  This process changes the nitrogen chemistry and in heat alters the bacterial reduction of its compost. (People who have installed cut sod may notice how quickly this bacterial heat can build).

That happens in the salt marsh except raking is replaced by tides (currents) and the mowing by waves.  Any lawn care taker realizes that removing the energy and raising the temperature can lead to turf sulfide rot, a death sentence to grass habitats.  In heat, salt marshes could outwell nutrients, in cold it would remove them for plant tissue.  The concept of “outwelling” is still controversial in the salt marsh literature – as climate was not factored into the bacterial complexing or releasing of nitrogen in many salt marsh studies.  In cold salt marshes can keep up with sea level rise, in extreme heat and sulfate reduction they cannot, they sink.  In cold peat bacterial with oxygen release and transfer ions forms of nitrite and nitrate quickly accessible to plant growth which traps organic matter.  In heat, bacterial reduction switches to ammonia, a much less active nitrogen for plants but favors harmful algae blooms.  In times of heat peat – sapropel deposits produce tremendous amounts of ammonium.  This is usually a period of low oxygen and nitrate and nitrite used as secondary oxygen sources.  This is when sulfate requiring bacteria increase and change shallow water chemistry.  This step now releases a plant toxin, sulfide.
In times of cold, seawater oxygen in its elemental form is often described as “non-limiting” and both 02 and NO3 are high.  This is critical as a strong thermocline (boundary) forms with oxygen poor waters below and those with higher oxygen levels above.  It is at this time the marine composting process changes, bottom waters will show less nitrate and more ammonia.  At the water bottom interface the pH will often rise (ammonia has a pH of 13 – basic) and if long enough cause a calcium precipitate.  The periods of cold and sufficient oxygen most of the ammonia was oxidized to nitrate and nitrate and that was accomplished by bacteria on the bottom of Long Island Sound.  From Harris “The Nitrogen Cycle pg. 59 of the Bulletin of the Bingham Oceanographic Collection – Oceanography of Long Island Sound (1959) has the segment:

“Von Brand et al. (1937) demonstrated that the bacterial liberation of ammonia from dead plankton proceeded rapidly at first and then more slowly.  The process virtually stopped in 8 to 20 days at which time some 20 to 35% of the nitrogen originally present in the plankton remained under composed or in bacterial cells.  The Ammonia was then transformed to nitrite and the nitrate, the whole process generally requiring two or three months.
In heat, this process breaks as oxygen is limiting and oxidation of ammonia to nitrate stops (this is the basis of most nitrogen filter systems in aquaculture) and ammonia levels rise, which benefits those algal species that need high ammonia – the Harmful Algal Blooms or “Brown Tides.”
From Harris the nitrogen cycle (1959) pg. 60 has this section (my comments, T. Visel):

“The ultimate oxidation of ammonia to nitrite and nitrate was obvious only in autumn and winter (when seawater is colder and chances oxygen levels are higher - T. Visel).  The fact that little nitrate was present at other times does not prove that it was not formed.  However, the slowness of the oxidation as described in experiments by Von Brand et al (1937) coupled with present evidence that phytoplankton readily utilized ammonia indicates that most of the ammonia was used before it could be oxidized.”

But despite the research of the 1930’s to 1950’s, the question of bacterial processes of nitrogen cycling was still being asked in the 1980’s.  In January 1986, the U.S. Environmental Protection Agency issued its final report on Technical Information and Research Needs to Support A National Estuarine Research Strategy – Contract No. 68-01-6986 – work assignment No. 18 Announcement #3 – Battelle 2010 M Street NW, Washington, DC 20036 the Nutrient Working Group leader Mr. Garry Powell, Director Bays and Estuaries Program Texas Water Development Board, page 33 contains specific objective 2:
“Determine the importance of chemical oxygen demand (COD) due to nitrification and sulfide oxidation such information is needed in order to determine if nitrogen should be controlled and to assess the efficacy of such control measures, i.e. should nitrogen be controlled in order to prevent prolific algal growth and associated oxygen demand or because of nitrification.”   

This research was not done – my view and was the foundation of the report titled “When It Came To Shellfish, Did We Take Out The Wrong Nitrogen” (See EC #10 Oxygen and Sulfur Reducing Questions, posted January 1, 2016, The Blue Crab Forum™).  A further recommendation of the nutrient working group included the following on pg. 33:

“It is recommended that available information on sediment oxygen demand be assessed and contrasted to data on total oxygen demand in selected estuarine systems.” 

And also -
“The group recommended that research be conducted on nitrification and sulfide oxidation in estuaries in order to determine the chemical oxygen demand associated with these processes.”

The largest difference between the Harris segments (1959) and the EPA study (1986) is that in the latter “bacteria” is not mentioned in regards to nitrogen.  For summary purposes the chemical and nitrogen generation from marine compositing was not included.  It is estimated that up to 50% of the nitrogen is in some regions from bacterial processes (Communication to Tim Visel from John Trefrey, FIT).

The question of nitrogen and bacteria were well known in the 1970’s the role of sulfide producing “deadlines” in the salt marshes.  In these salt marsh composts – when sulfur levels rose no plant growth occurred.

“The Ecology of Salt Marshes and Sand Dunes” by D. S. Ranwell, Head of the Coastal Ecology Station of The Nature Conservancy, 1972, pg. 203, mentions this deadline directly and the composting process associated with nitrogen enrichment as human pollution (my comments, T. Visel):

“No one has measured for example changes in the deadline for salt marsh growth in heavily polluted estuaries (referencing nitrogen above – T. Visel) due to the combined effect of all these influences close to the centuries of civilization.  It has been shown that overall productivity of macro algal communities on the Adriatic coast remains unpaired right up to the death line where macro-algal growth suddenly fails (submerged root grass and salt marsh grass dieback suspected, T. Visel) (Golubic, 1970) significantly as the point is approached (nitrate to ammonia, T. Visel) the species diversity is reduced from many to only two algal species Ulva lactuca and Hypnea musciformis (This plant species has sulfated compounds and has medical uses – Tim Visel).  Beyond this point persistently anaerobic organic rich mud forms a foul smelly bacterial soup virtually devoid of higher life forms.”

It is this foul smelly bacterial soup that forms a sapropel and is associated with thick growths of sea lettuce i.e., – Ulva lactuca, which utilizes high amounts of ammonia.  In fact, today Ulva is looked at a possible bio filter for ammonia in closed fish production systems.  It does well and in heat over composing sapropels.  Hypnea musciformis is a red algae, which has the ability to switch from nitrate to ammonia with no reduction in growth potential.  A transition to higher levels of ammonia would benefit these species – which it does and is confirmed by Ranwell, pg. 203 (my comments, T. Visel):

“Now these algae (Enteromorpha and Ulva, T. Visel) are capable of utilizing nitrogen in the ammonium form and these various effluents must contribute substantial quantities of organic or ammonia nitrogen which would normally be converted to readily assimilated nitrite or nitrate (by oxygen-requiring bacteria, T. Visel).  But it is significant that under anaerobic conditions, the conversion of organic nitrogen stops with the step of ammonium formation (Black, 1968).  It seems likely that accumulation of ammonium nitrogen may preferentially benefit algal, rather that salt marsh growth.  The growths are so extensive that in sheltered bays could act as nutrient traps.”           

It is during these hot stagnant low oxygen/no oxygen periods we see ammonia soar from sealed sapropel called “harbor mud” (first reported by the Maine Agriculture Experiment Station over a century ago).  It is the 1980’s that the nitrogen issue rose to be a critical public policy flash point, and difficult to portray salt marsh to be a nitrogen polluter so it was not included in many nitrogen TMDL’s and why our human efforts to take out nitrogen may be eclipsed by natural bacterial efforts often termed “benthic flux.”  Many researchers mention this bacterial loading as benthic flux – an oceanographic term I learned at the FIT School of Oceanography Jensen Beach Florida in 1973.  Benthic flux is a broad term that can describe several biochemical exchanges (flux) as interactions or discharges.

Researchers knew about these bacterial nitrogen pathways largely governed by climate.  Latimer and Charpentier (2010) – Nitrogen Inputs To Seventy-Four Southern New England Estuaries:  Applications of a watershed nitrogen load model (Estuarine, Coastal and Shelf Science, 2010) that bacterial nitrogen was not included because it was not “new nitrogen” while mentioning the controversy of a “sink” for nitrogen and in summer a “source” of nitrogen (outwelling) on pg. 5 contains this statement:

“Internal nitrogen regeneration from sediments and the water column is not considered in this paper, however, it is taken into account by the nitrogen loadings model ELM.  The sediment has been ascribed by others to be a net sink, except during summer periods where it may be a net source (Howes et al., 2003).  In either case it is not “new” nitrogen, therefore it was not included.”

The problem being of course when measurements are taken in the field it is impossible to differentiate between “old” nitrogen (once released by bacterial action) from “new” nitrogen from other sources.  Nitrate is nitrate there this is no way to tell bacteria nitrate from commercial prepared nitrate?  Once in the water column bacteria nitrogen moves with all other sources and is even more suspect by climate.  When Long Island Sound temperatures increased under the influence of a long positive NAO – a time of higher temps and less energy (energy is described here as tropical cyclones or immense Northeasters).  It was as if the raking and wave effect was lessened, leaf matter collected in bays and coves deepening as an ooze sulfide rich shedding ammonia and adding to nitrogen levels.  It is the hot and low energy levels that sapropels grow and again mentioned by Donald Rhoads at the 1985 Long Island Sound conference proposing a less expensive oxygen availability measure by simply checking sapropel growths – “we should map the sapropels.”

When one considers climate cycles (which are not reflected in many nitrogen models and puzzling considering all the recent media accounts – my view, T. Visel), it is not surprising to recall the rise of the brown algae species in Long Island Sound, which occurred as our winters were mild – waters warmed and became a huge source of ammonia (for a detailed explanation of this black mayonnaise (Sapropel) ammonium generation see Dr. John Trefry’s Florida Institute of Technology work in the Indian River Lagoon Florida).  Ammonium levels would build and support immense brown tide blooms (1980’s to 1990’s) that could use this nitrogen source while other algal species that needed nitrite and nitrate died off.  While many fish and shellfish studies look at elemental oxygen for respiration and life support this relationship is not true for bacteria.  Bacteria in the marine environment access oxygen indirectly from several sources as it appears in many compounds – remove the elemental oxygen source and include all oxygen compounds sources the largest oxygen source would then be sulfate, dissolved in sea water that is described as “non-limiting.”  Bacteria that depend upon sulfate as an oxygen source in heat will do fine – and in doing so generate huge amounts of ammonia while not “new” but nitrogen none the less.  Once climate is factored into the nitrogen model – the brown tide blooms become a natural response to heat, low oxygen and high ammonia.  By removing nitrite and nitrate in high heat, we may have even hastened the brown tide blooms.  I don’t think brown tide algae would avoid nitrogen that was not “new” – it would not be able to tell the difference.

The USGS correctly stated the dangers of not including benthic flux – bacterial nitrogen release of nitrogen and in this 2015 report, detailed below about Puget Sound on the West Coast (my comments, T. Visel):
“Quantifying Benthic Nitrogen Fluxes in Puget Sound Washington –
A Review of Available Data”

Scientific Investigations Report 2014-

US Dept of Interior
US Geological Survey
By Richard W. Sheibley and Anthony J. Paulson

“Three primary microbial processes influence the type and amount of generated nitrogen (N) (I term these pathways in many newsletter postings – T. Visel) ammonification, nitrification procedures ammonium NH4 from the breakdown of organic matter depositing to nitrogen regeneration from the sediments (2) nitrification converts NH4 to nitrate NO3 under aerobic conditions, and (3) denitrification converts N03 to nitrogen gas N2 under low oxygen conditions in the presence of organic carbon.  These three processes can concentration gradients between the overlying water and sediment resulting in exchanges between two compartments.  This exchange of N access the sediment – water interface is referred to as a benthic flux – pg. 2 figure 1.  And then issues a research caution (my comments, T. Visel).

“In Puget Sound, Washington, ignoring or under representing benthic flux as a source of nitrogen (N) to marine waters can result in ineffective management actions and can lead to chronic water quality problems in sensitive areas.  Shallow areas near the shores of Puget Sound are most likely to experience low levels of dissolved oxygen because of the combination of low relative circulation (sometimes referred to as “flushing,” T. Visel) warm summer water temperatures and proximity to watershed nutrient contributions; sediment fluxes may also dominate in these shallows.”

The rise and fall of habitat is often noted as species “extinction events” as related to habitat succession that for most purposes the habitat reversal mechanism of forest fires is our hurricane equivalent.  It is natural for monocultures to succumb to catastrophic failures, and then gradual restoration as a response to climate patterns.  Much of this process involves bacteria and the early grasses of habitat succession.  This is mirrored by the growth of eelgrass a grass adapted to live in the sea.

Although many reports point to nutrient enrichment nitrogen contamination for the decline of eelgrass and policies of non-disturbance, these beliefs are subject to a review, when eelgrass made its recovery in the 1950’s and 1960’s period of strong storms a negative NAO prevailed.  As eelgrass died off in the 1920’s and 1930’s it was often reported to die off first in the very shallow waters these waters subject to the greatest organic matter inputs (oak leaves are especially damaging because the leaf contains a high amount of leaf wax) – these would fail first because they had less energy and warmest of waters.  This is the black spot eelgrass that was also “brown and furry” eelgrass.  As the positive phase NAO climate pattern extended in the 1980’s these shallow meadows died off first while deeper eelgrass beds in more energy prevalent areas such as at the mouths of bays and coves “hung on” the longest.  A sudden storm or cooler temperatures can reactivate long dormant soils again for eelgrass, removing sulfide composts and restoring soil pores space and therefore raising pH.  A storm cultivates shallow marine soils improving them for eelgrass.  We do the same with terrestrial grass monocultures except it is called dethatching.

Nitrogen from Organic Matter in Shallow Waters

By the early 1900’s, the bacterial/organic pathway with oxygen termed aerobic and without oxygen, anaerobic composting were well understood.  With oxygen bacterial reduction yielded nitrate an “available” plant nitrogen nutrient source.  While this sounds like something new, it is the reason why manure exposed to air (oxygen) had been used to nourish terrestrial plants crops for all of history.  George Wilton Field understood these bacterial pathways and the agriculture practice to drain marsh peat, to allow air oxygen to penetrate it and allow the nitrate oxygen bacterial pathway to “win” and minimize the non oxygen pathway that yielded bacterial ammonia to “loose.”  George Wilton Field also knew that draining peat also reduced mosquito habitats that thrived in hot peat, but his shellfish research in 1899 looked at the waste of nitrogen and the need of nitrate the source nutrient for algae that fed shellfish.  Although he testified at the 1908 Wellfleet Mass hearing to build a dike across the Herring River he did so because of the nitrate pathway of exposed peat for farming – in the hearing transcripts of May to June 1908 that is the point he discussed – before this time he wrote about the waste of nitrogen being washed into streams and coves as runoff.

In 1898, Dr. Field had written a publication published by The Rhode Island Agricultural Experiment Station, Bulletin No. 50 titled “The Utilization of Waste Products and Waste Places, The Nitrogen Problem.”  George Wilton Field who conducted his research and writing when New England was in “the great heat” a period of extremely hot summers and mild winters (1890s) (See IMEP #45 John Hammond accounts).  As such the heat lowered the oxygen in the bacterial pathways and in heat bacteria consuming organic matter – used nitrate as a secondary oxygen source.  Nitrate soon became “limiting” and nutritious algal blooms that shellfish needed declined.  This was especially true for the bay scallop that needs high amounts of nitrate fed algae strains.  But this 1898 paper lists the bacterial pathways we still consider today – the waste of nitrogen an essential plant nutrient that is needed to produce food.  With changes to some words it is the same today.  On page 61, Dr. Field mentions this need for food – (and as part of his employment at the Rhode Island Agricultural Experiment Station)”.

Rhode Island Agricultural Experiment Station Bulletin No. 50.  The Utilization of Waste Products and Waste Places – The Nitrogen Problem.
“Undoubtedly the question of food supply for man, with the attendant chain of questions of varies sorts, is one of the most sordidly practical which confront us, since upon it depend all values wealth, and life.”
And further,

“It is the purpose here to speak merely of the economic advantage, even the necessity of utilizing certain nitrogenous waste products.  One of the most significant, probably the most extensive and therefore most important waste of nitrogen is that which naturally occurs through the washing of material by rains and flood water from the land into the streams and ponds, and ultimately into our bays and the ocean.”
Dr. Field alludes to the need not to waste this important source of nitrogen.  He was also one of the first to point to the role of bacteria in its reuse.
As for the Herring River dike, he was aware of its shellfisheries and the town as a place for growing shellfish and “I do not feel competent to speak on the navigability of the river.”  Objections to the dike had been as to restricting navigation but below the public discussions was an effort for mosquito control.  Lieutenant Col. Edward Burr (for the Army Corps) (Today termed hearing officer – Tim Visel) asks Dr. Field.  “How do you expect that this benefit will be brought about?

Dr. Field “It is known definitely that nitrification takes place more rapidly on fresh land than on brackish land, and the transformation of 1,500 acres from brackish land into fresh land will greatly increase the nitrification and increase the amount of shellfish food in the harbor.  And in this way great benefit will ensure.  Doubtless from your experience you know that the great sources of supply for shellfish are at the mouth of fresh rivers such as Chesapeake Bay and Narragansett Bay.  The growth is where the fresh material washes from the land; and we know that this process of making shellfish food goes on very much more rapidly in fresh than in brackish water, therefore, for this purpose the drainage from fresh meadows  is much more valuable than from brackish meadows.”

A 1906 act approved to build a dike across the Herring River in the Town of Wellfleet, Massachusetts.  From the transcripts, it soon became clear that this was more an attempt to reduce mosquito habitat than to promote the bacterial composting of nitrate.  The Army Corps of Engineers conducted the hearings because the placement of the dike would restrict navigation and thus under the authority of the Rivers and Harbor Act of 1899 a public hearing was held.
Testimony was obtained as part of the official record on pg. 7 from George W. Field.  Draining the marsh would allow faster composting by bacterial action producing more nitrate compounds that once formed would fertilize the nitrate dependent algae food for shellfish.  Thanks to the friends of the Herring River we can look at Dr. Field’s testimony from a century ago.

   Statement of Honorable George W. Field -
“So far as we are concerned officially as commissions of fish and game, we believe very strongly that the projected improvement of Herring River will be of great benefit.”   

The benefit was at the time a bacteria pathway that favored nitrate (exposing peat to air commonly referred as draining wetlands to dry them).  This was the same process underway across New England in an effort to reduce mosquito breeding habitats and prevent mosquito disease especially Malaria (See IMEP #16: Mosquito War Claims Connecticut Marshes 1901-1915, posted May 29, 2014, The Blue Crab ForumTM).

I think Dr. Field would be very surprised to look at recent media accounts that would mention the same two issues he mentioned, the need for food and the bacterial processes of nitrogen a century ago.  The issue of nitrogen waste and bacterial action an organic matter change with temperature and it is important to consider the climate period in which Dr. Field wrote and studied the nitrogen pathways – it was hot, hot seawater cannot hold much oxygen and the bacterial nitrogen “wars” that were occurring in New England’s then hot salt marshes. 

Dr. Field apparently understood this bacterial battle influenced nitrogen compounds formation, a drained peat exposed to oxygen shed nitrates – the algal food that shellfish needed, while oxygen limited peat (or pre peat sapropel) sheds ammonia.  Farmers long understood this bacterial battle – as manure composts exposed to air produced nitrates – and those wet sealed composted purged the sweet and smell of ammonia a far less valuable nitrogen that leaked into pools of water to be “lost to the farmer” (when it rained) who much preferred the soil nitrate rich compost which could be spread on fields than ammonia in water.  Many historical agriculture papers and Agriculture Experiment Station bulletins pointed out that.

The ammonia rich liquids were rinsed by rains and were not that desirable as these leachates entered the groundwater or surface water.  Rainwater near manure heaps fueled the farm pond green algal blooms.  But understanding the role of bacteria was key.  It was a bacterial conflict as to what types of bacteria that would get digest the plant, animal waste we call green manure.  In cold in the presence of oxygen nitrogen could be fixed – nitrate – in the absence of air oxygen (heat) nitrogen would be released in the form of ammonia.  That is the difference in nitrogen pathways that formed much of the Herring River Cape Cod dike testimony a century ago apart from the mosquito populations that threatened coastal “summer trade” tourism, that I believe was the real issue. 

In heat, nitrate was scarce and limiting at times for algal blooms that fed shellfish – in times of cold algal blooms were so intense that they themselves caused nitrate levels in sea water to crash.  It was possible at times for shellfish growth to suffer because of a lack of food.  We have some excellent examples of this in the bay scallop fisheries history these scallops that lived in or near eelgrass had smaller meats (weight) because lower currents (attributed to the eelgrass) meant less food to consume over a given tidal cycle.  In heat high levels of ammonia fed algal strains that provided little nutrition and in many cases were toxic.  These are called Harmful Algal Blooms or HABs for short (“tides” in the historical literature).  And these bacteria had the ability to create substances to kill one another.  It was a bacterial battle in the organic matter, itself unseen but having enormous policy nitrogen discharge implications.  In heat nitrate would be limiting in cold ammonia was - but for different reasons.  The oxygen bacteria held an advantage they could also use nitrite, nitrate and some iron compounds and was absent if sulfate rich.  These bacterial strains fought each other emitting substances deadly to each.  It was not surprising considering the above that Dr. Selman Waksman would term bacterial toxic substances to other bacteria as “antibiotics.”  Dr. Selman Waksman the discoverer of medically important antibiotics we call Streptomycin and Neomycin when he found this bacterial war in peat studies at the Rutger’s Agricultural Experiment Station (See his 1940’s studies while chairperson of the New Jersey Agricultural Experiment Station - Rutgers University, several of his papers are online).

When direct oxygen requiring bacteria “loose” in the marine environment – the bacteria that can access the oxygen bound in sulfur (sulfate) thrive as they “win” and the nitrate dependent seafood we value loose (See EC #7 Salt Marshes A Climate Bacterial Battlefield, posted Sept. 10, 2015, The Blue Crab ForumTM).  It is the sulfur-reducing bacteria (SRB) that shed ammonia into the water column, and in the process complex sulfide compounds that can gather chelate metal ions.  Hydrogen sulfide is purged into the water as such concentrations on hot summer nights the smell of rotten eggs permeates shorelines.  Researchers, including those of Dr. Field himself, experimented with adding nitrate to seawater to increase algal food for shellfish.  I wonder how he would react to the procedures in place today to remove it from seawater.

The conflict between which bacteria gets to sit at the dinner table is why aerobic composters turn over composts and why those who want ammonia seal them from oxygen.  We can influence which bacteria can win by controlling oxygen – but the outcomes remain the same the recycling of plant matter to nutrient compounds and minerals as they can be reformed again, often in agriculture – the end product over time is a rich carbon source.  In the marine world climate governs which bacteria can “win” even if it is for a short time.  In heat ammonia soars from the bacterial dinner table and in cold it is nitrate.  The left over from these bacterial feasts are called natural fertilizer, a carbon rich residue.

That is why, during the formation of Long Island Sound’s nitrogen TMDL, I urged that we should proceed with caution.  This paper was once a part Long Island Sound review of TMDL process.  The battle line between nitrate and ammonia was termed benthic flux – a newer term that describes the see saw battle line of bacteria on the submerged mud flats where the bacterial dinner table rests.  It does change at the bottom dinner table, how many chairs for the oxygen bacteria, those who need nitrate or nitrite, iron/oxygen compounds or even sulfate bacteria can sit.  In heat sulfate bacteria have the most chairs, in cold the oxygen bacteria hold a majority – it is very much temperature dependent.  Without accounting for the bacteria presence according to climate – nitrogen calculations would contain a horrific bias – and in some nitrogen removal studies “benthic flux” was not considered at all.  This allowed natural nitrogen to be at times perhaps counted as “human.”

This aspect of potential bias is magnified in importance as the size of the water body is reduced – heating and cooling happen faster – and changes at the organic matter (dinner table) also occurs quicker – that is the rise and fall of vibrio bacteria (See Megalops Report #4: Eelgrass Meadows As Possible Disease Inoculants, posted September 26, 2017, The Blue Crab ForumTM) and why Harmful Algal Blooms appear in heat with high ammonia.  As sulfate reducers are not as efficient as oxygen bacteria, they leave table scraps behind after the dinner table feast, this residue is the black greasy deposit many fishers and shellfishers call black mayonnaise.  But in the farm community today termed “digestate” a loose liquid sapropel that can be made by bacteria when sealed from oxygen.  By introducing organic waste and removing oxygen we can create “sapropels” and by controlling oxygen and sustaining the bacterial methanogens – and the result the production of methane gas which can be used as a fuel to lower farm production costs.  In effect we have created sapropels speeding up the high heat/low oxygen natural process found in salt marshes and estuaries – we have controlled the pathways of the benthic flux and by doing so obtained hydrocarbon fuel source (methane) using bacteria.

The agricultural community is looking into sapropel production as a way to concentrate carbon and release nitrogen compounds as well as producing methane.  These are also natural processes largely controlled by temperature.  My view Tim Visel.

Appendix #1
Nitrogen Concerns and Long Island Sound Fisheries
Timothy C. Visel
Submitted to The CAC September 15, 2015
-   Limited Distribution –
Revised to March 2016

This is the viewpoint of Tim Visel and does not represent the Citizens Advisory Committee of the EPA Long Island Sound Study

I was planning to attend the Long Island Sound meeting this Thursday but now with an additional dredging meeting in New Haven (which I suggested very strongly) I will miss it.  I also wanted to use some time to research some of my long concerns (questions) about our nitrogen reduction efforts before my response this summer to the CAC committee.  Since then my nitrogen/high heat concerns have increased.  During the July 2015 EPA Water Quality workshop at Avery Point UCONN and in response to my direct questions I learned that our Long Island Sound Nitrogen model was not aligned to climate change nor calibrated for the increase in Connecticut’s forest canopy (leaves).  Shortly after that meeting I suggested that all the New England Estuary Programs meet – to see if other New England Estuary Programs had done the same thing?  (These are the issues that I raised in #1, #2, #3 of my June 26th email).

1) It may not be possible to mandate oxygen saturation in the period of global warming - warmer water naturally contains less oxygen (inverse solubility law) for example Douglas Moss celebrated rising oxygen levels in the CT River in the 1960’s, not realizing than the reason the higher oxygen levels were more likely from a negative NAO - cooler water than pollution reduction that he mentioned was now showing the result of pollution abatement (see below).  Douglas Moss Chief of the Fish Division, Connecticut Board of Fisheries and Game wrote a bulletin about the Connecticut River in 1965.  On page 13 of “A History of The Connecticut River And Its Fisheries” is a section titled “Pollution Decreasing” he mentions that a sister agency – the Water Resources Commission reports dissolved oxygen sampling as evidence in 1914 (at the end of the Great Heat, T. Visel) percent saturation was just 26% (also a time of low shad returns) in 1929 was 43% - also after much colder winters after 1920 (T. Visel) and 1953 – 65%.  In all likelihood the increase of oxygen saturation was from colder water.  In 1958, shad returns would break records – under a cold negative NAO phase.   

2) More and more habitat history information is becoming available from Denmark the German bight region of the North Sea and Australia regarding nitrogen/and sulfide formation.  Aggressive nitrogen reduction plan targets need to include plant forest natural nitrogen sources (organic matter) in relation to sulfide and benthic ammonia generation (Sapropel).  Sulfide generation is now linked to acidic conditions in bodies of water with reduced or restricted flushing without realizing Western Long Island Sound may have suffered a major organic matter sulfide event related to those which occurs in the Black Sea and the Narrow River in RI.

3) Some harmful algae blooms could be related to winter overturn similar to fall over turn on lakes.  In 1981 I participated in a shellfish survey of Mumford Cove in which viable red tide cysts were found 1 to 2 meters below surface organic deposits.  See Mumford Cove Survey appendix #2.  The presence of these cysts at such depths is now linked to potential "bloom triggers" following massive bottom disturbance in areas of low flushing and high organic deposition.


This meeting did not occur but the issue of our continued concentration on the oxygen/nitrate pathway instead of the sulfate/ammonia pathway for nitrogen removal 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 assessing 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?  Both nitrate and nitrite contain oxygen.  (We may remove oxygen sources for some bacteria).

Since my June 26th (2015) email, 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 from a segment of the sulfur cycle.

A colder Long Island Sound in the 1950’s and 1960’s 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 was then termed “good” replacing it was thought lost nitrogen services from long ago 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 as it was cold and strong storms removed sapropel a marine compost subject to high heat sulfate reduction.  The cold helped oxygen levels remain saturated and cold water fisheries were “healthy.”

When Long Island Sound waters warmed (1980’s) 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 sulfur cycle near organic matter deposits – salt marshes or Sapropel.  There is much literature about this 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 – and cause the infamous “brown tides.”  At times aerial photographs of Long Island Sound along Connecticut’s coast had a brown color as waters warmed in the 1980’s.

Nitrogen pathways have changed with the climate and some of the first published reports mention a shift from denitrication to nitrogen fixation as our waters warmed came from 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, Vol. 629, No. 1, 147 - 156).  Some bacterial filter systems need nitrate and nitrate as an oxygen source, from Fulweiler – Nixon (2007).

“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 titled North Sea Source or Sink for Nitrogen and Phosphorus to the Atlantic Ocean (Biochemistry, Vol. 68, 277-296, 2004).  In the mid-1990’s, the role of Anammox bacterial in removing ammonia from coastal waters becomes 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 mentions “rates and relative importance of each process may be related to the availability of nitrate, or nitrite as well as organic matter” 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 3, 2007 fact sheet).  Robinson Fulweiler describes 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 1970’s.  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 warm 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 secondary 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 sulfur sulfate/ammonium pathway?  Did we with the nitrogen reduction programs actually remove beneficial buffering nitrogen compounds instead of focusing upon the sulfur/sapropel ammonia purging from Sapropel in very warm weather?

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 technically removed beneficial nitrogen filter sustaining compounds – those needed for nitrogen removal by 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 on Cape Cod.

The nitrogen reduction efforts needs a temperature climate change review – for fisheries and benthic habitat quality organic matter (leaves in run off) may have been more of a nitrogen problem than us.

As a first start, we need to review the impact of Sapropel formation and its potential to discharge ammonia.  To accomplish this we should review Sapropel, the sulfur cycle in shallow seas and its impacts to essential habitats for fish and shellfish.  This is something I feel CAC should carefully examine.

Thank you,
Tim Visel

March 16, 2016 – The use of the words nitrogen source and nitrogen contaminant is only possible when nitrogen a naturally occurring nitrogen compound was deemed to be a pollutant.  When this happened an effort occurred as to what is a natural source (related to the TMDL) and what is from man – a pollutant.  Unfortunately, reduction in nitrogen was linked to increases in seafood which largely excluded bacterial generation of natural nitrogen from organic matter.  Testing equipment cannot identify manmade nitrogen from natural nitrogen which is also different at different temperatures.  The relationship between nitrate and ammonia is variable and temperature sensitive.

 

Appendix # 2
Red Tide Cysts in Mumford Cove
URI

September 30, 1981

Mr. Edward Wong
U.S. Environmental Protection Agency
Surveillance & Analysis Division
60 Westview Street
Lexington, MA  02173

Dear Mr. Wong:

   I have received a copy of the Mumford Cove Shellfish Survey.  I found the section pertaining to the economic value of shellfish populations very interesting. Would it be possible for you to send me a copy of your publication titled:  A Multiplier for Computing the Value of Shellfish?  Eventually I would like to include such a section in future management proposals.

   The management plan for Old Saybrook got off to a rocky start, but is proceeding in the right direction. I have enclosed some newspaper articles for your interest relating to the program.  Hopefully, recreational shellfishing will occur shortly.

   Thank you for your assistance in May and for including me in the Mumford Cove study.

                                                               
                     Sincerely yours,

                     Timothy Visel



Appendix #3
Mumford Cove Shellfish Survey
Groton, Connecticut
June 1981-A
U.S. Environmental Protection Agency
Region I
Surveillance & Analysis Division
60 Westview Street
Lexington, MA 02173


Acknowledgement
The U.S. Environmental Protection Agency appreciates the interest and efforts of the people who volunteered and assisted in the completion of the Shellfish Survey of Mumford Cove, Groton, Connecticut.  We extend our thanks and acknowledgement to the following people:

U.S. ENVIRONMENTAL PROTECTION AGENCY
Edward F. M. Wong   Project Director

RHODE ISLAND DIVISION OF FISH AND WILDLIFE
Richard T. Sisson   Principle Marine Biologist
Arthur Ganz      Senior Marine Biologist
Barbara Simon      Computer Programmer

RHODE ISLAND YOUND ADULT CONSERVATION CORPS
Paul Baczenski      Group Leader

CONNECTICUT DEPARTMENT OF HEALTH
Malcolm C. Shute, Jr.   Principle Sanitarian
Donald Bell      Senior Sanitarian
James Citak      Senior Sanitarian

CONNECTICUT DEPARTMENT OF ENVIRONMENTAL PROTECTION
Edward Parker      Principle Sanitary Engineer
William Hogan      Principle Sanitary Engineer
James Grier      Principle Sanitary Engineer
Michael Powers   Sanitary Engineer
Gary Powers   Sanitary Engineer

MITCHELL COLLEGE, NEW LONDON, CONNECTICUT   
Dr. Thomas Hatfield   Chairman, Life Science Department
Virginia Magee   Instructor of Biology
Donna Magee   Student

UNIVERSITY OF RHODE ISLAND, KINGSTON, RHODE ISLAND
Timothy C. Visel   Instructor of Marine Science

The Study
Introduction

“Presently, and dating back for many years, Mumford Cove is closed to shellfish harvesting.  However, recreational sports such as fishing, boating and bathing on a private beach are available to residents of the immediate area.  The shellfish closure is due, in part, to a sewer outfall that empties into a stream at the Cove’s headwaters and also, discharges from a sanitary landfill located north of Mumford Cove may be involved.
The U.S. Environmental Protection Agency, State, local officials, and area residents of Mumford Cove know that unless the pollution standards are met, there will be no chance of lifting the shellfish closure imposed on Mumford Cove by the State Department of Health Services.  There are proposals to remove the sewer outfall and have it placed in an area remote from Mumford Cove.

Therefore, EPA with the help of several organizations, performed a shellfish survey in Mumford Cove to determine the densities, type and sizes of the shellfish in the beds.  Furthermore, the value of the shellfish will be estimated and compared with shellfish at the market level.

Cove Profile
The Cove bottom is mostly sand and gravel with a slight tendency toward siltation in certain areas.  The bottom of Area 1 consists mostly of sand and gravel.  The channel bottom, however, is mostly mud and becomes anoxic toward the headwaters.  We noted that the reaches of the headwaters had the appearance of septic conditions at the time of the examination.  Intertidal zones of Area 2 are mostly gravel, sand and silty-sand.  The northeastern portion of this area shows a heavy growth of a green sea lettuce.  Most of the shallow portions, averaging about two to four feet in depth, indicate a predominance of mud and some silty sand.  The outer portion of the Cove, adjacent to the closure line, is mostly gravel, sand and cobblestone.  The bottom is fairly firm at this point.”
[Note: During the shellfish survey, several Mumford Cove residents joined the group and asked questions about strong summer odors (perhaps sulfide?). I noticed that by raking below layers of Ulva (sea lettuce) in some areas had dead soft shell clams (shells still pared) and the smell of sulfide was evident even in June (Tim Visel observations).]
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A D V E R T I S E M E N T


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