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Author Topic: Salt Marshes - a Climate Change Bacterial Battlefield - T. Visel  (Read 6170 times)
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« on: September 10, 2015, 12:04:52 PM »

Salt Marshes - A Climate Change Bacterial Battlefield

Sea Level Rise, Climate Cycles and Salt Marshes
The Blue Crab Forum™ Environment and Conservation #7
Capstone Question:  Will Salt Marsh Habitats in High Heat
Kill Fish and Shellfish Eggs 
Will We Value The Salt Marshes of Tomorrow?
An ISSP/Capstone Proposal Series
ASTE Standards NRE #4, 5, 6, 9 
Tim Visel, The Sound School – July 2015

Environment and Conservation – The Blue Crab Forum™

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 seventh 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, 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.

   #7 Salt Marshes a Climate Change 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?  9/29/2014

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.
I respond to all emails at [email protected]


Fishers have provided us a rare insight of what global warming can do.  They are the first to ring the alarm as cold water species die off as they have in New England’s fisheries habitat history.  The problem is -- no one appears to listen to them (my view).  They with their habitat observations match the farm community only over a much greater time period.  Each of us has seen pictures of farmers looking over parched fields – drying soil as wind creates dust storms.  That weather can ruin a crop in a few weeks but always a chance of rainfall in time for next year’s plants.  Because of the moderating influence of the sea such habitat changes in the marine environments can take decades.  If you look at the hot periods – you can already see what the future will look like; sulfur likes heat, oxygen rules in cold.  That is why currently so much concerns about releasing sulfur compounds from smoke – and the efforts to sequester (lock up) carbon to diminish C02 in the atmosphere.  But those cycles have already happened in our estuaries and to assess potential future impacts we should review those cycles recorded in New England’s fisheries past.  Much of that fisheries history can be found in state and federal records landings and fish surveys from the last century.

Public policies also changes for example when I was in high school (Nixon was President) many of science books were concerned about locking up carbon in wood frame houses.  So much wood (carbon) was utilized in housing it would not recycle back for plant life and we would soon cause a carbon shortage, but 50 years later much emphasis today is spent on the need to lock up such carbon – there is too much.  The late 1960s our textbooks extolled the success of the green revolution – the use of insecticides, pesticides, commercial fertilizers were the answer then to a growing need of food to feed the world.  Only later did we learn what chemical excess could do – a modified green revolution exists today – use of fewer chemicals, genetics, low energy soil cultivation and biotic pest coupling (IPM).  Things that appear important even critical over time change.  With predictions of warm water we may find that change again for fish and shellfish habitats along our coast.

In time we may also need to reconsider many of the scientific values we hold today about the coast – a warming climate will return sulfur and vanquish oxygen as it had in the past.  Historical fisheries’ records it seems provide many features of habitat failures and changes in coastal fisheries.  Habitat observations of the shallow environments are so important just as agriculture field reports.  The glaciers have left Connecticut about 10,000 years ago, so technically our climate has “warmed” since then but we do have cold periods and those cycles are frequently mentioned in the historical fisheries literature.  So many of the collapses of fisheries appear to be natural cycles – and our ability to alter them part of any climate discussion, (my view) and fisheries could be an important piece in the climate change puzzle.  I feel until very recently this opportunity has been largely missed – it should not any longer.

Salt Marsh Public Policies Change

Most likely when one pictures the New England shore it is often a shore front barrier beach or rocky shore and behind it a coastal salt marsh.  I grew up living along one of them in Madison, CT along the western edge of Hammonaset State Park.  I watched and wandered on the marshes and marveled at what lived in them – blue crabbing in the summer and oystering in the fall.  In spring birds would come in the early spring to feed upon the first signs of life – killifish (mummies) that liked those shallow warm March and April pools.  In the fall birds would return on their migrating routes before winter, for shore life salt marshes, was a busy place but I also walked them in the snow and ice and sub zero temperatures.  It left me with a bitter cold feeling of what it was like to live in the Arctic Circle – at least for a short while.  Salt marshes were also the land of biting insects, unusual smells and at times dead zones.  At time they were places of incredible life while at others barren and desolate with some of the hardest climate extremes in the temperate zone.

I also was incensed by the filling of salt marshes – in the late 1960s after all they contained the pools, creeks even the mosquito control ditches had “valuable habitats” in them.  Creeks, I know they contained much life – oysters clams, blue crabs, you could see it, and the perception of marshes as disease vectors took a long time to extinguish and that happened in the 1970s.  But that also is part of salt marsh life.  That perception that marshes spread disease and vectored illness did have a foundation in truth, especially during the period I call the Great Heat, 1880-1920 summers here became very hot and a Malaria outbreak in Greenwich which spread to many coastal towns lead to efforts to fill them in, they had “bad” smells, biting insects – some that could infect you with parasites they were not the preferred coastal habitat type.  Salt marshes were accompanied by dread (insects) and fear disease – and at times noxious fumes.  Local Health Depts. (sometimes under State Connecticut public health directives) ordered them often filled a century ago.

Salt marshes have much different ecological services in different climate patterns – in cold amazing places of life in high heat, zones of death.  The salt marshes have a habitat history as well, born in periods of high heat and low energy and on occasion you could glimpse this habitat history.  I used to walk along the Hammonaset Beach after a February storm – long edges of peat/roots marsh banks were exposed filled with thousands of clam like borrowing shells – I had not seen before evidence of long ago marshes that over time been were claimed by the sea.  In the 1960s the State of Connecticut wanted to replenish (I guess today it is called beach nourishment) lost sand and along Hammonaset Beach by dredging up material about 1,500 feet offshore and in the process pumped up the remains of a prehistoric native American settlement placing many artifacts on the beach front.  I had watched this process not realizing what was happening in the late 1960s .  Hammonaset beach had lost about a foot a year for 1,500 year ago evidently the beach had extended much further out and sea level rise was an old feature of our shore.  In the 2000’s fill from this 1960s dredge project was again excavated (and created a great intertidal habitat) and placed in front of the remaining two west beach bath houses and artifacts again re exposed could easily be found again.  One day George Baldwin a Sound School teacher and I found several hammer, stones, cracking stones, George found a petrified tooth.  It was such a sight I had Sue Weber come out and see it also (she types many of these reports) and we had a great walk looking at these “old” shoreline relics. 

Much of these dredge deposits are still located on the park and reminders that this shoreline had been on the move retreating for hundreds of years. 

Salt marshes formed after the last ice age 10,000 years ago, in periods of heat and low energy – they need these periods to form and why in cold high energy periods they are apt to “disappear” along with the shoreline.  It’s not always constant heat and cold periods have happened before – heat and low energy they build in cold and energy periods they do not.  Nitrogen reduction does not impact the habitat quality in estuaries that obtain organic matter from land.  Bacteria in these salt marshes don’t need the oxygen from the short cycle they have already be sealed from it as Sapropel ages it collects and concentrates wax, as it becomes sulfide rich and purges H2S.  When it enters the sediment interface and disturbed forms a deadly sulfuric acid wash H2S04.  After storms this acid wash can be not only devastating to marine life but often dissolves metal lobster and crab traps – not unlike of the agricultural examples from the last century reported by the New Haven Agriculture Experiment Station.  When farmers re exposed it (Sapropel) to oxygen during land applications.  Rebuilding the short oxygen/nitrogen cycle does little to improve sulfate reduction below sapropel layers – dredging is the only to break this sulfide/ammonia cycle (or strong storms).  Therefore much of the habitat nitrogen problem can be linked to climate – not human factors and this includes a tremendous increase in organic matter from a rebuilt forest canopy.     

The Salt Marshes of Yesterday, Today and Tomorrow

In the 1870s here in Connecticut a cold and stormy period salt marshes were firm and hard – I recall some high school stories about that salt haying process from Charles Beebe (late of Madison) that the mashes were hard, then you could bounce a ball on them, but later to him the salt marshes became softer – horses had to wear special shoes (like snow shoes) to harvest this valuable salt hay crop.  At the lower edge of the East River he would point to a log (cord a row) road built to harvest the school meadow salt hay (Guilford’s early public schools were supported by selling public land salt hay crops) it was still visible in the 1990s about three feet below the present day salt marsh – he knew that salt marshes were building up because he could see the old road to support the wagons – it was no longer at the top, it was buried exposed by a dredge cut made by the Army Corps in the 1960s.  To him that was all the evidence he needed about sea level rise.  What had made the marshes in these low energy areas that would be leaves from terrestrial environments slowing over time collecting and composting in low energy regions behind barrier beach sand spits or bars built up at the mouths of rivers.  Heat is key because that typically meant that organic debris from land would slowly be reduced by bacteria slowing overtime in a long process I term the long sulfur nitrogen cycle – while cold and high energy periods favor the short oxygen nitrogen cycle – quickly rematerialized or moved by waves and currents.  The marsh surface would be firmer during these times.  Salt marsh habitats have two sides – the long cycle in heat/low energy and short cycle when it is cold and stormy.  In very cold times the short cycle can invade these deposits with bacteria consuming them in the presence of oxygen – they would appear to melt away or in heat/few storms to accumulate organic matter and grow up in response to constant sea level rise (estimated to be seven inches here in the last two centuries).

Just as sand dunes are deposits of sand that for a time can “protect a shore” salt marshes fulfill a different “bank” function only with organic matter.  In cold and stormy periods it is natural to have organic matter loss as oxygen levels favor faster “composting” processes and build up as leaves and organic matter slowly rot in heat in a very long process that overwhelmed bacteria as it collects in low energy areas.  These cycles are very long and we can’t see the entire process but reminders exist like the buried log corduroy road in Guilford’s salt marshes.

That is the problem with the global warming sea level rise – what we today value in salt marshes will turn against us – as what we perceive marshes to be and the role in marine ecology they enjoy while see a quantum shift.  In a global warming scenario with sea level rise salt marshes turn into natures killing fields vanquishing those organisms that need oxygen while furnishing those that prefer sulfur the food and nourishment they need long locked in these organic deposits with a “salt marsh crust” the vegetation that binds them.  The instruments that will wage war upon oxygen dependent life (and us) is bacteria and opens the door to bias in the literature about salt marshes and how we perceived them today.  This bias is connected to public policies of these hot and cold periods as well.  In high heat and during the Malaria outbreaks of the 1900s (see Climate Change in Public Opinion written in 2008 – IMEP #16).  Salt marshes were seen as deadly dangerous places and the public policy response was simply to fill them in – in the 1910s it was an honor to serve on such public good committees to fill them in – such as here in New Haven sometimes under State Health Dept directives).  In the colder periods salt mashes were valued as hunting grounds (ducks) or salt hay crops. 

The last Malaria outbreak in Connecticut occurred in 1938 as it turned colder here Malaria had ceased but the public perception of marshes as ill smelling disease ridden lands continued far beyond the Malaria outbreaks attributed to them.  With a colder negative North Atlantic Oscillation colder water meant more oxygen – with sea life abounding during a short cycle nitrogen reduction period.  Colder water naturally contains more oxygen – organic matter was quickly consumed reduced by oxygen reducing bacteria – but smells during the Great Heat (the infamous hydrogen sulfide smells frequently attributed to hydrogen sulfide heat or rotten eggs that quickly spoiled in the 1890s) had now disappeared, fish kills (now linked to sulfate reduction) became rare as the coastal energy now increased.  The 1950s and 1960s had cold winters and hurricanes the organic matter was quickly recycled or moved, Sapropel or “black mayonnaise” deposits subsided, inlets opened from strong storms and colder oxygen containing sea water entered again – killing off the sulfur bacteria and replacing bottoms with those bacteria that need oxygen.  Greater storms and now alkaline sea water assisted the removal of organic acids (mostly sulfuric acid) in marine soils and sets of quahog clams then soared as oyster recruitment declined.  Out of sight and leaving few clues of previous battles (other than in core samples) bacteria waged war and in this cold and energy period sulfur bacteria had now clearly “lost.”  Oxygen requiring bacteria had won and the organisms that needed them thrived.  The 1950s and 1960s are now recognized a being a negative NAO – a period of cold and many storms – it was the time of the “great quahog sets,” improved lobster recruitment and the return of the bay scallop.

Clint Hammond on Cape Cod often described the Atlantic Oscillation – during the fifties the term polar Vortex came into being.  (I was not familiar with this climate pattern at this time (1980s)).  After many decades the Chatham shore front was on the move again retreating from the relentless series of Northeasters each storm would change Monomoy a barrier spit in the southern section of Chatham, MA where he once shellfished it had a notebook filled with notebook habitat observations and sketches with descriptions of Powder Hole aquaculture experiments on Monomoy that no longer existed – they had been washed away.  Looking back I wish I had spent more time on these notebooks but at the time the study of shoreline change seemed so remote from the population changes in “sour bottoms,” he described to me but it was all connected and on the Cape these concerns thrust themselves into the print media.

-   Salt water intrusion into the ground water and the thin lens of fresh water in times of droughts.
-   Bacteria levels were high immediately after heavy rains
-   Warmer waters had more algal blooms and the “bad” summer smells from the marshes had returned.

Mr. Hammond felt the climate was turning against the in shore shellfishers and had linked in increase in foul smelling bottoms as evidence of this transition and wanted researchers to look at the bottom – he termed it compost (he called marine humus).   He had a practical example of this marine compost – mixed with oyster shell, huge tomatoes grew along his front walk.

He was concerned that with all the current debate about nitrogen no one was looking at what he termed “hard nitrogen” (hard because it was in a solid form mostly leaves) everyone was looking at nitrogen inputs from people or farmers.  What he called humus I called Black Mayonnaise and most likely he was emphatic regarding this research need to him was going nowhere – it had been missed but not by him or area shellfishers – it was for them hard to miss.  It had built upon shellfish bottoms and often contained a crust of eelgrass.  What he was concerned about climate change would be missed but not only from ignorance but public policy decisions made decades before.  In the 1960s after all it was policy to fill in salt marshes that would change in the 1970s.

Salt Marshes and Public Opinion

“Save the Salt Marshes” was the cause to finally galvanize public opinion in Connecticut much of that from Ann Conover in Guilford, CT (see climate change and public opinion IMEP #16.  Blue Crab Forum™ ( fishing, eels oystering  thread).  The salt marshes should have been saved, building close to the shore was something many coastal residents had already learned following the Great Heat (see Clinton Harbor and The Great Heat on the State of Connecticut Shoreline Task Force website) especially those in the middle to east sections of CT – subject to higher energy levels.  Their homes and land had been washed away.

Nixon and Oviatt 1973, Cordell 1975

Oviatt, A. S. Nixon 1975 – Sediment resuspension and deposition or organic matter in Narragansett Bay Estuaries Coast and Shelf Science 201-217.

Experimental Studies of the effect of organic deposition of the metabolism of a Coastal Marine Bottom community John R. Kelly – Scott W. Nixon Marine Progress Series Vol 47 157-169-1984.

A growing environmental movement soon saw the need for a massive educational effort to inform public policy makers about the value of salt marshes and in time sought out the education community to provide such an effort.  At first the process seemed sincere – after all salt marshes were important and integral parts of the shore and the web life in it.  But over time a bias in the research (much funded by environmental protection interests) became apparent to assist preservation and conservation efforts (It was the early 1970s in which public opinion changed from areas that needed to be filled) of salt marshes.  In time the value of salt marshes was highlighted and overtime increased – organic matter generation (grams of organic matter from square meter) and the grasses that lived in these grasses promoted the value to the marine “food web” one of largest education components (products) of this effort.  While salt marshes are important to numerous species it is a harsh environment in New England extreme heat and cold – they have far different ecological roles and “value” in different temperatures or climates.       

The University researchers often responded to this public policy agenda and naturally brought to the public information about the value of salt marshes – during that period in which the short oxygen nitrogen cycle had won – “forgotten” was The Great Heat (1890s), a previous time when sulfur reducing bacteria had won – sending oxygen requiring organisms into full retreat.  The “dead zones” created by sulfur bacteria or the toxic sulfides released by them so foul smelling that it would drive people at times from the shore itself in the 1890s.  The fish kills, red tides and black water deaths (now linked to sulfide purging of organic deposits) of the last century were forgotten – the long sulfur nitrogen cycle was replaced by studies of the short oxygen nitrogen cycle – it wasn’t that researchers did not access these historical records many did, it just did not fit what public policy decisions makers asked about or what conservation groups petitioned to do.  The bias came in around the value and benefits of salt marshes – from organic matter sources to bacterial respiration to ecological services.  In times of cold and sufficient oxygen levels salt marshes provided important habitat services to the species that the public could appreciate (USFWS Paul Galtsoff is credited with making that public policy connection) but in heat and low energy these same salt marshes became natures sulfur killing fields – toxic to many terms of good value marine life while becoming a source of pollutants and death to larval life forms.  That side is rarely presented to public policy decision makers but it is there none the less.

Fishers have experienced these bacterial habitat battles by the seafood they later catch, and a cycle of abundance that over the centuries would suddenly appear and just as quickly disappear.  Sometimes the appearance of new seafood was a “shock” or surprise.  These cycles give us a picture of what hot and cold periods would look like – warm in which sulfur will triumph in the shallows, cold in which oxygen life forms prevail or “return.”  And the organisms that shape the rise and fall of sulfur in seawater is bacteria.  They control to large extent the survival of the smallest life forms to the abundance of “forage” fish.  At times even adult fish can be killed by the residues of these bacterial battles – known as fish kills they frequently happen in the shallows.

Aquaculturists have known about bacterial habitat wars by using the same filtering mechanisms which nature provided.  Certain bacteria will convert some of the toxic ammonia compounds to nitrogen gas, others will change ammonia to less toxic ready nitrogen forms of nitrate and nitrate each in its own subject to chemical processes.  In closed systems and wastewater treatment plants we have cultured the “good bacteria” to make toxic compounds less toxic and facilitate nitrogen compounds forming a gas but in high heat these systems “fail” as the key ingredient in these bacterial reactions is oxygen.  (Often referred to as activated sludge).  Once oxygen is removed or lowered the sulfur bacteria “win” and the recipe for oxygen species down fall has already been scripted – sulfate a sulfur cycle compound that has four oxygen atoms around it is abundant in seawater.  Once the water warms the oxygen bacteria die off and the sulfate bacteria take over organic matter reduction and in the process release sulfur compounds toxic to oxygen requiring organisms – global warming would do much to change many salt marsh shaking current environmental beliefs and values namely –

-   Greater amounts of deadly toxic (antibiotic resistant bacteria strains) will be found in warm shallow organic deposits such as mud flats and salt marshes – some harmful even to us (That is already happening).

-   The good bacteria (many sustained by nitrate) will give way to sulfate reduction in salt marshes – releasing ammonia compounds that sustain toxic algal blooms.  In fact salt marshes will discharge now nitrogen “pollution.”

-   Bacteria counts in warm water are naturally higher and shallow areas (swimming fishing areas) will show naturally higher levels.  (In the 1950s, 1960s LIS water was colder and contained less bacteria) increased leaves and storm water organics will feed bacteria in or near salt marshes.  These deposits will culture enormous quantities of sulfur reducing bacteria.

-   Algal blooms prevent ultraviolet light from killing bacteria – a common filter system for pools and aquaculture for UV light tubes to work water must be clear.  Cloudy water will have more bacteria, ammonia discharged from water will nourish brown tides – making this condition even worse.

-   Natures filter which uses nitrate as a low oxygen buffer will fail producing increasing amounts of ammonia low oxygen conditions (Waste Water Treatment operators knew that nitrate was essential to keep filters alive in hot weather).

-   Years of environmental policies of non disturbance – anti dredging will give way to deeper colder water dredged to remove the food for bacteria in stagnant poorly flushed areas.  This is equivalent to aeration by mechanical means – energy is one of the few things we can do in a warming climate.

-   Oyster fishers would naturally rake off leaves from oyster beds each spring before they could kill oysters – later these leaves in hot weather became Sapropelic – the rotting of organic matter without oxygen creating a sulfur rich ooze Sapropel.  This is a form of turning the compost – both to remove it and oxygenate it.  Sapropel has left a habitat history in coastal core samples.  Deep Sapropel once disturbed will provide a sulfuric acid wash – minimized by the presence of estuarine shell.  Farmers in the last century had Sapropel tested by the New Haven Agricultural Experiment Station which consistently reported high sulfuric acid levels.  To offset this “harmful acidity” they blended in oyster shell (lobster shell was used in the northern).

-   Nitrite and nitrate nitrogen compounds will no longer be considered foes but friends in this bacterial conflict.  Evidence is already coming in that human nitrogen forms help prevent sulfur production and feeds natural bacterial systems (called annamox bacteria) that take ammonia out of seawater.  Bacteria filters in the natural environment take time to build and respond to cycles as well.  Aquaculture closed systems also have similar bacterial “filter start up” periods.

-   Dead zones will be associated to organic matter and temperature – dredging will be one of just a few tools we have to influence both allowing cool waters into warm shallows and depriving bacteria of its culture media, its food.  Cooler water can contain greater amounts of oxygen, but in heat greater amounts of sulfate as well.

-   This bacterial conflict has a direct impact over time to the rise and fall of coastal fisheries.  Oak leaves are particularly damaging as its leaf is both tough (complex cellulose) and contains wax (as a protection against water loss in droughts).  Oak leaves during dry periods will have a shine to protect the moisture that is the paraffin wax.  As sulfate reducing bacteria consume them they leave the wax behind the source of “sticky” bottoms.  As this occurs (when the wax (they cannot digest it) seals soil pores) forming Sapropel below.  In addition oak leaves have a low pH, 3.5 and release tannic acid which tends to clomp marine algal helping organic deposits to purge ammonia and sulfides – oak leaves can turn healthy bottoms into sulfur death traps.

-   Sulfate reducing bacteria naturally complex metal salts and over time various metal sulfides can increase in these organic deposits.  Over time (SRB) sulfur reducing bacteria concentrate these metals (including it seems under the correct conditions, even mercury compounds) especially aluminum which is acutely toxic to nearly all forms of marine life.  Some of the heaviest concentrations of metals and toxic discharges will come from salt marshes.  The affinity of Sapropel (sulfur reducing organic mater) to bind heavy metals so well it is considered overseas a method of cleaning up metal acid mining waste waters EPA investigated this possibility in 1982 and published some of the first papers suggesting the use of sulfur reducing bacteria to clean up acidic mine wastes (see EPA Study Tabak: et. al 2003).

Sulfur Sapropel Cycle – What fishers report –

This bacteria change which in itself may take decades, has a direct connection to shallow water nursery habitat, frequently termed “critical or essential” today.  Many fisheries depend upon these salt marsh habitats – creeks, ponds, coves and bays for segments of their life cycles, the egg and larval forms which contribute to diversity and biological richness – in the presence of oxygen. 

In the presence of sulfur compounds these areas are now barren and quite opposite, the perception of today mud flats that are nearly devoid of life (some sulfur tolerant worms can be present) and purge ammonia in high heat and sulfides in cold.  Both sulfide and ammonia are highly toxic to fish and shellfish, (even eelgrass) it is the rise and fall of many species that depends upon inshore nursery areas remaining viable habitats – they can look the same but have deadly consequences until bacteria types reverse. 

In hot periods of few storms organic pulse loading (after tropical rains for example) can overwhelm oxygen bacteria as sulfur reducing bacteria “take over” – in fact the same habitats that for so long were valuable and significant become natures killing fields wiping out reproductive capacity before fish and shellfish hatch – these toxins destroy the eggs themselves.  They rob the seafood cradle.  Years later as recruitment failures mount the fisheries collapse.  This is the “empty net syndrome” so often found in the historical literature and often attributed to “overfishing.”

Salt Marshes Habitat Failures - 

 The war between these bacteria have generally not been recognized by the marine community, some may be attributed to the public policy commitment of protection – another might be a funding bias called the funding effect, that grant supported research often has a institutional bias (whether we recognize it or not).  I feel it is a combination of both – for so long salt marshes have been a fixture of environmental protection – as something we should protect (which we should I agree) as it hard to explain that if the waters continue to warm – salt marshes will succumb to sulfate reduction – become rich in heavy metals and purge deadly ammonia.  Some highly toxic alone, like sulfide and purge substances toxic to oxygen requiring sea life.  The concept that Sapropel bottoms can produce toxins is opposite the non disturbance/no dredging policies of the last half century – cold water and energy are most likely two of most important tools to fight sulfate reduction – non disturbance is actually a policy that in this case helps “sulfur win.”  When sulfur wins the seafood we value loose.

 Salt Marshes Habitat Cycles –

Species that utilize salt marshes and have longer life cycles have a built in safety feature, they are outlast short term habitat failures.  (Hot climate cycles) short lived species such as bay scallops show wide swings in abundance.  That happened with striped bass – the young of the year index failed to produce for several years viable young – although suspected chemical pollution (that certainly did not help) these inshore habitats likely failed before other habitats were available, they became hot and in low dissolved conditions sulfur reducing.  When that happened ammonia levels most likely surged fueling opportunistic algal species that need ammonia – algal blooms strange to us (and deadly to others) we call today harmful or HABS for short.  Since sulfur reducing bacteria like hot shallow areas rich in organic matter they deliver the ammonia in areas that are also poorly flushed – so most HABS get their start in the shallows (most HABS cysts also in habitat these shallow areas even red tide species) and extend out when these algal blooms persist  they take any available oxygen with them as surface bacteria break them down on the immediate surface – a thin film of bacteria oxygen reducers and the ammonia surges get stronger, fueling the HABS and the cycle builds upon itself until storms or colder weather breaks it.  Much of this habitat cycle is first noticeable in shallow warm areas of salt marshes fishers often noticed blue crabs trying to climb out of the water during ‘events” when the sulfur cycle briefly triumphs in the historical literature they are called blue crab “jubilees.”

Over Fishing and Nursery Habitats – Salt Marsh Indicators

As many species can live past a short term habitat failure – over fishing can occur and many times masks the habitat failure – most of which start in the shallow salt marshes deprived of energy – from natural or manmade.  That is why winter flounder fishers first noticed “black mayonnaise” accumulating in these “quiet” low flow poorly flushed areas – in eastern CT it was often behind railroad tidal restricted causeways.  {But it can be any restriction, a culvert bridge restriction or dam – all have the ability to slow water and collect organic matter.  Many blue crabbers have experience this sulfur smelling compost while blue crabbing).

It was the shellfishers and winter flounder fisheries that reported first Sapropel deposits accumulating behind them.  When shellfishing areas where closed in Connecticut (from bacterial levels) inshore shellfish beds were deprived of “harvest energy” the raking scratching and lifting of leaf deposits that kept the marine soil cultivated and exposed clean shell cultch for oyster spat falls.  When these inshore areas many containing essential habitats for other species failed (they were covered with organic matter) they lost important ecological surfaces and in high heat – sulfate reduction. 

Striped bass for example would continue to lay eggs in habitats that in late summer that later turned deadly.  As no year classes survived eventually a fishery failure occurred, and lead to strict catch limits even moratoriums in some states.  Eventually some areas recovered sulfur bacteria had eaten huge volumes of marine compost Sapropel now suspected to have arrived in a pulse following Hurricanes Agnes in 1972.  It took almost two decades for these habitats to recover (my research) and again produce good young of the year – a series of storms can also sweep out Sapropel and the sulfur reducing bacteria with them.  This can cause reversals most often dramatic after hurricanes.  (The replacement of Sapropel eelgrass with kelp cobblestones after the 1938 Hurricane for example) and return under cold conditions oxygen where fisheries continue under many years of poor or no year classes it can collapse – giving the appearance of over fishing (this does not include discard waste of fishing mortality) but was really a series of habitat failures that in time produced a fishery failure.  The Southern New England die off of lobsters in 1898 and 1998 as past and current examples. 

When these shallow habitats salt marshes habitat are more closely examined evidence from other studies indicated they most likely became Sapropelic – Sulfur “had won” and had turned against the oxygen life forms.  When that happened aluminum most likely leached from marsh organic deposits (helped by acidic river washes from Tannin) and killed eggs by the millions, we have an example of the striped bass in the 1980s.  They life cycle of the striped bass enables it for a while to outline the short term habitat failure and can recover as habitat conditions improve.  The predator prey species adds another feature a good year class of stripers when forage fish is at a low level.  This is what I believe happened in 1932, the best year class of stripers were apparently born when there was little food (forage) and starved.  Not only do the species we consume have cycles but the forage and prey species as well. 

Sea Level Rise and Salt Marshes

Although it is difficult to imagine and only those with experience in bacteria culture media will recognize what salt marshes can do – they are natural organic supply (media) culture for sulfate reducing bacteria – the species that will turn salt marshes into a battle zone.  Sea water rich in sulfate (what SRB need) will now flow over the marshes bathing them in this sulfur/oxygen molecules as salt marshes now “burn” into the sulfur cycle.  This has happened before during the warm (hot) period of 1880-1920.  Nichols a botanist and researcher in this period often comments on salt marsh sudden “collapse” – pools left in salt marshes as sulfur reduction below eats the marshes from below – eventually releasing pockets of gas and the salt marsh surface sinks into a sink hole (This can happen on land as well – sink holes and areas in which wood (organic matter) was buried during construction projects).  In high heat the sulfur reduction takes place deep within the salt marsh deposits themselves and can leave depression or salt water pannes instead.  Researchers in the early teens had already noticed a sulfur link – in the heat the sulfur content of this hot surface pools became very high (sulfide) and helps explain the hardiness of these marsh plants to tolerate sulfides – up to a point – then a die off would occur in high heat it is not surprising that often the peat now is “barren” and easily washed away.

Salt Marshes and Deadly Bacteria

Salt marshes with rich amounts of partially decayed organic matter give rise to the first sulfur reducing bacteria.  They act as solar collectors warming in shallows as water can become “hot” and oxygen levels low.  The first necrotic bacteria disease for winter flounder came from the shallows.  Lobster shell disease also appeared first over organic sludge in the 105 dumpsite, it also is implicated know for vibrio bacteria series and other flesh eating bacteria (often termed antibiotic resistant).  As the climate warms these bacterial strains flourish in hot organic matter and appear to be increasing – as reports of dangerous bacterial infections appear to be on the rise as well.  But all shorelines have bacteria – a film of bacteria coats sand, pebbles almost any surface.  The ones in colder water are oxygen requiring and helpful.  Some of the first bio filters enclosed system aquaculture used oyster shell bio bacteria surfaces later a rotating contact filter had bacteria exposed to oxygen.  The industry today had gone over to a multi surface pack or ball in motion to help oxygen requiring bacteria to convert toxic ammonia to less toxic nitrogen compounds.  (Termed also bio extraction).

That is how in the natural environment the “good bacteria” help remove ammonia from the sea water – they need oxygen and when it is not in the water, use nitrite sulfur reducing bacteria strains increase – the hot water bacterial infections that have plagued fishers and beach goers of recent times (and serious if not life threatening bacterial infections have resulted).

In heat it is the marshes and soft organic deposits in them will culture the first generations of sulfur reducing bacteria – which has already occurred during long very hot weather and can be found in those habitats.  As these strains use sulfate as an oxygen source (and sulfate is not limiting in sea water) – eventually sulfur reducing bacteria will “win” and dominate the bacterial spectrum.  When that occurs the products of salt marshes we value will turn negative – bacteria that rots flesh, complexes heavy metals produces ammonia will cause new habitat profiles.  Many will not be liked or “valued” some outright dangerous to us, and the marshes of the 1950s and 1960s will not resemble the future salt marsh habitats of the sulfur cycle.


Did We Impact The Future of Salt Marsh Filters

As the climate in southern New England warmed we had indicators of bacterial changes – lobsters and winter flounder had bacterial infections, vibrio series closed shellfish beds and bacteria counts on beaches went up.  The flounder fin rot disease was mostly likely the first warning bell raised by fishers but bacteria is natures way of cleaning up excess and form complex filtering systems.  Some of which we use in closed system aquaculture and on a much larger scale waste water treatment plants – after all the term activated sludge is a nice way of saying bacteria rich organisms –we depend upon nitrogen filters to replicate what nature does naturally.

Since 1972 nitrogen has been linked to zones of low oxygen and programs have been initiated to remove the access.  In this process nitrate was removed so was nitrite, nitrate was a secondary oxygen source for good bacteria filters, and nitrite the source of a bacteria group that use it with Ammonia – both natural filter systems.  With annamox bacteria the result is the conversion of ammonia to nitrogen gas.  Both these filter systems would act to lower ammonia, the first by preventing its formation by sulfur reducing bacteria – the second by using nitrite to power annamox bacteria strains that would remove it.  Research today in looking at these complex bacteria filter systems and removing nitrite and nitrate in reducing water dissolved forms slow natures, natural filtering capacity?  By removing these nitrogen factions in low oxygen conditions, did that open the door so to speak to sulfate reduction – ammonia levels would soar and appear to by purging from hot organic matter deposits.  The first ammonia plants merely heated organic matter to produce it (see IMEP series #26).  (The American Fertilizer Magazine Jan. 1903, Vol 28, pg 14). 

One of the current questions is that nitrite/nitrate removal impact natural filter systems and did that influence high levels of ammonia from organic deposits.  Some of the first results of ammonia levels from organic matter (Sapropel) are coming in and they are large numbers.  The nitrogen compound flux (commonly called benthic flux) is now showing large amounts of ammonia the primary nutrient source that sustains Brown Tides (Harmful Algal Blooms).  In other words by removing nitrite and nitrate did we just make room for more ammonia production toxic to sea life itself but also sustains HABS which also create different toxins damaging to more sea life, including us with the red tides?  It’s a huge question and one that involves nitrogen removal programs along our coasts.  Sapropel formation and the chemical processes within them first occur in salt marshes, in terms of salt marsh ecology these factors appear to be missed in most of the recent nitrogen studies.

Salt Marshes of The Future?

As what will happen to salt marshes in the future has much in what direct bacteria pathway is “open” and at what climate period.  So much of what bacteria prevails “wins” in a long term habitat battle.  For dominance of each fishers’ have already experienced by observations of fish and shellfish cycles of abundance – in hot periods of relatively few storms.  The sulfate – sulfur cycle pathway is “open” and we see die offs and species shifts.  In times of cold the oxygen nitrate pathway is open as bacteria consumes organic matter in the presence of oxygen, we also see a species shift as well.  The cold water species suddenly “return.”

In continued heat and few storms salt marsh organic deposits will enter sulfate reduction – Sapropel will start to form with all of its deadly by products.  Salt marshes may recede below sea levels in tidally restricted areas.  Offsetting this subsistence is an increase in organic matter (primarily leaves) that are captured in estuaries but this organic matter (primarily leaves) that are captured in estuaries in high heat low energy become Sapropel’s.  Salt marshes are merely Sapropel deposits that have been colonized by grasses.  When chemical processes occur in Sapropel will eventually occur in salt marshes leaving holes that become salt pannes.  This has also been recorded in the historical literature – as sea levels rise sulfate in it will wash over salt marshes as they die back in the zones that obtain the most sulfate (usually creek banks because sulfate will flow in with the tides) and get “hot” with summer sun.

Eelgrass has a role in the final end of salt marshes it builds up along the edges of channels slowing tidal flows – less and less oxygen will become available – gradually opening the sulfur – sulfate pathway – closing the oxygen – nitrate pathway and Sapropel shedding of ammonia, aluminum and sulfide all toxic to marine life.

Marshes will produce sulfide rotten egg smells as they did during the recent hot periods – at the same time complex heavy metals and purge aluminum in deadly concentrations.  We have two studies one in Guilford (1994) and the Herring River Wellfleet (2012) tidally restricted that became a nutrient pollution source (ammonium) and seep toxic aluminum.  Salt marshes will become natures killing fields as the sulfur cycle tries to end the oxygen cycle – sulfides will increase and become intense (some sulfide events were so extreme they would oxidize paint on homes) the rotten egg smells of The Great Heat 1880-1920 permeate summer nights.

Sulfides will build up from below reaching the marsh surface damaging plant specialized root cells resistant to sulfide but in extreme conditions even the marsh grasses will weaken (many advantageous fungus infections now set in) the plants making them more susceptible to secondary infections.  As plants die the brown-black surface will act as a heat sink activity sulfate reduction deep below the marsh surface.  Natures marine compost pile will “burn” in intense heat as bacteria now consume it from below.  Sapropel ‘s will also now become warm and purge ammonia – as fresh organic matter is deposited on them they will also build up (constantly noticed by shellfishers and crabbers) become greasy to touch and acidic.  If Sapropel is dislodged the sulfides in them will turn to sulfuric acid – the acid wash that dissolves metal crab pots and in time anchor chains.  Many Cape Cod fishers would notice sulfide damage on salt pond moorings term it the “dead line.”  Acid washes will occur and die offs of fish/crabs become more evident – the waters may now be a continuous dead zone ruled by sulfur and toxic sulfides.  In the end heavy metals – by acid waters especially aluminum now are discharged killing the eggs and larval forms of fish and shellfish we value and algal species who can grow on ammonia – cloud the water preventing UV light (natures natural antibacterial agent) from killing the bacteria below.  A natures clean sweep of oxygen dependent life forms.  Salt marshes are in fact sulfur’s army in reserve – Sapropel just a battleground.

That is why it is so important to monitor Sapropel ‘s and ammonia discharges from them.  They are the sulfur/oxygen battlefield – did we help sulfur win by removing nitrate or remove nitrite a source to start ammonia removal by anammox?  Two good questions and why Sapropel study should be top of the climate change research storyboard – unfortunately it is not.

At a critical time in climate change discussions Sapropel was missed – we need to know much more about the bacterial communities in them – the battlefield is in full view – cold winters oxygen is returned, organic matter is digested and rematerialized Sapropel formation is limited, but in heat and warm winters Sapropel can grow – and in it sulfur reducing bacteria can increase.  In long hot low energy cycles we see Sapropel’s build up with its horrendous sulfur impacts, in cold and stormy periods Sapropel’s appear to melt back to the “black sands” described on Cape Cod when salt ponds cut off from tidal flows – suffered black water sulfide fish kills until good circulation was restored – frequently by dredging. 

Sapropel is natures living marine compost pile – and similar to land compost when oxygenated will slowly be reduced and appear to melt away.  It is also where the sulfur/oxygen struggle to dominate can be closely watched.  Since heat seems to be so critical to these bacterial reversals the shallows that warm and hold heat will show the first reversals.  Deep cores in salt marshes may also signal sulfate reduction below marsh surfaces and the formation of pools of liquid Sapropel beneath them.  In times as these pools form and move towards the surface a section of salt marsh may collapse forming a sink hole.  In warm climates entire salt marshes will retreat, as the leading edges succumb to increased sulfate reduction, and farthest from organic matter (closest to tidal waters with sulfate) a life or death battle between temperature organic matter and bacteria occurs.  Some salt marshes deprived of terrestrial organic matter – and restricted flows will “sink” and then as more sulfate saltwater flows in be consumed from the surfaces well.  Eventually the grass will be killed by sulfides and leave a bottom mud flat which now turns to Sapropel in low oxygen conditions.

The sulfur cycle is deadly to many of the marine life forms we value as food – that is why we try to limit sulfur in emissions into the atmosphere – after all that is how it got into coal – as fossilized Sapropel is just coal.  The sulfur cycle is very bad for us and the marine organisms we value as food – not so much nitrogen.  We decided to wage war on nitrogen but in a warm future sulfur will be much more of a foe.  In fact in time we may learn we focused on the wrong nitrogen compounds as well.

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« Reply #1 on: September 10, 2015, 04:53:20 PM »

good read once again


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« Reply #2 on: September 29, 2015, 06:43:58 AM »

Tremendous read.    Thank you.

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