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« on: April 12, 2022, 09:15:38 AM »

EC # 22-B Bacteria and Submerged Grasses
The Chemistry and Biochemical Processes of Sulfide Tolerant
Plants and Bacteria Nitrogen
The Nitrogen/Bacteria Series on The Blue Crab Forum™
Viewpoint of Tim Visel – No other agency or organization –
August, 2020 – This is a delayed report

Marine sapropels used in historical agricultural applications often required shells to offset sulfuric acid and also rain weather leaching of salt and in some cases heavy metals which is a natural sulfate bacteria reduction chelation process.  Mussel and oyster shells are the most frequently mentioned as offsetting acid conditions in the historical literature.  Although heavy metal content is often viewed as a negative soil component, in soils with a low clay content sapropel is being looked at replacing key metals needed for acid leached soils for plant growth.  An excellent write up of marine sapropel and humus harvests is found in a paper titled “Drawing Lines in the Ice Regulation Mussel Mud Digging in the Southern Gulf of St. Lawrence” by Joshua D. MacFadyen (2013).       

And after 115 years after the first agriculture Experiment Station report - A March 1994 US Army Corps of Engineers – New England Division section 22 grant for Connecticut titled Wetlands Restoration Investigation Leetes Island Salt Marsh, Guilford, CT foreword prepared by the Connecticut Dept of Environmental Protection, Office of Long Island Sound Programs for the Leetes Island report pages 1 and 2 contains these sections (author not identified).

“The soil in a salt marsh is known as peat, which is composed largely of decomposing remains of plant material.  Organic peats only form when the soil is water logged and anaerobic.  Under these conditions, iron combines with sulfate (a common constituent in sea water) to form the mineral known as pyrite.  Draining of the marsh causes the water table, which is normally within several inches of the surface, to drop several feet.  Thus the upper several feet of the soil are now exposed to oxygen or oxidized.  Under these conditions the organic component of the soil decomposes at a very rapid rate” (the marsh sinks or slumps – T. Visel).

However, the formation of iron sulfides (pyrite) deep in the peat leaves a potential to later purge sulfuric acid – something that the agricultural community had discovered a century before with the utilization of marine or mussel mud for terrestrial manure – once exposed to oxygen a dramatic release of acid and a lower pH.  This also tends to release metal sulfides from sulfate reducing bacteria which is found today in acid mine waste water.  This section also in the Leetes Island, Guilford, CT section 22 report (author not identified) from the 1995 CT DEP Office of Long Island Sound Programs Foreword, pg. ii –

“Draining causes chemical changes in the soil which cause the marsh to become a non-point source of water pollution.  Specifically, pyrite (iron sulfide FeS2 – T. Visel) is unstable when exposed to oxygen through a series of chemical reactions pyrite is converted to sulfuric acid which in turns causes a drastic decrease in soil and creek water pH.  Levels as low as 3 to 4 are not uncommon in drained salt marshes.  These altered soils are called acid sulphate soils.  Under such low pH values, the aluminum associated with natural clays is mobilized (released T. Visel) and this metal is toxic to aquatic organisms at very low concentrations.”

For marine soils and in which eelgrass lives, this sulfide – sulfuric acid relationship is also oxygen driven by seawater temperature over long periods of time.  A warming of seawater would tend to shift to lesser oxygen availability and sulfides would now increase and with that change greater acidity.  This change is only apparent in site specific studies with a composition to climate – the NAO.  One such study – Feasibility of Inactivating Phosphorous with Aluminum Salts in Ball Pond, CT – Wendell A. Norvell CT Agricultural Experiment Station, Bulletin 806 Sept 1982 (New Haven, CT).   

A transition occurs as water warm – organics are reduced in the absence of oxygen and sulfides rise, this can occur in the soil “black layer disease” or the sulfide deadline.  As sapropel can purge sulfides into the water – a rise in sulfides is a way to examine this change as compared to colder oxygen rich waters.  Only long term examinations of a site (which are relatively rare – T. Visel) can this be illustrated.  The study of Ball Pond provides a look at this important feature, from Norvell (1982).

“During 1980, hydrogen sulfide was found throughout most of the hypolimnion, (a layer of cooler water with warm water over it - little mixing, T. Visel) with concentrations approaching 2 ppm in the deeper waters.  This too is an index of eutrophy, and also of major change since 1939 when Deevey noted that iron dominated the redox system rather than hydrogen sulfide, Connecticut State Board of Fisheries and Game 1942.  (Note the winter of 1933-34 was very cold – followed by the Hurricane of 1938 - cooler and well mixed conditions – T. Visel).  At present, reducing conditions in the hypolimnion are much more severe with sulfate undergoing reduction and hydrogen sulfide accumulating “throughout the summer.  The anoxic sulfide rich waters of the hypolimnion are not suitable habitat for trout or most organisms.” 

As marine soils change so does the ability to eelgrass to live in them.  In fact, in times of heat and low energy (to cultivate soils) eelgrass is doomed by the sulfur cycle it helps create.  Although many reports continue to link the rise and decline of eelgrass to human activities, even the construction of roads or mooring anchors these are popular topics for grant funds rather than examination of the soil in which eelgrass lives.

When eelgrass is found in shallow bays or those with long connections to the sea it holds at thin grasp on the soils it can live in.  It should not be considered a permanent habitat type but one that is subject to changes in the soil itself governed by the chemistry of composting.  In this case the composting in high heat low energy conditions strengthens the sulfur cycle.  In the historical literature it is referenced as “stagnation” both for water and soils.  Kaare Munster Strom in his 1938 paper titled Land-locked Waters and Black Muds (Recent Marine Sediments, 1959) mentions the impact of hydrogen sulfide, Strom –

“The biological effect of stagnation are mainly a sterilization of the bottom sediments and the open waters from a certain depth downward.  If a total renewal of the bottom waters occurs, those containing hydrogen sulfide are sometimes lifted to the surface, and cause a catastrophic death of the fauna that normally lives in the upper waters.  In localities with nearly fresh surface waters, a salt water fauna may have a precarious existence between the fresh waters of the surface and the poisoned waters of the deep.” 

It is below the poisoned waters of the deep one can find the “dead soils.”

One feature of coastal marine soils is their ability to collect and hold clay particles.  Clay has a negative charge and holds positive charged ions called cations.  The amount of lay in the eelgrass soils may be an important indicator of CEC, cation exchange capacity of the soil.  Shellfish research conducted on Cape Cod by Karl Rask found the CEC was impacted by soil cultivation that cultivated soils has a lower CEC – likely do to removal of organic matter and clay particles.  Therefore, if CEC important to the growth of plants it may represent a way to determine eelgrass soil quality.  Shellfish researchers have reported slow or no growth attributes of marine soils for the quahog clam – Mercenaria mercenia for decades (Environmental Factors Affecting Growth in Venus Mercenaria, David M. Pratt and Donald A. Campbell, 1956).  As eelgrass can live in shallow soils after a period of strong events (a negative NAO), the soil health would naturally decline as these soils (eelgrass blades) collected clay particles. This could be measured as increasing CEC values.

One researcher who conducted research on this aspect of clay is Erin Aiello, Factors that Affect Eelgrass Growth in Morro Bay Sediment and Light Differences Part 1 (2019) – The Marro Bay National Estuary Program.  In this study the amount of clay in sediment (soil, T. Visel) was lowest at the estuary mouth and highest in the upper reaches of the estuary – it is an interesting review of soil capacity.  We need additional studies like the one above to more fully understand our eelgrass soils – my view. 

I respond to all emails at [email protected]

Fish-Sugar Cane and Sulfide Waters

One of the aspects of biological filters, the use of plants to absorb compounds from water, some of them toxic to seafood such as ammonia.  Sea lettuce for example can remove tremendous amounts of ammonia.  High ammonia levels fuel the rapid and thick blankets of Ulva lactuca – sea lettuce.  That ability of removing ammonia from the water is now considered a way to cleanse water of ammonia.  For decades, it was known that the Broadleaf Cattail, a fresh marsh plant Typha latifolia, could absorb heavy metals especially lead.  Its use in large manmade wetlands had one purpose, to absorb heavy metals.  Once completed into plant tissue the metals were now in a movable form.  Terrestrial plants have evolved to live in the peat soils above and below the surface and the most recognizable subtidal peat is perhaps eelgrass Zostera marina (species).

Metal consolidation in peat soil is well known, the Viking culture would take long stakes of hardwood and probe peat bogs until they hit a hardened substance a bog iron modules, once collected Vikings smelted these iron clumps in hot furnaces to produce bog iron.  Anaerobic bacteria complex the iron over time and large a harvestable clump below a red/organic discharge or the sheen of an oil residue.  That is why today acid mine waste water is often an orange color and something that indicated iron below.  Vikings were harvesting these sulfidic metal clumps 1,000 years ago.  These bacteria thrived in high sulfide environments sealed from oxygen complexed iron into a crude one.

One plant that has adapted to a wet high sulfur peat soil is sugar cana grass, Saccharum officinarum.  In fact, it thrives a high sulfur organic soil which requires large amounts of water and are known as acid sulfate soils.  The metals complexed into metal sulfides are released in a process that involves sulfuric acid formation when oxidized by bacteria to form sulfate S042 a potential oxygen source compound.  Waters with sulfate (like the sulfate already dissolved in seawater) is not toxic to fish but hydrogen sulfide is deadly.  Sulfur is oxidized by bacteria putting the peat/plant bacteria relationship governed by the presence of oxygen.  The sugar plant stalk and surface roots live in oxygen, the deep plant roots in sulfur.

The production of sugar cane requires a tremendous amount of water and draws upon the water in peat for its life cycle.  (The sugar cane juice and resultant processed sugar requires about 200 gallons of water for every pound of sugar).  In most areas of the world this high water requirement is a concern but in Florida, the high water levels of the Lake Okeechobee such plants that absorb water are looked as mitigating excess sulfide and nutrient rich waters that have caused so much harm with fish kills and red tides that poisoned seafood and animal life.  Florida ground water is found to contain high levels of sulfide.

Biochemistry and Functional Biology of Peat Soils

The consequences of excess-sulfur impact fish and shellfish or many excess sulfides is toxic to many organisms both land and sea.  Tidal peat is covered in Spartina, is open to air a part of the tidal cycle subtidal peat has submerged vegetation.  And the plants of tropical peat are some of the few organisms that can take sulfur out of peat soils – that are typically black and termed histosols which often start as brown peat but when re exposed to oxygen – turn black from iron in our salt marshes.  Histosols, when properly cultivated agriculturally, can be extremely productive.  (I pass a farm which specializes in field cultivation of peat soils every day to The Sound School.)  That is why farmers here a century ago found them suitable, level and containing few rocks and proceeded to drain them allowing oxygen requiring bacteria to replace sulfate reducing bacteria on the peat.  The surface exposed to oxygen as the reduction of organic matter to mineral fractions can occur naturally – from both bacterial pathways oxygen nitrate or sulfur ammonia.  The peat must be drained to prevent sulfide toxicity (the surface is exposed to oxygen) and prevent sulfuric acid build up.  Farmers a century ago who harvested sapropel from rivers and ponds soon learned the danger of peat sealed from oxygen and that re-exposed created sulfuric acid (today these soils carry part of the term).  Haplosaprists (See Nutrient requirements for sugar cane production on Florida Muck Soils) and saprist soils are those with highly decomposed organic materials or mucks, such as those that occur in coastal areas.  Sugar cane a grass from the tropics of Asia thrives in peat that does not freeze making southern Florida ideal for its culture.  The culture of sugar cane dates back to the first European settlers – only it was in a form of a thickened syrup or molasses of various grades.  The natural sugars in molasses consists of sucrose, glucose and fructose.  Originally sold in wood barrels molasses was used in baking and foods before the refined sugar crystals of today.  The most often uses today could be in gingerbread and beer.  One of the issues was cultivation of the sugar cane depleted peat carbon, its stalks need large amounts and if not replaced the peat tends to sink.  This happened here in New England, salt hay (Spartina patens) was harvested and the marshes were sinking (a combination of factors).  To keep salt hay thick and lush they spread mud over it (and also a terrestrial soils) to replace carbon in harvested organic matter.  This is more important on peat soils as this woody tissue is naturally under bacterial attack, bacteria trying literally to eat it, so peat is more susceptible to “shrinking” from water loss and harvests.  This mud is also the residue of bacterial digestion (also called digestate today) and in low or no oxygen conditions a marine compost properly termed a sapropel. 

At one time, New England and maritime coastal farms harvested sapropel for soil enrichment from an estimated 1,000 “mussel mud machines” soon learned of its high sulfur content which caused pH in soils to drop from sulfuric acid.  The negative effect is mentioned as a raised pH.  This is a comment from – one of the first CT Agricultural Experiment Station reports – Bulletin #49, October 30, 1890 “The bareness of the soil is due to iron salts soluble in water, many proto-sulphate of iron, the same thing as copperas or green vitriol, which is present in considerable proportion and which poisons and destroys all vegetation.  The remedy is a copious application of leached ashes or lime.”  A low pH is a concern in peat soils such as salt marshes, the acidity can release aluminum and then can complex phosphate.  A salt marsh that is drained and water table lowered exposes compost peat to oxygen bacteria which consume the organic matter much quicker.  The peat marsh surface can “sink” and needs what was termed a top dressing of organic matter to replace it.  Marshes cut off from organic matter from land can also subside or sink and become drowned peat bogs.  In heat black water is a natural lower no oxygen product of organic compost decomposition in lakes or streams.  Dr. Arthur Gaines (found that in the Narrow River system in Rhode Island – deep poorly flushed salt ponds could have sulfide levels higher that the Black sea (1975).  The upper portion of the Narrow River contain two salt pond lagoons in which a strong thermocline can be present.  This is an excerpt from a talk presented to the Narrow River Preservation Association by Dr. Veronica Berounsky and Rosemary Smith, December, 2012.  Which give us a view of the bacterial role of sulfide generation when stagnant oxygen poor water is quickly turned as in a compost turning process only this time in water termed on “over turn.”

“When the pond (upper Narrow River Lagoon – T. Visel) overturn on October 12, 2007 the anoxic water rose to the surface.  How did scientists and neighbors know that the upper pond was changing.  They could smell hydrogen sulfide, see the milkiness of the surface water and view evidence of dying fish and crabs.”

The depth of the lagoons in the upper reaches has sulfur reducing bacterial action that only becomes visible when these waters are “turned” (moved) to surface.  Peat residues are similar but lacking the fish kill potential only in very hot sea water and in low oxygen conditions.

The peat of coastal areas can be exposed such as bogs and marshes or subtidal, such as eelgrass or sapropels both can have similar chemical/bacterial reactions with or without oxygen.  When submerged peat is drained it can again support oxygen bacteria and sulfides converted into sulfuric acid.  In time the sulfuric acid toxicity is reduced and grass can grow again as oxygen bacteria are replenished.  Submerged peat (mostly eelgrass peat monocultures) can under go the same process, a serious storm may dislodge eelgrass releasing sulfides – oxygen levels of high enough van create a sulfuric acid released that with tidal mixing mixes with alkaline sea water and this acidic condition is lessened.  However, in times of little energy (few storms) and limited mixing, this acid water can grow – this was mentioned by S. W. Johnson, Director of the CT Agricultural Experiment Station, Bulletin #49, October 30, 1890, commenting on the use of sapropel organic composts of the sea that acid formation would be brief once exposed to air – unless the compost lie at the bottom of stagnant poisoned water.  S. W. Johnson provides this guidance – “The remedy (acid soil – T. Visel) is a copious application of leached ashes or lime.  Unless there is permanent bottom water also poisoned by iron salts, the lime will quickly cure the “difficulty.”  Permanent poised bottom waters are our “dead zones of today.”  In order words composts harvested from sulfide bottom waters would take longer to loose this acidity.  In today’s terms this is sulfide rich black water.  In times of extreme heat and little wind (or reduced tidal mixing) black water can form in our over submerged organic composts.  In the summer of 2016 these conditions occurred in Florida’s lake Okeechobee and a black water release was video recorded by The Harbor Branch Oceanographic Institution and can be seen in a video clip titled Blackwater Discharges Threaten Florida’s Indian River lagoon and St Lucie Inlet.  I feel all inshore fishers should view this outstanding clip (no endorsement or sponsorship provided).  The damaging impacts of bacterial reduction (term of breaking down structional cellulose in plant tissue – T. Visel) to fisheries is mentioned in historical references to fish and shellfish kills or as sulfide stains, a “deadline.”  Coastal residents often mention the by product of sulfide purging as a smell of putrid eggs.  This happens when the oxygen requiring bacteria die – and sulfate reducing bacteria replace them.  Some research is underway to study this bacterial battle, an excellent article July 1, 2019 titled “Bubbling.”  The Bay’s Dead Zone:  Breath of Fresh Air Or Pipe Dream by Len Lazorick (Maryland Reporter Com. referencing a Bay Journal article by Timothy B. Wheeler) mentions a Rock Creek, part of the Patapcio River system has supplied air to keep its bottom oxygen alive.       

Rock Creek, a tributary of the Patapcio River near Baltimore has had its aerator since 1988.  They were put there in response to complaints about the rotten egg odor given of by the creek in summer (this is the part that the bacteria are often left out of reports which is unfortunate – T. Visel).

“A 2014 study by researchers with the University of Maryland Center for Environmental Science rated the Rock Creek aerators a success they raised oxygen levels near the bottom enough to stop hydrogen sulfide (the source of bacterial black water – T. Visel) from bubbling out the sediments (again the absence of sulfate bacteria provides no direct link to the amount of sulfate dissolved in sea water to its ability to sustain bacteria that do not require oxygen – T. Visel) another by product of low – oxygen conditions.”

“The areators were incredibly effective at restoring dissolved oxygen to the creek” said Lora Harrison, Associate Professor at the UMCES Chesapeake Biology Laboratory and lead author of the study.”

However, those involved in aquaculture or even operating home aquariums will recognize the utility of supplemental air stones in life support – aerator and keeping ammonia levels low – as ammonia is extremely toxic to fish in fresh water.  However, in most fresh water systems dissolved sulfate is “limited” that is its abundance is a limiting factor for bacteria.  Salt water is another story, here the sulfur cycle from ages ago left a huge supply of sulfate dissolved in sea water and it is not limiting sulfate reducing bacteria in a hot climate in sea water they will never ran out – and thus the huge impact of heat upon the peat/compost in marine areas – the source of the rotten egg smell in heat is magnified.

When coastal residents report the smell of sulfur it tells of a bacterial battle out of sight but ragging below the water surface.  Bacteria need to electrons from oxygen and those that live in composts have a choice, C02 and S04 – carbon dioxide and sulfate.  Bacteria that use sulfate an electron acceptor “waste” hydrogen sulfide, and those who can utilize carbon dioxide purge methane.   

Many marinas in the 1980’s and 1990’s put in dock ice bubbler systems to prevent heavy build ups of ice in the winter.  These systems powered by electricity put a bottom stream of bubbles – that brings water on the bottom to the surface, keeping ice from forming or at least reducing it.  In 1998 or 1999 the marina basin next to The Sound School became hot, and wave attenuation barrier around it caused the water to partially stagnate, menhaden on the surface died and boaters complained about the sulfur smell and dead fish.  The owner called me about help – not realizing that the owner had recently installed the “winter” bubbler system I suggested, he just turn it back on – which he did and within a day or two the problem lessened.  What this was just a version of pond culture aquaculture aerators in use in southern states for decades.  In effect this ice bubble system was just a huge home aquarium air stone even though its original purpose was to prevent ice.  I see that today some bubbling systems are sold with two applications, preventing ice and helping to reduce fish kills.

While most of the environmental emphasis has been placed at removing nitrogen, a far larger issue is the build up of marine composts (often under eelgrass) during hot weather in poorly flushed bays and coves.  That process can increase ammonia levels and support massive algal blooms often called “brown tides.”

The exclusion of this marine composting in low or no elemental oxygen (elemental oxygen O2 is a frequently used indicator of water quality) i.e., the formation of sapropels tends to highlight chemical (industrial) inputs while minimize natural bacteriology responses.  This is often characterized by the blanket term of sediment instead of benthic bacteria or marine composting soil processes.  This approach while within geologic terminology minimizes the bacterial changes in nitrite, nitrate and bacterial ammonia generation although this impact has been recognized since the first biological filters used in aquaculture and home aquarium industries.  Many environmental reports use the term “fine grain sediment release” giving the impression that sediment particles provide work “somehow” that generates organic chemical compounds without bacteria.  It is often implied that sedimentation is the source of nitrogen compounds without definition of the term sediment, or inert particles such as sand cannot perform “work” but provide the collection and concentration of organic matter for bacteria that can perform that “work.”

This is one of the largest reasons why we may need to reevaluate research regarding nitrogen generation which is often classified as “new” or “old” nitrogen.  This process often termed “benthic flux” is the source of nitrogen compounds from the work of bacteria – not inert particles of rock washed from land into an estuary.  In many recent research papers the impact of sulfate reducing bacteria papers the impact of sulfate reducing bacteria (SRB) were not included in nitrogen reports.  Comparative Analysis of Eutrophic Condition and Habitat Status in Connecticut and New York Embayments of Long Island Sound LISS revised to February, 2016.

In a key and often referred EPA study – 2010 Nitrogen Inputs to Seventy-four Southern New England estuaries:  Application of a watershed nitrogen loading model, by James S. Latimer EPA Atlantic Ecology Division Narragansett RI and Michael A. Charpentier – Raytheon Information Solutions EPA Contractor Narragansett RI 2010 states on page 128 (Estuarine Coastal and Shelf Science 89 2010 pgs 125-136) the exclusion of bacterial release of nitrogen – described.

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

This would allow a difference (bias) in those areas that have little composting – high energy and good flushing compared to those with immense composting and restricted or poor “flushing.”  In areas of poor flushing high heat and heavy organic loadings would all contributed to sulfate bacterial processes.

Climate itself can cause a shift in the bacterial spectrum to produce more ammonia in heat and nitrate in cooler climate periods.  Human inputs of nitrogen is in two forms inorganic or reactive nitrogen, or organic – the nitrogen locked up in organic tissue.  This is the “solids” component in waste water treatment effluent commonly termed to as “suspended solids” as they are in a water transport solution.

The aspect of sea level rise a feature of coastline processes since the glaciers retreated from New England is an another important feature to consider when reviewing the nitrogen inputs.  As sea level rises and submerges more marsh peat it provides more sulfate – the oxygen source for sulfate reducing bacteria, so not only in hot seawater will marshes be covered with sea water, but it will seawater containing vast amounts of sulfate.  This sulfate can assist sulfate reducing bacteria in releasing huge amounts of “old” nitrogen locked in marsh peat plant tissue.  Marshes can therefore “sink.”  Increased sulfate metabolism by bacteria also increases sulfuric acid potential when marshes are exposed to oxygen – in fact the marsh peat becomes a source of natural nitrogen “pollution.”  This climate aspect has been known for many decades. 

This is a portion of a March 1994 study Leetes Island Salt Marsh Guilford, CT of the section 22 Connecticut Planning Assistance to States grant program Wetland Restoration Investigation administered by US Army Corps of Engineers, New England Division.  It highlights that marshes could be considered a non point source of pollution.

Foreword – for this study was prepared by the Connecticut Department of Environmental Protection Office of Long Island Sound Programs for the Leetes Island report.

Pg. ii

“Where dissolved oxygen levels have been monitored in drained salt marshes, low dissolved oxygen levels, known as hypoxia, have been observed during the summer months especially following rainstorms.  It appears that the leachates remove oxygen from the water. Fish kills have been observed in some of these wetlands.” 

Appendix #1
The Eelgrass Peat and Sapropel
The Connecticut Agriculture Experiment Station for 1884
New Haven Turtle Morehouse and Taylor – Printers 1885
State Board of Control – Thomas M. Waller, President
Honorable E. H. Hyde Stafford Vice President

Pg. 73

Tim Visel – This is rare comparison of marine mud compost fertilizer from three locations in CT – New Haven Harbor an 1860 dry sample and one sample form Old Saybrook and two samples from Guilford.  The New Haven dry sample contains almost one percent sulfuric acid. 
Direct from The Report pg. 73 – 1884

“A sample of Marine Mud #1082 sent to the station December last by W. T. foot of Guilford has the composition given below for comparison are given three other analysis.  One of New Haven Harbor mud, (1860) another of mud from Saybrook (1879) and a third of mud from Guilford (1882) (as well as a second Guilford sample #1082 December 1883).  The analysis of New Haven harbor mud was made on a dry sample and is not directly comparable with the others.”  (W. T. Foote of Guilford let it follow before use and shows a drop in sulfuric acid T. Visel)

New Haven Harbor    Saybrook    Guilford 1882      Guilford 1883                  
Water            Dry      71.32         45.68         49.11
Organic/Volatile Matter      10.56      2.79         4.54         3.20
Nitrogen      .52      (.14)         .18          Not recorded
Sand/Insoluble          17.63      20.82         40.99         33.90   
Oxide of Iron and       7.36      2.62         6.14         3.75
Lime            .73      .26         .90         3.62
Magnesia         .73      .51         .05         .73
Potash            .77      .17         .36         .34
Soda            .80      .69         .56         .83
Sulphuric Acid          .96      .39         .79         .18
Phosphoric Acid       .03      trace         trace         .69
Chlorine         .43      .51         0         .91
Carbonic Acid            0         0         0         2.92

It is also noted that in 1884 samples of fresh cow manure (pg 727) had .04 sulfuric acid while Old yard manure had even less just 01.

New England Homestead of Sept 6, 1884               

Appendix #2

Sapropel and Agriculture: The Impact of Composting Higher Plants
Recorded over a Century Ago

More than after the analysis and description of mussels mud, harbor mud or marine mud, marine composts that have sapropelic characteristics or sapropel itself by the Connecticut Agriculture Experiment Station, the positive impacts of soils is now accepted.  I Vanov et al. Effect of Phosphorous, Organic and Sapropel Amendments on Lead, Zinc and Codium uptake by Triticale from Industrially Polluted Soils, Agricultural University Bulgaria, 2008.

Pg. 255 – my comments T. Visel

It is known that adding sapropel in the soil leads to neutralization of the soil acidity, increases the moisture capacity of the soils and the content of microelements, and stimulates the growth of the plants by accelerating their maturity and increase the yields of some crops Lopotko et al., 1992.  Our preliminary study shows that DOMS (Sapropel – T. Visel) stimulate the vegetation of the growth of the root system of the cereal crops – wheat, corn and barley, and lead to increase of the chlorophyll content and soluble protein in the leaves.  It is also known that the sapropel has the ability to inactivate and restrict the entrance of heavy metals in the plants (Vashtou, 1996) (Other researchers – T. Visel) suggested that DOMS (Sapropel – T. Visel) could be used as absorbents for recultivating tailing dumps from Uranium processing and lead-zinc and copper mines.”   

Appendix #3

Recent Marine Sediments

A Symposium

Edited by





Scripps Institution of Oceanography, University of California, La Jolla, California

Aerobic as well as anaerobic bacteria are found in marine bottom deposits. They are most abundant in the topmost few centimeters of sediment below which both types of bacteria decrease in number with depth. A statistical treatment of the data on their vertical distribution suggests that aerobes are active to a depth of only 5-10 centimeters whereas anaerobes are active to depths of 40-60 centimeters below which they seem to be slowly dying off. However, microbiological processes may continue at considerably greater depths owing to the activity of the bacterial enzymes that accumulate in the sediments. The organic content is the chief factor which influences the number and kinds of bacteria found in sediments.

Bacteria lower the oxidation-reduction (O/R) potential of the sediments. Vertical sections reveal that the reducing intensity of the sediments increases with depth but the muds have the greatest reducing capacity near the surface. Three different types of oxygen absorption by the reduced muds are described, namely, chemical, enzymatic, and respiratory.

Bacteria that decompose or transform proteins, lipins, cellulose, starch, chitin and other organic complexes occur in marine sediments. These bacteria tend to reduce the organic matter content of the sediments to a state of composition more closely resembling petroleum although methane is the only hydrocarbon known to be produced by the bacteria. The precipitation or solution of calcium carbonate as well as certain other minerals is influenced by microbiological processes that affect the hydrogen-ion concentration. Other bacterial processes influence the sulphur cycle and the state of iron in the sediments. The possible role of bacteria in the genesis of petroleum is discussed.


Various physiological or biochemical types of bacteria have been demonstrated in the sediments that are capable of attacking most kinds of organic matter present in the sea. The rate and end-products of decomposition of the organic matter depend upon environmental conditions and the types of bacteria that are present. Waksman and Carey (49) have shown that diatoms, Fucus, alginic acid, copepods and other marine materials are utilized by bacteria with the rapid consumption of oxygen and the production of carbon dioxide and ammonia. More resistant fractions of marine plants and animals such as lignins hemicellulose-protein complexes may be only partially decomposed to give rise to marine humus (50).

Approximately one-fourth of the bacteria isolated from marine sediments are actively proteolytic (18,56) as indicated by their ability to attack proteinaceous materials and in so doing liberate ammonia, hydrogen sulphide and carbon dioxide. Presumably the topmost layer of sediment is the zone of greatest proteolytic activity below which there is a gradual, but not very appreciable, decrease in the nitrogen content of the sediments (30). According to Trask (45) amino acids and simple proteins constitute a very minor part of the organic-matter content. Hecht (23) reports that most simple proteins are completely decomposed even under anaerobic conditions and are not converted into adipocere. He records that about 90 percent of the nitrogen content sediments is due to chitin. Chitinoclastic bacteria are widely distributed (57) throughout the sea but chitin is only slowly attacked by bacteria even in the presence of oxygen and it may be more resistant under anaerobic conditions.

Most simple carbohydrates are readily decomposed (54) by the bacteria that occur in bottom sediments. Under aerobic conditions the end-products of the fermentation of carbohydrates are chiefly carbon dioxide and water. In the absence of oxygen, carbohydrates may be attacked and thus yield organic acids, methane, carbon dioxide, hydrogen and other products. Buswell and Boruff (9) noted the production of acetic, butyric and lactic acids, alcohol, methane, hydrogen, and carbon dioxide from the bacterial fermentation of cellulose under anaerobic conditions. Several types of cellulose-decomposing bacteria (48, 49, 51) have been isolated from bottom deposits but very little is known concerning their metabolism. The fact (45, 46) that less than 1 percent of the total organic-matter content of recent sediments is carbohydrate, whereas ancient sediments contain none, is indicative of the vulnerability of this class of compounds to bacterial attack. However, much remains to be done to ascertain the end-products of the reactions.

Perhaps bacteria have a greater influence than any other form of life on the hydrogen-ion concentration and O/R potential of sediments; properties that in turn tend to modify both the chemical composition and physical characteristics of the sediments. They may deplete the oxygen as noted above, they may liberate nitrogen from nitrites or nitrates and they may produce carbon dioxide, carbon monoxide and methane in appreciable amounts.”

Appendix #4

Long Island Sound: Issues, Resources,
Status and Management
Proceedings of a Seminar
Held May 10, 1985, Washington, D.C.

Edited by
Victoria R. Gibson & Michael S. Connor
New England Marine Research Laboratory
Duxbury, Massachusetts
Under contract #68-03-3319
To the U.S. Environmental Protection Agency
Office of Marine and Estuarine Protection
Washington, DC

U.S. Department of Commerce
Malcolm Baldrige, Secretary
National Oceanic and Atmospheric Administration
Anthony J. Calio, Under Secretary for Oceans and Atmosphere
NOAA Estuarine Programs Office
Virginia K. Tippie, Director

- Preface -

These proceedings are from a seminar on the status and management of living resources in Long Island Sound.  The seminar, sponsored jointly by the National Oceanic and Atmospheric Administration’s (NOAA) Estuarine Programs Office and the U.S. Environmental Protection Agency’s (EPA) Office of Marine and Estuarine Protection, was held in the main auditorium of the U.S. Department of Commerce on May 10, 1985.

The Benthic Ecosystem (Excerpts below pg. 47 and pg. 52, 56, 148)
D. Rhoads
Department of Geology and Geophysics
Yale University (1985)

“I have a difficult task, as all the speakers do, because we’re trying to summarize years of data and experience.  In my case, some 20 years, and I hope to do it in 20 minutes or less…

With the build-up of reactive organic matter in the sediment and a lack of pore water oxygen, hydrogen sulfide, ammonia, and methane gas may be generated and enter the overlying water column.  These reduced compounds, along with the reactive organic matter, may deplete water in contact with the bottom of its oxygen….

Underlying the dysaerobic and anaerobic water one typically finds organic-rich black (i.e., sulfidic) muds that are termed sapropels.  These are rich in iron mono-sulfides.  The physical properties of these muds are distinctive and the best description that I have heard of them is that they are like a “black mayonnaise.”

Dr. Rhoads:  Yes.  One reason I mentioned the importance of the sapropels –these black iron monosulfite muds on the bottom—was the direct point that Peter raised. The system is so dynamic that to measure the change from year to year is dissolved oxygen as measured in the water column would take more money than we have.  It’s not practical at all.

Given that kind of variability, what you need is a low-pass filter and an integrator, and that’s the sediment.  I suggest that a very sensitive index of the waxing and waning of this condition would be the map of where the sapropels terminate, whatever isobath that might be.  Follow the edge of those sapropels.  If they’re encroaching upwards into shallow water, it’s getting worse.  If they’re receding, it’s getting better.”   

Appendix #5

IAG NO: DW89938870-01-1

Executive Summary
This document is a final report on the performance of sulfate-reducing bacteria (SRB) bioreactors that were constructed and operated for Mine Waste Technology Program (MWTP) Activity III, Project 12, Sulfate-Reducing Bacteria Reactive Wall Demonstration. The MWTP is funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by the EPA and the U.S. Department of Energy (DOE) through an Interagency Agreement (IAG) and under DOE contract number DE-AC22- 96EW96405.
The organic matter, an electron donor and carbon source for the SRB, was provided as an 80% to 20% by volume mixture of cow manure and cut straw. The cut straw was added to provide secondary porosity to the mix and to prevent settling of the medium. TerraCellTM material, commonly used in landscaping for slope stabilization and made of high density polyethylene, was used to form a cellular containment system (CCS)1 to house the organic matter.
Overall, the project documented that SRB technology, as applied in this demonstration, is effective in removing Zn, Cu, and Cd by precipitating them as sulfides. Removal mechanisms for Fe, Al, Mn, and As were overshadowed by a dramatic change of the quality of the influent AMD (Acid Mine Drainage). The results of the project have also allowed the formulation of an important recommendation regarding the design and construction of SRB bioreactors.

Appendix #6
The Impact of Marine Soil Sulfides to Eelgrass

Two decades ago it was known that the biochemistry was changing the vegetation of salt marshes.  The cordgrass Spartina species was transitioning to plants that could tolerate higher levels of peat soil sulfide.  Coastal Connecticut residents have noticed the red coloration of Salicornia – salt marshes were turning a different color as this plant can tolerate high sulfide levels.  The same or very similar biochemistry (sulfide formation) was known in the 1980’s for eelgrass and turtle.  Sulfide was a plant toxin.  One of the major research papers on the impact of soil sulfides was conducted on Florida seagrass beds in 1994 by Paul Carlson, Laura Yarbo and Timothy Barber.  That reason was published in the Bulletin of Marine Science, 54(3), pgs. 731-746, University of Miami.  This article was titled “Relationship of Sediment Sulfide to Mortality of  Thalassia testudinum in Florida Bay.”  Similar research was presented in the 1992 Thesis by Jill Goodman at the College of William & Mary, Virginia.  “The Photosynthesis Responses of Eelgrass (Zostera marina) To Light and Sediment Sulfide In A Shallow Barrier Island Lagoon,” knowing the sulfide levels in peat and submerged peat.  (Eelgrass) is the most critical plant growth condition to measure – my view, T. Visel.  A portion of the introduction is reproduced below. 
Photosynthetic Responses of Eelgrass (Zostera marina L) to Light and Sediment Sulfide in a Shallow Barrier Island Lagoon
Jill Lynn Goodman
College of William and Mary - Virginia Institute of Marine Science, 1992

Recommended Citation
Goodman, Jill Lynn, "Photosynthetic Responses of Eelgrass (Zostera marina L) to Light and Sediment Sulfide in a Shallow Barrier Island Lagoon" (1992). Dissertations, Theses, and Masters Projects. Paper 1539617651.

Wetland sediments, where anaerobic metabolism and sulfate reduction dominate, have been the focus in studies on the effect of accumulation of H2S on plant responses. Seagrasses are also found in organic rich, highly reducing sediments. Shoot lacunal development and rates of photosynthesis are critical to the downward transport of 02 from the leaves to the roots of seagrasses (Pulich 1989). When photosynthetic activity is low, roots must tolerate significant periods of anoxia and/or hypoxia (Smith et al. 4 1984, Smith et al. 1988, Zimmerman et al. 1989).

When the 02 supply in the sediments becomes limiting, aerobic respiration is replaced by anaerobic metabolic processes (Koch et al. 1990). During these periods of anoxia, heterotrophic anaerobic bacteria use inorganic ions as terminal electron acceptors to break down organic matter (Hines et al. 1989). Where adequate supplies of sulfate and organic matter are present, sulfide is produced in these anaerobic sediments by sulfate reducing bacteria of the genus Desulfovibrio (Ingold & Havill 1984). These organisms use sulfate as their terminal electron acceptor for oxidative phosphorylation, the amount of hydrogen sulfide (H2S) present in marine sediments being dependent on this process (Ingold & Havill 1984, Howarth & Giblin 1983).

In salt marsh sediments, where Spartina alterniflora is found, H2S has been found to be the primary factor inhibiting plant growth and increasing mortality. The mechanisms for this apparent inhibition are not understood (Delaune et al. 1984, King et al. 1982). Several possibilities exist. For example, there is a reduction in ATP generation due to the switch from aerobic to anaerobic metabolic processes (Koch & Mendelssohn 1989). In addition, sulfide accumulation has been found to decrease the activity of root metallo-enzymes, such as important oxidases, used in the electron transport system of respiration (Koch et al. 1990). H2S may also affect alternate anoxic pathways by limiting the production 5 of ADH (alcohol dehydrogenase), which is the enzyme catalyzing the terminal step in alcoholic fermentation (Koch et al. 1990). Ethanol, the end product of alcoholic fermentation, when released to the sediment may be a major carbon drain from the plant (Hines et al. 1989). In order to eliminate this carbon drain, fermentative metabolism is maintained only at low levels (Smith et al. 1988). The reduction in nitrogen uptake caused by increases levels of sulfide in sediments surrounding S. alterniflora may also be detrimental to its growth and production.

Rice, which is also found in highly reduced, water saturated soils, has been found to be limited in growth, root hair development, and nutrient uptake by increased levels of sediment sulfide (Joshi & Hollis 1977). Chlorosis and stunted growth are indications that rice plants are being stressed by highly reduced soil conditions (Koch & Menselssohn 1989).

The growth of Salicornia europea, which is also associated with sulfide containing wetland sediments, has been found to be unaffected by increases in sediment sulfide (Wilkin-Michalska 1985). Sulfide pretreatment inhibited activity of two metallo-enzymes in plants from the upper marsh , such as Spartina foliosa and Scirpus robustus, but had no effect on enzymes from S. europea (Cooper 1984). Aster tripolum, a wide ranging halophyte, also appeared to be tolerant of sulfide at concentrations frequently encountered 6 in salt marshes (Cooper 1984).

“Relationship of Sediment Sulfide to Mortality of Thalassia Testudinum in Florida Bay”

Bulletin of Marine Science, 54 (3), 733-746, 1994

Paul R. Carlson, Jr., Laura A. Yarbro and Timothy R. Barber

My comments (    ) and identified as such (T. Visel)

Catastrophic mortality of the seagrass Thalassia testudinum (turtle grass, T. Visel) has occurred in Florida Bay since 1987.  Among the possible causes for Thalassia dieoff are increases in area, density and biomass of seagrass communities due to high salinities in Florida Bay, resulting from water management activities and a decade-long drought in south Florida (Zieman et. al., 1989).  The same authors have also suggested that the lack of a major hurricane in the past 27 years has caused high levels of inorganic and organic sedimentation (lack of soil cultivation – T. Visel) have restricted circulation (soil pore water exchange – T. Visel) and increased summertime salinity and temperature stress (conditions made worse in high heat – T. Visel).  A pathogen might also play a role in dieoff: Porter and Muehlstein (1990) reported the presence of a potentially pathogenic strain of the slime mold labrynthulla in lesions on thalassia leaves from dieoff sites.  Because many areas affected by dieoff are located far from potential sources of anthropogenic (man-made or man-caused – T. Visel) nutrients and toxic compounds, pollution is not considered a contributing factor (Robb Lee et. al., 1991).  (In other words, these turtle grass dieoffs appear to be natural – T. Visel).

As part of a collaborative research group study of Thalassia dieoff in Florida Bay, we have focused on the role of sediment (marine soil – T. Visel) sulfide in the dieoff process.  Sulfide is produced in anaerobic marine sediments (marine soils – T. Visel) by bacteria that use sulfate as a terminal electron acceptor (sulfate reducing bacteria or SRB – T. Visel) in the degradation of organic matter (Goldhaber and Kaplan, 1975; Sorensen et. al., 1979).  High temperatures, abundant organic matter, and low sulfide-binding capacity can result in extremely high pore water sulfide concentrations in sediment of Florida Bay seagrass beds (Barber and Carlson, 1993).  Sulfide is highly toxic to many plants and animals (Joshi et. al., 1975; Smith et. al., 1976; Bradley and Dunn, 1989; Koch and Mendelssohn, 1989) because of direct poisoning of cellular metabolism and indirect hypoxia due to the reaction of sulfide with molecular oxygen” (Pg. 734, Bulletin of Marine Science, Vol. 54, No. 3, 1994).



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