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« on: January 09, 2020, 02:27:35 PM »

The Cultivation and Chemistry of Marine Soils
The Clam Soils
IMEP #75
Understanding Science Through History
View All Habitat Newsletters on The Blue Crab ForumTM
Fishing, Eeling and Oystering Thread
Tim Visel, The Sound School, New Haven, CT
Part 2 of 3 Parts; Part 1 The Oyster Soils was posted on January 9, 2020
Viewpoint of Tim Visel only and no other agency or organization


The Clam Soils
A Note from Tim Visel
I recently read a manual on how to install a clam farm; it was very well organized and contained much useful information, but for me, it lacked a critical element – the soil.
Some of the most critical soil elements were missing such as pH, percent clay, percent organics and percent mineral – sand.  The next level was if the life of the soil was composting – gaining organic matter or depleting/losing organic matter.  The next soil factor was sorting which also tended to reveal soil pore capacity.  Well sorted soils tend to have less pore capacity and poorly sorted more (imagine the pore space of gravel compared to that of fine sand).  Additional soil questions respond to its biochemical aspects, how deep is the oxygen –sulfide sulfate “deadline,” does the presence of shell hash (bits of bivalve shell) moderate soil pH, whether cultivation is needed, and can the CEC value of the soil be determined?
Those questions seem commonplace for terrestrial farmers and soil surveys but in the marine clam soil farming, we don’t ask these questions.
Having worked for three Cooperative Extension Services, the importance of knowing your soil (terrestrial) was just accepted; it was ingrained into agriculture practices.  The value of knowing your soil has grown in importance, not less.  I don’t think many papers on agriculture would dismiss soil knowledge as not important to farmers, but step below the high tide line and soil knowledge soon disappears.  Soil characteristics become part of a confusing mixture of terms that describe erosion or geology rather than what soil bacteria is living in it - my view, Tim Visel. 
I respond to all emails at [email protected].

Symptoms of Declining Clam Soils - Sulfide
Crabbers’ or Clammers’ Itch – The Blood Fluke and Sulfide Tolerant Worms

One of the issues about heat and sapropel buildup was an increase in our area of the mud snail that sheds trematode worms.  The mud snail is properly termed; it lives among the mud flats of the shore and, in heat, this mud takes on sapropelic characteristics.  It is hot and the home of the mud snail and waterfowl (ducks, swans and geese).  You need all three for this small parasitic blood fluke (worm) to live and, at times, penetrate human skin.  This small parasitic worm can burrow into our skin, causing pustules and swelling (called swimmers’ itch) as our infection defenses isolate the small worm.  This worm, a parasite that is worldwide and can occur in freshwater lakes, is known to infect hundreds of millions of people each year although not widely reported in the U.S.  It is pathogenic but the species of schistosome is a parasitic worm-like organism but cannot survive long in our skin.  It burrows into human skin, mistaking us for duck feet.  The infection sites (I had 20 or so on each leg in 1984) was from working, planting seed oysters, in Tom’s Creek, a small, shallow, warm tidal creek next to my family home in Madison, CT (1980’s).  I had also examined some infections at Clinton Harbor in the mid-1980’s as well (See “A Caution Regarding Black Mayonnaise,” posted on The Blue Crab ForumTM on February 9, 2016 to the Northeast Crabbing Resources thread).  Each pustule can cause 1 to 2 days of incredible itching.  The worm is carried by the mud snail and matures in the feet of waterfowl.  It is worldwide and occurs in freshwater and marine waters.  Overseas it is called “rice puddy itch.”  Blue crabbers wading in warm, shallow water can also pick up these parasites.  It is associated with shallow mud flats and not the open shore.
Because it (the mud snail Ilyonassa obsoleta) lives in shallow, low energy soils with large amounts of organic matter; it is found in abundance in shallow tide pools (and therefore children playing in these shallow waters are very vulnerable).  It is also in the habitat of clammers and in Connecticut blood fluke infections are termed “clammers’ itch.”  It is a sign of a dying soil for clams and oysters, large mud snail populations signifying a composting soil as they live in this compost feasting on plant material, hence the name “mud snail.”  Waterfowl live in this shallow water habitat and consume subtidal vegetation such as eelgrass and macroalgae, such as sea lettuce.  Adult worms mature in the blood vessels of ducks, seagulls and geese and eggs are passed into the water in fecal droppings.  Once in the water, the eggs hatch and seek an intermediate vector – the mud snail.  The parasitic fluke matures in the snail and then is released, seeking waterfowl to complete its life cycle.  That is when they burrow into us.
Habitats that have a large population of mud snails in organic matter are soils that are composting (collecting organic matter) and being sealed by sapropel.  This signals a declining soil for clams, especially the softshell clam (Mya).  Such soils have shallow sulfide deadline and digging 12 inches or more can release a hydrogen sulfide smell into the air.  Such soils usually have large clams dead still in place deep but with shells still paired.  The organic matter is sealing the soils from oxygen and increasing the chance of hydrogen sulfide formation.
It is in these soils that soil pore circulation is low or even non-existent.  This soil now favors sulfide tolerant worms such as the sandworm, Nereis virens , which lives in soils of 50% sand or more and the milky ribbon worm, Cerebratulus marginatus, that lives in soils of 50% or more organic content.  “Sandworms” prefer a sandy soil, less sulfide, while ribbon worms thrive in composting soils of little oxygen.  Stagnant soils point to a drop of sandworms; in times of frequent storms, sandworms do better.
In fact, it is the milky ribbon worm that lives in a sulfide-rich environment.  If marine soils have successional attributes (which I believe they do), the population of milky ribbon worms may be one of the ways that will help identify the sulfide deadline.  As the sulfide deadline approaches the surface of the soil, the habitat conditions for sulfide tolerant worms improve.  Maine clammers are dealing with this issue currently.  As the milky worm increases, it shows that habitat conditions are improving for this vicious softshell clam predator and that as organic matter sulfide residues (acids) builds (usually in warm waters), there is little hope for clam culture in this soil without cultivation followed by predator protection – my view, Tim Visel.

The Clam Soils
It was the small boat fishers who most likely first noticed the Cation Exchange Capacity (CEC) and pH differences of soil  in clam and oyster growth.  On some bottoms oyster and clams grew quickly, while on others, growth was slow and yet on others caught a great set but over time slowly died out. These great sets frequently occurred after storms; waves could lift buried shells so that oysters could again set on them, while the same waves lift and drop marine soils, freeing them of organic matter and clays and rinsing them with alkaline seawater.  Some soils grew clams with thick shells while others very thin.  Some areas were better at obtaining seed while others had good adult growths.
Small boat fishers noticed this and at times moved seed from thick (stunted) sets to those that had plenty of growing room.  On Cape Cod, these seed beds of both soft and hard shell clams would stunt and growth could even stop completely.  But these were habitat capacity and succession fisher observations; submerged soils could change over time and raised questions about why.  Most of the traditional management policies reflected biological concepts, size, spawners and catch limits. Very little research was done about growth and seed capacity as to marine soils, except for four examples: The 1938 Virginia York River Oyster Study and sulfides, the 1957 study of the softshell clams in midcoast Maine by Spear and Glude, the 1956 studies of the Quahog Fishery conducted by Pratt and Campbell titled “Environmental Factors Affecting Growth in Venus mercenaria “– Contract NR 163-100 Office of Naval Research, Department of the Navy and the University of Rhode Island.  A final study (1987) conducted  on Cape Cod by H. Karl Rask looked at CEC values of marine soil before and after cultivating trials for the first time. 
This last study (See Appendix #4: “The Effect of Hydraulic Harvesting on Sediment Characteristics Related to Shellfish Abundance” by Rask, 1987) is one of a few that looked at soil differences (termed sediments) and found that high silt (organic matter)/clay content consistently slowed slower clam growth.  Further, researchers noticed that clams lived deeper in coarse sand than in silt/clay soils.  By doing this, they, at critical times, especially warm months, clams could live deeper below the crab predator zone.  Oyster farmers noted heavy sets of quahogs below a protective layer of “shell hash,” old oyster shells above sandy soils.  It was mentioned that these soils had a liming pH effect, preventing sour soils (See Sour Soil in Appendix).
But these shellfish growth observations are not uncommon.  Frank Dolan, a Guilford, Connecticut hydraulic hard clam fisher  in the late 1970’s, always mentioned clam growth in terms of better bottoms, that when clams were transplanted in shallow water sandy soils, they showed better growth and that moving clams from mud (soils) to sand always resulted in better shell thickness (comments to Tim Visel).  We know today that soils have a lower CEC value, and clams and oysters are able to build shells faster in them.  Marine soils high in clay have higher CEC values and H. Karl Rask completed the first CEC study of marine soils in 1988 with the Cape Cod Cooperative Extension Service, University of Massachusetts. 
I believe that Karl Rask on Cape Cod (who occupied my position after I left the University of Massachusetts Cooperative Extension to return to Connecticut to work for the University of Connecticut Sea Grant Cooperative Extension in 1983) can be considered to have the first modern marine soil study conducted at a land grant university.  It was Karl that implemented some of the first CEC marine soil experiments in the country and was decades ahead of most estuarine researchers.  His experiments detailed that after modest and controlled cultivation experiment measures, CEC values dropped.  In other words, it was now easier for shellfish to build shell material as the soil itself had less affinity to hold those calcium carbonate ions in place.  This aspect of the marine soil chemistry holding ions is frequently termed base saturation.  Karl’s soil study was printed in 1986 by the Cape Cod Extension Service UMASS and a section of the introduction can be found in Appendix #4: “The Effect of Hydraulic Harvesting on Sediment Characteristics Related to Shellfish Abundance” from Rask (1987, pg. 2):
“There is a link here to the excellent sets of shellfish found in new sand that has been deposited by storms or currents.  Clams (Mya), for example, are a colonizer species and can quickly populate an empty area.  New sand is not only free of decaying organic detritus, but is also free of predators (especially the numerous small invertebrates that prey on shellfish larvae and newly set seed).  Hydraulic action can easily be seen to imitate some of these natural phenomena, and could be used intentionally to benefit our shellfish resources.”
And reports on soil cultivation trials in Aquaculture Today (Rask, 1988) and contain graphed results of trials in the Centerville River (Barnstable), Widows Cove in Wareham.  Trials were triplicate both before and after hydraulic harvest.  Sediments (soils – T. Visel) were analyzed for grain size distribution, cation exchange capacity (CEC), content of nutrients, metals and pH.  On page 3, Rask reports on the following results:
“In all cases, hydraulic harvest had distinct noticeable effects on sediment quality.  The major physical effect is the reduction in the percentage of fine particles, such as clays, fine silt and small organics.  This is reflected in an increase in grain size (Tables 1 and 2) and a reduction in cation exchange capacity (Table 3).  Cation exchange capacity (CEC) measures the sediments ability to hold onto positively charged ions (such as calcium, potassium, magnesium, aluminum, etc.).  Sediments high in organic material or clays will tend to have higher CEC’s than those composed primarily of sand.  A reduction in the CEC therefore corresponds to some reduction in these fractions: the end result is a coarser grain sediment, having fewer clays, silts, and fine organic particles.”
The movement of seed by shellfishers is noted as both space and soil, similar to the agricultural concepts of capacity – thinning carrots.  This is more associated with “seed oysters” but is also found in some hard shell and soft shell clam studies.  The York River Study of slow or no growth of oysters by Galtsoff et al., U.S. Department of Commerce Bureau of Fisheries Preliminary Report on the Cause of the Decline of the Oyster Industry on the York River, VA and the Effects of Pulp– Mill Pollution on Oysters, Vol. 11, 1938 responded to poor meat quality that was initially reported by the oyster culturists who experienced slow or no growth.  Subject oysters were moved to good growth soils and oyster growth rates improved.  Oysters that were showing excellent growth were then moved into the York River “problem areas” where growth then stopped.  These studies usually then focused upon human pollution only as the factor in these observed growth changes.  The York River Study is an important study of both policy and pollution as soil climate chemistry – sulfate metabolism sulfide discharges from a York River (West Point) paper plant.  The policy of finding human causes only for growth failure is illustrated in the York Study and later reviewed by J.L. McHugh and J.D. Andrews (Status of Pollution and Oyster Culture in the York River, 1958) and noted “It is a weakness of the Galtsoff report that natural causes were not investigated thoroughly.”  Galtsoff found that when oysters were subjected to black liquor – a sulfide rich broth.  It is possible that much of the sulfide was not from the paper plant but from York River sapropels in heat.
Another growth study conducted in Maine (and free of human pollution concern) occurred in the 1950’s in the shore coves of MidCoast Maine, a study by Harlan Spear and John Glude, both fisheries research biologists with the U.S. Fish and Wildlife Service.  The study areas were Bedroom Cove and Sagadohoc Bay south of Georgetown Island, Maine.  At first, genetic differences were thought to explain the growth differences of softshell clams, that the clams living in Bedroom Cove were of another race of slow growing softshell clams while those living in the center of Sagadohoc Bay were of a fast growing heredity strain (title of the paper was “Effects of Environment and Heredity on Growth of the Soft Shell Clam” (Mya arenaria)), Fish Bulletin #57, pp. 279-292 (1957).  But as with studies of the hard shell clam beds of Chatham, Massachusetts Pleasant Bay (Marine Resources of Pleasant Bay, Cape Cod Monograph Series #5, 1967) issued by the State of Massachusetts documented, state shellfish managers and SCUBA divers found seed beds of quahogs stunting and moved them.  The oyster study of the York River several oyster culturists had done the same.  York River oysters transplanted to “good grounds” grew quickly; oysters that were growing fine once transplanted into the York River ceased growing.  Shellfishers had noticed these differences because they were “close to the resource” they depended on them and as such made them close observers of the populations.  The same thing occurred with the Spear and Guide Study. Clams from Bedroom Cove moved to other Maine clam flats grew fine.  Those from good growing areas (flats) moved into Bedroom Cove ceased growing.  The paper from the Spear and Glude Abstract concluded the following:
“The experiments demonstrated that environment, not heredity, is the important factor in growth.  Clams from one origin may have highly significant differences in growth rate when planted in different areas (and further).  Clams of different origins assume similar growth rates when transplanted to the same area.”
The growth differences can be explained in terms of soil science (In 1993, George Demas would breach this great research divide and is credited as being the first soil researcher since David Belding in 1912 to begin using the concept of marine soil - soil pore size, CEC, base saturation pH and organic matter/clay content in his research at NRCS in the early 1990’s from long accepted terrestrial agriculture concepts of pore size, pH and CEC).
But shellfishers have asked for a century for help in understanding why some marine soils change over time, and this involves temperature and the bacterial components of the sulfur cycle.  Soils high in clay and organic matter are the first types to become sulfide rich.  Sandy soils can be covered (buried) by organic matter also impacting soil pH.  Soil pore spaces over time are collapsed (by the weight of water – a slow hydraulic compaction) and clam sets in them grow weaker or sometimes fail.  In heat and low energy, fecal deposits can reduce soil pore exchange.  These are all concepts easily found in the study of terrestrial soil sciences but are not often found in shellfish culture guidebooks.
The relationship of pH to bicarbonate ions in seawater also impacts oysters’ and clams’ ability to access calcium carbonate (CaCo3), the building block of shell material.  Calcium ions (Ca++) abound in seawater and combine with carbonate CO3—to form CaCO3.  However in acid conditions, the carbonate ion below 6.5 pH in seawater falls, it decreases the relationship of supplemental carbonate ions and shell formation functions become more important.  Before this calcium can buffer the seawater, it first buffers the soil.  While many researchers have focused upon atmospheric CO2 as contributing to acid oceans, the near shore soils are more impacted by tannic and sulfuric acids, most often by sulfuric acid as a result of the sulfur cycle and sulfate metabolism from bacteria in the soil itself.
This gives marine soils an added restriction; the organic matter in them (compost) causes them to also attract calcium ions to offset negative charges from it (and clays also).  As clams live near or below the seawater interface, organic matter creates a physical and chemical barrier.  Organic matter may seal soils themselves from calcium and calcium carbonate in seawater.  Many shellfishers may have experienced these sealed soils as “sticky bottoms.”  It is these soils in which the ability to attract, retain and exchange cations, ions with a positive charge, such as calcium, which has a charge of positive 2 declines.  These soils over time have clams and oysters that show slow or no growth.  They contain organic matter (muck) or clays with negative charges that soak up the calcium positive ions, making it hard for clams and oysters to build shell.  In very acid soils or soils high in clay, that process takes away ions and can result in paper shells, shells so thin that they can be crushed between fingers.  Such thin shells provide little protection from crab or drill predation.  Well circulated soils, with good pore size and access to ions (a low CEC), will support firm, strong shells.  Sulfide levels far below the surface do not force clams to live in an active zone of predation but clams can live deeper below the crabs in soils with good access to ions (and usually a seawater pH of 7 or higher).  In times of heat, however, sulfide levels in soils can reach clams and in very hot high sulfide conditions clams can pop right out of the bottom (especially softshell clams) and shells can exhibit a black sulfide stain (personal observations – Green Pond, Falmouth, MA, Tim Visel, 1982).  It is suspected that this condition can even kill freshwater mollusks.  This was noted in the Rhode Island study of the Greenwich Bay fish kill, August 2003 issued September 3, 2003 by the Rhode Island Department of Environmental Management:
“Along the western shore of the bay, many noted a rotten egg smell associated with hydrogen sulfide (toxic to organisms) being produced by sediment chemistry and bacterial processes.”
When this happens, marine soils become sulfide-rich and toxic from bacteria that thrive in low or no oxygen conditions.  They utilize sulfate in seawater for oxygen and waste hydrogen sulfide.  Softshell clams, in the presence of high soil sulfide, leave the bottom and die.  The same report notes the following as well:
“Another indicator that impacts were occurring well before August 20th, and continued thereafter, is the dieoff of soft shell clams.  The first report of a clam kill in Greenwich Bay came several weeks before the fish kill.  And on August 25-26, a massive dieoff occurred, both within Greenwich Bay and at points north, with millions of juvenile soft shells washing ashore.”
(This, in effect, details that clams left the bottom or were killed as they left it – T. Visel).  The concern about ocean acidification is a low pH changing the bicarbonate ion relationship.  At a pH of 5, bicarbonate becomes scarce in seawater and that holds carbonate levels low and makes shell formation harder.   Calabrese, 1972 of NOAA, detailed the impact of low pH upon clam and oyster veligers.  If they landed on acid soils, they perished quickly (See “How Some Pollutants Affect Embryos and Larvae of American Oyster and Hard Shell Clam”, Marine Fisheries Review, Nov-Dec 1972, Vol. 34).  Acid rain does the same to terrestrial soils and slows bacterial growth, restricting nitrate and other ions crossing root tissue to support plant growth.  To keep pH levels at such to best support nitrogen-fixing bacteria, lime is added.  Oyster growers at the last century noticed that quahog sets were almost always enhanced at oyster bed edges, the buffering pH from shell to prevent  “sour bottoms.”   In fact, George McNeil, Hillard Bloom, J.R. Nelson, Frank Dolan, and Larry Malloy all said that when quahogs started coming up in commercial oyster dredges that they were close or at the end of the market beds (oysters) (personal communication – Tim Visel, 1975-1990).  The drift or roll of flat oyster shells termed “chips” was felt that shell calcium had encouraged quahog sets.  Luther Blount once explained to me while attending the University of Rhode Island that quahogs set frequently after hurricanes in “mixed bottoms,” that in the 1950’s contained oyster grow out production beds but still contained relic oyster shells (comments to Tim Visel, 1981, following an oyster production talk for the Rhode Island Aquaculture Association Meeting). 
In 1994, Jeffrey Kassner (Brookhaven, Division of Environmental Protection) reported that in Great South Bay, New York the most important quahog beds were those close or on once planted oyster grounds that contained relic oyster shell.  This observation led to a presentation at the Third Rhode Island Shellfisheries Conference in Narragansett, Rhode Island, August 18, 1994 (Sea Grant URI, Publication # P1394, titled “Habitat Enhancement as a Means to Increase the Abundance of the Northern Quahog, Mercenaria mercenaria”) and is found in this section:
“In 1990, 120 tons of clam shell were planted in Barneget Bay, New Jersey in six plots (trials – Tim Visel), each measuring 20 by 70 meters (Cronin, 1990).  Three of the plots were covered with “heavy” shell, and three were covered with “light” shell, while three unshelled plots served as controls.  Three years later, the shelled plots had slightly more than five times more recruits (set – T. Visel) than the unshelled control plots.” (Source: Clyde Mackenzie, National Marine Fisheries Service, Sandy Hook, N.J.- personal communication, pg. 53)
John Hammond of Cape Cod, a retired oyster grower, felt that the great sets occurred after severe storm events, “new sand” for softshell clams, and cultivated soils from powerful Noreasters for quahogs.  He provided the example of the once huge offshore quahog beds of Nantucket, which he felt occurred after the Portland Gale of 1898.  Mr. Hammond also felt that the discoveries of immense beds were the result of natural marine soil cultivation events.  What is consistently known and found in clam/oyster historical records are the benefits of “working the bottom.”  This was a much smaller version of natural soil disturbance usually from storms.  These powerful storms cultivated soils for the “great sets.”
Working the bottom would tend to increase soil pore function and circulation in the soil, long reported in terrestrial soil study.  Look at how David Belding incorporates many terrestrial soil attributes when it came to sulfate metabolism and the buildup of sulfide in Cape Cod marine soils a century ago:
The Softshell Clam Fisheries of Massachusetts - Belding
(Comments, Tim Visel)
Organic material – “Clams are usually absent from soils containing an abundance of organic material.  Even if the slimy surface (this mucous like covering is bacterial; it is the same growth that quickly coats planted oyster shell cultch – T. Visel) does not prevent the set. The clams that take lodgment soon perish.  Organic acids corrode their shells and interfere with the shell forming function of the mantle (acid conditions, T. Visel).  Such a soil indicates a lack of water circulation within (soil pore size and pore exchange capacity, T. Visel) the soil itself as indicated by the foul odor of the lower layers (most likely bacterial hydrogen sulfide, T. Visel) of soil, the presence of hydrogen sulfide, decaying matter, dead eelgrass, shells and worms.  If such a soil could be opened up by deep ploughing (cultivation by man, usually horse drawn cultivators, T. Visel) or resurfaced with fresh soil to sufficient depth (This is “new sand” as mentioned by John Hammond as storm driven, but new sands change CEC, the beach plum, and cranberry responds to new sand application in much the same way – T, Visel) it would probably favor the growth of clam.”
In the culture section of Belding’s softshell clam report, Belding again raises the issue of soil knowledge and shell formation, the ability of the clam to access calcium carbonate ions and soil stability, which is periodic and at times storm driven.
The following is a section titled “Selecting The Ground” from Belding (1931)
My Comments (T. Visel)
“Soils in which organic acids caused by vegetable decay (bacterial composting, T. Visel) are present (usually a sulfur or matchstick smell is present, often in the historical literature as the smell of rotten eggs, T. Visel) prove unsatisfactory for the catching of seed and interfere to a slight extent with growth by destroying the shell (most likely acid soils, T. Visel) often giving to the clam a black appearance (this is the sulfide stain, T. Visel), which makes it less suitable for marketing. (Note these soils often have only adult clams with few sets – it is a “dying” soil clam, T. Visel) (This is also where Belding mentions shell thickness and its direct relation to growth; soils with high CEC have skinny growing clams with thicker shells because for size, they are older. –T. Visel) Although the shell of the clam is secreted by the lime salts absorbed from food and water, nevertheless, the nature of the soil in some indirect way determines the appearance, the composition and the weight of the shell, as can readily be seen by comparing clams from various soils in the same localities.”
Clams growing in yellow or “honey sand” have large pore sizes, usually kept organic free by currents and contain low amounts of soil organic matter.  In these soils, growth can be almost twice as fast at times, producing shells of perfect shape but very thin shelled.  This is a soil with a low CEC.  Acid soils can exhibit the opposite.  Here clams grow slowly and may have thin shells but also watery (water belles) poor quality meats.  These soils have sulfides and can purge, at times, sulfuric acid.  Shells will appear pitted and flaky, hence, the effects of acids acting on the shell.  In high sulfides levels, shellfish simply stop feeding and, if long enough, starve – T. Visel.
Belding himself noticed this fast low CEC sand growth under a section on transportation of seed clams:
“In cases where the seed has to be carried many miles by rail, extreme care must be used in transit, since the shells of small clams are extremely fragile, especially the sand varieties, which are therefore less favorable for transporting than clams from gravel, stony or muddy soil.”
These “muddy” soils tend to have higher CEC levels; growth is slower, but shells are thicker.
Sulfate/Soils – Observations of Clam Growth
A Note From Tim Visel
On Cape Cod, John Hammond’s laboratory was Monomoy Pleasant Bay and Oyster Pond River.  After storms, “new sand” tore from the shore was rinsed and redeposited as a new sand bar or just a “new sand.”  After a period of time, these new sands held new sets of the softshell and hard shell clams.  These sets were great to those who saw them, thick and often shoulder to shoulder, so crowded they seemed to push themselves out.  Nature’s abundance did not go for long unnoticed for the many clams soon sustained many predators.  The attrition was recorded by shells with chipped edges or drilled holes washed to the tideline.  Clammers harvested them as well, but over time the clams stunted below legal size and it just didn’t pay to dig for them.  The new sands, once soft and clean, became soft, sticky and smelled of sulfur.  These soils had aged and now held few clams.  The clam predators suffered as well and these areas were called dead bottoms or exhausted beds until the next storm.  Then, according to Mr. Hammond, the process could repeat perhaps not exactly in the same location but was a combination of energy and temperature that could produce the next great sets in different sections along the coast.
New Sands and the Great Sets – Belding Studies of the Soft Shell Clam in Massachusetts
“In November 1906 (a very late set typical for these warm years – T. Visel), a heavy set of softshell clams was found on Rowley Reef Knobs, a sand flat on the form of a horseshoe in Plum Island Sound.  Set from an average square foot of sand in which every clam was burrowed out of sight, 1,397 clams averaging about one-half inch in length were dug from a square foot of sand into which the clams had not completely burrowed 2,416 clams were obtained.”
Further, Belding provides the reason for the set as movements of sands by energy – currents.  This was a frequent observation in the softshell historical literature, especially in Rhode Island after summer gales in 1904 and 1906 during heavy sets of softshells and then turned sands white when swept by waves and currents as shells were then exposed.
Belding, careful in his habitat observations, details this energy factor in his 1930 account of the Massachusetts softshell clam fishery in the movement of sand grains as for the Rowley Reef set, my comments (T. Visel):
“The cause of this enormous set was found in the arrangement of the currents (energy, T. Visel).  The main channel of Plum Island Sound took a bend of 90o just northeast of the reef.  Upon the western side of the channel was slack water.  The swift current bearing the larvae was suddenly checked and the larvae, as well as the sand grains, were deposited in the slack water (These newly deposited soils are low in organic matter and can have a low CEC value promoting shell growth (T. Visel)).  On the top of the reef and on the western side of the flat the waves beat with too great a force (energy – T. Visel) to permit any permanent set.  Upon the eastern side of the flat, the waves did not exert sufficient power to dislodge the clams, which explained the peculiar outline of the set.”
Even today, a century later, historical references still mention the impact of “new sand” in some of the greatest clam sets.  This reference from the Nantucket Shellfish Management Plan, written by the Nantucket Shellfish Management Plan Committee in October 2012 contains this section referring to historic sets of the quahog that mention “new” sand bars:
“Changes in habitat are another factor that can have an impact on quahog populations.  In 1890, the beach of Smith’s Point and Tuckernuck and Muskeyet began to break up and the sand pushed through these breaks produced new sand bars that provided habitat for great numbers of quahogs.”
New sand from dredge projects also appears in the eelgrass historical literature as helping improve soil conditions for it.  Cultivated marine soils are where eelgrass grows the best.  Eelgrass expands after such natural storms drive soil cultivation events.  This gives eelgrass the cycle of wax and wane.
A review of eelgrass and conditions on the east coast can be found in “Present Eelgrass Condition and Problems on the Atlantic Coast of North America,” by Clarence Cottam and C.E.  Addy  (both of the U.S. Fish & Wildlife Service), Transactions of the North American Wildlife Conference, Volume 12, 1947.  On page 394, Cottam comments about excellent eelgrass in “new sand” after dredging:
“This dike was built with sand pumped from the bottom of Buzzards Bay; work on this dike was beginning June 1936 and finished February 1937.  The dike thus consists of “new sand” that is sand which hasn’t’ been in the shallow water for many years, probably in historic times. Yet on both the north and south sides of this dike, are healthy stands of eelgrass, standing which are among the best when I saw during the entire summer.” (Stevens, 1946)
And further:
“It appears that fairly quiet water and freedom from deep mud and silt are major factors in the re-establishing of eelgrass.”
In other words, it is the soil condition that results in the differences of the habitat coverage of eelgrass and in time with habitat succession.  The storm energy, which occurs from the warm to cold or cold to warm periods for shellfish, is similar.  Mr. Hammond as part of his climate/shellfish study of Monomoy (Chatham) kept a journal of the number of storms and even what quadrant the wind vector which could change soil conditions and resultant clam sets.  (The difference in wind direction according to fetch could cultivate different sides of bays and coves and also change movement of larval forms). These soil conditions were in fact also mentioned by Cottam:
“In areas where that is not eelgrass, the bottom is covered with a rather deep layer of silt, and fine mud, quite in contrast to the condition for example, on Hog Island Dike (mentioned above) where there is abundant “clean sand”. (Cottam, Direct Quote)
So what makes sand soil so clean?  It is the absence of particles, organic matter or clay.  This is the same process in sand filters today.  Eventually, these sand filters will need a back flush.  I know that some colleagues were surprised that I would describe nature’s soil bacterial filters as getting a backwash by storms, but in many respects, that is essentially what happens even to the formation of black layer sulfides in the filter media itself (See EC # 8, Natural Nitrogen Bacteria Filter Systems, posted on The Blue Crab ForumTM, October 30, 2015, Environment & Conservation Thread).  I can recall cleaning sand filters at URI East Farms, trying to rid salmon tanks of shed fish skin mucus.  Fish secrete mucus cross-linked to protect skin from bacterial infections; in closed systems (or nearly closed), it is the buildup of mucus that clogs filters.  This substance is hard to break down and has a tendency to build up and then foam.  This was the basis of the foam protein fractionator – a more polite term for mucus remover.   It was supposed to be tough to break down as it was a protective coating.   We could eliminate much of the organic fecal material with a backwash but the mucus is sticky and coats sand particles and would eventually cause the filter media to “fail”.  The same thing occurs to nature’s filters as well.
In time, filters became sealed and could develop a black deposit, which when exposed to air, gave off the smell of sulfide.  The filter, without a backwash cycle, would soon fail, pore capacity/circulation declined and back pressure increased.  This assisted the formation of sulfides.  That is why the no energy or non-disturbance policies do not have a science but political basis (other than observation).  Remove nature’s backwash cycle and marine soils will also “fail.”  Storms act as a backwash and wind drives proteins ashore as bubbles (See Monahan & Van Patten, editors, The Climate and Health Implications of Bubble-Mediated Sea or Exchange, Connecticut Sea Grant, CT 5a-89-06, Groton, CT).
Coastal residents often experience this filter backwash after a strong storm, hence the brown or gray water of suspended clay and organic matter particles in seawater.  Clay particles are thrown up onto the beachfront and blown inland (Loess).  Heavy rains carry enormous quantities of clay and organic matter (brown tannins) from leaves that cloud waters for days at river mouths.  Coastal residents even witness nature’s own “protein fractioning process” as brown seafoam – sometimes feet deep after a series of strong storms or one strong storm that lasted several days.
I attended a presentation a few years ago about the negative impact of human feet on sand dunes, compacting soils (beach dune sand) that reduced pore exchange in them, causing dune grass to slow its growth and root penetration without a mention of the previous storms that cultivated dune soils that first gave them larger soil pore capacity?  The politicization of coastal habitat policy has given, in many respects, a “free pass” to nature that has resulted in a research bias so pervasive as to threaten decades of estuary study as faulty or at best insufficient in terms of natural soil succession.  This bias perhaps is best represented in the hundreds of articles about declines in eelgrass – much pointed to regulatory options to “protect it” while failing to consider (in the least possible way) the characteristics of the soil in which it grew best.
The clean sand could occur by dredging energy or natural storm energy as long as the soil was cultivated, freed of organic acids eelgrass could in time recover in them.  Clean and free of organic acids eelgrass could cover them much quicker and areas of bivalve shell hash, broken bits of soft and hard shell clamshells, a natural acid buffer material (lime for example in terrestrial soils) (coral down south) these soils eelgrass much preferred. The deep layers of mud and silt were terms used to describe the “dead muds.” Muds that seemed to support little or no life, now suspected of being sapropel deposits.  Many times in the historical literature these areas were noted as “dead bottoms” areas that contained little life – often called dead zones today.  Although the destructive storms often brought hardship to those on the coast they moved sapropel out and increased suitable habitats for all marine life, fish, shellfish and in time submerged vegetation, even eelgrass.  These marine soils were cultivated or rinsed and bacterial cultures/filter mechanisms again commenced.
New sand even comes up in the historical literature from dredging projects helping to sustain thick growths of healthy eelgrass by mixing of sand with organic matter, opening soil pores.  In a 2010 study, IJ Agricultural and Biosystem Engineering, Vol. 4, No. 1, 2010 (Utilizing Dredged Sediment for Enhancing Growth of Eelgrass in Artificially Prepared Substrates by Frade et al.) highlights the negative impacts of increasing organic matter to pH and sulfide:
“In a natural environment, seagrass beds sediments normally have lower pH than the overlying water column (around a pH of Cool and pH tends to decrease with increasing depth of the sediment” and further “decreased pore water exchange with the water column (with more silt-clay particles – T. Visel) could occur, leading to reducing environments which can be detrimental to seagrasses due to increased concentrations of phytotoxin like sulfide.”
Researchers found that above 15% silt/clay (85% sand), eelgrass growth was suppressed.  This is similar to storm energy cultivation by storms or observations of dredged material in shallow waters.  The best examples of man-made new sand or cultivated soil also comes from dredging projects, a thin layer deposit of what was then called spoils (Note the term spoil is an old one and from what I have determined equated to the stench of sulfide long associated with spoiled food – Tim Visel).   This material, although high in organics if it contained sand and bits of shell, could when re-oxygenated and rinsed of organic acids support immense sets similar to storm driven new sands, thus duplicating the sorting function of rebuilding stagnant or poor low pore capacity (circulation) soils.  Belding (1930) makes mention of not just one event but “several.”
Again, Belding made careful observations, recorded them and includes the term soil in his entry in the Massachusetts Soft Clam Bulletin (1930):
“Several instances of a large clam set occurring in barren flats which had been covered with material from dredging operations are on record.  In 1905 in the Annisquam River at Gloucester a heavy set of clams (Mya – Tim Visel) occurred on the flats which were resurfaced with the soil taken from the channel.  In 1920, the dredgings from the Yarmouth Cold Storage Company were placed on certain flats in Yarmouth.  These operations were followed by a heavy set over some fifty acres which yielded about 40,000 bushels of clams.  Experiments of this department have obtained similar results by resurfacing and building up flats, particularly with gravel.  The clam culturist by covering irregularly with gravel the smooth surface of his flat, particularly if a soft mud, can hope to obtain a set of clams provided current conditions are favorable.”
Changes in softshell clam populations after a storm event are often associated with shifts of “new sand” and appears in print media.  This soil frequently is recorded as having tremendous sets.  One Connecticut example occurred after 1898.  A breach in the barrier sand split, locally called the Dardanelles, occurred and Clinton Harbor (Clinton, CT) had increased softshell clams.  This created an interest in clam culture as in January 1903, the Clinton Recorder newspaper featured an article titled “To Propagate Shellfish” in which is mentioned new sand and directly quoted “S. G. Redfield said that by sprinkling a layer of sand over these mud flats clams would grow. He had written Congressman N. D. Sperry relative to the matter and had received from prominent shellfish expert report of clam culture in the vicinity of Essex, Mass., in which twenty-five acres of mud flat in two years’ time had been made to yield 2,500 bushels of clams where before there were next to none. The speaker said but little was being done toward the culture of clams. Professor Mead of Brown University had said that by strewing these mud flats with sand and small clams in a short time they could be made exceedingly profitable.  M.L. Blaisdell said he had experimented with a spot of mud flat about 30 feet square. He had sprinkled such a spot with sand to the depth of about two and one-half inches and in a short time clam holes were found so numerous that he could hardly put his fingers between the holes. One man he knew of had dug twenty bushels from this tract and another as many more.”
The oyster soils were quite different.  Here oysters grew over the soil sulfide and composting organic matter was a constant threat to oysters – burial.  Clams, when presented with burial, could move but oysters could not.  Their habitat history fate was sealed on the type of substrate/soil they set upon.  If that habitat changed, so could the fate of any oysters living upon it, leaving few clues except shell shape.  Oysters growing on soft bottoms tend to grow tall and thin to escape burial while hard bottom oysters often showed more circular zigzag growth and even ridges similar to the bay scallop.  Oysters needed a clean (bacteria-free) substrate upon which to glue themselves.  Much of the success is the presence of periodic energy to wash and tumble buried oyster shells to the surface providing a natural spat collector.  Without energy, oyster habitats tend to fail over time; a rain of organic particles can cause a type of marine snow covering shell surfaces with bacterial films, thus making them unavailable for a “spat fall.”  If organic deposition occurs while natural energy declines, sapropels can form.
Many oysters in high energy areas set upon sand wave bars driven by energy.  These bars have a high energy edge and low energy side.  Oyster shells that fall away are then swept over the bar covering it.  In time, both edges support oysters and may reef up, growing towards the surface.  In this way, an oyster reef is formed.  The high energy edge is a type of breakwater that can migrate toward the shore with storms with little energy.  It can remain stationary and even grow out; the back edge can be softer, the front or energy edge firmer.  Oyster bed renovation often involves lifting shell from a low energy edge and placing it on or near a high energy edge, the same impact as a seawall structure Instead of stopping energy, it deflects it. (Hardened shoreline increases energy at the interface, and why instead of vertical walls, wave energy is deflected at an angle or a tapered barrier such energy as hurricane barriers with graduated steps is often used instead.)  The oyster reef mimics this energy-moderating influence.   River oyster banks exhibit similar patterns; if the river changes course or shifts, the high energy bends show possible oyster expansion while the reduction in energy oysters are covered or buried completely.  With sea level rise, this pattern is repeated and can leave deposits of shell buried in bands below peat and in salt ponds that have been sealed for some time.  Cores of such deposits often yield bands of organic matter between those of bivalve shell.
And type of reef can be the result of massive underwater shell wrack, millions of oyster shells or other shells being cast into underwater windows, and if strong enough, cast upon beaches.  One area near West Wharf in Madison, CT has almost always had a beach shell wrack, sometimes two or three feet deep.  While this can cause beach walkers curiosity and an interesting sight, this also happens under water as well.  In a modest experiment in the 1970’s, I was curious about this shell movement.  So, I painted 500 shells orange/red and 500 shells blue.  The blue shells dumped on a bend moved over time, a considerable distance downstream (more energy).  The red shells planted a long, wide section and moved very little, if at all.  (This experiment was discussed in a paper I wrote in 2008 for the Fourth Annual Meeting of the Connecticut Shellfish Commissions, January 12, 2008, titled A Review of Fisheries Histories, Natural Oysters Populations in Tidal Rivers, pg. 25).  This tidal current energy was key to oyster habitats which had high energy and low energy oyster populations at different locations.
I am at a loss why the basic soil science principles have not been applied to clam culture except as previously mentioned the public policy bias regarding bottom disturbance.  Very few guides to Aquaculture or clam culture farming fail to mention even the basic soil characteristics.  One exception is the state of Florida and its extension services.  Here several publications have been made available to hard clam culturists and give an excellent background to understanding marine soils.  Most likely, the easiest to see the importance of knowing your marine soil is a publication titled “Differences in Soil Constitutents as Related to Energy” was found in a soil landscape assessment at Dog Island lease area, Cedar Key, Florida.  Online Resource Guide for Florida Shellfish Aquaculture, University of Florida.  Investigators Rex Ellis, Todd Osborne and Mark Clark mapped out the soil characteristics of a clam culture lease at Dog Island-Cedar Key, Florida.  The lease had an energy profile consistent with a sand bar subject to wave action.  Researchers found differences between “ocean” and “protected edges”:
•   Organic material and clay are lowest in the shallowest areas (e.g., the sand bar)
•   The Oceanside of the sand bar has depressed clay and organic material as well
•   The protected side of the bar has elevated clay and organic material
•   These likely drive the critical biogeochemical reactions that affect clam growth
Those reactions are now linked to successional increases of sulfate-reducing bacteria and pore water sulfides.   Florida has invested substantial resources investigating the culture attributes of marine soils and making this information available to clam farmers.
All of the literature to date appears to focus upon five basic characteristics, high sand fractions –low organic/clay soils that have a low CEC – aids in shell formation – a neutral to alkaline soil pH that is reflective of shell hash similar to lime, low sulfate metabolism (heat) which can both reduce pore capacity and increase pore soil sulfides.  Growth is best in moderate energy, circulated (open pore) soils as a source of nutrients for food and ability to clear soils of fecal deposits.  Cultivated soils that allow clams to live below a zone of predation can increase yields (See “Manual for Growing the Hard Clam Mercenarai” by Castagna, M. & Kraeuter, J., Virginia Institute of Marine Science, 1981) (my comments, T. Visel).
“One of the best methods of protecting small clams (small hatchery raised seed mercenaria, T. Visel) from crab predation has been the use of crushed aggregate (most likely large pore size, T. Visel) covering the substrate of the nursery plots.”
“The layer of aggregate (authors suggest angular crushed stone or pea gravel ½” in. to ¾” in. diameter ) will not protect them (hard clam seed – quahog, T. Visel) unless they are within or below the aggregate.”
The best clam soils resemble those long sought after terrestrial culture, non-acidic, good mixtures of organic matter (some organic matter make loose sand grains sticky and help stabilize the soil against erosion), low clay content and a good exchange of pore water with oxygen.  While terrestrial farmers have detailed soil maps and thousands of printed articles, clam farmers have little direct readable information – my view, Tim Visel (The Chemistry of Marine Soils -1 source-, P. Dyson 2019, “Streptomyces – Species Gram Positive Bacteria That Typically Colonize Terrestrial and Marine Soils as Free Living Saprophytes,” The Cultivation of Marine Soils – 1 recent citation is from Turkey).   
The designation of composting or depleting marine soils for shellfish research remains to be done – my view, Tim Visel.


APPENDIX #1
The Sound School Vibrio and Research Warning
Caution About Black Mayonnaise

The Search for Megalops Special Report #1
The Sound School Regional Vocational Aquaculture Center
A Caution About Sapropel and Vibrio Bacteria
Posted to The Blue Crab ForumTM on February 9, 2016 Northeast Crabbing Resources
“You Do Not Need to be a Scientist to Report”
Important Notice for Blue Crabbers – Estuarine Researchers
Timothy C. Visel
February 1, 2016

Last year’s many blue crabbers experienced the harmful impacts of Desulflovibrio bacteria – commonly known as sulfate reducing bacteria or SRB.  Sulfur – sulfate reducing bacteria need organic matter to live but exist in low or no oxygen environments.  At high tide waters have a fresh change of oxygen and blue crabs can forage over Sapropel deposits – deep blue – black organic deposits that form a marine compost (black mayonnaise).  This caution is for those crabbers who crab in these areas and may be exposed to these often dangerous bacterial strains.

Several southern states are reporting blue crabbers with serious skin and wound infections – as a result of puncture or cuts while crabbing.  Preliminary research indicates that this was first noticed in southern states in the 1980s (JW Davis et al 1982 Galveston Bay Texas) and as the heat continued to build north into the middle Atlantic and then by 2012 into New England as illness attributed to gram negative sulfur reducing bacteria increased.  The agent for these cautions were Vibrio vulnificus and V. parahaemolyticus also identified as being found in Blue Crabs.  These are members of a larger and dangerous bacterial group know as the Desulflovibrio series.  The most infamous perhaps of this Desuflovibrio group of the last century is desuflovibrio cholerae – shortened to cholera.  A Maryland Paper Rodgers et al. appeared in Society of Applied Microbiology Oct 2014, which comments on these bacteria.

Florida appears to be the hardest hit and issued a caution on them in May 2015 and again in June 2015.  The vector or host culture media (food) for these sulfate reducing bacteria is sapropel – large organic deposits found in hot shallow and often poorly flushed areas – ideal blue crabbing habitats at high tide but in heat and low tide with reduced oxygen conditions the breeding ground for these gram negative bacteria.

The Vibrio first caution was issued in 2012 as some of the seafood diseases – the necrotic flesh wasting strains necrotizing fasciitis (winter flounder fin rot) and shell dissolving bacteria (lobster shell disease strains chinoclastic Vibrio) were showing up in larger amounts in this warm marine compost – sapropel.

The caution now is for crabbers and researchers working in estuarine waters – sulfate reducing bacteria are being found in these warm water deposits and now suspected in dangerous bacterial infections.  Crabbers will recognize sapropel by its blue black color, sticky jelly or greasy consistency and the smell of sulfur.  It is also being associated with the blood fluke in our area termed clammers itch schistosomes and now potential links to the MSX oyster disease.  (An early MSX outbreak here in the 1980s occurred in the lower Hammonasett River near deep sapropel deposits).

When oxygen is low and the temperature goes up, sapropel (mostly leaf compost) provides the sugars or glucose (primarily terrestrial leaf material collecting in bays) to grow these sulfate reducing bacteria.  Extreme bacterial action is now suspected of creating sulfide Blue Crab Jubilees in historical events to our south during low energy (poor mixing or flushing) hot weather and storm free periods.

Gloves and aprons are suggested when working with sapropel – treat any puncture or cuts with serious and rapid antibacterial agents.  The problem with these gram negative bacteria is that they are often antibiotic resistant – as discovered in 1976 (Joel O’Connor, NOAA) in all of the New York dumpsites that obtained animal fats and grease.


Appendix #2

Recent Marine Sediments A Symposium

Edited by PARKER D. TRASK
U.S. GEOLOGICAL SURVEY, WASHINGTON, D.C.

PUBLISHED BY
THE AMERICAN ASSOCIATION OF  PETROLEUM GEOLOGISTS TULSA, OKALAHOMA, U.S.A.
___________________

LONDON, THOMAS MURBY & CO., I, FLEET LANE, E.C. 4
1939



OCCURRENCE AND ACTIVITY OF BACTERIA
IN MARINE SEDIMENTS

CLAUDE E. ZoBELL
Scripps Institution of Oceanography, University of California, La Jolla, California

ABSTRACT
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.

DECOMPOSITION CAUSED BY BACTERIA

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 #3

A Century Ago Sapropel Was Known to Have
Chemical Signatures
Low Oxygen Conditions Leave Chemical Residues of Nitrogen

Professional Paper – United States Geological Survey Issues
156-158  - 1920 – Edward Wilber Berry

{Brackets indicates T. Visel insertions}

Origin of the Varve (Layering) – Biochemical Evidence in Core Sample Reactions

“Of the three hypotheses that have been considered to explain the rhythmic alternation of carbonate and organic luminance of the varves {cores} in the Green River formation one depends upon biochemical reactions – Abundant evidence has been assembled to prove conclusively that the organic matter in the oil shale passed through a stage of putrefaction.  The ooze or sapropel which was later Lithified into oil shale must have been wholly analogous to the black fetid {often sulfide rich swamp stinks} organic oozes now forming in both fresh and salt lakes.  The characteristics of such locustrine ooze or “faul schlamm” have been described with considerable detail by Naumann, Potonie, Nadson, Wesenberg – Lund and others.  In the Microbian decomposition of such ooze the albumin is broken down and among other compounds ammonia and hydrogen sulphite are formed. Nadson isolated four bacteria and three fungi which play the principal part in the formatting of the fetid black ooze in the lake.  They (microbial organisms) all bring about the decomposition of albumin with the release of abundant ammonia and hydrogen sulfide.”

United States Department of The Interior
Ray Lyman Wilbur Secretary
Geological Survey
George Otis Smith, Director
Professional Paper 156
Revision of the Lower Eocene Wilcox Flora of the
Southeastern United States by Edward Wilber Berry
1920   

Appendix #4

Aquaculture Today, Fall 1988
“Getting More from Your Sediment Bottoms: The Effects of Hydraulic Harvesting”
By H.K. Rask
Regional Marine Resource
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