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Nitrogen and Eelgrass Habitat Questions
CT Fish Talk™ Environment and Conservation #9

Questions Remain about Eelgrass Habitat History and Nitrogen Research
To Crab and Shell Fisheries

Tim Visel, The Sound School*
Tim Visel – Member EPA – DEEP Long Island Sound Study Citizens Advisory Committee 2011 to present, Habitat Restoration Workgroup 2005 to present. These views do not represent either committee. This is the view point of Tim Visel. As of October 2014 no consensus has been reached regarding the existence of Sapropel in Long Island Sound, nor the significance of a Sapropel/sulfate reduction nitrogen pathway to fish and shellfish habitats. The Citizens Advisory Committee and Habitat Restoration Working Group continue to support eelgrass protection policies as of October 2014.

60 South Water St, New Haven, CT 06519
Questions about Eelgrass/Nitrogen Habitats

October 2014
Revised November 2015
Capstone Questions

• Did post 1982 research contain an accurate climate change habitat history for eelgrass?
• What is the role of dense submerged aquatic vegetation in habitat succession and habitat quality in high heat when sulfate is not limiting?
• Is the cycle of eelgrass abundance a form of marine habitat succession that is under represented in the current literature?

ASTE Performance Standards – Aquaculture #4, 5, 6
ISSP Capstone Eelgrass Habitat History Proposal

FFA Non Experimental Research SAE –
Students considering a public policy Capstone project should contact Tim Visel in the Aquaculture Office.

Environment and Conservation – The Blue Crab Forum™ - Bacteria Nitrogen Series

I want to thank the Blue Crab Forum for allowing me to post in a new thread – Environment and Conservation and also Connecticut Fish Talk for reposting these reports. This is my ninth report about bacteria and nitrogen cycles. Coastal habitats once praised for valuable habitat services are impacted by bacteria and at times become nature’s killing fields, eliminating critical nursery and spawning grounds for many inshore fish and shellfish species. Coastal fishers often observe these events, mats of bottom bacteria, chocolate or purple waters, brown tides, blue crab jubilees or just fish kills. Beyond these public events bacteria and nitrogen change the habitat qualities that we recognize today as “good” onto something that is “bad” for inshore fish and shellfishing. Out of sight and rarely discussed, these conflicting bacteria strains have important implications for estuarine health and seafood production worldwide.

#9 Nitrogen and Eelgrass Habitat Questions 11/18/2015

#8 Natural Nitrogen Bacteria Filter Systems 10/20/2015

#7 Salt Marshes a Climate Bacterial Battlefield 9/10/2015

#6 Bacteria Disease and Warm Water Concerns 7/23/2015

#5 Nitrogen, Inshore Habitats and Climate Change 1/12/2015

#4 Black Mayonnaise Impacts to Blue Crabs and Oysters 1972 to Present
10/16/2014

#3 A Caution Regarding Black Mayonnaise Habitats 10/2/2014

#2 Black Mayonnaise, Leaves and Blue Crab Habitats 9/30/2014

#1 What About Sapropel and the Conowingo Dam? 9/29/14

Fishers should follow this bacterial conflict as more and more information comes in regarding habitat quality and important recreational fisheries such as striped bass, winter flounder and blue crabs or lobster habitats are subject to bacterial impacts. It is also important that shallow water fishers be aware that sulfur bacteria contain a series of antibiotic resistant strains first identified in Contaminate Effects On Biota of the New York Bight by Joel, O’Connor, NOAA (1976). Soft organics with bacteria do pose risks to fishers and bathers – coastal bacteria benthic monitoring programs are needed.
I respond to all emails at tim.visel@new-haven.k12.ct.us

Tim Visel Special Note – Nitrogen and Eelgrass Habitat Questions

Years ago, I did not care much for fall yard cleanup. Some people look forward to the brilliant colors of fall leaves, others to harvesting the last summer crops. I just looked at fall as work—raking leaves.

I have taken a new interest in fall leaves, instead of the past summer’s growth or foliage, I now see sugar and acid – not the sugar we use on the table but cellulose a complex sugar, the product of photosynthesis. Oak leaves are also very acidic and add to reducing marine soils pH. Each fall thousands of tons of leaves fall, flow or are washed into Connecticut’s estuaries. Each fall is a harvest in itself, not for us, but for bacteria. It is now food for countless bacterial strains who consume it. This sugar is in a different form but it is a food for bacteria that breakdown this acidic plant tissue to obtain these sugars bound up in the leaf. I don’t think the above will be much of a surprise to terrestrial garden composters who often add lime to offset this low pH or turn composting deposits to gain oxygen, but we have marine composts as well, just with at times different bacteria.

Over the weekend, I mulched my oak and maple leaves all the while thinking how much “food” will be delivered into creeks, bays and coves in the form of leaves ground up by tires along roads all through New England to be washed into estuaries by fall rains. It was the shellfishers on Cape Cod of Lewis Bay who termed it “oatmeal”, the ground up chaff of oak leaves that now covered bay bottoms over once productive hard clam quahog areas sometimes measured in feet. Leaves had also filled in many “long run” alewife passage ways on the Cape as well. (Much after a regional leaf burning ban 1972-73). In time I learned that oak leaves were especially damaging to marine habitats. Oak trees to protect against water loss in times of drought produce a wax in its leaves- they often appear to glimmer or shine in summer breezes from it. Drivers in New England fear oak leaf wax as well in a heavy rain; they are “greasy” and cause many accidents. From time to time weather forecasters even issue “leaf warnings”; the slippery conditions of leaves and rain have caused many car accidents. The grease is the wax in the leaves themselves. In the marine environment, sulfate reducing bacteria in search of this cellulose (sugar) cannot digest the wax, so they just leave this residue behind; it is now the source of “sticky bottoms” that blue crabbers often experience. Even the old navigation charts mention “sticky bottoms”, nearly always in low energy areas or in areas that receive organic debris from land. These bottoms change only with the strongest of storms, nature’s way of turning its marine compost piles. This appears also to be cyclic.

Eelgrass is involved in this marine compost formation; it holds the leaves and reducing organic matter in the shallows and in times of heat helps form a deadly marine compost called Sapropel. In heat and low oxygen it can buildup rapidly – in colder periods, oxygen is “available” - cold water can hold more oxygen in the elemental form, the oxygen we need as well. However, in times of heat, oxygen solubility is lowered in seawater; the

oxygen requiring bacteria die off and sulfate reducing bacteria now “take over.” (Sulfate is plentiful in sea water even when it is “hot”). They are survivors of when sulfur, not oxygen, ruled our atmosphere. (Another survivor of this sulfur period is the amazing horseshoe crab who can live amongst these often dangerous sulfur bacterial strains with no harm, unfortunately not us as many blue crabbers have now experienced the ill effects of them (bacteria) introduced by simple cuts see Blue Crab Forum™ Science Discussion Thread – Marine Bacteria, September 12, 2015).

It is ironic that habitats in great cold contain the “friendly bacteria” and the same habitats in great heat now contain the flesh eating or shell destroying bacteria.
That is why coastal fishers are sometimes surprised by the seriousness of infections with cuts or scrapes today when decades ago meant little concern. In heat and high organic loading- that is not the case anymore.

Many swimmers and crabbers have experienced these dangerous bacterial strains in very hot weather, often with disastrous results as they live in Sapropel – the shallow wading areas. In times of great cold and storms, this greasy reside, Sapropel, (Black Mayonnaise) does not accumulate. It is quickly consumed (broken down) by bacteria and other organisms who utilize it. In times of heat and few storms, this compost builds up, harbors these sulfur bacteria strains that now purge ammonia and sulfides, very toxic compounds to fish and shellfish. It is the shallows that are so important habitats for “nursery areas” areas where the smallest life forms find shelter and food. Unfortunately nature delivers these bacterial foods into the same areas and as the sulfur reducing bacteria, do they break down leaf and organic matter very -very slowly. They themselves are overwhelmed (too much food) as a result the “marine compost” now builds and is noticeable to fishers. This is the cycle of Sapropel that New England farmers noticed and harvested over a century ago. (See IMEP # 26, Connecticut Rivers lead Sapropel production 1850-1885 - The Blue Crab.Info™ website: Fishing, eeling and oystering thread.

It is also the greasy sulfur smelling organic material fishers report covering previous habitat bottoms, such as the areas behind railroad causeways in eastern Connecticut in the late 1970s. (IMEP #15 Winter Flounder Fishers correct about habitat concerns April 2014 Blue Crab forum fishing eeling, oystering.) For decades these fisher habitat reports gained little recognition, but now other states have reported “Black Mayonnaise” as well; the organic composts trapped in poorly flushed lagoons, coves or built up behind reservoir dams. (A significant study of the Conowingo Dam organic deposits is now underway.)

Florida now is beginning to recognize the deadly impact of Sapropel, and a recent newspaper article contained this title:

“Muck Spreads Like a Cancer in Indian River Lagoon,” and was an article by Steven Thomas, Vero News, February 15, 2014 – it contains these quotes:

“The muck, when has been described as black mayonnaise, because of its consistency is made up of water, fine particles of soil or clay and rotting organic matter.”
“The topic came to forefront in December when John Trefrey, a professor of Marine and Environmental Chemistry at the Florida Institute of Technology appeared before the Senate
Committee in Environmental Reservation and Conservation to detail the ecological damage caused by muck.”

“It’s like a cancer that has been spreading,” he said. “There are now between 5 and 7 million cubic yards of muck along Brevard and Indian River County stretch of the lagoon. That’s enough to cover 1,000 football fields a yard high” and “It smothers all life forms other than bacteria and further, wherever the muck is, all habitable life is gone,” Trefrey said.

One of the signs that these shallow habitats are turning against fish and fishers is that Sapropel tends to build up. A caution was made to watch for this by Donald Rhoads to Long Island Sound Workshop attendees in 1985 as to this potential problem. In a May 10th, 1985 NOAA Estuary of the month workshop and report to the EPA has this section. (See Long Island Sound – Environmental status and Management of Living Resources – An Estuary of the month seminar US Dept of Commercial Main Auditorium May 10, 1985 sponsored by NOAA Estuarine Programs Office and the Environmental Protection Programs Agency EPA – Battelle contract #68-03-3319 to EPA January 15, 1986 Proceedings published January 1987 NOAA Estuary Seminar Series No 3 (note many of their Washington DC seminar participants later became part of the Long Island Sound Study committee membership by 1988 Tim Visel.)

Dr. Rhoads of Yale responds following a question from Dr. Schubel of the Marine Sciences Research Center State University of New York.

Dr. Rhoads responds, “Yes, one reason I mentioned the importance of the Sapropel – these black iron monosulfite muds on the bottom was the direct point that Peter raised (Dr. P.K. Weyl) the system is so dynamic that to measure the change from year to year in 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 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 Sapropel terminate whatever isobaths that might be follow the edge of those Sapropel. If they are encroaching upwards into shallow water, it’s getting worse. If they’re receding its getting better.”

Eelgrass is involved because by its natural characteristic to bind and gather organics in the most vulnerable habitats, it jumpstarts Sapropel. For over a century shellfish researchers have noted that eelgrass meadows over time tend to rise- that is why. Although in times of cold and high energy eelgrass provides significant positive habitat services to some fish species in high heat these eelgrass meadows begin the first Sapropel and in time become sulfide rich and purge deadly compounds as part of the sulfur reducing bacterial/nitrogen
cycle interactions. When that happens, eelgrass meadows protect the Sapropel deposits beneath them and become natures killing fields in heat, turning against those organisms that once lived near it. It can kill young and adult seafood alike.

Although numerous publications extol the positive habitat services of eelgrass very few mention the negative – almost none. We need to look at that very carefully (my view).

The current picture of eelgrass tended to be biased and portrayed the positive (cold and energy cycles) periods while ignoring the biological consequences of high heat, high organic eelgrass meadows even with global warming (heat and low energy cycles). A complicating factor is that eelgrass was utilized as a species to lower nitrogen inputs. That position has resulted in similar research balance/bias questions.

The capacity for sulfur reducing bacteria to alter the nitrogen cycle by purging ammonia was well known by the 1930s.

In times of high heat (global warming) an eelgrass “Sapropel habitat” is the least desirable habitat type to have in shallow water. It can kill quickly and leave very few clues behind other than dead or dying organisms and sulfur smells.

Introduction

One of the most serious questions regarding eelgrass habitat services to finfish and shellfish is an accurate portrayal of all conditions seasonally and over time. Habitat succession in marine shallow habitats appears to have been subject to “snapshot ecology” taking an isolated time (habitat condition) and extending it to basic habitat types with defined values. This is the equivalent of a newly cut lawn and then placing a sign “needs no cutting again” unless the lawn was artificial turf in a few days habitat succession would be quickly apparent. The sign and message contains a bias of time, a snap shot.

Many of the habitat benefits of eelgrass and other aquatic vegetation now appear to be linked to climate cycles. In times of energy and cold eelgrass provides “positive” services (very much highlighted in the current eelgrass literature) but in times of high heat and low energy (few storms) very negative habitat impacts. Those impacts are very much “missing” from current literature representing relatively short periods of successional habitat attributes linked to eelgrass over time. Is this a form of scientific or research misconduct – it could be more if the intended outcome was to prejudice a public policy outcome. Public policy decision makers may not have had all the important information upon which to make properly informed decisions.

There is also conflict emerging as to the habitat value of eelgrass/sapropel in shallow estuarine environments. It is not only in New England but in southern estuary programs as well. These are the same organic deposits linked to sulfuric acid fogs in the Niantic Bay area in the 1970s and hydrogen smells so intense as to drive Rhode Island Narrow River
residents from homes in the 1980s. It is these shallow areas that are so impacted by climate cycles, they heat up the fastest. In areas with organic deposits they support sulfur not oxygen reducing bacteria. As such in high heat they turn deadly in these shallow areas. It is these same shallow sediment – (organic matter) deposits that shelter the smallest sizes of fish and shellfish areas – often termed “nursery” areas because they in fact do act this way – they provide essential forage and protection habitat services (formerly associations) to a wide range of crabs, lobsters, benthic and pelagic fish and of course shellfish. In times of cool temperatures ample oxygen allows this nursery function to occur – Striped Bass fishers know how important these shallows can be with the young of the
year class failures of the 1980s – now linked to sulfate reduction of organic matter washed into the Chesapeake following Hurricane Ages (1972).

A huge rainfall can wash inches of organic matter downstream covering estuarine soils killing shellfish below. In time these organic deposits became even more deadly – they purge ammonia – sulfide and as it ages methane gas. These weather events (cycles) with huge pulse organic loadings are recorded as layer in core studies conducted by Wesleyan University in the early 1990s. Although some Connecticut State officials sent out letters to the effect that no shell/organic layers were found in Connecticut coves (as reported by winter flounder fishers) a shell/organic layers was found in every Connecticut Cove surveyed. Because sulfur reducing bacterial are slow composters it can (much slower than
terrestrial compost consumers) take decades to consume these organic deposits. In the process and during high heat it is possible to lose the shallows. Dr. Bernard Skud, one of my fisheries science teachers when I attended the University of Rhode Island (1978) mentioned this important relationship during class – “if you lose the shallows you will lose the fishery.”

Dr. Skud had a long history with the US Fish and Wildlife Service Bureau of Commercial Fisheries and later the National Marine Fisheries Service (NMFS) and of course this is absolutely correct but not instantaneous, except perhaps for bay scallops as most species can withstand one of two year class failures but cannot over extended periods of time such as the Striped Bass habitat failure of the 1980s illustrates. Eventually in time these organic deposits lessened and habitat quality improved and so did the survival of small stripers. Oysters fishers have also seen what several inches of organic matter will do to oyster bars covering them and sulfuric acid they produced and dissolved them. Most likely the most often used example for me is the loss of inshore winter flounder habitat as our climate warmed and energy levels decreased in CT. Fishers soon noticed the build up of Sapropel (Black Mayonnaise) in once sandy marine soils with bivalves – hard or soft shell clams. In times these once critical habitats became muck filled absent of fish and often when disturbed gave off strong sulfur smells. This is also the chemical/oxygen response as to why Cape Cod and Island residents would rush out to unblock salt pond inlets closed by a coastal storm – in time without tidal exchange these areas turned black and suffered fish kills – many times in the historical literature this is mentioned as “stagnation.”

Coastal Cove or salt pond residents could see the “black water” and fish kills that followed closures – what they did not realize perhaps the struggle between bacterial strains or the source of those sulfur compounds. From organic matter digestion in the historical records small coves and salt ponds do provide clues to these habitat struggles. One of the most detailed for energy is Pt. Judith Salt Pond in Rhode Island. (See Blue Crab Forum™ Northeast Crabbing Resources Megalops Special report #3).

Eelgrass in the historical literature was frequently linked to slowing flows, restricting channel widths, even at times interfering with navigation. In some regions special propellers were developed to cut through these dense eelgrass growths all of which helped collect organics and in high heat help the formation of Sapropel. When inlets were closed habitat succession events which naturally could take years as eelgrass meadows rose in height could happen in a few weeks or even days after a powerful storm in high heat.

What fishers and shore residents could observe is what happened to small bodies of water that warmed or got cut off from the sea – they could smell it. These are the marsh smells – the gases of bacterial composting only under water – sulfide at the surface (rotten egg smells of hydrogen gas) or methane gas attributed to “sour” bottoms far below. When this happened fish and shellfish larval forms can be killed by the billions.

Sulfate reducing bacteria is also a key component in carbon cycling systems as well (Baumgortner et al 2006 Sedimentary Geology 131-145 “Sulfate Reducing Bacteria in Microbial Mats”). A more recent work “Role of Sulfate Reduction and Methane Production by Organic Carbon Degradation in Eutrophic Fjord Sediments Jorgensen and Parkes 2010 (Limfjarden Denmark) describes how fine grained sediments with high organic matter accumulates in protected often euthrophic estuaries – escapes “aerobic mineralization” by burial in a sulfate zone where over time “methanogenesis is the terminal pathway of organic carbon mineralization” or just simply it seeps methane gas or it rots for a long time.

Sulfate bacterial reduction also has a role in acidification – early shellfish studies clearly detailed sulfate to sulfuric acid as increasing potential for carbonate dissolution (Effects of Sulfate Reduction on Calcium Carbonate Dissolution and Precipitation in Mixing Zone fluids). Ronald K. Stossell – Dept of Geology and Geophysics University of New Orleans. Acids in the marine environment can dissolve shell even metal at times and fishers have long seen the sulfide black “deadlines” and metal erosion in soft deep sediments. Blue crabbers in Chesapeake Bay often notice this impact after storms that re oxygenate organic deposits. Once this happens a sulfuric acid wash develops it eats metal blue crab traps.

Eelgrass and Nitrogen Questions -

Our freshmen students here at Sound School are exposed to the nitrogen cycle in closed aquaculture systems (crab shedding systems) and the role of bacterial in reducing toxic impacts of ammonia.

I just ran into a fact sheet that shows a cycle diagram from our Aqua Biology class – it clearly shows the role of ammonia to nitrite by nitrosomonas bacteria and nitrite to nitrate by nitrobacter bacteria in the ammonia nitrogen cycle. This ammonia pathway for nitrogen is clearly underrepresented in many Long Island Sound nitrogen studies. Ammonia with pH of 11 clearly can buffer acidic waters but is deadly to marine life that is why our aquaculture students closely monitor pH and ammonia levels in closed culture systems. A system or bay/cove or salt pond that receives organic matter in heat (and low oxygen) will see all of these processes and with devastating impacts to marine life – ammonia discharge from organic matter can more than offset acidic conditions it can make seawater more basic (tannic and sulfuric acids more dangerous to sea life in shallow seas than carbonic acid) discounting nitrogen releases from sulfate reducing bacteria can alter nitrogen levels, and now the implications of nitrate as a second source of oxygen that can buffer sulfate reduction and help other natural bacterial filter systems remove ammonia. But these processes are rarely discussed as a unit – more often than as fragmentary “pieces” part of a huge problem I term “snapshot ecology.” Eelgrass habitat succession only makes toxic sulfide and ammonia conditions worse in heat – especially over long periods of time that has few storms.

I often raise the concept of requiring long term historical reviews, which I feel is necessary by perhaps Congressional action but with this paper reinforce the concept of multidisplinary approach is so important (if not critical) so as to not repeat recent nitrogen
and eelgrass mistakes. It looks like a possibility of another one with the “blue carbon initiative” that seeks to declare organic deposits that undergo sulfate reduction as the most
precious mud on earth while it harbors some of the most deadliest bacterial strains and may soon be declared a public health hazard to us? It (organic sludge) in heat has been linked to fish and shellfish bacterial diseases for decades.

The “recent” blue carbon initiative appears to be in opposition to all biological oxygen demand nitrogen removal programs, (it is good to have excess organics) or perhaps to dump manure against the concept of habitat quality as it relates to soil pore water sulfide exchange and deadly methane and sulfide gas generation? It appears to only examine only a carbon retention “snapshot” (which is accurate) but ignores the horrific biological consequences of this carbon retention in organic deposits in high heat shallow habitats. Those habitats are now frequently associated with a warming global climate?

Several recent “blue carbon” studies correctly report that seagrass has extensive root structures and “accumulate large stores of carbon through the formation of “matters” beneath sea grass meadows – these mattes accrete vertically overtime, raising the seagrass meadow toward the surface of the water.” See State of The Science on Coastal Blue Carbon May 2011 Duke Nichols Institute pg 18. But does not include the biological consequences of the collection of organic matter in shallow seagrass habitats (Sapropel formation). Although the use of the term “matte” is used in several blue carbon papers the term matte has no biological reference as to the sulfate reduction process it contains.

Dr. David Belding a well respected shellfish researcher for the State of Massachusetts a century ago comments on the ability of eelgrass to suffocate clams, surface rises and the chemical implications of organic material in these soils. Pg 201, A report upon the soft shell lam fishery of Massachusetts – Reprinted by the State of Massachusetts and the Cape Cod Cooperative Extension Service – University of Massachusetts 2004 – The following sections pertain to Blue Carbon “mattes” my comments are between brackets.

Soils – “It occasionally happens that parts of a flat which seem similar in every respect exhibit extreme differences in the way they harbor or repel the clam set. It is almost as though on invisible line had been drawn beyond which did not grow. Hydrogen sulfide and other organic compounds in the soil may account in part for this condition.” {And the suspected presence of Sapropel conditions T. Visel}.

Eelgrass – Eelgrass as we have seen is fatal to a good clam bed. Many productive beds would be quickly spoiled by eelgrass if it were not for constant digging. The grass raises the surface of the bed above the normal level by bringing in silt, which smothers the clams. The reclamation of such flats can be accomplished by destroying the grass and allowing the water to carry away the accumulated muddy deposits.

Organic Material – “Clams are usually absent from soils containing an abundance of organic material. Even if the slimy surface (now suspected to be Sapropel – 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. Such a soil indicates a look of water circulation within the soil itself as indicated by the foul odor of lower layers of soil, the presence of hydrogen sulfide, decaying matter, dead eelgrass, shells, and worms. If such a soil could be opened up my deep ploughing, or resurfaced with fresh soil to sufficient depth, it would probably favor the growth of the clam.”

A recent Long Island Sound Study document titled “The Trillion Dollar Asset” Economic valuation of Long Island Sound Basin – indicates that marine compost (humis) that by location tends to create Sapropel as controlling climate factors pg 6 and has a dollar value as carbon accumulates in them. While carbon sequential collections occurs in all composts the report does not include habitat succession events, nor mentions the toxic materials that purge from them as bacterial processes collects the carbon or the negative seafood impacts from it, those sulfate reduction aspects are “missing” (pg 37 table 19 does lists a carbon stock storage value (high) at 135, 603, 756, 338 dollars or about 136 billion).

{The blue carbon initiative may surpass the concerns in eelgrass studies – my view}.
Ask any trout fisher what green leaves will do to trout stream or an oyster fisher what decaying oak leaves will do to oyster sets. Habitat specialists should have raised alarms to the types of bacteria that reproduce in accumulating organic deposits in high heat but they did not. If readers should like a review of what warm organic matter can do read on the Blue Crab Forum™ post titled Science Discussion “marine bacteria” it clearly describes some of the most dangerous bacteria infections – that blue crabbers are noticing and reporting now.

The bacterial sulfide/ammonia purging however is not new.

Claude E. ZoBell (Scripps Institution of Oceanography University of California, La Jalla California – new series #72 April 22, 1938 Recent Marine Sediments 1939, reprinted in 1965, detailed the impacts of organic matter that supports bacteria in the coastal zone half a century ago on pg 416, is found –this section which mentions these bacteria in the sulfur cycle (1939).

“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).”

Eelgrass has a special role in this habitat process as it holds and binds organic matter making it stable and by doing do enables sulfate reducing bacteria to digest it. The knowledge that in high heat organic deposits were able to purge ammonia and alter/enter the nitrogen cycle has been available for decades.

EPA – Region I Eelgrass Nitrogen TMDL

It appears EPA as an agency also strongly promoted nitrogen linkage to eelgrass health and connected it to seafood abundance as a way to bolster regulatory authority under the Clean Water Act1, See meetings and minutes of EPA eelgrass research team and EPA eelgrass reports ] [EPA also strongly promoted a nitrogen TMDL without apparently considering the sediment respiration of Sapropel (Benthic Flux) in many areas and now may be subject to pending litigation and allegations of scientific research questions or at the least, suspect research methods. This is especially true in terms of the law of habitat succession for eelgrass (See Daniel Pauly, Shifting Baselines, 1995) or marine habitat succession, as more and more research from overseas describes sulfide purging from eelgrass meadows – termed death rings. (IMEP 51-A, 51-B The Cycle of Eelgrass). Mervin Roberts a naturalist from Old Lyme raised questions about using populations in motion as to build public policy in 1985 as containing an institutional (and well known) bias – from The Tide Marsh Guide, Roberts 1985, is found this section -

“Biological surveys and censuses are difficult to design and sometimes impossible to carry out so as to be free of bias. They are often hard to compare since very few are conducted under identical circumstances; but then even the accuracy of our national census of people is frequently challenged. Now please come back to that word which appeared several paragraphs previous: bias and wondered how scientists apply it. As a matter of fact, scientists used it long before it became a catchword. Examples of bias in science are sometimes found in collections of living organisms whose population is in motion. To be without bias, such a collection would have to be made over an extended period with no regard to inclement weather, ice, time of day or holidays.” (Mervin Roberts The Tide Marsh Guide 1985).

Several environmental agencies including the EPA linked the protection of eelgrass (and other maritime grasses) to fisheries restoration and seafood abundance taking a slice of the habitat succession picture and promoting it to gain a public policy foothold by associating it to the Clean Water Act. Once included eelgrass became the hammer to drive the nitrogen nail home. This is mentioned by Walter Nelson, Western Ecology Division US. EPA Newport, Oregon in an EPA publication: EPA/600/R-09-050, June 2009. On page 1.1 the conceptual framework for a Review of Research News for Development of National Water Quality Criteria Protective of Seagrasses. “Background of EPA submerged Aquatic Vegetation Research Program” Walter G. Nelson is found this section.

“The U.S. Environmental Protection Agency is concerned with the protection of seagrasses under two sections of the Clean Water Act (33 U.S.C. 1252 et seq.), Section 304 (a) and Section 404 (c). Under section 304 (a) (1) the agency is charged with the development of water quality criteria reflecting the latest scientific knowledge on effects of pollutants on aquatic biota, including “plant life”. The agency is further charged (Section 304 (1) (2)) with providing timely scientific information on factors necessary to maintain the chemical, physical and biological integrity of the nations waters. Under section 404 which regulates dredging and dredged material disposal under the lead of the Army Corps of Engineers, EPA is authorized to deny issuance of dredged material disposal permits where such activity will have “an unacceptable adverse effect on municipal water supplies, shellfish beds and fishery areas (including spawning and breeding areas), wildlife, or recreational areas.” While seagrasses are not specifically named, it is clear that the protection of seagrass habitat is encompassed within both sections of the Clean Water Act.

Development of water quality criteria protective of seagrasses may be principally driven by the desire to restore a severely degraded resource. One example of a critical path (Figure 1.1) for seagrass protection derived from seagrass restoration goals is provided by the plan developed by the Tampa Bay National Estuary Program (Johansson and Greening 2000). Within the framework of the general designated use, targets for extent of seagrass restoration are first set. Setting of quantitative seagrass restoration targets may be based on a variety of lines of evidence. Seagrass conservation targets developed for the Indian River Lagoon of Florida (Virnstein and Morris 2000, Steward et al. 2005) involves three approaches, development of a potential target based on distribution in the best available
habitat (a reference condition approach), the use of a historically based distribution target, and a “critical minimum” approach which establishes the lowest threshold below which seagrass extent should not fall.

The specific site strategies developed by the Tampa Bay NEP (Johansson and Greening 2000), Texas Parks and Wildlife (1999), etc. can be generalized (Figure 1.2) to a critical process path (3.g.U.S. EPA 2001, Batelle 2008). Within the U.S. EPA Regional Offices, there are Nutrient Coordinators who establish Regional Technical Assistance Groups to assure that the best available current information is brought to the criterion development process, and inappropriate guidance is weeded out. As suggested by Figure 1.2, a critical early decision is the consideration of scale at which eco regional classifications can be applied are required in order to reach beyond a water-body by water-body approach to criteria setting.”

In a conference held in Maine seems to support that connection occurred in Tampa Bay. Researchers there found that in time at the end of habitat and succession these grasses
trapped organics that in time and appropriate climate conditions producing sulfide that could kill the grass itself (Carson et al 1994).

While the goal of including eelgrass under the Clean Water Act regulation umbrella its weakness of these efforts is that to accomplish its goal, climate cycles and habitat succession for eelgrass (as for any estuarine grass) were not included. If they had then the current damaging, organic deposit patterns in high heat would have been discussed as sulfate - sulfide toxicity. Some of the initial research on toxic sulfide formation in fact came from early submerged aquatic vegetation researchers, but were not included in later eelgrass studies.

The combined habitat impacts upon submerged aquatic grasses in this case turtle grass of high heat low energy and sulfide was first reported in the early 1990s. In a 1994 paper titled Relationship of Sediment Sulfide to Mortality of Thalassia Testudium in Florida, Paul Carlson, Laura Yarbro and Timothy Barber looked at bacterial reduction and sulfide
toxicity. On pages 733-734 (Bulletin of Marine Science, 54 (3) 7336 746 1994 provide some important habitat insights following a Thalassia (turtle grass) die off –

“As part of a collaborative research group studying Thalassia die off in Florida Bay, we have focused on the role of sediment sulfide in the die off process. Sulfide is produced in anaerobic marine sediments by bacteria that use sulfate as a terminal electron acceptor in the degradation of organic matter (Goldhaber and Kaplan, 1975; Sorensen et al., 1979). High temperatures, abundant organic matter, and low sulfide biding capacity can result in extremely high porewater sulfide concentrations in sediments 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 reaction of sulfide with molecular oxygen.”

The eelgrass effort appears to have looked at distinct short habitat views – snapshots that from it drew habitat conclusions for a very incomplete habitat history. It from the numerous reports ignores climate and energy cycles for explanation of eelgrass population shifts and dynamics for habitat coverage. It appears that perhaps a preselected process may have already been established by report statements that included on page 1.5 “and inappropriate guidance is weeded out” begs the question if these “site specific strategies” can be generalized to a “critical process path”. That path it seems always seemed to place eelgrass among other habitat types as more or most important that others. That is very easy
to see just from the volumes of reports/papers on eelgrass and very few that discuss sulfide, pH conditions of estuarine soils or the existence of Sapropel mentioned in the 1987 NOAA report referenced earlier.

In a conference held February 24 & 25, 2009, in Portland, Maine – Status Trends and Conservation of Eelgrass in Atlantic Canada and the Northeastern United States, details how public policy would be developed around eelgrass and then link its survival to water quality parameters that completely ignored habitat succession (soil pH and energy/ cultivation), but connect it to water quality conditions especially nitrogen.

The connection of water quality to eelgrass population was reinforced by many EPA studies and conference papers of EPA eelgrass researchers during this period as evidenced at a 2009 conference in Portland Maine.

Status, Trends, and Conservation of Eelgrass in Atlantic Canada and the Northeastern United States
February 24-25, 2009
Portland, Maine

“It’s the Water Quality, Stupid!

“The problem of cultural eutrophication of our coastal waters is a complex one that a multitude of state and federal agencies are attempting to address in a variety of ways.

Approaches to the protection of sea grasses from ever enrichment of nutrients vary widely. These approaches included development of ambient nitrogen criteria development of nitrogen loading models to watersheds, multimetric approaches to management of water quality, and ecosystem manipulations (e.g. adding oysters/shellfish to filter water, dredging to increase water movement/flushing). Our estuaries are physically, chemically and biologically complex and species, is not completely understood. Into this arena of uncertainty, resource managers must make very difficult decisions that have real societal costs.”

And another paper presentation at the same conference, continues this theme,

The Good, the Bad and the Ugly of Seagrass Protection in the Northeastern U.S.
“The Clean Water Act (CWA) has been the key tool in protecting aquatic resources since its inception. The general goals of the CWA are to ensure that the waters of the US are fishable and swimmable. Implied in this goal is protection of habitat that fish and other aquatic resources rely on for critical life functions. Thus, seagrass, defined as vegetated
shallows in the CWA, merits protection for its function as a nursery habitat. This talk will review seagrass regulation and management in New England over the last 20 years. The names have been changed to protect the innocent.”

In time, we may learn it was not the water quality at all, but the appearance of a water quality problem caused by climate conditions.

At least one area where this plan for protecting eelgrass related to nitrogen inputs or levels would become problematic in New England. Here colder temperatures and cycles of energy (now associated with a NAO climate pattern) caused great fluctuations of eelgrass over time.

In the case of linking eelgrass to water quality criteria (especially nitrogen) would backfire in Great Bay, New Hampshire. Here a report by the State of New Hampshire regarding its nitrogen TMDL would result in a special hearing of Congress looking into the
eelgrass/nitrogen linkage. A special panel would then be formed to give an outside review which did not support this single view that eelgrass populations is solely dependent upon water quality conditions or even nitrogen but listed several factors including environmental conditions.

February 12, 2014
Joint Report of Peer Review Panel
For Numeric Nutrient Criteria for the Great Bay Estuary
New Hampshire Department of Environmental services
June 2009

INTRODUCTION

This peer review was authorized through a collaborative agreement sponsored by the New Hampshire Department of Environmental Services (DDES) and the Cities of Dover, Rochester and Portsmouth, New Hamphire. The purpose was to conduct an independent scientific peer review of the document entitled, “Numeric Nutrient Criteria for the Great Bay Estuary, “dated June, 2009 (DES 2009 Report).

The peer review was conducted by a four-person panel (Panel) consisting of
Victor J. Bierman, Jr. Ph.D. BCEEM
Robert J. Diaz, Ph.D
W. Judson Kenworthy, Ph.D
Kenneth H. Reckhow, Ph.D.

The point of contact for the Panel throughout the review process was Ms. Sally I. Brabble, Litigation Paralegal, at the law firm of Sheehan Phinney Bass and Green in Manchester, New Hampshire.

Critical Evaluation of The DES Eelgrass Assessment Method {from the report}

“The DES assessment reports were correct in dividing the Great Bay Estuary into 11 distinct assessment zones, each with independent analyses of eelgrass states. This approach is consistent with the approach taken by the Massachusetts Estuaries Project in assessing nitrogen loading in coastal embayments. A main strength in this approach is that it implicitly recognizes heterogencity in the estuarine system as well as the possibility that there may be important differences in the biophysical characteristics of the zones which could affect eelgrass distribution and abundance. Spatial Variation in factors such as natural watershed landscape characteristics, non-point source water runoff, water depth, sediment type, substrate stability, wind and wave exposure, tidal velocities, freshwater discharge, non-point source runoff, groundwater discharge and land use are known to interact and determine different eelgrass distribution in shallow water coastal ecosystems (Thayer et al. 1984, Larkum et al. 2006 Orth et al, 2010a, b) Stochastic events like severe storms, ice scour and climate variations were not considered even though these are known to affect eelgrass (Frederiksen et al. 2000 a, b, Orth., and Moore 2006. Krause-Jensen et al 2008). The assessment completely ignored biological aspects of the system, including plant reproduction, grazing and bioturbation. Some these facts can limit eelgrass growth, reproduction and distribution to the extent that the species can be completely eliminated from an estuary (see Figure 5 in Krause-Jensen et al 2008) the importance of considering multiple controlling factors also directly applies to eelgrass restoration as empirically determined by Short et al. (2002) in Great Bay and elsewhere in New England estuaries. These confounding factors can obscure the relationship between nitrogen loading/eutrophication and eelgrass response, therefore the assessment was weakened by not explicitly considering any of these factors in their evaluation of eelgrass loss. The DES case was further weakened by only considering information for the anthropogenic effects of dredging and the existence of mooring fields as other potential factors controlling eelgrass distribution in the Great Bay estuary.”

Eelgrass Static Estuary Health Indicators are over estimated?

Eelgrass, like other terrestrial grasses have a habitat clock or in times of habitat history subject to change “value” according to the law of habitat succession in the marine environment. That is, any habitat services must be indexed with habitat change as plant species mature and exchange dominance on land. Habitat succession in the marine environment does not stand still, it is not static therefore snapshots that portray a lasting goal or benefit or contain constant habitat values are misleading at best and biased for habitat succession. It is certainly something upon which not to base long term public policy objectives.

The scientific community last February was startled by reports from Denmark that eelgrass was dying off from sediment sulfide toxicity. For some of us following the eelgrass research since the 1980s we were not surprised. In fact, some of the historical research conducted a century ago (also in Massachusetts) by Dr. David Belding clearly detailed observance of eelgrass holding organic matter in high heat as the source of sulfur emissions and negative habitat changes or direct impacts upon shellfish species, all of them including the bay scallop.

In the end, the sulfur compounds (sulfide) became so high it killed off eelgrass directly or weakened it enough to increase occurrence of fungal/mold infections. While creating vast mud flats unable to sustain any shellfish sets at all many researchers in the late 1990s identified the sulfide formation as a habitat SAV constraint and toxic impacts to eelgrass itself. Some of this pioneer sulfide toxic research to submerged aquatic vegetation SAV was conducted in Tampa Bay, Florida. (But not included in later eelgrass studies).[ Pauly defines a shifting baseline lack reference as a loss of the perception of change that occurs as each generation redefines what is considered “natural.”]

A Long Term Environmental History is Important to Coastal States

Beginning in 1880, and under the auspices of the Smithsonian, we saw the first U.S. records of fish and shellfish landings that could be indexed for climate/energy factors (US Fish Commission Reports). Important eelgrass observations were made but not reported in
the more recent scientific literature – in fact, much of this could have been prevented by a good balanced long term environmental fisheries history5. Nitrogen TMDL criteria formulated by ignoring organic primary and secondary source nitrogen are incorrect and now subject to potential scientific review investigations. An environmental history is very much needed as a bias in the research literature is now also being discovered in salt marsh studies (1971-1981) and also dredge windows (1985 to present). Very little correlation has been found long term to eelgrass populations and abundance of fish and shellfish. While it has been found to offer species shelter and forage habitat services in time (especially during periods of high heat and low energy) these habitat services very often become negative. That aspect appears to be missing from much of the current eelgrass research. While colder “green and clean” eelgrass provides significant habitat services that aspect is clearly promoted (even in pictures not indicative of location or functions) but the brown and furry eelgrass, slime covered and sulfide rich areas were “forgotten.”

Eelgrass/Nitrogen Indicators

In light of apparent omission of historical eelgrass habitat information and apparent bias with carefully scripted RFP nitrogen research proposals, omissions of both historic/period research and actions of public policy makers reflecting upon such research a funding relief action may be required. Peer review from the scientific community itself is not sufficient against science/research misconduct as evidenced by this eelgrass case6. (my view).[ Congress investigated EPA review panels and reaffirmed the National Academy of Science, National Research Council and the Science Advisory Board protocols which serves EPA were recoded in 2001 for conflict of interests. Findings showed transparency improved but did not exclude bias as qualified review members often worked or benefited from some of the same policies that were asked to review. That is currently under review for the 2012 Cape Cod TMDL panel, and New Hampshire Great Bay Nitrogen TMDL review.]

Scientific Review panels for example (based upon some degree of public perception of impartiality) were often members or individuals who worked or received university grants or funds that created much of the body of work being reviewed. Unfortunately as a result of the eelgrass-nitrogen issue, we need checks and balances in the University process also; as public funding dried up in the 1980s, public university agencies/groups forged new relationships with granting agencies that transitioned from a “publish or perish” to a much more colder “grants or gone” (see Nelson Marshall comments on this need for “grants” in his 1994 book titled – In the Wake of a Yankee Oceanographer). Some of the eelgrass/nitrogen researchers cannot take all the responsibility from a University system now that encourages such grant efforts and relationships while at the same time turns away from the consequences of the potential of introducing agenda based science into public policy decisions, such as we now face with eelgrass/nitrogen TMDL issues brought forth in the New Hampshire Great Bay report last year. There is also a growing ethical question of the expenditures of large amounts of public funds used to remove a plant nutrient, nitrogen a natural substance, when so many other larger toxic chemical questions relating to seafood quality (lead and PCB for example) remain unanswered.

Environmental Bias Ignores History

The notion of all negative environment impacts must be attributed to human actions has resulted in some extreme conservation protection policies. Although public policy intervention in the 1950s and 1960s had firm foundations (Love Canal, New York and Cuyahogo River Fire, Ohio), this has created a “baseline dilemma” as historical reviews were eclipsed by human existence “insulting nature” which was used quite effectively with the eelgrass/nitrogen indicators. In the Long Island Sound nitrogen issue we may have seen natural conditions given a “free pass,” and in terms of non point nitrogen given very low input allowances (10 percent) when forest organic matter overwhelmed estuaries in heat as ammonia levels increased – perhaps as high as 50 percent ammonia. (In Southern areas farms were blamed for nitrogen increases when in fact warmer winters had heavy rains wash manure (as leaves in the northern areas) off fields. Rain not people will be the largest climate feature of this 1972- 2012 period – (my view). In times of cold the oxygen/nitrate bacterial pathway was dominant – in times of heat the Sapropel/ammonia pathway “took over.” These also appear as long term cycles as seafood responds not only to temperature but to these bacteria pathways as well. [The DEEP Marine Fisheries office has 130 years of historical records of fish and shellfish reports, lobster hatchery records lobster (hatcheries were built in New England following the 1898 lobster die-off) catches as well as hundreds of fish census files and thousands of other historical fin and shellfish reports. These reports, journals fish census report will provide a key historical “habitat fisheries history” information for Connecticut.]

Much of the basis of the NEPA Act was to ascertain any (all) human impacts to the environment, usually in response to coastal development. The requirement of Environmental Impact Statement or “EIS” needs to be balanced by a mandatory natural history review of natural long-term climate and energy cycles for the coast (my view). Much of the controversy and confusion surrounding the 1999-2004 Southern New England lobster die-off for example a review of historical records would have shown that it resembled (precisely) the die-off of lobsters here before during 1898-1905. In both cases blue crab abundance suddenly soared in CT after each lobster die-off as what exactly recently happened here again7. (After the 1890s lobster die off New England States built lobster hatcheries (the largest being in Maine) most were closed or phased out when lobster habitats improved during the cooler 1950s and 1960s. (This is attributed to the return of the kelp/cobblestone habitats in southern New England).

Records of Native American shell middens may represent one of the few unbiased measures we have in determining the natural cycles of fin and shellfish species abundance, free of human climate/energy change discussions. The need of a long-term, unbiased environmental history therefore is critical8. [Several proposals have targeted species restoration without accurate long term habitat implications of land/climate changes. The return of Connecticut forests would combine with low energy and high heat to alternating subtidal habitats. Oak leaf litter is naturally acidic reversing pH of estuarine soils – preventing shellfish sets. That condition would favor the creation of Sapropel deposits in the 1980s.] Mervin Roberts in his (1985 book titled The Tide Marsh guide warned us of potential bias in surveys of marine populations in motion and closed with a statement that has for reaching impact. “I submit that we have no business establishing rigid categories for the works of Mother Nature” on pg 356.

When it came to eelgrass habitat services or eelgrass populations we did exactly that.

Capstone projects could include a US literature search of current eelgrass research to determine if any negative habitat conditions are included. Denmark has several researchers looking at eelgrass sulfide toxicity as well.
Demark researchers are scheduled to release additional eelgrass habitat reports by March 2016.

ENVIRONMENTAL ASSESSMENT OF THE USE OF EXPLOSIVES
FOR SELECTIVE REMOVAL OF EELGRASS (ZOSTERA MARINA)

Michael Ludwig
Environmental Assessment Division
National Marine Fisheries Service
National Oceanic and Atmospheric Administration
U.S. Department of Commerce
Milford, Connecticut 06460
(1977)

ABSTRACT

Data were obtained regarding the biological and physical impacts associated with using explosives as a herbicide for eelgrass (Zostera marina). Removal of the rooted marine vegetation from an area approximately 122 meter wide and 550 meters long within Niantic Estuary at Waterford, Connecticut has been proposed in an attempt to improve water quality and containment of egg and larval stages of the Bay Scallop (Argopectens irradians). Creation of a channel through dense stands of eelgrass should reestablish a persistent tidal eddy in the inner estuary which would improve dissolved oxygen levels and allow more complete habitation of the embayment. Relying on a physical model and in situa-generated information from both the private and public sectors it has been concluded that such an attempt, with proper constraints should be allowed.

Marshall’s 1960 discussion of this situation describes the scallops as setting on red algae in the absence of eelgrass within the estuary. Apparently the algae served as a suitable substitute for the destroyed eelgrass. As eelgrass reestablished itself along the coastline it also re-vegetated the estuary and had, by the early 1960s, extensively reduced the tidally-generated gyre’s persistence and mixing capabilities. During this same period bay scallop production suffered a serious decline. Compounding the reduction in numbers of juveniles the area experienced a series of concurrently occurring harsh winters which had caused the almost complete exclusion of bay scallops from the area.

Obtained from CT Board Fish and Game Files
1988 Waterford DEP Marine Fisheries Office
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.

THE COMMONWEALTH OF MASSACHUSETTS
Department of Natural Resources
BOARD OF NATURAL RESOURCES
Thomas a. Fulham, Chairman
William S. Brewster Joseph W. Lord Frederick G. Crane, Jr. Arnold D. Rhodes Robert L. Yasi Commissioner
DIVISION OF MARINE FISHERIES
A Study of the Marine Resources of the Westport River is the seventh in a series of monographs initiated by the Division of Marine Fisheries in 1963. These reports relate the extent and value of the marine resources of the major bays and estuaries in Massachusetts (page 32).
The major factor limiting quahog abundance seems to be lack of favorable bottom. During the