At such [peaceful] times, under an abated sun; afloat all day upon smooth, slow heaving swells; seated in his boat, light as a birch canoe; and so sociably mixing with the soft waves themselves, that like hearthstone cats they purr against the gunwale; these are the times of dreamy quietude, when beholding the tranquil beauty and brilliancy of the ocean's skin, one forgets the tiger heart that pants beneath it...
Melville, Moby Dick, Chapter CXIII

Lifting the skin of the sea. Dali at the age of six, when he thought he was a girl, lifting the skin of the water to see a dog sleeping in the shade of the sea
(1950 oil painting by Salvador Dali).     The ocean and the atmosphere constantly exchange gases and small particles (of things like salt), maintaining a rough equilibrium. The ocean also has a great heat capacity, that is, a great ability to hold heat. As the atmosphere heats up because of global warming, it transfers much of that heat to the ocean. Though the ocean absorbs that heat slowly, it will also (eventually) lose that heat very slowly, insuring that the heat we now inject into the atmosphere via carbon dioxide emissions will be around for a very long time.


In November of the year 2000, the Ocean Selector, a fishing trawler operating in the Pacific off the west coast of Vancouver Island, Canada, hauled up a very unusual catch. Along with the fish it obtained from a seafloor depth of about 800 meters (about half a mile) were numerous chunks of a white, frigid snowball-like substance. There was, in fact, a huge amount of the compacted but lightweight substance: perhaps 1000 kilograms (more than a ton), possibly more than had ever been netted before.

The catch of the Ocean Selector.

(Photo: Spence, 2001)

Most of the fishermen were perplexed about their unexpected catch, but a fisheries observer who happened to be on board suggested it might be something he had never personally seen before, something called methane hydrate, the mysterious "ice that burns" (Spence, 2001).

Methane is a tasteless, odorless, colorless gas. Along with tiny traces of other gases, it is the primary, almost exclusive, constituent of the "natural gas" which fuels many gas stoves and home heaters. Because it is a dangerous gas, potentially asphyxiating, flammable, and explosive, an unpleasant odor (that of methanethiol, or methyl mercaptan, CH¸3SH) is added to domestically used natural gas so that we can detect it by smell. In coal mines, however, methane provides no such warning; hence, the "miners' canary" was once used to give early notice of methane's presence, because canaries are more sensitive to methane than people. In spite of such precautions, many coal miners are nevertheless still lost every year in methane explosions.

Each molecule of methane is composed of four atoms of hydrogen held together by one atom of carbon (the chemical formula is CH¸4). With such a composition (hydrogen and carbon), methane is referred to as a hydrocarbon. Methane is a major component of the atmospheres of the "gas giants" of our solar system, Jupiter, Saturn, Uranus, and Neptune, and probably was a major constituent of the early atmosphere of Earth itself.

But methane is fairly active chemically and readily reacts in the atmosphere, and, to a lesser extent, in seawater, in a series of complex reactions whose end products are carbon dioxide and water. Once Earth's marine photosynthesizing organisms became plentiful in surface waters about two and a half billion years ago, producing a low level of free oxygen in our atmosphere and in the surface layer of the ocean, most free methane would have combined with that oxygen and disappeared. Because of the over 20% abundance of oxygen in our current atmosphere, there is little free methane around, though its quantity is slowly increasing. The presence of free oxygen, however, limits the lifespan of free methane in the atmosphere and most of the ocean to less than ten years.

The primordial methane of Earth's ancient atmosphere having long ago been oxidized, the subsequent atmospheric methane, ancient as well as modern, has been produced thermally or biologically. (The methane produced by these different processes is therefore referred to as thermogenic or biogenic methane.) Methane is produced thermally by the decomposition of organic matter by heat from the interior of the Earth. Most of the planet's methane, however, is probably produced biologically. Organisms called methanogens ("methane-makers") discard methane as a waste product of their metabolic activities, which take place in environments free from, or protected from, oxygen.

Archaea and Methanogens

The most important location for the formation of methane is in the sediments of the ocean floor. Within the sediments, in addition to the lithic (rock) particles, the dead organisms -- mostly microscopic -- which have rained down through the water column or been carried from the land, and various sorts of organic debris, are a multitude of living organisms including burrowing worms and mollusks (at shallow depths), and an awesome array of microorganisms (throughout the sediments: D'Hondt, 2004). Many of these microorganisms belong to the familiar category bacteria, but others are part of a group whose existence was not even suspected just a few decades ago. These microorganisms are Archaea.


Archaea is the name of the classification. The word archaea, with the "a" in lower case, is the plural form and refers to a number (two or more) of species or individual organisms within that class. (The term archaeans is also sometimes used to denote the plural form.) The word archaeon is the singular form, and refers to a single species or individual. Similarly, Eubacteria is the classification name; bacteria refers to more than one species or individuals; bacterium refers to a single individual or species. One does not often run across a reference to single individuals ( of either bacteria or archaea), however, so the singular and plural forms typically refer to species. The curious singular and plural forms (archaeon/archaea and bacterium/bacteria) derive from the fact that Greek and Latin words, respectively, are employed.

The term Archaea for these organisms, however, should not be confused with the term used for one of the oldest geologic time periods, the Archean Eon, often shortened simply to the Archean. (In some geologic time scales, the Archean includes the Hadean [Eon], the oldest time period.) Archaea refers to the group of organisms, Archean refers to the time period. Both terms derive from the Greek word 'archeo,' meaning primitive.

It used to be thought that the basic distinction in the living world was between bacteria, which are small, unicellular, and relatively simple (though indeed the simplicity is only relative, all living organisms being quite complex), and larger, often multicellular organisms. The bacteria are part of a group called the prokaryotes (in fact, they used to be considered the only members of that group), whose DNA is not enclosed in a nucleus.

All other organisms are eukaryotes, which do enclose their DNA with a nucleus, and which include all the multicellular organisms we routinely encounter in daily life, such as plants, fungi, and animals. The eukaryotes also include many creatures we do not encounter daily, organisms of the unicellular variety called protoctists (sometimes referred to as protists, but this term may also refer to any single-celled organism, even those which are not eukaryotes). Eukaryotic cells generally are considerably larger than prokaryotes, and they contain small but distinct organs, referred to as organelles (chloroplasts, which contain chlorophyll, and mitochondria, which provide cell energy, are the most obvious), which prokaryotes lack. (Some bacteria have now been found to contain an organelle also present in single-celled eukaryotes; see Seufferheld, 2003).

Microbiologists Lynn Margulis and Karlene Schwartz, noting the one large prokaryote group, the bacteria, and the four large groups of the eukaryotes proposed that all living things comprised five "kingdoms," the highest level of biological classification. Because the prokaryotes were quite distinct from the eukaryotes, they illustrated their proposal as a human hand, with the bacteria set off as the thumb, and the eukaryote groups as the fingers. Despite considerable variation in size, eukaryotic cells are typically about ten times the linear dimensions of prokaryotic cells, and their volumes are about 1000 times greater.

Eukaryote and prokaryotes, relative sizes. (Diagram from Gross, 1996, p. 134.)

In the '60's and 70's, however, some new organisms were discovered which, though unusual, were relegated to the classification bacteria largely because they were unicellular, small, did not have their DNA bound up in a nucleus, and, most importantly, because there was apparently no other biological category into which they might be fit. These unusual organisms were often found in environmental conditions considered extremely hostile to life, places of quite high temperature, salinity or acidity. Later, these inhospitable habitats would earn their inhabitants the name "extremophiles," that is, lovers of extreme (conditions).

With the development of new analytical methods by molecular biologists, the actual makeup of organisms at the molecular level -- a vastly smaller level than that of the cell -- began to be explored. The determination of the structure of DNA -- the famous double helix -- was one of the first triumphs of these new methods. By the mid 70's, molecular biology had advanced to the point that differences between the molecules of various organisms were being employed to examine the evolutionary relationships between them, just as DNA testing of human beings is today used to determine relations between individuals and groups.

In 1977, biologists using RNA from ribosomes, the protein factories of cells, to examine numerous species of bacteria made a startling discovery: that a few of the bacteria were vastly different, on a molecular level, than the many thought to be their biological cousins. In fact, biologists Carl Woese and George Fox, decided these organisms were so unlike other bacteria that they couldn't really be considered bacteria at all, but had to be assigned their own special classification, first called Archaebacteria, then changed and shortened to Archaea to make clear that they were entirely distinct living things.

The distinctiveness of the Archaea required a major revision in thinking about biological classification. No longer could the highest division of living things be considered the kingdom. Instead, while preserving the classification kingdom for the next lowest subdivisions, a new and higher division was created: the domain. Living things would be divided into three domains: Eubacteria, Archaea, and Eukaryota, the eukaryotes.

The three branches (domains) of life. Eubacteria and Archaea are prokaryotes, relatively simple, single-celled organisms. Eukaryotes (Eukaryota) possess complex cells; some are single-celled. All multicellular organisms, including animals, plants, and fungi, are eukaryotes. The line lengths are based on studies of the genetic information of the organisms; they indicate how closely the organisms are related. Note how closely animals, plants, and fungi (upper right) are related, and how far removed they are from many other organisms. (Howland, 2000, Figure 2.2, p. 29)

Not having their DNA enclosed in a nucleus, archaea are prokaryotes like bacteria. And there are other similarities: most prokaryotic DNA is found in the form of a single chromosome, a single large unbroken loop, sometimes together with smaller loops called plasmids. By contrast, eukaryotic DNA, enclosed in a nucleus, is divided into many chromosomes, and the chromosomes take the form of short spaghetti-like strands.

The difference is a critical one, one which goes far beyond the apparent shape and number: the short strands of the eukaryotic chromosomes have at their ends many copies of special units of DNA called telomeres, which have been likened to the plastic tips of shoelaces. Each time the cell reproduces, another unit is removed. Eventually, when all the telomere units are gone, the remaining DNA becomes unstable and the cell dies. Consequently eukaryotic cells have limited lifespans, programmed into their DNA from their inception. By contrast, the single loops of prokaryotic DNA, being loops, lack such telomeres, and thus are not programmed for eventual demise. Prokaryotic cells can divide and divide (a process called binary fission) and, in essence, live forever, while most eukaryotic cells, like the organisms of which they are a part, eventually must die. Sexual reproduction, by creating new individuals, is the eukaryotic organisms' hedge against oblivion.

One major difference between archaea and other living things, however, lies in the way they construct their outer cell membranes. Archaea employ ether links between the organic components of their cell membranes. Most other organisms use ester links. Ether links are chemically more stable, and such links may have helped archaea survive in the hostile conditions of early Earth. In addition, while all organisms have chains of fatty acids as essential components of their cell membranes, those chains are usually straight. In archaea they are branched, or "isoprenoid" (Howland, 2000, p. 74-79). Both the ether links and the isoprenoid configuration of the fatty acid chains provide biochemical indicators that archaea are present.

This biochemical evidence turns out to be quite important where other methods for detecting archaea are unsuccessful. Microorganisms generally cannot be identified where they are found, because they are too few and too small to be seen without substantial magnification. Indeed, one archaeal group, the Korarchaeota, has only been detected by its biochemical traces. No korarchaeon has ever been seen. But this is not surprising: microorganisms are notoriously difficult to isolate and identify, and the few that have been are generally those that fare well in laboratory conditions.

Only a tiny percentage (perhaps only 1%) of microorganisms can be cultured, that is, grown in the laboratory in significant numbers, outside of their natural habitats. Since the number of a particular microorganism in a given sample may be quite small, the ability to raise them in significant quantities is extremely important. Thus those microorganisms which cannot be cultured generally escape our attention. To increase the likelihood that particular microorganisms may be cultured and thereby identified, scientists attempt to replicate the precise conditions in which a sample was taken. If the sample were taken from one of the hot pools in Yellowstone National Park, for example, scientists will try to recreate the heat, acidity, dissolved gas and nutrient conditions found in the original pool, both during the transfer process and in the lab.

Nonetheless, the effort is often unsuccessful. A major reason for culture failure, it turns out, is that many microorganisms do not solely depend on the relatively large scale conditions mentioned above: heat, acidity, dissolved gas, and nutrients. Often they depend on very specific "local" conditions, which, in the case of microscopic creatures, can be very local indeed. Furthermore, the congeniality of these local conditions frequently requires close proximity to other particular microorganisms, which help provide the very specific conditions the organism of interest requires to thrive or even survive. It is not surprising, therefore, that recent efforts that include taking slabs of sediment rather than the small samples previously obtained should have allowed richer cultures to be grown.

Ecosystems comprised of different kinds of microorganisms living together are known as consortia. Consortia are a microscopic version of the ecological communities with which we are more familiar, like plant-herbivore-predator communities. Although most relationships between organisms in these consortia are only beginning to be investigated and understood, some organisms clearly provide products which are useful to other consortia members, and, in some cases, there is likely to be the kind of mutual exchange known as symbiosis. (In the case of microorganisms, symbiosis is known by the term syntrophy, literally, "eating together.")

Symbiotic processes are found throughout the natural world. In its broadest sense, symbiosis is much more common than many biology texts indicate. Lichens, for example, are typical textbook symbionts: they represent the simple pairing of an alga and a fungus, an arrangement that allows the lichen to live on the surface of rocks, frequently in quite dry, frigid, or otherwise inhospitable conditions. Surprisingly, however, as many as 20% of fungal species may engage in these partnerships.

Much more important to us is the symbiotic relationship between terrestrial plants and the fungi known as mycorrhizae (literally, "root fungus"). This is a relationship which began perhaps 450-500 million years ago, and was essential for the evolution and spread of plants onto the land. Mycorrhizal fungi are microorganisms which live on the roots of plants and allow plants to take up water and minerals from the soil. Quite recently, fungi have been found to inhabit almost all cells of photosynthetic land plants, in addition to their roots. Without these symbiotic organisms, we wouldn't have most of our food supply.

The digestive systems of cows, sheep, goats, giraffes, antelopes, buffalo, camels, and others -- those animals known as ruminants -- also house symbiotic organisms: methanogens. These methanogens live off the grass or leaves that the ruminants consume, and the ruminants in turn obtain much of their protein from digesting their store of methanogens and other gut microorganisms (Howland, 2000, p. 91). The by-product of this arrangement is methane, of use to neither cow (for example) nor methanogen, but released into the atmosphere as cow burps. A similar relationship between termites and methanogens allows termites to consume wood, again releasing methane as a waste product. Much atmospheric methane thus owes it origin to ruminants and termites.

The methanogens in which we are interested, however, live in the anoxic sediments of the ocean floor. These sediments, which can accumulate to depths of many hundreds of meters (well over a thousand feet), lack oxygen except in their topmost few centimeters (an inch or so). (Some oxygen, apparently from water flowing through bedrock, does seep into the base of the sediments [D'Hondt, 2004], but it is unimportant for our purposes.)

In the sediments, many microorganisms consume the organic detritus which has rained down through the water column. This process of consumption both depletes the remaining oxygen and releases carbon dioxide. That carbon dioxide, and other carbon sources, provide the carbon from which the methanogens manufacture methane. Other organisms contribute hydrogen (Gross, 1996), though hydrogen is also produced by inorganic means, through the interaction of ocean floor basalt and water (Stevens and McKinley, 1995), and even by a certain kind of radioactive decay (alpha particles -- helium nuclei -- colliding with water molecules, create hydrogen peroxide, oxygen, and hydrogen gas; Fields, 2003).


The Archaean domain is comprised of three different groups, based on where they live and what they do to make a living. (These groupings are similar to classifying people according to their home neighborhoods and occupations, and do not necessarily reflect how closely they may be related.) One group is the thermophiles, which, as their name implies, prefer hot conditions. These hot conditions are found in two situations, either where extremely hot water comes pouring out of the earth under the sea, at the sites of black smokers, white smokers, or hot seeps, or in the hot pools and geyser basins that are found in areas of volcanic activity, as at Yellowstone.

In these situations, water temperatures can exceed the boiling point of water (100°C; 212°F); in fact, the water that comes out of black smokers can be many hundreds of degrees hot. Nonetheless, some thermophiles, called hyperthermophiles, can survive temperatures above 100°C, because they exist at ocean depths where the pressure is so great (100 to 500 times that of the surface of the earth: Gross, 1996) that the water cannot become steam. Other thermophiles prefer somewhat cooler temperatures, in the 85°C range.

A second group of archaea are the halophiles ("salt-lovers"). These creatures prefer extremely saline conditions such as in deserts where high evaporation rates prevail. During wet seasons, thunderstorms, or in flash floods, rainwater washes down sediments and soluble materials from surrounding mountains into desert basin areas. There, without any outlet, the water evaporates under the unrelenting sun, eventually leaving behind only a dry playa. But before the basin gets to that stage, if it ever does, the salt content rises. The Dead Sea, between Israel and Jordan, is one well-known example, and the Utah's Great Salt Lake is another.

Water in the Great Salt Lake is about 25% salt, making it easy to float in (in fact, making it impossible not to float in), but unpleasant for getting in one's eyes. Halophiles don't find it unpleasant at all. While other microorganisms would find their water sucked from their bodies like prunes by the salinity, the halophiles protect themselves by incorporating a higher concentration of salt than is found in their environment. One curious feature of the Great Salt Lake, however, is that the water is pink. That pinkness is the consequence of the archaean halophiles which enjoy its salinity. Despite their extreme situations, they actually engage in a type of photosynthesis, though not using chlorophyll. It is the purple color of the pigment they employ for photosynthesis that makes the water pink.

The third group of archaea are the methanogens. The name derives from the fact that methanogens make (generate) methane, just as hydrogen, combined with oxygen (that is, when burned), makes water (hydro in Greek). The methanogens are divided into five subclassifications (called "orders"; see BOX: Biological classification, in Permian World section), Methanococcales (about 9 species), Methanobacteriales (about 25 species), Methanosarcinales (about 19 species), Methanomicrobiales (about 22 species), and Methanopyrales (1 species; Madigan, 2003). (The methano- indicates that these archaea are methanogens; the second part of the name refers to the organism's shape: coccus = sphere, bacteria = rod, sarcina = cubic, and microbiales = extremely small, round, flat, onion-flavored rolls: bialies are a breakfast favorite of many New Yorkers. The last order, Methanopyrales, derives its name not from the shape of its single species, methanopyrus, but rather from the ecological conditions in which that species lives. "Pyro," as in pyromaniac, comes from the Greek word for fire; methanopyrus lives in hot springs at extremely hot temperatures.)

Interestingly, it is clear that some methanogens can actually turn around and consume methane under particular conditions (Hinrichs, 1999; Hallam, 2004). These archaea, like some bacteria that also can consume methane, are referred to as methanotrophs (literally, "methane-eaters"). Some archaea, however, may be exclusively methanotrophic, and could therefore constitute a fourth division of the Archaea (Hinrichs, 1999).

 Archaea Classification

Formally, the archaean domain, Archaea, is divided into three groups. These groupings are based on the actual relatedness of the organisms, rather than how they make their livings. There is some disagreement as to the classification level (scientists use the term "taxonomic" level to refer to classification level; see BOX: Biological classification, in Permian World section) level in which these groups should be placed. The next lower level after domain is kingdom, and the one below that is the phylum, and some scientists have placed the basic archaeal division at the kingdom level, while others consider the main groups as at the phylum level. The classification level reflects how closely the groups are related: whether they are near or distant "cousins."

But while the classification level issue may be unresolved, there is general agreement on the main archaean groups. They are the Euryarchaeota, which contains the methanogens and halophiles and some of the thermophiles, and the Crenarchaeota, to which many of the thermophiles belong. A third group, the Korarchaeota, is known only from their organic residues rather than from the organisms themselves. Although the Korarchaeota may constitute a special side branch of the Crenarchaeota, there is no question that its members -- yet to be isolated -- are quite distinct from other archaea. Their RNA tells us so. In fact, it is the RNA differences among the archaea which has allowed biologists to distinguish the relations and divisions among the various groups. The recent discovery of a new archaeal organism, Nanoarchaeum (Huber, 2002), has led to a proposal that an additional group of archaea may exist, based, however, on the microbe's distinctive DNA.

As scientists have continued their investigations of the Archaea, they have made some stunning discoveries. Unknown and unsuspected until just two decades ago, archaeans turn out to be major, if not dominant, constituents of the biota of oceans and soils, and significant contributors to essential biochemical processes therein. In both oceans and soils, archaeans oxidize ammonia, a critical step in the production of biologically usable nitrogen compounds (a process called nitrogen fixation). It used to be thought that this process was carried on solely by bacteria, but it is now known that archaea oxidize tens to hundreds -- and, in some situations, perhaps thousands -- of times more ammonia than bacteria (Leininger, 2006; Wuchter, 2006). "Higher" plants, like photosynthesizing land plants, cannot accomplish this task on their own, and are completely dependent on microbes to provide them with this essential nutrient. In the oceans, it has been discovered, Crenarcheota "are the most abundant single group of prokaryotes" (Wuchter, 2006).

Living things make their livings in two basic ways: they either make and consume their own food (a process called autotrophy), or they consume other living things, or the organics they create (a process called heterotrophy. We are heterotrophs, and as such rely on other living things for our food supply, virtually all of which comes directly or indirectly from plants (with the minor exceptions of fungi and seaweed -- neither is a true plant, incidentally -- which provide rather little nutritional value).

The most familiar kind of autotrophy (photoautotrophy) is photosynthesis, which most commonly employs chlorophyll to facilitate the manufacture of a basic sugar unit (CH¸2O, six of which are assembled to form glucose, a simple sugar: C¸6H¸12O¸6) from the raw materials water and carbon dioxide. The chemical equation for this process is:

  H¸2O  +          CO¸2                Æ              CH¸2O          +     O¸2
(water) + (carbon dioxide) (yields) (basic sugar unit) + (oxygen)

It is important to note that the useful product of this process is the basic sugar unit, and not the oxygen, most of which is simply a waste product (though some is used for cellular respiration) and is dumped.

Photosynthesis is conducted in today's world by four main groups of organisms: cyanobacteria, two other kinds of marine phytoplankton, and the plant kingdom. Phytoplankton include all free-floating oceanic microorganisms that engage in photosynthesis, and therefore include cyanobacteria and two main groups of eukaryotic organisms: the diatoms and coccolithophorids. On land, green plants constitute the fourth group of photosynthesizers. All of these four groups with the exception of the coccolithophorids, also referred to as coccolithophores or coccoliths, were around in the Permian.

Cyanobacteria used to be called blue-green algae, because they used to be considered plants. But it is now clear that they belong to the classification Eubacteria, and are only very distantly related either to the photosynthesizing eukaryotes of the phytoplankton (the diatoms and coccolithophorids) or to the green plants of our ordinary experience. Despite that distant relationship, however, there is a very important connection between cyanobacteria and all other photosynthesizing eukaryotes, including green plants.

All eukaryotic photosynthesizers are able to photosynthesize because they contain chlorophyll, enclosed in cellular organelles called chloroplasts. In the 1960s the microbiologist Lynn Margulis recognized that many of the organelles of eukaryotes were actually former symbionts which more than a billion years ago lived independently of the eukaryotes in which they are now found. (They are referred to as endosymbionts because they are inside rather than outside the cell). It is now generally accepted that the original cyanobacterial ancestor of the chloroplast was captured during the early evolution of the eukaryotic cell, some billion and a half years ago.

There is a second kind of autotrophy which is far less familiar. This kind is labelled chemoautotrophy because it relies on chemical processes rather than light for the energy needed for food production. Instead of dumping oxygen, these organisms dump other metabolic waste products. Methanogens, the ones with which we are most concerned, dump methane. Although numerous organic molecules, including acetate, formate, and methyl alcohol, can be used as the source of carbon, the simplest methanogenesis reaction employs carbon dioxide and hydrogen:

         CO¸2           +       4H¸2           Æ          CH¸4      + 2H¸2O
(carbon dioxide) + (hydrogen) (yields) (methane) + (water)

The main product of this reaction for the methanogen is not methane, which is waste (at least for the methanogen), or water, which is obviously plentiful in the watery environments in which methanogens are found, but energy. The reaction releases a certain amount of energy which the organism then puts to use in assembling the organic molecules it needs for its existence.


A good deal of our atmosphere's methane comes from the activity of methanogens in wetlands, especially in colder regions, and in the rice paddies of warm climates. Although methanogens reside in numerous exotic environments -- the guts of cows and termites, swamps, northern peatlands, rice paddies, Yellowstone hot springs, and undersea vent communities -- those of greatest interest to us here live buried deep in the ocean-bottom sediments.

A huge quantity of methane is produced in the sediments of the ocean floor. When marine organisms and microorganisms die, their corpses rain slowly down to the bottom of the ocean. In the process, they are mixed with silty (fine-grained), sandy or pebbly sediments washed into the ocean by rivers. The sediments and the organic matter come to rest on the ocean floor, to be buried by further sedimentation. Because most marine organisms live relatively close to shore and because most of the sediment washing off the continents is carried only a short distance, a considerable portion of the organic debris and mud winds up on those parts of the ocean which are shallow and close to the continents.

These areas are called the continental margins. The part of the continental margin that is shallowest, flattest, and closest to shore is called the continental shelf. The continental shelf drops down to an average depth of about 130 meters (400 feet). At about this depth, there is a "shelf break," and the ocean floor drops more steeply down what is referred to as the continental slope, to the great depths of the oceans' abyssal plains, the deepest and flattest parts of the oceans.

The ocean floor off the Middle Atlantic states, New England, and eastern Canada. The number 1 indicates the continental shelf; 2, the continental slope; 3, the continental rise, 4, the abyssal plain, and 5, a submarine canyon cut by water from the Hudson River. Seamounts rise from the abyssal plain. Map from Siebold and Berger, 1982.

The dead organisms in the continental margin muds mostly decay in conditions that exclude the presence of free oxygen; these are called anoxic environments. Though there is often a good deal of oxygen in deep ocean water, the oxygen is rapidly depleted in the upper few centimeters (an inch or two) of sediment by microorganisms which employ that oxygen in the process of consuming organic debris. With the extreme oceanic cold at these depths, however, the process of organic decay is quite slow.

Below the oxic zone, those top few centimeters of sediment where oxygen is still present, the organic decay becomes even slower and much less efficient. This is because the process of anaerobic decay -- that is, the process of decay by organisms that do not use free oxygen -- is vastly slower than that by aerobic (oxygen using) organisms. But even in sediments hundreds of meters below the seafloor, decay is still going on. At such depths, in fact, the chill imparted by the overlying frigid ocean water begins to give way to the warmth generated from within the Earth. Because the efficiency of metabolism at these temperatures increases with warmth, decay may become more efficient, as long as chemical energy sources like hydrogen, sulfate, or various organic compounds such as acetate are available. It is in this region of sediment well below the seafloor that the methane-makers thrive, and the production of methane takes place.

Being a lightweight gas, the methane produced by the methanogens rises. Though -- as we shall see -- most methane never makes it so far, some eventually does reach the top five or so centimeters (about two inches) of the sediment.

The Seafloor

Though the term "seafloor" is regularly used herein, the seafloor in most parts of the ocean is not a simple, solid surface. It is not composed of rock, but of accumulations of sediment that have settled there from the time that the ocean basin originated. While the deepest sediments have been compressed by the weight of overlying sediments and sometimes turned to rock, the shallower sediments are less and less consolidated with decreasing age and depth. Approaching the surface, the sediments are the consistency of mud, though in places they are mostly water. Higher still, the sediment has such a high water content that it is like a soup or slurry. Near its contact with the ocean itself, the uppermost layer is nothing more than muddy water. Because of the lack of a solid surface, oceanographers often prefer the term "sediment-water interface" instead of seafloor.
Because much sediment originates on continents, it is generally more plentiful close to the continents, and particularly at the mouths of large rivers, creating their deltas. Rivers like the Nile, Mississippi, Niger, Chang Jiang (Yangtze), Ob, Indus, Ganges and Brahmaputra all have substantial deltas, but much of their sediment is carried far out to sea, accumulating on the continental margins, and especially on the continental slopes. In deeper ocean areas, the major sediment source are the organisms that live near the ocean surface, whose skeletons, feces, and other organic debris rain down slowly to the seafloor.
Not all of the seafloor has a sediment cover, however. In some places, strong currents scour the seafloor clean, exposing the bedrock below.

It is rare that nature produces anything as a waste product for which some organism cannot find a use. While methanogens simply dump the methane they produce, other organisms live on it. Much of the free methane which eventually finds its way up through the sediments is consumed by bacterial or archaeal methanotrophs. Some bacterial methanotrophs are aerobic, and therefore must live in the aerated (oxic) conditions at the top of the ocean sediment or in the ocean itself. Within the deeper, anoxic sediments, however, microorganisms frequently use sulfate (ions containing both sulfur and oxygen) to provide energy, a process known as sulfate-reduction.

Because sulfates is easily dissolved in seawater, numerous sulfate-reducers are found in oceanic sediments. (The amount of sulfate dissolved in seawater is truly extraordinary; it has been estimated at some 1376 trillion metric tons: Brock and Madigan, 1988, p. 630.) The higher concentrations of sulfate are found close to the sediment surface, where organic carbon debris, another essential foodstuff for sulfate-reducers, is also found. There the sulfate-reducers congregate, living in consortia with the methanotrophs, harvesting methane as it rises from below (DeLong, 2000). In northern peatlands, the methanotrophs consume as much as 90% of the methane available (Dedysh, 1998); it seems likely that a similar or greater percentage of the methane escaping from marine sediments may meet the same end.

Some methane undoubtedly makes it through the gantlet of the methanotrophs in the topmost sediment, then through the ocean itself and escapes into the atmosphere. Most methane, however, never makes it even as far as the sediments of the upper seafloor. Instead, as it rises through the deep sediments, it quickly becomes trapped in lattice-like structures or cages (called clathrates) composed of water ice. (Clathrates are microscopic crystalline chemical structures. They are highly efficient storage units and can contain several different kinds of gas, including carbon dioxide.) At the proper conditions of temperature and pressure, methane or other gases found in the porous sediments spontaneously react with seawater to produce these structures.

Those clathrates which specifically hold natural gas in their icy lattices are referred to as gas hydrates ("hydro" is the Greek word for water). There are three gas hydrate structures, referred to as Structure I (sI), Structure II (sII), and Structure H (sH). Structure I typically contains exclusively methane; the other two structures are slightly larger (though still microscopic) and can contain somewhat larger gas molecules, though their primary constituent (called guest molecules) remains methane. Structure I is the least stable, meaning that it can break up ("dissociate") at lower pressures and higher temperatures than the other structures. Structure II is the most stable, while Structure H, previously known exclusively from the laboratory and just recently found in the seafloor, is intermediate in stability (Lu, 2007).

While other hydrocarbon gases are frequently found together with methane in gas hydrates, the most common gas, by far, is methane. It comprises more than 99% of the gas in gas hydrates, with few other natural gases, like ethane, and occasionally propane. Though the term "methane hydrate," rather than gas hydrate is technically reserved for hydrates with greater than 99.9% of their contents as methane, the terms herein will be used interchangeably unless there is a specific reason to do otherwise.

Methane hydrates are extremely efficient in trapping methane, holding about 160 times the amount which would be occupied by the equivalent volume of free methane. In other words, a given volume of methane can be stored in a hydrate only 1/160th its size. Consequently, methane hydrates can contain huge quantities of methane.

Methane hydrate, the "ice that burns." As the methane burns, the ice which formerly trapped it melts. (US Department of Energy photo.)
Methane hydrates form wherever methane and water are present at the proper temperature and pressure conditions. In fact, an experiment in the Santa Barbara Basin off southern California revealed that just as soon as methane is released into deep, cold water, methane hydrates form. Because methane hydrate is lighter than water, it quickly floats to the surface. That is why chunks of methane hydrate as large as refrigerators have been spotted floating on the ocean surface, where they rapidly melt and their methane is released into the atmosphere. But because methane hydrate typically forms deep within the seafloor sediments, those sediments keep it in place. Consequently, despite the enormous quantity of methane hydrate that exists, only small amounts are found on the seafloor itself, where it can detach and float away, or, as happened with the Canadian fishing boat, where it can be scraped off the bottom itself. These chunks attract the curiosity of those who find them because they can easily be set on fire, burning off the methane and leaving just a puddle of water. Hence the name, "the ice that burns."

CONTINUE TO NEXT SECTION (Methane and methane hydrates, Part 2)