Water: The Vital Fluid

The atmosphere

Atmospheric Gases and The Elements of Life

Water droplets forming in clouds and rain passing through the atmosphere dissolve atmospheric gases containing carbon, sulfur, nitrogen, and oxygen. Like water, these gases were originally emitted from the earth's interior during volcanic eruptions in earth's earliest history. Large amounts accumulated overtime and now reside in the atmosphere, ocean, biosphere and sedimentary rocks. All are important to life, and life processes influence their partitioning among reservoirs and their rates of flow between reservoirs.

The role of life

These fluxes (rates of flow) are mediated by the metabolic processes of living creatures, most importantly the prokaryotes or bacteria. The simplest of non parasitic creatures, the prokaryotes are a most interesting and important group of creatures because of the variety of chemical reactions they catalyze to obtain energy. They were the only agents of biochemical change during the first half of earth's history, a time that saw great changes, including the introduction of molecular oxygen to the atmosphere. They still play a vital and dynamic role in the cycling of carbon, oxygen, sulfur, and nitrogen through the Earth's system.

Prokaryotes can be viewed as complex chemical catalysts that have evolved to exploit energy yielding chemical reactions. To extract energy and build organic structures, they can, in the absence of oxygen (anaerobic), reduce inorganic compounds of carbon, nitrogen, sulfur, and iron, or, in the presence of oxygen (aerobic), oxidize them. The former reactions occur in oxygen poor or anaerobic sediments of swamps, lakes or oceans and must have dominated organic processes in our earth's early history (prior to two billion years ago).

Photosynthesis and oxygen

One of the most important events in the history of our planet was the development, by the early bacteria, of the ability to utilize solar energy to reduce carbon dioxide and combine it with water to form organic compounds. Since the earth is daily flooded with sunlight, the utilization of this abundant energy set the stage for extraordinary developments. This process, photosynthesis, developed in both anaerobic and aerobic bacteria; the former do not produce oxygen as a product of their metabolism while the latter do. The photosynthetic reaction that occurs in plants and a large group of bacteria and produces oxygen as a product is the following;

6 H2O + 6 CO2 ---> C6H12 O6 + 6 O2

Complete oxidation of the produced organic matter on the right side of the equation reverses the reaction and consumes all the oxygen produced. This reverse reaction is the reaction of respiration, and through it the solar energy gained by the biosphere during photosynthesis is released. We release this same energy when we burn fossil fuels. If some of the organic matter on the right-hand side of the reaction is buried, thus escaping complete oxidation, there will be a net addition of oxygen to the environment. During the early history of the earth (up to about two billion years ago) the burying of photosynthetically produced bacterial organic matter gradually added oxygen to the environment. A number of oxygen sinks had to be filled before molecular oxygen could accumulate in the atmosphere. These included reduced atmospheric gases such as hydrogen sulfide, and reduced ions in sea water such as iron. Although iron in the oxidized state is nearly insoluble in water, in the reduced state it is much more soluble. During Earth's early history, when its atmosphere was reducing, large amounts of iron must have accumulated in the ocean as dissolved iron species. By about 2 billion years ago, this oceanic oxygen sink began to be filled and, as a consequence, iron minerals were precipitated. More than ninety percent of these deposits, known as banded iron formations (BIF's), were formed between 2.2 and 2 billion years ago. After this, oxidized subaerial sediments (redbeds) are found in the geological record, clear evidence of an oxidizing atmosphere. BIF's are our primary source of iron ore and are found on most continents.

Once free oxygen accumulated in the atmosphere, a new source of energy was available to Earth's resourceful bacteria. Oxygen could be used to oxidize inorganic and organic compounds, and a host of aerobic bacteria evolved to exploit these opportunities. Unfortunately for their predecessors, many of them found the new highly reactive oxygen poisonous and either became extinct, or retreated to restricted oxygen poor environments, where we find them today. In these anaerobic sediments they may reduce carbon dioxide (CO 2) with hydrogen (H2) to produce methane (CH4).

CO2 + 4 H2 ---> CH4 + 2 H2O

Although these bacteria are anaerobic, they obtain both hydrogen and carbon dioxide from the air. These bacteria are found world wide, in sewage, marine and freshwater sediments, and in the intestinal tracts of animals. They return carbon to the atmosphere helping to balance the amount removed by photosynthesis. Under aerobic conditions, another group of prokaryotes can oxidize CH4, using it as a source of energy and a source of carbon for building organic matter.

Thus, photosynthetic prokaryotes, algae and plants move oxygen from water to the atmosphere and reduce carbon while respiring prokaryotes, eucaryotes and animals use oxygen to oxidize carbon and return carbon dioxide to the atmosphere. Burial of some of this organic matter leaves excess oxygen in the system and much has accumulated in the atmosphere. As a result, it now constitutes twenty one percent of our modern atmosphere. Thus, the oxygen balance is dominated by life processes, and the large amount of oxygen in our atmosphere is, like the presence of liquid water at it's surface, one of the remarkable and unique characteristics of our planet.


Carbon is moved from the atmosphere through the ocean to the rock system and returned to the atmosphere not only in the reduced state fixed in organic matter, but by another pathway as well. Dissolved atmospheric carbon dioxide in clouds and rain undergoes a reaction with water to form a weak acid carbonic acid.

CO2 + H2O = H2CO3

H2CO3 ---> H+ + HCO3-

This changes the pH of rain water from 7.0 to 5.7. Hence, unpolluted rain is acidic.

The soluble HCO3- is carried by rivers to the sea, and there it combines, through the action of plants and animals, with calcium to form crystalline calcium carbonate. Some of this is deposited on the ocean floor carrying both calcium, carbon and oxygen into the sedimentary rock reservoir.

Most of Earth's original atmospheric carbon is now buried in sedimentary rocks; limestones through the deposition of plant and animal shells made of calcium carbonate and shales and fossil fuels through the burial of reduced carbon from the soft tissues of organisms. Therefore, on earth, life processes have removed carbon from the atmosphere and placed it in sedimentary rocks. The total amount of this buried carbon plus atmospheric, oceanic and biospheric carbon is about equal to the mass of carbon in the atmosphere of Venus. Although Earth and Venus may have had similar beginnings, they have evolved along very different paths.


Atmospheric gases are the prime sources of nitrogen and sulfur compounds for rainwater and subsequently for rivers, the ocean and living systems.

Nitrogen is the dominant element in the atmosphere, and 99.96% of noncrustal nitrogen is in the atmosphere as molecular nitrogen (N2). The other species of nitrogen in the atmosphere are nitrous oxide (N2O), and trace amounts of nitrogen dioxide (NO2), nitric oxide (NO) and ammonia (NH3). The gases NO and NO2 are collectively referred to as NOx. Like carbon and sulfur, nitrogen is important to life. However, it can be used by organisms only when changed from molecular nitrogen, which is chemically unreactive, to compounds of nitrogen through combination with carbon, hydrogen or oxygen. These compounds make nitrogen available to plants, and the processes that form these compounds are called nitrogen fixing processes. In biological fixation N2 is combined with C, H and O by marine and terrestrial prokaryotes.

All nitrogen fixing prokaryotes are capable of transforming atmospheric nitrogen, N2, into organic nitrogen, such as NH2. Without the nitrogen fixing capabilities of this group of bacteria, we would all die of protein deficiency. Thus, the major flux of nitrogen between the atmosphere and the biosphere is mediated by prokaryotes. Sometimes these prokaryotes are symbiotically associated with plant roots, e.g. the legumes (peas, lentils etc.). Nearly a third of the terrestrial fixation of nitrogen occurs in cultivated fields. A minor natural source of fixed nitrogen comes through the heating of atmospheric nitrogen by lightening and its oxidation to NOx and NO3. Humans also fix nitrogen by heating N2 in internal combustion engines, power plants, forest fires, and through the manufacture of fertilizers. Man is now a major supplier of oxidized nitrogen to the atmosphere and these products are important pollutants and contribute to acid rain.

N2 + O2 ---> 2 NO

NO2 + OH ---> HNO3

HNO3 ---> H+ + NO3-

Ammonium is the other major nitrogen containing compound found in rain. It forms from the reaction of ammonia gas, produced by bacteria, with water.

NH3 + H2O ---> NH4+ + OH-

Because hydroxyl ions are formed, this reaction tends to raise the pH of rain partially compensating for the acidifying effects of CO2, NOx, and SO2.

Nitrogen is returned to the atmosphere through denitrification or bacterial reduction of nitrate. Some of these bacteria have alternative forms of metabolism. In the presence of oxygen, they use it to oxidize organic matter; in its absence, or when it is at low levels, they can reduce NO3- to NO2- or N2 to N2O. All members of this group are chemoheterotrophic; they require reduced organic compounds both for energy and for growth.

Prokaryotes, therefore, play the dominant role in moving nitrogen between all reservoirs.


As with nitrogen, bacteria play a major role in the movement of sulfur between reservoirs. Sulfate SO4= or sulfite SO3- dissolved in the ocean may be reduced to hydrogen sulfide H2S or elemental sulfur S by sulfur reducing bacteria in anaerobic marine and fresh water sediments. Hydrogen sulfide usually combines with Fe in the sediments to form iron sulfide (FeS2), or "fool's gold", which then becomes part of the sedimentary reservoir. In similar environments, nitrates are reduced to molecular nitrogen.

In aerobic environments, sulfur oxidizing bacteria may oxidize elemental sulfur S, or sulfide S=4=. Bacteria can oxidize reduced sulfur compounds from sediments or volcanic eruptions, producing SO2

H2S + OH- ---> ... ---> SO2,

or from oceanic dimethylsulfide produced by marine plankton.

Dimethylsulfide (DMS) is the major volatile sulfur compound of biogenic origin emitted from the ocean into the atmosphere. Some 15 to 20 million metric tons of sulfur per year are estimated to move from the ocean to the atmosphere.

(CH3)2S + OH-... ---> SO2

The production of dimethylsulfide appears to be a major pathway by which sulfur is returned to the atmosphere from the ocean. The dimethylsulfide produced by marine algae reacts in the atmosphere to form sulfuric acid as a natural component of acid rain.

SO2 + 2 OH- ---> H2SO4

Rain can be further acidified by the bacterial oxidation of SO2 from volcanic eruptions and human production. This human added SO2 increases the acidity of rainfall near industrial plants where it is produced (Figure 6). In fact, the sulfur dioxide added to the atmosphere by humans is a major source of sulfur for the atmosphere equal to global natural inputs, and is the dominant source of sulfur to the atmosphere over continents.


Chlorine originally entered the atmosphere through volcanic eruptions as a gas and subsequently acculmulated in the ocean as the most abundant anion, chloride. Today it is introduced to rain, not as a gas, but by sea salt, small particles of sea spray that form when air bubbles break at the surface of the ocean. Its concentration in rain is closely tied to the proximity of the ocean ( Fig. 7, Fig. 8).

Acid rain

The combination of the following reactions of oxidized compounds of sulfur, nitrogen and carbon with water in the atmosphere results in naturally acidic rain.

H2O + CO2 ---> H2CO3 <---> H+ + HCO3-

NO2 + OH- ---> HNO3 ---> H+ + NO3-

SO3 + H2O ---> H2 SO4 --->2H+ + SO4-

Humans now add substantial amounts of oxidized nitrogen and sulfur to the atmosphere further acidifying rain. Whether naturally acidic or with enhanced acidity from pollution, rain water reacts with rock-forming minerals to release additional cations and anions. Although in some arid regions atmospheric dust may bring soil particles to rain, more commonly rain water that seeps into the soils becomes groundwater and releases ions through chemical reactions with crustal rocks. The major species released are K+, Mg2+, Ca2+, Na+, Si(OH)4, HCO3-, Cl- and SO42-.

The hydrosphere

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