The Carbon Cycle

Carbon is the fourth most abundant element in the universe, and essential to life on earth. Carbon is the element that provides the backbone of all organic molecules (see Chapter 2, Chemistry of Life). All living organisms from microorganisms, to plants and animals, contain a large number of organic compounds and therefore a large amount of carbon. Thus the carbon cycle is considered to be the primary biogeochemical cycle.

For the carbon cycle to start, autotrophic organisms are necessary, either photoautotrophs or chemoautotrophs—organisms that use carbon dioxide as their primary source of carbon. Photoautotrophs are the primary organisms in the carbon cycle and include cyanobacteria, green and purple bacteria (sulfur and nonsulfur), algae, photosynthetic protozoa, and plants. All these organisms convert carbon dioxide (CO₂) to organic molecules via carbon fixation during photosynthesis. Photoautotrophs require sunlight and for that reason are restricted to soil and water surfaces. Chemoautotrophs can also fix carbon dioxide into organic matter, but because they cannot use the energy of the sun, they need to metabolize compounds such as hydrogen sulfide for energy.

The next step in the carbon cycle involves the consumption of autotrophs by chemoheterotrophs such as animals and protozoans, which then catabolize the organic molecules for energy, resulting in the release of CO₂. Some organic molecules produced by the autotrophs may be incorporated into the tissues of heterotrophs, where they remain until that organism dies. Dead organisms are decomposed with the help of microorganisms, metabolizing organic molecules and releasing CO₂ in the process. The release of CO₂ into the atmosphere starts the cycle over again (Figure 24.2).

The Nitrogen Cycle

Nitrogen gas is the most abundant gas in the earth’s atmosphere, representing about 79% of all the gases in air. Unfortunately, the nitrogen in the atmosphere is unusable by most organisms. Only about 0.03% of the earth’s nitrogen is fixed in the form of nitrates, nitrites, ammonium ion, and organic compounds. Nitrogen is necessary for all living organisms for the synthesis of proteins, nucleic acids, and other nitrogen-containing compounds. The nitrogen cycle consists of several steps as illustrated in Figure 24.3.

Nitrogen fixation is a process by which nitrogen gas (N₂) is reduced to ammonia (NH₃), a process catalyzed by the enzyme nitrogenase. Only a limited number of prokaryotes are capable of performing this process. Nitrogenase functions only in the complete absence of oxygen, which does not present a problem for anaerobic microbes. Aerobic nitrogen fixers must protect nitrogenase from oxygen, which is done in several ways. Some of these microbes use oxygen at such a high rate that it never enters the cell and therefore does not come in contact with the enzyme. Some cyanobacteria fix nitrogen only at night, when the oxygen-producing cycle of photosynthesis does not occur; other cyanobacteria form nonphotosynthetic cells referred to as heterocysts to protect the enzyme from oxygen in the atmosphere as well as from the oxygen produced during photosynthesis. Nitrogen fixers can be free-living or symbiotic.

Free-living, nitrogen-fixing bacteria include aerobic species of Azotobacter, aerobic cyanobacteria, and anaerobic species of Bacillus and Clostridium. They are found in particularly high concentrations in the rhizosphere, a region about 2 mm in diameter around the roots of plants. As these organisms die, they release the fixed nitrogen into the upper layers of the soil, where it then becomes available to plants and to the animals that graze on the plants.

Symbiotic nitrogen-fixing bacteria live in direct symbiosis with plants. The main organism in this category is Rhizobium, which is especially adapted to leguminous plant species, on which the organism forms root nodules. Nitrogen is fixed in the nodules, the plant provides an anaerobic environment and nutrients to the bacteria, and the bacteria then provides the plant with usable nitrogen. The nitrogen fixers provide enough nitrogen to the leguminous plants so that the farmer does not have to apply nitrogen fertilizers.

Lichens, which are a symbiotic (mutualistic) combination of a fungus and an algae or cyanobacteria, also play an important role in nitrogen fixation in the forest environment. If the symbiont is a nitrogen-fixing cyanobacterium, the fixed nitrogen will eventually enrich the forest soil.

Ammonification is the process by which amino groups are converted to ammonia. Almost all nitrogen in the soil is present in organic molecules of organisms. Bacteria and fungi decompose wastes and dead organisms and break down proteins into amino acids, which are then transported into the microbial cells. Next, in the process of deamination the amino groups of amino acids are removed and converted to ammonia. In dry or alkaline soil ammonia will escape as gas; however, in moist soil it is converted to ammonium ion, which can be absorbed by bacteria and plants and used for amino acid synthesis.

Nitrification involves oxidation of nitrogen in the ammonium ion to produce nitrate (NO₃⁻). This is a two-step process involving two genera of autotrophic nitrifying bacteria, which oxidize ammonia or nitrite (NO₂⁻) to obtain energy. The first step involves the oxidation of ammonia to nitrites, performed by Nitrosomonas spp. Nitrites are toxic to plants, but in the second stage Nitrobacter oxidize nitrites into nitrates, which are soluble and can be used by plants.

Denitrification is the process by which nitrate is reduced to nitrogen (N₂) by anaerobic cellular respiration. The gas then escapes into the atmosphere. Denitrification takes place in waterlogged soils where little oxygen is available. Pseudomonas species seem to be the most prevalent group of bacteria involved in the denitrification of soil. This conversion of valuable nitrate into nitrogen gas represents a considerable economic loss in agriculture.

Anammox is the acronym for anaerobic ammonium oxidation and is a recent addition to knowledge of the nitrogen cycle. In this process, performed by anammox bacteria (previously thought to be denitrifying bacteria), nitrite and ammonium are directly converted to dinitrogen gas. This process accounts for up to 50% of the dinitrogen gas produced in the oceans. Ammonia is the major source of fixed nitrogen in the oceans and because the anammox bacteria remove ammonia efficiently from those bodies of water, these organisms limit oceanic primary productivity. On the positive side, the ability of anammox bacteria to convert ammonium and nitrite directly to dinitrogen gas provides a promising alternative to current methods of removal of nitrogen from wastewater (see Life Application: Anammox and Wastewater Treatment).

The Sulfur Cycle

Sulfur is the tenth most abundant element in the universe and is present in vitamins, proteins, and hormones. Sulfur is important for the appropriate functioning of proteins and enzymes in plants, as well as in animals that depend on plants for sulfur. Plants absorb sulfur when it is dissolved in water, and animals consume the plants for their sulfur needs. The majority of earth’s sulfur is stored underground in rocks and minerals, and as sulfate salts deep within the ocean sediments.

The sulfur cycle is similar to the nitrogen cycle, except that sulfur originates from natural sedimentary deposits. The sulfur cycle includes both atmospheric and terrestrial processes (Figure 24.4). The terrestrial process begins with the weathering of rocks, resulting in the release of stored sulfur. Subsequently, the sulfur comes in contact with air and is then converted into sulfate (SO₄). Plants and microorganisms will take up the sulfate and convert it into organic forms. Animals will consume the organic forms via food they consume, thereby moving the sulfur through the food chain. As organisms die, bacteria decompose them, releasing sulfur-containing amino acids into the environment. The sulfur released from the amino acids is converted by microorganisms to its most reduced form, hydrogen sulfide (H₂S). This process is called sulfur dissimulation. H₂S is then oxidized to elemental sulfur and then to sulfate by various microorganisms under various conditions. These organisms include nonphotosynthetic autotrophs such as Thiobacillus and Beggiatoa and photoautotrophic green and purple sulfur bacteria. The cycle starts again with the uptake of sulfate by plants and algae that animals eat. Anaerobic respiration by the bacterium Desulfovibrio reduces sulfate back to H₂S.

Sulfur can also be found in the atmosphere. A variety of natural sources emit sulfur directly into the atmosphere, including volcanic eruptions, bacterial processes, decaying organisms, and the evaporation of water. When sulfur dioxide enters the atmosphere it will react with oxygen to produce sulfur trioxide gas, or it can react with other chemicals in the atmosphere to produce sulfur salts. Furthermore, sulfur dioxide can react with water to produce sulfuric acid. All these particles will eventually settle back onto the earth, or react with rain and fall back to earth as acid deposition. The particles will then be absorbed by plants, and the sulfur cycle will start over again.

The Phosphorus Cycle

Phosphorus is an essential nutrient for plants, animals, and microorganisms. It is part of nucleic acids (DNA, RNA, ATP, and ADP) and of the plasma membranes (phospholipids). Phosphorus can be found in water, soil, and sediments. Unlike nitrogen and sulfur, phosphorus cannot be found in the atmosphere in the gaseous state. Phosphorus exists in the form of phosphate ion and undergoes little change in its oxidation state. The phosphorus cycle (Figure 24.5) involves changes of phosphorus from insoluble to soluble forms that are available for uptake by organisms, and from organic to inorganic forms by pH-dependent processes. Because no gaseous form of phosphorus exists it has the tendency to accumulate in the seas and other bodies of water.

Excess phosphorus can present a problem in a habitat. Agricultural fertilizers rich in phosphate and nitrogen are easily leached from the fields by rain. The resulting runoff into rivers and lakes can cause eutrophication, the overgrowth of microorganisms in nutrient-rich waters. The organisms involved include mainly algae and cyanobacteria. Such overgrowth, referred to as a bloom, depletes oxygen from the water, resulting in the death of aerobic organisms such as fish. Anaerobic organisms then take over, leading to increased production of H₂S and resulting in the release of foul odors.

Microbial Populations in Soil

The microbial populations in soil vary depending on the type of soil. Bacteria are the most abundant and diverse soil inhabitants; they are found in all layers and often form biofilms, especially around plant roots. Bacteria are highly adaptable to changing environments, and therefore are plentiful in most soils. Fungi are next in numbers. Both free-living and symbiotic fungi are present only in topsoil, where they can form large mycelia (mats of fibrous hyphae) that potentially cover several acres. Algae and protozoa are also present in soil but in smaller numbers than bacteria and fungi. Soil algae are photoautotrophs and therefore exist on or near the soil surface. Protozoans are mobile and move around the soil feeding on other microbes, especially bacteria. Although viruses are present within microorganisms, they generally are not found free.

Freshwater Ecosystems

About 3% of the world’s water is freshwater, 99% of which is either frozen in glaciers and pack ice, or is buried in aquifers. The remainder of the freshwater is found in lakes, ponds, rivers, and streams. Microorganisms are dispersed vertically within lake and pond systems, according to the availability of oxygen, light intensity, and temperature. Surface waters are higher in oxygen and light intensity, and warmer than deeper waters. In contrast to stagnant waters where oxygen is readily depleted, in larger lakes the wave action continuously mixes nutrients, oxygen, and organisms, resulting in efficient use of its resources. In stagnant waters, because of the depletion of oxygen, anaerobic organism will dominate and a lesser water quality will be the result. Four distinct vertical zones can be observed in lakes and ponds (Figure 24.6): a littoral zone, a limnetic zone, a profundal zone, and a benthic zone:

• The littoral zone (Figure 24.7) is the area along the shoreline with considerable rooted vegetation and good light source. This is the zone where nutrients enter the lake or pond, providing an abundance of food and promoting a high diversity of animals and bacteria in the biotope.

• The limnetic zone is the well-lit, upper layer of water away from the shore. This area is occupied by phytoplankton consisting of algae and cyanobacteria, and zooplankton, small crustaceans, and fish. Areas of the limnetic zone with sufficient oxygen supply also contain Pseudomonas spp., Cytophaga, Caulobacter, and Hyphomicrobium.

• The profundal zone is the deeper water located below the limnetic zone. It is characterized by limited light penetration (diffuse light), lower oxygen content, and lower temperature. The organisms of this zone depend on import of organic matter drifting down from the littoral and limnetic zones. This zone is inhabited mainly by primary consumers that are either attached to or crawl along the sediments at the bottom of the lake. These bottom-dwelling organisms are referred to as benthos. Purple and green sulfur bacteria can also be found in this zone.

• The benthic zone consists of the sediments at the bottom of a lake; it includes the sediment surface as well as some subsurface layers. This layer also contains benthos, which generally live in close relationship with the substrate bottom. These life forms can tolerate cool temperatures and low oxygen levels. Bacteria found in this zone include Desulfovibrio, methane-producing bacteria, and Clostridium species.

Contrary to the vertical stratification of lakes and ponds, rivers and streams lack this stratification because the organisms and nutrients are continuously swept along and mixed. Many organisms live toward the edges, where currents are low and organic material enters the water. Furthermore, biofilms can readily be found on rocks of rivers and streams.

Marine Ecosystems

Marine (saltwater) ecosystems are part of the largest aquatic system on earth, covering more than 70% of the earth’s surface. Marine ecosystems host many different species ranging from planktonic organisms that comprise the base of the marine food web, to fish, and large marine mammals. These ecosystems have some unique qualities, specifically the presence of dissolved compounds, particularly salts. As in freshwater systems the oceans can also be divided into layers, but they do have a fifth zone, the abyssal zone, which encompasses the deep ocean trenches (Figure 24.8). The majority of marine microorganisms are present in the littoral zone, where light is readily available and nutrient levels are high. The upper 200 m of ocean contains an unseen population of microbes that supports oceanic life. These are photosynthetic organisms called the marine phytoplankton. The many kinds of different bacteria among the phytoplankton are a food source for protozoa, which in turn are prey for the multicellular organisms among the zooplankton. The zooplankton is a source of food for the fish. The carbon dioxide and mineral nutrients released as by-products of the metabolic activities of bacteria, protozoa, and zooplankton are recycled into the photosynthetic phytoplankton.

The benthic abyssal zones have sparse nutrients, but they still support microbial growth, especially around hydrothermal vents. These vents release superheated, nutrient-rich water, providing nutrients and energy for thermophilic chemoautotrophic anaerobes. These organisms in turn support a variety of invertebrate and vertebrate animals.