How Matter Cycles on Earth – The Biogeochemical Cycles

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Looking Ahead

For a detailed explanation of photosynthesis, see the Energy Chapter.

As explained above, biogeochemical cycles move elements through the biosphere, lithosphere, atmosphere, and hydrosphere. Through these cycles and other biological processes, the elements that serve as the building blocks for life on Earth are incorporated into microorganisms, plants, and animals, and are transformed from organic to inorganic forms and back again at various rates. Some cycles process elements quickly, on the scale of a human lifetime or less, and result in renewable resources. Nonrenewable resource cycles, however, take much longer, operating on geological timescales. The biogeochemical cycles of four elements of particular environmental significance are described below.

The Carbon Cycle

Carbon serves as the ‘structural skeleton’ of every type of organic molecule.  It enters the biosphere as carbon dioxide (CO2) from the atmosphere. Plants use CO2 in photosynthesis. Sunlight fuels the reaction of photosynthesis which transforms carbon (CO2) and water (H2O) molecules into glucose, a simple sugar (C6H12O6), and oxygen (O2) molecules. You will learn the details of the physiological process of photosynthesis in the Energy Chapter, since the sugar that plants produce is the primary source of caloric energy to food webs.

Plant glucose is consumed by aerobic (i.e. oxygen-requiring) animals and microorganisms, who harness its chemical energy through the process of cellular respiration. In cellular respiration, glucose molecules are broken down in order to provide energy that fuels basic cellular metabolic processes. The aerobic metabolism of glucose produces waste products; CO2 and H2O. These waste products are released back into the atmosphere or hydrosphere for re-use by plants and microbes, thereby forming a mutually dependent cycle of elements and compounds (carbon, water, oxygen) between plants and animals. In nature there is no build-up of waste. The byproducts of one organism’s metabolism are the necessary nutrients for another’s. In this way, the biogeochemical cycles keep the living organisms in ecosystems in balance with their natural resources.

In environments that are without oxygen, like the fine sediments of swamps, the water and sediments in the deep ocean, or the stomachs of ruminants (mammals that have a specialized anaerobic digestive compartment where they ferment plant materials prior to digesting them), anaerobic (i.e. non-oxygen-requiring) microorganisms utilize a different type of metabolism. They extract their energy from the chemical bonds of CO2 and release methane (CH4) as a waste product through the process of methanogenesis.

Figure 10: The Global Carbon Cycle. This diagram of the carbon cycle shows the movement of carbon between land, atmosphere, and oceans in billions of tons of carbon per year. Yellow numbers are natural fluxes, red are human contributions in billions of tons of carbon per year. White numbers indicate stored carbon.1

In addition to the biological processes (“biological pumping” of CO2) through photosynthesis and respiration which dominate the natural cycling of carbon on Earth, there exist non-biological chemical pathways in which carbon molecules flow. For example, both CO2 and CH4 molecules can be emitted into the atmosphere from the lithosphere through volcanic activity, and carbonates in the lithosphere (for example, calcium carbonate, CaCO3) can be dissolved in water through weathering and enter into the hydrosphere.

Because carbon uptake and release is mediated in large part by biological activity, carbon is cycled more rapidly than most other elements. However, while the vast majority of the carbon atoms on Earth cycle relatively quickly among the atmosphere, biosphere, and hydrosphere (Figure 10), some have resided for hundreds of millions of years in the lithosphere as fossil fuels. The largest perturbation to the natural carbon cycle is the relatively recent human extraction and combustion of stored geological reserves of organic carbon in the form of fossil fuels (coal, oil, and natural gas), which are transformed when they are burned, and released as CO2 into the atmosphere.

Looking Ahead

The idea of 'balance' is also important when considering natural resource ethics. This will be discussed in the Ethics Section

The extraction and combustion of these fossil fuels has thrown the Earth’s natural carbon cycle out of balance. Earth’s natural atmospheric concentrations of CO2 (the major greenhouse gas), have recently increased from 280ppm (parts per million) prior to the Industrial Age to over 400ppm today, causing global climate change and the acidification of the oceans.

The Nitrogen Cycle

Nitrogen is an essential component of a number of different kinds of organic molecules, including proteins, DNA (deoxyribonucleic acid), and chlorophyll (the primary photosynthetic pigment in plants). In the atmosphere, nitrogen occurs as a stable, inert, diatomic (consisting of 2 atoms) form, N2

N2 is the most abundant element found in the atmosphere, accounting for 78% of all atmospheric gases.  However, in order for diatomic nitrogen to be used in the biosphere, it must be converted into a form that is biologically available, that is, a form that can be metabolized by living organisms. This transformation occurs through a biologically mediated process called nitrogen fixation (Figure 11), which changes N2 gas into the more bio-usable form of ammonia (NH3).

Figure 11: The Nitrogen Cycle1

There are two natural ways that nitrogen gas is fixed into ammonia; a very small amount of N2 is fixed by lightning, and the vast majority of N2 is fixed by the activity of specialized nitrogen-fixing bacteria and cyanobacteria (blue-green algae), that we call nitrogen fixers. Nitrogen fixing bacteria and cyanobacteria possess a unique enzyme called nitrogenase. Enzymes are a class of proteins produced by organisms that act as catalysts to facilitate specific biochemical reactions in the cells. The function of nitrogenase is to catalyze the fixation of N2 into NH3 by first breaking the three strong chemical bonds that bond the two N atoms together in N2, then facilitating the formation of new bonds in NH3 (ammonia).

The biogeochemical cycling of nitrogen includes transforming numerous forms of nitrogen. These transformations are greatly facilitated by specialized groups of microorganisms. First, we have the nitrogen fixers who transform N2 gas into ammonia NH3. When in soil or in the sediments of freshwater or marine systems, ammonia can be further converted to ammonium (NH4+) through a process called ammonification, achieved by another specialized group of bacteria called ammonifiers. Ammonium can then be transformed to nitrites (NO2-) and nitrates (NO3-) through the microbial process called nitrification.  Both steps of nitrification are facilitated by specialized bacteria called nitrifying bacteria. Finally, the oxidized states of nitrogen (NO2- and NO3-) can be reduced to N2 gas through the process of denitrification, which is facilitated by another group of specialized bacterial called denitrifiers.  Where nitrogen fixers begin the nitrogen cycle by sequestering N2 gas from the atmosphere, denitrifying bacteria complete the cycle by transforming nitrogen back to N2 gas.

The ionic forms of nitrogen, particularly NH4+ and NO3- are the forms of nitrogen that are the most biologically available and easily utilized by the metabolic pathways of plants. Herbivore animals do not possess metabolic pathways to consume inorganic NH4+ and NO3-. Therefore, their nitrogen needs are met by consuming nitrogen-rich plants that have already done the work of converting inorganic nitrogen into organic forms, such as the nitrogen present in plant amino acids and proteins. Carnivorous animals consume herbivores, obtaining their nitrogen primarily in the form of animal amino acids and proteins.

When dead plant and animal material is decomposed by the group of microorganisms called decomposers (mostly fungi and bacteria), the nitrogen in their tissues is reduced to inorganic forms that return to the soil and water for reuptake by plants (Figure 11).

Closer Look

Read about how the current imbalanced nitrogen cycle can effect health in this article from the National Center for Biotechnology Information.

Because the cycling of nitrogen through its various molecular forms is mediated by so many different specialized bacteria, it is a relatively fast biogeochemical cycle. This cycle naturally maintains a balance in the amount of nitrogen found in its various forms in the biosphere, lithosphere, hydrosphere, and atmosphere. However, as you will read later in this section, humans have modified the nitrogen cycle through industrial nitrogen fixation so that it is far out of its natural balance. Today this imbalance poses great threats to the stability of our natural ecosystems. Figure 12 was first introduced in the Biodiversity Chapter (as figure 24) to demonstrate the planetary boundaries of various natural processes. Notice again that the nitrogen cycle in its current state is one of the most disproportionate from its natural homeostasis.

Figure 12: The inner green shading represents the proposed safe operation space for humans within nine planetary system threats. The red wedges represent an estimate of the current position for each variable. The boundaries in three systems (rate of biodiversity loss, climate change, and human interference with the nitrogen cycle), have already been exceeded, with the rate of biodiversity loss being exceeded most profoundly.1

The Phosphorus Cycle

Figure 13: Phosphate rock is a solid material
which varies from a hard rock to loosely
consolidated grains. It is found in the Earth’s
crust and the color may be brown, gray,
bluish gray, white, or black depending on
what other minerals it is bound to.1

Like nitrogen, phosphorus is an essential element for life, present in DNA, RNA (ribonucleic acid), cell membranes, and ATP (adenosine tri-phosphate, the critical molecule responsible for storing chemical energy in cells and releasing it for metabolic processes). Unlike carbon and nitrogen, the cycling of phosphorus is not mediated by the activity of organisms. Phosphorus is found in the Earth’s crust. It is the 11th most abundant chemical element in the crust, and it exists primarily as calcium phosphate (Ca3 (PO4)2) (Figure 13), a mineral called apatite. As sedimentary rock containing apatite weathers through rain and wind erosion, calcium phosphate is dissolved in water and can be transported into soils, rivers, lakes, and oceans.

Closer Look

Check out this video demonstration of the phosphate cycle.

Plants sequester the dissolved inorganic phosphorus in the form of orthophosphate (PO43-), and incorporate it into organic molecules that make up the plants’ metabolic molecules and structural tissues (Figure 14). Animals, in turn, fulfill their phosphorus requirements by eating plants containing these synthesized organic forms of phosphorous. In terrestrial ecosystems, animals and microorganisms return phosphate to the soil through excretion of waste. Phosphate also returns to the soil and hydrosphere through the decomposition of dead plants and animals. Once in the soil, the phosphate is typically quickly sequestered by new plant growth, completing the cycle.

The soluble orthophosphate can also be carried to oceans by rivers, where it is used by marine organisms in similar ways as described above for terrestrial organisms. Once the marine organisms die, their remains sink to the ocean bottom, and phosphate returns to the sediment. Under anaerobic conditions of deep lakes and ocean bottoms, phosphate is very soluble, and can be redistributed to upper aerobic water through currents. Over hundreds of thousands to millions of years geologic uplift returns the old sedimentary phosphorus to Earth’s surface (Figure 14).

Figure 14: The Phosphorus Cycle1

As with the other biogeochemical cycles, nature itself maintains balance within the cycling of phosphorus through the lithosphere, hydrosphere, and biosphere. You will note that there are no gaseous forms of phosphorus, so this element does not cycle through the atmosphere.

The Sulfur Cycle

Figure 15: Sulfur; at room temperature, elemental
sulfur is a bright yellow crystalline solid. Visit for pictures, stories, and facts
about sulfur. 1

Sulfur is among the 16 most abundant elements on Earth. The vast majority of it is bound in rock as sulfur salts (Figure 15), such as gypsum (CaSO4) and pyrite (FeS2), or as dissolved sulfate anions (SO4-) (Figure 16) in freshwater bodies and oceans. Of the 20 amino acids required to build all of the various kinds of plant and animal proteins, two of them (cystine and methionine) contain sulfur, making sulfur critical for all forms of life. Plants sequester sulfur from the soil in the form of dissolved inorganic sulfate (SO42-).

Figure 16: Dallol sulfur spring in the Afar Depression in Ethiopia and Djibouti, Africa. The spring releases dissolved sulfates from the ground. The high concentration of sulfates precipitate out of the water as white and grey solids, which then turn yellow and then orange as it becomes more oxidized by oxygen in the air. Read more about this part of Africa in a story from National Geographic’s website.1

Like phosphorus, sulfur can be bound in biologically unavailable forms in the crust of the earth for millennia. It becomes biologically available through weathering of sulfite - or sulfide-containing rock (Figure 17). Specialized bacteria can extract chemical energy to fuel their cellular metabolism by extracting dissolved sulfate (SO42-), reducing it to hydrogen sulfide (H2S) through a process called sulfate reduction. The hydrogen sulfide can then be oxidized back to SO42- by different bacteria in a process called bacterial oxidation.

Figure 17: The Sulfur Cycle1

Like carbon and nitrogen, sulfur also occurs in a gaseous phase (primarily as SO2). When sulfur in its gaseous form combines with water vapor (H2O) in the atmosphere it forms an acid, (H2SO4 or sulfuric acid), which contributes to the phenomenon called acid rain

While we have only touched on four of the many biogeochemical cycles, the other elements on Earth go through similar cycles. The different forms of these elements in their biogeochemical cycles are naturally in balance and provide humans and all other life forms with sustainable supplies of the resources required for life.

Questions to Consider

Where would you look for evidence of the carbon cycle in the area where you live? How would you explain the carbon cycle with this example form the area where you live? How about the other cycles: nitrogen, phosphorous, sulfur - do you find evidence of these cycles where you live? Explain.