Chapter 22
Biogeochemical Cycles

Links for Enrichment and Further Learning

• Biogeochemistry - Wikipedia
• NOVA: Hunt for Alien Worlds
• Planet Quest
• Planetary Biology

• Visualize and explain the general flow of materials between living things and the environment.
• Comprehend the rewarding structural and functional components of life in terms of useful chemicals, molecules, cells, biochemical processes and the Earth’s surface environment.
• Identify and trace major biogeochemical cycles involving carbon, nitrogen and oxygen.
• Distinguish between a substance’s environmental importance and its biological importance.
• Using gained knowledge in biogeochemistry, critically evaluate the notion that the Earth’s surface environment is largely the result of life.
• Using gained knowledge in biogeochemistry, critically evaluate its usefulness in understanding global climate and in the emerging field of astrobiology.

Study Questions / Quiz Prep. (Consult Required Reading and lecture notes for answers.)

1. Describe the flow of elements in the nonliving and living components in biogeochemical cycles.
2. Bio = ___________, geo = ______________ chemical = _______________.
3. Which three gases are most important to life?
4. Available forms of mineral elements occur as __________________ dissolved in soil water, or in lakes, streams and seas.

Carbon Cycle

5. What is the source of all carbon in living organisms?
6. What biochemical process removes carbon from the environment and incorporates it into living things?
7. Primary producers (photosynthesizers) and consumers (all other living things) release carbon back into the atmosphere as CO2, by what biochemical process?
8. Compare the rates in which dead organic matter accumulates in the following environmental settings: tropical rain forest; Alaskan forest; swamps and marshes.
9. How does the deposition and burial of fixed carbon influence the amount of CO2 in the atmosphere?
10. How does the deposition and burial of carbonates influence the amount of CO2 in the atmosphere?
11. Compare the amount (low or high) of carbon stored in soils in the following environmental settings: tropical rain forest; frozen tundra.
12. Why are the amounts so different?

Nitrogen Cycle

13. Nitrogen is available to plants generally in which two chemical forms?
14. Which three kinds of living things perform the process of nitrogen fixation?
15. Describe the process of nitrogen fixation.
16. Denitrification is a chemical process that does what?
17. What kinds of organisms perform denitrification?
18. What kind of ecosystem accounts for more than half of terrestrial denitrification?

Oxygen Cycle

19. What is the main biological process that releases O2 into the atmosphere?
20. If cellular respiration and decay normally consume O2 produced by photosynthesis, why has O2 accumulated in the atmosphere?
21. Chemically, what is ozone?
22. How can ozone be beneficial to life in one situation, and harmful in another?

From this presentation page

23. Review (written response not necessary) the following:

• Carbon dioxide gas
• Solid carbon
• Calcium carbonate
• Molecular nitrogen
• Nitrate salt
• Molecular oxygen
• Ozone
• Water
• Molecule
• Proteins
• Carbohydrates
• Fats
• Nucleic acids
• Chlorophyll
• DNA
• Living cell

24. Briefly describe the process of photosynthesis.
25. Write the general chemical expression for photosynthesis.
26. Briefly describe the process of cellular respiration.
27. Write the general chemical expression for cellular respiration.
28. Review (written response not necessary) the following:

• Photosynthetic types
• Non-photosynthetic types
• Non-photosynthetic decomposers
• Nitrogen-fixing types
• Denitrifying types

Global Carbon Cycle

29. Environmental Importance = ?
30. Biological Importance = ?
31. Study and understand the images of the Global Carbon and Oxygen Cycles on the presentation page.
32. How is carbon normally returned to the atmosphere?
33. How is carbon deposited in the Earth’s crust?
34. Does the burial of fixed carbon in the earth's crust result in a net reduction of CO2 in the atmosphere? How about O2?
35. How is coal made?
36. How is petroleum made?
37. Study and understand the image depicting the deposition of calcium carbonate on the presentation page.
38. Does the deposition and burial of calcium carbonate in the Earth's crust result in a net reduction of CO2 in the atmosphere? How about O2?
39. How were the White Cliffs of Dover made?
40. What extraordinary ways of returning carbon to the atmosphere?

Nitrogen Cycle

41. Environmental Importance = ?
42. Biological Importance = ?
43. Study and understand the image of the global nitrogen cycle on the presentation page.
44. Can plants take nitrogen directly out of the atmosphere?

Oxygen Cycle

45. Environmental Importance = ?
46. Biological Importance = ?
47. Study and understand the images of the Global Carbon and Oxygen Cycles on the presentation page.

Synthesis (These are not official study questions. But just for fun, you should try to answer them on your own.)
These are hypothetical situations.

1. A planet orbits a nearby star. This exoplanet is similar to Earth in many ways except there is no surface water. No lakes, no rivers, no oceans. The atmosphere is 95% CO2, 2% O2 and 3% N2. The surface of the planet is covered with living objects, including carbon-fixing, oxygen-producing photosynthesizers. Why is there so little O2 in the atmosphere?
2. A planet orbits a nearby star. This exoplanet is similar to Earth in many ways except that there is no life on it. There are oceans and continents and clouds. But, unlike early Earth, this planet's original (and current) atmosphere contains 78% O2. What are the prospects for "life" on this planet, and what would its chemical platform be?
3. On Earth, scientists discover that cyanobacteria populations are rapidly decreasing in the oceans, in the soil and in lakes. Based on recent trends, cyanobacteria will be extinct in 50 years. With the loss of cyanobacteria from the planet, what will the long-term consequences be to the atmosphere and biosphere?
4. Oceanographers report that global ocean acidity has "flipped" to a new stable state. Oceans now are strongly acidic -- similar to that of vinegar. An accompanying report by marine biologists describes whole coral reefs dissolving in this new acid regime. Predict atmospheric fluxes of key gases as well as changes in the mix of gases in the atmosphere.
5. Engineers have developed effective techniques to quickly extract every last ton of coal and petroleum from the Earth's crust. Predict what would happen to the mix of gases in the atmosphere if all of this coal and petroleum is burned in just a few years.

Review of useful environmental chemicals

A kid sprays carbon dioxide gas onto a demonstration fire. Carbon dioxide (CO₂ ) is a molecule composed of one atom of carbon and two atoms oxygen. It's normally a gas in Earth's atmosphere.

A piece of solid carbon. Carbon atoms form the main structure of all biological molecules.

A dish of calcium carbonate. Calcium carbonate is a solid substance made from calcium and carbon salts (carbonates). Carbonates are made from CO₂.

A pan of boiling liquid, molecular nitrogen (N₂ ). Molecular nitrogen is normally a gas in Earth's atmosphere. Nitrogen atoms are very useful components in important biological molecules like: proteins, DNA, vitamins, chlorophyll and cell membranes.

Nitrate salt. Nitrate is a kind of nitrogen-containing salt. Bacteria pull molecular nitrogen out of the atmosphere and convert it into this solid form. Nitrate is water soluble, so it can dissolve in lakes and oceans, and it can be carried by ground water. Photosynthetic organisms use nitrogen in this form to construct important biological molecules.

Pouring liquid molecular oxygen (O₂ ). Molecular oxygen normally is a gas in Earth's atmosphere. Its ability to rapidly collect hydrogen wastes supports energy extraction chemistry in most living things (cellular respiration). Oxygen atoms also are important components in most biological molecules.

A side view of Earth's atmosphere. High up in the stratosphere, molecular oxygen undergoes reactions that produce ozone. This ozone production results in an enriched ozone region -- otherwise known as the "ozone layer."

Liquid water. Chemically, water is H₂O. Water is the main original source of oxygen atoms used in the production of atmospheric oxygen (O₂).

Review of molecules and cells

A molecule. Molecules are discrete objects composed of atoms. This molecule is constructed out of different kinds of atoms including: carbon, hydrogen, oxygen, nitrogen and sulfur.

The biological world contains hundreds of thousands (if not millions) of unique molecular formulations. Biologists recognize that molecules, rather than being random lumps of matter, perform rewarding services for their biological unit. The nature of a molecule's activity is determined by the specific placement of different kinds of atoms, and the shape of the final construction.

Biological molecules are constructed out of many different kinds of atoms including: carbon, hydrogen, oxygen, nitrogen and sulfur atoms.

There are several main categories of biological molecules including:

• proteins - structural materials and enzymes (action molecules that do work)
• carbohydrates - energy storage, include sugars and starches
• fats - energy storage and other uses
• nucleic acids - information management, including DNA and RNA

A diagram of a chlorophyll molecule. Notice the presence of several different kinds of atoms: carbon, hydrogen, oxygen, nitrogen and magnesium. The specific order and arrangement of these atoms results in rewarding energy-capturing services.

A model of a DNA molecule. It takes a great deal of resources to construct a DNA molecule -- specifically atoms of carbon, hydrogen, oxygen, nitrogen and phosphorous.

A false color image of a living cell. The cell is the fundamental living unit in living things. It is composed of complex operating systems that are self maintaining. Cells exploit their surroundings for resources in support of the self-maintenance component. The combined activities of living cells in all living things churn the planetary surface environment -- with remarkable results.

Living things grow by the addition of cells much in the same way that a wall grows by the addition of bricks. So, in order to support the growth and maintenance of new cells, living things constantly consume resources from their surrounding environment.

And as the cells in living things do their work, they are constantly producing wastes that are released to the  surrounding environment.

Review of related biochemical processes

Photosynthesis

Photosynthesis uses CO₂, H₂O and light energy to build short chains of carbon (fixed carbon). Water is used as a source of hydrogen atoms to stabilize the chains, and resultant oxygen atoms are released as waste O₂.

The carbon chains then can be passed to other biochemical streams inside the cell for the assembly of carbohydrates, proteins, fats, nucleic acids and other kinds of biological molecules. Apart from other functional properties, all molecules of fixed carbon store sizeable amounts of chemical energy.

The general chemical expression for photosynthesis is:

CO₂ + H₂O + light --> carbon chains (fixed carbon) + O₂

Cellular Respiration

Cellular respiration disassembles molecules of fixed carbon, releasing the chemical energy stored in them. The disassembly process produces large amounts of unescorted hydrogen atoms that, if allowed to accumulate, could clog up the system. Molecular oxygen (O₂ ) is brought in to clear out these hydrogen atoms by combining with them to make water (H₂O). The disassembled carbon is released as CO₂.

The general expression for cellular respiration is:

Fixed carbon + O₂ --> CO₂ + H₂O + biological energy

Review of different kinds of living things

Photosynthetic types

Photosynthetic organisms usually require simple resources from their surroundings. These resources come in material form, such as carbon dioxide, molecular oxygen, nitrate salts (and other mineral salts) and water. Additional resources come in the form of energy, mainly sunlight.

Photosynthetic types also release materials back into their surroundings. Released chemicals include, carbon dioxide, molecular oxygen, water, nitrogen oxides and dimethyl sulfide.

Cyanobacteria are microscopic aquatic organisms that are responsible for the overwhelming majority of photosynthesis in the world's oceans, lakes and rivers.

Diatoms. Photosynthetic, single-celled plankton that float in the oceans, especially in cold waters.

Plants. Mostly terrestrial (on land). Plants are the main photosynthesizers on the continents.

Non-photosynthetic: animals

Animals require a mix of simple and complex materials from their surroundings. Simple materials include molecular oxygen, water and mineral salts. More complex materials includes the bodies, products or remains of other living things -- otherwise referred to as food.

Animals return simple materials to their surroundings such as carbon dioxide, water and nitrogen salts. They also return complex materials including digestive wastes and their own bodies after death.

Beetle -- an insect	Sea star	Barracuda -- a fish	Tree frog -- an amphibian
Desert iguana -- a reptile	Deer -- a mammal	Baby chicken -- a bird

Non-photosynthetic: decomposers

Decomposers consume and process the remains and wastes of all living things. Decomposition converts biological molecules into their basic components. For example, decomposers would convert a dead leaf into: carbon dioxide, nitrate salts, sulfur salts, phosphorous salts and water. The results of decomposition are released into the surrounding environment.

Fungi

Bacteria. Many bacteria species behave as decomposers. When you have a bacterial infection, bacteria are trying to decompose you.

Nitrogen fixing types

Cyanobacteria also fix nitrogen in addition to being photosynthetic.

Root nodules containing symbiotic nitrogen-fixing bacteria.

Denitrifying types

Denitrifying bacterium. Denitrification converts nitrate salts to molecular nitrogen.

How do the activities of life cause changes in the atmosphere?

The above image illustrates the long-term trends for atmospheric CO2, atmospheric O2, and the sun's energy output. As the sun has grown older, it has grown hotter. Atmospheric CO2 has been reduced because of the burial of calcium carbonate and the burial of fixed carbon. Atmospheric O2 has increased because of the burial of fixed carbon.

1. Burial of Fixed Carbon Reduces Atmospheric CO₂ and Increases Atmospheric O₂

First, Scenarios WITHOUT Burial (no atmospheric changes)

In this scenario, there is no burial of fixed carbon. Perfect recycling of CO2 and O2 on the continents results in no net increases or decreases in the amount of CO2 and O2 in the atmosphere. Photosynthetic plants remove carbon dioxide from the environment and use it to build biological molecules and wood (fixed carbon). Afterwards, all living things break down biological molecules (cellular respiration, decomposition), releasing carbon dioxide back into the surrounding environment. As a result, all CO2 and O2 are perfectly recycled, and there is no net change of CO2 or O2 in the atmosphere.

In this scenario, there is no burial of fixed carbon. Perfect recycling of CO2 and O2 in the oceans results in no net increases or decreases in the amount of CO2 and O2 in the atmosphere. Photosynthetic plankton remove carbon dioxide from the environment and use it to build biological molecules. Afterwards, all living things break down biological molecules (cellular respiration, decomposition), releasing carbon dioxide back into the surrounding environment. As a result, all CO2 and O2 are perfectly recycled and there is no net change of CO2 or O2 in the atmosphere.

Next, Scenarios WITH Burial (result in atmospheric changes)

In this scenario, there is burial of fixed carbon. Burial of fixed carbon on the continents results in a decrease in the amount of atmospheric CO2 and an increase in the amount of atmospheric O2. Some undecomposed biological molecules from plants and animals get carried to the bottom of lakes where they accumulate and get buried in the Earth's crust. This process results in a one-way movement of CO2 from the atmosphere and into the crust, causing a net reduction of atmospheric CO2. Also, the burial of this fixed carbon prevents its further contact with O2, resulting in an accumulation of O2 in the atmosphere. Long term accumulations on the continents can result in the production of peat and coal.

In this scenario, there is burial of fixed carbon. Burial of fixed carbon on the ocean bottom results in a decrease in the amount of atmospheric CO2 and an increase in the amount of atmospheric O2. Some undecomposed biological molecules from plankton and animals get carried to the bottom of the ocean where they accumulate and get buried in the Earth's crust. This process results in a one-way movement of CO2 from the atmosphere and into the crust, causing a net reduction of atmospheric CO2. Also, the burial of this fixed carbon prevents its further contact with O2, resulting in an accumulation of O2 in the atmosphere. Long term accumulations on the ocean bottom can result in the production of petroleum and natural gas.

Deposition and Burial of fixed carbon in the Earth's crust

Sometimes the remains of living things are added to an environmental setting faster than decomposers can, well... decompose them. As a result, remains of living things accumulate and are eventually buried. The burial of these remains represents an interruption in the normal carbon cycle.

    Turning buried fixed carbon into coal

If the buried, undecomposed remains of plants are compressed and heated for millions of years, the result is a coal deposit.

Coal miners

A chunk of coal. Made from the buried, undecomposed remains of trees and other plants.

    Terrestrial depositional environment for coal formation

Dead trees and tree parts collect in this lake and accumulate on the lake bottom in massive, cellulose-rich organic deposits.

Dead trees and tree parts collect in this lake and accumulate on the lake bottom in massive, cellulose-rich, organic deposits.

    Turning buried fixed carbon into petroleum

The main photosynthesizers in the ocean are tiny phytoplankton creatures that float near the surface along the coasts. In some places, phytoplankton grow rapidly (phytoplankton bloom). When they die, they sink to the shallow bottom and their undecomposed remains accumulate into massive organic deposits.

If the buried, undecomposed remains of marine plankton are compressed and heated for millions of years, the result is a petroleum deposit.

Oil well.

A jar of fresh petroleum (crude oil) made from the buried, undecomposed remains of marine plankton.

    Coastal marine depositional environment for petroleum formation

Phytoplankton bloom off of La Jolla, CA.

Phytoplankton bloom in the Bohai Sea near Beijing, China. Enclosed seas such as this one are excellent environments for rapid plankton deposits.

2. Burial of Calcium Carbonate Reduces Atmospheric CO₂

Turning carbon into buried calcium carbonate deposits

Deposition of calcium carbonate results in a net reduction of the amount of CO2 in the atmosphere. In one pathway, carbon dioxide spontaneously dissolves in water to become a carbonate salt called bicarbonate. In another pathway, on the continents, CO2 spontaneously reacts with freshly exposed, calcium-rich rocks in a chemical process called "rock weathering." During rock weathering, CO2 is taken out of the atmosphere to become a solid in the form of carbonate or bicarbonate. Calcium salts are freed from the rock. Both calcium and bicarbonate are carried by running water to lakes or the ocean. Many different kinds of aquatic organisms use bicarbonate salts along with dissolved calcium to make a new solid substance called calcium carbonate. They use the solid calcium carbonate to make their shells. If these creatures die and settle to the ocean or lake bottom in large numbers, then deposits of calcium carbonate accumulate. Such deposits permanently remove carbon from the normal carbon cycle.

Coccolithophores are planktonic creatures that use calcium carbonate to make their shells.

Many kinds of creatures in the coral reef use calcium carbonate to make hard body parts.

The white cliffs of Dover. These cliffs are composed of calcium carbonate from the deposited remains of plankton over millions of years. An ancient burial ground for carbon dioxide.

Returning Carbon to the Atmosphere

1. Normal return of carbon to the atmosphere

Plants and animals release carbon dioxide back into the environment usually after extracting energy from carbon-rich molecules (cellular respiration).

Fires rapidly return carbon dioxide to the atmosphere. A fire basically is the result of molecular oxygen performing rapid thievery of hydrogen atoms from biological molecules -- leaving the orphaned carbon behind as solid carbon and carbon dioxide(Fixed carbon + O2 + heat --> Co2 +H20).

Decomposers use the remains of all kinds of organisms for a variety of purposes. The final result is the release of carbon back into the atmosphere usually as carbon dioxide or methane (cellular respiration).

2. Extraordinary return of carbon to the atmosphere

Humans return buried carbon to the atmosphere by digging up and burning petroleum (gasoline), natural gas, and coal.

Volcanoes release large amounts of carbon dioxide gas to the atmosphere. Plate tectonics theory suggests that much of the carbon dioxide from volcanoes along crustal plates comes from the carbon deposits on subducted ocean plates.

Oxygen, Carbon, and Nitrogen Cycles

All of the above scenarios illustrate oxygen and carbon cycles on Earth. In addition to these cycles, the nitrogen cycle is presented below. Each of these cycles is summarized below.

Carbon Cycle

Environmental Importance of carbon
    Global temperature - greenhouse effect

Biological Importance of carbon
    Carbon is the main atom for the construction of all biological molecules

SUMMARY - The global carbon cycle is driven by photosynthesis.

• Photosynthesizers remove carbon dioxide from the environment and use it to build biological molecules (fixed carbon).
• Afterwards, all living things break down biological molecules (cellular respiration, decomposition), releasing carbon dioxide back into the surrounding environment.
• Some undecomposed biological molecules get buried and accumulate in the Earth's crust (burial of fixed carbon), resulting in a net reduction of atmospheric CO₂. Long term accumulations can result in the production of peat, coal, petroleum and natural gas.
• The decomposition of some biological molecules in the soil results in the production of carbonate salts (such as, calcium carbonate). Some carbonate salts wash into aquatic environments like rivers, lakes and oceans.
• Corals, mollusks, sea stars, coccolithophores and many other kinds of aquatic animals turn carbonate salts into solid calcium carbonate. When they die their bodies remain on or settle to the bottom and accumulate (burial of calcium carbonate).
• The accumulation of calcium carbonate deposits on the ocean bottom results in a net reduction of atmospheric CO₂.

Oxygen Cycle

Environmental Importance of oxygen
    Global temperature - by mass; O₂ makes up 21% of the atmosphere
    Stratospheric ozone -- Ozone (O₃) is made out of O₂.

Biological Importance of oxygen
    Important in supporting cellular respiration and the extraction of energy from fixed carbon
    Oxygen is a major building material for all biological molecules

SUMMARY - The global oxygen cycle is mainly the outcome of the biological processes of:1) photosynthesis (makes O2) and cellular respiration (consumes O2).

• While making chains of carbon (fixed carbon), photosynthesizers remove hydrogen atoms from water (H₂O) and eject O₂ as a waste.
• Photosynthesizers and most other kinds of living things use cellular respiration to extract energy from molecules of fixed carbon. During cellular respiration, hydrogen atoms accumulate inside the cell as wastes. So, living things take in O₂ which combines with the waste hydrogen atoms to make water (H₂O).
• If photosynthesis and cellular respiration are equally balanced in the world, there would be no net buildup of oxygen in the atmosphere.
• Molecular oxygen builds up in the atmosphere because some of the remains of living things (fixed carbon) get buried in the Earth's crust (burial of fixed carbon). To the extent that fixed carbon is buried, O₂ will accumulate in the atmosphere.
• Geologic movements sometimes expose deposits of fixed carbon. Once exposed to the atmosphere, atmospheric O₂ recombines with this fixed carbon. When this happens, the result is a reduction in atmospheric O₂.
• Fires are chemical reactions in which O₂ reacts with fixed carbon (among other possible materials) to become H₂O -- reducing the amount of O₂ in the atmosphere.
• Humans purposely dig up buried fixed carbon in the form of coal, petroleum and natural gas. Atmospheric O₂ is used in the combustion (burning) of these substances, resulting in a reduction in atmospheric O₂.

Nitrogen Cycle

Environmental Importance of Nitrogen
    Global temperature - by sheer mass; N₂ makes up 78% of the atmosphere
    Local and regional air pollution; photochemical smog, acid rain

Biological Importance of Nitrogen
    Nitrogen is a very useful atom for the construction of proteins, DNA, chlorophyll, vitamins

The global nitrogen cycle is mostly the outcome of bacteria.

SUMMARY

• Nitrogen-fixing bacteria remove molecular nitrogen (N₂ ) from the atmosphere and convert it to ammonium salts.
• Nitrifying bacteria convert ammonium salts to nitrate salts.
• Photosynthesizers take in nitrate salts and use them to build biological molecules.
• Decomposers disassemble nitrogen-containing molecules and release ammonium salts back into the environment.
• Denitrifying bacteria convert nitrate salts into molecular nitrogen which is released back into the atmosphere.

Using our understanding of biogeochemistry to do interesting things

	Gaia theory -- seeing life on Earth from the perspective of the whole planet. Gaia theory was developed by James Lovelock and Lynn Margulis in the 1970s. Gaia theory was the first comprehensive model to portray the Earth's surface environment largely as the result of biological activity over billions of years.
	Understanding how biogeochemistry affects climate and making predictions about climate change. Here is a simple introduction into this idea. Forests release water vapor which stimulates the formation of local clouds. Plankton in warming ocean waters release dimethyl sulfide -- which can increase cloud production over oceans. Since clouds can either trap more heat (warming the planet) or reflect more sunlight (cooling the planet), anything that influences their production has the potential to influence global climate as well.
	Assessing the possibilities for life-influenced environments on worlds outside of our solar system As of November 2006, astronomers have discovered 209 planets around 179 other stars in the galaxy. About 41 of those planets could be the right distance from their host stars to support liquid surface water. These are compelling findings. The science of astrobiology applies biogeochemical theory to develop and evaluate possible surface environments on these distant worlds.

End