EarthLabs > Climate and the Carbon Cycle: Unit Overview > Lab 5: Soil and The Carbon Cycle > 5A: Soil, Carbon and Microbes

Lab 5: Soil and The Carbon Cycle

Part A: Soil, Carbon and Microbes

When we stand on soil, we are standing on an important reservoir of the carbon cycle, one that has great potential to add large amounts of carbon to the atmosphere if global climate continues to warm. Conversely, many ranchers, farmers and soil scientists now feel that soil may also be a solution to rising levels of atmospheric CO2.

Like oceans, soils are highly complex ecosystems where the carbon cycle interacts with other biogeochemical cycles such as nitrogen, phosphorus and sulfur. And, to add to soil's complexity, microbes that live in the soil mediate many of these biogeochemical interactions in addition to driving important carbon cycle processes.

In this Lab section, you will explore how soil carbon is formed and stored. This will include exploring the critical role of soil microbes and the nitrogen cycle in storing carbon in soil. Then, you will design and carry out a laboratory investigation on the effect of temperature on soil respiration rates. Finally, you will learn how ranchers and farmers are using new agricultural and range methods that build healthy carbon-rich soil, a process that has the potential to mitigate climate change. First, watch this video to take a look below ground. As you watch, make note of the different types of organisms that live in soil and their role in the soil carbon cycle.

If the above video does not load, you can also view the video above at The Living Soil Beneath Our Feet | California Academy of Sciences - YouTube


With a partner or a group, discuss the following:

  • What organisms exist below ground.
  • Using information from the video and what you have learned about carbon so far in this module, describe the role these organisms have in carbon cycle processes, moving carbon from one place to another, and/or transforming carbon compounds to new carbon compounds.

More carbon is stored in soil than in Earth's vegetation and atmosphere combined

In soils, you can find carbon in both organic carbon compounds and inorganic carbon compounds. In most soils, carbon exists predominately in the form of soil organic carbon (SOC) the amount of carbon contained in the organic carbon compounds found in soil. .

Soil organic carbon (SOC) is the main constituent of soil organic matter (SOM) organic matter component of soil, consisting of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms.. SOM is formed by the biological, chemical and physical decay of organic materials on the soil surface and below the ground. Basically, soil organic matter (SOM) is composed of anything that once lived, including:

  • organic bits and pieces of plant and animal remains in various stages of decomposition, sloughed off cells and tissues of soil organisms, and substances from plant roots and soil microbes.
  • living soil microbes (bacteria, fungi, archaea, nematodes and protozoa) and plant roots. If we weighed all of the organisms found in soil, soil microbes would comprise about 90-95% of that weight.
  • humus, a chemically stable type of organic matter composed of large, complex organic carbon compounds, minerals, and soil particles. Humus is resistant to further decomposition unless disturbed by a change in environmental conditions. If undisturbed, humus can store soil carbon for hundreds to thousands of years. This makes humus a very important carbon sink.
  • charcoal(biochar), incompletely burned plant material. Charcoal can remain undecomposed in the soil for decades to centuries.

The carbon balance within soil is controlled by carbon inputs from photosynthesis, carbon losses by respiration and carbon storage in humus

Examine the image pictured on the right showing the flow of carbon into and out of soil. If plants transfer more carbon into soil than is released via soil respiration, more carbon will get stored in humus via the process of humification formation of humus during the decomposition of organic matter in soils..

For years, soil scientists and farmers have known that carbon can persist for long periods of time in carbon-rich humus. Humus is formed when soil organic material is degraded by soil microbes that reside in the soil. However, humus is a very complex substance and not fully understood. Current research indicates that the length of time soil carbon persists in humus and other SOM components depends on many ecosystem interactions between SOM and microbes, minerals, moisture and temperature. (Schmidt, M., Torn, M., et al). Scientists do not know yet how long this carbon will stayed stored in soil or if environmental disturbances will move large amounts into the atmosphere amplifying climate change.

Plant root exudation oozing out of complex carbon compounds such as sugars, protein proteins through the pores of roots to the surrounding soil. transfers a variety of complex organic carbon compounds such as acids, sugars and protein enzymes from the roots of trees and shrubs into the surrounding soil and into a symbiotic ecosystem of mycorrhizal fungi. fungi that have a symbiotic relationship with plants, living on and in plants' roots. These fungi get sugars from the plant in return for greatly enhancing the plant's ability to take up water and nutrients from the soil. Mycorrizal fungi eat the sugars and then deposit carbon-containing residue in the surrounding soil. Recent research indicates some types of these fungi (ectomycorrhizal fungi) can lead to up to 70% more carbon stored in soil. (Averill, C., et al)

Next, watch the video from the International Year of Soil, 2015. As you watch, make note of:
  • how carbon moves into, around and out of soil; and
  • the role of vegetation in recycling CO2 back into soil.

If the video above does not load, you can also see the video at The Science of Soil Health: Cycle, Re-cycle, Repeat - YouTube


With a partner or with a group, discuss the following:

  • Describe how carbon can be recycled back into the soil if the soil is covered by vegetation.
  • Many areas of soil have very little vegetation on top of the soil or no vegetation at all. How might this influence the amount of carbon stored in the soil? Why?

Soil microbes move and transform carbon compounds and make nitrogen bioavailable to plants.

Some of the smallest organisms in both soil and the oceans have key roles in moving and transforming carbon compounds in their ecosystems. In soils, microbes directly and indirectly mediate about 90% of soil functions, such as:

  • decomposing dead matter into SOM;
  • respiring CO2 and methane (CH4) to the surrounding soil and air;
  • making essential biogeochemical nutrients such as nitrogen compounds bioavailable to plants and other soil organisms;
  • storing carbon in soil humus; and
  • decomposing humus which releases CO2 to the air via soil respiration.

All organisms in the Biosphere need nitrogen to build their DNA, RNA and protein molecules. Because plants transfer carbon into the soil via photosynthesis, the nitrogen cycle becomes critical to building strong healthy soil. Take a few minutes to examine the image of the nitrogen cycle above and then watch the Soil Microbes video. Then answer the discussion questions that follow.


With a partner or the class, discuss the following:

  • Compare the specific roles of nitrifying bacteria, decomposers and denitrifying bacteria in the plant/soil ecosystem.
  • Explain why soil microbes are critical to carbon storage in soil.
  • Describe at least one way the nitrogen cycle and the carbon cycle are interconnected in soil.
  • Explain why soil microbe diversity is important to building rich soil.

Active soil microbes respire CO2 at greater rates

Soil microbes have a busy lifestyle! When soil microbes are carrying out their life activities such as reproducing, eating, metabolizing, biosynthesizing, transforming nitrogen compounds, decomposing dead organisms, humus and SOM, they need lots of energy. Burning sugars via respiration provides that energy and releases CO2as a by-product. This CO2can be used by plants covering the soil surface for photosynthesis and/or drift up to the air to join other CO2 molecules in the atmosphere. Several abiotic and biotic environmental variables can make microbes very active or can slow down that activity. How active or inactive microbes are depends on the many ecosystem interactions between microbes, minerals, SOM, moisture and temperature.

Checking In

Based on your knowledge of soil microbes, soil respiration and the carbon and nitrogen cycles, which of the following statements would most likely be true? Choose all that apply. NOTE: Remember that soil respiration is a short-hand term for respiration by soil microbes.










Stop and Think

1: Describe the role of soil in the carbon cycle.

2: How do microbes change the amount of carbon compounds in the soil and carbon dioxide in the air?

Soil microbes, soil respiration and climate changeIs there a connection?

When scientists discuss global climate change, they often focus on the amount of carbon in the atmosphere and vegetation. In reality, soil contains more carbon than Earth's vegetation and atmosphere combined. For this reason, even a minor change in soil carbon could have major implications for Earth's atmosphere and climate. Scientists are especially concerned about changes in rates of decomposition and soil respiration in permafrost - a frozen soil found in cold latitudes like Alaska, Canada, Siberia and the Arctic. You will learn more about permafrost soil in Lab 5B.

Scientists agree that they have many unanswered questions about how soil will respond to climate change and more research needs to be done. Key research questions scientists are exploring are:

  • How will soil and soil microbes respond to a warming climate?
  • Will a warming climate result in higher amounts of carbon transferring from soils to the atmosphere as CO2 and methane (CH4), both greenhouse gases that could create additional warming.
To find answers to these important questions, scientists need to know more about how soil microbes respond to changes in climate environmental variables such as temperature and moisture. To that end, you will design and carry out an experiment to test the effect of temperature on soil respiration rates.

Laboratory investigation: How Do Different Temperatures Affect the Rate of Soil Respiration by Soil Microbes?

In this laboratory investigation, your class will collectively design a controlled experiment that tests the effect of different temperatures on rates of soil microbe respiration. You will be given a core set of equipment and materials to use but you are encouraged to use other equipment and materials in your design. This could include other equipment and materials in your classroom or even your own kitchen! Additionally, you must design the experimental control(s) for this investigation. Begin by reviewing the materials and equipment needed and then answer the pre-lab discussion questions that follow.


  • Soil microbial respiration apparatus (20 fluid oz plastic soda bottles )
  • CO2 gas delivery mechanism (#4 one-hole stopper, attached glass tube and rubber tubing. One per bottle.)
  • Collecting vessels (small jars, flasks, beakers, etc.)
  • 50-100 ml graduated cylinders (to measure limewater and sugar water)
  • Celsius thermometers (to test ambient temperatures)
  • Vernier CO2 probe (optional) This probe will give you quantitative data of respired CO2 over time. If using a probe, you will need to make sure that you have a soil respiration chamber bottle with a wide enough mouth for the probe. Bottles like VitaminWater work well.
  • N-P-K nutrient soil testing kit (optional)


  • Limewater - 50 ml Limewater per collecting vessel. Safety Alert: Do not get in eyes, on skin or on clothing. Wear safety goggles and a lab apron. Wash hands after handling.
  • Duct tape and scissors (to cut and tape the bottle)
  • Well-dried topsoil (Its important that the soil is very dry!)
  • Sugar water - 70 ml from a class stock solution of 5g of sugar dissolved in 500ml of distilled or filtered water.
  • Dry Topsoil: You need to ensure that the soil you are using is rich with soil microbes. Topsoil is usually the most humus-rich portion of soil, indicating presence of soil microbes. It should be dry, dark, almost black in color, have small particles and smell musty indicating presence of fungi.

    Sugar Water: It takes a long time for microbes to decompose and digest tough plant lignans and cellulose in the top soil, so sugar water is used to provide an immediate food resource for the soil microbes. This rapid resource of food, combined with using a very dry soil, stimulates respiration. This phenomenon is an example of an environmental resourcepulse which is a natural event of increased resource availability that happens suddenly, doesn't last very long, is rare but has a large magnitude. (Yang, LH et al.,)

    Limewater is used in many experiments to indicate the presence of CO2. When carbon dioxide is bubbled through limewater, the limewater turns from clear to cloudy with a white precipitate. The cloudier the water, the more CO2 has reacted with the limewater. Limewater is made of calcium hydroxide in solution. The chemical formulas for the reaction you will be seeing are calcium hydroxide + carbon dioxide → calcium carbonate + water Ca(OH)2 (aq) + CO2 (g) → CaCO3 (s) + H2O (l) Calcium carbonate (chalk) is the white precipitate you will see if CO2 reacts with the limewater.


As a class, discuss the following pre-lab questions:

  • What will be the various temperatures conditions you will be testing for in your experiment? How will you set them up?
  • Describe the experimental control(s) you will use and how they might help you analyze your results.
  • The experiment's instructions tell you to use the same amount of sugar water and to stop your observations all at the same time. Why is this important?
  • Why is it a good practice to determine the amount of N-P-K in the top soil you will be using?
  • If using the optional CO2 probe, explain how and why you will use it.

Laboratory investigation instructions:

  1. Prepare your bottle. Use scissors or safety blade to start a cut about 4-5 cm from the top of the bottle. Then, cut approximately 8/10 of the way around the bottle. DO NOT cut all the way around. You want to be able to fold the top of the bottle back as you fill the bottle with soil and water.
  2. NOTE: Your teacher may have bottles already cut for you.
  3. Test the soil for N-P-K nutrients (optional)
  4. Put the soil and sugar water into the bottle in increments:
    • Fill the bottles approximately 1/3 to the top, add 20 ml of water and then gently tap the bottle on the counter several times to compact the soil.
    • Repeat the above. Add more soil to 2/3 full and add 20 ml of sugar water and tap to compact.
    • Fill bottle with soil up to the cut rim. Add 20 ml of sugar water and tap.
  5. Close and seal the bottle cut with duct tape. Add more soil through the mouth of the bottle to bring the level of soil up to 1 cm below the mouth of the bottle where the rubber stopper will go. Add 10 more ml of sugar water.

  6. Insert the #4 one-hole stopper gas delivery apparatus into the bottle top. Insert the tubing into the collecting vessel that contains 50 ml of limewater. Make sure the end of the tubing is in the limewater.
  7. Use the aluminum foil to cover the collecting vessel and wrap tightly to make sure no water from the lime water can evaporate and that no CO2from the surrounding air can get into the limewater.
  8. Put your bottle, soil and limewater set-up under the different temperature conditions your class has identified.
  9. Use a Celsius thermometer to take the ambient temperature for each different temperature condition.
  10. Observe over the next 2-3 days. Look for tiny "flakes" of white, chalky calcium carbonate and/or cloudiness forming in the limewater. NOTE: Because you are doing this as a class, you should stop all observations at the same time.
  11. Record your results in your lab notebook if your teacher requires you to keep one.
  12. Answer the discussion questions below.

NOTE: While you are waiting for results from your experiment, read the section at the bottom of this page then move on to Lab 5B to learn about permafrost, a frozen soil that is starting to thaw.


As a class, share and discuss the results of the experiment:

  • Describe any differences you observed in the limewater as soil was exposed to different temperatures.
  • What evidence from your experiment, if any, supports a causal (causal and effect) relationship between changes in temperature and changes in soil respiration rates?
  • How did the experimental controls you designed inform your analysis of your results?
  • What evidence from your experiment, if any, supports or refutes the claim that a warming climate could cause changes (increase or decrease) in the rates of soil respiration?
  • Explain how soil carbon can regulate climate.

Soil carbon cowboys are putting carbon back into the soil where it belongs

The Keeling Curve graph on the right tells us that the amount of CO2in the atmosphere continues to increase from fossil fuel emissions. But, wouldn't it be great if we could use plants to take some of that excess CO2out of the atmosphere and store the carbon away in soil humus?

Could soils be a viable solution to mitigating climate change? To find out, watch the two videos below.

As you watch the videos, make note of the following:

  • the causes of soil carbon loss over time
  • the strategies to put carbon back into the soil
  • the multiple benefits of building healthy carbon-rich soil

NOTE: This video is also available on Vimeo: Soil Solutions to Climate Problems - Narrated by Michael Pollan on Vimeo

NOTE: This video is available without Spanish subtitles here: SOIL CARBON COWBOYS on Vimeo


  • With a partner or your class, discuss how the following strategies would increase carbon in soil and protect crops against drought:
    • rotating cattle grazing instead of grazing in one large field all season
    • planting a cover crop instead of letting fields lie bare
    • using polyculture instead of monoculture
    • creating natural fertilizer instead of using artificial fertilizer (N-P-K)
  • What could you do store carbon in soil in your community or in your own back yard?

Optional Extensions

Want to learn more about soil carbon? Check out the following resources: