Biological Pump

Katherine Heal


This module is an introduction to the marine biological pump and uses representative organisms to demonstrate the interconnectivity between the biosphere and the global carbon cycle.  Created by Katherine Heal while she was a graduate student in Oceanography at UW, this module complements other labs created by the UW PCC team as part of a year long high school climate science curriculum.  May be readily used in non-major college courses that build on student knowledge of food webs to gain understanding of the carbon cycle.

Grade level: 9-12

Focus Questions

  • How are photosynthesis and respiration related to the global carbon cycle?
  • How does the biological pump work to maintain the oceanic carbon reservoir?
  • What controls the biological pump?

Learning Goals:

  1. To relate the ocean’s primary producers to terrestrial plants as and acting as consumers of CO2
  2. To be introduced to a variety of globally important marine organisms
  3. To understand how the biology of the ocean is important in the global carbon cycle
  4. To understand why phytoplankton growth is limited in some areas of the ocean
  5. To appreciate the ecological balance of a few different organisms contributing to the upkeep of the biological pump

Background Information for Teachers

What is the biological pump? As we know, photosynthesis consumes CO2 while respiration produces it. In the ocean, these two processes can be spatially separated. Net photosynthesis occurs in the sunlit (upper) portion of the ocean, while net respiration occurs deeper. As CO2 dissolves in the ocean, it becomes available to phytoplankton that fix it into organic carbon (photosynthesis), or used to form calcium carbonate shells (CaCO3). Some of this organic carbon (in the form of biological matter) sinks and is consumed (respiration) or dissolves (in the case of CaCO3 shells) in the deeper ocean. Because the deeper ocean does not come in contact with the atmosphere very often, it traps the carbon in the deeper ocean, creating a large reservoir of carbon. The biological pump is thought to be bottom-up limited, meaning that the ocean would be able to act as a larger sink for CO2 if there were more phytoplankton growth. In this way, the marine biological pump is closely related to other biogeochemical cycles, especially nitrogen, phosphorus, and iron which make up the main nutrients needed by phytoplankton to grown.

Prior Knowledge for Students

Students should be familiar with the importance of CO2 as a greenhouse gas and be introduced to different global carbon reservoirs. Students have been introduced to photosynthesis and respiration as important biologically important mechanisms, but may have not yet related this to the marine carbon cycle, except as an aspect of short-term variability. Introduction to the solubility of CO2 in the oceans would be helpful before this module, but not necessary.


  • Projector and screen
  • Introductory presentation – can be edited (.pptx)
  • Suggested readings from:
    • The Earth System (3rd Edition) (Kump et al.)

  • Other reference books on marine biology or biology of microorganisms
  • Access to reference articles
  • Whiteboard/chalkboard with colored markers/chalk or projector and screen
  • Template for Facebook profiles (Teacher needs to create)



It may be helpful to assign pages 154-159 as reading from Kump et al. before this module.

Write the equations for photosynthesis and respiration on a whiteboard so the students may refer back as necessary during the powerpoint presentation. It would also be helpful to provide the slides to the students to follow along and take notes. The key words provided here are important for students to know to understand the slides. They are introduced and defined on the indicated slides.

Keywords mentioned on slides:

  • Photosynthesis – slide 2
  • Respiration – slide 2
  • Phytoplankton – Slide 6
  • Zooplankton – slide 10
  • Filter Feeders – slide 10
  • Decomposition – slide 12
  • Nutrient Limitation – slide 19
  • Nitrogen Fixation – slide 20

The following are notes for the instructors to accompany the provided slides:

  • Photosynthesis and Respiration – The presentation begins with a review of photosynthesis and respiration as chemical formulas. It is not important for students to memorize these, but to know which is a sink and which is a source for CO2.
  • Photosynthesis and Respiration and atmospheric CO2 – On the second slide of the Keeling curve, probe the students to identify how photosynthesis and respiration affect the Keeling curve (the short term variations). This is an example of how seasonal differences in photosynthesis and respiration can change atmospheric CO2.
  • The ocean is a large carbon reservoir – The ocean is a large and important carbon reservoir. Only the upper ocean is in equilibrium with the atmosphere (exchanging carbon), but the deep ocean holds much more carbon than both the upper ocean and the atmosphere. Remember that the deep ocean only comes in contact with the atmosphere every 1000 years and that the upper ocean is usually considered only the top 100 m while the deep ocean can be over 4000 m deep.
  • Photosynthesis and Respiration in the Ocean – Much like land plants and animals, there are many organisms that photosynthesize and respire in the ocean – in fact, a huge amount of the global fixation of carbon takes place in the ocean!
  • The following slides are taken from MBARI’s lesson plans for introducing the biological pump. They go through the steps of the biological pump .
  • Overview of the Biological Pump (slide 19) – Each of the organisms mentioned in the previous slides are here, but in a better representation. We will be coming back to this figure in Part III, so make sure that the students are very familiar with it. Also, this figure shows how this system is balanced by upwelling. Stress that the pump is not a sink for carbon, but rather just a mechanism that maintains the large carbon reservoir in the deep ocean.
  • What limits phytoplankton growth? – This slide presents a question that is the topic of many oceanographers research. It also gives one commonly accepted school of thought that most of phytoplankton growth is limited by nutrients. Part III of this module deals with the complexity of nutrient limitation and how it is connected to the biological pump in further detail.
  • Sources of N, P, and Fe – This slide is a super quick overview of the sources of the major limiting nutrients in the ocean. It is important to emphasize that

A good reading that could be inserted here for homework or class discussion is the recent review article by Falkowski called “The Power of Plankton.” 2012. Nature. 483, S17-S20.

Group Presentations:

In this lab, groups of students will put together a short presentation and Facebook profile page on a different marine organism. Groups of 2-4 would work well for this. Use all of the first 5 organisms, and if there is a larger class, use the optional additions.

Each of these organisms represents an important part of the biological pump. The teacher is not expected to be an expert on any of these organisms, so it is up to the groups of students to introduce the organisms to the class by presenting their own research. The will include an internet search (good websites to start at are provided in the student handout), using textbooks (a list of texts that can be used is provided and could be rented from a local university library), and one provided piece of primary literature or relevant review article.

Assign groups of 3-4 an organism and provide them with the appropriate primary literature article and the student handout (both provided). Each of these organisms is important and unique, so below is a very brief description of each of the organism. I suggest that after the groups have broken off and started the research, that the teacher visit each group and prompt the group to make sure that they understand the important information they should be conveying by using these talking points. The teacher should also be available as a resource for where to start looking (see provided list of appropriate resources), but it should be stressed that the students are to become the experts. Many of these articles will be vocabulary- heavy so use the glossaries in the books listed to help students understand the vocabulary. Important terms that students should introduce to the class within each organism group are listed below.


Your assignment is to become an expert on a globally important marine organism. You will use the provided resources to answer the following questions about your organism. You will then make and present a Powerpoint presentation that will answer these questions and provide background on your organism for your peers. Finally, you will create a Facebook profile for your organism for distribution that will synthesize what you have learned about your organism. Use the provided template for your Facebook page, but feel free to get creative. If you want to add a category or something doesn’t make sense with your organism, change the template, not all organisms are created equal! Remember to cite your sources.

Questions to address in Presentation and on Profile:

1. What type of organism is it?

2. What do they look like? How big are they? How common are they?

3. Where are they located in the ocean?

4. What do these organisms eat/need to survive?

5. What are some other important or interesting facts about this organism?

6. How is this organism related to the biological pump?


1. Your teacher will provide a piece of primary literature that will provide answers to many of these questions – remember that these are written by scientists who study these organisms every day so they will probably be very scientific, don’t be discouraged.

2. Your teacher will also have a number of textbooks available for

3. Microbewiki is wiki created for microbes (and their fans) – some of your organisms will have information here


(citations of the primary literature sources are located at the end of the chapter)

  • Prochlorococcus
    • Prochlorococcus is a genus of one of the smallest and most common photosynthetic organisms on earth. Prochlorococcus dominate in nutrient-poor regions of the ocean.
    • Keywords: cyanobacteria, picoplankton, oligotrophic
    • Primary literature: pages 116-120 of “Prochlorococcus, a Marine Photosynthetic Prokaryote of Global Significance” by Partensky Hess and Vaulot, in Microbiology and Molecular Biology Reviews, 1999.
  • Thalassiosira
    • Thalassiosira is a genus of important photosynthetic eukaryotes called Diatoms. Diatoms dominate in nutrient-rich areas of the ocean, but in addition to the N, P, and iron requirements, also require silica to make beautiful shells. Due to their rather large size, diatoms sink quickly and are often cited as important to the flux of the biological pump.
    • Keywords: diatom, frustule
    • Primary literature: “The life of diatoms in the world’s oceans” by Armbrust in Nature, 2009.
  •  Trichodesmium
    • Trichodesmium is a genus of cyanobacteria that can perform nitrogen fixation and photosynthesis. This provides an essential nutrient to areas of the ocean that otherwise have very little nitrogen. They have very high iron requirements.
    • Keywords: Nitrogen fixation, diazotroph, colonial cyanobacteria
    • Primary literature: “Trichodesmium, a Globally Significant Marine Cyanobacterium” by Capone, Zehr, Paerl, Bergman, and Carpenter in Science, 1997
    • Optional 2nd primary literature: “Marine nitrogen fixation: what’s the fuss?” by Capone in Current Opinion in Microbiology, 2001.
  • Planktonic Copepods
    • Copepods are important zooplankton and voracious grazers of phytoplankton. Their fecal matter is especially dense and significantly contributes to sinking particles. Vertical migration also contributes to the biological pump.
    • Keywords: zooplankton, vertical migration
    • Primary literature: pages 55-58 of “Upper Ocean Carbon Export and the Biological Pump” by Ducklow, Steinberg, and Buessler in Oceanography, 2001
  •  Pelagibacter
    • Pelagibacter is a genus of the globally important heterotrophic bacteria in the SAR11 clade. The SAR11 clade of organisms were not known until very recently, and they might be the most numerous bacteria on earth! They can thrive in low-nutrient waters and are important recyclers of organic carbon
    • Keywords: heterotrophic bacteria, mesopelagic
    • Primary literature: “SAR11 clade dominates ocean surface bacterioplankton communities” by Morris, Rappe, Connon, Vergin, Siebold, Carlson and Giovannoni in Nature, 2002.
  •  Optional – Emiliania huxleyi
    • Emiliania huxleyi is a species of important algae, coccolithophores. Emiliania huxleyi are calcifiers and can form huge blooms in the oceans and therefore cause large carbon export events.
    • Keywords: phytoplankton bloom, calcifiers
    • Primary literature: “Emiliania huxleyi: bloom observations and the conditions that induce them.” By Toby Tyrrell and Agostino Merico
  • Optional – Roseobacter
    • Roseobacter is a genus of heterotrophic bacteria in the ocean and our example of very important particle associated bacteria.
    • Keywords: heterotrophic bacteria, marine snow, particle associated
    • Primary literature: “Possible Quorum Sensing in Marine Snow Bacteria: Production of Acylated Homoserine Lactones by Roseobacter Strains Isolated from Marine Snow” by Gram, Grossart, Schlingloff, and Kiørboe in Applied and Environmental Microbiology 2002.
  •  Optional – Planktonic Salps
    • Salps are zooplankton that filter feed on phytoplankton (and whatever else may be in its path). They respond very quickly to blooms and their death result in a sticky substance which can sink, significantly contributing to marine snow.
    • Keywords: filter feeder, marine snow
    • Primary literature: pages 55-58 of “Upper Ocean Carbon Export and the Biological Pump” by Ducklow, Steinberg, and Buessler in Oceanography, 2001

After an appropriate amount of time working on the presentations, students should present each organism as a group and handing out their Facebook page as a resource for the other students. Each student will end up with a packet of Facebook pages for each organism and can take notes on these.v

Class Synthesis:

The final part of this module is to have a class discussion about the interconnectivity of their organisms and to understand how each of the groups’ organisms fit into the biological pump by connecting them in a “carbon web.” This idea will be familiar to the students who have made food webs in introductory biology courses. The figure is based on the figure from Part I on the final overview of the biological pump slide, from Z. Johnson in the Nature Magazine.

First I would encourage each group to come up with a simple way to draw each of the organisms and to define each drawing on the board. Having different colors would be helpful (little green = Prochlorococcus, little blue = heterotrophic bacteria). As you go farther along, define other symbols (flow of carbon, sinking organic material).

Encourage students to use colored pencils or different colored pens and provide blank sheets of paper to take notes and create their own drawing. The provided slides goes through these steps as well.

Draw on the board a schematic of the ocean with the surface ocean, deep ocean, and seafloor. Stress that only CO2 in the surface ocean is in equilibrium to the atmosphere. Probe the class to identify which of the presented species are phytoplankton. Add the phytoplankton – Prochlorococcus, Thalassiosira, Trichodesmium, and Emiliania huxleyi – to the surface ocean. They live only in the surface ocean because they require light to survive.

Next add grazers to the surface ocean (those who eat phytoplankton, copepods and salps). They are in the surface ocean because their food (phytoplankton) are in the surface ocean.

Now add sinking organic material throughout the water column. Brainstorm different sources of sinking organic material in this small system.

  • Fecal pellets from grazers
  • Death of a large phytoplankton bloom
  • Dead grazers
  • “Messy” feeding by grazers resulting in sinking “crumbs” of their food

Add heterotrophic bacteria to surface and deep ocean. Roseobacter should be particle associated, pelagiabacter can be on or off particles.

Add direction of CO2 to or from each depicted organism/group of organisms. Which are the organisms that respire (give off carbon) and which are the ones that photosynthesize (consume carbon)? Overall, you should have net photosynthesis in the upper ocean and net respiration in the deep ocean.

Quantifying the biological pump is an active area of research in oceanography. Probe the students to understand why. Why is the biological pump important? Pumps CO2 from the surface ocean to the deep ocean

  • Why is the biological pump important?
    • Pumps CO2 from the surface ocean to the deep ocean
  •  Would the atmospheric CO2 be different if the biological pump didn’t exist?
    • Yes!!!!! The CO2 of the atmosphere would be much higher than current if there was no biological pump.
  • How does the biological pump affect climate?
    • Lowers atmospheric CO2 and therefore decreases the greenhouse gas effect.

Using our small-system example of organisms, discuss the interconnectivity of the different organisms

  • What limits the growth of each type of phytoplankton?
    • Tricho – generally thought to be iron or phosphorus limited since it can fix its own nitrogen
    • Thaps – could be limited by N, P, Fe or Si (to grow shells)
    • Prochlorococcus – could be limited by N, P, Fe (but can survive at much lower concentrations than other phytoplankton), can’t survive well in cold environments
    • Ehux – could be limited by N, P, or Fe, doesn’t survive well in warm environments What limits the growth of the grazers?
  • Both copepods and salps are limited by their food source, phytoplankton (and oxygen) What limits the growth of the heterotrophic bacteria?
    • Both types of heterotrophic bacteria are limited by their food supply, decaying organic matter (and oxygen )
  • What if there were no phytoplankton? What would happen to this food web and the biological pump of our system?
    • It would collapse! No phytoplankton = no food for grazers = no food for heterotrophs = no biological pump!!
  •  What if there were no grazers? What would happen to this food web and the biological pump of our system?
    • No grazers = much less respiration in the upper ocean. Bacteria would only feed on decaying phytoplankton material and no fecal matter. This would lead to a much more efficient biological pump, less atmospheric CO2, cooler planet!
  • What if one or more species/groups of species were affected by a viral attack?
    • Depending on the species/group of species affected, this could increase or decrease the biological pump’s strength.

A lot of research is being put into predicting how the biological pump will change with global climate change. Discuss possible scenarios of both ocean acidification and increased stratification and how they could change the biological pump. Please note that there really is no consensus on this yet scientifically as there are many.

  • Ocean Acidification
    • Could affect the ability for coccoliths to grow and affect blooms, decreasing strength of bio pump (because they grow calcium carbonate shells)
    • Could affect nitrogen fixation by Trichodesmium (quite a bit of literature on this)– increasing N2 fixation could increase the strength of the biological pump, decreasing N2 fixation could decrease the strength of the biological pump.
    • Could have physiological effects on higher trophic levels
  • Increased stratification leading to less mixing nutrients
    • Especially affecting diatoms (who thrive in nutrient-rich areas and require the extra nutrient of silica), could decrease bio pump
    • Overall the phytoplankton would be under nutrient limitation more than now – decreasing the biological pump

If students have other ideas of what could change the biological pump – open the floor to them.

Primary Literature Sources

Armbrust, E. The life of diatoms in the world’s oceans. Nature 459, 185–192 (2009).

Capone, D. G. (2001). Marine nitrogen fixation: what’s the fuss? Current Opinion in Microbiology, 4(3), 341–348.

Capone, D. G. (1997). Trichodesmium, a Globally Significant Marine Cyanobacterium. Science, 276(5316), 1221–1229.

Ducklow, H., Steinberg, D., & Buesseler, K. (2001). Upper Ocean Carbon Export and the Biological Pump. Oceanography, 14(4), 50–58.

Falkowski, P. Ocean Science: The power of plankton. Nature 483, S17–S20 (2012).

Gram, L., Grossart, H.-P., Schlingloff, A., & Kiørboe, T. (2002). Possible Quorum Sensing in Marine Snow Bacteria: Production of Acylated Homoserine Lactones by Roseobacter Strains Isolated from Marine Snow. Applied and Environmental Microbiology, 68(8), 4111–4116.

Morris, R., Rappé, M., Connon, S. et al. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420, 806–810 (2002).

Partensky, F., Hess, W. R., & Vaulot, D. (1999). Prochlorococcus, a Marine Photosynthetic Prokaryote of Global Significance. Microbiology and Molecular Biology Reviews, 63(1), 106–127.

Tyrrell, T., & Merico, A. (2004). Emiliania huxleyi: bloom observations and the conditions that induce them. In Coccolithophores (pp. 75–97). Springer Berlin Heidelberg.

Attribution:  Heal, Katherine. “Biological Pump” Climate Science for the Classroom edited by Bertram and Biyani, 2020. Date of Access.



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