Oceanography The Official Magazine of
The Oceanography Society
Volume 27 Issue 03

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Volume 27, No. 3
Pages 10 - 16


COMMENTARY • Understanding the Role of the Biological Pump in the Global Carbon Cycle: An Imperative for Ocean Science

By Susumu Honjo , Timothy I. Eglinton , Craig D. Taylor , Kevin M. Ulmer, Stefan M. Sievert , Astrid Bracher, Christopher R. German , Virginia Edgcomb , Roger Francois, M. Debora Iglesias-Rodriguez , Benjamin Van Mooy , and Daniel J. Repeta  
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First Paragraph

Anthropogenically driven climate change will rapidly become Earth’s dominant transformative influence in the coming decades. The oceanic biological pump—the complex suite of processes that results in the transfer of particulate and dissolved organic carbon from the surface to the deep ocean—constitutes the main mechanism for removing CO2 from the atmosphere and sequestering carbon at depth on submillennium time scales. Variations in the efficacy of the biological pump and the strength of the deep ocean carbon sink, which is larger than all other bioactive carbon reservoirs, regulate Earth’s climate and have been implicated in past glacial-​interglacial cycles. The numerous biological, chemical, and physical processes involved in the biological pump are inextricably linked and heterogeneous over a wide range of spatial and temporal scales, and they influence virtually the entire ocean ecosystem. Thus, the functioning of the oceanic biological pump is not only relevant to the modulation of Earth’s climate but also constitutes the basis for marine biodiversity and key food resources that support the human population. Our understanding of the biological pump is far from complete. Moreover, how the biological pump and the deep ocean carbon sink will respond to the rapid and ongoing anthropogenic changes to our planet—including warming, acidification, and deoxygenation of ocean waters—remains highly uncertain. To understand and quantify present-day and future changes in biological pump processes requires sustained global observations coupled with extensive modeling studies supported by international scientific coordination and funding.


Honjo, S., T.I. Eglinton, C.D. Taylor, K.M. Ulmer, S.M. Sievert, A. Bracher, C.R. German, V. Edgcomb, R. Francois, M.D. Iglesias-Rodriguez, B. Van Mooy, and D.J. Repeta. 2014. Understanding the role of the biological pump in the global carbon cycle: An imperative for ocean science. Oceanography 27(3):10–16, https://doi.org/10.5670/oceanog.2014.78.

Supplementary Materials

Alldredge, A.L., and J.L. Cox. 1982. Primary productivity and chemical composition of marine snow in surface waters of the Southern California Bight. Journal of Marine Research 30:517–527.

Alldredge, A.L., and M.W. Silver. 1988. Characteristics, dynamics and significance of marine snow. Progress in Oceanography 20:41–82, https://doi.org/10.1016/0079-6611(88)90053-5.

Alvain, S., C. Moulin, Y. Dandonneau, and F.M. Breon. 2005. Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS imagery. Deep Sea Research 52(11):1,989–2,004, https://doi.org/10.1016/j.dsr.2005.06.015.

Angel, M.V., and A. de C. Baker. 1982. Vertical distribution of the standing crop of plankton and micronekton at three stations in the northeast Atlantic. Biological Oceanography 2:1–30.

Antoine, D.M. 1996. Oceanic primary production: Part 1. Adaptation of a spectral light-photosynthesis model in view of application to satellite chlorophyll observations. Global Biogeochemical Cycles 10:43–55, http://dx.doi.org/10.1029/95GB02831.

Arístegui, J., J.M. Gasal, C.M. Duarte, and G.J. Herndl. 2009. Microbial oceanography of the dark ocean’s pelagic realm. Limnology and Oceanography 54(5):1,501–1,529, https://doi.org/10.4319/lo.2009.54.5.1501.

Behrenfeld, M.J., and P.G. Falkowski. 1997. Photosynthetic rates derived from satellite-based chlorophyll concentration. Limnology and Oceanography 42:1–20, https://doi.org/10.4319/lo.1997.42.1.0001.

Berger, W.H. 1989. Global maps of ocean productivity. Pp. 429–455 in Productivity of Oceans, Past and Present. W.H. Berger, V.S. Smetacek, G. Wefer, eds, Dahlem Konferenzen, 1989, Life Science Research Report 44, J. Wiley & Sons, New York.

Bishop, J.K.B. 2009. Autonomous observations of the ocean biological carbon pump. Oceanography 22(2):182–193, https://doi.org/10.5670/oceanog.2009.48.

Bracher, A., M. Vountas, T. Dinter, J.P. Burrows, R. Röttgers, and I. Peeken. 2009. Quantitative observation of cyanobacteria and diatoms from space using PhytoDOAS on SCIAMACHY data. Biogeosciences 6:751-764, https://doi.org/10.5194/bg-6-751-2009.

Buesseler, K.O., C.H. Lamborg, P.W. Boyd, P.L. Lam, T.W. Trull, R.R. Bidigare, J.K.B. Bishop, K.L. Casciotti, F. Dehairs, M. Elskens, and others. 2007. Revisiting carbon flux through the ocean’s “twilight zone.” Science 316:567–570, https://doi.org/10.1126/science.1137959.

Chavez, P.C., M. Messié, and J.T. Pennington. 2011. Marine primary production in relation to climate variability and change. Annual Review of Marine Science 3:227–260, https://doi.org/10.1146/annurev.marine.010908.163917.

Church, M.J., M.W. Lomas, and F. Muller-Karger. 2013. Sea change: Charting the course for biogeochemical ocean time-series research in a new millennium. Deep-Sea Research Part II 93:2–15, https://doi.org/10.1016/j.dsr2.2013.01.035.

Falkowski, P., R.J. Scholes, E. Boyle, J. Canadell, D. Canfield, J. Elser, N. Gruber, K. Hibbard, P. Hogberg, S. Linder, and others. 2000. The global carbon cycles: A test of our knowledge of Earth as a system. Science 290:291–296, https://doi.org/10.1126/science.290.5490.291.

Gowing, M.M., and K.F. Wishner. 1998. Feeding ecology of the copepod Lucicutia aff. L. grandis near the lower interface of the Arabian Sea oxygen minimum zone. Deep Sea Research Part II 45:2,433–2,459, https://doi.org/10.1016/S0967-0645(98)00077-0.

Hansell, D.A., and C.A. Carlson. 2013. Localized refractory dissolved organic carbon sinks in the deep ocean. Global Biogeochemical Cycles 27(3):705–710, https://doi.org/10.1002/gbc.20067.

Honjo, S. 1997. The rain of ocean particles and the Earth’s carbon cycle. Oceanus 40:4–7, https://www.whoi.edu/oceanus/feature/the-rain-of-ocean-particles-and-earths-carbon-cycle.

Honjo, S., S. Manganini, R.A. Krishfield, and R. Francois. 2008. Particulate organic carbon fluxes to the ocean interior and factors controlling the biological pump: A synthesis of global sediment trap programs since 1983. Progress in Oceanography 76:217–285, https://doi.org/10.1016/j.pocean.2007.11.003.

IPCC (Intergovernmental Panel on Climate Change). 2007. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. S. Solomon, D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M. Tignor and H.L. Miller, eds, Cambridge University Press, Cambridge, UK, and New York, USA, 996 pp.

Johnson, K.S., W.M. Berelson, E.S. Boss, Z. Chase, H. Claustre, S.R. Emerson, N. Gruber, A. Körtzinger, M.J. Perry, and S.C. Riser. 2009. Observing biogeochemical cycles at global scales with profiling floats and gliders: Prospects for a global array. Oceanography 22(3):216–225, https://doi.org/10.5670/oceanog.2009.81.

Kallmeyer, J., R. Pockalny, R.R. Adhikari, D.C. Smith, and S.C. D’Hondt. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America 109(40):16,213–16,216, https://doi.org/10.1073/pnas.1203849109.

Kwon, E.Y., F. Primeau, and J.L. Sarmiento. 2009. The impact of remineralization depth on the air–sea carbon balance. Nature Geoscience 2:630–635, https://doi.org/10.1038/NGEO612.

Lauro, F.M., and D.H. Bartlett. 2008. Prokaryotic lifestyles in deep-sea habitats. Extremophiles 12(1):15–25, https://doi.org/10.1007/s00792-006-0059-5.

Levin, L.A., and M. Sibuet. 2012. Understanding continental margin biodiversity: A new imperative. Annual Review of Marine Science 4:79–112, https://doi.org/10.1146/annurev-marine-120709-142714.

Longhurst, A., S. Sathyendranath, T. Platt, and C. Caverhill. 1995. Estimate of global primary production in the ocean from satellite radiometer data. Journal of Plankton Research 17:1,245–1,271, https://doi.org/10.1093/plankt/17.6.1245.

Montes, E., F. Muller-Karger, R. Thunell, R.D. Hollander, Y. Astor, R. Varela, I. Soto, and L. Lorenzoni. 2012. Vertical fluxes of particulate biogenic material through the euphotic and twilight zones in the Cariaco Basin, Venezuela. Deep Sea Research Part I 67:73–84, https://doi.org/10.1016/j.dsr.2012.05.005.

Muller-Karger, F., E. Varela, R.C. Thunell, M.I. Scranton, G.T. Taylor, Y. Astor, C.R. Benitez-Nelson, L. Lorenzoni, K.A. Fanning, E. Tappa, and others. 2010. The Cariaco Basin: The CARIACO Oceanographic Time Series. Pp. 454–463 in Carbon and Nutrient Fluxes in Continental Margins: A Global Synthesis. JGOFS Continental Margins Task Team (CMTT), K.-K. Liu, L. Atkinson, R. Quinones, L. Talaue-McMan, eds, Springer-Verlag, Berlin/Heidelberg.

Siegel, D.A., K.O. Buesseler, S.C. Doney, S.F. Sailley, M.L. Behrenfeld, and P.W. Boyd. 2014. Global assessment of ocean carbon export by combining satellite observations and food-web models. Global Biogeochemical Cycles 28:181–196, https://doi.org/10.1002/2013GB004743.

Sarmiento, J.L. and N. Gruber. 2006. Ocean Biogeochemical Dynamics. Princeton University Press, New Jersey, 503 pp.

Steinberg, D.K., S.A. Goldthwait, and D.A. Hansell. 2002. Zooplankton vertical migration and the active transport of dissolved organic and inorganic nitrogen in the Sargasso Sea. Deep-Sea Research Part I 49:1,445–1,461, https://doi.org/10.1016/S0967-0637(02)00037-7.

Swan, B.K., M. Martinez-Garcia, C. Preston, A. Sczyrba, T. Woyke, D.E. Lamy, D.P. Masland, M.L. Gomez, M.E. Sieracki, E.F. DeLong, and others. 2011. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 33:1,296–1,299, https://doi.org/10.1126/science.1203690.

Taylor, C.D., and B.L. Howes. 1994. Effect of sampling frequency on measurements of primary production and oxygen status in near-shore coastal ecosystems. Marine Ecology Progress Series 108:193–203, http://www.int-res.com/articles/meps/108/m108p193.pdf.

Thunell, R., C. Benitez-Nelson, R. Varela, Y. Aster, and F. Muller-Karger. 2007. Particulate organic carbon fluxes along upwelling-dominated continental margins: Rates and mechanisms. Global Biogeochemical Cycles 21(1):1–12, GB1029, https://doi.org/10.1029/2006GB002793.

Thunell, R.C., R. Varela, M. Llano, J. Collister, F. Muller-Karger, and R. Bohrer. 2000. Organic carbon fluxes, degradation, and accumulation in an anoxic basin: Sediment trap results from the Cariaco Basin. Limnology and Oceanography 45:300–308, https://doi.org/10.4319/lo.2000.45.2.0300.

Tsunogai, S., S. Watanabe, and T. Sato. 1999. Is there a “continental shelf pump” for absorption of atmospheric CO2? Tellus 51B:701–712.

Wefer, G., G. Fischer, D. Füetterer, and R. Gersonde. 1988. Seasonal particle flux in the Bransfield Strait, Antarctica. Deep-Sea Research 35:891–898, https://doi.org/10.1016/0198-0149(88)90066-0.

Whitman, W.B., D.C. Coleman, and W.J. Wiebe. 1998. Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences of the United States of America 95(12):6,578–6,583, http://www.pnas.org/content/95/12/6578.full.

Wunsch, C., R.W. Schmitt, and D.J. Baker. 2013. Climate change as an intergenerational problem. Proceedings of the National Academy of Sciences of the United States of America 110:4,435–4,436, https://doi.org/10.1073/pnas.1302536110.

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