The organic carbon that forms the biological pump is transported primarily by sinking particulate material, for example dead organisms (including algal mats) or faecal pellets. However, some carbon reaches the deep ocean as dissolved organic carbon (DOC) by physical transport processes such as downwelling rather than sinking.
Carbon reaching the deep ocean by these means is either organic carbon or particulate inorganic carbon such as calcium carbonate (CaCO3). The former is a component of all organisms, the latter only of calcifying organisms, for example coccolithophores, foraminiferans or pteropods. In reference to the different use of these materials in organisms, the organic carbon portion of this transport is known as the soft tissues pump, while the inorganic carbon portion is known as the hard tissues pump.
In the case of organic material, remineralisation (or decomposition) processes such as bacterial respiration, return the organic carbon to dissolved carbon dioxide. Calcium carbonate dissolves at a rate dependent upon local carbonate chemistry. As these processes are generally slower than synthesis processes, and because the particulate material is sinking, the biological pump transports material from the surface of the ocean to its depths.
As the biological pump plays an important role in the Earth's carbon cycle, significant effort is spent quantifying its strength. However, because they occur as a result of poorly-constrained ecological interactions usually at depth, the processes that form the biological pump are difficult to measure. A common method is to estimate primary production fuelled by nitrate and ammonium as these nutrients have different sources that are related to the remineralisation of sinking material. From these it is possible to derive the so-called f-ratio, a proxy for the local strength of the biological pump. Applying the results of local studies to the global scale are complicated by the role the ocean's circulation plays in different ocean regions.
Anthropogenic changes 
Changes in land use, the combustion of fossil fuels, and the production of cement have led to an increase in CO2 concentration in the atmosphere. At present, about one third (approximately 2 Gt C y−1)[clarification needed]  of anthropogenic emissions of CO2 are believed to be entering the ocean. However, the biological pump is not believed to play a significant role in the elevation in CO2. This is because the biological pump is primarily limited by the availability of light and nutrients, and not by carbon. This is in contrast to the situation on land, where elevated atmospheric concentrations of CO2 may increase primary production because land plants are able to improve their water-use efficiency (= decrease transpiration) when CO2 is easier to obtain. However, there are still considerable uncertainties in the marine carbon cycle, and some research suggests that a link between elevated CO2 and marine primary production exists.
However, climate change may affect the biological pump in the future by warming and stratifying the surface ocean. It is believed that this could decrease the supply of nutrients to the euphotic zone, reducing primary production there. Also, changes in the ecological success of calcifying organisms caused by ocean acidification may affect the biological pump by altering the strength of the hard tissues pump. This may then have a "knock-on" effect on the soft tissues pump because calcium carbonate acts to ballast sinking organic material.
See also 
- Marinov, I.; Gnanadesikan, A., Toggweiler, J. R. and Sarmiento, J. L. (2006). "The Southern Ocean biogeochemical divide". Nature 441 (7096): 964–967. doi:10.1038/nature04883. PMID 16791191.
- Raven, J. A.; and P. G. Falkowski (1999). "Oceanic sinks for atmospheric CO2". Plant, Cell and Environment 22 (6): 741–755. doi:10.1046/j.1365-3040.1999.00419.x.
- Takahashi, T., S. C. Sutherland, C. Sweeney, A. Poisson, N. Metzl, B. Tilbrook, N. Bates, R. Wanninkhof, R. A. Feely, C. Sabine, J. Olafsson and Y. C. Nojiri (2002) Global sea-air CO2 flux based on climatological surface ocean pCO2, and seasonal biological and temperature effects. Deep-Sea Res. Pt. II 49, 1601-1622.
- Orr, J. C., E. Maier-Reimer, U. Mikolajewicz, P. Monfray, J. L. Sarmiento, J. R. Toggweiler, N. K. Taylor, J. Palmer, N. Gruber, C. L. Sabine, C. Le Quéré, R. M. Key and J. Boutin (2001). Estimates of anthropogenic carbon uptake from four three-dimensional global ocean models. Global Biogeochem. Cycles 15, 43-60.
- Cox, P. M., Betts, R. A., Jones, C. D., Spall, S. A. and Totterdell, I. J. (2000). Acceleration of global warming due to carbon-cycle feedbacks in a coupled climate model. Nature, 408, 184-187.
- Riebesell, U., Schulz, K.G., Bellerby, R.G.J., Botros, M., Fritsche, P., Meyerhöfer, M., Neill, C., Nondal, G., Oschlies, A., Wohlers, J. and Zöllner, E. (2007). Enhanced biological carbon consumption in a high CO2 ocean. Nature 450, 545-548.
- Orr, J. C. et al. (2005). Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437, 681-686.
- Armstrong, R.A., Lee, C., Hedges, J.I., Honjo, S. and Wakeham, S.G. (2002). A new, mechanistic model for organic carbon fluxes in the ocean: Based on the quantitative association of POC with ballast minerals. Deep Sea Res. Part II 49, 219—236.