Aggregation of Thalassiosira weissflogii as a function of pCO2, temperature and bacteria - Aggregation Phase - Sinking Velocity from a from 2009 to 2010 (OA - Ocean Acidification and Aggregation project)

Version: 05 September 2013
Version Date: 2013-09-05

» Will Ocean Acidification Diminish Particle Aggregation and Mineral Scavenging, Thus Weakening the Biological Pump? (OA - Ocean Acidification and Aggregation)

» Ocean Carbon and Biogeochemistry (OCB)
» Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)
Passow, UtaUniversity of California-Santa Barbara (UCSB-MSI)Principal Investigator, Contact
Seebah, ShalinUniversity of California-Santa Barbara (UCSB-MSI)Student
Gegg, Stephen R.Woods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Dataset Description

Series 4: Aggregation of Thalassiosira weissflogii as a function of pCO2, temperature and bacteria: Aggregation Phase - Sinking Velocity

Related Reference:
Aggregation and Sedimentation of Thalassiosira weissflogii (diatom) in a Warmer and More Acidified Future Ocean

Acquisition Description

Processing Description

See: Series 4: Aggregation of Thalassiosira weissflogii - Methods

BCO-DMO Processing Notes
Original file: "BCODMO_Shalin Data.xlsx" contributed by Uta Passow
Sheet: "Agg.-SinkingVelocity"
- Approx Lat/Lon of Passow Lab appended to enable data discovery in MapServer
- "nd" (no data) inserted into blank cells
- "NV" contributed identifier for no value converted to BCO-DMO standard of "nd" (no data)
- Parameter names edited to conform to BCO-DMO naming convention found at Choosing Parameter Name

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Lab_IdLab Id – Lab identifier where experiments were conducted text
LatApproximate Latitude Position of Lab; South is negative decimal degrees
LonApproximate Longitude Position of Lab; West is negative decimal degrees
TempTemperature degrees C
pCO2pCO2 conditions text
HP15_additionHP15 Addition text
sampling_pointSampling Point hrs
fractionFraction text
agg_num_per_tankAggregate Number per Tank count/tank
ESDEquivalent Spherical Diameter mm
VelocityAggregate sinking velocity meters/day

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Dataset-specific Instrument Name
Inverted Axiovert 200 Microscope
Generic Instrument Name
Inverted Microscope
Dataset-specific Description
Diatom cell abundance was monitored daily by counting cells in a Sedgwick-Rafter Cell S50 (SPI Supplies, West Chester, PA, USA) using an inverted Axiovert 200 microscope (Zeiss, Jena, Germany).
Generic Instrument Description
An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana). Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives. The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.

Dataset-specific Instrument Name
Sedgwick-Rafter Cell S50
Generic Instrument Name
Dataset-specific Description
Diatom cell abundance was monitored daily by counting cells in a Sedgwick-Rafter Cell S50 (SPI Supplies, West Chester, PA, USA) using an inverted Axiovert 200 microscope (Zeiss, Jena, Germany).
Generic Instrument Description
A hemocytometer is a small glass chamber, resembling a thick microscope slide, used for determining the number of cells per unit volume of a suspension. Originally used for performing blood cell counts, a hemocytometer can be used to count a variety of cell types in the laboratory. Also spelled as "haemocytometer". Description from:

Dataset-specific Instrument Name
Generic Instrument Name
Dataset-specific Description
The pH (total scale) was measured with a spectrophotometer using the indicator dye m-cresol purple (Sigma-Aldrich) within 1-2 hours of sampling at 25 oC (Clayton and Byrne 1993).
Generic Instrument Description
An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Dataset-specific Instrument Name
dissecting microscope
Generic Instrument Name
Microscope - Optical
Dataset-specific Description
The dimensions of the aggregate axes (x, y, and z direction) were measured under a dissecting microscope, and the aggregated volume calculated assuming an ellipsoid shape.
Generic Instrument Description
Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

Dataset-specific Instrument Name
Roller Tank
Generic Instrument Name
Roller Tank
Dataset-specific Description
During this acclimatization phase diatoms were kept in the exponential growth by regular dilutions. The diatom was grown in artificial seawater (Kester et al. 1967), the bacteria in marine broth prepared with ASW. After the acclimatization, aggregation experiments were conducted in duplicates in roller tanks in darkness. Replicate roller tanks were set-up with diatom cells at a final concentration of 3 x 103 cells ml-1 and – where appropriate - bacteria at a final concentration of 3 x 105 cells ml-1.
Generic Instrument Description
Rolling tanks, which keep particles in suspension, thus simulating aggregate formation in situ. Marine snow experiments are conducted in roller tanks, which turn continuously, keeping marine snow in suspension. It is important for marine snow not to touch surfaces. The rolling tanks, which keep particles in suspension, thus simulate aggregate formation in situ. Marine snow formation due to different types of oil was tested. Some treatments are easily identifiable as containing oil by their color (middle). UCSB, CA 2012.

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Start Date
End Date
Results form a series of controlled laboratory experiments investigating the effect of altered carbonate system chemistry on the abiotic formation of TEP

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Project Information

Will Ocean Acidification Diminish Particle Aggregation and Mineral Scavenging, Thus Weakening the Biological Pump? (OA - Ocean Acidification and Aggregation)

Coverage: Passow Lab, Marine Science Institute, University of California Santa Barbara

Will Ocean Acidification Diminish Particle Aggregation and Mineral Scavenging, Thus Weakening the Biological Pump?

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

The pH of the ocean is predicted to decrease by 0.2-0.5 pH units in the next 50 to100 years as a result of increasing atmospheric CO2. To date almost all the research on impending ocean acidification has focused on the impacts to calcifying organisms and the carbonate system. However, ocean acidification will also affect other significant marine processes that are pH dependent.

In this project, researchers at the University of California at Santa Barbara will investigate the impact of ocean acidification on the organic carbon or 'soft tissue' biological pump. They predict that a decline in oceanic pH will result in an increase in the protonation of negatively charged substances, especially of Transparent Exopolymer Particles (TEP), the gel-like particles that provide the matrix of aggregates and bind particles together. A decreased polarity of these highly surface-active particles may reduce their "stickiness" resulting in decreased aggregation of organic-rich particles and a decreased ability of aggregates to scavenge and retain heavy ballast minerals. A reduction in aggregation will lower the fraction of POC enclosed in fast-sinking aggregates. Decreased scavenging of minerals by aggregates will result in reduced sinking velocities and consequently a decline in the fraction of material escaping degradation in the water column. Both processes ultimately reduce carbon flux to depth. The resulting weakening of the biological pump will alter pelagic ecology and potentially produce a positive feed-back pathway that further increases atmospheric CO2 concentrations.

The research team will experimentally investigate TEP-production, aggregation rates and aggregate characteristics, mineral scavenging and sinking velocity as a function of ocean acidification, because these parameters are susceptible to pH and central in determining sedimentation rate of organic carbon. They will determine potential changes in the abiotic formation of TEP or in the release rate of TEP or TEP-precursors by phytoplankton that have been adapted to increased CO2 regimes for multiple generations, up to 1000 doublings. Additionally, they will experimentally test potential changes in the aggregation rate of adapted phytoplankton and natural particles, and measure impacts on scavenging rates of ballast minerals by aggregates. Effects of various acidification levels on aggregate characteristics, including size, composition, density, and sinking velocity will also be determined. These results are expected to provide parameterization for a predictive model that will be used to investigate the impact of changing ballasting or aggregation on carbon flux.

Broader impact: Climate and environmental change are a global challenge to society. We need to know if possible positive feed back mechanisms to the biological pump will further increase atmospheric CO2 in order to prepare for and hopefully manage future climate changes.

These data are also available at Pangea

Passow U (2012) The Abiotic Formation of Tep under Ocean Acidification Scenarios. Marine Chemistry 128-129:72-80

Bathmann U, Passow U. "Global Erwaermung. Kohlenstoffpumpen im Ozean steuern das Klima.," Biologie in unserer Zeit 5, v.5, 2010.

Benner I, Passow U. "Utilization of organic nutrients by coccolithophores," Marine Ecology Progress Series, v.404, 2010, p. 21.

Feng Y, Hare C, Leblanc K, Rose J, Zhang Y, DiTullio G, Lee P, Wilhelm S, Rowe J, Sun J, Nemcek N, Gueguen C, Passow U, Benner I, Brown C, Hutchins D. "Effects of increased pCO2 and temperature on the North Atlantic spring bloom. I. The phytoplankton community and biogeochemical response," Marine Ecology Progress Series, v.388, 2009, p. 13.

Gaerdes A, Iversen MH, Grossart H-P, Passow U, Ullrich M. "Diatom associated bacteria are required for aggregation of Thalassiosira weissflogii.," ISME Journal, 2010, p. 1.

Leblanc K, Hare CE, Feng Y, Berg GM, DiTullio GR, Neeley A, Benner I, Sprengel C, Beck A, Sanudo-Wilhelmy SA, Passow U, Klinck K, Rowe JM, Wilhelm SW, Brown CW, Hutchins DA. "Distribution of calcifying and silicifying phytoplankton in relation to environmental and biogeochemical parameters during the late stages of the 2005 North East Atlantic Spring Bloom," Biogeosciences, v.6, 2009, p. 2155.

Ploug H, Terbruggen A, Kaufmann A, Wolf-Gladrow D, Passow U. "A novel method to measure particle sinking velocity in vitro, and its comparison to three other in vitro methods.," Limnolgy and Oceanography Methods, v.8, 2010, p. 386.

Passow, U., Rocha, C.L.D.L., Fairfield, C., Schmidt, K., 2014. Aggregation as a function of pCO2 and mineral particles. Limnology and Oceanography 59 (2), 532-547.

De La Rocha, C.L., Passow, U., 2014. The biological pump. In: Turekian, K.K., Holland, H.D. (Eds.), Treatise on Geochemistry. Elsevier, Oxford, pp. 93-122.

Boyd, P., Rynearson, T., Armstrong, E., Fu, F., Hayashi, K., Hu, Z., Hutchins, D., Kudela, R., Litchman, E., Mulholland, M., Passow, U., Strzepek, R., Whittaker, K., Yu, E., Thomas, M., 2013. Marine Phytoplankton Temperature versus Growth Responses from Polar to Tropical Waters - Outcome of a Scientific Community-Wide Study. PLoS ONE 8 (5), e63091.

Passow, U., Carlson, C., 2012. The Biological Pump in a High CO2 World. Marine Ecology Progress Series 470, 249-271.

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Program Information

Ocean Carbon and Biogeochemistry (OCB)

Coverage: Global

The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.

The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.

The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.

The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.

Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)

Coverage: global

NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (

In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.

Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.

PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)

NSF media releases for the Ocean Acidification Program:

Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification

Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?

Discovery - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)

Press Release 12-179 - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)

Press Release 13-102 World Oceans Month Brings Mixed News for Oysters

Press Release 13-108 - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)

Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants

Press Release 13-148 - Video - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)

Press Release 14-010 - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)

Press Release 14-116 - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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