Ocean Carbon & Biogeochemistry
Studying marine ecosystems and biogeochemical cycles in the face of environmental change
  • Home
  • About OCB
    • About Us
    • Scientific Breadth
      • Biological Pump
      • Changing Marine Ecosystems
      • Changing Ocean Chemistry
      • Estuarine and Coastal Carbon Fluxes
      • Ocean Carbon Uptake and Storage
      • Ocean Observatories
    • Code of Conduct
    • Get Involved
    • Project Office
    • Scientific Steering Committee
    • OCB committees
      • Ocean Time-series
      • US Biogeochemical-Argo
      • Ocean-Atmosphere Interaction
  • Activities
    • Summer Workshop
    • OCB Webinars
    • Guidelines for OCB Workshops & Activities
    • Topical Workshops
      • CMIP6 Models Workshop
      • Coastal BGS Obs with Fisheries
      • C-saw extreme events workshop
      • Expansion of BGC-Argo and Profiling Floats
      • Fish, fisheries and carbon
      • Future BioGeoSCAPES program
      • GO-BCG Scoping Workshop
      • Lateral Carbon Flux in Tidal Wetlands
      • Leaky Deltas Workshop – Spring 2025
      • Marine CDR Workshop
      • Ocean Nucleic Acids ‘Omics
      • Pathways Connecting Climate Changes to the Deep Ocean
    • Small Group Activities
      • Aquatic Continuum OCB-NACP Focus Group
      • Arctic-COLORS Data Synthesis
      • BECS Benthic Ecosystem and Carbon Synthesis WG
      • Carbon Isotopes in the Ocean Workshop
      • CMIP6 WG
      • Filling the gaps air–sea carbon fluxes WG
      • Fish Carbon WG
      • Meta-eukomics WG
      • mCDR
      • Metaproteomic Intercomparison
      • Mixotrophs & Mixotrophy WG
      • N-Fixation WG
      • Ocean Carbonate System Intercomparison Forum
      • Ocean Carbon Uptake WG
      • OOI BGC sensor WG
      • Operational Phytoplankton Observations WG
      • Phytoplankton Taxonomy WG
    • Other Workshops
    • Science Planning
      • Coastal CARbon Synthesis (CCARS)
      • North Atlantic-Arctic
    • Ocean Acidification PI Meetings
    • Training Activities
      • PACE Hackweek 2025
      • PACE Hackweek 2024
      • PACE Training Activity 2022
  • Science Support
    • Data management and archival
    • Early Career
    • Funding Sources
    • Jobs & Postdocs
    • Meeting List
    • OCB Topical Websites
      • Ocean Fertilization
      • Trace gases
      • US IIOE-2
    • Outreach & Education
    • Promoting your science
    • Student Opportunities
    • OCB Activity Proposal Solicitations
      • Guidelines for OCB Workshops & Activities
    • Travel Support
  • Publications
    • OCB Workshop Reports
    • Science Planning and Policy
    • Newsletter Archive
  • Science Highlights
  • News

Archive for chlorophyll

Photoacclimation by phytoplankton under clouds

Posted by mmaheigan 
· Thursday, May 29th, 2025 

Unlike most remote sensing products, Net Primary Production (NPP) is computed under clouds. Since satellites can’t see through clouds, NPP models rely on clear-sky observations, interpolate model inputs, and assume that phytoplankton behavior stays the same, regardless of light conditions.

Figure caption: (a) Schematic of the photoacclimation process. In yellow, a standard photoacclimation curve where θ (the chlorophyll to phytoplankton carbon ratio), adjusts as a function of light in the mixed layer (Eg). In blue, the schematic when we do not consider photoacclimation under cloud: Eg is reduced due to cloud-cover, but θ remains the same as it was under cloud, resulting in a strongly reduced μ (a proxy for growth rate). When considering photoacclimation under clouds (red), θ increases because of a reduced Eg, resulting in a μcloudy(photo) > μcloudy(no photo). (b) Histogram of the distribution of θ*Eg (a proxy for growth rate) from BGC-Argo floats separated by whether under cloudy (red) or clear (yellow) skies.

But phytoplankton are known to photoacclimate, adjusting their internal chlorophyll to carbon ratio in response to changes in light. In this study published in GRL we used data from BGC-Argo floats to show that this acclimation occurs consistently under both clear and cloudy skies across the global ocean. Despite reduced light, phytoplankton maintain similar growth rates, suggesting that current estimates of NPP may be biased low when cloud cover is present.

Recognizing and correcting this bias could improve satellite-based NPP estimates, particularly in persistently cloudy regions like the Southern Ocean or eastern boundary upwelling zones. This, in turn, would refine models of the ocean’s biological carbon pump, leading to better projections of CO₂ uptake and export.

 

Authors
Charlotte Begouen Demeaux (Univ Maine)
Emmanuel Boss (Univ Maine)
Jason R. Graf (Oregon State Univ)
Michael J. Behrenfeld (Oregon State Univ)
Toby Westberry (Oregon State Univ)

Using BGC-Argo to obtain depth-resolved net primary production

Posted by mmaheigan 
· Friday, July 23rd, 2021 

Net primary production (NPP)—the organic carbon produced by the phytoplankton minus the organic carbon respired by phytoplankton themselves—serves as a major energy source of the marine ecosystem. Traditional methods for measuring NPP rely on ship-based discrete sampling and bottle incubations (e.g., 14C incubation), which introduce potential artifacts and limit the spatial and temporal data coverage of the global ocean. The global distribution of NPP has been estimated using satellite observations, but the satellite remote sensing approach cannot provide direct information at depth.

Figure 1. Panel A. Trajectories of 5 BGC-Argo and 1 SOS-Argo with the initial float deployment locations denoted by filled symbols. The dash-line at 47° N divided the research area into the northern (temperate) and southern (subtropical) regions. Stars indicate ship stations where 14C NPP values were measured during NAAMES cruises and compared with NPP from nearby Argo floats. Panels B and C. Monthly climatologies of net primary production (NPP, mmol m-3 d-1) profiles in the northern and southern regions of the research area, derived from BGC-Argo measurements using the PPM model. The shadings indicate one standard deviation. The red dotted line indicates mixed layer depth (MLD, m), and the yellow dashed line shows euphotic depth (Z1%, m).

To fill this niche, a recent study in Journal of Geophysical Research: Biogeosciences, applied bio-optical measurements from Argo profiling floats to study the year-round depth-resolved NPP of the western North Atlantic Ocean (39° N to 54° N). The authors calculated NPP with two bio-optical models (Carbon-based Productivity Model, CbPM; and Photoacclimation Productivity Model, PPM). A comparison with NPP profiles from 14C incubation measurements showed advantages and limitations of both models. CbPM reproduced the magnitude of NPP in most cases, but had artifacts in the summer (a large NPP peak in the subsurface) due to the subsurface chlorophyll maximum caused by photoacclimation. PPM avoided the artifacts in the summer from photoacclimation, but the magnitude of PPM-derived NPP was smaller than the 14C result. Latitudinally varying NPP were observed, including higher winter NPP/lower summer NPP in the south, timing differences in NPP seasonal phenology, and different NPP depth distribution patterns in the summer months. With a 6-month record of concurrent oxygen and bio-optical measurements from two Argo floats, the authors also demonstrated the ability of Argo profiling floats to obtain estimates of the net community production (NCP) to NPP ratio (f-ratio), ranging from 0.3 in July to -1.0 in December 2016.

This work highlights the utility of float bio-optical profiles in comparison to traditional measurements and indicates that environmental conditions (e.g. light availability, nutrient supply) are major factors controlling the seasonality and spatial (horizontal and vertical) distributions of NPP in the western North Atlantic Ocean.

 

Authors:
Bo Yang (University of Virginia, UM CIMAS/NOAA AOML)
James Fox (Oregon State University)
Michael J. Behrenfeld (Oregon State University)
Emmanuel S. Boss (University of Maine)
Nils Haëntjens (University of Maine)
Kimberly H. Halsey (Oregon State University)
Steven R. Emerson (University of Washington)
Scott C. Doney (University of Virginia)

A close-up view of biomass controls in Southern Ocean eddies

Posted by mmaheigan 
· Thursday, August 20th, 2020 

Southern Ocean biological productivity is instrumental in regulating the global carbon cycle. Previous correlative studies associated widespread mesoscale activity with anomalous chlorophyll levels. However, eddies simultaneously modify both the physical and biogeochemical environments via several competing pathways, making it difficult to discern which mechanisms are responsible for the observed biological anomalies within them. Two recently published papers track Southern Ocean eddies in a global, eddy-resolving, 3-D ocean simulation. By closely examining eddy-induced perturbations to phytoplankton populations, the authors are able to explicitly link eddies to co-located biological anomalies through an underlying mechanistic framework.

Figure caption: Simulated Southern Ocean eddies modify phytoplankton division rates in different directions of depending on the polarity of the eddy and background seasonal conditions. During summer anticyclones (top right panel) deliver extra iron from depth via eddy-induced Ekman pumping and fuel faster phytoplankton division rates. During winter (bottom right panel) the extra iron supply is eclipsed by deeper mixed layer depths and elevated light limitation resulting in slower division rates. The opposite occurs in cyclones.

In the first paper, the authors observe that eddies primarily affect phytoplankton division rates by modifying the supply of iron via eddy-induced Ekman pumping. This results in elevated iron and faster phytoplankton division rates in anticyclones throughout most of the year. However, during deep mixing winter periods, exacerbated light stress driven by anomalously deep mixing in anticyclones can dominate elevated iron and drive division rates down. The opposite response occurs in cyclones.

The second paper tracks how eddy-modified division rates combine with eddy-modified loss rates and physical transport to produce anomalous biomass accumulation. The biomass anomaly is highly variable, but can exhibit an intense seasonal cycle, in which cyclones and anticyclones consistently modify biomass in different directions. This cycle is most apparent in the South Pacific sector of the Antarctic Circumpolar Current, a deep mixing region where the largest biomass anomalies are driven by biological mechanisms rather than lateral transport mechanisms such as eddy stirring or propagation.

It is important to remember that the correlation between chlorophyll and eddy activity observable from space can result from a variety of physical and biological mechanisms. Understanding the nuances of how these mechanisms change regionally and seasonally is integral in both scaling up local observations and parameterizing coarser, non-eddy resolving general circulation models with embedded biogeochemistry.

Authors:
Tyler Rohr (Australian Antarctic Partnership Program, previously at MIT/WHOI)
Cheryl Harrison (University of Texas Rio Grande Valley)
Matthew Long (National Center for Atmospheric Research)
Peter Gaube (University of Washington)
Scott Doney (University of Virginia)

A new tidal non-photochemical quenching model reveals obscured variability in coastal chlorophyll fluorescence

Posted by mmaheigan 
· Tuesday, October 15th, 2019 

Although chlorophyll fluorescence is widely-used as a proxy for chlorophyll concentration, sunlight exposure makes fluorescence measurements inaccurate through a process called non-photochemical quenching, limiting its proxy accuracy during daylight hours. In the open ocean, where time and space scales are large relative to variability in phytoplankton concentration, daytime chlorophyll fluorescence—necessary for satellite algorithm validation and for understanding diurnal variability in phytoplankton abundance—can be estimated by averaging across successive nighttime, unquenched values. In coastal waters, where semidiurnal tidal advection drives small scale patchiness and short temporal variability, successive nighttime observations do not accurately represent the intervening daytime. Thus, it is necessary to apply a non-photochemical quenching correction that accounts for the additional effect of tidal advection.

In a recent study in L&O Methods, authors developed a model that uses measurements of tidal velocity to correct daytime chlorophyll fluorescence for non-photochemical quenching and tidal advection. The model identifies high tide and low tide endmember populations of phytoplankton from tidal velocity, and estimates daytime chlorophyll fluorescence as a conservative interpolation between endmember fluorescence at those tidal maxima and minima (Figure 1). Rather than removing nearly 12 hours’ worth of hourly chlorophyll fluorescence observations (i.e., all of the daytime observations) as was previously necessary, this model recovers them. The model output performs more accurately as a proxy for chlorophyll concentration than raw daytime chlorophyll fluorescence measurements by a factor of two, and enables tracking of phytoplankton populations with chlorophyll fluorescence in a Lagrangian sense from Eulerian measurements. Finally, because the model assumes conservation, periods of non-conservative variability are revealed by comparison between model and measurements, helping to elucidate controls on variability in phytoplankton abundance in coastal waters.

Figure 1: Model (light blue line) is a tidal interpolation between high tide (blue points) and low tide (red points) phytoplankton endmembers. The model represents nighttime, unquenched chlorophyll fluorescence measurements well (black points), while daytime, quenched measurements are visibly reduced (gray points).

This result is a critical achievement, as it enables the use of daytime chlorophyll fluorescence, which increases the temporal resolution of coastal chlorophyll fluorescence measurements, and also provides a mechanism for satellite validation of the ocean color chlorophyll data product in coastal waters. The model’s capacity to accurately simulate the pervasive effect of non-photochemical quenching makes it a vital tool for any researcher or coastal water manager measuring chlorophyll fluorescence. This model will help to provide new insights on the movement of and controls on phytoplankton populations across the land-ocean continuum.

Authors:
Luke Carberry (University of California, Santa Barbara)
Collin Roesler (Bowdoin College)
Susan Drapeau (Bowdoin College)

 

Nutrient and carbon limitation drive broad-scale patterns of mixotrophy in the ocean

Posted by mmaheigan 
· Tuesday, May 14th, 2019 

In the ocean, unicellular eukaryotes are often mixotrophic, which means they photosynthesize and also consume prey. In recent decades, it has become clear that mixotrophs are ubiquitous in sunlit ocean habitats. Additionally, models predict that mixotrophs have important impacts on productivity, nutrient cycling, carbon export, and food web structure. However, there is little understanding of the environmental conditions that select for a mixotrophic lifestyle, and it is unclear how mixotrophs succeed in competition with autotrophic and heterotrophic specialists. A recent study in PNAS that synthesized measurements of mixotrophic nanoflagellates showed that mixotrophs are more abundant in stratified, well-lit, low latitude environments (Figure 1A). They are also more abundant, relative to pure heterotrophs, in productive coastal environments (Figure 1B). A trait-based model analysis revealed that the success of mixotrophs depends on the fact that they are less nutrient-limited than autotrophs (due to prey-derived nutrients) and less carbon-limited than heterotrophs (due to photosynthesis). This synergy requires sufficient light, leading to success in low latitude environments. Similarly, a greater supply of dissolved nutrients relative to prey, as commonly observed in coastal environments, favors mixotrophs relative to heterotrophs. One implication of these results is that carbon fixation at lower latitudes may be enhanced by mixotrophy, while limiting nutrients may be more efficiently transferred to higher trophic levels.

Figure 1. Estimated abundance of autotrophic, mixotrophic, and heterotrophic nanoflagellates across environmental gradients in the ocean.

 

Author:
Kyle Edwards (Univ. Hawaii at Manoa)

A half century perspective: Seasonal productivity and particulates in the Ross Sea

Posted by mmaheigan 
· Tuesday, April 2nd, 2019 

Studies of cruise observations in the Ross Sea are typically biased to a single or a few year(s), and long-term trends have predominantly come from satellites. Consequently, the in situ climatological patterns of nutrients and particulate matter have remained vague and unclear. What are the typical patterns of nutrients and particulate matter concentrations in the Ross Sea in spring and summer? How do these concentrations affect annual productivity estimates?

Patterns of nutrient and particulate matter in the Ross Sea can play a wide-ranging role in a productive region like the Ross Sea. Smith and Kaufman (2018) recently synthesized austral spring and summer (November to February) observations from 42 Ross Sea research cruises (1967-2016) to analyze broad biogeochemical patterns. The resulting climatologies revealed interesting seasonal patterns of nutrient uptake and particulate organic carbon (POC) to chlorophyll (chl) ratios (POC:chl). Temporal patterns in the nitrate and phosphate climatologies confirm the role of early spring haptophyte (Phaeocystis antarctica) growth, followed by limited nitrogen and phosphorus removal in summer. However, a notable increase in POC occurred later in summer that was largely independent of chlorophyll changes, resulting in a dramatic increase in POC:chl. A gradual decline in silicic acid concentrations throughout the summer, along with an increased occurrence of biogenic silica during this time suggest that diatoms may be responsible for this later POC spike. Revised estimates of primary productivity based on these observed climatological POC:chl ratios suggests that summer blooms may be a significant contributor to seasonal productivity, and that estimates of productivity based on satellite pigments underestimate annual production by at least 70% (Figure 1).

Figure 1. Bio-optical estimates of mean productivity using a constant POC:chl ratio (black dots and lines) and modified estimates of productivity using the monthly climatological POC:chl ratios (red dots and lines), in a) the Ross Sea polynya region and b) the western Ross Sea region.

 

By clarifying typical seasonal patterns of nutrient uptake and POC:chl, these climatologies underscore the biogeochemical importance of both spring haptophyte growth and previously underestimated summer diatom growth in the Ross Sea. Further investigation of the causes and consequences of elevated summer ratios is needed, as assessments of regional food webs and biogeochemical cycles depend on more accurate understanding of primary productivity patterns. Likewise, these results highlight the need for continued efforts to constrain satellite productivity estimates in the Ross Sea using in situ constituent ratios.

For other relevant work on seasonal biogeochemical patterns in the Ross Sea, please see https://doi.org/10.1016/j.dsr2.2003.07.010. And for intra-seasonal estimates of particulate organic carbon to chlorophyll using gliders, please see: https://doi.org/10.1016/j.dsr.2014.06.011.

 

Authors:
Walker O. Smith Jr. (VIMS, College of William and Mary)
Daniel E. Kaufman (VIMS, College of William and Mary; now at Chesapeake Research Consortium)

 

 

 

Filter by Keyword

abundance acidification additionality advection africa air-sea air-sea interactions algae alkalinity allometry ammonium AMO AMOC anoxic Antarctic Antarctica anthro impacts anthropogenic carbon anthropogenic impacts appendicularia aquaculture aquatic continuum aragonite saturation arctic Argo argon arsenic artificial seawater AT Atlantic atmospheric CO2 atmospheric nitrogen deposition authigenic carbonates autonomous platforms AUVs bacteria bathypelagic BATS BCG Argo benthic bgc argo bio-go-ship bio-optical bioavailability biogeochemical cycles biogeochemical models biogeochemistry Biological Essential Ocean Variables biological pump biophysics bloom blue carbon bottom water boundary layer buffer capacity C14 CaCO3 calcification calcite carbon carbon-climate feedback carbon-sulfur coupling carbonate carbonate system carbon budget carbon cycle carbon dioxide carbon export carbon fluxes carbon sequestration carbon storage Caribbean CCA CCS changing marine chemistry changing marine ecosystems changing marine environments changing ocean chemistry chemical oceanographic data chemical speciation chemoautotroph chesapeake bay chl a chlorophyll circulation clouds CO2 CO3 coastal and estuarine coastal darkening coastal ocean cobalt Coccolithophores commercial community composition competition conservation cooling effect copepod copepods coral reefs CTD currents cyclone daily cycles data data access data assimilation database data management data product Data standards DCM dead zone decadal trends decomposers decomposition deep convection deep ocean deep sea coral denitrification deoxygenation depth diatoms DIC diel migration diffusion dimethylsulfide dinoflagellate dinoflagellates discrete measurements distribution DOC DOM domoic acid DOP dust DVM ecology economics ecosystem management ecosystems eddy Education EEZ Ekman transport emissions ENSO enzyme equatorial current equatorial regions ESM estuarine and coastal carbon fluxes estuary euphotic zone eutrophication evolution export export fluxes export production extreme events faecal pellets fecal pellets filter feeders filtration rates fire fish Fish carbon fisheries fishing floats fluid dynamics fluorescence food webs forage fish forams freshening freshwater frontal zone functional role future oceans gelatinous zooplankton geochemistry geoengineering geologic time GEOTRACES glaciers gliders global carbon budget global ocean global warming go-ship grazing greenhouse gas greenhouse gases Greenland ground truthing groundwater Gulf of Maine Gulf of Mexico Gulf Stream gyre harmful algal bloom high latitude human food human impact human well-being hurricane hydrogen hydrothermal hypoxia ice age ice cores ice cover industrial onset inland waters in situ inverse circulation ions iron iron fertilization iron limitation isotopes jellies katabatic winds kelvin waves krill kuroshio lab vs field land-ocean continuum larvaceans lateral transport LGM lidar ligands light light attenuation lipids low nutrient machine learning mangroves marine carbon cycle marine heatwave marine particles marine snowfall marshes mCDR mechanisms Mediterranean meltwater mesopelagic mesoscale mesoscale processes metagenome metals methane methods microbes microlayer microorganisms microplankton microscale microzooplankton midwater mitigation mixed layer mixed layers mixing mixotrophs mixotrophy model modeling model validation mode water molecular diffusion MPT MRV multi-decade n2o NAAMES NCP nearshore net community production net primary productivity new ocean state new technology Niskin bottle nitrate nitrogen nitrogen cycle nitrogen fixation nitrous oxide north atlantic north pacific North Sea NPP nuclear war nutricline nutrient budget nutrient cycles nutrient cycling nutrient limitation nutrients OA observations ocean-atmosphere ocean acidification ocean acidification data ocean alkalinity enhancement ocean carbon storage and uptake ocean carbon uptake and storage ocean color ocean modeling ocean observatories ocean warming ODZ oligotrophic omics OMZ open ocean optics organic particles oscillation outwelling overturning circulation oxygen pacific paleoceanography PAR parameter optimization parasite particle flux particles partnerships pCO2 PDO peat pelagic PETM pH phenology phosphate phosphorus photosynthesis physical processes physiology phytoplankton PIC piezophilic piezotolerant plankton POC polar polar regions policy pollutants precipitation predation predator-prey prediction pressure primary productivity Prochlorococcus productivity prokaryotes proteins pteropods pycnocline radioisotopes remineralization remote sensing repeat hydrography residence time resource management respiration resuspension rivers rocky shore Rossby waves Ross Sea ROV salinity salt marsh satellite scale seafloor seagrass sea ice sea level rise seasonal seasonality seasonal patterns seasonal trends sea spray seawater collection seaweed secchi sediments sensors sequestration shelf ocean shelf system shells ship-based observations shorelines siderophore silica silicate silicon cycle sinking sinking particles size SOCCOM soil carbon southern ocean south pacific spatial covariations speciation SST state estimation stoichiometry subduction submesoscale subpolar subtropical sulfate surf surface surface ocean Synechococcus technology teleconnections temperate temperature temporal covariations thermocline thermodynamics thermohaline thorium tidal time-series time of emergence titration top predators total alkalinity trace elements trace metals trait-based transfer efficiency transient features trawling Tris trophic transfer tropical turbulence twilight zone upper ocean upper water column upwelling US CLIVAR validation velocity gradient ventilation vertical flux vertical migration vertical transport warming water clarity water mass water quality waves weathering western boundary currents wetlands winter mixing zooplankton

Copyright © 2025 - OCB Project Office, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, MS #25, Woods Hole, MA 02543 USA Phone: 508-289-2838  •  Fax: 508-457-2193  •  Email: ocb_news@us-ocb.org

link to nsflink to noaalink to WHOI

Funding for the Ocean Carbon & Biogeochemistry Project Office is provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). The OCB Project Office is housed at the Woods Hole Oceanographic Institution.