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Tracing the biological carbon pump across diverse export regimes

Posted by mmaheigan

· Thursday, May 29th, 2025

The ocean’s biological carbon pump (BCP) plays a crucial role in regulating Earth’s climate. But how efficiently does it transport carbon to the deep? It has been difficult to answer this question because observations are sparse, labor-intensive, and the uncertainties of the BCP’s magnitude, which are nearly equivalent to human emissions. Fortunately, autonomous vehicles unlock our ability to observe the upper ocean in three dimensions, garner a greater spatial and temporal range than a research vessel and, unlike a satellite, enable us to see into the deep.

Figure caption: This figure compares mean daily organic carbon flux (blue bars) with ship-based particulate organic carbon (POC) flux (purple bars) to show the different export regimes at 60 and 100 m depth at each study site (left panel: the subpolar northeast Pacific late summer; right panel: North Atlantic spring bloom. The inferred net DOC production (orange bars) was calculated as the difference between the organic carbon flux and the ship-based POC. At times, net community production (NCP, yellow bars) is smaller than the export terms, which suggests a contribution from earlier productivity to export that is consistent with the cruise period beginning on the tail end of a previous bloom. The error bars depict the 95% confidence interval.

A new paper in Limnology & Oceanography leverages these vehicles to autonomously characterize the BCP in two dramatically diverse carbon export regimes. The results reveal strong variability in carbon export efficiency, and further comparison with ship-based data informed the transport pathways. At the lower productivity site, nearly all of the carbon fixed by phytoplankton was routed into sinking particulate organic carbon, while at the highly productive site, nearly half was diverted to dissolved organic carbon. These insights refine our understanding of carbon transport processes and highlight the strength of multiple observational approaches used in tandem. This work is part of the NASA-led EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) program, that ultimately seeks to reduce the uncertainty in the global BCP through improved remote sensing algorithms.

Why does this matter? With climate change mitigation at the forefront of global policy, improving our understanding of the marine carbon cycle is essential. By providing continuous, high-resolution observations, autonomous platforms offer critical data to inform climate predictions, carbon sequestration strategies, and ocean conservation efforts.

Authors
Shawnee Traylor (MIT-WHOI Joint Program)
David P. Nicholson (Woods Hole Oceanographic Inst.)
Samantha J. Clevenger (MIT-WHOI Joint Program)
Ken O. Buesseler (Woods Hole Oceanographic Inst.)
Eric D’Asaro (Univ Washington)
Craig M. Lee (Univ Washington)

New over-determined CO2 system solver QUODcarb

Posted by mmaheigan

· Thursday, May 29th, 2025

Do you work with over-determined datasets of seawater carbon dioxide system chemistry? QUODcarb (Quantifying Uncertainty in an Over-Determined marine carbonate system), a new over-determined CO2-system solver is described in the recently published “QUODcarb: A Bayesian solver for over-determined datasets of seawater carbon dioxide system chemistry.” The Bayesian formulation of the novel solver and demonstrates its use on an over-determined dataset from the Gulf of Mexico (COMECC-3) that included measurements of DIC, AT, pH, pCO2, and [CO3]. The over-determined calculations, with self-consistent uncertainty quantification, can calculate carbonate ion concentration uncertainty within the GOA-ON climate uncertainty target of 1% with implications for ocean acidification monitoring projects.

Find the Matlab code on GitHub: https://github.com/fprimeau/QUODcarb

Figure caption: Diagram depicting the measured quantities (left side) and the use of thermodynamic constant (pK) formulations and mass balance total (_T) formulations in seawater carbonate chemistry calculations. Adapted from Figure 1 in Carter et al., 2024 a, to illustrate how QUODcarb can replace CO2SYS calculations to include three or more carbonate variable measurements in over-determined calculations while also enabling uncertainty quantification.
Physical measurements are shown with pink backgrounds, mass balance total contents are shown with light green backgrounds, thermodynamic constants are in gray, and carbonate chemistry variables are in yellow. Temperature dependent carbonate chemistry measurements (e.g., pH and pCO2) may be included at different input temperatures. The calculator reflects the analogy that QUODcarb acts as a calculator for solving the system of nonlinear equations.

Authors
Marina Fennell (University of California, Irvine)
Francois Primeau (University of California, Irvine)

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)

Microbial Iron limitation in the ocean’s twilight zone

Posted by mmaheigan

· Monday, March 31st, 2025

How deep in the ocean do microbes feel the effects of nutrient limitation? Microbial production in one third of the surface ocean is limited by the essential micronutrient iron (Fe). This limitation extends to at least the bottom of the euphotic zone, but what happens below that?

In a study that recently published in Nature we investigated the abundance and distribution of siderophores, small metabolites synthesized by bacteria to promote Fe uptake. When environmental Fe concentrations become limiting and microbes become Fe deficient, some bacteria release siderophores into the environment to bind iron and facilitate its uptake. Siderophores are therefore a window into how microbes “see” environmental Fe. We found that siderophore concentrations were high in low Fe surface waters, but surprisingly we also found siderophores to be abundant in the twilight zone (200-500 m) underlying the North and South Pacific subtropical gyres, two key ecosystems for the marine carbon cycle. In shipboard experiments with siderophores labeled with the rare ⁵⁷Fe isotope, we found rapid uptake of the label in twilight zone samples. After removing ⁵⁷Fe from the ⁵⁷Fe-siderophores complex, bacteria released the now unlabeled siderophores back into seawater to complex additional Fe (Figure. 1).

Figure 1: Iron-siderophore cycling in the twilight zone. When the seawater becomes Fe-deficient, some bacteria are able to synthesize siderophores and release them into the environment (middle left). These metabolites bind Fe (middle right) and the Fe-siderophore complex is taken up by bacteria using specialized TonB dependent transporters (TBDT; bottom right). Inside the cell, Fe is recovered from the Fe-siderophore complex (bottom left) and the siderophore excreted back into the environment to start the cycle anew.

Our results show that in large parts of the ocean microbes feel the effects of nutrient limitation deep in the water column, to at least 500 m. This greatly expands the region of the ocean where nutrients limit microbial metabolism. The effects of limitation this deep in the water column are unexplored, but twilight zone Fe deficiency could have unanticipated consequences for the efficiency of the ocean’s biological carbon pump.

Authors
Jingxuan Li, Lydia Babcock-Adams and Daniel Repeta
(all at Woods Hole Oceanographic Institution)

How do ocean microbes share the job of denitrification?

Posted by mmaheigan

· Monday, March 31st, 2025

Denitrification is a crucial multi-step process for ecosystem productivity and sustainability because some of its steps can result in the loss of the essential nutrient nitrogen or the production of greenhouse gas nitrous oxide. We do not understand why microbial functional groups conducting different steps of denitrification can coexist in the ocean and why certain groups are more abundant than others.

In a recent study published in PNAS, we uncover ecological mechanisms that govern the coexistence of these microbes. For the microbial groups utilizing different nitrogen substrates, the “stronger” groups rely on the “weaker” groups to feed them nitrogen (with respect to the organic substrates that they compete for), enabling them to coexist. For the groups competing for the same nitrogen substrates, microbes that invest more to build longer denitrification steps win the competition when nitrogen is limiting, but lose the game when nitrogen is repleted and organic carbon is limiting. The spatial and temporal variability of nutrients in the ocean allows these microbes to be observed in the same water mass.

Figure caption: Temporal and spatial heterogeneity in nutrients promotes the coexistence of functionally diverse denitrifiers in the ocean.

These hypothesized coexistence patterns help us predict where and when nitrogen loss and nitrous oxide production may occur. As human activities continue to alter marine nutrient balances, these predictions help us better anticipate ocean responses and design better strategies for mitigating negative anthropogenic impacts on the ocean.

Authors
Xin Sun (Carnegie Institution for Science) @xinsun-putiger.bsky.social
Emily Zakem (Carnegie Institution for Science) @carnegiescience.bsky.social

The ocean is shifting toward phosphorus limitation

Posted by mmaheigan

· Friday, February 28th, 2025

Biogeochemical models predict that ocean warming is weakening the vertical transport of nutrients to the upper ocean, with severe implications for marine productivity. However, nutrient concentrations across the ocean surface often fall below detection limits, making it difficult to observe long-term changes.

In a recent study in PNAS, we analyzed over 30,000 nitrate and phosphate depth profiles observed between 1972 and 2022 to quantify nutricline depths, where nutrient concentrations are reliably detected. These depths accurately represent nutrient supplies in a global model, allowing us to assess long-term trends. Over the past five decades, upper ocean phosphate has mostly declined worldwide, while nitrate has remained mostly stable. Model simulations support that this difference is likely due to nitrogen fixation replenishing upper ocean nitrate, whereas phosphate has no equivalent biological source.

Figure caption: Five decades of global and regional nutricline depth data reveal declining phosphate-to-nitrate trends. Nutricline depths were defined based on threshold concentrations of 3 μmol kg−1 nitrate (TNO3) and 3/16 μmol kg−1 phosphate (TPO4). Site-specific trends were quantified for each unique pair of geographic coordinates where sufficient data was available (TNO3, n = 1,859 sites; TPO4, n = 1,641 sites). Shown are 95% confidence intervals (CI95%) calculated for each median trend by generating 10,000 bootstrap samples. The curves over the histograms depict the kernel densities. The sets of error bars from top to bottom are the interquartile ranges of TNO3 and TPO4 from a monthly climatology, the total observations, and the total observations with added measurement error.

These findings suggest that the ocean is becoming more limited in phosphorus. This decline could make phytoplankton less nutritious for marine animals. Fish larvae growth rates correlate with phosphorus availability in the ecosystem, so intensifying phosphorus limitation may greatly impact fisheries worldwide.

Authors
Skylar Gerace (University of California, Irvine)
Jun Yu (University of California, Irvine)
Keith Moore (University of California, Irvine)
Adam Martiny (University of California, Irvine)

@UCI_OCEANS

Persistent bottom trawling impairs seafloor carbon sequestration

Posted by mmaheigan

· Friday, February 28th, 2025

Bottom trawling, a fishing method that uses heavy nets to catch animals that live on and in the seafloor, could release a large amount of organic carbon from seafloor into the water, that metabolizes to CO₂ then outgasses to the atmosphere. The magnitude of this indirect emission has been heavily debated, with estimates spanning from negligibly small to global climate relevant. Thus, a lack of reliable data and insufficient understanding of the process hinders management of bottom trawling for climate protection.

We set out to solve this problem in two steps. First, we analyzed a large field dataset containing more than 2000 sediment samples from one of the most intensely trawled regions globally, the North Sea. We identified a trawling-induced carbon reduction trend in the data, but only in samples taken in persistently intensively trawled areas with multi-year averaged swept area ratio larger than 1 yr^-1. In less intensely trawled areas, there was no clear effect. In a second step, we applied numerical modelling to understand the processes behind the observed change (Fig. 1). Our model results suggest that bottom trawling annually releases one million tonnes of CO₂ in the North Sea and 30 million tonnes globally. Along with sediment resuspension in the wake of the trawls, the main cause for altered sedimentary carbon storage is the depletion of macrofauna, whose locomotion and burrowing effectively buries freshly deposited carbon into deeper sediment layers. By contrast, macrofauna respiration is reduced owing to trawling-caused mortality, partly offsetting the organic carbon loss. Following a cessation of trawling, the simulated benthic biomass can recover in a few years, but the sediment carbon stock would take several decades to be restored to its natural state.

Figure 1. (a) Benthic–pelagic coupling in a natural system. (b) Processes involved in bottom trawling. (c) Model-estimated source and sink terms of organic carbon in surface sediments in the No-trawling (solid fill, n = 67 annual values for 1950–2016) and trawling (pattern fill, n = 67 ensemble-averaged values for 1950–2016) scenarios of the North Sea. © 2024, Zhang, W. et al., CC BY 4.0.

Marine conservation strategies traditionally favor hard bottoms, such as reefs, that are biologically diverse but accumulate limited amounts of organic carbon. Our results indicate that carbon in muddy sediments is more susceptible to trawling impacts than carbon in sand and point out a need to safeguard muddy habitats for climate protection. Our methods and results might be used in the context of marine spatial planning policies to gauge the potential benefits of limiting or ending bottom trawling within protected areas.

Zhang, W., Porz, L., Yilmaz, R. et al. Long-term carbon storage in shelf sea sediments reduced by intensive bottom trawling. Nat. Geosci. 17, 1268–1276 (2024). https://doi.org/10.1038/s41561-024-01581-4

Authors
Wenyan Zhang (Hereon)
Lucas Porz (Hereon)
Rümeysa Yilmaz (Hereon)
Klaus Wallmann (GEOMAR)
Timo Spiegel (GEOMAR)
Andreas Neumann (Hereon)
Moritz Holtappels (AWI)
Sabine Kasten (AWI)
Jannis Kuhlmann (BUND)
Nadja Ziebarth (BUND)
Bettina Taylor (BUND)
Ha Thi Minh Ho-Hagemann (Hereon)
Frank-Detlef Bockelmann (Hereon)
Ute Daewel (Hereon)
Lea Bernhardt (HWWI)
Corinna Schrum (Hereon)

Rain increases the global carbon sink

Posted by mmaheigan

· Tuesday, January 28th, 2025

The global ocean dampens the anthropic CO₂ increase in the atmosphere by absorbing around 25% of the carbon emitted each year. Of the processes involved in exchanges of energy and mass between ocean and atmosphere that may impact this carbon sink, rainfall has never been systematically and comprehensively quantified. A study recently published in Nature Geosciences suggests that about 6% of the global ocean CO₂ sink is mediated by rainfall.

Figure 1. Histograms of 2008-2018 global ocean (60°S-60°N) CO2 sink increase due to rain-induced turbulence only, rain-induced dilution only, the resultant of turbulence and dilution (named the interfacial effect), the wet deposition of CO2 absorbed during the raindrops fall and the total (interfacial plus wet deposition) using 1-h rain rates from IMERG (blue) and ERA5 (red). The rain-induced dilution is diagnosed from a satellite-derived empirical relationship (full) or a 1D physical model (stripes). Figure based on Parc et al. (2024) Table 1.

The exchange of CO₂ at the ocean interface is controlled by chemical, physical, and biological properties and processes. Rainfall, one of these processes, can alter the properties of the ocean surface and perturb the carbon exchange in three ways:

(i) Turbulence: Raindrops increase the momentum transfer to the ocean and generate turbulence enhancing the renewal of interfacial water (first column in Fig. 1). This tends to increase both in- and out-gassing. The impact of this effect alone is weak because wind dominates the generation of turbulence in the ocean;

(ii) Dilution + Interfacial: Rain dilutes and cools the near surface waters, which perturbs chemical equilibria and leads the ocean to absorb more CO₂ (second column in Fig. 1). The result of dilution and turbulence effects of rain, which is named “Interfacial”, is a clear increase in global CO₂ sink (third column in Fig. 1);

(iii) Wet deposition: Finally, raindrops directly inject CO₂ molecules into the ocean that they absorbed during their fall through the atmosphere (fourth column in Fig. 1).

Using two rainfall datasets (the satellite-derived product IMERG and the ERA5 reanalysis) and two ways to quantify the rain-induced dilution, the authors show that rain increases the ocean carbon sink by 140 to 190 million tonnes of carbon per year, equivalent to 5% to 7% of the 2.66 billion tonnes of carbon absorbed annually by the oceans. Because rainfall amounts and patterns will change in the future, impacting the ocean carbon sink, these results call for explicitly including rain effects in the annual global carbon budget estimates.

Authors
Laëtitia Parc (Laboratoire de Météorologie Dynamique)
Hugo Bellenger (Laboratoire de Météorologie Dynamique)
Laurent Bopp (Laboratoire de Météorologie Dynamique) @bopplaurent.bsky.social
Xavier Perrot (Laboratoire de Météorologie Dynamique)
David T. Ho (University of Hawaii at Manoa; [C]Worthy) @davidho.bsky.social

Parc, L., Bellenger, H., Bopp, L., Perrot, X., and Ho, D. T. Global ocean carbon uptake enhanced by rainfall.Nat. Geosci. 17, 851–857 (2024). https://doi.org/10.1038/s41561-024-01517-y

Deep dive into carbon transport: How bacteria feast and compete on lipids in sinking particles

Posted by mmaheigan

· Tuesday, January 28th, 2025

What drives carbon from the atmosphere to the deep ocean? The journey of phytoplankton-derived carbon is critical in the global carbon cycle, yet the influence of interacting bacteria in degrading lipid-rich particles during their descent has remained a mystery—until now.

Using an innovative combination of nano-scale lipidomics and microscopy, researchers investigated how bacteria target and degrade diverse lipid molecules in sinking oceanic particles. The study, published in Science, revealed that bacteria exhibit distinct dietary preferences, governed by their lipid-degrading genes rather than taxonomic affiliation. Interactions among bacteria influenced both degradation rates and timing, together reshaping our view on the efficiency of lipid transport to the ocean depths. These findings were incorporated into a mathematical model, revealing how microbial communities could regulate the carbon transfer efficiency.

This research enhances our understanding of the ocean’s carbon pump, highlighting the pivotal role of bacterial communities in carbon sequestration. By uncovering how microbial interactions affect carbon transfer, these findings improve climate models and support the development of strategies to mitigate atmospheric CO₂.

Authors
Lars Behrendt (Uppsala University, Sweden)
Benjamin van Mooy (Woods Hole Oceanographic Institution)

Twitter: LarsBehrendt4
Bluesky: @belab1.bsky.social

OA could boost carbon export by appendicularia

Posted by mmaheigan

· Wednesday, December 4th, 2024

Gelatinous zooplankton comprise a widespread group of animals that are increasingly recognized as important components of pelagic ecosystems. Historically understudied, we have little knowledge of how much key taxa contribute to carbon fluxes. Likewise, there’s a critical knowledge gap of the impact of ocean change on these taxa.

Appendicularia are the most abundant gelatinous zooplankton in the world oceans. Their population dynamics display typical boom-and-bust characteristics, i.e. high grazing rates in combination with a short generation time and life cycle, results in intense blooms. The most prominent feature of appendicularians is their mucous feeding-structure (“house”), which is produced and discarded several times per day. These sinking houses can contribute substantially to carbon export.

Figure 1: Influence of ocean acidification on the Appendicularia Oikopleura dioica and carbon export. Appendicularian populations display typical boom-and-bust characteristics, resulting in intense blooms. The sinking of appendicularians’ discarded mucous feeding-structure several times per day can contribute substantially to carbon export. Low pH conditions (as expected for future ocean acidification extreme events) enhanced its population growth and contribution to carbon fluxes shown above (red lines/diamonds) vs ambient (blue lines/diamonds).
(Figure sources: Picture by Jean-Marie Bouquet, data plots from Taucher et al. (2024): The appendicularian Oikopleura dioica can enhance carbon export in a high CO2 ocean. Global Change Biology, doi:10.1111/gcb.17020)

A recent study in Global Change Biology quantified how much appendicularia can contribute to carbon export via the biological pump, and how this carbon flux could markedly increase under future ocean acidification and associated extreme pH events.

The findings are based on a large-volume in situ experimental approach that allowed observing natural plankton populations and carbon export under close-to-natural conditions for almost two months. Thereby, O. dioica population dynamics could be directly linked to sediment trap data to quantify the influence of this key species on carbon fluxes at unprecedented detail. During the appendicularia bloom up to 39% of total carbon export was attributed to them.

The most striking finding was that high CO₂ conditions elevated carbon export by appendicularia increased by roughly 50%. Appendicularians physiologically benefit from low pH conditions, giving them a competitive advantage over other zooplankton, allowing them to contribute to a disproportionally large role in carbon export from the ecosystem.

Authors
Jan Taucher (GEOMAR)
Anna Katharina Lechtenbörger (GEOMAR)
Jean-Marie Bouquet (University of Bergen)
Carsten Spisla (GEOMAR)
Tim Boxhammer (GEOMAR)
Fabrizio Minutolo (GEOMAR)
Lennart Thomas Bach (University of Tasmania)
Kai T. Lohbeck (University of Konstanz)
Michael Sswat (GEOMAR)
Isabel Dörner (GEOMAR)
Stefanie M. H. Ismar-Rebitz (GEOMAR)
Eric M. Thompson (University of Bergen)
Ulf Riebesell (GEOMAR)

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.

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