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New software enables global ocean biogeochemical modeling in Python

Posted by mmaheigan

· Friday, September 5th, 2025

Have you ever wondered what life would be like if you could write and run complex biogeochemical models easily and conveniently in Python? Wonder no more. In a paper published in J. Adv. Model. Earth Syst., Samar Khatiwala (2025; see reference below) describes tmm4py, a new software to enable efficient, global scale biogeochemical modelling in Python.

tmm4py is based on the Transport Matrix Method (TMM), an efficient numerical scheme for “offline” simulation of tracers driven by circulations from state-of-the-art physical models and state estimates. tmm4py exposes this functionality in Python, providing the tools needed to implement complex models in pure Python using standard modules such as NumPy, and run them interactively on hardware ranging from laptops to supercomputers. No knowledge of parallel computing required! tmm4py even extends the interactivity to models written in Fortran, allowing the many existing models coupled to the TMM, e.g., MITgcm, to be used from the familiar comfort of Python. Whether you’re a seasoned modeler, just want to try out an idea, or illustrate a concept in your teaching, tmm4py is designed to make biogeochemical modeling more widely accessible.

Download the code from: https://github.com/samarkhatiwala/tmm

Figure: Schematic illustrating the structure of tmm4py and its relationship with the various libraries and components it is built on or interacts with. Outlined boxes represent user‐supplied code (such as the “Hello World” example of the ideal age tracer shown on the left). Other low-level libraries on which tmm4py depends, for example, BLAS and LAPACK for linear algebra, MPI for parallel communication, and CUDA for GPUs, are not shown.

Author
Samar Khatiwala (Waseda Univ)

Joint Science Highlight with GEOTRACES.

Migrating zooplankton increase N2 production in Oxygen Deficient Zones

Posted by mmaheigan

· Friday, August 15th, 2025

Diel Vertically Migrating Zooplankton that spend their day in an Oxygen Deficient Zone to avoid predators are a previously ignored source of organic matter for N₂ producing bacteria.

A recent study in GBC, examined biogeochemical cycling in the offshore Eastern Tropical North Pacific Oxygen Deficient Zone. They found that the daytime maximum in backscattering, used as a proxy for zooplankton and forage fish, corresponded to quantitative PCR maxima in zooplankton and forage fish (metazoan) DNA and to the maximum in biological N₂ gas, and a shoulder of the nitrite maximum. At the same time, the C:N ratio of both suspended and sinking organic matter were reduced, indicating less degraded organic matter. These data strongly suggest that N₂ production in the core of the Oxygen Deficient Zone is stimulated by the daily migration of zooplankton and forage fish in the Oxygen Deficient Zone. These results decouple N₂ production from sinking organic matter fluxes. This work indicates that multicellular animals can affect key ocean biogeochemical cycles, and can cause hot spots of microbial activity well below the sunlit ocean.

Figure caption: Offshore Eastern Tropical North Pacific Oxygen Deficient Zone. The dashed black line indicates the top of the ODZ, the gray lines indicate the boundaries of the deep vertical migration maximum. A) Concentrations of nitrite and oxygen, B) C:N of suspended and of sinking (sediment trap) organic matter, C) Day and night backscattering, a proxy for zooplankton and forage fish, and D) Biological N2 gas concentrations and day and night quantitative PCR data for zooplankton and forage fish (metazoans).

Authors
Clara Fuchsman (UMCES Horn Point Laboratory)
Megan Duffy (Univ Vermont)
Jacob Cram (UMCES Horn Point Laboratory)
Paulina Huanca-Valenzuela (UMCES Horn Point Laboratory)
Louis Plough (UMCES Horn Point Laboratory)
James Pierson (UMCES Horn Point Laboratory)
Catherine Fitzgerald (UMCES Horn Point Laboratory)
Allan Devol (U. of Washington)
Richard Keil (U. of Washington)

Paper: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2024GB008365

Giant iceberg meltwater supplies nutrients to upper ocean layers

Posted by mmaheigan

· Friday, August 15th, 2025

Iceberg meltwater induces mixing which erodes upper-ocean layers. This supplies nutrients, both released from the iceberg and entrained from deeper waters, to surface waters which stimulates phytoplankton growth.

Meltwater from the base, sidewalls and surface of giant icebergs influences upper ocean stratification and mixing. Containing a substantial micro-nutrient load, (incorporating nutrient-rich deep waters along with mineral-rich particles, such as iron and silica, from the melting iceberg), this meltwater is thought to relieve nutrient limitation in surface ecosystems, impacting ocean biological productivity and carbon drawdown. A recent paper in Nature Geoscience provides high-resolution glider measurements right next to giant iceberg A-68A; elucidating the effects of meltwater on water mass modification and near-surface productivity.

The number of calving icebergs is expected to increase in the near future, however the impact of iceberg meltwater on the hydrography, circulation and mixing of the upper ocean is poorly quantified. Understanding the complex physical and biological impacts on the ocean waters through which icebergs transit is difficult to represent in global ocean models, precipitating complexity in prediction of future ocean circulation and the health of Antarctic ecosystems.

Authors
Natasha S Lucas (British Antarctic Survey)
J. Alexander Brearley (British Antarctic Survey)
Katharine R Hendry (British Antarctic Survey)
Theo Spira (University of Gothenburg)
Anne Braakmann-Folgmann (The Arctic University of Norway)
E. Povl Abrahamsen (British Antarctic Survey)
Michael P Meredith (British Antarctic Survey)
Geraint A Tarling (British Antarctic Survey)

Social media:
@krhendry.bsky.social
@TashaOcean
www.bas.ac.uk
@britishantarcticsurvey
@bangor_university
@bangor.sos
@polarwomen @womeninoceanscience
#TashaGoesSouth #PolarResearch #SouthernOcean #AgulhasII #WomenInPhysics #WomenInScience #ExperimentalPhysics #Oceanography #Antarctica

A little extra background:

Roughly a quarter the size of Wales at 5800 square kilometres, A-68A was the biggest iceberg on Earth when it calved from the Larsen-C Ice Shelf in 2017. It arrived at South Georgia as the sixth largest giant iceberg on record. A-68A deposited an estimated 152 billion tonnes of nutrient-rich fresh water, equivalent to 61 million Olympic sized swimming pools, and 27 times the annual freshwater outflow from South Georgia, into the seas around this sub-Antarctic island during the three months of this glider survey.

Ocean gliders are a type of small, robotic underwater vehicle that use density differences, or buoyancy, to move up and down through the water column with wings to create lift, propelling it forward. While ‘flying’ through the water, from the surface to 1 km in depth, the gliders’ sensors measure the water’s properties. The glider surfaces at regular intervals to check its position by GPS, transmit sparse data back to the UK using a satellite phone system, and check for new instructions on where to go and what instruments to turn on.

Research Briefing https://rdcu.be/eg39r

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)

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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