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New algorithm unclogs major bottleneck in ocean geochemical and biogeochemical modelling

Posted by mmaheigan

· Thursday, May 16th, 2024

Numerical models are some of the principal tools for understanding the cycling of geochemical and biogeochemical tracers in the ocean, with the latter also being important components of the Earth System Models used to project future climate change. However, in order to use these models they must first be integrated to a seasonally-repeating equilibrium with minimal drift, a computationally expensive calculation that can take months on supercomputers given the long turnover timescale – many thousands of years – of the ocean. This “spin-up” problem has long been a major bottleneck in marine geochemical and biogeochemical modelling.

In a study published last year in J. Adv. Model. Earth Sys (2023, see reference below), a new algorithm was shown to speed-up by a factor of between 10-25 the spin-up of a wide range of geochemical tracers, such as radiocarbon, protactinium/thorium and zinc. It can be applied to any model in a “black box” manner.

Now, a follow up study published recently in Sci. Adv. (2024, see reference below) extends the previous results to complex marine biogeochemical models such as those used in the Coupled Model Intercomparison Project (CMIP) that underpin IPCC reports on climate change. The algorithm can accelerate the spin-up of seasonally-forced models by over an order of magnitude, and by a factor of 5 when driven with interannually forcing as is typical in CMIP simulations.

The ability to efficiently spin-up geochemical and biogeochemical models should enable their more effective use, for example making it feasible to calibrate models against observations and performing simulations at resolutions higher than has been previously possible.

Caption: Spin-up to equilibrium of the PISCES marine biogeochemical model. PISCES is coupled to the NEMO ocean circulation model and has 24 prognostic tracers. Left: Drift in dissolved inorganic nitrate concentration (mean squared difference at all grid points between consecutive years) as a function of time. Right: Globally-integrated air-sea flux of CO2 as a function of time. The solid horizontal line is the criterion for convergence established by the Ocean Model Intercomparison Project (OMIP). The blue lines are the conventional direct integration solution and the red lines the accelerated solution using the new algorithm.

This is a joint highlight with the GEOTRACES program.

Reference:

Khatiwala, S. (2024). Efficient spin-up of Earth System Models using sequence acceleration. Science Advances, 10. Access the paper: 10.1126/sciadv.adn2839

Khatiwala, S. (2023). Fast Spin‐Up of Geochemical Tracers in Ocean Circulation and Climate Models. Journal of Advances in Modeling Earth Systems, 15. Access the paper: 10.1029/2022ms003447

Looking for easy data access to high quality time-series data? SPOTS is out!

Posted by mmaheigan

· Thursday, April 18th, 2024

Whether we aim to disentangle anthropogenic driven trends from naturally variability or we want to assess and improve our ocean model’s capabilities to correctly display changes in time, all require high-quality observational data from multiple fixed time-series data. Until now access to these data was difficult, time-consuming, and often required solving multiple data challenges before these data were fit for the purpose. Following the successful examples set by well-known ocean synthesis products, the idea for SPOTS – the Synthesis Product for Ocean Time-Series – was born from this need to address these challenging.

The recently published SPOTS pilot provides biogeochemical essential ocean variables from 12 ship-based fixed time-series scattered around the globe covering the period from 1983 until 2021. An extensive quality assessment enables the straightforward detection of method changes, and in combination with further introduced data quality indicators, the pilot enhances the inter- and intra-station comparability of the included time-series stations. The stations in SPOTS represent unique open ocean and coastal marine environments in the Atlantic, Pacific, Mediterranean, Caribbean, and the Nordic Seas. More than 100,000 water samples are harmonized into one consistent, FAIR, and readily available data synthesis product.

The SPOTS pilot drastically reduces the amount of time needed to obtain high quality and comparable time-series data from multiple programs around the globe. SPOTS facilitates a variety of applications that benefit from the collective value of biogeochemical time-series observations, complementing relevant products for the global ocean that don’t offer the temporal variability and quality of data that fixed time-series programs have. This pilot gives a first glance of what SPOTS has to offer and hopefully many updates of a sustained time-series living data product, SPOTS, will follow.

Read more in the SPOTS paper and access data via BCODMO at https://www.bco-dmo.org/dataset/896862.

Mixotrophs in the northern North Atlantic

Posted by mmaheigan

· Tuesday, April 16th, 2024

Mixotrophs (or mixoplankton) are now accepted as a third group of plankton alongside phytoplankton and zooplankton. Our knowledge of mixotrophs lags far behind that of the other two groups. We currently have only a limited understanding of mixotrophs’ biogeographical distribution across ocean basins, and what environmental factors are associated with their distribution.

The authors of a study recently published in Frontiers in Marine Science reviewed nearly 230,000 individual microplankton samples collected by the North Atlantic Continuous Plankton Recorder program between 1958 and 2015 and calculated the proportion of organisms that are considered mixotrophs in each sample. They classified protist species in the dataset as phytoplankton, mixotrophs, or microzooplankton (heterotrophs), based on existing literature. Taken together across seasonsin shelf waters (depth ≤ 300m), mixotrophs comprise a greater proportion of the microplankton community when nitrate is high and photosynthetically available radiation (PAR) is low (e.g. during the late fall and winter), or when nitrate is low and PAR is moderate to high (e.g. during the summer and early fall). When both nitrate and PAR are high, mixotrophs comprise less of the community compared to phytoplankton. The same pattern was found in offshore waters (depth > 300m), but the key macronutrient was phosphate rather than nitrate. The annual average proportion of mixotrophs in microplankton samples compared to phytoplankton has increased since 1958 in the offshore portion of the study region, with a notable changepoint in 1993; this increasing trend is strongest in the winter season.

This paper is useful for aquatic ecologists who want to integrate mixotrophic plankton into their understanding of marine food webs and biogeochemical cycles. Understanding mixotroph temporal and spatial distributions, as well as the environmental conditions under which they flourish, is imperative to understanding their impact on trophic transfer and biogeochemical cycling.

Authors
Karen Stamieszkin (Bigelow Laboratory for Ocean Sciences)
Nicole Millette (Virginia Institute of Marine Science)
Jessica Luo (NOAA Geophysical Fluid Dynamics Laboratory)
Elizabeth Follett (University of Liverpool)
Nick Record (Bigelow Laboratory of Ocean Science)
David Johns (Marine Biological Association)

Backstory
This work and the collaboration that made it possible was catalyzed by the Eco-DAS XII symposium, attended by Karen Stamieszkin, Nicole Millette, Jessica Luo, and Elizabeth Follett in 2016. Nicole had an idea for an analysis but lacked collaborators, just as she was ready to give up on it, Karen, Jessica, and Elizabeth expressed interest in the project. Karen, Jessica, and Elizabeth each brought a unique perspective that helped make Nicole’s original idea more practical and ensured that the analysis would come to life.

The collaboration that began with this paper lead to the OCB Mixotrophs & Mixotrophy Working Group led by Karen, Jessica, and Nicole, and a successful grant proposal to study mixotrophy awarded to Nicole and Karen by NSF’s Biological Oceanography program. This story shows the importance and power of programs that connect researchers across disciplines, especially in the early stages of their careers.

Carbon sequestration by the biological pump is not exclusive to the deep ocean

Posted by mmaheigan

· Tuesday, April 16th, 2024

The biological carbon pump plays a key role in ocean carbon sequestration by transporting organic carbon from the upper ocean to deeper waters via three broad processes: the sinking of organic particles, vertical migration of organisms, and physical mixing. Most studies assume that century-scale carbon sequestration occurs only in the deep ocean, thus have missed sequestration that happens in the water column above 1,000m.

A recent publication reassessed the biological pump’s century-scale (≥100 years) carbon sequestration fluxes throughout the water column, by implementing the concept of ‘continuous vertical sequestration’ (CONVERSE). The resulting CONVERSE estimates were up to three times higher than those estimated at 1,000 m. This method shows that not only are these fluxes higher than previously thought, but also that vertical migration and physical mixing, which are generally neglected, make a significant contribution (20-30%) to carbon sequestration.

The CONVERSE method provides a new metric for calculations of the biological pump’s century-scale carbon sequestration flux that can be used to diagnose future changes in carbon sequestration fluxes in prognostic models of ocean biogeochemistry.

Interested in learning more? View more results and figures here.

Authors
Florian Ricour (Institute of Natural Sciences, Belgium)
Lionel Guidi (CNRS and Sorbonne University, France)
Marion Gehlen (CEA, CNRS and Paris-Saclay University, France)
Timothy Devries (University of California at Santa Barbara, USA)
Louis Legendre (Sorbonne University, France)

@LionelGuidi
@ComplexLov
@CNRS_INSU

Turbulent Mixing: A Dominant Source of Oxygen in the Upper Equatorial Pacific

Posted by mmaheigan

· Tuesday, March 12th, 2024

What balances oxygen removal in the equatorial Pacific? For a long time, oxygen in the eastern and central tropical Pacific was assumed to be mainly supplied by the large-scale advection of remotely ventilated waters via the equatorial current system and meridional circulation. A recent study used an eddy-resolving simulation of a global ocean model to show that turbulent mixing and its regulation by mesoscale eddies play a critical role in balancing oxygen removal (by consumption and upwelling) in the upper thermocline. Deeper in the water column, mean advection by the zonal currents and meridional circulation dominates. This mixing is tightly regulated by tropical instability waves, which intensify the shear between the equatorial currents and enhance the downward turbulent mixing flux of oxygen into the thermocline. Mesoscale phenomena thus play an indirect yet critical role as a local pathway of ventilation in this region. Testing these model-based hypotheses in the real ocean through dedicated field studies and long-term observations is needed to advance our understanding of the observed expansion of the oxygen deficient zones (ODZs) and model their future trajectory in a warmer and more stratified ocean.

Figure: The main processes that set the mean structure of oxygen in the equatorial Pacific are assessed in an eddy resolving simulation of the Community Earth System Model (CESM). Panel a shows the climatological oxygen distribution on the 26.25 isopycnal in CESM. Panels b-e show the contribution of advection by mean circulation and eddies, vertical mixing, and production and consumption. These processes are illustrated in panel f). Figure adapted from Eddebbar et al (2024).

Authors
Yassir A. Eddebbar (Scripps Institution of Oceanography)
Daniel B. Whitt (NASA Ames)
Ariane Verdy, (Scripps Institution of Oceanography)
Matthew R. Mazloff (Scripps Institution of Oceanography)
Aneesh C. Subramanian (CU Boulder)
Matthew C. Long, (National Center for Atmospheric Research)

Tiny parasites, big impact: Species networks and carbon recycling in an oligotrophic ocean

Posted by mmaheigan

· Tuesday, March 12th, 2024

Parasites are everywhere in the ocean. Including the microbial realm where a diverse, widespread group of protist parasites (Syndiniales) infect and kill a range of hosts, such as dinoflagellates, radiolarians, and even larger zooplankton. A complete Syndiniales infection cycle is only 2-3 days. First, the parasite is a free-living spore. Once inside a host, the parasite consumes the host’s carbon and becomes a larger multicellular organism (a trophont) eventually causing the host to burst open and release hundreds of new spores.

Like viruses, parasite lysis is expected to reroute organic carbon to the microbial loop, potentially decreasing the amount of carbon available for export to the deep sea. Yet, the role of Syndiniales in carbon cycling has been hard to define, as depth-specific infection dynamics and links to carbon export remain poorly understood.

Parasites are everywhere in the ocean. Including the microbial realm where a diverse, widespread group of protist parasites (Syndiniales) infect and kill a range of hosts, such as dinoflagellates, radiolarians, and even larger zooplankton. A complete Syndiniales infection cycle is only 2-3 days. First, the parasite is a free-living spore. Once inside a host, the parasite consumes the host’s carbon and becomes a larger multicellular organism (a trophont) eventually causing the host to burst open and release hundreds of new spores.

Figure 1. The mean relative abundance of Syndiniales (purple) in the photic zone (<140 m) is negatively correlated with particulate organic carbon (POC) flux at 150 m (p-value < 0.001). Similar correlations are not significant (p-values > 0.05) for other major 18S taxonomic groups, like Dinophyceae (red) and Arthropoda (green).

In a recent study published in ISME Communications, authors analyzed an 18S rRNA gene metabarcoding dataset from the Bermuda Atlantic Time-series Study (BATS) site that included 4 years (2016-2019) and twelve depths (1-1000 m). Syndiniales were the most dominant 18S group at BATS, present throughout the photic and aphotic zones. These parasites were prominent in species networks constructed with 18S sequence data, with significant associations with dinoflagellates and copepods in the surface, and with radiolarians in the aphotic zone. In addition, Syndiniales were the only major 18S group to be significantly (and negatively) correlated to particulate carbon flux (at 150 m), which was estimated from sediment trap data collected concurrently at BATS (Figure 1). This is in situ evidence of flux attenuation among Syndiniales, as they recycle host carbon that would otherwise transfer up to larger organisms (e.g., via grazing). Lastly, authors found 19% of the Syndiniales community is linked between photic and aphotic zones, indicating that parasites are sinking on particles and/or are recirculated via diel vertical migration. Overall, these findings elevate the role of Syndiniales in microbial food webs and further emphasize the importance in quantifying parasite-host dynamics to inform ocean carbon models.

Authors
Sean Anderson (University of New Hampshire / Woods Hole Oceanographic Institution)
Leocadio Blanco-Bercial (Bermuda Institute of Ocean Sciences / Arizona State University)
Craig Carlson (University of California, Santa Barbara)
Elizabeth Harvey (University of New Hampshire)

Coastal DOM database – CoastDOM v1

Posted by hbenway

· Wednesday, February 28th, 2024

We present the first edition of a global database (CoastDOM v1) and a resulting data manuscript, which compiles previously published and unpublished measurements of DOC, DON, and DOP in coastal waters, consisting of 62,338 (DOC), 20,356 (DON), and 13,533 (DOP) data points, respectively.

CoastDOM v1 includes observations of concentrations from all continents between 1978 and 2022. However, most data were collected in the Northern Hemisphere, with a clear gap in DOM measurements from the Southern Hemisphere.

This dataset will be useful for identifying global spatial and temporal patterns in DOM and will help facilitate the reuse of DOC, DON, and DOP data in studies aimed at better characterizing local biogeochemical processes; closing nutrient budgets; estimating carbon, nitrogen, and phosphorous pools; and establishing a baseline for modelling future changes in coastal waters.

The aim is to publish an updated version of the database periodically to determine global trends of DOM levels in coastal waters, and so if you have DOM data lying around, please submit it to Christian Lønborg (c.lonborg@ecos.au.dk).

CITATIONS

Lønborg et al. 2024. A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v1), Earth Syst. Sci. Data, 16, 1107–1119, https://doi.org/10.5194/essd-16-1107-2024

Lønborg et al. 2023.A global database of dissolved organic matter (DOM) concentration measurements in coastal waters (CoastDOM v.1). PANGAEA, https://doi.org/10.1594/PANGAEA.964012

Two OCB-led articles featured in AGU Eos Feb. Oceans Issue

Posted by hbenway

· Friday, January 26th, 2024

A Closer Look-Sea at the Ocean’s Carbon Cycle

AGU Eos highlights the following two articles emerging from OCB-led activities, including the OCB 2022 plenary session on the biological carbon pump and the 2022 OCB Workshop Marine Carbon Dioxide Removal: Essential Science and Problem Solving for Measurement, Reporting, and Verification.

New synthesis of global ocean greenhouse gas fluxes

Posted by hbenway

· Friday, January 26th, 2024

Resplandy, L., Hogikyan, A., Müller, J. D., Najjar, R. G., Bange, H. W., Bianchi, D., et al. (2024). A synthesis of global coastal ocean greenhouse gas fluxes. Global Biogeochemical Cycles, 38, e2023GB007803. https://doi.org/10.1029/2023GB007803.

New framework reveals gaps in US ocean biodiversity protection

Posted by hbenway

· Friday, January 26th, 2024

Gignoux-Wolfsohn et al., New framework reveals gaps in US ocean biodiversity protection, OneEarth (2023), https:// doi.org/10.1016/j.oneear.2023.12.014. (accompanying fact sheet)

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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A Closer Look-Sea at the Ocean’s Carbon Cycle

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