Matt Long (Aug 06 2020 at 14:38): Matt Long (Aug 06 2020 at 14:38):Marine heatwaves: https://www.nature.com/articles/s41586-020-2534-z
(@Precious Mongwe, this is relevant to your current paper.)
Precious Mongwe (Aug 06 2020 at 17:04):@Matt Long got it, thanks
Matt Long (Aug 22 2020 at 13:17):Simple Global Ocean Biogeochemistry with Light, Iron, Nutrients and Gas version 2 (BLINGv2): Model description and simulation characteristics in GFDL’s CM4.0
https://doi.org/10.1029/2019MS002008
Matt Long (Aug 22 2020 at 13:17):Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and CMIP6
https://doi.org/10.1007/s40641-020-00160-0
Keith Lindsay (Aug 22 2020 at 14:24):It appears that the registration of the DOI for the BLINGv2 paper isn't complete.
In the meantime, I'm able to access the paper via
https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2019MS002008
Matt Long (Oct 30 2020 at 16:14):Biological nitrogen fixation detected under Antarctic sea ice
Nitrogen fixation is the primary source of reactive nitrogen in the ocean. Most ecological models do not predict nitrogen fixation in the Antarctic Ocean because of the low availability of iron and high abundance of nitrogen. Here we extensively examined nitrogen fixation in the Antarctic Ocean, and found substantial nitrogen fixation (maximum: 44.4 nmol N l−1 d−1) near the Antarctic coast, especially around ice-covered regions. The nitrogenase gene (nifH) was detected at all coastal stations, including stations where no nitrogen fixation was found. At the stations where nitrogen fixation was detected, the nitrogen-fixing cyanobacterium UCYN-A (Candidatus ‘Atelocyanobacterium thalassa’) dominated nifH gene expression, and the nifH sequence was identical to that of the major oligotype in tropical and subtropical oceans. Our results suggest that marine nitrogen fixation is a ubiquitous process in the global ocean, and that UCYN-A is the keystone species for making it possible.
https://www.nature.com/articles/s41561-020-00651-7
Matt Long (Nov 02 2020 at 15:50):Planet Microbe
Enabling the discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers.
https://www.planetmicrobe.org/
Matt Long (Nov 03 2020 at 13:10):PhytoBase: A global synthesis of open-ocean phytoplankton occurrences
Marine phytoplankton are responsible for half of the global net primary production and perform multiple other ecological functions and services of the global ocean. These photosynthetic organisms comprise more than 4300 marine species, but their biogeographic patterns and the resulting species diversity are poorly known, mostly owing to severe data limitations. Here, we compile, synthesize, and harmonize marine phytoplankton occurrence records from the two largest biological occurrence archives (Ocean Biogeographic Information System, OBIS; and Global Biodiversity Information Facility, GBIF) and three independent recent data collections. We bring together over 1.36 million phytoplankton occurrence records (1.28 million at the level of species) for a total of 1704 species, spanning the principal groups of the diatoms, dinoflagellates, and haptophytes, as well as several other groups. This data compilation increases the amount of marine phytoplankton records available through the single largest contributing archive (OBIS) by 65 %. Data span all ocean basins, latitudes, and most seasons. Analyzing the oceanic inventory of sampled phytoplankton species richness at the broadest spatial scales possible using a resampling procedure, we find that richness tends to saturate at ∼93 % of all species in our database in the pantropics, at ∼64 % in temperate waters, and at ∼35 % in the cold Northern Hemisphere, while the Southern Hemisphere remains under-explored. We provide metadata on the cruise, research institution, depth, and date for each data record, and we include phytoplankton cell counts for 193 763 records. We strongly recommend consideration of spatiotemporal biases in sampling intensity and varying taxonomic sampling scopes between research cruises or institutions when analyzing the occurrence data spatially. Including such information into predictive tools, such as statistical species distribution models, may serve to project the diversity, niches, and distribution of species in the contemporary and future ocean, opening the door for quantitative macroecological analyses of phytoplankton. PhytoBase can be downloaded from PANGAEA: https://doi.org/10.1594/PANGAEA.904397 (Righetti et al., 2019a).
https://essd.copernicus.org/articles/12/907/2020/
cc @Kristen Krumhardt
Precious Mongwe (Nov 03 2020 at 16:46):Let more big fish sink: Fisheries prevent blue carbon sequestration—half in unprofitable areas
Gaël Mariani et al., 2020
Contrary to most terrestrial organisms, which release their carbon into the atmosphere after death, carcasses of large marine fish sink and sequester carbon in the deep ocean. Yet, fisheries have extracted a massive amount of this “blue carbon,” contributing to additional atmospheric CO2 emissions. Here, we used historical catches and fuel consumption to show that ocean fisheries have released a minimum of 0.73 billion metric tons of CO2 (GtCO2) in the atmosphere since 1950. Globally, 43.5% of the blue carbon extracted by fisheries in the high seas comes from areas that would be economically unprofitable without subsidies. Limiting blue carbon extraction by fisheries, particularly on unprofitable areas, would reduce CO2 emissions by burning less fuel and reactivating a natural carbon pump through the rebuilding of fish stocks and the increase of carcasses deadfall.
https://advances.sciencemag.org/content/advances/6/44/eabb4848.full.pdf
Yassir Eddebbar (Nov 06 2020 at 00:56):Metabolic trait diversity shapes marine biogeography:
Deutsch, et al.
Climate and physiology shape biogeography, yet the range limits of species can rarely be ascribed to the quantitative traits of organisms1–3. Here we evaluate whether the geographical range boundaries of species coincide with ecophysiological limits to acquisition of aerobic energy4 for a global cross-section of the biodiversity of marine animals. We observe a tight correlation between the metabolic rate and the efficacy
of oxygen supply, and between the temperature sensitivities of these traits, which suggests that marine animals are under strong selection for the tolerance of low O2 (hypoxia)5. The breadth of the resulting physiological tolerances of marine animals predicts a variety of geographical niches—from the tropics to high latitudes and from shallow to deep water—which better align with species distributions than do models based on either temperature or oxygen alone. For all studied species, thermal and hypoxic limits are substantially reduced by the energetic demands of ecological activity, a trait that varies similarly among marine and terrestrial taxa. Active temperature-dependent hypoxia thus links the biogeography of diverse marine species to fundamental energetic requirements that are shared across the animal kingdom.
https://www.nature.com/articles/s41586-020-2721-y
Precious Mongwe (Nov 06 2020 at 14:53):Precious Mongwe7:52 AM
:+1:, thanks Yassir
Matt Long (Dec 09 2020 at 13:25):The potential role of turbulence in modulating the migration of demersal zooplankton
Despite suggestions that turbulence can affect the migration of zooplankton, field observations of such effects are scarce. This is especially the case for bottom‐associated (demersal) zooplankton that reside in the typically turbulent near‐bottom environment. Using moored sensors deployed at two coastal sites in the North Pacific and the Red Sea, we present observations of the effects of turbulence on the nocturnal emergence of demersal zooplankton. A cabled observatory consisting of a plankton camera, an acoustic current profiler and environmental sensors, was deployed near bottom in 20 m of water near Oshima Island, Japan. Observations were also obtained from a second site near a coral reef in 16 m of water in the Red Sea. Acoustic backscatter data obtained from current profilers at both sites provided a proxy for zooplankton density. Combined with simultaneous estimates of turbulence intensity, the observations suggest that the nocturnal emergence of demersal zooplankton was hindered by elevated levels of turbulence. While our findings are inferred from acoustic data, agreement between the two different sites supports our hypothesis that demersal zooplankton may remain near the bed during times of strong turbulence.
https://doi.org/10.1002/lno.11646
Precious Mongwe (Dec 09 2020 at 23:03)::+1:
Matt Long (Jan 05 2021 at 12:25):Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill fecal pellets
Detritivores need to upgrade their food to increase its nutritional value. One method is to fragment detritus promoting the colonization of nutrient-rich microbes, which consumers then ingest along with the detritus; so-called microbial
gardening. Observations and numerical models of the detritus-dominated ocean mesopelagic zone have suggested microbial gardening by zooplankton is a fundamental process in the ocean carbon cycle leading to increased respiration of carbon-rich detritus. However, no experimental evidence exists to demonstrate that microbial respiration rates are higher on recently fragmented sinking detrital particles.
https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7119
Michael Levy (Jan 21 2021 at 19:07):Two papers by Moha about DA for parameter estimation in ocean BGC models. Both are available for download using the NCAR Library proxy:
Online tuning of ocean biogeochemical model parameters using ensemble estimation techniques: Application to a one-dimensional model in the North Atlantic
Given the recent focus on developing new data assimilation systems for biological models, we present in this study the application of a newly developed state-parameters estimation tool for a marine ecosystem model. The data assimilation scheme is based on the original Ensemble Kalman Filter (EnKF) algorithm and further applies a One-Step-Ahead smoothing to the state variables.
https://www.sciencedirect.com/science/article/abs/pii/S0924796316304407
Ensemble data assimilation for ocean biogeochemical state and parameter estimation at different sites
We develop an efficient data assimilation system that aims at quantifying the uncertainties of various biogeochemical states and parameters. We explore the use of four different ensemble estimation techniques for tuning poorly constrained ecosystem parameters using a one-dimensional configuration of the Ocean Biogeochemical General Circulation Model. The schemes are all EnKF-based operating sequentially in time but have different correction equations.
https://www.sciencedirect.com/science/article/abs/pii/S1463500317300215
Matt Long (Feb 03 2021 at 17:30):A Roadmap for Using the UN Decade of Ocean Science for Sustainable Development in Support of Science, Policy, and Action
https://doi.org/10.1016/j.oneear.2019.10.012
cc @Zephyr Sylvester
Matt Long (Feb 03 2021 at 20:16):Opinion: Will understanding the ocean lead to “the ocean we want”?
https://doi.org/10.1073/pnas.2100205118
Matt Long (Feb 16 2021 at 16:10):Global Drivers on Southern Ocean Ecosystems: Changing Physical Environments and Anthropogenic Pressures in an Earth System
https://doi.org/10.3389/fmars.2020.547188
Matt Long (Feb 25 2021 at 20:49):Identifying global favourable habitat for early juvenile loggerhead sea turtles
Matt Long (Oct 01 2021 at 11:09):What’s the Least Bad Way to Cool the Planet?
https://www.nytimes.com/2021/10/01/opinion/climate-change-geoengineering.html?smid=url-share
Matt Long (Oct 05 2021 at 18:49):Some interesting new papers in Nature Geoscience:
Sensitivity of Holocene East Antarctic productivity to subdecadal variability set by sea ice
Katelyn M. Johnson, Robert M. McKay, Johan Etourneau, Francisco J. Jiménez-Espejo, Anya Albot et al.
doi:10.1038/s41561-021-00816-y
A mid-Holocene expansion of coastal sea ice led to phytoplankton blooms’ becoming less frequent off East Antarctica, according to a suite of annually resolved physical and geochemical analyses performed on a marine sediment core.
Constraint on net primary productivity of the global ocean by Argo oxygen measurements
Kenneth S. Johnson & Mariana B. Bif
doi:10.1038/s41561-021-00807-z
Argo measurements provide a constrained estimate of net primary productivity of the global ocean of 53 Pg C y–1, according to a global analysis of diel oxygen variations.
Sinking enhances the degradation of organic particles by marine bacteria
Uria Alcolombri, François J. Peaudecerf, Vicente I. Fernandez, Lars Behrendt, Kang Soo Lee et al.
doi:10.1038/s41561-021-00817-x
Faster sinking rates can enhance bacterial degradation of organic particles in the ocean due to flow-induced removal of waste products, according to laboratory experiments and modelling of the marine carbon pump.
Matt Long (Nov 10 2021 at 16:45):Baleen whale prey consumption based on high-resolution foraging measurements
Baleen whales influence their ecosystems through immense prey consumption and nutrient recycling1,2,3. It is difficult to accurately gauge the magnitude of their current or historic ecosystem role without measuring feeding rates and prey consumed. To date, prey consumption of the largest species has been estimated using metabolic models3,4,5,6,7,8,9 based on extrapolations that lack empirical validation. Here, we used tags deployed on seven baleen whale (Mysticeti) species (n = 321 tag deployments) in conjunction with acoustic measurements of prey density to calculate prey consumption at daily to annual scales from the Atlantic, Pacific, and Southern Oceans. Our results suggest that previous studies3,4,5,6,7,8,9 have underestimated baleen whale prey consumption by threefold or more in some ecosystems. In the Southern Ocean alone, we calculate that pre-whaling populations of mysticetes annually consumed 430 million tonnes of Antarctic krill (Euphausia superba), twice the current estimated total biomass of E. superba10, and more than twice the global catch of marine fisheries today11. Larger whale populations may have supported higher productivity in large marine regions through enhanced nutrient recycling: our findings suggest mysticetes recycled 1.2 × 104 tonnes iron yr−1 in the Southern Ocean before whaling compared to 1.2 × 103 tonnes iron yr−1 recycled by whales today. The recovery of baleen whales and their nutrient recycling services2,3,7 could augment productivity and restore ecosystem function lost during 20th century whaling12,13.
https://doi.org/10.1038/s41586-021-03991-5
Matt Long (Nov 16 2021 at 21:57):Seasonal Arctic sea ice forecasting with probabilistic deep learning
https://www.nature.com/articles/s41467-021-25257-4
@Dan Amrhein
Matt Long (Dec 02 2021 at 19:30):Strong Southern Ocean carbon uptake evident in airborne observations
The Southern Ocean plays an important role in determining atmospheric carbon dioxide (CO2), yet estimates of air-sea CO2 flux for the region diverge widely. In this study, we constrained Southern Ocean air-sea CO2 exchange by relating fluxes to horizontal and vertical CO2 gradients in atmospheric transport models and applying atmospheric observations of these gradients to estimate fluxes. Aircraft-based measurements of the vertical atmospheric CO2 gradient provide robust flux constraints. We found an annual mean flux of –0.53 ± 0.23 petagrams of carbon per year (net uptake) south of 45°S during the period 2009–2018. This is consistent with the mean of atmospheric inversion estimates and surface-ocean partial pressure of CO2 (PCO2)–based products, but our data indicate stronger annual mean uptake than suggested by recent interpretations of profiling float observations.
https://www.science.org/doi/10.1126/science.abi4355
Matt Long (Jan 07 2022 at 19:22):@Dan Amrhein, it would be fun to find a time to discuss this paper. Note the sentence in the abstract below:
a Green's function approach is used to optimize the biogeochemistry
The ECCO-Darwin Data-Assimilative Global Ocean Biogeochemistry Model: Estimates of Seasonal to Multidecadal Surface Ocean pCO2 and Air-Sea CO2 Flux
Quantifying variability in the ocean carbon sink remains problematic due to sparse observations and spatiotemporal variability in surface ocean pCO2. To address this challenge, we have updated and improved ECCO-Darwin, a global ocean biogeochemistry model that assimilates both physical and biogeochemical observations. The model consists of an adjoint-based ocean circulation estimate from the Estimating the Circulation and Climate of the Ocean (ECCO) consortium and an ecosystem model developed by the Massachusetts Institute of Technology Darwin Project. In addition to the data-constrained ECCO physics, a Green's function approach is used to optimize the biogeochemistry by adjusting initial conditions and six biogeochemical parameters. Over seasonal to multidecadal timescales (1995–2017), ECCO-Darwin exhibits broad-scale consistency with observed surface ocean pCO2 and air-sea CO2 flux reconstructions in most biomes, particularly in the subtropical and equatorial regions. The largest differences between CO2 uptake occur in subpolar seasonally stratified biomes, where ECCO-Darwin results in stronger winter uptake. Compared to the Global Carbon Project OBMs, ECCO-Darwin has a time-mean global ocean CO2 sink (2.47 ± 0.50 Pg C year−1) and interannual variability that are more consistent with interpolation-based products. Compared to interpolation-based methods, ECCO-Darwin is less sensitive to sparse and irregularly sampled observations. Thus, ECCO-Darwin provides a basis for identifying and predicting the consequences of natural and anthropogenic perturbations to the ocean carbon cycle, as well as the climate-related sensitivity of marine ecosystems. Our study further highlights the importance of physically consistent, property-conserving reconstructions, as are provided by ECCO, for ocean biogeochemistry studies.
https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2019MS001888
Matt Long (Jan 11 2022 at 17:41):Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus
https://doi.org/10.1073/pnas.2110993118
Matt Long (Feb 08 2022 at 20:36):@Kristen Krumhardt and others,
Here are some discussion papers from Lennart Bach's group on CDR
BGD - Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
https://bg.copernicus.org/preprints/bg-2022-17/
BGD - Investigating the effect of nickel concentration on phytoplankton growth to inform the assessment of ocean alkalinity enhancement
https://bg.copernicus.org/preprints/bg-2021-312/
BGD - Ocean Alkalinity Enhancement – Avoiding runaway CaCO3 precipitation during quick and hydrated lime dissolution
https://bg.copernicus.org/preprints/bg-2021-330/
Matt Long (Mar 12 2022 at 00:02):@Kristen Krumhardt Colleen just shared this with me:
Oceanic and Atmospheric Drivers of Post-El-Ni o Chlorophyll Rebound in the Equatorial Pacific
https://doi.org/10.1029/2021GL096113
Matt Long (Apr 05 2022 at 18:55):Reliable information about the future state of the ocean and fish stocks is necessary for informed decision-making by fisheries scientists, managers and the industry. However, decadal regional ocean climate and fish stock predictions have until now had low forecast skill. Here, we provide skilful forecasts of the biomass of cod stocks in the North and Barents Seas a decade in advance. We develop a unified dynamical-statistical prediction system wherein statistical models link future stock biomass to dynamical predictions of sea surface temperature, while also considering different fishing mortalities. Our retrospective forecasts provide estimates of past performance of our models and they suggest differences in the source of prediction skill between the two cod stocks. We forecast the continuation of unfavorable oceanic conditions for the North Sea cod in the coming decade, which would inhibit its recovery at present fishing levels, and a decrease in Northeast Arctic cod stock compared to the recent high levels.
https://www.nature.com/articles/s43247-021-00207-6
Yassir Eddebbar (Jun 10 2022 at 01:00):Strong Habitat Compression by Extreme Shoaling Events of Hypoxic Waters in the Eastern Pacific
Ocean deoxygenation has led to a measurable shoaling of subsurface hypoxic waters ([O2] < 60 mmol m−3) in the tropical Pacific and elsewhere. This shoaling compresses the vertical habitat of heterotrophic organisms between the well oxygenated surface and the hypoxic interface. Superimposed on this long-term trend, natural variability can cause shorter-term, extreme habitat compression events, which we term Transient Habitat Reduction Extreme Events (THREEs). Here, we investigate THREEs in the Eastern Pacific (EP) between 1979 and 2016 using output from a high-resolution hindcast simulation with the coupled physical-biogeochemical ocean model ROMS-BEC. We identify THREEs on the basis of the hypoxic interface being shallower than the 99th percentile of its variability and requiring a minimum duration of 5 days. We find that THREEs compress the aerobic habitat by up to 50-70% (locally exceeding 80%) in the subtropical and tropical EP and reach horizontal scales exceeding 300 km in the tropical EP. There, THREEs are pre-conditioned by La Nin ̃a conditions and occur primarily in boreal winter and spring. In the subtropical EP, THREEs are associated with mesoscale eddies and occur independently of the season. 71% (32%) of all THREEs are characterized by unusually high acidity (cold) conditions (i.e., below the 1st percentile), thus constituting compound events. The strong habitat compression during THREEs is bound to lead to substantial changes in water column biogeochemistry, in food-web interactions, and in ecosystem structure. Yet, so far, very little is known about the impact of these transient phenomena.
https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2022JC018429
Matt Long (Aug 15 2022 at 22:23):Vertically migrating phytoplankton fuel high oceanic primary production
https://www.nature.com/articles/s41558-022-01430-5
Matt Long (Aug 16 2022 at 17:01):What controls the large-scale efficiency of carbon transfer through the ocean’s mesopelagic zone? Insights from a new, mechanistic model (MSPACMAM)
https://doi.org/10.1029/2021GB007131
Frank Bryan (Sep 28 2022 at 15:42):From the co-developer of the EBM:
(https://bg.copernicus.org/articles/19/4479/2022/)
Whitney, MM, Observed and projected global warming pressure on coastal hypoxia, Biogeosciences
Volume19, Issue18, 4479-4497
DOI10.5194/bg-19-4479-2022
Matt Long (Jan 11 2023 at 18:29):Quantifying the Ocean’s Biological Pump and Its Carbon Cycle Impacts on Global Scales
Here's a nice review by Dave Siegel on the biological pump.
@Elizabeth Yankovsky, @Kristen Krumhardt see section on the "migrant pump."
Yassir Eddebbar (Feb 24 2023 at 22:30):Preprint Discussion for: GOBAI-O2: temporally and spatially resolved fields of ocean interior dissolved oxygen over nearly two decades By Jonathan Sharp et al.
https://essd.copernicus.org/preprints/essd-2022-308/essd-2022-308.pdf
Yassir Eddebbar (Feb 24 2023 at 22:34): Keith Lindsay (May 23 2023 at 19:06):Kane, A., Moulin, C., Thiria, S., Bopp, L., Berrada, M., Tagliabue, A., Crépon, M., Aumont, O., and Badran, F. (2011), Improving the parameters of a global ocean biogeochemical model via variational assimilation of in situ data at five time series stations, J. Geophys. Res., 116, C06011, doi:10.1029/2009JC006005.
Keith Lindsay (May 23 2023 at 19:11):M.E. Gharamti, J. Tjiputra, I. Bethke, A. Samuelsen, I. Skjelvan, M. Bentsen, L. Bertino,
Ensemble data assimilation for ocean biogeochemical state and parameter estimation at different sites,
Ocean Modelling, Volume 112, 2017, Pages 65-89, https://doi.org/10.1016/j.ocemod.2017.02.006.
Last updated: May 16 2025 at 17:14 UTC