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  • 1
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    Modeling phytoplankton blooms and inorganic carbon responses to sea-ice variability in the West Antarctic Peninsula (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schultz, C., Doney, S. C., Hauck, J., Kavanaugh, M. T., & Schofield, O. Modeling phytoplankton blooms and inorganic carbon responses to sea-ice variability in the West Antarctic Peninsula. Journal of Geophysical Research: Biogeosciences, 126(4), (2021): e2020JG006227, https://doi.org/10.1029/2020JG006227.
    Description: The ocean coastal-shelf-slope ecosystem west of the Antarctic Peninsula (WAP) is a biologically productive region that could potentially act as a large sink of atmospheric carbon dioxide. The duration of the sea-ice season in the WAP shows large interannual variability. However, quantifying the mechanisms by which sea ice impacts biological productivity and surface dissolved inorganic carbon (DIC) remains a challenge due to the lack of data early in the phytoplankton growth season. In this study, we implemented a circulation, sea-ice, and biogeochemistry model (MITgcm-REcoM2) to study the effect of sea ice on phytoplankton blooms and surface DIC. Results were compared with satellite sea-ice and ocean color, and research ship surveys from the Palmer Long-Term Ecological Research (LTER) program. The simulations suggest that the annual sea-ice cycle has an important role in the seasonal DIC drawdown. In years of early sea-ice retreat, there is a longer growth season leading to larger seasonally integrated net primary production (NPP). Part of the biological uptake of DIC by phytoplankton, however, is counteracted by increased oceanic uptake of atmospheric CO2. Despite lower seasonal NPP, years of late sea-ice retreat show larger DIC drawdown, attributed to lower air-sea CO2 fluxes and increased dilution by sea-ice melt. The role of dissolved iron and iron limitation on WAP phytoplankton also remains a challenge due to the lack of data. The model results suggest sediments and glacial meltwater are the main sources in the coastal and shelf regions, with sediments being more influential in the northern coast.
    Description: C. Schultz, S. C. Doney, M. T. Kavanaugh, and O. Schofield acknowledge support by the US National Science Foundation (Grant no. PLR-1440435), and C. Schultz and S. C. Doney acknowledge support from the University of Virginia. This research has also received funding from the Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys), Grant number VH-NG-1301.
    Keywords: Air-sea fluxes ; Biogeochemical modeling ; Inorganic carbon cycle ; Phytoplankton bloom ; Sea ice ; West Antarctic Peninsula
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    WAP-1D-VAR v1.0: development and evaluation of a one-dimensional variational data assimilation model for the marine ecosystem along the West Antarctic Peninsula (2021)
    European Geosciences Union
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, H. H., Luo, Y.-W., Ducklow, H. W., Schofield, O. M., Steinberg, D. K., & Doney, S. C. WAP-1D-VAR v1.0: development and evaluation of a one-dimensional variational data assimilation model for the marine ecosystem along the West Antarctic Peninsula. Geoscientific Model Development, 14(8), (2021): 4939–4975, https://doi.org/10.5194/gmd-14-4939-2021.
    Description: The West Antarctic Peninsula (WAP) is a rapidly warming region, with substantial ecological and biogeochemical responses to the observed change and variability for the past decades, revealed by multi-decadal observations from the Palmer Antarctica Long-Term Ecological Research (LTER) program. The wealth of these long-term observations provides an important resource for ecosystem modeling, but there has been a lack of focus on the development of numerical models that simulate time-evolving plankton dynamics over the austral growth season along the coastal WAP. Here, we introduce a one-dimensional variational data assimilation planktonic ecosystem model (i.e., the WAP-1D-VAR v1.0 model) equipped with a model parameter optimization scheme. We first demonstrate the modified and newly added model schemes to the pre-existing food web and biogeochemical components of the other ecosystem models that WAP-1D-VAR model was adapted from, including diagnostic sea-ice forcing and trophic interactions specific to the WAP region. We then present the results from model experiments where we assimilate 11 different data types from an example Palmer LTER growth season (October 2002–March 2003) directly related to corresponding model state variables and flows between these variables. The iterative data assimilation procedure reduces the misfits between observations and model results by 58 %, compared to before optimization, via an optimized set of 12 parameters out of a total of 72 free parameters. The optimized model results capture key WAP ecological features, such as blooms during seasonal sea-ice retreat, the lack of macronutrient limitation, and modeled variables and flows comparable to other studies in the WAP region, as well as several important ecosystem metrics. One exception is that the model slightly underestimates particle export flux, for which we discuss potential underlying reasons. The data assimilation scheme of the WAP-1D-VAR model enables the available observational data to constrain previously poorly understood processes, including the partitioning of primary production by different phytoplankton groups, the optimal chlorophyll-to-carbon ratio of the WAP phytoplankton community, and the partitioning of dissolved organic carbon pools with different lability. The WAP-1D-VAR model can be successfully employed to link the snapshots collected by the available data sets together to explain and understand the observed dynamics along the coastal WAP.
    Description: Hyewon Heather Kim and Scott C. Doney were supported by the National Aeronautics and Space Administration Ocean Biology and Biogeochemistry Program (grant no. NNX14AL86G) and the US National Science Foundation Office of Polar Programs (grant no. PLR-1440435 to Hugh W. Ducklow at Columbia University; Palmer LTER). Hyewon Heather Kim was additionally supported by the Investment in Science Fund and the Reuben F. and Elizabeth B. Richards Endowed Fund from Woods Hole Oceanographic Institution. Oscar M. Schofield and Deborah K. Steinberg were supported by US NSF grant no. PLR-1440435. Ya-Wei Luo was supported by National Natural Science Foundation of China project no. 41890802.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, Y., Moreno, C., Marchetti, A., Ducklow, H., Schofield, O., Delage, E., Meredith, M., Li, Z., Eveillard, D., Chaffron, S., & Cassar, N. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula. Nature Communications, 12(1), (2021): 4948, https://doi.org/10.1038/s41467-021-25235-w.
    Description: Since the middle of the past century, the Western Antarctic Peninsula has warmed rapidly with a significant loss of sea ice but the impacts on plankton biodiversity and carbon cycling remain an open question. Here, using a 5-year dataset of eukaryotic plankton DNA metabarcoding, we assess changes in biodiversity and net community production in this region. Our results show that sea-ice extent is a dominant factor influencing eukaryotic plankton community composition, biodiversity, and net community production. Species richness and evenness decline with an increase in sea surface temperature (SST). In regions with low SST and shallow mixed layers, the community was dominated by a diverse assemblage of diatoms and dinoflagellates. Conversely, less diverse plankton assemblages were observed in waters with higher SST and/or deep mixed layers when sea ice extent was lower. A genetic programming machine-learning model explained up to 80% of the net community production variability at the Western Antarctic Peninsula. Among the biological explanatory variables, the sea-ice environment associated plankton assemblage is the best predictor of net community production. We conclude that eukaryotic plankton diversity and carbon cycling at the Western Antarctic Peninsula are strongly linked to sea-ice conditions.
    Description: This work is supported by NSF OPP-1643534 to N.C., NSF OPP-1341479 to A.M., and NSF PLR-1440435 to H.D. and O.S. (Palmer LTER).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits (2022)
    European Geosciences Union
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, H. H., Bowman, J. S., Luo, Y.-W., Ducklow, H. W., Schofield, O. M., Steinberg, D. K., & Doney, S. C. Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits. Biogeosciences, 19(1), (2022): 117–136, https://doi.org/10.5194/bg-19-117-2022.
    Description: Heterotrophic marine bacteria utilize organic carbon for growth and biomass synthesis. Thus, their physiological variability is key to the balance between the production and consumption of organic matter and ultimately particle export in the ocean. Here we investigate a potential link between bacterial traits and ecosystem functions in the rapidly warming West Antarctic Peninsula (WAP) region based on a bacteria-oriented ecosystem model. Using a data assimilation scheme, we utilize the observations of bacterial groups with different physiological traits to constrain the group-specific bacterial ecosystem functions in the model. We then examine the association of the modeled bacterial and other key ecosystem functions with eight recurrent modes representative of different bacterial taxonomic traits. Both taxonomic and physiological traits reflect the variability in bacterial carbon demand, net primary production, and particle sinking flux. Numerical experiments under perturbed climate conditions demonstrate a potential shift from low nucleic acid bacteria to high nucleic acid bacteria-dominated communities in the coastal WAP. Our study suggests that bacterial diversity via different taxonomic and physiological traits can guide the modeling of the polar marine ecosystem functions under climate change.
    Description: This research has been supported by the NASA (grant no. NNX14AL86G) and the NSF (grant no. PLR-1440435).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) (2022)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-27
    Description: Dataset: cluster analysis - Carbonate Organic Matrix proteins
    Description: This dataset includes results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/536485
    Description: NSF Emerging Frontiers Division (NSF EF) EF-1041143
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 6
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    FIReglider: mapping in situ chlorophyll variable fluorescence with autonomous underwater gliders (2020)
    Association for the Sciences of Limnology and Oceanography
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), [year]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carvalho, F., Gorbunov, M. Y., Oliver, M. J., Haskins, C., Aragon, D., Kohut, J. T., & Schofield, O. FIReglider: mapping in situ chlorophyll variable fluorescence with autonomous underwater gliders. Limnology and Oceanography: Methods, (2020), doi:10.1002/lom3.10380.
    Description: Nutrient and light availability regulate phytoplankton physiology and photosynthesis in the ocean. These physiological processes are difficult to sample in time and space over physiologically and ecologically relevant scales using traditional shipboard techniques. Gliders are changing the nature of data collection, by allowing a sustained presence at sea over regional scales, collecting data at resolution not possible using traditional techniques. The integration of a fluorescence induction and relaxation (FIRe) sensor in a Slocum glider allows autonomous high‐resolution and vertically‐resolved measurements of photosynthetic physiological variables together with oceanographic data. In situ measurements of variable fluorescence under ambient light allows a better understanding of the physical controls of primary production (PP). We demonstrate this capability in a laboratory setting and with several glider deployments in the Southern Ocean. Development of these approaches will allow for the in situ evaluation of phytoplankton light stress and photoacclimation mechanisms, as well as the role of vertical mixing in phytoplankton dynamics and the underlying physiology, especially in remote locations and for prolonged duration.
    Description: This work was supported by National Science Foundation (NSF Palmer LTER program, grant 0823101), National Oceanographic Partnership Program (NOPP, grant NA05OAR4601089), and NASA Ocean Biology and Biogeochemistry Program (grants NNX16AT54G and 80NSSC18K1416). Filipa Carvalho was funded by a Portuguese doctoral fellowship from Fundação para a Ciência e Tecnologia (FCT, grant DFRH ‐ SFRH/BD/72705/2010), a Teledyne Marine Graduate Fellowship and a European Research Council Consolidator grant (GOCART, agreement number 724416).
    Repository Name: Woods Hole Open Access Server
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  • 7
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    On the development of SWOT in situ calibration/validation for short-wavelength ocean topography (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-11-01
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 39(5), (2022): 595–617, https://doi.org/10.1175/jtech-d-21-0039.1.
    Description: The future Surface Water and Ocean Topography (SWOT) mission aims to map sea surface height (SSH) in wide swaths with an unprecedented spatial resolution and subcentimeter accuracy. The instrument performance needs to be verified using independent measurements in a process known as calibration and validation (Cal/Val). The SWOT Cal/Val needs in situ measurements that can make synoptic observations of SSH field over an O(100) km distance with an accuracy matching the SWOT requirements specified in terms of the along-track wavenumber spectrum of SSH error. No existing in situ observing system has been demonstrated to meet this challenge. A field campaign was conducted during September 2019–January 2020 to assess the potential of various instruments and platforms to meet the SWOT Cal/Val requirement. These instruments include two GPS buoys, two bottom pressure recorders (BPR), three moorings with fixed conductivity–temperature–depth (CTD) and CTD profilers, and a glider. The observations demonstrated that 1) the SSH (hydrostatic) equation can be closed with 1–3 cm RMS residual using BPR, CTD mooring and GPS SSH, and 2) using the upper-ocean steric height derived from CTD moorings enable subcentimeter accuracy in the California Current region during the 2019/20 winter. Given that the three moorings are separated at 10–20–30 km distance, the observations provide valuable information about the small-scale SSH variability associated with the ocean circulation at frequencies ranging from hourly to monthly in the region. The combined analysis sheds light on the design of the SWOT mission postlaunch Cal/Val field campaign.
    Description: The research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004). All authors are supported by the SWOT project. J. T. Farrar was partially supported by NASA NNX16AH76G.
    Description: 2022-11-01
    Keywords: Internal waves ; Ocean dynamics ; Small scale processes ; Altimetry ; Global positioning systems (GPS) ; In situ oceanic observations ; Ship observations
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    Results of cluster analysis and gene ontology: cross-phyla clustering of non-redundant carbonate organic matrix proteins from coral, mollusk, and sea urchin grouped by hierarchical clustering; analyzed in the Falkowski lab at Rutgers from 2010-2014 (2022)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-27
    Description: Dataset: cluster analysis - cross-phyla protein clustering
    Description: This dataset includes the results of cluster analysis and gene ontology: cross-phyla clustering of non-redundant carbonate organic matrix proteins from coral, mollusk, and sea urchin grouped by hierarchical clustering; analyzed in the Falkowski lab at Rutgers from 2010-2014. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/536074
    Description: NSF Emerging Frontiers Division (NSF EF) EF-1041143
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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