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  • Modeling  (12)
  • Oxygen  (8)
  • Dissolved organic carbon
  • Flow-through
  • John Wiley & Sons  (20)
  • American Chemical Society  (2)
  • American Chemical Society (ACS)
  • 1
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    Emerging opportunities and challenges in phenology : a review (2016)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecosphere 7 (2016): e01436, doi:10.1002/ecs2.1436.
    Description: Plant phenology research has gained increasing attention because of the sensitivity of phenology to climate change and its consequences for ecosystem function. Recent technological development has made it possible to gather invaluable data at a variety of spatial and ecological scales. Despite our ability to observe phenological change at multiple scales, the mechanistic basis of phenology is still not well understood. Integration of multiple disciplines, including ecology, evolutionary biology, climate science, and remote sensing, with long-term monitoring data across multiple spatial scales is needed to advance understanding of phenology. We review the mechanisms and major drivers of plant phenology, including temperature, photoperiod, and winter chilling, as well as other factors such as competition, resource limitation, and genetics. Shifts in plant phenology have significant consequences on ecosystem productivity, carbon cycling, competition, food webs, and other ecosystem functions and services. We summarize recent advances in observation techniques across multiple spatial scales, including digital repeat photography, other complementary optical measurements, and solar-induced fluorescence, to assess our capability to address the importance of these scale-dependent drivers. Then, we review phenology models as an important component of earth system modeling. We find that the lack of species-level knowledge and observation data leads to difficulties in the development of vegetation phenology models at ecosystem or community scales. Finally, we recommend further research to advance understanding of the mechanisms governing phenology and the standardization of phenology observation methods across networks. With the opportunity for “big data” collection for plant phenology, we envision a breakthrough in process-based phenology modeling.
    Description: U.S. National Science Foundation Grant Numbers: PLR-1417763, DBI-959333, AGS-1005663; University of Chicago and the MBL Lillie Research Innovation Award; NEXT Program; KAKENHI (MEXT, Japan); National Science Foundation of China Grant Number: 41571103; NERC Grant Number: NE/J02080X/1
    Keywords: Cameras ; Greenness ; ILTER ; Modeling ; Phenology ; Scale ; International LTER
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Forum for Arctic Modeling and Observational Synthesis (FAMOS) : past, current, and future activities (2016)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 121 (2016): 3803–3819, doi:10.1002/2016JC011898.
    Description: The overall goal of the Forum for Arctic Modeling and Observational Synthesis (FAMOS) community activities reported in this special issue is to enhance understanding of processes and mechanisms driving Arctic Ocean marine and sea ice changes, and the consequences of those changes especially in biogeochemical and ecosystem studies. Major 2013–2015 FAMOS accomplishments to date are: identification of consistent errors across Arctic regional models; approaches to reduce these errors, and recommendations for the most effective coupled sea ice-ocean models for use in fully coupled regional and global climate models. 2013–2015 FAMOS coordinated analyses include many process studies, using models together with observations to investigate: dynamics and mechanisms responsible for drift, deformation and thermodynamics of sea ice; pathways and mechanisms driving variability of the Atlantic, Pacific and river waters in the Arctic Ocean; processes of freshwater accumulation and release in the Beaufort Gyre; the fate of melt water from Greenland; characteristics of ocean eddies; biogeochemistry and ecosystem processes and change, climate variability, and predictability. Future FAMOS collaborations will focus on employing models and conducting observations at high and very high spatial and temporal resolution to investigate the role of subgrid-scale processes in regional Arctic Ocean and coupled ice-ocean and atmosphere-ice-ocean models.
    Description: National Science Foundation Office of Polar Programs. Grant Number: PLR-1313614 and PLR- 1313647
    Keywords: Introduction ; Arctic ; Modeling
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Quantifying subtropical North Pacific gyre mixed layer primary productivity from Seaglider observations of diel oxygen cycles (2015)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geophysical Research Letters 42 (2015): 4032–4039, doi:10.1002/2015GL063065.
    Description: Using autonomous underwater gliders, we quantified diurnal periodicity in dissolved oxygen, chlorophyll, and temperature in the subtropical North Pacific near the Hawaii Ocean Time-series (HOT) Station ALOHA during summer 2012. Oxygen optodes provided sufficient stability and precision to quantify diel cycles of average amplitude of 0.6 µmol kg−1. A theoretical diel curve was fit to daily observations to infer an average mixed layer gross primary productivity (GPP) of 1.8 mmol O2 m−3 d−1. Cumulative net community production (NCP) over 110 days was 500 mmol O2 m−2 for the mixed layer, which averaged 57 m in depth. Both GPP and NCP estimates indicated a significant period of below-average productivity at Station ALOHA in 2012, an observation confirmed by 14C productivity incubations and O2/Ar ratios. Given our success in an oligotrophic gyre where biological signals are small, our diel GPP approach holds promise for remote characterization of productivity across the spectrum of marine environments.
    Description: The authors acknowledge support from the National Science Foundation (NSF) through an NSF Science and Technology Center, the Center for Microbial Oceanography Research and Education (C-MORE; NSF EF-0424599). D.N. also was supported by NSF (OCE-1129644) and an Independent Study Award from the Woods Hole Oceanographic Institution (WHOI). D.M.K. was also supported by the Gordon and Betty Moore Foundation. WHOI Summer Student Fellow Cole Stites-Clayton, Stanford University, contributed to early stages of Seaglider data analysis and was supported by an NSF REU grant to WHOI (OCE-1156952).
    Keywords: Primary productivity ; Glider ; Diel ; Oxygen ; Net community production ; Hawaii
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Variability in the mechanisms controlling Southern Ocean phytoplankton bloom phenology in an ocean model and satellite observations (2017)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 31 (2017): 922–940, doi:10.1002/2016GB005615.
    Description: A coupled global numerical simulation (conducted with the Community Earth System Model) is used in conjunction with satellite remote sensing observations to examine the role of top-down (grazing pressure) and bottom-up (light, nutrients) controls on marine phytoplankton bloom dynamics in the Southern Ocean. Phytoplankton seasonal phenology is evaluated in the context of the recently proposed “disturbance-recovery” hypothesis relative to more traditional, exclusively “bottom-up” frameworks. All blooms occur when phytoplankton division rates exceed loss rates to permit sustained net population growth; however, the nature of this decoupling period varies regionally in Community Earth System Model. Regional case studies illustrate how unique pathways allow blooms to emerge despite very poor division rates or very strong grazing rates. In the Subantarctic, southeast Pacific small spring blooms initiate early cooccurring with deep mixing and low division rates, consistent with the disturbance-recovery hypothesis. Similar systematics are present in the Subantarctic, southwest Atlantic during the spring but are eclipsed by a subsequent, larger summer bloom that is coincident with shallow mixing and the annual maximum in division rates, consistent with a bottom-up, light limited framework. In the model simulation, increased iron stress prevents a similar summer bloom in the southeast Pacific. In the simulated Antarctic zone (70°S–65°S) seasonal sea ice acts as a dominant phytoplankton-zooplankton decoupling agent, triggering a delayed but substantial bloom as ice recedes. Satellite ocean color remote sensing and ocean physical reanalysis products do not precisely match model-predicted phenology, but observed patterns do indicate regional variability in mechanism across the Atlantic and Pacific.
    Description: NDSEG Graduate Fellowship; National Aeronautics and Space Administration Ocean Biology and Biogeochemistry Program Grant Number: NNX14L86G; NSF Poloar Programs Award Grant Number: 1440435; National Aeronautics and Space Administration Grant Number: NNX14AL86G; NDSEG; National Science Foundation Grant Number: 1440435
    Description: 2017-11-30
    Keywords: Southern Ocean ; Phytoplankton ; Bloom phenology ; Top-down controls ; Bottom-up controls ; Modeling
    Repository Name: Woods Hole Open Access Server
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  • 5
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    The role of external inputs and internal cycling in shaping the global ocean cobalt distribution : insights from the first cobalt biogeochemical model (2018)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Global Biogeochemical Cycles 32 (2018): 594-616, doi:10.1002/2017GB005830.
    Description: Cobalt is an important micronutrient for ocean microbes as it is present in vitamin B12 and is a co‐factor in various metalloenzymes that catalyze cellular processes. Moreover, when seawater availability of cobalt is compared to biological demands, cobalt emerges as being depleted in seawater, pointing to a potentially important limiting role. To properly account for the potential biological role for cobalt, there is therefore a need to understand the processes driving the biogeochemical cycling of cobalt and, in particular, the balance between external inputs and internal cycling. To do so, we developed the first cobalt model within a state‐of‐the‐art three‐dimensional global ocean biogeochemical model. Overall, our model does a good job in reproducing measurements with a correlation coefficient of 〉0.7 in the surface and 〉0.5 at depth. We find that continental margins are the dominant source of cobalt, with a crucial role played by supply under low bottom‐water oxygen conditions. The basin‐scale distribution of cobalt supplied from margins is facilitated by the activity of manganese‐oxidizing bacteria being suppressed under low oxygen and low temperatures, which extends the residence time of cobalt. Overall, we find a residence time of 7 and 250 years in the upper 250 m and global ocean, respectively. Importantly, we find that the dominant internal resupply process switches from regeneration and recycling of particulate cobalt to dissolution of scavenged cobalt between the upper ocean and the ocean interior. Our model highlights key regions of the ocean where biological activity may be most sensitive to cobalt availability.
    Description: EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC) Grant Number: 724289; Natural Environment Research Council (NERC) Grant Number: NE/N001079/1; Gordon and Betty Moore Foundation Grant Number: 3738; NSF OCE Grant Numbers: 0929919, 0752832, 0649639, 0223378, 1658030, 1736599; NERC Grant Number: NE/N001079/1; European Research Council Grant Number: 724289
    Keywords: Biogeochemistry ; Trace elements ; Modeling
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Estimating hypoxic volume in the Chesapeake Bay using two continuously sampled oxygen profiles (2018)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 6392-6407, doi:10.1029/2018JC014129.
    Description: Low levels of dissolved oxygen (DO) occur in many embayments throughout the world and have numerous detrimental effects on biota. Although measurement of in situ DO is straightforward with modern instrumentation, quantifying the volume of water in a given embayment that is hypoxic (hypoxic volume (HV)) is a more difficult task; however, this information is critical for determining whether management efforts to increase DO are having an overall impact. This paper uses output from a three‐dimensional numerical model to demonstrate that HV in Chesapeake Bay can be estimated well with as few as two vertical profiles. In addition, the cumulative hypoxic volume (HVC; the total amount of hypoxia in a given year) can be calculated with relatively low uncertainty (〈10%) if continuous DO data are available from two strategically positioned vertical profiles. This is because HV in the Chesapeake Bay is strongly constrained by the geometry of the embayment. A simple Geometric HV calculation method is presented and numerical model results are used to illustrate that for calculating HVC, the results using two daily‐averaged profiles are typically more accurate than those of the standard method that interpolates bimonthly cruise data. Bimonthly data produce less accurate estimates of HVC because high‐frequency changes in oxygen concentration, for example, due to regional‐weather‐ or storm‐induced changes in wind direction and magnitude, are not resolved. The advantages of supplementing cruise‐based sampling with continuous vertical profiles to estimate HVC should be applicable to other systems where hypoxic water is constrained to a specific area by bathymetry.
    Description: NOAA Grant Number: NA13NOS0120139
    Keywords: Chesapeake Bay ; Oxygen ; Dead zone ; Hypoxia ; Observing systems ; Estuary
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  • 7
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    Impact of seabed resuspension on oxygen and nitrogen dynamics in the northern Gulf of Mexico : a numerical modeling study (2018)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 7237-7263, doi:10.1029/2018JC013950.
    Description: Resuspension affects water quality in coastal environments by entraining seabed organic matter into the water column, which can increase remineralization, alter seabed fluxes, decrease water clarity, and affect oxygen and nutrient dynamics. Nearly all numerical models of water column biogeochemistry, however, simplify seabed and bottom boundary layer processes and neglect resuspension. Here we implemented HydroBioSed, a coupled hydrodynamic‐sediment transport‐biogeochemical model to examine the role of resuspension in regulating oxygen and nitrogen dynamics on timescales of a day to a month. The model was implemented for the northern Gulf of Mexico, where the extent of summertime hypoxia is sensitive to seabed and bottom boundary layer processes. Results indicated that particulate organic matter remineralization in the bottom water column increased by an order of magnitude during resuspension events. This increased sediment oxygen consumption and ammonium production, which were defined as the sum of seabed fluxes of oxygen and ammonium, plus oxygen consumption and ammonium production in the water column due to resuspended organic matter. The increases in remineralization impacted biogeochemical dynamics to a greater extent than resuspension‐induced seabed fluxes and oxidation of reduced chemical species. The effect of resuspension on bottom water biogeochemistry increased with particulate organic matter availability, which was modulated by sediment transport patterns. Overall, when averaged over the shelf and on timescales of a month in the numerical model, cycles of erosion and deposition accounted for about two thirds of sediment oxygen consumption and almost all of the sediment ammonium production.
    Description: DOC | National Oceanic and Atmospheric Administration (NOAA); U.S. National Oceanic and Atmospheric Administration's National Centers for Coastal Ocean Science Center for Sponsored Coastal Ocean Research Grant Numbers: NA09NOS4780231, NA09NOS4780229
    Keywords: Regional Ocean Modeling System (ROMS) ; Northern Gulf of Mexico continental shelf hypoxia ; Sediment transport and resuspension ; Particulate organic carbon (POC) ; Nitrogen ; Oxygen
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Coastal flooding in Scituate (MA) : A FVCOM study of the 27 December 2010 nor'easter (2014)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 118 (2013): 6030–6045, doi:10.1002/2013JC008862.
    Description: A nested Finite-Volume Coastal Ocean Model (FVCOM) inundation forecast model has been developed for Scituate (MA) as part of the Northeast Coastal Ocean Forecast System (NECOFS). Scituate Harbor is a small coastal lagoon oriented north-south with a narrow entrance (with opposing breakwaters) opening eastward onto Massachusetts Bay and the Gulf of Maine. On 27 December 2010, a classic nor'easter produced a ∼0.9 m high surge, which when added to the ∼1.5 m high tide and seasonal higher mean water level, produced significant inundation in Scituate. The Scituate FVCOM inundation model includes flooding/drying, seawall/breakwater, and wave-current interaction capabilities, and was driven by one-way nesting with NECOFS. Hindcasts of the 27 December nor'easter event were made with two different resolution Scituate FVCOM grids with and without inclusion of wave-current interaction to examine the influence of spatial resolution and model dynamics on the predicted flooding. In all simulations, a wind-driven coastal current flowed southward across the harbor entrance, with an attached separation eddy forming downstream of the northern breakwater and rapid decrease in wave energy entering the harbor. With wave-current interaction, the southward coastal current was strongly enhanced and currents within the separation eddy increased to more than 1 m/s, making it highly nonlinear with large lateral shears. Comparisons of the model water elevation time series with harbor tide station measurements showed that inclusion of wave-current interaction increased the peak model surge by ∼8 cm, in closer agreement with the observed peak.
    Description: This project was supported by NOAA via the U.S. IOOS Office (Award: NA10NOS0120063 and NA11NOS0120141) and was managed by the Southeastern Universities Research Association. The Scituate FVCOM setup was supported by the NOAA-funded IOOS NERACOOS program for NECOFS and the MIT Sea grant College Program through grant 2012-R/RC-127.
    Description: 2014-05-13
    Keywords: Modeling ; Inundation
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Seasonal and interannual oxygen variability on the Washington and Oregon continental shelves (2015)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 608–633, doi:10.1002/2014JC010254.
    Description: The coastal waters of the northern portion of the California Current System experience a seasonal decline in oxygen concentrations and hypoxia over the summer upwelling season that results in negative impacts on habitat for many organisms. Using a regional model extending from 43°N to 50°N, with an oxygen component developed in this study, drivers of seasonal and regional oxygen variability are identified. The model includes two pools of detritus, which was an essential addition in order to achieve good agreement with the observations. The model was validated using an extensive array of hydrographic and moored observations. The model captures the observed seasonal decline as well as spatial trends in bottom oxygen. Spatially, three regions of high respiration are identified as locations where hypoxia develops each modeled year. Two of the regions are previously identified recirculation regions. The third region is off of the Washington coast. Sediment oxygen demand causes the region on the Washington coast to be susceptible to hypoxia and is correlated to the broad area of shallow shelf (〈60 m) in the region. Respiration and circulation-driven divergence contribute similar (60, 40%, respectively) amounts to the integrated oxygen budget on the Washington coast while respiration dominates the Oregon coast. Divergence, or circulation, contributes to the oxygen dynamics on the shelf in two ways: first, through the generation of retention features, and second, by determining variability.
    Description: This work was supported by a postdoctoral fellowship to Samantha Siedlecki from JISAO and the Program on Climate Change at the University of Washington, and grants from the Coastal Ocean Program of the National Oceanic and Atmospheric Administration (NOAA) (NA09NOS4780180) and the National Science Foundation (NSF) (OCE0942675) as part of the Pacific Northwest Toxins (PNWTOX) project.
    Description: 2015-08-05
    Keywords: Hypoxia ; Oxygen ; Respiration ; Upwelling
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Effect of a sheared flow on iceberg motion and melting (2017)
    John Wiley & Sons
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 43 (2016): 12,520–12,527, doi:10.1002/2016GL071602.
    Description: Icebergs account for approximately half the freshwater flux into the ocean from the Greenland and Antarctic ice sheets and play a major role in the distribution of meltwater into the ocean. Global climate models distribute this freshwater by parameterizing iceberg motion and melt, but these parameterizations are presently informed by limited observations. Here we present a record of speed and draft for 90 icebergs from Sermilik Fjord, southeastern Greenland, collected in conjunction with wind and ocean velocity data over an 8 month period. It is shown that icebergs subject to strongly sheared flows predominantly move with the vertical average of the ocean currents. If, as typical in iceberg parameterizations, only the surface ocean velocity is taken into account, iceberg speed and basal melt may have errors in excess of 60%. These results emphasize the need for parameterizations to consider ocean properties over the entire iceberg draft.
    Description: National Oceanic and AtmosphericAdministration Grant Number: NA14OAR4320106; National Oceanic and Atmospheric Administration, U.S. Department of Commerce NSF Grant Numbers: PLR-1332911, OCE-1434041, OCE-1434041, PLR-1332911
    Description: 2017-06-27
    Keywords: Icebergs ; Freshwater flux ; Modeling ; Greenland ; Dynamics
    Repository Name: Woods Hole Open Access Server
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