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Archive for modeling – Page 2

Chemical thermodynamic models of artificial seawater and the Tris buffers used to define the ‘total’ pH scale

Posted by mmaheigan

· Thursday, August 25th, 2022

The total pH scale used by oceanographers (for salinities 20 – 40, and temperatures 0 to 45°C) is calibrated from a combination of electromotive force measurements of artificial seawaters containing either added HCl of various molalities, or equimolal Tris and its protonated form TrisH⁺. In both cases, the added H⁺ or TrisH⁺ is substituted for Na⁺ on a mole-for-mole-basis, so as to change the properties of the artificial seawater medium as little as possible. The artificial seawater itself consists of the major ions of seawater (those present in constant ratios to one another in natural seawater), with substitutions for the inorganic acid-base species present in natural seawater (principally carbonate and borate). Figure 1 shows the composition of a typical Tris buffer.

Figure 1. The composition of a buffer solution containing 0.04 mol kg-1 of Tris and TrisH+ in artificial seawater of salinity 35. The TrisH+ is substituted for an equal amount of Na+, so that the buffer has the same ionic strength as a pure artificial seawater of the same nominal salinity.

The operational definition of the total pH scale in use today involves a number of assumptions associated with the small differences between pure artificial seawater, and artificial seawater containing the buffer substance. These cannot be determined experimentally. However, a chemical thermodynamic model of the ion activities and concentrations in the buffer solutions can be used to calculate these quantities and to link measured total pH to the conventional thermodynamic total of H⁺ and HSO₄^–. Such a model can also address a series of important future applications and uses of the total pH scale:

The measurement of the total pH of natural waters whose compositions differ from seawater stoichiometry, and the extension of the scale to low salinity waters
Conversion between total pH, a measure of [H⁺] + [HSO₄^–], and ‘free’ pH (a measure of [H⁺])
Calibration of electrode pairs such as H⁺/Cl^– or H⁺/Na⁺ for the potentiometric measurement of pH

Figure 2 shows a model simulation of the operationally defined total pH and the conventional thermodynamic sum [H⁺] + [HSO₄^–] in a buffer solution of salinity 35. The linear extrapolation to zero buffer molality yields a hypothetical total pH that is used by oceanographers and is shown to be the same for both cases, demonstrating that they are the same.

Figure 2. Modelled values of the operational total pH (dashed blue line) and the conventional thermodynamic total pH (solid red line) plotted against buffer molality (mBuffer) for a salinity 35 artificial seawater at 25°C. The fine dotted lines are extrapolations of linear fits to the two groups of points. The vertical distance between marked points A and B (about 0.0045 pH units) represents the effect of differences between the two solutions – hitherto assumed out of necessity to be zero, and here calculated for the first time. The two extrapolations (fine dotted lines) intercept at point C, for which mBuffer is equal to zero and the two definitions are numerically the same.

In these two papers, we describe the development of the model of solutions containing the ions of artificial seawater plus Tris buffer. The models include uncertainty propagation (a first, for models of this type). We assess the needs for further measurements to both improve the accuracy of the model and extend it over the full range of temperatures of interest to oceanographers. We have an ongoing programme of measurements to support this work involving colleagues at the National Institute of Standards and Technology and its equivalents in Germany and Japan. In late 2022, we will be releasing for public use the software that implements two models, and also one of seawater electrolyte. If interested, please contact Heather Benway to be added to our email list, and check the website of SCOR Working Group 145 (marchemspec.org).

Read the papers about the pH buffer and artificial seawater in Marine Chemistry.

Authors:
Simon L. Clegg (School of Environmental Sciences, University of East Anglia, United Kingdom)
Matthew P. Humphreys (NIOZ Royal Netherlands Institute for Sea Research, Netherlands)
Jason F. Waters (National Institute of Standards and Technology, Gaithersburg, USA
David R. Turner (University of Gothenburg, Sweden)
Andrew G. Dickson (Scripps Institution of Oceanography, La Jolla, USA)

How do coccolithophores survive the darkness?

Posted by mmaheigan

· Friday, April 1st, 2022

Coccolithophores have survived several major extinction events over geologic time. The most significant was the asteroid impact at the K/T boundary, followed by months of darkness. Additionally, coccolithophores regularly reside in the twilight zone, just beyond the reach of sunlight. A paper recently published in the New Phytologist addresses how these photosynthetic algae can persist and grow, albeit slowly, in darkness using osmotrophy.

The authors discovered that the osmotrophic uptake of certain types of dissolved organic carbon (DOC) can support survival in low light. They completed a 30-day darkness experiment to determine how the concentration of several DOC compounds affects growth. The coccolithophore species Cruciplacolithus neohelis growth rate increased with the increasing concentration of dissolved organic compounds. They also examined the kinetics of short-term uptake of radiolabeled DOC compounds and found that the uptake rate generally showed Michaelis-Menten-like saturation kinetics. All radiolabeled DOC compounds were incorporated into the POC fraction, but surprisingly also into the particulate inorganic carbon (PIC) fraction (i.e., calcite coccoliths).

These results suggest that osmotrophic uptake in coccolithophores may be significant enough to be included in carbon cycle models, especially if they can simultaneously take up a wide range of organic compounds. Surprisingly, we detected ¹⁴C-DOC in the PIC fraction after only 24 hours. This remarkably rapid incorporation is most likely due to the respiration of radiolabeled DOC into dissolved inorganic carbon (DIC), subsequently used by coccolithophores for calcification. These results have implications for the biological carbon pump and alkalinity pump paradigms, as we confirmed that both POC and PIC originate from DOC on short time scales.

Introducing the Coastal Ocean Data Analysis Product in North America (CODAP-NA)

Posted by mmaheigan

· Friday, October 22nd, 2021

Coastal ecosystems are hotspots for commercial and recreational fisheries, and aquaculture industries that are susceptible to change or economic loss due to ocean acidification. These coastal ecosystems support about 90% of the global fisheries yield and 80% of the known marine fish species, and sustain ecosystem services worth $27.7 Trillion globally (a number larger than the U.S. economy). Despite the importance of these areas and economies, internally-consistent data products for water column carbonate and nutrient chemistry data in the coastal ocean—vital to understand and predict changes in these systems—currently do not exist. A recent study published in Earth Syst. Sci. Data compiled and quality controlled discrete sampling-based data—inorganic carbon, oxygen, and nutrient chemistry, and hydrographic parameters collected from the entire North American ocean margins—to create a data product called the Coastal Ocean Data Analysis Product for North America (CODAP-NA) to fill the gap. This effort will promote future OA research, modeling, and data synthesis in critically important coastal regions to help advance the OA adaptation, mitigation, and planning efforts by North American coastal communities; and provides a foothold for future synthesis efforts in the coastal environment.

Figure caption. Sampling stations of the CODAP-NA data product.

Authors:
Li-Qing Jiang (University of Maryland; NOAA NCEI)
Richard A. Feely (NOAA PMEL)
Rik Wanninkhof (NOAA AOML)
Dana Greeley (NOAA PMEL)
Leticia Barbero (University of Miami; NOAA AOML)
Simone Alin (NOAA PMEL)
Brendan R. Carter (University of Washington; NOAA PMEL)
Denis Pierrot (NOAA AOML)
Charles Featherstone (NOAA AOML)
James Hooper (University of Miami; NOAA AOML)
Chris Melrose (NOAA NEFSC)
Natalie Monacci (University of Alaska Fairbanks)
Jonathan Sharp (University of Washington; NOAA PMEL)
Shawn Shellito (University of New Hampshire)
Yuan-Yuan Xu (University of Miami; NOAA AOML)
Alex Kozyr (University of Maryland; NOAA NCEI)
Robert H. Byrne (University of South Florida)
Wei-Jun Cai (University of Delaware)
Jessica Cross (NOAA PMEL)
Gregory C. Johnson (NOAA PMEL)
Burke Hales (Oregon State University)
Chris Langdon (University of Miami)
Jeremy Mathis (Georgetown University)
Joe Salisbury (University of New Hampshire)
David W. Townsend (University of Maine)

The ephemeral and elusive COVID blip in ocean carbon

Posted by mmaheigan

· Monday, September 20th, 2021

The global pandemic of the last nearly two years has affected all of us on a daily and long-term basis. Our planet is not exempt from these impacts. Can we see a signal of COVID-related CO₂ emissions reductions in the ocean? In a recent study, Lovenduski et al. apply detection and attribution analysis to output from an ensemble of COVID-like simulations of an Earth system model to answer this question. While it is nearly impossible to detect a COVID-related change in ocean pH, the model produces a unique fingerprint in air-sea DpCO₂ that is attributable to COVID. Challengingly, the large interannual variability in the climate system makes this fingerprint difficult to detect at open ocean buoy sites.

This study highlights the challenges associated with detecting statistically meaningful changes in ocean carbon and acidity following CO₂ emissions reductions, and reminds the reader that it may be difficult to observe intentional emissions reductions — such as those that we may enact to meet the Paris Climate Agreement – in the ocean carbon system.

Figure caption: The fingerprint (pink line) of COVID-related CO2 emissions reductions in global-mean surface ocean pH and air-sea DpCO2, as estimated by an ensemble of COVID-like simulations in an Earth system model. While the pH fingerprint is not particularly exciting, the air-sea DpCO2 fingerprint displays a temporary weakening of the ocean carbon sink in 2021 due to COVID emissions reductions.

Authors:
Nikki Lovenduski (University of Colorado Boulder)
Neil Swart (Canadian Centre for Climate Modeling and Analysis)
Adrienne Sutton (NOAA Pacific Marine Environmental Laboratory)
John Fyfe (Canadian Centre for Climate Modeling and Analysis)
Galen McKinley (Columbia University and Lamont Doherty Earth Observatory)
Chris Sabine (University of Hawai’i at Manoa)
Nancy Williams (University of South Florida)

Counterintuitive effects of shoreline armoring on estuarine water clarity

Posted by mmaheigan

· Wednesday, February 24th, 2021

Around the world, human-altered shorelines change sediment inputs to estuaries and coastal waters, altering water clarity, especially in areas of dense human population. The Chesapeake Bay estuary is recovering from historically high nutrient and sediment inputs, but water clarity improvement has been ambiguous. Long-term trends show increasing water clarity in terms of deepening light attenuation depth, yet degrading clarity in terms of shallowing Secchi depth over time. High water clarity is needed to support seagrass meadows, which act as nursery habitats for commercially important fish species such as striped bass. How are these opposing water clarity trends possible?

In a recent paper published in Science of the Total Environment, researchers performed experiments with a coupled hydrodynamic-biogeochemical model to test a simulated Chesapeake Bay under realistic conditions, more shoreline erosion, and highly armored shorelines. Comparing the two extreme conditions (Figure 1), there was a striking difference between (a) an estuary experiencing more shoreline erosion and greater resuspension versus (b) a highly armored estuary with decreased resuspension. Reduced erosion yielded improved water clarity in terms of light attenuation depth, but a shallower Secchi depth (reduced visibility). In estuaries, reducing sediment inputs is often proposed as a strategy for improving water quality. This study shows that, under certain conditions in a productive estuary, reduced sediments can have unintended secondary effects on water clarity due to enhanced production of organic particles. This study also highlights the need to consider other sediment sources in addition to rivers, such as seabed resuspension and shoreline erosion, especially at times and locations of low river input.

Figure 1. Schematic of how shoreline armoring causes deepening light attenuation depth (navy) yet shallowing Secchi depth (green) during the spring growing season in the mid-bay central channel.

Authors:
Jessica S. Turner
Pierre St-Laurent
Marjorie A. M. Friedrichs
Carl T. Friedrichs
(all Virginia Institute of Marine Science)

Species loss alters ecosystem function in plankton communities

Posted by mmaheigan

· Monday, February 8th, 2021

Climate change impacts on the ocean such as warming, altered nutrient supply, and acidification will lead to significant rearrangement of phytoplankton communities, with the potential for some phytoplankton species to become extinct, especially at the regional level. This leads to the question: What are phytoplankton species’ redundancy levels from ecological and biogeochemical standpoints—i.e. will other species be able to fill the functional ecological and/or biogeochemical roles of the extinct species? Authors of a paper published recently in Global Change Biology explored these ideas using a global three-dimensional computer model with diverse planktonic communities, in which single phytoplankton types were partially or fully eliminated. Complex trophic interactions such as decreased abundance of a predator’s predator led to unexpected “ripples” through the community structure and in particular, reductions in carbon transfer to higher trophic levels. The impacts of changes in resource utilization extended to regions beyond where the phytoplankton type went extinct. Redundancy appeared lowest for types on the edges of trait space (e.g., smallest) or those with unique competitive strategies. These are responses that laboratory or field studies may not adequately capture. These results suggest that species losses could compound many of the already anticipated outcomes of changing climate in terms of productivity, trophic transfer, and restructuring of planktonic communities. The authors also suggest that a combination of modeling, field, and laboratory studies will be the best path forward for studying functional redundancy in phytoplankton.

Figure caption: Examples of the modelled ecological and biogeochemical responses to the extinction of different phytoplankton species.Figure caption: Examples of the modelled ecological and biogeochemical responses to the extinction of different phytoplankton species.

Authors:
Stephanie Dutkiewicz (Massachusetts Institute of Technology)
Philip W. Boyd (Institute for Marine and Antarctic Studies, University of Tasmania)
Ulf Riebesell (GEOMAR Helmholtz Centre for Ocean Research Kiel)

Climate-driven pelagification of marine food webs: Implications for marine fish populations

Posted by mmaheigan

· Friday, January 22nd, 2021

Global warming changes the conditions for all ocean life, with wide-ranging consequences. It is particularly difficult to predict the impact of climate change on fish because fish production is conditioned on both temperature and food resource (zooplankton and benthic organisms) changes. Climate change projections from Earth system models show a negative amplification of changes in global ocean net primary production (NPP), with an approximate doubling of production decreases from net primary producers to mesozooplankton. This “trophic amplification” continues up the marine food web to fishes. A new study published in Frontiers in Marine Science illustrates this amplification clearly when fishes are defined by their maximum body size, which describes their position in the food web (Figure 1a). However, decreases in globally integrated biomass and production were not limited to differences in size alone. Importantly, reduced abundances also varied by fish functional type (Figure 1b).

Figure 1: a) Percent change in net primary production (NPP), mesozooplankton (MesoZ) production, all medium (M) fishes, and all large (L) fishes from Historic (1951-2000) to the RCP 8.5 Projection (2051-2100). b) Percent change in production of forage fish, large pelagic fish, demersal fish, and benthic invertebrates in Projection (2051-2100) from Historic (1951-2000). c) Absolute change in the ratio of zooplankton production to seafloor detrital flux as the difference of the Projection (2051-2100) from the Historic (1951-2000). d) Percent change in zooplankton production (dashed grey), percent change in seafloor detrital flux (solid grey), and absolute change in the ratio of their means during the Historic and Projection time periods relative to 1951.

Despite the “pelagification” of marine food webs caused by unequal decreases in secondary production (Figure 1d) and subsequent increases in pelagic zooplankton production relative to seafloor detritus production (Figure 1c,d), large pelagic fish (e.g., tunas and billfishes) suffered the greatest declines and the highest degree of projection uncertainty. The result was a shift from benthic-based ecosystems historically dominated by large demersal fish (e.g., cods and flounders) towards pelagic-based ones dominated by smaller forage fish (e.g., sardines and herring). Any positive impacts of the pelagification of food resources on large pelagic fish were overwhelmed by the negative impacts of the overall reduction in global productivity, compounded by warming-induced increases in metabolic demands. Both the degree of change in the productivity of large pelagic fish and the magnitude of trophic amplification were sensitive to the temperature dependence of metabolic rates. Thus, better constraints are needed on empirical estimates of the effect of temperature on physiological rates to project the impacts of climate change on fish biomass and marine ecosystem structure.

Ocean fish harvests currently supply ~15% of global protein demand. Reduced primary production will decrease the total amount of fish available to harvest for human food, while the pelagification of ecosystems could require large and expensive structural modifications to fisheries, including gear, location, regional and international management plans, consumer demands, and market values.

Authors:
Colleen M. Petrik (Texas A&M University)
Charles A. Stock (Geophysical Fluid Dynamics Laboratory)
Ken H. Andersen (Technical University of Denmark)
P. Daniël van Denderen (International Council for the Exploration of the Seas)
James R. Watson (Oregon State University)

Water clarity impacts temperature and biogeochemistry in Chesapeake Bay

Posted by mmaheigan

· Thursday, December 3rd, 2020

Estuarine water clarity is determined by suspended materials in the water, including colored dissolved organic matter, phytoplankton, sediment, and detritus. These constituents directly affect temperature because when water is opaque, sunlight heats only the shallowest layers near the surface, but when water is clear, sunlight can penetrate deeper, warming the waters below the surface. Despite the importance of accurately predicting temperature variability, many numerical modeling studies do not adequately parameterize this fundamental relationship between water clarity and temperature.

In a recent study published in Estuaries and Coasts, the authors quantified the impact of a more realistic representation of water clarity in a hydrodynamic-biogeochemical model of the Chesapeake Bay by comparing two simulations: (1) water clarity is constant in space and time for the calculation of solar heating vs. (2) water clarity varies with modeled concentrations of light-attenuating materials. In the variable water clarity simulation (2), the water is more opaque, particularly in the northern region of the Bay. During the spring and summer months, the lower water clarity in the northern Bay is associated with warmer surface temperatures and colder bottom temperatures. Warmer surface temperatures encourage phytoplankton growth and nutrient uptake near the head of the Bay, thus fewer nutrients are transported downstream. These conditions are exacerbated during high-river flow years, when differences in temperature, nutrients, phytoplankton, and zooplankton extend further seaward.

Figure 1: Top row: Difference in the light attenuation coefficient for shortwave heating, kh[m-1] (variable minus constant light attenuation simulation). June, July, and August average for (A) 2001, (B) average of 2001-2005, and (C) 2003; difference in bottom temperatures [oC] (variable minus constant). Bottom row: Difference in June, July, and August average bottom temperature for (D) 2001, (E) average of 2001-2005, and (F) 2003. Data for 2001 are representative of low river discharge, and 2003 are representative high river discharge years.

This work demonstrates that a constant light attenuation scheme for heating calculations in coupled hydrodynamic-biogeochemical models underestimates temperature variability, both temporally and spatially. This is an important finding for researchers who use models to predict future temperature variability and associated impacts on biogeochemistry and species habitability.

Authors:
Grace E. Kim (NASA, Goddard Space Flight Center)
Pierre St-Laurent (VIMS, William & Mary)
Marjorie A.M. Friedrichs (VIMS, William & Mary)
Antonio Mannino (NASA, Goddard Space Flight Center)

A new Regional Earth System Model of the Mediterranean Sea biogeochemical dynamics

Posted by mmaheigan

· Thursday, November 19th, 2020

The Mediterranean Sea is a semi-enclosed mid-latitude oligotrophic basin with a lower net primary production than the global ocean. A west-east productivity trophic gradient results from the superposition of biogeochemical and physical processes, including the biological pump and associated carbon and nutrient (nitrogen, phosphorus) fluxes, the spatial asymmetric distribution of nutrient sources (rivers, atmospheric deposition, coastal upwelling, etc.), the estuarine inverse circulation associated with the inflow of Atlantic water through the Gibraltar Strait. The complex and highly variable interface between land and sea throughout this basin add a further layer of complexity in the Mediterranean oceanic and atmospheric circulation and on the associated biogeochemistry dynamics, emphasizing the need for high-resolution truly integrated Regional Earth System Models to track and understand fine-scale processes and ecosystem dynamics.

In a recent paper published in the Journal of Advances in Modeling Earth System, the authors introduced a new version of the Regional Earth System model RegCM-ES and evaluated its performance in the Mediterranean region. RegCM-ES fully integrates the regional climate model RegCM4, the land surface scheme CLM4.5 (Community Land Model), the river routing model HD (Hydrological Discharge Model), the ocean model MITgcm (MIT General Circulation model) and the Biogeochemical Flux Model BFM.

A comparison with available observations has shown that RegCM-ES was able to capture the mean climate of the region and to reproduce horizontal and vertical patterns of chlorophyll-a and PO₄(the limiting nutrient in the basin) (Figure 1). The same comparison revealed a systematic underestimation of simulated dissolved oxygen (which will be fixed by the use of a new parametrization of oxygen solubility), and an overestimation of NO₃, possibly due to uncertainties in initial and boundary conditions (mostly traced to river and Dardanelles nutrient discharges) and an overly vigorous vertical mixing simulated by the ocean model in some parts of the Basin.

Figure.1 Distributions of chlorophyll-a mg/m³ (top) and PO₄ mmol/m³ (bottom) in the Mediterranean Sea as simulated by RegCM-ES.

Overall, this analysis has demonstrated that RegCM-ES has the capabilities required to become a powerful tool for studying regional dynamics and impacts of climate change on the Mediterranean Sea and other ocean basins around the world.

Authors:
Marco Reale (Abdus Salam International Centre for theoretical physics-ICTP, National Institute of Oceanography and Experimental Geophysics-OGS)
Filippo Giorgi (Abdus Salam International Centre for theoretical physics-ICTP)
Cosimo Solidoro (National Institute of Oceanography and Experimental Geophysics-OGS)
Valeria Di Biagio (National Institute of Oceanography and Experimental Geophysics-OGS)
Fabio Di Sante (Abdus Salam International Centre for theoretical physics-ICTP)
Laura Mariotti (National Institute of Oceanography and Experimental Geophysics-OGS)
Riccardo Farneti (Abdus Salam International Centre for theoretical physics-ICTP)
Gianmaria Sannino (Italian National Agency for New Technologies, Energy and Sustainable Economic Development-ENEA)

Austral summer vertical migration patterns in Antarctic zooplankton

Posted by mmaheigan

· Thursday, October 15th, 2020

Sunrise and sunset are the main cues driving zooplankton diel vertical migration (DVM) throughout the world’s oceans. These marine animals balance the trade-off between feeding in surface waters at night and avoiding predation during the day at depth. Near-constant daylight during polar summer was assumed to dampen these daily migrations. In a recent paper published in Deep-Sea Research I, authors assessed austral summer DVM patterns for 15 taxa over a 9-year period. Despite up to 22 hours of sunlight, a diverse array of zooplankton – including copepods, krill, pteropods, and salps – continued DVM.

Figure caption: Mean day (orange) and night (blue) abundance of (A) the salp Salpa thompsoni, (B) the krill species Thysanoessa macrura, (C) the pteropod Limacina helicina, and (D) chaetognaths sampled at discrete depth intervals from 0-500m. Horizontal dashed lines indicate weighted mean depth (WMD). N:D is the night to day abundance ratio for 0-150 m. Error bars indicate one standard error. Sample size n = 12 to 22. Photos by Larry Madin, Miram Gleiber, and Kharis Schrage.

The Palmer Antarctica Long-Term Ecological Research (LTER) Program conducted this study using a MOCNESS (Multiple Opening/Closing Net and Environmental Sensing System) to collect depth-stratified samples west of the Antarctic Peninsula. The depth range of migrations during austral summer varied across taxa and with daylength and phytoplankton biomass and distribution. While most taxa continued some form of DVM, others (e.g., carnivores and detritivores) remained most abundant in the mesopelagic zone, regardless of photoperiod, which likely impacted the attenuation of vertical carbon flux. Given the observed differences in vertical distribution and migration behavior across taxa, ongoing changes in Antarctic zooplankton assemblages will likely impact carbon export pathways. More regional, taxon-specific studies such as this are needed to inform efforts to model zooplankton contributions to the biological carbon pump.

Authors:
John Conroy (VIMS, William & Mary)
Deborah Steinberg (VIMS, William & Mary)
Patricia Thibodeau (VIMS, William & Mary; currently University of Rhode Island)
Oscar Schofield (Rutgers University)

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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