Numerical Modeling of Hypoxia and Its Effects: Synthesis and Going Forward

  • Kenneth A. Rose
  • Dubravko Justic
  • Katja Fennel
  • Robert D. Hetland


Numerical models can provide the needed information for understanding hypoxia and ensuring effective management, and this book provides a snapshot of representative modeling analyses of hypoxia and its effects. In this chapter, we used the modeling and analyses across the other 14 chapters to illustrate 8 themes that relate to the general strengths, uncertainties, and future areas of focus in order for modeling of hypoxia and its effects to continue to advance. These themes are role of physics; complexity of the dissolved oxygen (DO) models; oxygen minimum zones (OMZs) and shallow coastal systems; observations; vertical dimension; short-term forecasting; possible futures; and ecological effects of hypoxia. Modeling the dynamics and causes of hypoxia has greatly progressed in recent decades, and modern models routinely simulate seasonal dynamics over 0.1–1 km scales. Despite these advances, prevailing model limitations include uncertain specification of boundary conditions and forcing functions, challenges in representing the sediment-water exchange and multiple nutrient limitation, and the limited availability of observations for multiple contrasting years for model calibration and validation. A major challenge remains to effectively link the water quality processes to upper trophic levels. A variety of approaches are illustrated in this book and show that quantifying this linkage is still in the formative stages. There will be increasing demands for predicting the ecological responses to hypoxia in order to quantify the ecological benefits and costs of management actions and to express the simulated effects of coastal management and climate change in terms of direct relevance to managers and the public.


Hypoxia Nutrients Simulation Modeling Ecological effects Food webs Climate change Fisheries Management 



Funding for the preparation of this chapter (KAR) was partially provided by the National Oceanic and Atmospheric Administration, Center for Sponsored Coastal Ocean Research (CSCOR), NGOMEX16 grant number NA16NOS4780204 awarded to Louisiana State University. This is publication number 218 of the NOAA’s CSCOR NGOMEX program.


  1. Ainsworth CH, Kaplan IC, Levin PS, Mangel M (2010) A statistical approach for estimating fish diet compositions from multiple data sources: Gulf of California case study. Ecol Appl 20:2188–2202CrossRefPubMedGoogle Scholar
  2. Altieri AH, Gedan KB (2015) Climate change and dead zones. Glob Change Biol 21:1395–1406CrossRefGoogle Scholar
  3. Anderson CR, Moore SK, Tomlinson MC, Silke J, Cusack CK (2015) Living with harmful algal blooms in a changing world: strategies for modeling and mitigating their effects in coastal marine ecosystems. Coastal and marine hazards, risks, and disasters. Elsevier BV, Amsterdam, pp 495–561Google Scholar
  4. Ayata SD, Lévy M, Aumont O, Sciandra A, Sainte-Marie J, Tagliabue A, Bernard O (2013) Phytoplankton growth formulation in marine ecosystem models: should we take into account photo-acclimation and variable stoichiometry in oligotrophic areas? J Mar Syst 125:29–40CrossRefGoogle Scholar
  5. Bestley S, Jonsen I, Harcourt RG, Hindell MA, Gales NJ (2016) Putting the behavior into animal movement modeling: improved activity budgets from use of ancillary tag information. Ecol Evol 6:8243–8255CrossRefPubMedPubMedCentralGoogle Scholar
  6. Blumberg AF, Kantha LH (1985) Open boundary condition for circulation models. J Hydraul Eng 111:237–255CrossRefGoogle Scholar
  7. Bonachela JA, Klausmeier CA, Edwards KF, Litchman E, Levin SA (2015) The role of phytoplankton diversity in the emergent oceanic stoichiometry. J Plankton Res p fbv087Google Scholar
  8. Breitburg DL, Hondorp DW, Davias LA, Diaz RJ (2009) Hypoxia, nitrogen, and fisheries: integrating effects across local and global landscapes. Ann Rev Mar Sci 1:329–349CrossRefPubMedGoogle Scholar
  9. Chan F, Barth JA, Lubchenco J, Kirincich A, Weeks H, Peterson WT, Menge BA (2008) Emergence of anoxia in the California Current large marine ecosystem. Science 319:920CrossRefPubMedGoogle Scholar
  10. Chesney EJ, Baltz DM (2001) The effects of hypoxia on the northern Gulf of Mexico coastal ecosystem: a fisheries perspective. In: Rabalais NN, Turner RE (eds) Coastal hypoxia: consequences for living resources and ecosystems. American Geophysical Union, Washington, DC, pp 321–354CrossRefGoogle Scholar
  11. Cohen JH, Forward RB (2009) Zooplankton diel vertical migration—a review of proximate control Oceanog. Mar Biol Annu Rev 47:77–109Google Scholar
  12. DeAngelis DL, Grimm V (2014) Individual-based models in ecology after four decades. F1000 prime reports 2014, 6:39. doi: 10.12703/P6-39
  13. Denman KL (2003) Modelling planktonic ecosystems: parameterizing complexity. Prog Oceanogr 57:429–452CrossRefGoogle Scholar
  14. Diaz RJ, Rosenberg R (2008) Spreading dead zones and consequences for marine ecosystems. Science 32:926–929CrossRefGoogle Scholar
  15. Fennel K, Laurent A, Hetland R, Justić D, Ko DS, Lehrter J, Murrell M, Wang L, Yu L, Zhang W (2016) Effects of model physics on hypoxia simulations for the northern Gulf of Mexico: a model intercomparison. J Geophys Res Oceans 121. doi: 10.1002/2015JC011577
  16. Fennel K, Hu J, Laurent A, Marta-Almeida M, Hetland R (2013) Sensitivity of hypoxia predictions for the northern Gulf of Mexico to sediment oxygen consumption and model nesting. J Geophys Res 118:990–1002CrossRefGoogle Scholar
  17. Flint LE, Flint AL (2012) Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis. Ecol Proces 1:2CrossRefGoogle Scholar
  18. Flynn KJ (2003) Modelling multi-nutrient interactions in phytoplankton; balancing simplicity and realism. Prog Oceanogr 56:249–279CrossRefGoogle Scholar
  19. Friedrichs MA, Dusenberry JA, Anderson LA, Armstrong RA, Chai F, Christian JR, Doney SC, Dunne J, Fujii M, Hood R, McGillicuddy DJ, Moore JK, Schartau M, Spitz YH, Wiggert JD (2007) Assessment of skill and portability in regional marine biogeochemical models: role of multiple planktonic groups. J Geophys Res Oceans 112(C8)Google Scholar
  20. Glibert PM, Kana TM, Brown K (2013) From limitation to excess: the consequences of substrate excess and stoichiometry for phytoplankton physiology, trophodynamics and biogeochemistry, and the implications for modeling. J Mar Syst 125:14–28CrossRefGoogle Scholar
  21. Grantham BA, Chan F, Nielsen KJ, Fox DS, Barth JA, Huyer A, Lubchenco J, Menge BA (2004) Upwelling-driven nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific. Nature 429:749–754CrossRefPubMedGoogle Scholar
  22. Grimm V, Railsback SF (2013) Individual-based modeling and ecology. Princeton University PressGoogle Scholar
  23. Gutowsky LF, Harrison PM, Martins EG, Leake A, Patterson DA, Power M, Cooke SJ (2013) Diel vertical migration hypotheses explain size-dependent behaviour in a freshwater piscivore. Anim Behav 86:365–373CrossRefGoogle Scholar
  24. Heip CHR, Goosen NK, Herman PMJ, Kromkamp J, Middelburg JJ, Soetaert K (1995) Production and consumption of biological particles in temperate tidal estuaries. In: Ansell AD, Gibson RN, Barnes M (eds) Oceanography and marine biology: an annual review, vol 33. University College London Press, pp 1–149Google Scholar
  25. Hetland RD (2017) Suppression of baroclinic instabilities in buoyancy-driven flow over sloping bathymetry. J Phys Oceanogr 47:49–68CrossRefGoogle Scholar
  26. Hetland RD, DiMarco SF (2008) How does the character of oxygen demand control the structure of hypoxia on the Texas-Louisiana continental shelf? J Mar Syst 70:49–62CrossRefGoogle Scholar
  27. Hetland RD, DiMarco SF (2012) Skill assessment of a hydrodynamic model of circulation over the Texas-Louisiana continental shelf. Ocean Model 43:64–76CrossRefGoogle Scholar
  28. Holt J, Allen JI, Anderson TR, Brewin R, Butenschön M, Harle J, Huse G, Lehodey P, Lindemann C, Memery L, Salihoglu B (2014) Challenges in integrative approaches to modelling the marine ecosystems of the North Atlantic: physics to fish and coasts to ocean. Prog Oceanogr 129:285–313CrossRefGoogle Scholar
  29. Howarth RW (1988) Nutrient limitation of net primary production in marine ecosystems. Annu Rev Ecol Syst 19:89–110CrossRefGoogle Scholar
  30. Howes EL, Joos F, Eakin M, Gattuso JP (2015) An updated synthesis of the observed and projected impacts of climate change on the chemical, physical and biological processes in the oceans. Front Mar Sci 2:36. doi: 10.3389/fmars.2015.00036 CrossRefGoogle Scholar
  31. Ibarra D, Fennel K, Cullen J (2014) Coupling 3-D Eulerian bio-physics (ROMS) with individual-based shellfish ecophysiology (SHELL-E): a hybrid model for carrying capacity and environmental impacts of bivalve aquaculture. Ecol Model 273:63–78CrossRefGoogle Scholar
  32. Justic D, Wang L (2014) Assessing temporal and spatial variability of hypoxia over the inner Louisiana-upper Texas shelf: application of an unstructured-grid three-dimensional coupled hydrodynamic-water quality model. Cont Shelf Res 72:163–179CrossRefGoogle Scholar
  33. Justić D, Bierman VJ, Scavia D, Hetland RD (2007) Forecasting Gulf’s hypoxia: the next 50 years? Estuaries Coasts 30:791–801CrossRefGoogle Scholar
  34. Justic D, Rabalais NN, Turner RE (1996) Effects of climate change on hypoxia in coastal waters: a doubled CO2 scenario for the northern Gulf of Mexico. Limnol Oceanogr 41:992–1003CrossRefGoogle Scholar
  35. Kemp WM, Sampou PA, Garber J, Tuttle J, Boynton WR (1992) Seasonal depletion of oxygen from bottom waters of Chesapeake Bay: roles of benthic and planktonic respiration and physical exchange processes. Mar Ecol Prog Ser 85:137–152CrossRefGoogle Scholar
  36. Kim DK, Zhang W, Watson S, Arhonditsis GB (2014) A commentary on the modelling of the causal linkages among nutrient loading, harmful algal blooms, and hypoxia patterns in Lake Erie. J Great Lakes Res 40:117–129CrossRefGoogle Scholar
  37. Kirtman BP, Bitz C, Bryan F, Collins W, Dennis J, Hearn N, Kinter JL, Loft R, Rousset C, Siqueira L, Stan C (2012) Impact of ocean model resolution on CCSM climate simulations. Clim Dyn 39:1303–1328CrossRefGoogle Scholar
  38. LaBone E (2016) Modeling the effects of hypoxia on fish movement in the Gulf of Mexico hypoxic zone. PhD dissertation, Louisiana State University, Baton RougeGoogle Scholar
  39. Laurent A, Fennel Cai W-J, Huang W-J, Barbero L, Wanninkhof R (2017) Eutrophication-induced acidification of coastal waters in the northern Gulf of Mexico: insights into origin and processes from a coupled physical-biogeochemical model. Geophys Res Lett 44. doi: 10.1002/2016GL071881
  40. Lévy M, Ferrari R, Franks PJ, Martin AP, Rivière P (2012) Bringing physics to life at the submesoscale. Geophys Res Lett 39:L14602. doi: 10.1029/2012GL052756 Google Scholar
  41. Lehrter JC, Beddick DL, Devereux R, Yates DF, Murrell MC (2012) Sediment-water fluxes of dissolved inorganic carbon, O2, nutrients, and N2 from the hypoxic region of the Louisiana continental shelf. Biogeochemistry 109:233–252CrossRefGoogle Scholar
  42. Levin LA, Breitburg DL (2015) Linking coasts and seas to address ocean deoxygenation. Nat Clim Change 5:401–403CrossRefGoogle Scholar
  43. Li Y, Li M, Kemp WM (2015) A budget analysis of bottom-water dissolved oxygen in Chesapeake Bay. Estuaries Coasts 38:2132–2148CrossRefGoogle Scholar
  44. Litchman E, Klausmeier CA, Miller JR, Schofield OM, Falkowski PG (2006) Multi-nutrient, multi-group model of present and future oceanic phytoplankton communities. Biogeosci Discuss 3:607–663CrossRefGoogle Scholar
  45. Mahadevan A (2016) The impact of submesoscale physics on primary productivity of plankton. Ann Rev Mar Sci 8:161–184CrossRefPubMedGoogle Scholar
  46. Marta-Almeida M, Hetland RD, Zhang X (2013) Evaluation of model nesting performance on the Texas-Louisiana continental shelf. J Geophys Res Oceans 118:2476–2491. doi: 10.1002/jgrc.20163 CrossRefGoogle Scholar
  47. Mattern JP, Fennel K, Dowd M (2013) Sensitivity and uncertainty analysis of model hypoxia estimates for the Texas-Louisiana shelf. J Geophys Res Oceans 118:1316–1332CrossRefGoogle Scholar
  48. McClintock BT, Russell DJ, Matthiopoulos J, King R (2013) Combining individual animal movement and ancillary biotelemetry data to investigate population-level activity budgets. Ecology 94:838–849CrossRefGoogle Scholar
  49. Meier HM, Andersson HC, Eilola K, Gustafsson BG, Kuznetsov I, Müller-Karulis B, Neumann T, Savchuk OP (2011) Hypoxia in future climates: a model ensemble study for the Baltic Sea. Geophys Res Lett 38:L24608. doi: 10.1029/2011GL049929 CrossRefGoogle Scholar
  50. Melzner F, Thomsen J, Koeve W, Oschlies A, Gutowska MA, Bange HW, Hansen HP, Körtzinger A (2013) Future ocean acidification will be amplified by hypoxia in coastal habitats. Mar Biol 160:1875–1888CrossRefGoogle Scholar
  51. Middelburg JJ, Levin LA (2009) Coastal hypoxia and sediment biogeochemistry. Biogeosciences 6:1273–1293CrossRefGoogle Scholar
  52. Miller SH, Breitburg DL, Burrell RB, Keppel AG (2016) Acidification increases sensitivity to hypoxia in important forage fishes. Mar Ecol Prog Ser 549:1–8CrossRefGoogle Scholar
  53. Monteiro PM, Dewitte B, Scranton MI, Paulmier A, Van der Plas AK (2011) The role of open ocean boundary forcing on seasonal to decadal-scale variability and long-term change of natural shelf hypoxia. Environ Res Lett 6. doi: 10.1088/1748-9326/6/2/025002
  54. Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW, Galbraith ED, Geider RJ, Guieu C, Jaccard SL, Jickells TD (2013) Processes and patterns of oceanic nutrient limitation. Nat Geosci 6:701–710CrossRefGoogle Scholar
  55. Obenour DR, Scavia D, Rabalais NN, Turner RE, Michalak AM (2013) Retrospective analysis of midsummer hypoxic area and volume in the northern Gulf of Mexico, 1985–2011. Environ Sci Technol 47:9808–9815CrossRefPubMedPubMedCentralGoogle Scholar
  56. O’Neil JM, Davis TW, Burford MA, Gobler CJ (2012) The rise of harmful cyanobacteria blooms: the potential roles of eutrophication and climate change. Harmful Algae 14:313–334CrossRefGoogle Scholar
  57. Paulmier A, Ruiz-Pino D (2009) Oxygen minimum zones (OMZs) in the modern ocean. Prog Oceanogr 80:113–128CrossRefGoogle Scholar
  58. Paerl HW, Gardner WS, Havens KE, Joyner AR, McCarthy MJ, Newell SE, Qin B, Scott JT (2016) Mitigating cyanobacterial harmful algal blooms in aquatic ecosystems impacted by climate change and anthropogenic nutrients. Harmful Algae 54:213–222CrossRefPubMedGoogle Scholar
  59. Rabalais NN, Turner RE, Diaz RJ, Justic D (2009) Global change and eutrophication of coastal waters. ICES J Mar Sci 66:1528–1537CrossRefGoogle Scholar
  60. Reed DC, Algar CK, Huber JA, Dick GJ (2014) Gene-centric approach to integrating environmental genomics and biogeochemical models. Proc Natl Acad Sci 111:1879–1884CrossRefPubMedPubMedCentralGoogle Scholar
  61. Roman MR, Pierson JJ, Kimmel DG, Boicourt WC, Zhang X (2012) Impacts of hypoxia on zooplankton spatial distributions in the northern Gulf of Mexico. Estuaries Coasts 35:1261–1269CrossRefGoogle Scholar
  62. Rose KA, Adamack AT, Murphy CA, Sable SE, Kolesar SE, Craig JK, Breitburg DL, Thomas P, Brouwer MH, Cerco CF, Diamond S (2009) Does hypoxia have population-level effects on coastal fish? Musings from the virtual world. J Exp Mar Biol Ecol 381:S188–S203CrossRefGoogle Scholar
  63. Rose KA, Sable S, DeAngelis DL, Yurek S, Trexler JC, Graf W, Reed DJ (2015a) Proposed best modeling practices for assessing the effects of ecosystem restoration on fish. Ecol Model 300:12–29CrossRefGoogle Scholar
  64. Rose KA, Fiechter J, Curchitser EN, Hedstrom K, Bernal M, Creekmore S, Haynie A, Ito SI, Lluch-Cota S, Megrey BA, Edwards CA (2015b) Demonstration of a fully-coupled end-to-end model for small pelagic fish using sardine and anchovy in the California Current. Prog Oceanogr 138:348–380CrossRefGoogle Scholar
  65. Rose KA, Creekmore S, Thomas P, Craig JK, Rahman MS, Neilan RM (in review) Modeling the population effects of hypoxia on Atlantic croaker (Micropogonias undulatus) in the northwestern Gulf of Mexico: part 1—model description and idealized hypoxia. Estuaries CoastsGoogle Scholar
  66. Scully ME (2013) Physical controls on hypoxia in Chesapeake Bay: a numerical modeling study. J Geophys Res Oceans 118:1239–1256CrossRefGoogle Scholar
  67. Shen J, Wang T, Herman J, Mason P, Arnold GL (2008) Hypoxia in a coastal embayment of the Chesapeake Bay: a model diagnostic study of oxygen dynamics. Estuaries Coasts 31:652–663CrossRefGoogle Scholar
  68. Sippel T, Eveson JP, Galuardi B, Lam C, Hoyle S, Maunder M, Kleiber P, Carvalho F, Tsontos V, Teo SL, Aires-da-Silva A (2015) Using movement data from electronic tags in fisheries stock assessment: a review of models, technology and experimental design. Fish Res 163:152–160CrossRefGoogle Scholar
  69. Soetaert K, Middelburg JJ (2009) Modeling eutrophication and oligotrophication of shallow-water marine systems: the importance of sediments under stratified and well-mixed conditions. Hydrobiologia 629:239–254CrossRefGoogle Scholar
  70. Stramma L, Johnson GC, Sprintall J, Mohrholz V (2008) Expanding oxygen-minimum zones in the tropical oceans. Science 320:655–658CrossRefPubMedGoogle Scholar
  71. Tabor K, Williams JW (2010) Globally downscaled climate projections for assessing the conservation impacts of climate change. Ecol Appl 20:554–565CrossRefPubMedGoogle Scholar
  72. Testa JM, Brady DC, Di Toro DM, Boynton WR, Cornwell JC, Kemp WM (2013) Sediment flux modeling: Simulating nitrogen, phosphorus, and silica cycles. Estuar Coast Shelf Sci 131:245–263CrossRefGoogle Scholar
  73. Thomas LN, Tandon A, Mahadevan A (2008) Submesoscale processes and dynamics. In: Hecht MW, Hasumi H (eds) Ocean modeling in an eddying regime. American Geophysical Union, Washington, DC, pp 17–38. doi: 10.1029/177GM04
  74. Thomas P, Rahman MS, Picha ME, Tan W (2015) Impaired gamete production and viability in Atlantic croaker collected throughout the 20,000 km2 hypoxic region in the northern Gulf of Mexico. Mar Pollut Bull 101:182–192CrossRefPubMedGoogle Scholar
  75. Trenberth KE (2011) Changes in precipitation with climate change. Clim Res 47:123–138CrossRefGoogle Scholar
  76. Treseder KK, Balser TC, Bradford MA, Brodie EL, Dubinsky EA, Eviner VT, Hofmockel KS, Lennon JT, Levine UY, MacGregor BJ, Pett-Ridge J (2012) Integrating microbial ecology into ecosystem models: challenges and priorities. Biogeochemistry 109:7–18CrossRefGoogle Scholar
  77. Tyler RM, Brady DC, Targett TE (2009) Temporal and spatial dynamics of diel-cycling hypoxia in estuarine tributaries. Estuaries Coasts 32:123–145CrossRefGoogle Scholar
  78. Voss M, Bange HW, Dippner JW, Middelburg JJ, Montoya JP, Ward B (2013) The marine nitrogen cycle: recent discoveries, uncertainties and the potential relevance of climate change. Philos Trans R Soc Lond B 368:20130121. doi: 10.1098/rstb.2013.0121
  79. Wainwright J, Mulligan M (2005) Modelling and model building. In: Wainwright J, Mulligan M (eds) Environmental modelling: finding simplicity in complexity. Wiley, West Sussex, pp 7–73Google Scholar
  80. Watson SB, Miller C, Arhonditsis G, Boyer GL, Carmichael W, Charlton MN, Confesor R, Depew DC, Höök TO, Ludsin SA, Matisoff G (2016) The re-eutrophication of Lake Erie: harmful algal blooms and hypoxia. Harmful Algae 56:44–66CrossRefPubMedGoogle Scholar
  81. Yu L, Fennel K, Laurent A (2015) A modeling study of physical controls on hypoxia generation in the northern Gulf of Mexico. J Geophys Res Oceans 120:5019–5039CrossRefGoogle Scholar
  82. Zhang H, Mason DM, Stow CA, Adamack AT, Brandt SB, Zhang X, Kimmel DG, Roman MR, Boicourt WC, Ludsin SA (2014) Effects of hypoxia on habitat quality of pelagic planktivorous fishes in the northern Gulf of Mexico. Mar Ecol Prog Ser 505:209–226CrossRefGoogle Scholar
  83. Zhang J, Gilbert D, Gooday A, Levin L, Naqvi SWA, Middelburg JJ, Scranton M, Ekau W, Pena A, Dewitte B, Oguz T, Monteiro PMS, Urban E, Rabalais NN, Ittekkot V, Kemp WM, Ulloa O, Elmegen R, Escobar-Briones E, Van der Plas AK (2010) Natural and human-induced hypoxia and consequences for coastal areas: synthesis and future development. Biogeosciences 7:1443–1467CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Kenneth A. Rose
    • 1
  • Dubravko Justic
    • 1
  • Katja Fennel
    • 2
  • Robert D. Hetland
    • 3
  1. 1.Department of Oceanography and Coastal SciencesLouisiana State UniversityBaton RougeUSA
  2. 2.Department of OceanographyDalhousie UniversityHalifaxCanada
  3. 3.Department of OceanographyTexas A&M UniversityCollege StationUSA

Personalised recommendations