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Infrastructure for collaborative science and societal applications in the Columbia River estuary

Abstract

To meet societal needs, modern estuarine science needs to be interdisciplinary and collaborative, combine discovery with hypotheses testing, and be responsive to issues facing both regional and global stakeholders. Such an approach is best conducted with the benefit of data-rich environments, where information from sensors and models is openly accessible within convenient timeframes. Here, we introduce the operational infrastructure of one such data-rich environment, a collaboratory created to support (a) interdisciplinary research in the Columbia River estuary by the multi-institutional team of investigators of the Science and Technology Center for Coastal Margin Observation & Prediction and (b) the integration of scientific knowledge into regional decision making. Core components of the operational infrastructure are an observation network, a modeling system and a cyber-infrastructure, each of which is described. The observation network is anchored on an extensive array of long-term stations, many of them interdisciplinary, and is complemented by on-demand deployment of temporary stations and mobile platforms, often in coordinated field campaigns. The modeling system is based on finiteelement unstructured-grid codes and includes operational and process-oriented simulations of circulation, sediments and ecosystem processes. The flow of information is managed through a dedicated cyber-infrastructure, conversant with regional and national observing systems.

References

  1. Anderson C R, Davis R E, Bandolin N S, Baptista A M, Tebo B M (2011). Analysis of in situ manganese (II) oxidation in the Columbia River and offshore plume: linking Aurantimonas and the associated microbial community to an active biogeochemical cycle. Environ Microbiol, 13(6): 1561–1576

    Article  Google Scholar 

  2. Baptista A M (2006). CORIE: the first decade of a coastal margin collaborative observatory. In: Proceedings of MTS/IEEE Oceans '06. Boston, Massachusetts: IEEE, 1–6

    Google Scholar 

  3. Baptista AM(2015). The power of estuarine collaboratories: can lessons learned in the Columbia River inform a global vision? In: Proceedings of IEEE/OES Underwater Technologies 2015. Chennai, India: IEEE/OES, 1–7

  4. Baptista A M, Howe B, Freire J, Maier D, Silva C (2008). Scientific exploration in the era of ocean observatories. Comput Sci Eng, 10(3): 53–58

    Article  Google Scholar 

  5. Baptista A M, Wilkin M, Pearson P, Turner P J, McCandlish C, Barrett P (1999). Coastal and estuarine forecast systems: a multi-purpose infrastructure for the Columbia River. Earth Syst Monit, 9(3): 1–2, 4–5, 16

    Google Scholar 

  6. Baptista A M, Zhang Y L, Chawla A, Zulauf M, Seaton C, Myers E P III, Kindle J, Wilkin M, Burla M, Turner P J (2005). A cross-scale model for 3D baroclinic circulation in estuary-plume-shelf systems: II. application to the Columbia River. Cont Shelf Res, 25(7–8): 935–972

    Article  Google Scholar 

  7. Barbier E B, Hacker S D, Kennedy C, Koch E W, Stier A C, Silliman B R (2011). The value of estuarine and coastal ecosystem services. Ecol Monogr, 81(2): 169–193

    Article  Google Scholar 

  8. Barnes C A, Duxbury A C, Morse B A (1972). Circulation and selected properties of the Columbia River effluent at sea. In: Pruter A T, Alverson D L, eds. The Columbia River Estuary and Adjacent Ocean Waters. Seattle: University of Washington Press, 41–80

    Google Scholar 

  9. Bottom D L, Simenstad C A, Baptista A M, Burke J, Jay D A, Burke J, Jones K K, Casillas E, Schiewe M H (2005). Salmon at river’s end: the role of the estuary in the decline and recovery of Columbia River salmon. NOAA Technical memorandum NMFS-NWFSC-68

    Google Scholar 

  10. Bräuer S L, Adams C, Kranzler K, Murphy D, Xu M, Zuber P, Simon H M, Baptista A M, Tebo B M (2011). Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environ Microbiol, 13(3): 589–603

    Article  Google Scholar 

  11. Bräuer S L, Kranzler K, Goodson N, Murphy D, Simon H M, Baptista A M, Tebo B M (2013). Dark carbon fixation in the Columbia River’s estuarine turbidity maxima: molecular characterization of red-type cbbL genes and measurement of DIC uptake rates in response to added electron donors. Estuaries Coasts, 36(5): 1073–1083

    Article  Google Scholar 

  12. Burke B J, Anderson J J, Baptista A M (2014). Evidence for multiple navigational sensory capabilities by Chinook salmon. Aquat Biol, 20(1): 77–90

    Article  Google Scholar 

  13. Burla M (2009). The Columbia River estuary and plume: natural variability, anthropogenic change and physical habitat for salmon. Dissertation for Ph.D Degree. Beaverton, Oregon: Oregon Health & Science University

    Google Scholar 

  14. Burla M, Baptista A M, Casillas E, Williams J G, Marsh D M (2010b). The influence of the Columbia River plume on the survival of steelhead (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha): a numerical exploration. Can J Fish Aquat Sci, 67(10): 1671–1684

    Article  Google Scholar 

  15. Burla M, Baptista A M, Zhang Y, Frolov S (2010a). Seasonal and interannual variability of the Columbia River plume: a perspective enabled by multiyear simulation databases. Journal of Geophysical Research. Oceans, 115(C2): C00B16

    Google Scholar 

  16. Chawla A, Jay D A, Baptista A M, Wilkin M, Seaton C (2008). Seasonal variability and estuary-shelf interactions in circulation dynamics of a river-dominated estuary. Estuaries Coasts, 31(2): 269–288

    Article  Google Scholar 

  17. DeLorenzo S, Bräuer S L, Edgmont C A, Herfort L, Tebo B M, Zuber P (2012). Ubiquitous dissolved inorganic carbon assimilation by marine heterotrophic bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing. PLoS ONE, 7(10): e46695

    Article  Google Scholar 

  18. Diaz R J, Rosenberg R (2008). Spreading dead zones and consequences for marine ecosystems. Science, 321(5891): 926–929

    Article  Google Scholar 

  19. Durkin C A, Bender S J, Chan K Y K, Gaessner K, Grunbaum D, Armbrust E V (2013). Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnol Oceanogr, 58(5): 1707–1726

    Article  Google Scholar 

  20. Evans W, Hales B, Strutton P G (2013). PCO2 distributions and air–water CO2 fluxes in the Columbia River estuary. Estuar Coast Shelf Sci, 117: 260–272

    Article  Google Scholar 

  21. Fortunato C S, Crump B C (2011). Bacterioplankton community variation across river to ocean environmental gradients. Microb Ecol, 62(2): 374–382

    Article  Google Scholar 

  22. Fortunato C S, Eiler A, Herfort L, Needoba J A, Peterson T D, Crump B C (2013). Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME J, 7(10): 1899–1911

    Article  Google Scholar 

  23. Fortunato C S, Herfort L, Zuber P, Baptista A M, Crump B C (2012). Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME J, 6(3): 554–563

    Article  Google Scholar 

  24. Frolov S, Baptista A M, Wilkin M (2008). Optimizing fixed observational assets in a coastal observatory. Cont Shelf Res, 28 (19): 2644–2658

    Article  Google Scholar 

  25. Gilbert M, Needoba J A, Koch C, Barnard A, Baptista A M (2013). Nutrient loading and transformations in the Columbia River estuary determined by high resolution in situ sensors. Estuaries Coasts, 36(4): 708–727

    Article  Google Scholar 

  26. Green V, Watts N B, Wegner K, Thompson M, Johnson A, Peterson T, Baptista AM(2013). Coastal margin science and education in the era of collaboratories. Current, 28(3): 27–31

    Google Scholar 

  27. Herfort L, Peterson T D, Campbell V, Futrell S, Zuber P (2011a). Myrionecta rubra (Mesodinium rubrum) bloom initiation in the Columbia River estuary. Estuar Coast Shelf Sci, 95(4): 440–446

    Article  Google Scholar 

  28. Herfort L, Peterson T D, McCue L A, Crump B C, Prahl F G, Baptista A M, Campbell V, Warnick R, Roegner G C, Zuber P (2011b). Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquat Microb Ecol, 62(1): 85–97

    Article  Google Scholar 

  29. Herfort L, Peterson T D, McCue L A, Zuber P (2011c). Protist 18S rRNA gene sequence analysis reveals multiple sources of organic matter contributing to turbidity maxima of the Columbia River estuary. Mar Ecol Prog Ser, 438: 19–31

    Article  Google Scholar 

  30. Herfort L, Peterson T D, Prahl F G, McCue L A, Needoba J A, Crump B C, Roegner G C, Campbell V, Zuber P (2012). Red waters of Myrionecta rubra are biogeochemical hotspots for the Columbia River estuary with impacts on primary/secondary productions and nutrient cycles. Estuaries Coasts, 35(3): 878–891

    Article  Google Scholar 

  31. Herfort L, Seaton C, Wilkin M, Seitz K, Lopez J, Smith M, Haynes V, Baptista A M, Simon H M. Autonomous adaptive sampling of microbial processes in a dynamic estuary. Limnol Oceanogr Methods, (in press)

  32. Hey T, Tansley S, Tolle K (2009). The Fourth Paradigm–Data-Intensive Scientific Discovery. Berlin, Heidelberg: Springer

    Google Scholar 

  33. Hickey B M, Kudela R M, Nash J D, Bruland K W, Peterson W T, MacCready P, Lessard E J, Jay D A, Banas N S, Baptista A M, Dever E P, Kosro P M, Kilcher L K, Horner-Devine A R, Zaron E D, McCabe R M, Peterson J O, Orton P M, Pan J, Lohan M C (2010). River influences on shelf ecosystems: introduction and synthesis. Journal of Geophysical Research, 115(2): C00B17

    Google Scholar 

  34. Howarth R, Chan F, Conley D J, Garnier J, Doney S C, Marino R, Billen G (2011). Coupled biogeochemical cycles: eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems. Front Ecol Environ, 9(1): 18–26

    Article  Google Scholar 

  35. HSBC (2012). Exploring the links between water and economic growth. A report prepared for HSBC by Frontier Economics: Executive Summary

    Google Scholar 

  36. IPCC (2014). Climate change 2014: impacts, adaptation, and vulnerability. Part B: regional aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, United Kingdom and New York, USA

  37. Kahn P, Herfort L, Peterson T D, Zuber P (2014). Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element. MicrobiologyOpen, 3(5): 764–776

    Article  Google Scholar 

  38. Kärnä T, Baptista A M, Lopez J E, Turner P J, McNeil C, Sanford T B (2015). Numerical modeling of circulation in high-energy estuaries: a Columbia River Estuary benchmark. Ocean Model, 88: 54–71

    Article  Google Scholar 

  39. Lave J, Wenger E (1991). Situated Learning: Legitimate Peripheral Participation. Cambridge: Cambridge University Press

    Book  Google Scholar 

  40. Liu Y, MacCready P, Hickey B M (2009). Columbia River plume patterns in summer 2004 as revealed by a hindcast coastal ocean circulation model. Geophys Res Lett, doi: 10.1029/2008GL036447

    Google Scholar 

  41. Lopez J E, Brown J (2014). Improving the performance of the coastal ocean model SELFE. In: SIAM Conference on Parallel Processing for Scientific Computing, Portland, Oregon

    Google Scholar 

  42. Lopez J, Baptista A M, Spitz Y (2012). Modeling estuarine turbidity maxima in the Columbia River estuary. In: 2012 Columbia River Estuary Conference: New Scientific Findings and their Management Implications. Astoria, Oregon, US

    Google Scholar 

  43. Lotze H K, Lenihan H S, Bourque B J, Bradbury R H, Cooke R G, Kay M C, Kidwell S M, Kirby M X, Peterson C H, Jackson J (2006). Depletion, degradation, and recovery potential of estuaries and coastal seas. Science, 312(5781): 1806–1809

    Article  Google Scholar 

  44. Maier M A, Peterson T D, Needoba J A, Bartowicz K, Baptista A M (2012). Phytoplankton seasonal dynamics and ecological interactions in the lower Columbia River. In: AGU Ocean Sciences Meeting, Salt Lake City, Utah

    Google Scholar 

  45. MEA (2005). Ecosystems and human well-being: current state and trends: findings of the Condition and Trends Working Group of the Millennium Ecosystem Assessment. Washington D C: Island Press

    Google Scholar 

  46. Megler V M, Maier D (2013). Data near here: bringing relevant data closer to scientists. Comput Sci Eng, 15(3): 44–53

    Article  Google Scholar 

  47. Miller J A, Teel D J, Peterson W T, Baptista A M (2014). Assessing the relative importance of local and regional processes on the survival of a threatened salmon population. PLoS ONE, 9(6): e99814

    Article  Google Scholar 

  48. Miller J A, Teel D, Baptista A M, Morgan C, Bradford M (2013). Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon. Can J Fish Aquat Sci, 70(4): 617–629

    Article  Google Scholar 

  49. NOAA (2014a), U.S. population living in coastal watershed counties, in NOAA’s State of the Coast

    Google Scholar 

  50. NOAA (2014b), The coast–our nation’s economic engine, in NOAA’s State of the Coast

    Google Scholar 

  51. NSF (2005). Ocean Observatories Initiative. Science Plan Report

    Google Scholar 

  52. OGE (2014). Our Global Estuary: U.S. NationalWorkshop, October 21–23, 2013. Editor: M. Davis. Harbor Branch Oceanographic Institute, Harbor Branch, FL, USA

    Google Scholar 

  53. Peterson T D, Golda R L, Garcia M L, Li B, Maier M A, Needoba J A, Zuber P (2013). Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquat Microb Ecol, 68(2): 117–130

    Article  Google Scholar 

  54. Pinto L, Fortunato A B, Zhang A, Oliveira A, Sancho F E P (2012). Development and validation of a three-dimensional morphodynamic modelling system for non-cohesive sediments. Ocean Model, 57–58 (C): 1–14

    Article  Google Scholar 

  55. Rathmell K, Wilkin M, Welle P, Mattson T, Baptista A M (2013). A Very Smart Kayak. Current: The Journal of Marine Education, 28(3): 32–33

    Google Scholar 

  56. Robinson P, Leight A K, Trueblood D D, Wood B (2013). Climate sensitivity of the national estuarine research reserve system. NOAA Special Report

    Google Scholar 

  57. Roegner C G, Needoba J A, Baptista A M (2011b). Coastal upwelling supplies oxygen-depleted water to the Columbia River estuary. PLoS ONE, 6(4): e18672

    Article  Google Scholar 

  58. Roegner G C, Seaton C, Baptista A M (2011a). Climatic and tidal forcing of hydrography and chlorophyll concentrations in the Columbia River estuary. Estuaries Coasts, 34(2): 281–296

    Article  Google Scholar 

  59. Scholin C A (2013). Ecogenomic sensors. In: Levin S A, eds. Encyclopedia of Biodiversity. Waltham, Massachusetts: Academic Press, 690–700

    Chapter  Google Scholar 

  60. Seaton C, Turner P J, Kärnä T, Baptista A M (2014). Columbia River channel improvement project. Post-project analysis. Final Report to the U.S. Army Corps of Engineers, Portland, Oregon: Oregon Health & Science University

    Google Scholar 

  61. Simmons S, Casavant K (2010). Historical waterborne commerce on the Columbia Snake River system: commodity movements up and down river, 1991–2010. Freight Policy Transportation Institute, Pullman, Washington, Washington State University

    Google Scholar 

  62. Smith M W, Allen L Z, Allen A E, Herfort L, Simon H M (2013). Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front Microbiol, 4: 120

    Google Scholar 

  63. Smith M W, Herfort L, Tyrol K, Sucui D, Campbell V, Crump B C, Peterson T D, Zuber P, Baptista A M, Simon H M (2010). Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients of the Columbia River coastal margin. PLoS ONE, 5(10): e13312

    Article  Google Scholar 

  64. Smith M W, Maier M, Suciu D, Peterson T D, Bradstreet T, Nakayama J, Simon H M (2012). High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae, 19: 169–180

    Article  Google Scholar 

  65. Spitz Y H (2011). Ecosystem modeling of the Oregon shelf: everything but the kitchen sink. In: Omori K, Guo X, Yoshie N, Fujii N, Handoh I C, Isobe A, Tanabe S, eds. Interdisciplinary Studies on Environmental Chemistry—Marine Environmental Modeling & Analysis. TERRAPUB, 1–9

    Google Scholar 

  66. Spitz Y H, Moisan J R, Abbott M R (2001). Configuring an ecosystem model using data from the Bermuda Atlantic time series (BATS). Deep Sea Res Part II Top Stud Oceanogr, 48(8–9): 1733–1768

    Article  Google Scholar 

  67. Statham P J (2012). Nutrients in estuaries—An overview and the potential impacts of climate change. Sci Total Environ, 434: 213–227

    Article  Google Scholar 

  68. Swalwell J E, Ribalet F, Armbrust E V (2011). SeaFlow: a novel underway flow-cytometer for continuous observations of phytoplankton in the ocean. Limnol Oceanogr Methods, 9(October): 466–477

    Article  Google Scholar 

  69. Towns J, Cockerill T, Dahan M, Foster I, Gaither K, Grimshaw A, Hazlewood V, Lathrop S, Lifka D, Peterson G D, Roskies R, Scott J R, Wilkens-Diehr N (2014). XSEDE: accelerating scientific discovery. Computing in Science & Engineering, 16(5): 62–74

    Article  Google Scholar 

  70. U.S. Entity (2013). Regional recommendation for the future of the Columbia River Treaty after 2024. http://www.crt2014-2024review.gov/Files/Regional Recommendation Final, 13 DEC 2013.pdf

    Google Scholar 

  71. Wenger E (1998). Communities of Practice: Learning, Meaning, and Identity. Cambridge: Cambridge University Press

    Book  Google Scholar 

  72. Zhang Y, Baptista A M (2008). SELFE: a semi-implicit Eulerian Lagrangian Finite-element model for cross-scale ocean circulation. Ocean Model, 21(3–4): 71–96

    Article  Google Scholar 

  73. Zhang Y, Baptista A M, Myers E P (2004). A cross-scale model for 3D baroclinic circulation in estuary-plume-shelf systems: I. formulation and skill assessment. Cont Shelf Res, 24(18): 2187–2214

    Article  Google Scholar 

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Correspondence to António M. Baptista.

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António M. Baptista has a B.Sc. in Civil Engineering from Academia Militar, Portugal and M.Sc. and Ph.D. degrees in Civil Engineering from the Massachusetts Institute of Technology, United States. He is a Professor at the Oregon Health & Science University, U.S. and serves as the Director of the Center for Coastal Margin Observation & Prediction, a multi-institutional Science and Technology Center funded by the National Science Foundation. Prof. Baptista’s research is broadly interdisciplinary, anchored on a core expertise in estuarine science and in observation & modeling systems. He has published about 70 peerreviewed articles, often collaboratively, in areas including computational science; physical, biogeochemical & microbial oceanography; fisheries; natural hazards; and computer science. He provides scientific and operational coordination for the SATURN collaboratory.

Charles Seaton has a B.Sc. in Botany from the University of Massachusetts at Amherst and a M.S. in Environmental Science and Engineering from the Oregon Graduate Institute of Science & Technology. He is a Research Associate at the Oregon Health & Science University, U.S., and the coordinator of the cyber-infrastructure team for the Center for Coastal Margin Observation & Prediction. Mr. Seaton has published 9 peer-reviewed articles.

Michael P. Wilkin has a B.Sc. in Oceanography from University of Southampton, United Kingdom. With over 25 years of experience in the design and deployment of oceanographic instrumentation, he is a Senior Research Associate at Oregon Health & Science University, U.S., and manages the design, implementation and maintenance of the estuarine and coastal elements of the SATURN observation network from a field station in Astoria, Oregon, U.S. Mr. Wilkin has published 10 peerreviewed articles.

Sarah F. Riseman has a B.Sc. in Zoology from the University of Massachusetts, U.S., and a M.Sc. in Marine Biology from the College of Charleston, U.S. She is a Research Associate at Oregon Health & Science University, U.S., working on quality assurance and quality control of biogeochemical data for the Center for Coastal Margin Observation & Prediction. Before joining the center in 2010, she had over 10 years of oceanographic research experience including operation and maintenance of a diversity of instrumentation for biogeochemical measurements and over 13 cumulative months of research at sea or in remote field locations. She has published 13 peer-reviewed articles.

Joseph A. Needoba has a B.Sc. (Biology) degree and a Ph.D. (Botany) degree from the University of British Columbia, Canada. He is an Assistant Professor at Oregon Health & Science University, U.S, and an Investigator in the Center for Coastal Margin Observation & Prediction. He has published more than 20 peer-reviewed papers in the fields of oceanography and estuarine science.

David Maier is Maseeh Professor of Emerging Technologies in the Department of Computer Science at Portland State University, U.S. His research interests include scientific information management, datastream systems, superimposed information and declarative cloud programming. Prof. Maier has a dual BA (Honors College) in Mathematics and Computer Science from the University of Oregon, U. S. and a Ph.D. in Electrical Engineering and Computer Science from Princeton University, U.S. He is an ACM Fellow, a Senior Member of IEEE and a member of SIAM. He has published 95 peer-reviewed articles in journals and selective conferences. He is a member of the CMOP cyber-infrastructure team.

Paul J. Turner has a B.Sc in Mathematics from Boise State University. He is a Senior Research Assistant at the Oregon Health & Science University, U.S. As a member of the cyber-infrastructure team, he manages operational details of the Virtual Columbia River for the Center for Coastal Margin Observation & Prediction. He has published 9 peerreviewed articles.

Tuomas Kärnä has a M.Sc in Technology from Helsinki University of Technology, Finland and a Ph.D. in Applied Mathematics from Université Catholique de Louvain, Belgium. He is a Post-Doctoral Fellow at the Oregon Health & Science University, U.S. He has published 14 peer-reviewed articles.

Jesse E. Lopez has a B.A. in History from the University ofWashington, U.S. He is a Ph.D. candidate at the Oregon Health & Science University, U.S. and a Department of Energy Computational Science Graduate Fellow.

Lydie Herfort received an undergraduate diplomat (D.E.U.G.) in Biology from the University of Caen, France, and a third year of B.Sc. and a Ph.D. degree in aquatic biology from Queen Mary University London, United Kingdom. She is a Senior Research Associate at the Center for Coastal Margin Observation & Prediction at Oregon Health & Science University, U.S. Dr. Herfort studies the ecology and physiology of aquatic microorganisms—specifically bacteria, archaea and protists— to assess their impacts on biogeochemical cycles. Her work involves many aspects of SATURN’s collaboratory, including traditional vessel-based campaigns and adaptive microbial water sample collection with an Environmental Sample Processor. She has published 23 peerreviewed articles.

V.M. Megler is a Post-Doctoral Fellow in Computer Science at Portland State University, U.S., having received a Ph.D. there in 2015. Megler's most recent industry position was as Executive IT Architect at IBM, publishing more than 20 industry technical papers on applications of emerging technologies to industry problems. Current research centers on applying Information Retrieval techniques to scientific data, ranging from oceanographic to genomic data. General research interests include applications of emerging technologies, scientific information management and spatio-temporal databases. Megler has 11 peer-reviewed research articles and holds 2 patents.

Craig McNeil has a B.Sc. in physics from Heriot-Watt University, Scotland and a Ph.D. from University of Victoria, Canada. He is a Principal Oceanographer at the Applied Physics Laboratory at the University of Washington, U.S. His multi-disciplinary research focuses on upper ocean processes and interactions. He has published more than 20 peer-reviewed articles. He coordinates the CMOP autonomous underwater vehicles program.

Byron C. Crump has a M.S. and Ph.D. in Oceanography from the University of Washington, U.S. He is an Associate Professor in Ocean Ecology and Biogeochemistry at the College of Earth, Ocean and Atmospheric Sciences, Oregon State University, U.S. His research explores the ecology, biodiversity and genomics of microbes in lakes, rivers, estuaries and coastal oceans. He has published 55 peer-reviewed articles and is an editor for the textbook Estuarine Ecology 2nd Ed. (Wiley Interscience).

Tawnya D. Peterson has a B.Sc. in Biology from Mount Allison University (Sackville, Canada) and a Ph.D. in Oceanography from the University of British Columbia (Vancouver, Canada). She is an Assistant Professor at Oregon Health & Science University, U.S., and an Investigator in the Center for Coastal Margin Observation & Prediction. She has published over 30 peer-reviewed papers in the fields of oceanography and environmental science.

Yvette H. Spitz has a B.Sc. in Physics and a M.Sc. in Oceanography from the University of Liège, Belgium, a M.Sc. in Physical Oceanography from Florida State University, U.S., and a Ph.D. in Oceanography from Old Dominion University, U.S. She is a Professor in Ocean Ecology and Biogeochemistry at the College of Earth, Ocean and Atmospheric Sciences at Oregon State University, U.S., and has served for the last two years as co-director of the Center for Coastal Margin Observation & Prediction. Her research includes ecosystem dynamics and physical-biological interactions in the world ocean, with ecosystem modeling spanning tropical microbes to ice algae. She is an expert in data assimilation applied to coupled circulation and ecosystem models. She has published ~45 peer-reviewed articles in areas including circulation and biogeochemical models from coastal to open ocean and ice cover ocean; particle filter and variational adjoint data assimilation.

Holly M. Simon has B.S. (Biology) and B.A. (Chemistry) degrees from the Metropolitan State College of Denver, U.S., and a Ph.D. degree (Bacteriology) from the University ofWisconsin at Madison, U.S. She is an Associate Professor in the Institute of Environmental Health and an Investigator in the Center for Coastal Margin Observation & Prediction at Oregon Health & Science University, U.S. She has published over 20 peer-reviewed articles across diverse areas of environmental microbiology, with emphasis on the application of gene sensing technologies to assess the provisioning of, and perturbations to, microbial ecosystem services.

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Baptista, A.M., Seaton, C., Wilkin, M.P. et al. Infrastructure for collaborative science and societal applications in the Columbia River estuary. Front. Earth Sci. 9, 659–682 (2015). https://doi.org/10.1007/s11707-015-0540-5

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Keywords

  • estuaries
  • observations
  • numerical modeling
  • cyber-infrastructure
  • Columbia River