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Science Initiative III: Lateral Bays


The Lateral Bays science initiative aims to understand the biogeochemical exchange between lateral bays and the estuary, and to develop approaches and models to quantify the contribution of these exchanges to the functioning of the estuary bioreactor.

  • Observe, describe and quantify biogeochemical transformations (e.g. nutrients, DIC, methane, gene expression) in lateral bays at multiple time scales (daily, tidal monthly, and seasonal).
  • Identify the dominant microbial assemblages and metabolisms responsible for carbon respiration in three distinctive lateral bays (freshwater marsh, mudflat, and saltwater marsh) within the estuary, which differ in the degree to which the coastal ocean influences them.
  • Quantify the extent to which lateral bays contribute to the net heterotrophy in the estuary.
  • Develop models of varying complexity that (a) describe the nitrogen and carbon exchanges between lateral bays and the main stem of the contemporary river-to-estuary continuum, and (b) have the potential to anticipate the evolution of these exchanges relative to climate and land-use change.

Chart summarizing the various types of metabolisms capable of organic matter decomposition and key products of those metabolisms that are or potential could be measurable.Chart summarizing the various types of metabolisms capable of organic matter decomposition and key products of those metabolisms that are or potential could be measurable. The types of lateral bays where each metabolism might be expressed are indicated using a zone 1 (fresh), 2 (brackish) or 3 (marine) notation.

Biogeochemical transformations within lateral bays

Energy in the form of organic carbon flows downstream and fuels the ecosystem through a variety of metabolic pathways along the Columbia River river-to-ocean continuum. It has been hypothesized that successive microbial assemblages are adapted to capitalize on inefficiencies in the processing of organic matter and thus result in a myriad of probable redox transformations that effect multiple biogeochemical cycles. Most of these metabolic activities are predominant in lateral bays, where the residence times of water and its constituents (both dissolved and particulate) are the longest. In addition, the interaction with the hyporheic zone through tidally driven pressure gradients further enhances metabolism of the estuarine water column by continuously exchanging reduced substrates from the sediments (e.g. Mn2+) and electron acceptors (e.g. nitrate, sulfate) from the water column. In addition, lateral bays are critical habitats for benthic organisms and marsh vegetation that contribute to the overall metabolic fluxes. The geographic focus of this initiative is on three of the major bays along the salinity gradient: Cathlamet Bay (mostly freshwater), Youngs Bay (brackish), and Baker Bay (marine). Due to circulation features and different salinity levels, the energy transfers and metabolic processes within each bay are expected to be very different and thus provide for an excellent comparative model.

Tidal transport and mixing of river and ocean waters are driving forces that determine the structure and function of lateral bay communities. These habitats, represented by tidal marshes and mudflats, are vital components of the overall estuarine ecosystem because they are regions of high autotrophic and heterotrophic productivity that together contribute to Net Community Metabolism. As a detritus-driven ecosystem fueled mainly by allochthonous inputs of organic matter, the Columbia River estuary is generally considered net heterotrophic. Within the lateral bays, however, autotrophy is accomplished by benthic or epiphytic phytoplankton communities (e.g. diatoms), macrophytes or rooted aquatic vegetation. Heterotrophy encompasses microbial metabolisms ranging from aerobic to facultative anaerobic (denitrifiers; metal reducers: Mn and Fe) to strict anaerobic (sulfate reducers; methanogens; fermentors). Net Community Metabolism depends upon seasons as well as the location along the tidal fresh-to-salt water gradient that ultimately defines the importance of physical factors such as river flow and tidal forcing and by factors that impact physiology such as temperature and resource limitations including low light and nutrient depletion. Through the variety of metabolic processes, lateral bay communities contribute significantly to the biogeochemical breathing cycle at the sea-land margin, and provide multiple ecosystem benefits such as pollutant filtering and sediment stabilization.

A detailed quantitative understanding of the biogeochemistry of intertidal regions has been limited by our inability to resolve the temporal and spatial dynamics using traditional field sampling approaches. This initiative will utilize SATURN observational platforms within the estuary and lateral bays to facilitate a comprehensive ecological study of the dynamics of intertidal biogeochemistry and metabolic processes. Through this initiative we will develop quantitative understanding of lateral bay ecosystem metabolism that will allow us to assess the role of these hotspots on the estuary bioreactor and on future environmental impacts such as increasing acidification and hypoxic events in the estuary. It is essential to identify the main factors that drive organic matter input and decomposition by which acidity (in the form of CO2) is added to the water column. Efficient downstream passage of this central product of Net Community Metabolism would act to exacerbate the impact of ocean acidification on the upwelling-dominated coastal margin.

Science Initiative III Team

Lead Investigator
Fred Prahl, Oregon State University (OSU)

António Baptista (OHSU), Jim Lerczak (OSU), Joe Needoba (OHSU), Gyorgyi Nyerges (Pacific Unv.) Tawnya Peterson (OHSU),  Holly Simon (OHSU), Yvette Spitz (OSU), Brad Tebo (OHSU)

Students, Post-Docs, and Staff
David Langner (OSU), Emily Lemagie (OSU), Anne Pfeifer-Herbert (OSU), John Roque, Mariya Smith (OHSU), Jessica Sweeney, Marnie Jo Zirbe

Operational Team Support
Astoria Field Team: Michael Wilkin (OHSU), Katie Rathmell (OHSU), Jo Goodman (OHSU)
Cyber Team: Charles Seaton (OHSU), Paul Turner (OHSU)
Clatsop Community College: Faculty and students of the Maritime Science Program and Integrated Technologies Program