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Research Priorities
Introduction
research skiff
Research activities undertaken by the South Slough NERR will address an interdisciplinary array of estuarine science questions and management issues defined by national priorities and regional needs. Priority research issues will be addressed by Reserve staff, visiting researchers, and graduate students, and through collaborations with existing partners and other interested groups.

Priority Research Issues
Native Olympic Oysters (Ostreola conchaphila)
The Development of Best Management Practices for Estuarine Aquaculture Activities
Extensive areas of estuarine tidelands in the Pacific Northwest are currently used for commercial cultivation of Pacific oysters (Crassostrea gigas). Coastal aquaculture practices, however, have recently come under scrutiny regarding the potential impacts oyster mariculture may have on estuarine ecosystems. Over the past 15 years, South Slough NERR has studied the effects of oyster mariculture and will seek support for additional research on this issue. Future research will emphasize comparing and contrasting ecological impacts of various oyster mariculture methods in order to develop best management practices for the industry.

Interactive Hydrodynamic Model of the South Slough and Coos Estuary
Hydrology and circulation patterns of estuarine waters are fundamentally important to ecological processes and commercial activities in Coos Bay. Hydrodynamics within the Coos estuary and South Slough are complex and affected by large-scale perturbations of the shoreline and bathymetry of the tidal basin, tidal forcing from the adjacent nearshore ocean, changes in local wind conditions, and inputs from the watershed.  Information about estuarine hydrodynamics is essential to many of the decisions that influence the management of coastal areas. With datasets available from the long-term monitoring of estuarine water conditions, the opportunity exists for South Slough NERR to investigate the hydrology and circulation patterns of tidal waters in the South Slough and greater Coos estuary. South Slough NERR will seek partnerships to develop and validate a hydrodynamic model that will link movement of the estuarine waters with time-series measurements for several ambient water parameters.

Assessment and Mapping of Intertidal and Subtidal Estuarine Habitats and Communities
New field surveys of the distribution and spatial extent of habitats and communities are required throughout the intertidal and subtidal regions of the South Slough estuarine tidal basin. The Reserve will participate in an environmental characterization, biotic inventory, and mapping effort of the estuarine habitats and communities found in the South Slough, and will facilitate the development of similar products for the greater Coos estuary.
 

Restoration and Recovery of Native Olympic Oysters
Native Olympia oysters (Ostreola conchaphila), historically abundant in the Coos estuary and South Slough, became locally extinct prior to written history due to basin-wide changes in sedimentation. Since that time, aquatic habitats in Coos Bay have been degraded by the cumulative effects of sedimentation, bark decay, dredging, diking, filling, domestic and industrial pollution, and by colonization by non-indigenous aquatic species. Despite these changes, water column and sediment conditions have improved considerably within the tidal basin to the point where they are now conducive to the recovery of native oysters. Discontinuous populations of O. conchaphila have become re-established in the Coos estuary over the past two decades in the low intertidal and shallow subtidal zone.  The restoration of self-sustaining populations of Ostreola conchaphila in Coos Bay and South Slough will be a research focus for the Reserve. In particular, efforts will be focused on investigating the genetic identity of potential brood stock sources, oyster transplant and cultivation techniques, life history patterns and the resistance of Ostreola conchaphila to colonization by non-indigenous species, and studying ecological interactions within tideflat communities.

Salt Marsh and Eelgrass Communities as Biotic Indicators of Estuarine Ecosystem Function
Emergent tidal marshes and submerged aquatic vegetation (SAV) are critically important habitats in the South Slough estuary. Salt marshes and eelgrass beds are widely recognized as indicators of coastal ecosystem health, contributing to fundamental ecological processes including the production and decomposition of organic matter, cycling of organic and inorganic nutrients, alteration of hydrologic flow patterns, and improvement of estuarine water quality. In addition, emergent tidal marshes and eelgrass beds provide essential habitat for populations of fish and shellfish, and offer resting and forage areas for migratory and resident shorebirds and waterfowl.
Despite the recognized value of emergent tidal wetlands and SAV, the spatial extent, distribution, biotic diversity, and ecosystem functions have not been fully described and documented for these communities in the South Slough estuary.  Building on past and current research projects, South Slough NERR will participate in projects to further investigate the dynamics of salt marshes and eelgrass beds within the South Slough and greater Coos Bay.  Additional research will focus on understanding how the density, productivity, and spatial extent of emergent and submerged vegetation fluctuates over seasonal, annual, and longer time scales in Pacific Northwest estuaries in response to large-scale changes in nearshore ocean conditions as well as anthropogenic perturbations.

Bioinvasions and Ecological Impacts of Aquatic Non-Indigenous Species
Biological invasions pose a considerable threat to the ecological integrity of the South Slough and Coos estuaries. The South Slough tidal basin, including the Reserve, is inhabited by nearly 50 species of aquatic non-indigenous organisms, and over 100 aquatic non-indigenous species have been identified in the adjacent waters of Coos Bay. Coos Bay and the South Slough are susceptible to accelerated rates of invasion by new species due to international shipping, interstate commerce, shellfish mariculture, and recreational activities.  South Slough NERR will continue to monitor the appearance, abundance, and distribution of target non-indigenous species. In addition, the Reserve will respond to opportunities to monitor the arrival of new non-native species and to investigate the ecological impacts of these aquatic invasive species on estuarine habitats and native estuarine communities.

Community Development by Dominant Estuarine Ecological Engineering Species
Several organisms function as dominant ecological engineering species in the South Slough estuary. These include burrowing shrimp (Neotrypaea californiensis and Upogebia pugettensis), eelgrass (Zostera marina and Z. japonica), and Pacific oysters (Crassostraea gigas).  The establishment, maintenance, and decline of these distinct communities is particularly interesting because they can exist as alternative states in the lower to mid intertidal zone of unconsolidated tideflats.  Although the upper and lower boundaries of these communities appear to be established by physical and biotic factors, respectively, the lateral extents of these communities appear to fluctuate dramatically over time and to be determined to some extent by changes in estuarine conditions and characteristics of the communities themselves. For example, preliminary observations within several Oregon estuaries suggest that the spatial distribution of burrowing
shrimp populations may be determined by a combination of salinity tolerances, predation, and larval recruitment.  Research efforts at South Slough NERR will be directed towards further understanding the functional role of estuarine ecological engineering species in tideflat communities.

Physical and Biotic Links between the South Slough/Coos Estuary and the Nearshore Pacific Ocean
Since 1995, South Slough NERR has been involved in research to improve the understanding of the dynamics of nearshore ocean/estuary connections in the Pacific Northwest region, and to shed new light on the ecological consequences of ocean forcing for special interest species including Dungeness crabs (Cancer magister), burrowing shrimp (Neotrypaea californiensis), and populations of Pacific salmon and groundfish. In support of this research, the Reserve will seek assistance to analyze data collected during five NOAA research cruises to develop quantitative descriptions of physical and biotic linkages between the protected waters of Oregon estuaries (Coos, Coquille, and Umpqua) and the nearshore Pacific Ocean.  Future research cruises are planned for alternating years to continue these investigations, and NOAA ship time has been requested for the years 2004, 2006, 2008, and 2010.  Additional research will focus on characterization of spatial and temporal variability in the continental shelf waters (2-50 miles offshore) from the mouths of estuaries, and comparisons will be made with ocean conditions immediately offshore from rocky headlands and stretches of sandy beaches. Repeated surveys of the ocean transects will be completed whenever possible to describe changes in nearshore water column conditions over short (seasonal) time scales and longer time scales (El Niño - Southern Oscillation, Pacific Decadal Oscillation). Simultaneous characterization of estuarine waters within Coos Bay/South Slough will provide direct measures of the extent of the nearshore ocean influence on tidal waters managed by the state of Oregon.

Determination of Bacterial Sources in Estuarine Tidal Waters
South Slough NERR will seek support and partnerships to further investigate sources and dynamics of bacteria in the tidal waters of the South Slough estuary. Additional research will use microbial source tracking techniques to identify the specific sources of bacteria from the vicinity of the Charleston development area (i.e., recreational/industrial marina, residential developments, shoreline seafood processing plants, and sewage treatment plant outfalls). Expansion of the estuarine monitoring and assessment program will include most probable number estimates for Enterococcus in tidal waters. This project will also provide the Reserve with the opportunity to incorporate water quality data in the development of a hydrodynamic model. The model will use movement of bacteria and other parameters to determine water circulation patterns throughout the South Slough.