Fourth Annual Report: 2007 Pre-Construction Eelgrass Monitoring and Propagation for King County Outfall Mitigation

King County proposes to build a new sewer outfall discharging to Puget Sound near Point Wells, Washington. Construction is scheduled for 2008. The Point Wells site was selected to minimize effects on the nearshore marine environment, but unavoidable impacts to eelgrass (Zostera marina) beds are anticipated during construction. To mitigate these impacts and prepare for post-construction restoration, King County began implementing a multiyear eelgrass monitoring and restoration program in 2004, with the primary goal of returning intertidal and shallow subtidal habitat and eelgrass to pre-construction conditions. Major program elements related to eelgrass are (a) pre-construction monitoring, i.e., documenting initial eelgrass conditions and degree of fluctuation over 5 years prior to construction, (b) eelgrass transplanting, including harvesting, offsite propagating, and stockpiling of local plants for post-construction planting, and (c) post-construction planting and subsequent monitoring. The program is detailed in the Eelgrass Restoration and Biological Resources Implementation Workplan (King County 2006). This report describes calendar year 2007 pre-construction activities conducted by Pacific Northwest National Laboratory (PNNL) for King County. Activities included continued propagation of eelgrass shoots at the PNNL Marine Sciences Laboratory (MSL) in Sequim, Washington, and monitoring of the experimental harvest plots in the marine outfall corridor area to evaluate recovery rates relative to harvest rates. In addition, 490 eelgrass shoots were also harvested from the Marine Outfall Corridor in July 2007 to supplement the plants in the propagation tank at the MSL, bringing the total number of shoots to 1464. Eelgrass densities were monitored in four of five experimental harvest plots established in the Marine Outfall Corridor. Changes in eelgrass density were evaluated in year-to-year comparisons with initial harvest rates. A net increase in eelgrass density from 2004 post-harvest to 2007 was observed in all plots, despite density decreases observed in 2006 in all plots and at most harvest rates. Eelgrass densities within individual subplots were highly variable from year to year, and the change in density in any interannual period was not related to initial 2004 harvest rate. Harvest rates of neighboring subplots did not appear to affect subplot eelgrass density (Woodruff et al. 2007). Three years post-harvest, eelgrass shoot densities were not significantly different from pre-harvest shoot densities at any harvest level. Additional plans are being discussed with King County to harvest all eelgrass from the construction corridor and hold in the propagation tanks at the MSL for post-construction planting. Under this plan, plants that would have been lost to construction will be held offsite until construction is completed. This strategy reduces and possibly eliminates the need to harvest eelgrass from donor beds located south of the construction area, allowing them to remain undisturbed. However, if eelgrass is harvested from donor beds, the monitoring of eelgrass growth at different harvest rates should help determine an optimum harvest rate that supports rapid recovery of donor eelgrass beds

Eelgrass donor sites: potentially overlooked impacts of restoration in Puget Sound

Eelgrass (Zostera marina) is an important habitat in the Salish Sea and restoration efforts are being undertaken around the region to increase eelgrass abundance and resilience. Eelgrass restoration is typically performed by transplanting whole shoots or dispersing viable seeds collected from reproductive shoots to a site. Most of the restoration efforts in the Pacific Northwest utilize whole shoots harvested from donor meadows and transplanted into restoration areas, but little work has been done to look at the impacts of the harvest on the donor stock. In response to the lack of existing data for Puget Sound, Washington Department of Natural Resources and Pacific Northwest National Laboratory’s Marine Sciences Laboratory conducted a controlled harvest experiment in two regions of the Salish Sea at sites associated with ongoing restoration activities. These meadows were harvested under different pressure (i.e., different percentage of plants taken from 0 to 50%) using traditional harvesting techniques. The meadows were then monitored for two years for changes in density. The results indicated that the eelgrass meadows were surprisingly resilient to all levels of harvest under ideal conditions and in small harvest areas. Interpretation and implications of these results will be discussed, as well as potential considerations for choosing potential donor sites for future restoration efforts

Third Annual Report: 2006 Pre-Construction Eelgrass Monitoring and Propagation for King County Outfall Mitigation

King County proposes to build a new sewer outfall discharging to Puget Sound near Point Wells, Washington. Construction is scheduled for 2008. The Point Wells site was selected to minimize effects on the nearshore marine environment, but unavoidable impacts to eelgrass (Zostera marina) beds are anticipated during construction. To mitigate for these impacts and prepare for post-construction restoration, King County began implementation of a multi-year eelgrass monitoring and restoration program in 2004, with the primary goal of returning intertidal and shallow subtidal habitat and eelgrass to pre-construction conditions. Major program elements are a) pre-construction monitoring, i.e., documenting initial eelgrass conditions and degree of fluctuation over 5 years prior to construction, b) eelgrass transplanting, including harvesting, offsite propagating and stockpiling of local plantstock, and post-construction planting, and c) post-construction monitoring. The program is detailed in the Eelgrass Restoration and Biological Resources Implementation Workplan (King County 2006). This report describes calendar year 2006 pre-construction activities conducted by Pacific Northwest National Laboratory (PNNL) in support of King County. Activities included continued propagation of eelgrass shoots and monitoring of the experimental harvest plots in the marine outfall corridor area to evaluate recovery rates relative to harvest rates. Approximately 1500 additional shoots were harvested from the marine outfall corridor in August 2006 to supplement the plants in the propagation tank at the PNNL Marine Sciences Laboratory in Sequim, Washington, bringing the total number of shoots to 4732. Eelgrass densities were monitored in the five experimental harvest plots established in the marine outfall corridor. Changes in eelgrass density were evaluated in year-to-year comparisons with initial harvest rates. Net eelgrass density decreased from 2004 post-harvest to 2006 in all plots, despite density increases observed in 2005 in some plots and at some harvest rates. Eelgrass densities within individual subplots were highly variable from year to year, and the change in density in any interannual period did not correlate to the initial 2004 harvest rate. Continued monitoring should help project managers determine an optimum harvest rate that supports rapid recovery of donor eelgrass beds

Automated Thermal Image Processing for Detection and Classification of Birds and Bats - FY2012 Annual Report

Surveying wildlife at risk from offshore wind energy development is difficult and expensive. Infrared video can be used to record birds and bats that pass through the camera view, but it is also time consuming and expensive to review video and determine what was recorded. We proposed to conduct algorithm and software development to identify and to differentiate thermally detected targets of interest that would allow automated processing of thermal image data to enumerate birds, bats, and insects. During FY2012 we developed computer code within MATLAB to identify objects recorded in video and extract attribute information that describes the objects recorded. We tested the efficiency of track identification using observer-based counts of tracks within segments of sample video. We examined object attributes, modeled the effects of random variability on attributes, and produced data smoothing techniques to limit random variation within attribute data. We also began drafting and testing methodology to identify objects recorded on video. We also recorded approximately 10 hours of infrared video of various marine birds, passerine birds, and bats near the Pacific Northwest National Laboratory (PNNL) Marine Sciences Laboratory (MSL) at Sequim, Washington. A total of 6 hours of bird video was captured overlooking Sequim Bay over a series of weeks. An additional 2 hours of video of birds was also captured during two weeks overlooking Dungeness Bay within the Strait of Juan de Fuca. Bats and passerine birds (swallows) were also recorded at dusk on the MSL campus during nine evenings. An observer noted the identity of objects viewed through the camera concurrently with recording. These video files will provide the information necessary to produce and test software developed during FY2013. The annotation will also form the basis for creation of a method to reliably identify recorded objects

Assessing harmful algal bloom risk in Puget Sound: a coupled modeling-data analysis approach

The increased frequency, duration and geographic extent of toxic Alexandrium blooms in Puget Sound presents new challenges of how to best allocate resources available for toxin monitoring of shellfish in order to protect human health. Monitoring plans are typically based on shellfish toxicity patterns from the recent past; however, the increasing trend in Alexandrium blooms means that managers are chasing a moving target. With projected future changes in global and regional climate, the risk of toxic Alexandrium blooms is expected to increase. Through funding from NOAA’s Coastal and Ocean Climate Applications Program, we are developing a harmful algal bloom (HAB) risk index that will provide another source of information to the Washington State Department of Health (WDOH) and local health jurisdictions for allocating paralytic shellfish poisoning (PSP) monitoring resources in the Sound. The HAB risk index is being developed from existing modeling capabilities and six years of year-round PSP toxin data in mussels collected by the WDOH. Climate/meteorological data produced by the University of Washington Climate Impacts Group, was used to drive the Puget Sound hydrologic and coastal hydrodynamic models developed by Pacific Northwest National Laboratory. Temperature and salinity output from the modeling framework provided input to an Alexandrium growth rate model developed by the Puget Sound Alexandrium Harmful Algal Bloom (PS-AHAB) program. Output from these models was calculated for spatially-explicit WDOH biotoxin closure zones. Statistical correlations between model outputs were examined for trends related to initiation of biotoxin zone closures and changes in shellfish PSP toxin levels. These relationships are being used to develop a risk index that can inform decisions about resource allocation for PSP monitoring in the future at the county, regional, and state level. Changes in risk factors based on a future climate scenario are also being examined. Results of the modeled data and development of the risk index will be presented at the conference

Methods for Assessing the Impact of Fog Oil Smoke on Availability, Palatability, & Food Quality of Relevant Life Stages of Insects for Threatened and Endangered Species

A methodology for quantifying population dynamics and food source value of insect fauna in areas subjected to fog oil smoke was developed. Our approach employed an environmentally controlled re-circulating wind tunnel outfitted with a high-heat vaporization and re-condensation fog oil generator that has been shown to produce aerosols of comparable chemistry and droplet-size distribution as those of field releases of the smoke. This method provides reproducible exposures of insects under realistic climatic and environmental conditions to fog oil aerosols that duplicate chemical and droplet-size characteristics of field releases of the smoke. The responses measured take into account reduction in food sources due to death and to changes in availability of relevant life stages of insects that form the prey base for the listed Threatened and Endangered Species. The influence of key environmental factors, wind speed and canopy structure on these responses were characterized. Data generated using this method was used to develop response functions related to particle size, concentration, wind speed, and canopy structure that will allow military personnel to assess and manage impacts to endangered species from fog oil smoke used in military training

Effects of Total Dissolved Gas on Chum Salmon Fry Incubating in the Lower Columbia River

This report describes research conducted by Pacific Northwest National Laboratory in FY 2007 for the U.S. Army Corps of Engineers, Portland District, to characterize the effects of total dissolved gas (TDG) on the incubating fry of chum salmon (Onchorhynchus keta) in the lower Columbia River. The tasks conducted and results obtained in pursuit of three objectives are summarized: * to conduct a field monitoring program at the Ives Island and Multnomah Falls study sites, collecting empirical data on TDG to obtain a more thorough understanding of TDG levels during different river stage scenarios (i.e., high-water year versus low-water year) * to conduct laboratory toxicity tests on hatchery chum salmon fry at gas levels likely to occur downstream from Bonneville Dam * to sample chum salmon sac fry during Bonneville Dam spill operations to determine if there is a physiological response to TDG levels. Chapter 1 discusses the field monitoring, Chapter 2 reports the findings of the laboratory toxicity tests, and Chapter 3 describes the field-sampling task. Each chapter contains an objective-specific introduction, description of the study site and methods, results of research, and discussion of findings. Literature cited throughout this report is listed in Chapter 4. Additional details on the study methdology and results are provided in Appendixes A through D

Total Dissolved Gas Effects on Incubating Chum Salmon Below Bonneville Dam

At the request of the U.S. Army Corps of Engineers (USACE; Portland District), Pacific Northwest National Laboratory (PNNL) undertook a project in 2006 to look further into issues of total dissolved gas (TDG) supersaturation in the lower Columbia River downstream of Bonneville Dam. In FY 2008, the third year of the project, PNNL conducted field monitoring and laboratory toxicity testing to both verify results from 2007 and answer some additional questions about how salmonid sac fry respond to elevated TDG in the field and the laboratory. For FY 2008, three objectives were 1) to repeat the 2006-2007 field effort to collect empirical data on TDG from the Ives Island and Multnomah Falls study sites; 2) to repeat the static laboratory toxicity tests on hatchery chum salmon fry to verify 2007 results and to expose wild chum salmon fry to incremental increases in TDG, above those of the static test, until external symptoms of gas bubble disease were clearly present; and 3) to assess physiological responses to TDG levels in wild chum salmon sac fry incubating below Bonneville Dam during spill operations. This report summarizes the tasks conducted and results obtained in pursuit of the three objectives. Chapter 1 discusses the field monitoring, Chapter 2 reports the findings of the laboratory toxicity tests, and Chapter 3 describes the field-sampling task. Each chapter contains an objective-specific introduction, description of the study site and methods, results of research, and discussion of findings. Literature cited throughout this report is listed in Chapter 4. Additional details on the monitoring methodology and results are provided in Appendices A and B included on the compact disc bound inside the back cover of the printed version of this report

Ecosystem Diagnosis and Treatment Planning Model as Applied to Supplementation : Model Description, User Guide, and Theoretical Documentation for the Model Introduced in the Summary Report Series on Supplementation in the Columbia Basin.

This document describes the formulation and operation of a model designed to assist in planning supplementation projects. It also has application in examining a broader array of questions related to natural fish production and stock restoration. The model is referred to as the Ecosystem Diagnosis and Treatment (EDT) Model because of its utility in helping to diagnose and identify possible treatments to be applied to natural production problems for salmonids. It was developed through the Regional Assessment of Supplementation Project (RASP), which was an initiative to help coordinate supplementation planning in the Columbia Basin. The model is operated within the spreadsheet environment of Quattro Pro using a system of customized menus. No experience with spreadsheet macros is required to operate it. As currently configured, the model should only be applied to spring chinook; modifications are required to apply it to fall chinook and other species. The purpose of the model is to enable managers to consider possible outcomes of supplementation under different sets of assumptions about the natural production system and the integration of supplementation fish into that system. It was designed to help assess uncertainty and the relative risks and benefits of alternative supplementation strategies. The model is a tool to facilitate both planning and learning; it is not a predictive model. This document consists of three principal parts. Part I provides a description of the model. Part II is a guide to running the model. Part III provides theoretical documentation. In addition, a sensitivity analysis of many of the model's parameters is provided in the appendix. This analysis was used to test whether the model produces consistent and reasonable results and to assess the relative effects of specific parameter inputs on outcome