Ocean 443 Abstracts - 2000 thru 2005
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Biological Oceanography

Abrams, Jessica. 2001. Comparison of bacterial abundance and growth dynamics in the Puget Sound Main Basin and Hood Canal

Bacteria are classified both as remineralizers, through the degradation of organic matter, and as a food source for higher marine organisms such as microflagellates. These functions put bacteria in a critical role in estuarine ecosystems, with changes in bacterial health likely being manifested in the population of organisms it helps to support. The evaluation of bacterial growth and abundance is the topic of many investigations; however, little effort has focused on the estuarine environment of Puget Sound. Described here are the results of an experiment designed to quantify the growth and abundance of bacteria in this area. Incubations with 3H thymidine and 3H leucine (radiolabeled precursors to DNA and protein, respectively) allowed for the quantification of bacterial growth. The use DAPI and CTC stains provided information about bacterial abundance, and further, an assessment of whether bacterial cells were active or inactive. Bacterial abundances were within a normal range for estuarine systems (~108 cells L-1). The bacterial growth rates were also found to be within normal limits for Hood Canal (0.13 d–1) and the Main Basin (0.16 d-1). Comparisons of bacterial abundances and growth rates with in-situ conditions revealed that bacteria in Hood Canal are replicating, while bacteria in the Main Basin are getting fatter.

Bailey, Jennifer. 2004. Absence of fecal coliform contamination in Pacific oysters (Crassostrea gigas) and surrounding waters in northwestern Hood Canal and south Puget Sound, Washington

Sanitation and agriculture problems in areas that drain into shellfish growing waters may contaminate shellfish with a number of pathogens. Concentrations of fecal coliform bacteria in marine waters are used as an indicator of sanitation problems and are routinely sampled by the Washington State Department of Health, as well as by tribes and local health departments. This research sought to assess the variability of fecal coliform contamination in oysters and surface waters in areas of high urbanization compared to low populated areas. Fecal coliform bacteria concentrations in Pacific oysters and the nearby surface water from northwestern Hood Canal (Quilcene Bay) and south Puget Sound (north of Mud Bay), Washington were measured using three-tube most-probably number techniques. Three samples of oysters and the surrounding waters were collected from each site where fecal coliform contamination due to leaking septic tanks or agriculture waste draining from storm water drainage systems, was thought to be present. Both the water and the oyster samples were measured for fecal coliform bacteria to compare the accumulation in oysters to the ‘snapshot' levels obtained in water samples. No fecal coliform contamination was found in the water or oyster samples in either location of this study. Since these results were unexpected due the relative urbanization of south Puget Sound, the lack of fecal coliform from these sites could be due to revisions and improvements of storm water drainage systems, improvements in agriculture practices or routine maintenance of septic tanks.

Bernhardt, Megan. 2003. The effects of sediment grain size on benthic protozoans in the Snohomish River and Possession Sound, Washington

To better understand the coupling between sediment grain size and the distribution of benthic protozoans, sediment samples were collected from the Snohomish River and Possession Sound, Washington. Sediment grain size, bacterial abundance and porewater salinity were measured to study the relationship between these factors and protozoan abundances. Sediments in Possession Sound had higher proportions of silt and clay while sand was the dominant component in the Snohomish River. Protozoan abundances were highest in Possession Sound ranging between 2.34 x 104 – 5.12 x 105 cells cm-3. Bacterial abundances were also highest in Possession Sound ranging between 5.57 x 108 – 1.22 x 109 cells cm-3. Porewater salinity was highest in Possession Sound measuring ~ 32 ‰ whereas in the river porewater salinity ranged from 0 ‰ - 6 ‰. The factors influencing the abundances of benthic protozoans vary in marine and riverine environments and are likely to be extremely complex. Porewater salinity was considered an unlikely factor to affect the abundances in either Possession Sound or the Snohomish River. Oxygen concentrations, microhabitats and currents are possible contributors to changes in abundances with depth in the sediments. Higher protozoan abundances in Possession Sound may be the result of higher bacterial abundances or increased organic matter with finer sediments.

Boruch-McDonough, Teegan. 2004. Presence of proteorhodopsins similar to known green-light absorbing proteorhodosin in the Main Basin of Puget Sound, Washington

Bacteria are ubiquitous in the marine environment and are essential in recycling nutrients for phytoplankton usage. Recently a protein called proteorhodopsin was found in some bacteria; this protein enables the bacteria to absorb light energy and convert it into kinetic energy in the form of ion movement. It has also been found that wavelengths absorbed by bacteria with this protein correspond to the wavelengths available in the surrounding environment. The objective of this study is to find out if proteorhodopsin is present in the nutrient rich, estuarine system of Puget Sound and if proteorhodopsin sequences vary with light availability here. Water samples were collected from the main basin on 31 March 2004 at the chlorophyll maximum, mid-euphotic zone and just below the euphotic zone (10 m, 28 m, and 70 m respectively). These samples were analyzed for proteorhodopsin presence using polymerase chain reactions, cloning and sequencing techniques. Analysis of sequence data provided convincing evidence that proteorhodopsin is present in Puget Sound. There appear to be two primary groups of sequences resulted that are both related to green light absorbing proteorhodopsin. Sequence diversity does not appear to be correlated with depth. The presence of proteorhodopsin indicates that bacteria in Puget Sound are able to use light energy and may therefore need carbon-derived energy to survive. Sequence similarity from all depth samples indicates that there is not a significant difference in the wavelengths of light available between the surface and base of the euphotic zone in Puget Sound, WA.

Brown, Rusty. 2005. Effects temporal variation on the spectral signature of eelgrass (Zoestra marina L.) in Hood Canal, Washington

Remote sensing is a fast growing field of technology and its applications to research and science are becoming more and more important. The ability to study change on a daily time scale of an area as large as 100km without having to traverse said area in the field is priceless. This technology can readily be applied to the study of eelgrass (Zoestra marina) in the near-shore environment. The spectral signature of eelgrass is hypothesized to change with regards to time of day, amount of daylight, and turbidity of surrounding water. Studying eelgrass at the Guillemot Cove Nature Preserve in Seabeck, WA we were able to acquire 2 days of sampling totaling 24 individual samples. These samples spanned a time period of both low tide exposed eelgrass and a period of time as the eelgrass was submerged by the approaching tide. When analyzed our data shows that a single spectral band may fluctuate up to two fold in a fifteen minute period. We also find that while all visible spectra appear to behave the same (i.e. same plotted curve over time) the smaller fluctuations do not follow same patterns. Most fluctuations found are attributed to turbidity in the water column and reflectance of surrounding sediment.

Buell, Christina. 2001. Comparison of bacterial activity and 14C phenanthrene degradation rates in surface sediments around Puget Sound

In April 2001, sediment samples were taken from five locations around the Puget Sound Main Basin and Hood Canal. Sediment slurries were enriched with radioactive tracers in an effort to attain a quantitative sense of the bacterial productivity in Puget Sound in near-shore sediments and assess the ability of bacteria to utilize and degrade polycyclic aromatic hydrocarbons (PAHs). Site locations include near the current effluent of King County wastewater treatment facilities, the proposed site for the new wastewater treatment plant effluent at Point Wells, the sill in Hood Canal, where an ammonium plume has been measured, and two sites near Dabob Bay. Bacterial activity was measured in the surficial sediments by 3H-TdR incorporation, as an estimate of bacterial production. Hydrocarbon degradation rates were analyzed by injecting 14C phenanthrene substrate into sediments and measuring uptake rates as respired 14CO2 released. Bacteria that have never been exposed to petroleum byproducts were expected to show a lag time in their incorporation of the injected substrate compared to those that had at some time previously fed on hydrocarbon.

Caldwell, Jennifer. 2000. Determination of the quality and movement of proteins and amino acids in eelgrass beds

Little is known about eelgrass beds and the role they play in coastal carbon and nitrogen fluxes. By studying the amino acid concentrations in the sediment (inside and outside the bed), eelgrass, epiphytes and particulate matter in the water column, I determined that eelgrass beds are acting as a net sink for carbon and nitrogen. Water samples were taken from a boat using a Niskin bottle; samples of eelgrass, epiphytes, and sediment were collected from Padilla Bay by walking from shore at low tide. Samples were analyzed by high-pressure liquid chromatography and an amino acid degradation index. Understanding how eelgrass beds utilize labile organic carbon is essential to understanding their ecology and their role in the coastal ecosystem, and is fundamental to properly protect and maintain eelgrass beds in the future.

Cary, Scott. 2003. Calanus pacificus collocation with their food source during a phytoplankton bloom in Dabob Bay

Calanus pacificus females in Dabob Bay, a temperate fjord in the state of Washington, migrate out of the surface layer during daytime to avoid visual predators. During nighttime copepods must balance the risk of predation with the physiological need for energy obtained from food. The diel migratory behavior of C. pacificus females in Dabob Bay has been extensively studied; interannual, intergenerational, and seasonal variation has been observed. A significant relationship between diel vertical migration and the abundance of planktonic predators has been shown, but there was no clear evidence to show the effect of food availability on vertical migration. The abundance and vertical distribution of C. pacificus females was determined over a 14-hour-long period on 9 and 10 April 2003 in Dabob Bay. Samples were collected with a vertically hauled Puget Sound net deployed 9 times throughout the night and two times during the day. Results show a migration up into the surface waters, 10m to 0m, at 0252 and a migration out of the surface after 0500. This is evidence that vertical migration is effected by food availability.

Conrad, Stephanie. 2005. Polycyclic aromatic hydrocarbon bioaccumulation in Mytilus edulis in Seattle, Washington

Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants derived from the incomplete combustion of organic material, such as petroleum. Solubility of PAHs decreases with increasing molecular weight, making sediment a natural reservoir. PAHs bioaccumulate in organisms such as mussels, causing cancer, narcosis, and genetic mutations. Mussels are often used in pollutant analysis due to their abundant and sessile nature; as filter feeders, they indiscriminately feed on dissolved and particulate matter in the water column. Different species of mussels show the same trend in PAH accumulation, making worldwide PAH comparisons possible. Turbulence increases the bioavailability of PAHs to mussels. Three sites in Seattle were analyzed: West Seattle, Magnolia, and Ballard. No mussels in this study were found in turbid waters, possibly because phytoplankton (mussels' main food source) grow more efficiently in calmer waters where they can stay in the euphotic zone. Each site was evaluated for turbidity, PAH concentrations in mussel tissue and sediment, mussel shell length, and percent water in both mussel and sediment samples. The turbidity of the sites had a small range, and was green in color suggesting phytoplankton particulate matter, not sediment particles due to turbulent water. The method used to analyze PAHs had a 0% efficiency, indicating a loss of PAHs in the extraction process.

Cordray, Benjamin. 2005. Biological effect on the corrosion rates of three alloys in a marine environment

The effects of corrosion may endanger the health and safety of the general public. The annual economic cost of corrosion prevention and repair in the United States is significant. The causes and prevention of corrosion have long been studied, but the effect of bacteria and biofilms on the corrosion of metals in a marine environment has only recently gained attention from the scientific community. This experiment was conducted to quantify the corrosion rates of stainless steel 316L, aluminum 5052 and high-strength steel HY-80. Samples of the three alloys were placed in the surface waters of Puget Sound (a fjord like estuary in western Washington), Lake Washington (a freshwater lake in Seattle, Washington) and sterile seawater. After 1, 2, 4, or 6 weeks of exposure, the samples were collected, cleaned and weighed. The change in mass of the samples was used to calculate corrosion rates for the respective alloys. There was very little to no corrosion of the stainless steel samples. The aluminum samples in Puget Sound and Lake Washington were slightly corroded, while the samples in the sterile seawater formed a protective oxide layer and did not corrode. There was significant corrosion of the high-strength steel samples in all environments. These observations indicate that the presence of bacteria or biofilms may have an effect on the corrosion of aluminum, but does not have an effect on stainless steel or high-strength steel in a marine environment.

Crowley, Jennifer. 2000. The flux of particulate organic matter across an eelgrass system located in Padilla Bay

The carbon to nitrogen ratio of organic matter was determined for all major components of an eelgrass system in Padilla Bay, Washington, during spring 2000. The particles suspended directly in the eelgrass had a higher average C:N ratio than the POM surrounding the bed, 8.95 and 8.26 respectively. Likewise, the sediments in the bed had higher average C:N ratios than the sediments outside the bed (9.73 and 8.889). Due to the high level of eelgrass production during this time it was assumed that the particulate organic matter in the eelgrass bed was comprised of new production (phytoplankton) and resuspended sediment. From this assumption a mixing model was constructed to determine the origin of the water taken from within the bed. From the model results, suspended particles from within the bed were determined to be composed of 11% phytoplankton and 89% sediment-derived particulate organic matter. Using the mixing model results and a comparison of all C:N ratios, the path of organic carbon and nitrogen through an eelgrass system were determined.

Delwiche, Leon. 2003. The effects of chlorophyll and total suspended solids on water-leaving radiance in the Snohomish River region of freshwater influence

When remote sensing algorithms developed for the open ocean (Case I) are applied to coastal estuarine waters (Case II) problems of overestimating chlorophyll concentrations are encountered. Case II water optical properties are complicated by the presence of substances that don't covary with phytoplankton abundances. However, a strong need exists to optically characterize these waters in order to develop regional remote sensing algorithms for chlorophyll estimates. This study examines the effects of chlorophyll and total suspended solids (TSS) on light attenuation and water leaving radiance in a coastal region of freshwater influence. Chlorophyll and TSS were measured to a depth of 10 m at five stations west of the Snohomish River mouth in Puget Sound, Washington. Water leaving radiance and light attenuation were measured at the 443 nm and 550 nm wavelengths. A sum difference of TSS and chlorophyll was utilized in the analysis of water leaving radiance measured at each station. The sum difference was highest at station 1 closest to the river and decreased along the transect. However, no relationship could be established between the sum difference and the observed water leaving radiance. The station 1 outlier (closest to the river) can be described as sharing characteristics common to Case II waters whereas the other stations show more Case I properties. Development of regional algorithms for environments characterized by mixing between Case I and Case II waters may require defining the boundaries that exist due to this duality. The results of this study contribute to the use of remote sensing as a tool to monitoring phytoplankton communities within regionally-important waters such as Puget Sound.

Dignon, Andrea. 2001. The relationship between low dissolved oxygen and euphausiid abundance and distribution in Puget Sound

This paper examines the relationship between low dissolved oxygen (DO) and euphausiid abundance and distribution in Puget Sound, Washington. Euphausiids were collected at night by triplicate downward hauls using a plummet closing net. Two species of euphausiids, Euphausia pacifica and Thysanoessa raschii, are found in Puget Sound. Gut pigment analysis was performed on these two species of euphausiids in order to determine if they were consuming the same amount of phytoplankton. Although there was individual variability, both euphausiid species were found to graze upon similar quantities of phytoplankton. Oxygen levels, as measured by oxygen titrations, were found to affect the abundance and distribution of euphausiid species in Puget Sound. E. pacifica was the dominant species found in Port Susan and southern Hood Canal, which both have levels of oxygen below the biological stress level of 5.0 mg L-1. T. raschii was the dominant species found in the Main Basin and northern Hood Canal, where the oxygen levels remained above the biological stress level. Temperature, vertical mixing, and the ammonium plume in northern Hood Canal did not directly influence the abundance and distribution of the euphausiid, but they may possibly have indirect affects. Euphausiids are a major prey item of commercially important fish and larger benthic invertebrates. The alteration of euphausiid abundance and distribution due to low oxygen could cause an effect on the important predators of euphausiids.

Dugaw, Erin. 2001. Chlorophyll concentrations and taxonomic compositions in the ‘snake:' Implications for the food web in Puget Sound

The ‘snake' is a high-transport stream fed by south Sound rivers that flows northward in the Main Basin originating from Colvos Passage. The objective of the current study was to determine whether there was more chlorophyll inside vs. outside the snake, if taxonomic compositions changed from north to south, and the implications of the latter to the food web in Puget Sound. Four east-west thermoslinograph transects across the Main Basin of Puget Sound were conducted, beginning in Colvos Passage and ending near Admiralty Inlet. Each transect had three CTD stations from which water was collected. The chlorophyll concentrations, following Lorenzen (1966) and taxonomic compositions, using the inverted microscope method (Hasle 1978), were determined for each station. It was found that the chlorophyll and taxonomic compositions differed slightly inside vs. outside the ‘snake', but the greatest difference was seen from north to south. Diatoms were by far the dominant taxa. A recent study has shown that diatom diets could possibly have an impact on copepods (Lee et al. 1999) by having a detrimental effect on their egg production and hatching success. If the zooplankton of Puget Sound are living off of diatom dominated diets, then diatoms could have a cascading effect on the higher trophic levels of the food chain.

Durkin, Colleen. 2004. Predator avoidance as a possible driver of heterotrophic dinoflagellate diel vertical migration

Heterotrophic dinoflagellates are significant grazers of spring phytoplankton blooms and provide vital nutrients to higher trophic levels. They commonly undergo reverse diel vertical migration, although the benefits of this energetically costly behavior are not fully understood. This study investigates predator avoidance as a possible motivation for heterotrophic dinoflagellate diel vertical migration. The study was conducted in Dabob Bay, Puget Sound 22-24 March, 2004 during a spring bloom of Phaeocystis. Diel water sampling and microscopic counts of the dinoflagellate Gyrodinium showed that no migration was occurring at this time. Gyrodinium were consistently concentrated at the surface (860-1445 organisms L-1). Shipboard dilution and copepod predation (Calanus pacificus) experiments did not detect grazing by either microzooplankton or C. pacificus. The lack of predation pressure on Gyrodinium may explain why they were not migrating, although other characteristics of the phytoplankton bloom may also have influence. Phaeocystis is nutrient poor and perhaps could not provide enough energy to support migration. These results, combined with a 2003 study in Dabob Bay, suggest that phytoplankton composition may also be a factor in driving diel vertical migration.

Evans, Colleen. 2004. Carbon limitation of heterotrophic bacteria in Dabob Bay, WA

To evaluate carbon limitation of heterotrophic bacteria in Puget Sound, WA, bacterial productivity, dissolved organic carbon (DOC) concentrations, and bacterial community structure (using T-RFLP and sequencing of the 16S rRNA gene) were measured from surface seawater samples collected at the Dabob Bay Buoy. Seawater cultures were either amended with 8.3 µmol L-1 glucose or left unamended and incubated on deck in the dark for 30 h. Bacterial productivity was measured in triplicate 3H-Thymidine assays every 6 h for 30 h from both glucose-amended and unamended samples using the microcentrifuge technique. Rates of incorporation ranged from 9.56 - 65.99 pmol TdR L-1 h-1 for unamended samples and 9.56 - 117.11 pmol TdR L-1 h-1 for those amended with glucose. The ambient DOC concentration was 110.4 µmol L-1 C. After the addition of glucose, DOC concentration increased to 177.4 µmol L-1 C and fluctuated over the course of the 30 h incubation period, indicating that it was being both utilized and possibly produced by heterotrophic bacteria. Cloning of the 16S rRNA indicated that bacteria of the a-Proteobacteria and Cytophaga Flexibacter Bacteriodes groups were present. T-RFLP was used to further assess the bacterial community, verifying the presence these two groups of marine bacteria as well as showing the dynamic nature of the heterotrophic bacterial community. Approximately 31 total OTUs were obtained in samples digested with BsuRI while 37 OTUs were obtained following digestion with Hin6I. The distribution of these OTUs varied over the course of the 30 h incubation. It is apparent from these data, with productivity in amended samples as much as twice that in unamended samples, that heterotrophic bacteria in Dabob Bay, while having a dynamic community structure, are carbon limited in the surface waters. Carbon limitation yields decreased bacterial activity thus hindering the crucial role of bacteria in aquatic environments as remineralizers.

Frechette, David. 2000. Development of a molecular technique to assess particle-attached and free-living bacterial communities in marine environments

A qualitative molecular technique was developed for rapid analysis of microbial diversity in marine environments. A protocol for terminal restriction fragment length polymorphism (T-RFLP) was developed to detect the minimum number of bacterial species present in samples obtained from Puget Sound, WA. The technique used a polymerase chain reaction (PCR) in which one of the two primers was fluorescently labeled at the 5' end and was used to amplify bacterial 16S rDNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently-labeled terminal restriction fragment was detected by laser-scanning with a fluorimager. The T-RFLP technique was tested on samples from two sites in Puget Sound. For both sites, particle-attached and free-living bacterial communities were compared at the surface and the chlorophyll maximum. Different bacterial communities were found at the different sampling sites. Additionally, there were differences in species richness between the particle-attached and free-living communities.

Galindo, Heather. 2000. Development of a method to study the specificity of associations between a pelagic diatom, Ditylum brightwelli, and its epibiotic bacterial assemblages in Hood Canal

Sampling and molecular techniques were developed to characterize the epibiotic bacterial assemblages attached to single cell isolates of the centric diatom Ditylum brightwelli. The first part of the study involves culture maintenance, filtration, and DNA extraction in a 96-well format for the rapid processing of large numbers of samples. The second part develops molecular techniques involving the use of Terminal Restriction Fragment Length Polymorphisms to determine the minimum level of genotypic diversity of the epibiotic assemblages using the 16s ribosomal gene. Preliminary results indicate that individual diatoms isolated from a single water sample exhibit both genetically similar and distinct bacteria in their epibiotic assemblages.

Goodman, Christian. 2002. Flow cytometric evidence of phytoplankton photoacclimation in the mixed waters of Puget Sound

This study tested the open ocean hypothesis that phytoplankton isolated at different light intensities will photoacclimate, make short-term changes in their cellular biology, to maximally use ambient light. In Puget Sound, different types of mixing regimes were considered potential phytoplankton isolators. If the time scale for phytoplankton response to different ambient light levels (photoacclimation) is shorter than that for vertical mixing, phytoplankton cellular chlorophyll a content will increase in low light. In March 2002, this hypothesis was tested at four Puget Sound stations characterized by different mixing intensities: Hood Canal, Possession Sound, Dalco Passage, and the Tacoma Narrows. Qualitative mixing intensity was determined from water column density profiles. Collected water samples were analyzed for cell specific chlorophyll a content and cell size using flow cytometry to measure chlorophyll fluorescence. Cell specific fluorescence results revealed two different populations with one type present at all stations and the other type only found in Hood Canal. Cell specific chlorophyll content increased for both populations from the surface to 5 m but differed at 10 m. Size changes were more variable, but at 60% of the different sites, cell size data were similar to data for chlorophyll changes. Further evaluation and understanding of individual phytoplankton response to ambient light changes may lead to a better understanding and estimation of water column productivity, and the depth preferences of some phytoplankton species.

Goyt, Rebecca. 2005. Marine sediment toxicity bioassay testing using amphipods (Ampelisca abdita) to assess the EPA designated Superfund site: Commencement Bay, Washington

Commencement Bay, located in Puget Sound, Washington was designated by the EPA as Superfund site in 1981, due to the presence of toxins such as heavy metals, PCBs, and PAHs. Restoration efforts were completed in 2004 and consisted of controls over sources to prevent further contamination of groundwater and marine sediments, creation of mitigation areas to promote natural recovery, and sediment dredging, backfilling and capping. Marine sediments serve as a reservoir for these toxins, and marine sediment bioassay testing has been validated as a way to determine their effects upon live organisms using amphipods. Sediments were collected from 3 sampling sites in Commencement Bay, and bioassay testing chambers were set up using the amphipod A. abdita. The hypothesis was that bioassay test results would be positive (dead amphipods) for sediments within Commencement Bay, despite restoration efforts under the Superfund designation. Comparisons of the percentage of amphipod mortalities between the 3 Commencement Bay sampling sites indicated that the site closest to the point sources at the nearshore area (T1) was the least toxic, followed by the site closest to the Asarco area at the mouth of the bay (T3), and the site in the middle of the bay (T2) was the most toxic. Further statistical analysis performed using ANOVA indicated that the differences between the negative controls to the testing groups, as well as amongst the 3 testing groups, were not statistically significant. The results of this research project confirmed the hypothesis, bioassay testing results indicated the sediments were toxic, but were inconclusive in assessing the comparative levels of toxicity within the Commencement Bay Superfund site.

Graff, Jason. 2003. The temporal and spatial response of microzooplankton to a spring bloom in Dabob Bay

Microzooplankton abundance and biomass was measured in Dabob Bay, Puget Sound, Washington from 12 February to 1 May 2003. During this time period, maximum chlorophyll concentrations ranged from 1.05 to 38.35 mg Chl a m-3 and remained above 14 mg Chl a m-3 for 6 of the ten weeks. Microzooplankton biomass positively co-varied with chlorophyll concentrations. Vertical migration by ciliates and a large Gyrodinium was determined to occur within the upper 50 meters. Ciliates migrated to the surface at night and large Gyrodiniums migrated to depths of 25-50 meters. Vertical net tow samples from 9-10 April 2003 indicated diel vertical migration by Calanus pacificus in Dabob Bay with maximum concentrations in the upper 25 meters during the night. This nightly upward migration is a potential forcing factor for the apparent microzooplankton migrations. A simple carbon budget for feeding copepods is constructed from which an estimated 1.5 to 30% of carbon available to mesozoooplankton comes from three categories of microzoopolankton.

Grocock, Jaime. 2002. Distribution of picophytoplankton chlorophyll and cyanobacterial rDNA in Puget Sound, WA

Size-fractionated chlorophyll experiments examine picophytoplankton (cell size <3 µm) concentrations and distinguish what percent they compose of the total photosynthetic biomass. Amplification of 16S-23S cyanobacterial ribosomal DNA positively identify cyanobacteria in Puget Sound. There were seven stations, with two stations in the Main Basin, one in Admiralty Inlet, three in Hood Canal, and one outside Puget Sound in the Strait of Juan de Fuca. From the size-fractionated chlorophyll experiments total and picophytoplankton chlorophyll were high at the surface (2-30 mg L-1) and low at depth (0.3-2.5 mg L-1). In the Main Basin, and the Strait of Juan de Fuca the percent picophytoplankton was consistently greater at depth than at the surface. In Admiralty Inlet, a well-mixed water column, the percent picophytoplankton was constant with depth. Hood Canal shows a very high percentage of picophytoplankton chlorophyll with values ranging from 9-43% at the surface and was 30-59% at depth. Possible factors affecting the relative contribution of picophytoplankton to the phytoplankton biomass and picocyanobacteria communities are salinity, nutrients, temperature, and percent light transmittance; these properties change from coastal to estuarine environments, and vary with increasing depth.

Hageman, Garrett. 2001. The distribution and abundance of picophytoplankton and Phaeocystis in Puget Sound during spring

The picophytoplankton (0.2 to 2.0 mm) assemblage, consisting of both prokaryotes and eukaryotes, was sampled from Puget Sound, WA, during 2-6 April 2001, in order to make estimates of the importance of this size class to the total phytoplankton community and total primary production. Picophytoplankton can be an important food source, apart from heterotrophic bacteria, for microzooplankton. However, picophytoplankton abundance in coastal and estuarine waters is thought to be low, although this assumption has not been rigorously tested for Puget Sound waters. Sampling stations in Puget Sound included Possession Sound, Main Basin, Carr Inlet, Admiralty Inlet, northern Hood Canal, southern Hood Canal, and Dabob Bay. Seawater samples were analyzed by chlorophyll size fractionation to determine the percent of the total phytoplankton community comprised of pico-sized phytoplankton, whereas epifluorescence microscopy was used to estimate picophytoplankton abundance and the relative proportions of the major types of picophytoplankton. At Admiralty Inlet, the phytoplankton biomass was low, and the picophytoplankton comprised a relatively large percentage of total phytoplankton. Generally, the percentage of phytoplankton that was picophytoplankton decreased as the phytoplankton biomass increased. The cyanobacterium Synechococcus was present throughout Puget Sound, with the highest concentration of ~3000 ± 300 cells mL-1 observed in Admiralty Inlet. Synechococcus was generally less than 1000 cells mL-1, and it is probably not an important food source in Puget Sound. Phaeocystis was found at concentrations up to ~50000 cells mL-1 in Hood Canal. Due to the presence of Phaeocystis in high concentrations, picophytoplankton should not be assumed insignificant in Puget Sound.

Heller, Marlene. 2000. Distribution and sources of Vibrio parahaemolyticus in the water column of Hood Canal, Washington in March and April 2000

This paper presents new data on abundances of Vibrio parahaemolyticus in the water column of Hood Canal, Washington during March and April 2000. V. parahaemolyticus is a pathogenic bacterium found in estuaries that causes the disease gastroenteritis, and in some cases primary septicimia, as a result of the consumption of contaminated seafood. Salinity, temperature, chlorophyll, oxygen and V. parahaemolyticus abundances were determined for both free-living and particle-attached bacteria at the surface, the chlorophyll max and 1-5 m from the bottom at sites in the main channel, the Skokomish river outflow, and along the shoreline and in the mid-channel around the Great Bend. V. parahaemolyticus abundances were usually greatest in particle-attached size fractions as compared to free-living. A geographic trend was also seen where V. parahaemolyticus was more likely to grow within the canal. V. parahaemolyticus abundances were also seen to be greatest at intermediate levels within the water column and where concentrations of chlorphyll and temperatures were highest. These observations suggest that V. parahaemolyticus is introduced into Hood Canal primarily from bottom currents where they are transported in a cyst phase and that V. parahaemolyticus may proliferate in association with zooplankton and other chitinous material. From a public health and fisheries management perspective, these results suggest that V. parahaemolyticus abundances may increase with increasing eutrophication; an effect that is compounded by the addition of nutrients that pollution adds to the water column of Hood Canal.

Hoover, Joe. 2003. Do methane-producing zooplankton microflora explain elevated CH4 levels in marine environments?

Despite the highly oxygenated state of the surface ocean, supersaturation of methane a reduced volatile gas, can reach levels of up to 700% above background levels. Some sources for this methane have been described such as hydrocarbon seeps and anoxic slope sediments but these cannot explain the entire supersaturation. A biological process performed by methanogenic microbial communities, potentially inhabiting anaerobic environments within the guts of marine animals is thought to contribute to this flux. Two species of zooplankton, Euphausia pacifica and Cyphocaris challengeri, were investigated from Dabob Bay in Puget Sound, Washington. Samples were prepared for analysis of methane production in laboratory experiments and for examination of gut microflora. The production of small quantities of methane was observed in laboratory experiments (<0.1 ppm individual-1 day-1). One percent of the microbial population was identified as methanogens through microscopy. Bacterial 16S genes could be PCR amplified while methanogen mcrA and archaeal 16S genes could not. These data point towards low abundances of methanogenic microorganisms under the conditions sampled. However, the presence of methanogenic populations suggests that zooplankton gut microflora could explain the supersaturation of methane in the surface ocean and play important roles in the carbon cycle of pelagic marine environments.

Hope, Erin. 2004. Diversity of benthic diatom communities along a salinity gradient in Big Beef Creek, Puget Sound

Benthic diatoms are important primary producers in shallow aquatic environments. Serving as a food source for heterotrophic protozoans and invertebrate grazers and important players in carbon cycling, benthic diatoms are integral to the health of the eutrophic benthic region. Several variables including sediment type and salinity, can affect the distribution and diversity of benthic diatom communities. Species diversity of benthic diatoms has been investigated in varying environments including saline lakes where a negative correlation between salinity and community diversity was observed. In this study the effects of salinity on diversity were examined in Big Beef Creek, and estuary in Hood Canal, Puget Sound, Washington. Two sets of sediment samples were taken from six locations within the estuary: one for pore water salinity analysis, and the other for microscopic genera identification and counts. Pore water salinity increased with distance from station 1. Cell counts were highest at stations 1 and 2 (7.6-7.9x106 +/- 2.5x106 cells cm-3) and lowest at station 3 (1.7x106 +/- 4.4x105 cells cm-3). Diversity was also highest at station 1 and decreased with distance. Each station had a different community composition, but each had one to four genera that comprised more than 80% of the community. Most common genera included Navicula and Stauroneis. A direct correlation between community diversity and salinity was not observed, but additional salinity measurements at other points in the tidal cycle could have an effect on correlation. Additional sampling at other points in the estuary could provide a more complete survey of community diversity.

Hudson, Jeremy. 2005. Dissimilatory nitrate reduction to ammonium as a potential mechanism for seasonal ammonium production at the northern Hood Canal sill sediment-water interface

Dissolved oxygen within the Hood Canal basin has been thought to have progressively declined during the past several years. As recent as 1998, an ammonium plume has been measured annually at the northern Hood Canal sill. Increasing hypoxic conditions within the Hood Canal basin could favor nitrate-reducing bacteria at the sediment-water interface, including those bacteria that can reduce nitrate to ammonium, a process termed dissimilatory nitrate reduction to ammonium (DNRA). Here I demonstrate that DNRA can occur at the northern Hood Canal sill. On 23 March 2005 samples were collected at the northern Hood Canal sill aboard the R/V Thomas G. Thompson. In order to isolate the ammonium produced via DNRA, intact sediment cores were incubated with nitrogen-15 sodium nitrate (Na15NO3) and analyzed for nitrogen-15 ammonium (15NH4+). Results indicate that DNRA can occur at the northern Hood Canal sill: overlying water and pore water from 1, 2, 3, and 4 day intact core incubations measured an order of magnitude greater than natural abundance for 15NH4+ enrichment. Although DNRA occurred, it did not account for the majority of the ammonium produced. Future studies should concentrate on estimating the rate of DNRA, particularly during the summer when the ammonium concentration at the northern Hood Canal sill typically peaks. If the DNRA rate is significant enough to contribute to the ammonium plume at the northern Hood Canal sill, it could have drastic implications for primary production and could lead to increased hypoxia for the Hood Canal region through feedback mechanisms.

Johnson. Benjamin. 2005. Spatiotemporal distribution of the Puget Sound Virioplankton

Viruses are the most abundant biological particle in the oceans, ranging between 10 to >108 virus-like particles ml-1. Marine viruses have direct connections to host population dynamics, community genetics, and ultimately biogeochemical cycling. Virus and bacteria concentrations were observed between 16-18 February and 30 March 2005 at three locations in Puget Sound. Virus concentrations ranged from 1.63 to 3.96x107 viruses ml-1, with a mean of 2.60x107 viruses ml-1 (1.31x106 standard error). Virus concentrations measured over approximately 9 hours in Lynch Cove varied by 1.77-fold, but the variance was not statistically significant. Bacteria concentrations ranged from 5.32x105 to 2.26x106 bacteria ml-1, with a mean of 9.26x105 bacteria ml-1 (standard error 1.24x105). Bacteria concentrations measured over approximately 9 hours in Lynch Cove varied by 1.56-fold, but the variance was not statistically significant. Strong correlation (r=0.92) was observed between bacterial abundance and chlorophyll concentrations, while strong negative correlation (r=-0.92) was observed between viral abundance and the ≥0.2μm<2μm size-fraction of chlorophyll-containing organisms. Virus to bacterium ratios were calculated for each sampling site and period, ranging from 17 to 35, with a mean ratio of 30.2 (standard error 0.626). The virioplankton is poorly understood, and has never been explored in an ecological setting in the Puget Sound. These data are the first exploration of the Puget Sound virioplankton distribution and dynamics, and will form the basis for future marine virus studies.

Jorgenson, Ann Willow. 2004. Vertical migration and the ecological role of hydromedusae Aglantha digitale in the plankton community of Dabob Bay, Puget Sound, Washington

Hydromedusae, Aglantha digitale is commonly abundant in the temperate fjord, Dabob Bay (Washington). The ecological role of A. digitale is not well understood. Little is known about A. digitale's vertical migration patterns, the predators of A. digital, or the predatory impacts by A. digitale on its primary prey copepods. It was found that A. digitale in Dabob Bay exhibits a reverse diel migration pattern. Abundance and distribution was calculated from vertically stratified samples spanning 165 m, the depth of the basin. The peak abundance of A. digitale was 5.3 individuals m-3 and occurred in the top 25 m during the day. The distribution shifted during the night when peak abundance occurred between 25-50 m. Potential predatory impact of A. digitale on copepod populations was evaluated by comparing the relative distribution and migration patterns. It is not likely that predation by A. digitale has a large impact on copepod abundance. This research elucidated the possible selective advantage of migration by A. digitale. The migration pattern of A. digitale did not optimize contact with their primary prey and suggested predator avoidance as a major selective advantage of reverse migration. Species distribution indicates Euphausia pacifica is likely the dominate predator of A. digitale but additional research is necessary to confirm this hypothesis.

Larson, Noel. 2000. Spectral absorption of colored dissolved organic matter (CDOM) in the waters of Puget Sound, Washington

Spectral values of light absorption by colored dissolved organic matter (CDOM) in seawater (CDOM; also known as gelbstoff, gilvin, or yellow substance) play an important part in understanding radiation absorption in surface waters. Seawater samples containing CDOM were collected along a transect in Puget Sound which followed a salinity gradient beginning near the mouth of the Skagit River through the Whidbey Basin, Admiralty Inlet, and into the Strait of Juan de Fuca. Samples were gathered from three depths (0 m, 10 m, near bottom) at twelve stations. Light absorption by each sample was measured throughout the UV- visible range (350 nm- 750 nm) using a spectrophotometer. The range of absorption at 400 nm was 0.702 m-1 to 0.231 m-1. The highest absorption by CDOM was found in surface waters near the Snohomish River. The lowest value was in surface waters in the Strait of Juan de Fuca. Absorption coefficients at 400 nm were compared to salinity and DOC. A positive relationship between CDOM absorption coefficients at 400 nm and salinity was observed in samples at all depths. There was a good relationship between CDOM absorption coefficients at 400 nm and DOC in surface samples. These findings may have important applications in the field of optical oceanography to correct for biases in radiation measurements in surface waters and chl a estimates based on remote sensing methods. There may prove to be an alternative method for measuring DOC concentrations in surface waters.

Leiker, Shauna. 2002. Can nitrogen loading affect trophic structure in estuarine food webs? Using nitrogen stable isotopes to determine trophic length in nutrient enriched waters

In this project, food webs in areas of Puget Sound characterized by nitrogen loading (Nisqually Reach, Poverty Bay) were studied and compared to similar areas not affected by nitrogen loading (Murden Cove, Hood Canal). Trophic structure was determined using stable isotope analysis of nitrogen and carbon in tissues of collected zooplankton, using the ratio of the heavier isotope to the lighter isotope (given in d notation). There is a 2-4‰ enrichment per trophic level due to fractionation, which allows for determining the trophic position of organisms. Nutrient and POC/PON samples were taken as well, to determine relative concentrations of nitrate, nitrite, ammonium, and POM. The surface concentration of nitrate was highest in Hood Canal, and lowest in Murden Cove. Poverty Bay had the highest concentration of nitrite, whereas Hood Canal had the lowest concentration. Ammonium was highest at Nisqually Reach, and lowest in Hood Canal. POC and PON concentrations were similar at all stations. There was more taxonomic diversity in Hood Canal and Murden Cove, and d15N were higher in organisms at these stations as well. Carbon values did not show a correlating increase in d13C, proving that carbon is a better tracer of a consumer's food source than of trophic position. Given the results of this study, food webs in Nisqually Reach and Poverty Bay may have fewer trophic levels than Murden Cove and Hood Canal.

Marks, Ryan. 2004. Eutrophication susceptibility of phytoplankton in Port Gardner, Washington

Port Gardner, located in Puget Sound, is an area which is monitored by the Washington State Department of Ecology (DOE) for water quality concerns, and specifically for low dissolved oxygen (DO). Levels below 5 mg L-1 have been measured, giving rise to eutrophication concerns in the area. One warning sign of eutrophication is consistently low dissolved inorganic nitrogen in coastal waters, a condition that is especially likely in stratified waters. The DOE sampled a transect in Port Gardner in September of 1995, from marine waters near the outskirts of the port to fresher stations near the mouth of the Snohomish River. Phytoplankton located at the more marine stations showed greater nutrient limitation than those in the fresher stations, most likely due to the fact that there was more nitrogen in the fresher water than in the marine stations. A similar transect of five stations was covered on 29 March, 2004, to examine whether proximity to the river influences the effect of nutrient incubations on phytoplankton growth. At each station, a CTD cast was made for physical characteristics of the water column, and water samples were taken from the surface. Sub-samples were taken from these for nutrient analysis, chlorophyll analysis, and a 24 hour incubation, part of which was a nutrient enrichment study. Primary production was measured before and after the incubation using the light-dark bottle oxygen method. Physical conditions, including depth and turbulence, were likely controls on phytoplankton growth in March, rather than nutrient concentrations, as nutrients were abundant at all stations ( > 13 µM NO3). Chlorophyll values were slightly higher in marine stations, ranging from 0.71 mg m-3 to 1.01 mg m-3, with the highest values seen at the middle station. Phaeopigment values increased toward the river mouth, likely due to shallow water and turbulent mixing destroying phytoplankton cells. This physical influence on phytoplankton survival is a large control on growth in March, before stratification and resulting nutrient limitation occur. Nutrient enrichment showed no effect on production, though large variation among small production values prevented significant conclusions.

Maurer, Jennifer. 2005. Spatial Variability: Determining length scales and small-scale variability of biogeochemical properties in Hood Canal, Washington

Traditional shipboard sampling regimes often fail to comprehensively capture biogeochemical patterns, because temporal coverage is often at most seasonal, with limited spatial resolution. Recent technological developments, including moored profilers and remote sensing, have added to the ability to study small-scale processes. Despite these advances, there remains a great need to understand spatial and temporal variability – and the scales upon which they should be studied – in biogeochemical processes. The Oceanic Remote Chemical/Optical Analyzer (ORCA) buoy is an autonomous moored profiler monitoring water quality parameters in Hood Canal, Washington; despite sampling every two hours, large shifts in properties such as chlorophyll have been recorded by the ORCA buoy. This study examines the small-scale variability of chlorophyll and oxygen surrounding the ORCA buoy. Sampling was conducted on a pattern of several interlocking grids – the inner, smallest grid had 50m spacing, with the outermost grid comprised of 400 m spacing. Chlorophyll levels surrounding the ORCA buoy ranged from m 1.72-8.38 μg/L, while oxygen values ranged from 8.12-9.81 mg O2/L. Semivariograms were used to determine the appropriate length scales for oxygen and chlorophyll sampling in Hood Canal. Both oxygen and chlorophyll displayed high directional variability, with variation lowest in a cross-channel direction. The level of chlorophyll variation indicated length scales of 280 m for chlorophyll sampling, while ³500 m sampling appears necessary for oxygen. The high variability in chlorophyll coincided with a jump in the chlorophyll data recorded by the ORCA buoy, indicating that spatial variability is the likely cause of the jumps in data recorded.

McKay, Melissa. 2004. A comparison of egg production and hatching success for Metridia pacifica during variable phytoplankton bloom conditions in Dabob Bay, Puget Sound, Washington

Metridia pacifica, a crustaceous zooplankter, exhibits low fecundity when compared to other dominant copepods, such as Calanus pacificus, in Puget Sound and in the temperate and subarctic Pacific. M. pacifica is an omnivorous copepod that exhibits strong diel vertical migration and tends to winter-over in the adult female stage instead of entering a diapause phase, unlike most calanoid copepods. Previous research in the subarctic and temperate Pacific has shown that egg production is low for M. pacifica during the early spring phytoplankton bloom and increases in post-bloom conditions. Zooplankton samples were collected in early March and again in April for the purpose of quantifying egg production and hatching success. Taking samples beginning 4 March 2004, when diatoms were expected to dominate the phytoplankton community, and weekly or biweekly through 21 April 2004, when other planktonic populations had emerged, allowed for the comparison of egg production and hatching success temporally and the opportunity to look for diet variability which may contribute to low fecundity in M. pacifica. This experiment tested the hypothesis that if diatoms dominate an early spring phytoplankton bloom in Dabob Bay, Puget Sound, then M. pacifica, which feed on diatoms during such a bloom, will exhibit lower egg production and hatching success compared to later in the spring when the food supply is more diverse. The experimental results indicate that egg production was higher in April (2.1 vs. 19.6 eggs female-1 day-1), when the food supply was more diverse, and average hatching success was relatively low (between 35% and 60%) over the experimental period.

Nichols, Crystal. 2000. Comparison of importance of different size classes of phytoplankton in Puget Sound, Washington

Size fractionated 14C primary productivity and biomass of picoplankton (0.2 to 2 mm), nanoplankton (2 to 20 mm), and microplankton (>20 mm) were measured in Hood Canal, Admiralty Inlet, and Main Basin, Puget Sound, Washington State in April 2000. Highest integrated productivity occurred at the transition between Hood Canal and the Main Basin with 12292.32 mg·C·m-2·d-1. Microplankton dominated the size-specific primary productivity and biomass at four of the six stations whereas nanoplankton dominated at the remaining two stations from Hood Canal. Nutrient concentrations were found to be fairly high at all stations except the two stations in southern Hood Canal where nanoplankton dominated.

Odum, Chris. 2003. Spatial distribution of phytoplankton within the Triple Junction of Puget Sound

The correlation of phytoplankton was examined within the triple junction of Puget Sound, Washington using geostatistics. Semivarience of forty one stations shows a boundary in which data-collecting stations can be considered correlated. The distance is smaller than that of a single ocean satellite pixel.

Pratt, Andrea. 2004. Pre- and post-industrial deposition of black carbon in Puget Sound sediments

Black carbon (BC) is derived from anthropogenic activity such as fossil fuel combustion, and biomass burning and also from natural processes such as river runoff over exposed graphite. Sources are linked to climate history and changes in land-use and industrialization. Historic BC deposition from the atmosphere and river run off can be measured in marine or lake sediments and represent a significant sink in the global carbon cycle. A 3.38-m-long piston core was collected from the Main Basin of Puget Sound (47° 45.33, 122° 24.84). Accumulation rates were determined using the 210Pb chronology method. Sediments were then analyzed for BC concentrations using thermal oxidation, acidification and elemental analysis techniques. BC deposition was constant until the mid 1850's and has increased since the Industrial Revolution. A steady decrease is observed since the 1970's. The % wt of BC in sediments ranged from 0.13%-0.95% with a subsurface maximum in 1895 and a smaller peak in 1969. A similar trend was found in Lake Washington where the subsurface maximum occurred around 1900 and the smaller peak in the mid 1960's, yet both peaks were smaller in magnitude. BC trends are correlated to population and energy source patterns in the Puget Sound region. No data on this topic existed for Puget Sound prior to this study. Isotope fractionation analysis could later be preformed in an attempt to quantify source strength of natural and anthropogenic sources.

Putnam, Shelley. 2001. Can the natural isotope 15N be used as a trophic level tracer in the Puget Sound food chain?

Stable isotope 15N increases with each trophic level. Phytoplankton preferentially assimilate 14N, causing the remaining dissolved organic nitrogen (DIN) pool to be increasing higher in 15N (Wada 1987). Animals preferentially excrete 15N-depleted nitrogen, causing a magnification of 15N in the food chain. A fairly constant enrichment of 1 to 2 ppm has been observed at each step of the food web (Libes 1992). Thus the 15N of an organism can be used to infer its trophic level. In this study, 15N values of phytoplankton, Copepods, Aetideus sp., Amphipods, Euphausiids, and Euchaeta sp. were sampled from several different basins of Puget Sound in order to develop a partial food web in the Puget Sound. Samples were collected in both winter and spring to see if there were any consistent differences in the entire food web. Winter 15N values showed food web increases of approximately 0.75 ppm from Aetideus sp. through Euchaeta sp. Spring 15N values put each step of the food web at about 1.4 ppm from phytoplankton through Amphipods. The importance of this is that it shows a strong possibility of a different diet for the sample species between the two seasons.

Rodriguez, David. 2003. The presence of Synechococcus in different aquatic environments around Puget Sound, Washington

Cyanobacteria ascribed to the genus Synechococcus are widely distributed in various aquatic environments around the world, yet they are poorly represented in Puget Sound, an important marine ecosystem in Washington State. Water samples were taken from river, estuarine, and lake environments around Puget Sound in order to determine if Synechococcus were present in these different aquatic systems. Samples from the Snohomish River, Possession Sound, Northern Main Basin and Lake Washington were analyzed utilizing flow cytometry, epifluorescence microscopy and PCR. Through these methods, Synechococcus was positively identified in all of the samples. Flow cytometry complimented by epifluorescence microscopy revealed that concentrations of Synechococcus cells were extremely low in the river and estuarine stations, ranging from 3-5 cells ml-1. As a result there was no amplification of 16S-23S cyanobacterial ribosomal DNA in these samples because of insufficient amounts of DNA template. Cell concentrations in Lake Washington were determined to be 1x103 cells ml-1 and were close to anticipated values. This higher concentration of cells enabled some amplification of Synechococcus 16S-23S rDNA genes as seen in the PCR analysis. This study was conducted during an El Nino year and it is likely that increased mixing in the surface layer due to an El Nino event is responsible for the very low cell concentrations.

Sackmann, Brandon. 2000. Variability in egg production of natural populations of Calanus pacificus from Puget Sound, Washington

Mesozooplankton secondary production in aquatic food webs is critical in the energy transfer of primary producers to higher trophic levels. Detailed knowledge of copepod reproductive behavior, especially egg production, is required to understand marine heterotrophic food webs. The specific goal of this study was to determine the degree to which egg production of Calanus pacificus correlates with egg size, female prosome length, egg hatching success, and available food concentrations. Samples were collected by vertical net tow from the R/V Thomas G. Thompson on 3-7 April 2000, at six stations along a transect extending from the Main Basin of Puget Sound into lower Hood Canal, Washington. Calanus pacificus females (10-40 individuals per station) were sorted under a dissecting microscope to conduct short-term incubation experiments. After 24-28 hrs the incubations were terminated and released eggs were counted and a random subsample of eggs was sized using an inverted microscope at 250X. The remaining eggs were allowed to hatch for an additional 48 hrs in order to estimate hatching success. Female prosome length was measured using a dissecting microscope and available food concentrations were estimated from fluorescence profiles developed at each station. Egg production was correlated with egg size and female size, but not with hatching success or available food concentrations. This study may elucidate ways in which these parameters can be used to predict and quantify secondary production in many marine systems.

Satterberg, Jessica. 2001. Distribution and production of transparent exopolymer particles (TEP) in Puget Sound, WA

Transparent exopolymer particles (TEP) are composed of dissolved carbohydrates exuded from phytoplankton. TEP particles are believed to be coupled with aggregation of phytoplankton blooms and formation of marine snow, and can provide a potential means for transporting organic matter to the sediments. The objectives of this study were to determine the relationships between phytoplankton productivity and TEP production in the Main Basin and Hood Canal of Puget Sound. Chlorophyll and TEP samples were taken at three depths, including the chlorophyll maximum, and four-day-long incubations were constructed using seawater from the chlorophyll maximum at one Hood Canal and one Main Basin station. TEP concentrations were determined spectrophotometrically using an alcian blue stain. Phytoplankton productivity was measured using 14C incubations to quantify TEP production with respect to phytoplankton productivity. A positive correlation between TEP concentration and productivity was observed in Main Basin incubations where the dominant plankton were diatoms. However, in Hood Canal incubations no TEP, productivity correlation was observed. TEP concentrations measured in the Main Basin were significantly lower then expected ranging from 21.8 µg xanthan equiv. L-1 to 76.4 µg xanthan equiv. L-1. Single cells of Phaeocystis were dominant in Hood Canal and are known to produce larger amounts of carbohydrates. Higher TEP concentrations were therefore measured in Hood Canal incubations, up to 1579 µg xanthan equiv. L-1. Relating TEP production and abundance to productivity, chlorophyll a, and phytoplankton abundances will increase our understanding of the timing and mechanisms involved in TEP interactions, aggregation, and sedimentation.

Sawyer, Richard. 2000. Nutritional quality of phytoplankton as a food source for zooplankton in Puget sound, WA, determined by chemical composition

Various properties of phytoplankton that determine their quality as a food source for zooplankton have been determined through years of research. This study focused on one set of phytoplankton properties (chemical composition) and several food quality indicators (prosome length, egg diameter, and egg production rates) in Hood Canal and the Main Basin. Phytoplankton samples and zooplankton (Calanus pacificus) were collected along a six station transect of these two basins in Puget Sound, WA aboard the R/V Thomas G. Thompson during 3-7 April 2000. Phytoplankton food quality was analyzed for total protein content, carbon/nitrogen ratios, chlorophyll a concentrations, and phaeopigment concentrations using conventional methods. The first goal of this study was to quantify potential spatial variability in chemical composition between the two basins. Second, a correlation between chemical composition and food quality indicators was determined. Variability was evident in all chemical analyses conducted, particularly Hood Canal, which contained steady gradients with most parameters. Chemical composition also correlated well with Calanus pacificus prosome length and egg diameter, and to a lesser extent with egg production suggesting that these parameters were accurate measurements for determining zooplankton size and fecundity.

Scansen, Brian. 2000. Discriminating the relative impact of point vs non-point sources of fecal coliform contamination in Hood Canal, Washington

Fecal coliform abundance was measured in the main channel of Hood Canal, along the shore, and at the mouth of the Skokomish River, to characterize the extent of fecal contamination in the Hood Canal system. Samples were collected from R/V Thomas G. Thompson and R/V Wee Lander and analyzed via membrane filtration and culture techniques to discriminate the relative impact of a point source of fecal contamination - the Skokomish River - versus a non-point source - land runoff, agriculture, etc. - in the Hood Canal estuary. High coliform abundances were found at the mouth of the Skokomish; the abundances decreased with distance from the river. These high abundances, coupled with a correlation between coliform abundance and salinity, implicate the Skokomish River as a point source of coliform bacteria into the system. Higher and more variable coliform abundances along the shore of Hood Canal as compared to the mid-canal imply non-point sources of fecal coliform entry into the system as well.

Soterhou, Patricia. 2004. Influences on the abundance of sediment bacteria in an estuarine system, Big Beef Creek, Washington

Marine sediments are inhabited by bacteria from the exposed tidal flat into the deep sea. To better understand what influences the abundance of bacteria at Big Beef Creek Estuary, associated factors that can affect bacterial abundance were examined: porewater salinity, organic carbon, nitrogen, oxygen and sediment type. Sediment samples were collected, stained and counted by epifluorescence microscopy to determine bacterial abundance. The range of salinity had no effect on the abundance from 1.33 to 26.67 ‰. There were two types of sediment present, sand and mud. Bacterial abundances throughout the creek were not significantly different, ranging from 4.86 x 109 to 1.04 x 1010 bacteria per ml with one standard deviation. The difference in the sediment types did not affect the abundance of bacteria. Organic carbon and nitrogen levels corresponded to the vegetation and animals inhabiting the area. No correlation was found between organic carbon, nitrogen and bacterial abundance. The factors influencing the abundances of sediment bacteria may be complex. The current levels may reflect the pressure of grazing by other organisms.

Straza, Tiffany. 2005. Bacterial richness along an oxygen gradient in Hood Canal, Washington, determined using terminal restriction fragment length polymorphism

Bacterial populations are an integral component of the marine environment, playing several roles in the ecosystem. Because different species of bacteria play different roles, measuring the species richness of bacteria in a given environment is an important start toward understanding the complexity of the system. In this study, the bacterial diversity in Hood Canal was measured using terminal restriction fragment length polymorphism (tRFLP) analysis. Hood Canal's oxygen trends – low oxygen particularly in the deeper and southern waters – made possible an analysis of bacterial richness with comparison to a critical environmental factor, oxygen. Samples were taken throughout the water column at four stations, including the northern and southern endpoints of the Canal. At the time of this study, oxygen values ranged from 8.84 mg O2 L-1 in the surface water of the northern station to 2.75 mg O2 L-1 in the deepest sample of the southern station. Bacterial richness ranged from 40 to 1 bacterial types. The bacterial richness at the site with lowest oxygen was 25; the richness at the site with highest oxygen was 7. No significant trends were observed between richness and the environmental variables tested. The similarity of types was greatest between surface and mid-column samples at the same sites, and least between sites at the opposite extremes of oxygen concentrations.

Sutton, Lesa. 2000. Relationship of oxygen concentration to euphausiid abundance, species composition, and vertical distribution in Hood Canal, Washington

Dissolved oxygen (DO) concentrations below the biological stress level of 5.0 mg/L persist at depths greater than 15 m in southern Hood Canal. Because this low DO appears to be increasing spatially and temporally, it is important to determine if the low DO has a significant effect on the biological community of Hood Canal. DO concentrations were measured and euphausiids collected throughout the water column at two stations, one in northern and one in southern Hood Canal. Two species of euphausiids, Euphausia pacifica and Thyanoessa raschii were collected. There were significantly more euphausiids collected at the southern than northern station. Euphausia pacifica was the dominant species at the southern station and nearly absent from the northern station. Thyanoessa raschii was found in low, but similar abundance at the northern and southern stations. However, evidence is weak for a relationship between euphausiid abundance, species composition, and distribution and DO concentrations in Hood Canal. Possible alternate explanations for the observed euphausiid community structure include an unexplained NH4 plume, temperatures below Euphausia pacifica spawning range, and vertical mixing at the northern station.

Vaughan, Meredith. 2003. Photorespiration and glycine decarboxylase expression in phytoplankton communities in Puget Sound, WA

Photorespiration is the process by which the photosynthetic enzyme, ribulose biphosphate carboxyalse/oxygenase (RUBISCO), rather than binding to carbon dioxide, binds to oxygen. This leads to loss of energy, and release of carbon dioxide and organic compounds into the environment. On a 5-6 March 2003 cruise on Puget Sound, Washington, water samples were collected from Main Basin and Dabob Bay, to assess the presence of photorespiration in phytoplankton communities. RNA was extracted from the samples and converted to cDNA for analysis. Degenerate primers were used to detect gene expression of glycine decarboxylase (GDC), an enzyme tied to the photorespiratory cycle. PCR of the surface samples from Main Basin and Dabob Bay, as well as the 20 m sample from Main Basin showed successful amplification of GDC with the primers. Four sequences were obtained from the Dabob Bay surface sample, confirming expression of GDC. While photorespiration could not be demonstrated conclusively, it is the likely source of GDC expression in these samples.

Wagar, Paul. 2002. Aldehyde effects on hatching success of Calanus pacificus

In the first two trophic levels of a marine food web, primary producing diatoms often constitute a major dietary portion of secondary producing copepods. The copepod Calanus pacificus reproduces by spawning fertilized eggs freely into the water column. A paradox has been observed that hatching success of C. pacificus eggs decreases when certain species of diatoms are a major portion of the copepod's diet. The presence of a hatching-inhibiting compound in diatoms has long been suggested and recently 3 aldehydes isolated from different diatoms have been proposed as possible hatching inhibitors. In this paper, C. pacificus eggs collected from two locations in southern Hood Canal, Puget Sound USA were exposed to the aldehyde 2-trans­-4-trans-decadienal in varying concentrations to test the hatching-inhibiting hypothesis of 2-trans­-4-trans-decadienal. C. pacificus were also collected from a third location in Hood Canal (Dabob Bay) and fed a diatom diet and a non-diatom control for 6 days. Eggs collected from these copepods were exposed to one concentration of aldehyde to test hatching inhibition. Neither of the hatching experiments resulted in significant differences in hatching success between aldehyde-treated eggs and controls. These findings contradict the hypothesis that 2-trans­-4-trans-decadienal reduces hatching success of Calanus pacificus eggs.

Welch, Matt. 2000. Spring abundance of zooplankton related to particulate organic material across the Hood Canal sill, Puget Sound, Washington

The density of four classes of zooplankton was calculated from vertical net tows done at three stations around the Hood Canal sill, Puget Sound, Washington. Suspended particulate matter, particulate organic matter, chlorophyll a, and CTD data were taken and used to determine the most important factor in zooplankton distribution. Comparisons were made between stations and day vs. night at each station. A significant link between zooplankton abundance and the availability of food could not be determined, and advection is thought to be the primary factor governing the distribution of zooplankton at this location.

Williams, Cheryl. 2004. Size distribution and genetic diversity of phytoplankton in Dabob Bay, Washington

The size spectra and diversity of phytoplankton have an enormous effect on carbon and nutrient cycling and food web dynamics. In order to characterize the phytoplankton community in Dabob Bay in Puget Sound, Washington, seawater was collected on 25 February, 4, 11, 25 March, 8 and April 2004, at the surface and between 7 and 15 m. The seawater was filtered through 20, 5, and 0.7 mm filters consecutively. Nutrient, chlorophyll, and TRFLP analyses were conducted. Nitrate was the primary nitrogen source ranging from 0.01 to 0.32 mmol L-1. The >20 mm size fraction dominated at the surface and at 7-15 m for all cruises except cruises 1 and 2, when the 0.7-5 mm size fraction comprised 60 and 50% of the total chlorophyll. TRFLP was performed with the gene psbA to quickly assess the diversity of phytoplankton. The number of terminal fragment peaks and their lengths were highly variable for cruises 1 through 4, however, on cruise 5 all three size classes shared three of four terminal fragments. The highest diversity was found in the 0.7-5 mm size class on cruise 1 and the lowest diversity was found in the >20 mm size class on cruise 2. Understanding the size distribution and genetic diversity of the phytoplankton in Dabob Bay will aid in the understanding of the estuarine food web as a whole.

Wood, Neil. 2000. A comparison of phytoplankton community compositions and species diversity in Puget Sound, Washington: Main Basin vs Hood Canal

Phytoplankton species diversity and dominant phytoplankton species were determined in two different regions (Hood Canal and Main Basin) of Puget Sound, Washington. Samples from three stations in each region were collected from two depths (surface and chlorophyll maximum) to determine local differences in the phytoplankton community in Puget Sound. Main Basin stations were dominated by the diatoms Skeletonema costatum, Thalassiosira nordenskioeldii, and Ditylum brightwellii. In general, Hood Canal stations were dominated by the dinoflagellate Scrippsiella trochoidea and the diatoms Pseudo-nitzschia spp and Chaetoceros spp. With two minor exceptions, no substantial differences in dominant phytoplankton were observed between the two sampled depths. Mixing of water bodies at the transition of the two regions appears to have created a composite of predominant Main Basin and Hood Canal species at the closest adjacent regional stations. The strong presence of S. trochoidea in the southern Hood Canal stations, in conjunction with lower chlorophyll-a to phaeopigment ratios, point to the end of a recent phytoplankton bloom in this area. Phytoplankton species diversity was higher in Hood Canal than in the Main Basin; this difference may be attributed to the presence of a greater number of microhabitats in Hood Canal (greater shore to volume ratio). While neither hydrographic conditions (temperature, salinity, dissolved oxygen) or nutrient concentrations appeared to be associated with species diversity, the presence of available nutrients may have been related to levels of species diversity at the Hood Canal stations.

Wood, Theresa. 2005. The effects of nutrient concentrations on jellyfish abundance in Puget Sound

Due to increasing anthropogenic input, eutrophication in some areas is becoming a problem. Eutrophication may change the composition of the higher trophic levels in marine systems from fish to jellyfish. By looking at food webs in different bodies of water, it can be shown that jellyfish populations are enhanced in eutrophic conditions. Non-eutrophic water would support a diatom/large zooplankton/fish food chain, while eutrophic water would support a flagellate/small zooplankton/jellyfish food chain. Nutrients, chlorophyll a, microzooplankton, zooplankton, and jellyfish were sampled at five different stations in Puget Sound. The nutrient values compared to the amount of chlorophyll a present showed that all of the stations were eutrophic. The data showed a mix of the two food chains not just one or the other present at each station. Two of the five stations support the hypothesis that jellyfish populations are enhanced in eutrophic conditions.

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Chemical Oceanography

Boyd, Jason. 2001. Coliphages as an indicator of fecal contamination in northern Puget Sound

This study was prompted by the concern over the increased discharge of treated sewage that will occur upon implementation of King County's proposed wastewater treatment plant in northern Puget Sound. The purpose of this study was to assess the use of coliphages as a fecal pollution indicator. Concentrations of coliphages and the traditional coliform indicator of fecal pollution were measured at five sites between March and May 2001. Of 40 water samples tested, coliforms were present in 39 and coliphages in all 40. The means of all samples, per 100 ml, were 174.2 ± 112.7 pfu (range: 13-464) for coliphages and 51.3 ± 75.6 cfu (range: 0-430) for fecal coliforms. Coliphage concentrations were higher than coliforms in all samples, suggesting that they are a more reliable fecal indicator. Non-point source discharges appeared to be more important in the distribution of fecal indicators in Puget Sound than point sources. Based on the results of this study and recent reports on the association of coliphages with enteric diseases, future studies on the determination of water quality should involve coliphage enumeration.

Bui, Tan. 2003. Examination of the main food source for the amphipod Cyphocaris challengeri in Puget Sound using stable isotopes

The main food source for the amphipod Cyphocaris challengeri in Puget Sound, Washington was defined by stable isotope analyses of amphipods, the copepod Calanus, and organic matter deposited in surface sea-floor sediments. Samples were collected November 25, 2002 and again April 8, 2003 aboard the R/V Clifford A. Barnes. Prior studies suggest a 3.2 (ppt) bioamplification in the d15N of marine animals versus their diet. The d15N data on fall samples excluded organic matter from sea-floor sediments as the main food source for Cyphocaris because the difference in their d15N was 7.59 (ppt). The d15N shift of 1.44 (ppt) between Cyphocaris and Calanus from fall samples did not indicate copepod as the sole food source either, but suggest Cyphocaris may also feed on organisms besides the copepods when copepod availability is reduced. The bioamplification in the d15N shift of Cyphocaris versus Calanus in the spring was 3.13 (ppt). The d15N shift of 3.13 (ppt) indicate that Calanus is indeed the main food source for Cyphocaris when copepods are more abundant in the spring. This is supported by the d13C shift between the two organisms of 0.88 (ppt), which agreed with the literature value of 0.75-1.0 (ppt). An overall decrease in d15N shift that was observed from fall to spring can be attributed to the greater availability of food in spring when continuous feeding of 14N enriched organisms would cause a decrease in d15N.

Chaney, Matthew. 2001. Concentrations of Ag, As, Cu, and Sn in Mytilus edulis from the Whidbey Basin, Puget Sound

The main goals of this study were: 1) to determine the levels of the metals of interest present in mussels collected from the Whidbey Basin, in northern Puget Sound, 2) to identify any possible point sources of metal pollution, and 3) to compare data from this study with time series data from the NOAA Mussel Watch program. Concentrations for Ag and Sn were at or below the quantification limits for all sites. The concentrations of As and Cu were fairly uniform throughout the basin. As averaged 17.0 ± 0.7 ppm and Cu concentrations averaged 12.7 ± 0.7 ppm with the exception of Everett Marina. The samples in Everett Marina had Cu concentrations of 48.28 ± 0.04 ppm. The data for this study are 2.3X higher in As and 1.5X higher in Cu than the data from the NOAA Mussel Watch Program at the same sites. Possible explanations for this difference are based primarily on differences in collection month, December for NOAA vice April in this study. These temporal differences could yield differences in food availability/intake, metal availability, or physiological differences (i.e. mating cycle). Recent studies also suggest that there is significant seasonal variability in the concentrations of Cu and other metals accumulated by some species of macroalgae (Teresa et al. 2001). It seems unlikely that the high metal concentrations observed in this study are the result of procedural or analytical error, because laboratory blanks yielded consistent numbers below quantification limits and analysis of NIST Standard Reference Material corresponded to the certified values for Cu and As.

Grissom, Karen. 2001. Comparative survival of fecal coliforms and enterococcus native to Puget Sound and the Snohomish river with variation in sunlight, temperature, and salinity

Enteric bacteria and viral contamination of recreational and drinking water poses an important health risk. Therefore, accurate prediction of the survival rate of fecal coliforms and enterococcus is crucial when assessing the threat to human health. Different bacteria are affected differently by such factors as UV radiation, temperature, and salinity. The inactivation rates of wild strains fecal coliforms (FC) and enterococcus (Ent) from Puget Sound and the Snohomish River were compared to determine susceptibility to environmental stresses. The traditional membrane filtration method was used for enumeration of the daily subsamples. Inactivation coefficients (kT) were measured from a log-linear % survival curve. The kT for FC was approximately 1.3 times that for Ent, and inactivation was generally slower at lower radiation and salinity. The time necessary for 90 % of the enterococcus to die off (T90) showed a significant increase with increasing salinity. The 13° C chamber T90 for Ent was 4.35 days at 0.00 psu and increased to 5.50 days at 24.30 psu, whereas FC T90 decreased from 3.94 days at 0.00 psu to less than one day at 24.30 psu. Most of the inactivation appeared to be a result of increasing salinity and UV radiation. The inactivation rates for both types of bacteria in the dark chamber showed a similar trend, with the inactivation coefficients similar to the lower radiation levels. The combined data gave a general inactivation ranking of FC> Ent and warm > cold. However there were significant differences in inactivation rates between experiments, indicating the contribution to inactivation of factors other than temperature, salinity, and UV radiation.

Kassakian, Steve. 2004. Nitrogen isotopic variations in nitrate in the Hood Canal, Puget Sound Washington: Confirmation of the kinetic isotope effect of sedimentary denitrification

The southern end of the Hood Canal exhibits low oxygen, ~60 µmoles L-1, in the deeper layers. The dissolved oxygen levels measured in early March 2004 were the lowest values ever reported for this time of year. As the remineralization of organic material in the Hood Canal occurs, there is clear evidence of denitrification. The amount of nitrate lost, assuming Redfield ratio for the organic material, is on the order of 28 µmoles L-1 in the southern end of the Hood Canal. The d15NO3- of the nitrate does not increase with the occurrence of denitrification, confirming that denitrification occurs in the sediments rather than the water column, as expected given the results of previous studies. The fact that d15NO3- shows no increase in the water column overlying areas of intense sedimentary denitrification confirms a small or non-existent kinetic isotope effect (e) for sedimentary denitrification.

Kollasch, Lisa. 2000. The transfer of Ag from sewage effluent to copepods, amphipods, arrow worms, and euphausiids in Hood Canal and at West Point, Puget Sound

Silver (Ag) concentrations were determined in samples of West Point sewage effluent as well as Puget Sound zooplankton species including amphipods, arrow worms, euphausiids and copepods. The zooplankton collection sites included Hood Canal and just off West Point. Higher Ag concentrations were found in the zooplankton from the West Point station, presumably due to the closer proximity to the wastewater treatment plant effluent. Ag concentrations were lower in copepods compared to the other species sampled (which prey on copepods). This suggests bioaccumulation.

Louis, Cindy. 2000. Particulate arsenic concentrations in Puget Sound and Lake Washington

Box core sampling occurred during spring 2000 to determine particulate arsenic, iron, and antimony concentrations from two stations in Puget Sound (Quartermaster Harbor and Fox Island) and one station in Lake Washington (Madison Park). Samples were partially digested and then analyzed using ICP-AES. The highest particulate arsenic concentrations occurred at the Lake Washington station, followed by Quartermaster Harbor and then Fox Island. The Lake Washington station was the station most enriched in arsenic from the smelter, has the slowest sedimentation rate of the three stations and no visible signs of bioturbation. Both Puget Sound cores had signs of bioturbation, which may have led to some of the inconsistency in the profiles there. The faster sedimentation rates and dilution effect due to bioturbation make it not surprising for the Puget Sound cores to have lower particulate arsenic concentrations.

Norbeck, Angela. 2000. Sediment fluxes as the main source of high ammonium concentrations in northern Hood Canal and the Main Basin of Puget Sound, Washington

Two seasonal ammonium plumes have been detected in the Puget Sound water column, one over the northern Hood Canal sill, and the other in the Main Basin, near Alki Point. Causes of these occurrences were previously unknown. To test the hypothesis that diffusive ammonium sediment fluxes are high enough to provide the necessary amount of ammonium in the water column, flux rates and nitrogen isotopes were measured. Benthic ammonium fluxes were determined using concentration gradients in the sediments and overlying water. A diffusive flux of ammonium, measuring 0.756 pmol·cm-2·s-1, leaving the sediment/water interface in April 2000 appears adequate to supply 23% to 92% of the necessary quantity of ammonium over the Hood Canal sill, the exact value depending on the rate of irrigation. The sediment ammonium flux in the Main Basin, 0.580 pmol·cm-2·s-1, is only sufficient to supply 9.5% of the observed ammonium concentration in the overlying water at that location, with a maximum of 38% when irrigation is included. Nitrogen isotopes, determined by mass spectrometry, in the pore water of the sediments at Hood Canal average 13.70 ‰, while the water column above has an average isotope value of 12.07 ‰, suggesting a benthic origin of the nitrogen in the ammonium in the water column at the Hood Canal station.

Ruef, Wendi. 2000. Tracing seasonal changes in circulation of Hood Canal, Puget Sound, Washington State, using chlorofluorocarbons as conservative tracers

Changes in seasonal circulation may be a contributing factor to the intensification of naturally low dissolved oxygen concentrations observed at the southern end of Hood Canal, Puget Sound. Chlorofluorocarbon concentrations measured in water samples taken in December 1999 and April 2000 were used as conservative tracers to observe general circulation patterns and calculate seasonal flow rates and residence times in a 3-box model of the Hood Canal. Flow rate through the deep water at the southern end increased between December and April, from 6.04 x 102 to 1.14 x 103 m3·s-1, with a consequent decrease in residence time from 153 to 81 d. An increase in flow rate would generally not contribute to low dissolved oxygen concentrations, since more water would flow through at depth and up to the surface, where it could be re-saturated with atmospheric oxygen. Because of annual and seasonal variability, these data are only applicable for the time period between December 1999 and April 2000, but can be added to a larger data set of more seasons and years, which can then be used to make conclusions about the effect of seasonal circulation changes on dissolved oxygen concentrations.

Salnick, Erica. 2000. An investigation into the possible use of caffeine as a tracer for sewage effluent in Puget Sound, Washington, USA

The presence of caffeine in Puget Sound, Washington, USA, in association with sewage effluent discharge could be used as a tracer for the discharge plume. Water samples of 4 L were collected in a transect across a pipe used for the dispersion of sewage effluent by the West Point, Seattle, sewage facility. Duplicate 1 L water samples were filtered through solid phase extraction cartridges and eluted with methanol and an 80%/20% methylene chloride/methanol solution. The resulting 7 mL were evaporated under a gentle stream of nitrogen and re-suspended in 0.5 mL of methylene chloride. Caffeine standards tended to have retention times between 13.9 min to 14.1 min when analyzed by gas chromatography flame ionization detection and sample from the sampling stations near West Point contained chromatographic peaks of differing heights at similar retention times. Upon investigation of these samples by gas chromatography mass spectrometry the peaks were determined to be caused by the presence of phthalates. The results of this study did not provide any indication that caffeine could be used as a tracer for the discharge plume caused by the release of sewage effluent into Puget Sound.

Stewart, Keith. 2002. Temporal changes in dissolved iron concentrations during the spring algal bloom in Hood Canal, Puget Sound

There is compelling evidence that phytoplankton growth in the open ocean is limited by iron concentrations. Typical high nutrient low chlorophyll (HNLC) regimes (iron < 1nM) give rise to surprisingly low phytoplankton growth and production. Iron limited phytoplankton growth has not been thoroughly documented in estuarine environments, although some coastal studies have been done with mixed results. This research analyzed dissolved iron concentrations within Hood Canal to establish possible correlations between iron concentrations and phytoplankton biomass. Strong correlations between these two factors might suggest that iron limiting conditions have the potential to influence phytoplankton growth. Samples were analyzed with the MASTER (MBARI Analytical System for Trace Element Research) resin chemiluminescence technique. It was hypothesized that dissolved iron concentrations in Dabob Bay, Hood Canal, would decrease from February to April with the arrival of the annual spring phytoplankton bloom. Dissolved iron concentrations showed atypical limiting nutrient profiles and were found to be between 1.2 nM and 12.7 nM. Total acid soluble iron concentrations, however, were much higher and showed more classically limited depth profiles, ranging between 12.2 nM and 238.6 nM. Concentrations of iron found in this study are higher than that of other coastal studies and show clear relationships with chlorophyll concentrations. Nutrient limited profiles as well as inverse relationships with chlorophyll existed, but the dissolved iron concentrations did not decrease appreciably over the three month long sampling period. Had concentrations decreased it might have indicated that iron limiting conditions exist in Dabob Bay.

Stratton, Virginia. 2004. Determining temporal changes in carbon sources and d13C ratios in sediment cores due to anthropogenic activity near the West Point sewage treatment facility

The purpose of this study was to determine the importance of marine and terrestrial sources of organic matter flux into sediments in the main basin of Puget Sound, Washington. A 3.3-meter -long piston core and four Van Veen grab samples were collected near the West Point sewage outfall. Sub-samples were analyzed for d13C and d15N as well as molar C:N ratios. The stable isotope ratios of both C and N underwent a roughly 20% shift toward more terrestrial values approximately 150 years before present. This shift, concurrent with the industrial revolution and a drastic increase in human activity in the Puget Sound region, indicated that anthropogenic activity has had a significant effect on organic matter sources. While this study did not conclusively establish a single primary source for the terrestrial organic matter, when coupled with previous studies on polycyclic aromatic hydrocarbon (PAH) concentrations in Puget Sound sediments, a correlation with anthropogenic combustion-derived hydrocarbon concentrations was indicated.

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Geological Oceanography

Bever, Aaron. 2003. Concentration of heavy metals in sediments beneath tidal eddies: A case study from Hood Canal, Puget Sound, Washington

Heavy metals contained within the sediments can significantly harm the organisms with which they come into contact. Traditionally it has been those locations near point sources (smelters, sewer outfall sites, highly industrialized areas) that are thought of as at risk for becoming contaminated with heavy metals. There are other locations that are also at risk. This study proves that tidally induced eddies within Hood Canal, Puget Sound, Washington are actively concentrating heavy metals at their centers. Seabed sediment samples were collected from14 stations on 1-2 April 2003 using the R/V Clifford A. Barnes and a 0.1 m2 Van Veen grab. These samples underwent grain size analysis using standard sieve and pipette techniques (median grain sizes (Mgs) ranged from 7.25 f to 1.83 f) and heavy metal concentration analysis using EPA method 3050B and an ICP-MS. The samples were analyzed for Al, Ar, Cu, Fe, Sc and Zn. Average concentrations were found to be: [Al] = 14.4 mg kg-1, [Ar] = 7.1 mg kg-1, [Cu] = 29.3 mg kg-1, [Fe] = 4.5 mg kg-1, [Sc] = 16.23 mg kg-1, [Zn] = 84.0 mg kg-1. Acoustic Doppler current profiler (ADCP) data was used together with information developed using the Puget Soundf and current velocities (Cv) of ~ 50 mm s-1 within the eddy, Mgs ~3.9 f and Cv ~ 500 mm s-1 outside the eddy). Decreasing median grain size also shows a positive trend with heavy metal concentration; smaller grain sizes have higher heavy metal concentrations (Mgs = 4.68 f, [Cu] = 27.9 mg kg-1 and Mgs = 1.83 f, [Cu] = 9.2 mg kg-1. The map resulting from mapping heavy metal concentrations with the eddy location shows that the eddy is concentrating heavy metals. The highest sediment heavy metal concentrations are located near the center of the eddy ([Cu]inside ~ 27.27 mg kg-1, [Cu]outside ~ 23.42 mg kg-1). hydrodynamic model to determine the exact location of the eddy. When the sediments median grain size is mapped at its corresponding station location a distinct trend between the median grain size and eddy location is observed; the smaller median grain sizes are contained within the eddy (Mgs values of ~4.7

Clement, Curtis. 2004. Seismic reflection imaging across steep gravity and magnetic anomaly gradients in southern Puget Sound, WA: Future fault or benign block?

Marine seismic reflection data were collected across gravity and magnetic anomalies associated with the Olympia Structure in southern Puget Sound (Budd, Eld, and Totten Inlets). The project was designed to test the hypothesis that the potential field gradients are caused by a fault. Eighty seven km were surveyed in the three inlets; the track lines ran parallel with the length of the inlets to transect as much of the anomalies as possible. Evidence for a strike slip fault was found at the mouth of Budd Inlet with a strike of ~300o (NW) across channel. The best evidence is 1 m of displacement across a sag in subhorizontal bedding that is directly above a dipping reflector with equal displacement only with opposite throw. Approximately 150 m to the north of the sag is a band of acoustic diffractions. Across the band was 1.5 m of displacement. The strike of the fault is aligned with lineaments mapped on land using LiDAR data, which indicates that motion could have occurred as recently as the late Pleistocene. In the southern end of Budd Inlet is a basin 140 m deep and approximately 3.5 km long filled with horizontal layers. This basin is interpreted as a glacial outwash channel and is presumably filled with sub-glacial alluvium at depth and covered with marine muds and clays. The existence of this fault has important implications for the apportionment of seismic hazard per fault within the Lowland.

Coyle, Jill. 2003. Sediment transport regime and seasonal changes in beach morphology at Cama Beach, Camano Island: Implications for the stability of eelgrass habitat

A 1.3-km-long portion of Cama Beach was surveyed in the summer of 2002 and winter 2003 to assess the possible impact of the sediment transport regime and seasonal changes in beach morphology on eelgrass habitat. Nine elevation transects were surveyed in the southern third of the beach; thirteen were surveyed in the northern third. Slopes ranged from 4°-7°; showing little change in slope occurred between summer and winter. However, profiles indicated that approximately 4800 m3 of material had been removed (probably to the north) from the northern area during the ~6-month long period. Little erosion occurred in the southern area during the same time period. A wave (pressure) gauge deployed off the southern end of the beach measured wave heights of 0.7 m during a March 2003 storm. In April 2003 near-bottom currents ranging from 1.1 to 16.8 cm s-1 were measured in the lower intertidal zone along 1.3 km of the beach; these velocities are capable of moving coarse sand. Sediment samples collected from a single transect across the beach showed find sand dominating in the eelgrass beds; beach sediment coarsens to medium sand in the upper part of the intertidal zone. Cama Beach eelgrass beds, covering an area of 22.4 x 103 m2, occur in water depths up to 7 m, the upper extent exposed during low tide. Physical conditions measured in this study, covering two seasons, do not appear to pose a threat to stability of eelgrass beds. Erosion in the northern part of the beach should, however, be carefully monitored.

Crouch, John. 2003. Holocene faulting in the Tacoma basin: Implications for the thrust sheet hypothesis and potential earthquake hazards

Seismic reflection data were collected in Carr Inlet, Case Inlet, and Hood Canal of the Puget Lowland in effort to reveal pertinent subsurface information about the inferred Tacoma Fault zone. Gravity, tomography and LiDAR (Light Detection And Ranging) data infer the existence of a major feature separating Seattle Basin and the Tacoma Basin. During this study 110 km of seismic reflection data were collected and analyzed for faulting. The survey lines were chosen to profile along known fault scarps located on land adjacent to the study areas. Sub-bottom penetration in the data varied from 1 m up to 130 m, inferred muddy or hard bottom regions provided minimal penetration. Imaging in areas closest to fault scarps that have been mapped on land (Case Inlet) was poor and penetration was minimal. In these regions bathymetry was mapped for anomalies found in the basin. Although faulting was not imaged in Case Inlet, it can be inferred from subsurface features and their alignment with faults scarps found on land. In Hood Canal disruptions in the sedimentary sequence through the northeastern part of the survey area revealed features to align with inferred fault scarps displayed on LiDAR maps and a possible uplifted terrace. All of these features combined provide evidence for shallow (<60 m) faulting in Hood Canal. Carr Inlet generated conclusive imaging of Holocene faulting with ~4m of uplift displayed. North of this fault, seismic reflection data show disruptions and methane gas saturated sections that align generally east-west across the basin. This study has found conclusive evidence supporting faulting along the Tacoma fault zone during the Holocene. The faulting found in this study, however, does not align closely east-west through the lowland. For this reason the data seem to point toward the existence of a deep-seated thrust fault (3 km) with a series of blind faults above it.

Davies, Maureen. 2004. The role of modern sedimentation and particulate transport processes in the formation of central submarine rises in the bathymetry of Puget Sound, Washington

At three locations in Puget Sound, Washington, the bottom is characterized by deep (250-280 m) troughs separated by a shallow (~215 m) central rise, forming a striking W-shaped cross-section atypical of glaciated fjord-type estuaries. Formation hypotheses were tested by a detailed examination of the W-shaped bottom morphology in the Main Basin of Puget Sound southwest of Edmonds. Seismic reflection profiles were examined for indications of glacial scouring and nearby large-scale submarine landslides. Bathymetric site surveys were performed to accurately determine the bottom profile. Bottom samples, including 10 grab samples, 3 box cores, and 3 piston cores, were collected in late March 2004 along a transect crossing the morphological feature in question. Samples were analyzed for accumulation rates and grain size distributions for the axial rise and the flanking depressions. The accumulation rate on the central rise was found to be higher (6.2 mm y-1) than that of the axial depressions (1.9 mm y-1 – 2 mm y-1). Mean grain size on the rise (17.18 µm) was found to be finer than in the depressions (20.30 µm). Stronger near-bottom currents along the flanks, produced by tides, preclude deposition of all but the coarsest sediment in the depression. This results in low sediment accumulation rates compared to rates in the low energy axial area, as well as coarser sediment in the troughs compared to the axial high. Results primarily suggest that the W-shaped bathymetry is due to post-glacial sedimentary processes governed by tidally induced current regimes, although submarine landslides in the region undoubtedly play a role.

DeGeest, Amy. 2003. Temporal variations in trace metal concentrations in Lake Washington sediments: An estimation of sediment response to airborne pollutants

Arsenic concentration profiles measured in modern sediments were used to determine if the reduced input of anthropogenic arsenic to the atmosphere created by the closure of the ASARCO Tacoma copper smelter in 1985 is reflected in the concentrations of recently deposited Lake Washington sediments. Subsamples from two cores collected on 4 March 2003 were analyzed for concentrations of arsenic, antimony, aluminum, iron, and manganese using an Inductively Coupled Plasma-Mass Spectrometer. Concentration profiles reveal that arsenic, iron, and manganese are increasing in surface sediments, while antimony and aluminum do not show consistent change over time. The highest modern arsenic concentrations, 95 and 117 mg kg-1 at LW1 and LW3, respectively, are located within the upper 2 cm of sediment. However, the total arsenic flux into the surface mixed layer at present is 1,700 ± 700 kg y-1, compared to 2,600 ± 700 kg y-1 as was calculated in 1974. This indicates that surface sediment concentrations are decreasing in response to the reduced arsenic input, but some previously deposited arsenic can be remobilized and move along gradients within anoxic sediments. It can then precipitate in the oxygenated surface layer, causing the increased surface concentration relative to depth. An estimation of response times of Lake Washington sediment is 82 ± 38 years, although there is high spatial variability. Results from this study show that sediments create a dynamic environment in which anthropogenic impacts can cause potentially hazardous conditions that remain for extensive periods of time after the source has been eliminated.

Gendron, Austin. 2005. Water table dynamics at Lowell Point, Camano Island, Washington: A designer study for Puget Sound

An ebbing tide will cause fluctuations in a beach watertable sometimes resulting in a decoupling of the two water masses. The decoupling results in the falling watertable lagging behind the ebbing tide creating a exfiltrating seepage face. A hydrological field study involving a series of measurements profiling the fluctuating water table over an eight hour April ebbing spring tide in 2005 was conducted on Lowell Point at Camano Island State Park. The sequence is relative to tidal elevation, and was measured using a well method consisting of a series of peizometers on a transect perpendicular to the shoreline. The linear profile was constructed of 6 evenly placed wells within the inter-tidal zone allowing the elevation of the water table to be easily measured. A measurement of the tide elevation over the ebbing tide was calculated using the Puget Sound Tide Channel Model (PSTCM). Seepage face and exit point was identified and profiled. Comparison of the recorded tidal elevations and watertable heights to a qualitative interpretation of the Darcian based SEEP model proved to coincide with hydrological surveys of finer grained beaches, suggesting a relative example for the mixed beaches of the Puget Sound.

Krynytzky, Marta. 2005. Humongous subaqueous sand dunes in Admiralty Inlet, Puget Sound, Washington

A large (3.5 km2) field of subaqueous sand dunes has been mapped in Admiralty Inlet, Puget Sound, in 20-127 m of water. The field was surveyed using a swath mapping system and a 3.5 kHz subbottom profiler. The largest dunes are 20 m high, with a wavelength of 375 m. Wavelength to water depth (L/h) ratio is 4.36 which is typical for intertidal dunes, height to water depth (H/h) ratio is 0.23 which is larger than usually found in any environment, and vertical form index (L/H) is 18 which is unusually steep. Bedforms range from symmetric to highly asymmetric. In some areas of the field, mega ripples (2-5 m high) are superimposed on large dunes at oblique angles. Bottom sediments collected using a grab sampler at four sites within the bedform field show the bedforms to consist of well sorted coarse sands. Five samples taken near the field were poorly sorted and slightly coarser grained. Acoustic Doppler current profiler measurements show maximum mean tidal currents in the water column were 1.4 and 0.9 m s-1 for ebb and flood flows, respectively, whereas modeling predicts peak bottom currents of 0.2 and 0.4 m s-1 for ebb and flood flows. These currents are capable of transporting coarse sand, suggesting that the bedforms are active. A differencing analysis between two bathymetric surveys (2002 and 2005) shows net northwest migration of ~10 m yr-1. Rapidly eroding shore bluffs on nearby Whidbey Island could be a sediment source for the bedforms.

Schacht, Kathleen. 2002. Gas charged sediments and seafloor pockmarks in Puget Sound: Implications for submarine geomorphology and slope stability

This study shows that gas charged sediments contribute to the geomorphology of Puget Sound and that pockmarks are surface expressions of vented gas. A subbottom profiler and multibeam swath mapping system were used. An area just south of the Elliott Bay pockmark shows irregular features indicative of erosion and a large slump is seen to the southeast. Gravity and box cores were taken from the pockmark and off-site stations. These cores showed that the pockmark was formed from liquefaction of the sediments, mixing the sediments found at depth with the surface sediments, creating a hummocky and shell hashed surface. The methane analysis of the sediments from these cores was not conclusive because the depth of penetration for the pockmark and for the down current site was not more than 5 cm and 14 cm, respectively. A methane analysis was done of the water column above the stations and found not to have any significant anomalies. During the underway survey, a gas charged ridge was found and a methane analysis was done on the 80 cm of sediment collected. This analysis showed an increase of 10 nM g-1 to 1200 nM g-1 in methane content with depth. From these analyses, a method for testing gas charged sediments and slope stability with respect to nearshore and offshore construction should be developed.

Smith, Colin. 2005. A pæleo-oceanographic survey of past bottom water oxygen conditions in Hood Canal

Three piston cores, representing approximately 247 years of sedimentary record, were obtained from the southern half of the Hood Canal basin on 30 March 2005 to investigate past bottom water oxygen (BWO) conditions and to determine if they are proceeding toward a great hypoxic state. In recent times there has been much concern as to whether or not anthropogenic modifications to the water shed have contributed to eutrophication of Hood Canal. Classification and quantification of sedimentary structures via X-radiography, and organic carbon to surface area (OC:SA) analyses were performed on the 210Pb geochronology dated cores in an attempt to determine if any trends indicating BWO states coincide with the general increase in human population and related changes to the Hood Canal water shed. X-radiograph results indicate the presence of mottled sedimentary structures in all three cores. The cores from the southernmost reaches of the basin display characteristics indicative of BWO conditions proceeding towards a greater hypoxic state. The northernmost core indicates the exact opposite. Organic carbon to surface area ratios indicate Hood Canal has never experienced any prolonged periods of anoxia during the dates sampled. The higher end of the range from OC:SA values obtained do coincide with those from a nearby seasonally anoxic fjord which may indicate that Hood Canal is a basin that has a similar BWO regime, though care must be taken in interpreting this finding because of an analytical step that was not performed in preparing the samples.

Staly, John. 2002. Sediment transport processes on Possession Point Shoal, southern Whidbey Island: Implications for tidal flow along the northern margin of the Triple Junction

Bathymetry was mapped and sediment samples were taken on Possession Shoal, southern Whidbey Island. Megaripples found on the south side of shoal cover an area of 1.5 km2 and have a 14 m period and between 0.6 m and 1.0 m amplitude. The megaripples appear to be propagating southeastward towards a sediment fan south of Possession Sound. Megaripples within a south trending canyon that partially bisects the shoal cover an area of 0.1 km2. Megaripples within the canyon have differing periods depending on which side of the canyon axis (thalweg) they lie. The megaripples on the east side of the canyon, which have a 10 m period and 1 m amplitude, appear to be propagating southward whereas the megaripples on the west side of the canyon, that have a 35 m to 40 m period and a 3 m to 5 m amplitude, appear to be propagating northward. The west side of the shoal, which lacks bedforms, consists of a 1-km2-area of hard rock (pavement). A 45-cm-thick turbidite layer was sampled at a depth of 4.5 m below the seafloor in the axis of the canyon system in 250 m of water. The base of the turbidite consisted of coarse shell hash containing abundant fragments of Macoma brota, an intertidal dwelling mollusk. Acoustic profiles across the canyon at the piston core site show flank levee systems typical of active turbidity flow channels. The geometry of channel and levees were used to estimate a turbidity current velocity of 419 m s-1. Extrapolation of modern sediment accumulation rates suggest that the turbidite was deposited between 900 and 1000 yBP. Results suggest that during the ebb tide, bottom currents travel northward through Possession Shoal canyon, hugging its west side, and eventually spilling over the west side of the shoal. During the flood tide, however, bottom currents are forced to the east over the west side of the shoal. They then travel southward down the canyon along its east side and southeast over the east side of the shoal towards the sediment fan.

White, Theodore. 2002. Geologic evolution of the Possession Point submarine fan

The circulation in the triple junction region of Puget Sound is of interest to many different groups of people for various reasons. The local bathymetry has a large effect on the circulation. The Possession Point submarine fan is a feature of the local bathymetry and may play a role in circulation. The geologic history of the fan and how it has changed over time has the possibility to reveal insights into its role in circulation. The history of the fan was studied by examining the changes in mass accumulation rates and by examining its change in shape. Using box core samples, modern deposition rates were studied by comparing 210Pb profiles at three locations down the fan. Using seismic profiles, ancient deposition rates were studied by estimating the amount of sediment accumulated in the fan and approximating how long it took to accumulate. To see if turbidites affected mass accumulation, a piston core was taken at the foot of the fan and piston core data from the middle of the fan were examined. The shape of the fan was examined using 3.5 kHz profiles and by Simrad EM300 mapping. Differences in ancient and modern mass accumulation rates reveal that the submarine fan is growing at a slower rate than in the past and that it may therefore be inactive. Differences in mass accumulation rates of the fan vs. adjacent areas confirm the concept that the fan is acting as a sill and may play a large role in the circulation of the triple junction.

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Physical Oceanography

Alvarado, Luke. 2002. A survey of the tidal circulation patterns near a sewage outfall site in Poverty Bay, Puget Sound, Washington

Recently, the Puyallup Tribe processed a request to the Department of Health to classify Geoduck tract #09950 as a suitable area for commercial harvesting in Poverty Bay, Puget Sound, Washington. Assessment of this specific Geoduck tract requires a knowledge of the tidal circulation patterns inside the bay. This report estimates the circulation patters during an ebb tide and approximates current structure during a flood tide. The hydraulic model at the University of Washington was used to predict results and guide the field research. Twelve free floating drifters estimated surface current velocities and current velocities at 5 m depth. Results indicate current velocities of 0.11 m s-1 and 0.08 m s-1 respectively. The ADCP data collected documents an average southwest current over a tidal cycle. The current velocities are greater during a flood tide and thus, the current structure is tidally dominated by the flood tide. Geoduck tract #09950 lies on the northeastern shore of Poverty Bay and proves to be a suitable location for commercial harvest.

Burcal, Rene. 2001. Surface water circulation characteristics of the Triple Junction for model comparisons

Observed temporal characteristics made using satellite-tracked drifters provide an analysis of how accurate models are. Parameters observed with the use of drifters include the spatial and temporal variations of the surrounding water. Such information, paired with observed freshwater discharge, tidal phase, bathymetry and wind-forcing data, provides the variables needed to derive a working model. Factors responsible for driving the surface current were mostly due to tidal forcing, followed by wind and bathymetry. Areas of converging saltier water from Main Basin and fresh Possession Sound water in the Triple Junction were shifted depending on wind forcing. An area of continuous fresh water was evident over the shoal as the portable CTD data showed as water moved closer to the shoal salinity dropped.

Curry, Lauren. 2005. Dissipation of internal waves in Port Susan, Puget Sound

Internal waves have been observed in Port Susan, Puget Sound. Their timing with tides, speed and amplitudes were well documented in a previous study, but the reason they decay remained unknown. On April 8th 2005 the R/V WeeLander was taken to Port Susan with a Seacat CTD to observe the decay of the internal wave. Internal waves create regions of convergence and divergence that are observable as surface slicks. The CTD was yo-yoed at seven stations in these surface features. I will show observations that demonstrate that the internal waves respond to changes in the channel width and to decreases in the stratification of the water column as the wave propagates out of Port Susan. At the surface, I observed a strong foam front in Port Susan, where the foam disintegrates after reaching the end of Camano Island and spreads over a much larger area. Wave amplitudes are seen to dramatically decrease in size from 9 meters to 4 meters over the course of our observations, while the wavelengths increase with distance. The final end of the wave is a region of well mixed water south of Gedney Island in Port Gardner. The loss of stratification here is theorized to be the cause of the decay of the internal wave, because the interface on which the wave propagates no longer exists.

Determan, Luke. 2002. An investigation to track the effluent output from Redondo wastewater treatment plant in Poverty Bay, Puget Sound, WA

After receiving a request from the Puyallup Native Tribe, it became necessary for the Washington State Department of Health to classify geoduck tract #09950 for commercial harvest. Very near the shellfish beds lies a sewer outfall from the Redondo Wastewater Treatment Plant. Past studies at station EAP001 nearby in East Passage show a well mixed water column and a mean southwesterly current; however, after closer investigation, a stratified water column was observed. Five stations were chosen along a transect starting southwest of the outfall and terminating northeast of the outfall, just offshore from the shellfish beds. The plume was believed to be a warm, fresh water lens near the surface, and the nutrient depletion was expected to occur at the stations to the southwest of the outfall. CTD casts were done and samples were collected for ammonium analysis during the ebb and flood tides. The temperature and salinity, combined with model data in the lab, confirmed the southwestward flow theory. Oxygen and nutrients were ambiguous but did, after close examination, also confirm a southwesterly current.

Falkner, James. 2005. Investigation of mixing processes at the Hood Canal Sill

The Hood Canal is one of four basins associated with the Puget Sound system. It has experienced problems of low oxygen in the past. Many biological hypotheses are put forth to explain these problems. This paper looked at the physical characteristics of the Hood Canal sill to determine if it added to the problem. It was found that circulation during a flood tide into the canal slowly increases in velocity, near 0 mm s-1, until reaching a maximum, 200 mm s-1, just after max flood and then slowly decreases in velocity. The maximum was found at the bottom of the water column between 60 m and 100 m. Refluxing was found to occur at the very end stages of the flood tide, causing perturbations in the water column properties of salinity, temperature, density and oxygen concentrations. The water column properties ranged from 29.4-30.2 psu for salinity, 8.2-9.6 °C for potential temperature, 1022.8-1024 kg m-3 for density and 6.6-6.8 ml L-1 for oxygen. These properties advanced from values similar to those taken inside the sill to values similar to those taken outside the sill as the time series progressed. This is consistent with expected behavior for an estuarine system.

Harris, Jeffrey. 2003. Internal solitary waves in Port Susan, Puget Sound

On 30 April 2003, a group of at least six internal solitary waves (ISWs) were observed to propagate south in Port Susan, Puget Sound. Prior to this study, no direct measurements of ISWs in the region were on record. Measurements were made from CTD observations from a small boat, the R/V Weelander. From the CTD observations, the ISW amplitudes were about 10 m. The boat stopped at seven stations, and wave positions were recorded by GPS. The ISWs could be seen as a series of surface slicks. The least-squares fit for the velocity was 63 ± 4 cm s-1. From this, the ISWs appear to be generated by the interaction of the ebb tide with the Stillaguamish River delta. The simplest nonlinear wave theory, based on the Korteweg-de Vries equation, underestimates the ISW amplitudes for the measured velocity. An empirical formula is put forward in an attempt to explain the observed wave speed: , where c is the wave speed, N is the average buoyancy frequency in the surface layer, h is the depth of the surface layer, and a is the amplitude of the wave. The waves appear to decay near Gedney Island by shear instabilities in on their trailing edges. Interestingly, the waves decay soon after the background flow switches from moving against to moving with the waves. This further suggests that the ISWs are sensitive to background flow.

Heinze, Kurt. 2002. A study of the salt flux through Deception Pass, Washington

During the period 22 March – 17 April 2002, two tide gauges were placed in Bowman and Cornet Bays near Deception Pass. Tidal height differences were calculated from the tide gauges. Using the tidal height differences in a simple model, the flow through Deception Pass was determined. It was then possible to calculate the salt flux through Deception Pass. By assuming the Whidbey Basin to be in steady state over long time scales, it was possible to determine if salt is being entrained from the Triple Junction into the Whidbey Basin. A salt flux of -6.5x104 kg s-1 was found to be flowing through Deception Pass during the study period; this suggests that salt is entrained from the Triple Junction into the Whidbey Basin. CTD casts were taken between the two bays on different tidal cycles to determine the short term effects of the tidal forcing on the flow through Deception Pass. Periods of slack water showed a normal estuarine flow; saline water entered Deception Pass at depth and fresh water exited in a surface layer. During an ebb tide, the flow fields in Deception Pass were more complicated; normal estuarine flow did not develop.

Higgins, Eric. 2004. Deep Water Intrusions in Hood Canal, a basin in Puget Sound, Washington

Recent fish kills in the southern regions of Hood Canal due to dangerously low dissolved oxygen concentrations have prompted interest into the existence and magnitude of deep-water intrusions over the sill of Hood Canal. Such deep intrusions may be a major mechanism for the replenishment of deep-water oxygen in this system. CTD casts were performed both north and south of the sill in order to locate any deep intrusion and ADCP velocity data was collected in order to obtain an estimate of intrusion volume transport once they were identified. An intrusion was identified for the first CTD station just south of the sill but no intrusion signals were found for stations further south. The identified intrusion was determined to extend from 75-meters depth to the bottom (~118). A volume transport of 307.47 m3 s-1 was then determined from velocity measurements taken at this site, yielding a flushing time of 209.64 days. Measured velocities were small since ADCP data was collected near slack tide. A theoretical extrapolation of tide data available for Hood Canal yielded a shorter 151.86-day flushing time for flows averaged over the entire tidal cycle. Both flushing times exceeded flushing times obtained from previous studies.

Hoglund, McArthur. 2001. A Lagrangian study of surface circulation in the Main Basin of Puget Sound using ARGOS/GPS-tracked drogues

The circulation of the 10-m-thick surface layer in the Main Basin and Admiralty Inlet, Puget Sound, Washington, was tracked from 26 March 2001 through 2 April 2001 using satellite-tracked drogues. The drogues were deployed just north of Vashon Island. The drogues consisted of an electronics float and a 10-m-long mesh sail at depth from the surface. The drogues measured currents as fast as 1.16 m/s, and a mean current velocity of 0.26 m/s. The net paths of the floats were north through the southern Main Basin and up and into Admiralty Inlet in an average of five days. The results correlate with a hypothesized narrow, seaward-directed, stream-like current. Results suggest a wider ‘snake' is present in Puget Sound. The University of Washington Puget Sound Model was used to compare the drogue results. The model proposed that wind was the major factor in the net northern flow, which allows one to believe that the model's circulation is slow compared to actual Puget Sound circulation.

Jenks, Katie. 2004. Is Dabob Bay a closed system? Water exchange in the western channel as a means for renewal of water in Dabob Bay, Puget Sound, Washington

Dabob Bay is located in Hood Canal, Puget Sound, Washington, and is a center of biological research. Understanding the circulation of Dabob Bay is important for both physical and biological reasons. Physically, understanding the dynamics of Dabob Bay will allow for a greater understanding of the entire Hood Canal system. Biologically, the studies conducted in Dabob Bay assume that it is a closed system—that is, advection is minimal and can be ignored. This study tests that hypothesis, as well as contributes to the overall body of knowledge about and understanding of Dabob Bay. ADCP transects across the sill at the entrance to Dabob Bay measured water velocities on five cruises in the spring of 2004: 24-26 February 2004, 3-5 March 2004, 10-12 March 2004, 22-26 March 2004, and 7-9 April 2004. CTD casts collected potential temperature and potential density data on two of those cruises: 3-5 March 2004 and 7-9 April 2004. Warm (10-11 ˚C), dense (23.0-23.5 kg m-3) water was repeatedly observed at depth at the entrance sill. In the western channel of the entrance to Dabob Bay the transport showed no significant correlation with the tides, however, an upper bound of the transport gave an estimated residence time of 1.3 years. Considering the entire channel, the data support previous three-layer models of Dabob Bay. The transport in this three-layer model gives an estimated residence time of 0.88 years. Thus, Dabob Bay can only be considered a closed system for processes acting on shorter time scales than the residence time.

Kang, Jeong-In. 2003. Water circulation in Dabob Bay: Focus on the exchange of flows during the diurnal tide transitions

The project concentrates on the exchange flows across the entrance sill in Dabob Bay, Washington. Dabob Bay is one of the closed fjord-like basins in Puget Sound. Water circulation has received considerable attention since it distributes the nutrients into the basin. Water velocity data were obtained by using a ship-mounted 150 kHz acoustic Doppler current profiler (ADCP), and water property data were gathered by conductivity-temperature-depth (CTD) aboard R/V Clifford A. Barnes during a complete diurnal tide on March 10th - 12th, 2003. Averaged water velocities at certain waypoints and depths were plotted along two transects: one is along the sill or across the channel, and the other is along the channel in the basin. Currents across the entrance over the sill were the greater and more variable.

Kellogg, Jonathan, and Noel Gray. 2004 Seiche dynamics and energy dissipation in the Hood Canal basin

Hood Canal, the westernmost arm of the Puget Sound fjord in Washington State, was instrumented for the month of March 2004 with two tide gages on either side of the South Point sill and two moorings at either end of the basin. The southern mooring had a conductivity, temperature and depth (CTD) recorder while the northern mooring only recorded temperature. The energy dissipation across the sill was calculated from the tide gages using previously developed equations. A total of 1.72 MW was dissipated by the M2 tide; 0.067 MW was dissipated by the K1 tide. Potential density from the CTD at the south mooring was used to estimate the pycnocline excursion from a historical average density profile. Internal waves oscillating on ~30 hour timescales are observed. These internal waves can also be seen in the low pass filtered sea level height data from Seabeck. When also considering the hourly wind record from Olympia, three storm events stood out with strong southerly winds. It was also found that these wind events were intense enough to bring water from beneath the pycnocline (10 m) to the surface such that oxygen was injected into the deep waters of this area. This is important because these waters are regularly hypoxic and have recently been anoxic. Bubble injection likely has great impact on the oxygen budget and could have both positive and negative impacts on the organisms in south Hood Canal.

Kende, Andrea. 2001. Characterization of current behavior and circulation in the Triple Junction of Puget Sound, WA

Characterization of current structure in the Triple Junction, an area joining the Main Basin, Admiralty Inlet, and Possession Sound, of Puget Sound, Washington, was completed using a ship-mounted 150 kHz acoustic Doppler current profiler (ADCP) during one tidal cycle on 5 and 6 April 2001. Tidally averaged current velocities across the basins in the area were correlated with previous, long-term ADCP studies at fixed locations. Cross-channel variability was seen in both ebb and flood tides, as well as the tidal average. Seaward flow dominated the eastern sides of the Main Basin and Admiralty Inlet entrance at midlevel to shallow depths, reaching up to 60 cm/s. Landward flow dominated the western sides of the two basins at all depths, reaching velocities of 50 cm s-1. Currents across the Possession Sound entrance were slower and more variable. This general flow structure corresponds with the previous studies, but differs in the East/West velocity components. Like the previous study, results show evidence of a core of seaward flow, flowing into the Triple Junction, where bathymetry influences the currents' path. Results suggest further study is needed to resolve the ultimate path of the currents and flow on the eastern side of study area to determine the suitability of a sewage outfall into the Triple Junction.

Macdonald, Eric. 2000. Flow properties of the water column over the Hood Canal sill, Puget Sound, Washington

The physical properties of the Hood Canal sill were examined in an attempt to further our understanding of water properties over a sill, and extend these results to the physical properties of the entire estuary. A high salinity, low temperature water mass was observed at depth during the flood tide and a fresher, warmer water mass was observed at the surface during an ebb tide. A mean flux of dense water was also seen over the entire study period. And, although they are arguably suspect, Richardson numbers indicated immense mixing over the sill. The movement of distinct density water masses suggested a dense water intrusion over the sill, while also indicating the occurrence of a two-layer exchange flow. The mean landward flux of dense water was also an indication of two-layer exchange flow. Water velocity profiles were obtained by RD Instruments ADCP along a single track above the sill. A Seabird CTD was used concurrently in tow-yo mode to examine the density, temperature, and salinity structure from the higher high water to the lower high water of a spring, semi-diurnal tide.

Maynor, Shannon. 2004. The near-bottom current regime and the role of the benthic nepheloid layer in transport and accumulation of particulate matter in Puget Sound, Washington

Historical data reveal the presence of an approximately 70-m-thick, turbid benthic nepheloid layer (BNL) in the near-bottom waters of Puget Sound, a fjord in western Washington. The BNL is likely formed during neap tides when intrusions of dense, salty Pacific Ocean waters are able to move southward into Puget Sound. Where headlands constrict water moving through the Sound, the estuary floor is characterized by pairs of depressions separated by a shallower axial ridge. The origin of this W-shape has never been investigated. Constriction of the channel tends accelerate tidal flow, resulting in faster flood currents on the western side of the basin, and faster ebb currents on the eastern side. The anticipated relationship between tidal currents, development of the BNL, and the W-shaped bottom morphology was investigated using an array of measurements over a transect from Richmond Beach to Jefferson Head in central Puget Sound. Twice in March 2004, an acoustic Doppler current profiler (ADCP) measured tidal currents across the channel, revealing speeds of 50 to 70 cm s-1 in the western depression. A 20 % decrease in light transmission corresponded to a 0.5 kg m-3 increase in water density as measured by the conductivity, temperature, and depth profiler (CTD). Sediment grain sizes on the rise were 3 mm finer on average than in the depressions, and accumulation rates were about 3 times greater on the rise. These results imply that tidal currents are primarily responsible for the W-shaped morphology, and that periodic transport by the BNL has a significant impact on particulate transport in Puget Sound.

Sauers, Kari. 2000. Tidal current structure around Point Edwards in Puget Sound, Washington

Field measurements of tidal flow in the triple junction of Puget Sound, Washington, were taken during a 6.5-hour-long maximum ebb tide on 7 April 2000 aboard the R/V Thomas G. Thompson using an RD Instruments ADCP. The objective of this research was to determine if a flow separation occurred north of Point Wells, and then to identify any evidence of eddy formation in this region during an ebb tide. Vertical velocity profiles suggested the possibility of eddy formation just north of Point Edwards; however, the measurement array did not provide enough spatial and temporal coverage to be conclusive. The flow patterns observed in this study demonstrated that the currents in the Main Basin are primarily controlled by local bathymetry.

Stumbaugh, Matt. 2002. Passive acoustic observations of geophysical phenomena in the Puget Sound estuary

In situ measurements of geophysical, anthropogenic, and biological phenomena occurring below and at the ocean-atmosphere interface are needed for meteorological, oceanographic, climatological, and ecological studies. In this research, passive acoustic and ground truth observations of rain, wind, and vessel traffic were made and synthesized for comparison of Acoustic Rain Gauge (ARG) measurements to surface measurements. The cumulative probability distribution of sound levels was calculated to determine the temporal variability of spectral levels within Puget Sound. Low frequency sound levels determined by the probability distribution function for Puget Sound were compared to observations from 1994-2000 on the continental slope off Point Sur, CA. Variability within Puget Sound is ~1.6 times greater than that of Point Sur and for the median spectrum higher by 4 and 6.5 [dB re 1 mPa2 Hz-1] at 300 and 500 Hz respectively and 2 [dB re 1 mPa2 Hz-1] lower at 100 Hz. Ship presence was identified acoustically on time scales of hours but a global algorithm to quantify the total number of shipping events was not determined. Consequently, the presence of ship traffic contaminated acoustic wind speed measurements. Acoustic trends in wind speed are in agreement with ground truth observations but an average of 5 m s-1 greater than measured on land. Rainfall accumulation determined by ARG is very similar to land based tipping rain gauge measurements.

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