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In Their Own Words - Project Summaries for Ocean 443

Matthew Chien-Hom: Mysterious mounds of southern Hood Canal: dump sites, landslide deposits or glacial debris

In 2005, the University of Washington research ship, R/V Thomas G. Thompson

discovered two large mounds in southern Hood Canal just west of Dewatto Bay and Long Point. These mounds are large bathymetric features in a basin that for the most part lacks such features and their origins have yet to be determined. Three possible mechanisms for their formations are being considered. These mechanisms are spoil deposits, landslide deposits, and glacial debris. Bathymetric and sub-bottom profiles will be gathered of the two mounds. These data will be used to search for any exposed or buried landslide features around the mounds. A total of 12 grab samples will be taken over and around the

mounds along the sub-bottom profile tracks for an analysis of the spatial distribution of grain sizes on the horizontal plain. This will help establish whether or not the mechanism that deposited these features could have been dumping events, such as disposal of spoils or from glacial debris. If possible, cores will be taken with a spade box core for 210Pb analysis of sediment deposition rates for dating of the mounds or possible landslide features.

Adam Fleischer: An exploration of the changing diversity and distribution of ichthyoplankton within the Puget Sound

The objective of this study is to achieve a greater understanding of the distribution and diversity of ichthyoplankton within the Puget Sound. A 60 cm bongo net with 505 μm mesh will be used to obtain samples from five stations within the Puget Sound, including Hood Canal and San Juan Island. These samples will be counted and identified in a laboratory. Little has been done concerning larval fishes in the study area and some species heavily rely upon the estuary as a nursery, which would have management and ecological ramifications. It is expected that a higher diversity will be found at the northern sites, closer to the Pacific Ocean, considered the source of many species. If this

proves to be wrong, and there is a uniform diversity within the Puget Sound, then it may indicate that Puget Sound does not function as a nursery for some species of fishes.

Brianna Fox: A quantitative look at the possible effect of the common pesticide carbaryl on the copepod Calanus pacificus

In recent years the pesticide carbaryl has been measured at elevated levels in

Seattle area watersheds. In 2004, in an effort to protect endangered salmon, a court imposed a pesticide buffer around west coast waterways that are known to support these salmon. Copepods and other zooplankton represent a major food source for the juvenile fish, including salmonoids, which may be equally at risk in Puget Sound. This project will consider a potential indirect effect on salmonoids by quantifying the acute toxicity of carbaryl to the copepod Calanus pacificus. C. pacificus will be collected in Hood Canal during the week of March 19 from the R/V Thomas G. Thompson. Adult females, their eggs and the resulting nauplii will be exposed to carbaryl, at levels they may encounter in Puget Sound. Egg production and/or mortality will be measured in the adults, hatching success will be measured in the eggs, and mortality will be measured in the nauplii. It is

expected that there will be a positive correlation between carbaryl concentration and mortality, with a possibly greater correlation with the juveniles (nauplii). Additionally, it is expected that both egg production and hatching success will decrease with increased carbaryl concentration. This study will improve our understanding of how urban populations directly and indirectly impact salmon.

Rachel Halfhill: Evaluation of chlorophyll concentration and wavelength specific light attenuation

The effect of light on chlorophyll concentration of phytoplankton is relatively known, yet it is still unknown what affect changes in light quality will have on phytoplankton. Specifically, the affect of the attenuation of red wavelengths of light on chlorophyll concentration in surface waters is understudied considering the potential use of these wavelengths in remote sensing of algal blooms. Chlorophyll concentrations should change along with changes in the attenuation of red wavelengths in the water column. Changes in the light quality in various waters of Puget Sound will be measured using a PAR sensor and Hobo light and temperature sensor pendants attached to a red and a blue band pass filter. These sensors will be mounted on a CTD rosette and deployed from the R/V Thomas G. Thompson. Water samples will be analyzed for chlorophyll a

concentrations and will be counted for phytoplankton composition. Three transects of four stations will be used; each represents a different turbidity regime in Puget Sound. These transects will be near Elliot Bay in the Main Basin, in Saratoga Passage near the Skagit River, and in Dabob Bay in Hood Canal. Since water absorbs longer wavelengths of light preferentially, PAR composition in deeper waters is mainly due to blue light, while there is a higher proportion of red light in surface waters. Because of this, increases in red light should increase the chlorophyll concentration at the surface.

Chet Harrison: A cross channel survey of southern Rosario Strait, Puget Sound, Washington during a flood tide using ADCP/CTD methods

The vertical structure of the Southern portion of Rosario Strait will be surveyed using an ADCP/ CTD/ nutrient analysis method to measure the velocities and physical properties of the water will be measured. The purpose of this project is to gain a greater understanding of the vertical based structure of the waters in this region where a significant number of tankers pass by carrying much needed crude oil. With this knowledge one may be able to more accurately predict where an oil spill may go due to oil droplets typically not moving past the thermocline or pycnocline, would one happen to occur near March Point. The project will also provide a greater understanding of basic oceanography in the region.

Shane Hollrah: Model/data comparison of a sewage outfall in Puget Sound using ammonium as a tracer

An EPA model, applied to the South Treatment Plant’s Sewer Outfall during an

ebb tide in Puget Sound will show where the plume’s movement in the marine water is predicted to exist during this time. The model will be compared to data to test whether or not the discharge stays submerged near a depth of 100-150m as reported by one source (Ebbesmeyer, 1998). If the plume has high concentrations of ammonium, it could promote a phytoplankton bloom if the depth of the plume reaches into the photic zone. Using ammonium as a tracer I will test the water quality where excessive ammonium could cause eutrophication. I expect to see high concentrations of ammonium that advect horizontally, not reaching the surface directly above the plume which is good for the surface water quality. This model will also make a good comparison to modeling work completed on the West Point outfall.

Brittany Kimball: Estradiol accumulation in Puget Sound sediments and the implications for native fish populations

Estrogenic pollution within Puget Sound is a growing concern for the citizens that

care for it. Estradiol (E2) and Ethynylestradiol (EE2) are two of the main estrogenic compounds that have recently been recognized as contaminants and possible catalysts to fish abnormalities. English Sole (Parophrys vetulus), a native sediment-dwelling species of fish in the Pacific Northwest, have been documented with lesions, reduced fertilization, decreased egg and larval viability, and levels of vitellogenin in males, indicating estrogenic pollution. It has been concluded that sediments are a viable sink for estrogenic pollution and consequently contaminating fish populations. To determine if Puget Sound sediments contain concentrations of these estrogenic compounds, six

stations will be sampled from 19-23 March 2007 using a Van Veen grab sampler and Multi-Corer. The stations of most concern are those in Elliot Bay, Seattle, and near Victoria, BC in the Strait of Juan de Fuca where the urban populations are greatest. Detailed lab procedures will be utilized to detect these compounds within the sediment and Gas Chromatography – Mass Spectrometry (GC-MS) will be used to calculate the concentrations of the two hormones in question. The accumulation and concentration of these compounds could provide a link to the developmental abnormalities in benthic fish.

Claire Landowski: Relict ‘Ediz Hooklets’ on the Elwha River delta, Olympic Peninsula, WA: Implications for Holocene sea level rise

Three morphological features on the submarine delta of the Elwha River on the northern coast of the Olympic Peninsula (WA) offshore may be relict spits that can provide insight into the rise in sea level following the last (Fraser) glaciation. Analysis of three seismic reflection profiles and 3.5 kHz subbottom profiles (~5 km each) collected across the spits and the Elwha River delta shelf will be used to determine (1) if the features are indeed spits and (2) the shape of the “basement” surface underlying the spit-like features (SFLs). If this basement surface is terraced, it would indicate that the delta was exposed to waves and currents long enough to produce a platform, indicating a still stand in sea level rise. If the basement surface is straight, it would indicate that the SFLs were formed by episodic deposition during constant sea level change. Spit development is an important character of sediment transport along the coastal margin, and understanding the response of sediment movement to a changing sea level could aid in the development of effective coastal policies as global sea level continues to rise throughout the Holocene.

Deni Malouf: Alexandrium catenella encystment and temperature control in the sediment of Discovery Bay and Penn Cove, Washington

Alexandrium catenella is a dinoflagellate that produces saxitoxin, a neurotoxin that is bioaccumulated in shellfish and passed to humans when shellfish are consumed. The abundance of the organism in Puget Sound is an economic threat to the shellfish industry, as well as a health threat to the general public. All regions in Puget Sound have had shellfish harvest closures due to Hazardous Algal Blooms (HABs) caused by A. catenella with the exceptions of Southern Hood Canal and the Southern Puget Sound (Rensel, 1993). Understanding of the bloom dynamics of A. catenella is necessary to help sustain the economic stability of the shellfish industry and provide advanced warnings for consumers. These cells have been found in high abundance in Discovery Bay and Penn Cove, Washington where the cell presence has also caused shellfish farm closures (Horner et al., 2007). This dinoflagellate has a complex life cycle: under warm conditions, it is actively swimming and dividing in the water column but under cold conditions it forms a resting cyst in the sediment. I will quantify A. catenella cyst abundance in sediment samples from Discovery Bay, Penn Cove, and the Main Basin of Puget Sound in Washington aboard the R/V Thomas G. Thompson from 19 March 2007 to 23 March 2007. I will also measure the temperature decrease necessary to cause encystment of the active cells. I hypothesize that enclosed regions, such as Discovery Bay and Penn Cove, have the preferred environment in which cells most readily encyst. Enclosed regions have different circulation patterns, nutrient levels, and water temperature than open regions, contributing to unique conditions supporting increased encystment. If the enclosed regions have predictable encystment patterns based on temperature, the magnitude of a potentially toxic bloom can be anticipated based upon the cyst abundance in the sediment the season before the bloom. With this information, farmers can take precautions to minimize the risk of harvest poisoning.

Liana Singh: An experiment to identify the harmful levels of antibacterial triclosan to bacteria in Puget Sound

Triclosan is an antibacterial agent commonly used in household personal care

products because of its high bactericidal performance against many bacteria including ram positives and gram negatives. I propose antibacterial substances like triclosan are potentially toxic to the natural bacterial population in Puget Sound. My project aims to determine the concentrations at which this antibacterial substance become harmful to the bacterial population in Puget Sound. The research will take place on board R/V Thomas G. Thompson from 19 March 2007 to 23 March 2007. Bacterial population samples will be collected at two depths at each location using a CTD with Niskin bottles and then incubated with tritium-labeled thymidine (to measure bacterial growth) and four

different concentrations of triclosan. Growth rate will be measured in the lab by counting the radioactive thymidine incorporated into bacterial biomass. By comparing the growth rates with and without triclosan I will be able to determine at which concentration triclosan is harmful to the bacterial population in Puget Sound.

Bruce Titius: Distribution of the dinoflagellate Alexandrium catenella in sediment cores from Discovery Bay, Washington

Paralytic Shellfish Poisoning (PSP) closures have been documented from the late 1950’s to the present. Alexandrium catenella is the dinoflagellate usually associated with PSP outbreaks. Changes in environmental conditions cause A. catenella to form resting cysts that deposit on the bottom sediments. If bottom sediments accumulate quickly, the resting cyst will become trapped in the sediment thereby indicating level of cyst abundance over time. I hypothesize that the occurrence of Alexandrium catellena resting cysts will be present in bottom sediments that were deposited prior to formal documentation of PSP outbreaks. The history of these outbreaks will be a useful tool to indicate the presence

and abundance of a dinoflagellate associated with PSP. To test this hypothesis, near surface and sub-surface sediments will be collected using both a spade box core and kasten core. Sediments will be collected at one location each in Discovery Bay and Penn Cove, Washington, using the shipboard capabilities R/V Thomas G. Thompson during the week of 19-23 March 2007. Post-cruise analysis of the sediments will include; 210 Pb isotope analysis for sediment accumulation rate and sediment layer dating , grain size analysis for sediment porosity information and Alexandrium catenella cyst enumeration using an epifluoresent microscope. The objectives of this study are 1) to determine if A.

catenella cysts can be found with increased depth of the bottom sediments, 2) to

determine if A. catenella cysts are present in sediments dated prior to documented PSP outbreaks, 3) to relate A. catenella cysts occurrence with industrial anthropogenic changes and/or local climate variations. This study will provide insight into what happens to resting cysts as they become buried in the sediment, and present possible variables that may influence Alexandrium catenella cyst abundance.

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 north