Thesis (Ph. D.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 130-135). Also available on the World Wide Web.

Thesis (Ph. D.)--University of Washington, 1994. / Vita. Includes bibliographical references (leaves [240]-273).

Thesis (M.S.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 80-96). Also available on the World Wide Web.

Thesis (Ph. D.)--Oregon State University, 1992. / Typescript (photocopy). Includes bibliographical references (leaves 96-103). Also available online.

Thesis (M.S.)--California Polytechnic State University, 2009. / Mode of access: Internet. Title from PDF title page; viewed on June 18, 2009. Major professor: Lars Tomanek. "Presented to the faculty of California Polytechnic State University, San Luis Obispo." "In partial fulfillment of the requirements for the degree [of] Master of Science in Biological Sciences." "June 2009." Includes bibliographical references (p. 33-37). Also available on microfiche.

Thesis (Ph. D.)--Oregon State University, 2009. / Printout. Includes bibliographical references. Also available on the World Wide Web.

Food production systems need to keep pace with the rising global population. Food from aquatic environments comes from both capture fisheries and aquaculture. Industrial fishing pressure has caused a global loss of more than 90% of large predatory fishes and 80% of the world’s fish stocks are reported as fully exploited or overexploited. Global finfish, shellfish and aquatic plant aquaculture has been steadily increasing to meet the global demand for seafood. In British Columbia, aquaculture is primarily marine, with salmon and shellfish accounting for the majority of species cultured. Although shellfish aquaculture accounts for significantly less production and value compared to salmon aquaculture, the amount of foreshore dedicated to farming shellfish is nearly half (44%) the total area utilized by all aquaculture in the Province. Introduced Pacific oysters (Crassostrea gigas) (74%) dominate shellfish aquaculture in British Columbia. Pacific oysters are known to be very efficient generalist filter feeders that can grow faster and larger than native species. Extensive aquaculture is a form of aquaculture, where farmed animals feed exclusively on naturally occurring food in the surrounding water column. The goal of this research was to determine if there was a measureable depletion of phytoplankton around shellfish farms along the west coast of Canada and the United States. Chlorophyll-a, a pigment found within phytoplankton, was used as a proxy for phytoplankton abundance for this study. In field season one, two bays were studied, one exposed to shellfish culture (Westcott Bay) and one not exposed to shellfish culture (Fisherman Bay). The concentration of chlorophyll-a was measured in each bay at three locations at two depths (0.5 and 3 meters) and at two tidal heights (high and low). Chlorophyll-a concentration was found to be related to either depth or tide, with location in a bay showing no difference in either of the bays studied. In addition to water column measurements, 100 Pacific oysters were placed at two locations within Westcott Bay Seafarm to test for local differences in oyster growth. The results from this experiment showed that Pacific oysters grown in the center of a shellfish farm were smaller than oyster grown at the farm’s periphery. Field season two tested for spatial patterns between chlorophyll-a concentration and proximity to a shellfish farm in three different bays (Westcott Bay, Trevenon Bay and Gorge Harbour). A measureable depletion footprint of chlorophyll-a concentration was detected in the two sheltered shallow bays tested (Westcott Bay and Gorge Harbour), whereas no depletion footprint was detected in the exposed, deep bay (Trevenon Bay). Tide height played a significant role in predicating chlorophyll-a concentration in all three of the bays studied. These results suggested that some areas may be more suitable for shellfish culture than others. Taken together, this research demonstrated a measureable gradient of phytoplankton in sheltered shallow bays exposed to shellfish culture with depletion closest to the farm site, as well as greater oyster growth at the periphery of shellfish farms where phytoplankton would be predictably in greater abundance. / Graduate

In recent years, mortalities of unknown aetiology have occurred in Pacific oyster aquaculture in Baynes Sound, BC during the summer. Field studies were conducted to examine environmental, reproductive and microbial factors that could be contributing to these mortalities. In 2017, oysters were observed at three sites from July 5 to September 15. Each intertidal site had three modules containing seven stacked trays with 80 oysters per tray. Final mortalities ranged from 9.3 ± 1.9 to 38.8 ± 4.9% per module. The mortality per module correlated significantly with gonad length and the proportion of oysters that were female in a multiple linear regression model (R2=0.824, p=0.002). Vibrio aestuarianus, a well-documented pathogen of farmed Pacific oysters in France, was well represented in bacterial cultures from intertidal oysters in 2017 based on recA gene sequencing of 158 bacterial isolates. In 2018, juvenile Pacific oysters were monitored to characterize the onset of a summer mortality event in suspended culture. From May 11 to September 17, data on shell size, reproductive development, environmental conditions, and the microbial community of gill tissue was tracked at culture densities of 150, 300, 450, and 600 oysters tray-1. The onset of mortality was associated with a period of rapid growth, reproductive development, and elevated temperatures. Cumulative mortality per tray ranged from 34 to 75%, with the highest density trays having significantly lower mortality (p=0.023), smaller shell width (p=0.001), smaller shell length (p=0.002) and smaller gonad length (p=0.049) than the lowest density trays in a linear mixed-effects regression. Histology of oysters from August 12, during the mortality event, showed a mixed microbial infection in peripheral gill tissue. High-throughput sequencing of the 16S rRNA gene and qPCR of V. aestuarianus using species-specific recA primers suggest V. aestuarianus is temporally associated with summer mortality. Mortalities observed in 2017 and 2018 occurred in different age classes and with different oyster culture techniques, but all were associated with elevated water temperature, increased reproductive effort, and the presence of V. aestuarianus. / Graduate / 2021-08-06

Vibrio parahaemolyticus is a Gram-negative, halophilic, human pathogenic bacterium ubiquitous in the marine environment. Like many Vibrio species, V. parahaemolyticus commonly associates with shellfish, particularly oysters. Ingestion of a raw or under cooked oysters contaminated with V. parahaemolyticus can cause gastroenteritis, which is typically self-limiting and rarely causes death. Globally, oyster production is highly lucrative, especially on the West Coast of the United States where approximately 60% of oyster production occurs each year. Outbreaks of V. parahaemolyticus can result in a significant public health problem as well as an economic burden for the oyster farms implicated in the outbreak. With the increase in overall V. parahaemolyticus outbreaks, improved post-harvest processing strategies have been developed to reduce this natural contaminant. Depuration was developed to allow shellfish to purge contaminants from their tissues into the clean, flowing seawater where they are held. This post-harvest processing technique can typically reduce fecal contaminants from the oyster tissues but is relatively ineffective at eliminating V. parahaemolyticus and other Vibrio species.. Thus, improved methods for reducing this and other human pathogenic Vibrio are needed to effectively produce safer oysters for the consumer. To develop more effective and novel V. parahaemolyticus intervention strategies, first we must identify the factors that are involved in V. parahaemolyticus colonization of the oyster, allowing them toresist depuration. This study sought to investigate specific factors utilized by V. parahaemolyticus and, in the process, determined that various strains of V. parahaemolyticus have different alleles of the Type IV pili, mannose-sensitive hemagglutinin (MSHA)and chitin-regulated pilus (PilA). In addition, we expanded our investigations into the allelic diversity of MSHA and PilA from Vibrio cholerae and Vibrio vulnificus and found that V. cholerae strains that possess the Type IV toxin co-regulated pilus (TCP) maintained highly conserved MSHA and PilA sequences while strains of V. cholerae without TCP, and all of the V. vulnificus and V. parahaemolyticus strains examined, had highly divergent sequences with no discernable connection to isolation source or observed phenotype. Following that discovery, we determined that Type I, and Type IV pili, as well as polar and lateral flagellar systems contribute to V. parahaemolyticus persistence in the Pacific oyster during depuration, while Type III secretion systems and phase variation do not. Overall, we have identified factors involved in colonization of the Pacific oyster by V. parahaemolyticus. Future studies investigating conditions that affect pili and flagella production in V. parahaemolyticus may provide novel depuration conditions that could easily and effectively increase the efficiency of oyster depuration, ultimately reducing the risk of seafood-borne illness by V. parahaemolyticus associated with oysters. / Graduation date: 2013

Vibrio parahaemolyticus is a Gram-negative, halophilic pathogen that occurs naturally in coastal and estuarine environments. This human pathogen is frequently isolated from a variety of seafood, particular oysters, and is the leading cause of gastroenteritis associated with seafood consumption. Several outbreaks of V. parahaemolyticus infections linked to consumption of raw oysters have been documented. Contamination of oysters with V. parahaemolyticus is a concern for public health. This study investigated the efficacy of high pressure processing (HPP) in inactivating V. parahaemolyticus in raw Pacific oysters (Crassostrea gigas) and identified a process condition capable of achieving greater than 3.52-log reductions of V. parahaemolyticus in raw oysters for commercial application. Raw Pacific oysters were inoculated with a clinical strain of V. parahaemolyticus 10293 (O1:K56) to levels of 10⁴⁻⁵ cells per gram and processed at 293 MPa (43K PSI) for 90, 120, 150, 180 and 210 s. Populations of V. parahaemolyticus in oysters after processes were analyzed with the 5-tube most probable number (MPN) method. A minimum HPP of 293 MPa for 120 s at groundwater temperature (8±1 °C) was identified capable of achieving greater than 3.52-log reductions of V. parahaemolyticus in Pacific oysters. The HPP (293 MPa for 120 s at 8±1 °C) was validated at a commercial scale according to the FDA's National Shellfish Sanitation Program Post Harvest Processing (PHP) Validation/Verification Interim Guidance for Vibrio vulnificus and Vibrio parahaemolyticus. Negative results obtained by the MPN method were confirmed with a multiplex PCR detecting genes encoding thermolabile hemolysin (tl), thermostable direct hemolysin (tdh) and TDH-related hemolysin (trh). Oysters processed at 293 MPa for 120 sec had a shelf life of 6-8 days when stored at 5 °C or 16-18 days when stored in ice. This validated HPP was accepted by the FDA as a post harvest process to eliminate V. parahaemolyticus in raw oysters. / Graduation date: 2012