Document Type


Degree Name



Oregon Health & Science University


The California Current Large Marine Ecosystem (CCLME) spans the coastal waters of Northern Washington through Baja California and is one of five Large Marine Ecosystems in the world that are subject to seasonal upwelling of cold nutrient rich water (Chavez and Messié, 2009). Upwelling promotes areas of intense localized primary productivity, which supports a vast array of fisheries vital to the Pacific Northwest economy. Recent seasonal occurrences of near-shore hypoxia off the coast of Oregon between 44oN and 45oN within the 100m depth contour, and the development of a 3,000 km2 dead zone in 2006, are indicators of ecosystem stress. The expansion of oxygen minimum zones (OMZs) in the continental shelf, (Grantham et al., 2004; Karstensen et al., 2008) and blooms fueled by upwelled nutrients are possibly the result of shifts in oceanic climate regimes due to global climate change. Increases in thermocline depth and the intensification of upwelling are predicted responses of eastern boundary current systems to climatic warming, however the role of climate and seasonal changes in the energy flow and population dynamics of microbial species within the CCLME has yet to be elucidated and are essential to identifying changes in ecosystem health (Grantham et al., 2004). The long-term goal of this research is to assess the microbial involvement in the biogeochemical cycling of carbon and nitrogen in relation to hypoxic events in coastal Oregon and Washington. The aim of this project was to identify seasonal variations in active dissolved inorganic carbon (DIC) -assimilating microbial populations in the water column off the coast of Oregon through stable isotope probing (SIP). The identification of active microbial populations promotes a greater understanding of the biogeochemical complexity and processes operating within the Pacific Northwest Coastal Margin while providing a basis for evaluating ecosystem change. xiv Hypoxic or low oxygen environments (DO < 2.0 mg/L) are generally associated with chemoautotrophic organisms that are able to thrive with little to no oxygen and utilize inorganic carbon. Stable isotope probing (SIP) with 13C-NaHCO3, a technique utilized as the foundation of this dissertation research, was used to examine the diversity of bacteria actively assimilating DIC in the Pacific Northwest coastal margin. SIP results ultimately revealed that that DIC-assimilation is ubiquitous in the Pacific Northwest marine environment, is utilized by both heterotrophic and autotrophic bacteria alike, and may represent a significant metabolic process in transient hypoxic waters. During the phylogenetic analysis of the active DIC-assimilating fractions, two observations were made. First, organisms previously found to be associated with hypoxic and low-oxygen environments all over the world (Canfield et al., 2010; Fuchs et al., 2005; Lavik et al., 2009a; Walsh et al., 2009a), gamma sulfur oxidizing (GSO) clade bacteria SUP05 and ARCTIC96BD-19, were implicated in DIC-assimilation in all SIP samples. Second, sequences for organisms involved in the nitrogen cycling pathways such as ammonia oxidation and heterotrophic denitrification were elevated in the SIP samples from areas that experience hypoxic events. The coupling of ammonia oxidation and low oxygen environments has been observed previously, particularly in the eastern tropical Pacific OMZ where ammonia oxidation was found to account for 6-33% of total NO2- production (Lam et al., 2009). While this does not imply that these organisms are absent from oxic environments it suggests that these organisms are potentially more active in these unique environments possibly due to reduced competition for ammonia. To assess the abundance and distribution of SUP05 and ARCTIC96BD-19 GSO clade bacteria, identified in SIP experiments in relation to environmental variables, we conducted qPCR analysis on 49 samples collected from the Oregon and Washington coasts between 2007 and xv 2009. QPCR results presented evidence of the widespread occurrence of both SUP05 and ARCTIC96BD-19 in near-shore environment regardless of sampling location or season. SUP05 correlated negatively with dissolved oxygen and was most abundant in hypoxic waters. ARCTIC96BD-19 was much more prominent in inner-shelf samples, and its presence was strongly correlated to the coastal upwelling index, suggesting that wind-driven upwelling events, which pull nutrient-rich OMZ waters onto the continental shelf, influence the presence of GSO bacteria in the coastal margin. The identification of organisms involved in ammonia oxidation led us to assess amoA gene transcription in the Pacific Northwest coastal margin in relation to low oxygen and the influence of freshwater from the Columbia River. Ammonia oxidation was studied by RT-qPCR amplification of amoA gene transcripts to assess the levels and distribution of Betaproteobacterial ammonia oxidizing bacteria (AOB), Thaumarchaeota Group A ammonia oxidizing archaea (AOA-A) and Thaumarchaeota Group B ammonia oxidizing archaea (AOA-B) amoA gene expression in water collected at two different depths in May and July 2010 from two sampling lines subject to varying influence of freshwater discharge from the Columbia River. Sample sites subject to the greatest Columbia River influence experienced dramatic shifts in DO and nutrient levels possibly linked to the onset of upwelling and decrease river discharge. These samples showed the greatest variability in AOA-A and AOA-B contribution to amoA transcription. Our results demonstrate the biogeochemical potential of DIC-assimilating organisms in carbon and nitrogen cycling pathways in the Pacific Northwest coastal margin, influenced by the dynamic environment of the Northeast Pacific coastal zone.




Institute of Environmental Health


School of Medicine



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.