The high productivity of Eastern Boundary Upwelling Ecosystems (EBUE), some of the most productive ecosystems in the globe, is attributed to the nutrient rich waters brought up through upwelling. Climate change scenarios for coastal upwelling systems, predict an intensification of coastal upwelling winds. Associated with intensification in upwelling are biogeochemical changes such as ocean hypoxia and ocean acidification. In recent years, the California Current System (CCS) has experienced the occurrence of nearshore hypoxia and the novel rise of anoxia. This has been attributed to changes in the intensity of upwelling wind stress. The effects of some of the more severe hypoxia and anoxia events in the CCS have been mass mortality of fish and benthic invertebrates. However, the impacts on zooplankton in this system are not known. Meroplankton, those organisms which have a planktonic stage for only part of their life cycle, are an important component of zooplankton communities. The larval stage of benthic invertebrates forms an important link between benthic adult communities and planktonic communities. Larvae serve to disperse individuals to new locations and to link populations. They are also food for fish and planktonic invertebrates. This important life stage can spend long periods in the plankton (from days to months) where environmental conditions can affect larval health, subsequent settlement and recruitment success, and juvenile health. This research assesses the role of hypoxia and larval survivorship, and the relationship between individual abundance and community structure of larvae to environmental factors in the field. In laboratory experiments (Chapter 2), a suite of 10 rocky intertidal invertebrate species from four phyla were exposed to low oxygen conditions representative of the nearshore environment of the Oregon coast. Results revealed a wide range in tolerances from species with little tolerance (e.g. the shore crab Hemigrapsus oregonensis) to species with high tolerance (e.g. the California mussel Mytilus californianus). The differential responses across larvae to chronic hypoxia and anoxia potentially could affect their recruitment success and consequently, the structure and species composition of intertidal communities. Field studies (Chapter 3 & 4) explore the relationship between environmental variables and larval abundance and community structure. Chapter 3 focuses on broad taxonomic groups, while Chapter 4 focuses on larval decapods in particular. Fine focus was devoted to decapod larvae, due to laboratory findings of heightened sensitivity to hypoxia of decapod crabs. A finding that is also supported in the literature. The goal of field studies was to identify the environmental parameters that structure meroplankton and larval decapod communities and identify which of these parameters play a significant role in influencing larval abundance. A number of environmental variables contributed to meroplankton assemblage structure and larval decapod assemblage structure. These included distance from shore, depth, date, upwelling intensity, dissolved oxygen, and cumulative wind stress. Some of these factors occurred frequently in larval abundance models. In Chapter 3, individual abundance across broad taxonomic groups was most commonly explained by upwelling intensity while in Chapter 4, individual abundance of different decapod species was explained by cumulative wind stress, which is a proxy for upwelling intensity. The prominent role of upwelling related factors in explaining individual abundance is important considering climate change projections of an increased intensification of upwelling winds in EBUE. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Jan. 6, 2012 - Jan. 6, 2013

Continental shelves located along eastern boundary currents occupy relatively small volumes of the world’s oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of hypoxia and anoxia, events that are detrimental to larger macro-faunal species. Microbial communities, however, are metabolically diverse, capable of utilizing alternative electron donors and acceptors, and can withstand transient periods of low dissolved oxygen. Understanding the phylogenetic and metabolic diversity of microorganisms in these environments is important for assessing the impact hypoxic events have on local and global biogeochemistry. Several molecular ecology tools were used to answer questions about the distribution patterns and activities of microorganisms residing along the coast of Oregon in this dissertation. Ribosomal rRNA fingerprinting and sequence analyses of samples collected during 2007-2008 suggested that bacterial community structure was not substantially influenced by changes in dissolved oxygen. However, substantial depth dependent changes were observed, with samples collected in the bottom boundary layer (BBL) displaying significant differences from those collected in the surface layer. Phylogenetic analyses of bacterial rRNA genes revealed novel phylotypes associated with this area of the water column, including groups with close evolutionary relationships to putative or characterized sulfur oxidizing bacteria (SOB). Analysis of metagenomes and metatranscriptomes collected during 2009 suggested increasing abundances of chemolithoautrophic organisms and their activities in the BBL. Thaumarchaea displayed significant depth dependent increases during the summer, and were detected at maximal frequencies during periods of hypoxia, suggesting that nitrification maybe influenced by local changes in dissolved oxygen. Metagenomic analysis of samples collected from 2010 revealed substantial variability in the metabolic potential of the microbial communities from different water masses. Samples collected during the spring, prior to upwelling clustered independently of those collected during the summer, during a period of upwelling, and did not display any clear stratification. Samples collected during the summer did cluster based on depth, consistent with previous observations, and increases in the relative abundances of chemolithotrophic gene suites were observed in the BBL during stratified conditions, suggesting that the metabolic potential for these processes is a repeatable feature along the Oregon coast. Overall, these observations suggest that depth impacts microbial community diversity, metabolic potential, and transcriptional activity in shallow areas of the Northeast Pacific Ocean. The increase in lithotrophic genes and transcripts in the BBL suggests that this microbial community includes many organisms that are able to use inorganic electron donors for respiration. We speculate that the dissolved organic material in the BBL is semi-labile and not available for immediate oxidation, favoring the growth for microorganisms that are able to use alternative electron donors. / Graduation date: 2012