Thesis (M.S.) OGI School of Science & Engineering at OHSU, June 2007. / Includes bibliographical references (leaves 136-140).

Most Australian studies on estuarine plankton have examined distribution and abundance in relation to hydrological changes, primary productivity and associated nutrient dynamics. Relatively few have examined the complex interactions between zooplankton grazers and the type and quality of food available, or the role of zooplankton grazers in structuring phytoplankton communities, or their contribution to the nutrient pool. The ecological role of zooplankton grazers in the Swan River estuary, Perth, Western Australia, was examined as part of a collaborative research project directed by the Western Australian Estuarine Research Foundation, which was established in response to concern about increasing intensity and persistence of algal blooms. The present study focussed on one component of the zooplankton, the Copepoda, as model zooplankton grazers. A regular zooplankton monitoring programme, undertaken over a two year period, provided data on seasonal patterns of abundance and distribution of zooplankton over a broad spectrum of physical conditions. Relationships were identified between habitat variables, such as algal biomass, dissolved oxygen, salinity and suspended solids and zooplankton distribution, relative abundance and species composition. Prior to the inception of this study, it was assumed that copepod species composition, abundance and richness in the Swan River estuary may have changed over time, in response to long-term declines in water quality. Comparison of historical copepod monitoring data with current data did not detect any such change and it was concluded that there was greater variation in copepod species composition, abundance and richness within years than between years and that no significant change had occurred between 1966 and 1997. / However, an absence or reduction in abundance of copepods in areas of very high algal biomass (>80 pg chlorophyll a.L-1) suggests that local loss of water quality may have an impact on copepods over a small spatial scale within the estuary. Different aspects of the interactions between zooplankton grazers and phytoplankton were studied. Zooplankton grazing rates were measured in situ during algal blooms and in the laboratory under controlled conditions to determine the potential for zooplankton grazers to reduce algal biomass. Field and laboratory experiments supported the hypothesis that copepods and other zooplankton can exert 'top-down control' over phytoplankton biomass, but that the type and biomass of phytoplankton present affected their ability to exert this control. The results of the field and laboratory grazing experiments, along with literature data, were used to provide input data for a model of zooplankton and phytoplankton dynamics during a dinoflagellate bloom in the Swan River estuary. The model was tested against biomass measurements of zooplankton and phytoplankton to determine how well it predicted actual changes in the plankton community. The simulated output closely followed the measured Page x field data and fitted regression curves and provided information about diurnal patterns of phytoplankton production, respiration and migration and hydrodynamic transport, which was not available from field data. It was shown that zooplankton grazing, particularly grazing by microzooplankton, was the process contributing most to the observed decline in dinoflagellate biomass. Nutrient availability is one of several factors determining productivity of phytoplankton. Nutrients within copepod faecal pellets are relocated by faecal deposition to sediments, where microbial activity leads to the remineralisation of these nutrients. / Quantification of metabolic excretion of nutrients by copepods and the rate at which pellets are produced by copepod grazers, the concentration of nutrients within faecal pellets and the rate at which these nutrients are released indicated that copepods may play an important role in nutrient regeneration during summer and autumn when allochthonous nutrients are unavailable. At other times of the year, it is unlikely that copepods play an important role in nutrient regeneration. The research has provided a more detailed level of understanding of the interactions between zooplankton, phytoplankton and their environment. The data is ideally suited for use in a computer model to predict the effects of management actions on the Swan River estuary. This would allow pre-emptive management strategies to be developed and lessen the focus on reactive management.

Characterized by high levels of terrestrial organic carbon inputs, estuaries and coastal marshes are among the most productive ecosystems on earth and significantly impact the global carbon cycle. Unfortunately, rates of natural organic matter (NOM) degradation in these environments are difficult to quantify directly due to the complex interaction between microbial respiration processes and abiotic reactions in these sediments, yet estuaries and marshes are considered both net sources and sinks of carbon. Typically carbon remineralization rates are determined by measuring total (TOU) and diffusive (DOU) oxygen uptake fluxes assuming oxygen is the ultimate oxidant. This assumption, however, requires any reduced metabolites produced during microbial respiration to be reoxidized by oxygen. In this study, voltammetric sensors were used to measure terminal electron acceptors or their reduced by-products. By simultaneously considering oxygen as well as anaerobic respiration accepting processes, this study demonstrates that oxygen does not function as the ultimate oxidant in coastal marine sediments due to precipitation and burial of reduced species. Furthermore, the biogeochemistry of coastal sediments is typically investigated ex situ after collection of sediment cores. However, coastal sediments are subject to complex subsurface hydrological forcing that cannot be accounted for with ex situ measurements. Consequently, in situ approaches are required to better understand the impact of physical processes on sediment biogeochemistry, and two novel in situ voltammetric systems were developed as part of this research. First, a new autonomous benthic lander equipped with a benthic chamber to measure TOU fluxes with a high temporal resolution and a potentiostat and micromanipulator to simultaneously acquire voltammetric depth profiles of the main redox species in pore waters was deployed in a pristine river-fed estuary to characterize the seasonal variability of coastal sediment biogeochemistry and examine the impact of riverine discharge on carbon remineralization processes. Simultaneously, a new electrochemical analyzer equipped with a solar and wind power charging system to ensure continuous monitoring capability and a VHF radio to transmit data was operated remotely via the internet from the Georgia Tech campus to investigate the dynamic coupling between hydrological, chemical, and biological processes in intertidal marsh sediments. Finally, new microelectrodes were deployed in microbial mats to examine the chemical and biological oxidation of sulfide with submillimeter resolution. Typically, only biological processes are considered to oxidize sulfide in these environments. Depth profiles during diel studies were able to demonstrate the formation of thiosulfate as an intermediate oxidation product of sulfide oxidation, suggesting that the chemical oxidation of sulfide is much more prevalent than previously recognized when compared to biological oxidation. Overall, using a novel in situ sampling technique with high temporal resolution, these studies confirm that biogeochemical processes in coastal sediments vary seasonally. More importantly, these studies also reveal that estuarine sediments are significantly influenced by riverine discharge, demonstrate that the biogeochemical response of these sediments to natural perturbations is rapid, and indicate that respiration processes in continental shelf sediments are controlled by a combination of temperature, supply of inorganic and organic substrates, and hydrological processes, which has important implications regarding the effect of climate change on the biogeochemical cycling of carbon in these environments.

Coastal transition zones form important interlinking regions where marine ecosystems, rivers and estuarine environments significantly influence each other. Coastal rocky shores are key habitats that sustain a variety of primary producers and invertebrates and due to the dynamic nature of coastal ecosystems, suspension-feeders on rocky shores can be influenced by an array of autochthonous and allochthonous food sources. Fatty acid and stable isotope trophic markers were employed to distinguish between regional and temporal changes in the potential food sources to rocky shore suspension-feeders in the Eastern Cape Province of South Africa. The primary aim was to assess the spatial and temporal influences of contrasting river flows on the available food sources to three indigenous coastal suspensionfeeders, namely the volcano barnacle Tetraclita serrata, brown mussel Perna perna and tubebuilding polychaete Gunnarea capensis. This was done by examining the intra- and interspecific changes in the fatty acid and stable isotope signatures of the barnacles, mussels and polychaetes in the adjacent marine environment of a freshwater-restricted (Kariega) and freshwater-dominated (Great Fish) estuary during austral summer and winter. Multivariate and Kruskal-Wallis analyses of variance on the fatty acid and isotopic signatures, respectively, identified significant regional changes in the barnacles and mussels, while only stable isotopes distinguished between the Kariega and Great Fish polychaetes (P < 0.05). In addition, significant temporal changes were observed in consumer fatty acids and isotope values in both regions (P < 0.05). Bacterial sources, detritus and phytoplankton assemblages, which are influenced by hydrology and vegetation, differed between regions and were mainly responsible for the regional and temporal separations. Principal component analyses on the consumer fatty acid signatures distinguished between animals situated upstream (i.e. north) and downstream (i.e. south) of the Kariega Estuary mouth in summer. The north/south separation was mainly due to greater contributions of diatoms to northernlocated animals and dinoflagellates and detritus to southern-located consumers. In addition, the south-flowing Agulhas Current on the eastern shores of southern Africa appeared to influence the north/south separation in the Kariega region, as water leaving the estuary was probably entrained into the south-easterly flowing currents, thereby depositing estuarinederived detritus to southern populations. In general, diatoms and detritus were essential food sources to the filter-feeders in summer, and flagellates, diatoms, zooplankton and detritus were important in winter. Coastal macroalgae was a key food source in the Kariega and Great Fish regions during both seasons. Consistently large levels of diatom markers (16:1n-7 and 20:5n-3) and dinoflagellate markers (22:6n-3) in consumer tissues in the Kariega and Great Fish regions identified that phytoplankton was their dominant food source. The barnacles, mussels and polychaetes had similar fatty acid markers and a fairly narrow δ¹³C range (-16.5 to -14.4 ‰), suggesting that they probably consumed similar food. Carbon isotope analyses, however, separated the suspension-feeders into slightly depleted (barnacles; -16.5 to -16.1 ‰), intermediate (mussels; -15.8 to -15.0 ‰) and enriched (polychaetes; -15.0 to -14.4 ‰) consumers, but did not provide conclusive evidence of their preferences for specific phytoplankton. Conversely, fatty acid analyses highlighted that barnacles and mussels had greater proportions of dinoflagellate markers (22:6n-3; 7.0-15.3 % TFA), while polychaetes had larger diatom levels (20:5n-3; 15.1-22.2 % TFA). In addition, all three species had consistently large contributions from bacterial fatty acids (15:0, i-16:0, 17:0 and i-18:0; 4.2-13.6 % TFA) in summer and winter, and large proportions of saturated fatty acids (33.3-53.1 % TFA) including those with 14 to 18 carbons, indicating that bacterial and detritus food sources played an important role in their diets. Barnacles had small levels of terrestrial markers (18:2n-6 and 18:3n-3; <2.5 % TFA) and demonstrated increased omnivorous feeding compared with the other suspension-feeders [increased levels of 20:1n-11 and 20:1n-9, higher 18:1n-9/18:1n-7 ratios at ~2.1, enriched δ¹⁵N values at ~10.6 ‰; zooplankton (potentially including microzooplankton, larvae and protists) contribution of up to 61 % of the diet]. Mussels contained significant proportions of the terrestrial markers (18:2n-6 and 18:3n-3; >2.5 % TFA) and exhibited intermediate omnivory (intermediate levels of 20:1n-11 and 20:1n-9, intermediate 18:1n-9/18:1n-7 ratios at ~1.3, less enriched δ¹⁵N values at ~7.9 ‰; zooplankton contribution of 10-15 % of the diet). The more depleted nitrogen signatures in the mussels relative to the barnacles and polychaetes possibly illustrated a stronger preference for autotrophic food. Polychaetes mainly consumed plant food sources (i.e. microalgae, macroalgae and detritus; high levels of i-18:0, 18:1n-9, 18:4n-3 and 20:5n-3) and displayed little omnivory (low levels of 20:1n-11 and 20:1n-9, low 18:1n-9/18:1n-7 ratios at ~0.4, intermediate δ¹⁵N values at ~9.1 ‰; zooplankton contribution of <10 % of the diet). The barnacles, mussels and polychaetes are all suspension-feeders, originally presumed to consume the same food sources. The variations observed among the species, therefore, may result from differences in the proportional contributions of the various food sources to their diets as well as distinctions in metabolism. The distinct changes in the fatty acid and stable isotope signatures in all three filter-feeders in the Kariega and Great Fish regions are likely influenced by the diversity in regional vegetation and hydrology in the different systems, combined with interspecific differences in resource partitioning among the species.

The aims of this study were to determine the potential use of biomarkers at multiple levels of biological organisation together with a fish community bioindicator to assess the estuarine health status of three temporarily open/closed estuaries. The estuaries investigated were the East Kleinemonde (EK), Old Woman's (OW) and Mtana (MTN), all of which are situated in the Eastern Cape Province. Three biomarkers, the acetylcholinesterase (AChE) assay, lipid peroxidation (LPx) assay, liver histopathology and a condition factor were used to determine sub-organism health and one bioindicator, the Estuarine Fish Community Index (EFCI), was used as a bioindicator of community health. The estuarine-dependent marine species Rhabdosargus holubi was selected as an indicator species for the sub-organism level analyses. The results from the community analyses indicated that the EK and OW estuaries were in 'good' condition, while the MTN was found to be in 'moderate' condition. Histological analyses revealed that R. holubi from all three estuaries showed signs of pathological changes to the liver, with the fish from the MTN eliciting the highest occurrence of these changes. The LPx assay found that R. holubi from both the OW and MTN showed signs of oxidative damage in the liver tissue, but those from the EK did not appear to be affected. The AChE assay showed that only the fish from the OW had been affected by anticholinesterase compounds. A laboratory study was undertaken using R. holubi as a positive control for the AChE and LPx assay. The fish were exposed to 3 μg/L chlorpyrifos, a known cholinesterase inhibitor, for six hours and their tissues were examined for changes to LPx levels and AChE activities. AChE activity was significantly inhibited (Mann Whitney U test, Z = 3.65, n = 38, P < 0.001) by the exposure, but LPx levels were not significantly affected. A composite index incorporating the biomarkers at different biological levels of organisation was developed. The index was designed to assist managers and scientists to determine whether the ichthyofauna of a system was being affected by environmental stressors and what management interventions could be undertaken to ameliorate the water quality in an estuary. The index was applied to the three estuaries investigated during the present study and both the OW and MTN were assessed to be in need of immediate management intervention. The fish in the OW were found to be stressed at all the sub-organism levels measured and the reason for this was hypothesised to be as a result of golf course activities in this adjacent estuary. A number of management actions are proposed to reduce the sub-organism stress observed in the fish from the OW. The livers of fish from the MTN were shown to be under stress; however the causative agent of this stress was unknown because there is no formal development in the MTN catchment. However, a possible contaminant source is proposed and management interventions to alleviate the stress on the biota of the MTN are suggested. The EK does not require immediate management intervention, however, continuous routine monitoring is recommended to ensure that conditions do not deteriorate. Shortcomings of the index were outlined and a number of suggestions were made in terms of other measures of biological health which could be incorporated into the index.

Sharks are considered top predators in many marine ecosystems, and can play an important role in structuring those communities. As a result, it is necessary to understand the factors that influence their abundance and distribution. This is particularly important as fishery managers develop fishery management plans for sharks that identify areas that serve as essential fish habitat (EFH). This includes nursery habitat where sharks are born and juveniles spend the early part of their life. However, our understanding of shark habitat use in the northeast Florida waters is limited. The goal of this thesis was to characterize the abundance and distribution of sharks in northeast Florida estuaries, and to examine the effect of abiotic and biotic factors affecting shark habitat use. A bottom longline survey conducted from 2009 – 2011 indicated that 11 shark species use the estuarine waters of northeast Florida during summer months. Atlantic sharpnose (Rhizoprionodon terraenovae), blacktip (Carcharhinus limbatus), bonnethead (Sphyrna tiburo), and sandbar sharks (Carcharhinus plumbeus) were the most abundant species and made up 87.1% of the total catch. Month, bottom water temperature, and depth were the most important factors determining the presence and abundance of these species. This study also examined the role of prey abundance in determining the abundance of Atlantic sharpnose sharks. The probability of catching an Atlantic sharpnose shark, and the abundance of Atlantic sharpnose sharks, were most influenced by site. Neither potential prey abundance nor preferred prey abundance were not significant factors effecting Atlantic sharpnose abundance. This may be a result of prey sampling not providing an accurate measure of the true availability of prey resources. Other factors, such as predation risk, may better explain habitat use patterns of Atlantic sharpnose sharks. Continued sampling will give a better understanding of the factors influencing shark habitat use in this area.