Thesis (Ph. D.)--University of Chicago, Dept. of Ecology and Evolution, August 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Texas at Austin, 1999. / Vita. Includes bibliographical references (leaves 200-215). Available also in a digital version from Dissertation Abstracts.

Estuaries are intrinsically complex and dynamic ecosystems that display marked spatial and temporal variability. Because estuaries are situated at the receiving end of catchment activities, they are at particular risk of alterations to their natural complexity. The overarching objective of this study was to gain an overview of the abiotic conditions and biotic response of the Goukamma Estuary, a small temporarily open/closed estuary (TOCE) which is situated in a relatively undisturbed catchment in the Southern Cape. Physico-chemical properties drive estuarine ecology, and together with biological indicators, are commonly assessed to determine the present status of an estuary. During the study, physico-chemical parameters reflected great spatial and temporal variability in response to the mouth state over a 13 month period. Parameters ranged within expected limits, as proposed by the conceptual model for water quality of TOCE’s (Snow and Taljaard 2007). Of particular importance was the prominent occurrence of salinity stratification and hypoxic conditions (dissolved oxygen [DO] < 3 mg l-1) during both open and closed mouth states. Data indicated that in the wide and shallow lower reaches, weak stratification gradients were present and oxygenated conditions (DO > 6 mg l-1) were maintained throughout the water column mainly by wind and tidal action. However, stratification increased towards the deeper, channel-like middle and upper reaches of the estuary, followed by a significant reduction in bottom DO concentrations and development of hypoxia and anoxia. Bottom water hypoxia commonly occurs in microtidal estuaries due to the limited influence of mixing forces, mainly by wind and tidal action. The Goukamma Estuary is a channel-like microtidal estuary where stratification effectively limited oxygenation of the bottom water which resulted in frequent occurrence of bottom water hypoxia. During June 2010 when the highest local rainfall (75 mm) was recorded for the region, salinity and DO data showed that this amount of rainfall was insignificant as it did not replenish the water column of oxygen. Only the surface 0.5 m layer was fresh and oxygenated while below this, the water column was completely hypoxic. In an unimpacted state, the Goukamma Estuary is a blackwater system and is expected to be nutrient poor; however, farming activities in the catchment have resulted in elevated nutrient concentrations. This study showed that significantly higher nutrient concentrations were measured in the middle and upper reaches of the estuary, adjacent to cattle farms situated in the floodplain of these reaches. Nutrient concentrations represented mesotrophic (dissolved inorganic nitrogen [DIN] > 500 μg l-1) to eutrophic conditions (dissolved inorganic phosphorus [DIP] > 25 μg l-1). Nutrient input stimulated phytoplankton to attain a significantly high biomass, ranging between 0.3 – 112 μg l-1 (~ 7.7 ± 1.3 μg l-1; n = 128) and 0.8 – 289 μg l-1 (~ 21.1 ± 4.4 μg l-1; n = 80) during the open and closed states, respectively. High organic loads are associated with high oxygen demands which consequently result in hypoxia following decomposition. Exacerbated by natural salinity stratification which effectively limits oxygenation of the water column, unnaturally high nutrient concentrations and coinciding organic loads place the estuary at particular risk of degradation. This study captured key patterns and processes by quantifying salinity, oxygen and nutrient concentrations in addition to biological indicators (phytoplankton biomass and community composition). Considering possible budget constraints, it is recommended that monthly salinity and oxygen concentrations should be monitored as well as seasonal nutrient concentrations. It is also recommended that riparian buffer zones should be established in the middle and upper reaches of the estuary, as these vegetation buffers have been well documented to contribute to nutrient attenuation and improved water quality from agricultural run-off.

Links between nitrification rates and betaproteobacterial ammonia oxidising bacteria (AOB) community structure in estuarine sediments were determined in relation to changes in salinity and substrate concentrations associated with these environments.  Sediment was collected from the upper, middle and lower reaches of the estuary and incubated with water amended with either a range of salinities from marine to freshwater, or a range of ammonia concentrations.  Ammonia consumption, nitrate and nitrite production were measured at regular intervals as an indicator of nitrification rates and 16S rRNA gene-targeted analysis of betaproteobacterial AOB community structure was carried out by denaturing gradient gel electrophoresis of amplified genes from original sediment, at the beginning of nitrate production, and after a period of incubation.  Salinity and ammonia concentrations were shown to influence both nitrification rates and betaproteobacterial AOB community structure in estuarine sediments, in particular increased ammonia concentrations lead to increased nitrification regardless of the origin of the sediment.  A shift in the dominant betaproteobacterial AOB community structure was observed in microcosms with both salinity and ammonia treatments, but particular treatments did not lead to the selection of a common community structure.  Members of the <i>Nitrosomonas </i>cluster 5 were selected for in most sediments and treatments, regardless of salinity and ammonia treatments, while others, such as members of the <i>Nitrosospira</i>-lineage cluster 1 group, were restricted to low ammonia microcosms.  This study indicates that community members are capable of functioning at a wide range of estuarine salinity and ammonia conditions but that these are eventually replaced by community members better suited to these conditions.

Seagrass beds of Zostera capricorni are an integral part of the estuarine landscape along the east coast of Australia forming important habitats for juvenile fish and macroinvertebrates. Seagrass beds can vary in their spatial structural such as their size, shape and patchiness of seagrass cover. They can also be located within the estuarine landscape context such as their proximity to other habitats or their location within the estuary. The influence or correlation of these landscape or seascape spatial features of seagrass beds on the assemblages of seagrass fauna (fish and macroinvertebrates) was tested in this thesis. It was found that the spatial structure of seagrass beds (size and shape), their patchiness of the seagrass cover and location within the estuary (close or far from estuary mouth) were correlated with the assemblages of fish within seagrass beds. In particular it was demonstrated that there were greater densities of small fish species in the small compared to the large beds of Z. capricorni. This occurred regardless of the placement of the seagrass bed within the estuary context, its proximity to other habitats or patchiness of cover. Further experimentation using artificial seagrass patches demonstrated that this effect of patch size was independent of the perimeter length or perimeter to area ratio of the seagrass beds. It was hypothesised that the greater density of small fish species in small seagrass beds could be attributed to the greater proportion of edge habitats in small beds i.e. edge-mediated effects. However, the number of fish species per net haul in edges and inner regions of small and large seagrass beds were measured and found not to be different. The outcomes of this research suggest that to conserve the small fish species within an estuary, it is essential to protect even the small and patchy seagrass beds. A network of seagrass beds from all regions of the estuary is also required and the adjacent mangrove forests must be included / Doctor of Philosophy (PhD)

Thesis (Ph.D.)--Murdoch University, 2009. / Thesis submitted to the Faculty of Sustainability, Environmental and Life Sciences. Includes bibliographical references.

Thesis (M.S.)--University of North Carolina at Wilmington, 2003.

Not available / text

Aim: This series of studies assessed the influence that digenean parasites exert on a host population beyond the initial cost of infection. It aimed to address the discrepancy between the exclusion of parasites from most ecological studies, and their functional importance within the wider free-living community. It also assessed methodologies that utilise the diversity of the parasite community as well as the phenotypic effects of parasitism, as potential tools for ecology and palaeoecology. Results: From 2004-2007, in excess of 53,000 snails were dissected during the course of these studies. Making it one of the most detailed parasitological studies undertaken on a single host parasite interaction in this field. Community studies - Parasite diversity was found to be influenced by local scale abiotic, as well as large scale environmental patterns. Parasite diversity correlates with the distribution of definitive avian hosts, which in turn correlates with intertidal benthic communities. These correlations provide an effective methodology for monitoring ecosystem health. Behavioural studies - A critical assessment of parasite mediated behavioural change revealed the indirect cost of gigantism in the host population to be a side effect, and that differences in behaviours were often a result of size rather than infection. Growth/Morphometric studies - Gigantism was revealed as both infection and environment driven. Finally, morphometric analysis revealed conchiometric markers that provide tools for reconstructing past environments and infection prevalence. Main conclusions: The functional importance of digenean parasitism within the intermediate host snail Hydrobia ulvae, extends far beyond the individual. Digeneans directly and indirectly manipulate the host population, in turn affecting wider community structure. Environmental, abiotic and biotic factors can leave observable imprints on the infected and uninfected host population. Such markers can provide tools and methodologies for furthering our understanding of both extinct and extant host-parasite populations.

Diets of large marine predators have been extensively studied to assess interactions with fisheries, monitor links between diet and reproductive success, and understand trophic interactions in marine ecosystems. Since marine species can rarely be observed foraging directly, most studies rely on the identification of prey remains in stomach contents or faeces to determine the prey items being consumed. While this approach has provided a wealth of information, it has several limitations resulting primarily from difficulties identifying digested prey and from biased recovery of remains due to differential digestion. My thesis explores the use of molecular genetic methods in dietary studies of large marine predators. DNA-based identification techniques have been used in several diet studies, but the methods and applications are still in the early stages of development. Through a number of studies, I investigated the ability to recover genetic data from various dietary samples using a range of genetic techniques. A) Genetic screening for prey in the gut contents from a giant squid - I assessed the use of polymerase chain reaction (PCR)-based methods for isolation of prey DNA from an Architeuthis gut content sample. A taxonomically informative molecular marker was selected and a screening method developed using denaturing gradient gel electrophoresis. The methodology was used to identify prey from otherwise unidentifiable hard-part remains and the amorphous slurry component of the squid gut sample. The techniques developed here provided a framework for later chapters. B) Analysis of prey DNA in faeces of captive sea lions Part I: DNA detection, distribution and signal persistence - A feeding trial with captive Steller sea lions (Eumetopias jubatus) was carried out to investigate the use of genetic faecal analysis as a tool to study diet. I used group-specific PCR detection to determine: (i) the reliability of prey DNA recovery, (ii) the distribution of prey DNA within faeces and (iii) the persistence of the genetic signal after a prey item was removed from the diet. The proportions of prey DNA in several samples were also determined using a clone library approach to determine if DNA quantification could provide semi-quantitative diet composition data. Results show that the prey DNA could be reliably detected in sea lion faeces and the genetic signal could persist in samples up to 48 hours after ingestion. Proportions of prey DNA isolated from faeces were roughly proportional to the mass of the prey items consumed. Part II: DNA quantification - Quantitative real-time PCR was used to further investigate if quantitative diet composition data could be obtained through quantification of the DNA present in faeces. I quantified the relative amounts of DNA in three fish species being fed to captive sea lions, then determined the amount of DNA recovered from these prey items in the sea lions - faeces. The results indicate that diet composition estimates based on the relative amounts of DNA in faeces can be biased due to the differential survival of DNA from different fish species; however, these biases may be less than those commonly observed in the conventional analysis of prey hard remains. C) Quantification of damage in DNA recovered from faecal samples - I developed a general method to quantify the frequency of DNA damage present in specific gene regions. The technique was applied to assess the amount of DNA damage in predator and prey DNA recovered from sea lion faeces. The estimated frequency of DNA damage was always higher for the prey DNA than for the predator DNA within a faecal sample. The findings have implications for marker development and comparison of results obtained in future DNA-based diet studies. D) Studying seabird diet through genetic analysis of faeces - I investigated the diet of macaroni penguins (Eudyptes chrysolophus) through conventional analysis of stomach contents and through the analysis of prey DNA extracted from faeces. Genetic data was obtained from faecal samples using PCR tests to determine the presence or absence of DNA from potential diet items and also using a clone library approach. Approximately half of the faecal samples tested positive for one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in early stages of chick rearing and DNA from a myctophid fish was prevalent in faeces collected later; this trend mirrored the data obtained from the stomach contents. Analysis of prey sequences in 'universal'clone libraries revealed a highly biased recovery of sequences from fish prey; this bias is most likely caused by the use of degenerate primers with a higher binding affinity for fish DNA template compared to DNA from other prey groups. Results obtained from the genetic and traditional approaches are compared, and potential future applications of the genetic techniques to studying seabird diet are discussed. This series of studies has contributed significantly to our understanding of the strengths and the limitations of DNA-based diet analysis. The work identifies situations where genetic methods can be successfully applied to study the diet of marine predators and provides guidance for future studies in this emerging field.