published_or_final_version / Environmental Management / Master / Master of Science in Environmental Management

The Avon-Heathcote Estuary is of significant value to Christchurch due to its high productivity, biotic diversity, proximity to the city, and its cultural, recreational and aesthetic qualities. Nonetheless, it has been subjected to decades of degradation from sewage wastewater discharges and encroaching urban development. The result was a eutrophied estuary, high in nitrogen, affected by large blooms of nuisance macroalgae and covered by degraded sediments. In March 2010, treated wastewater was diverted from the estuary to a site 3 km offshore. This quickly reduced water nitrogen by 90% within the estuary and, within months, there was reduced production of macroalgae. However, a series of earthquakes beginning in September 2010 brought massive changes: tilting of the estuary, changes in channels and water flow, and a huge influx of liquefied sediments that covered up to 65% of the estuary floor. Water nitrogen increased due to damage to sewage infrastructure and the diversion pipeline being turned off. Together, these drastically altered the estuarine ecosystem. My study involves three laboratory and five in situ experiments that investigate the base of the food chain and responses of benthic microalgae to earthquake-driven sediment and nutrient changes. It was predicted that the new sediments would be coarser and less contaminated with organic matter and nutrients than the old sediments, would have decreased microalgal biomass, and would prevent invertebrate grazing and bioturbation activities. It was believed that microalgal biomass would become similar across new and old sediments types as the unstable new sediments were resuspended and distributed over the old sediments. Contact cores of the sediment were taken at three sites, across a eutrophication gradient, monthly from September 2011 to March 2012. Extracted chlorophyll a pigments showed that microalgal biomass was generally lower on new liquefied sediments compared to old sediments, although there was considerable site to site variation, with the highly eutrophic sites being the most affected by the emergence of the new sediments. Grazer experiments showed that invertebrates had both positive and negative site-specific effects on microalgal biomass depending on their identity. At one site, new sediments facilitated grazing by Amphibola crenata, whereas at another site, new sediments did not alter the direct and indirect effects of invertebrates (Nicon aestuariensis, Macropthalmus hirtipes, and A. crenata) on microalgae. From nutrient addition experiments it was clear that benthic microalgae were able to use nutrients from within both old and new sediments equally. This implied that microalgae were reducing legacy nutrients in both sediments, and that they are an important buffer against eutrophication. Therefore, in tandem with the wastewater diversion, they could underpin much of the recovery of the estuary. Overall, the new sediments were less favourable for benthic microalgal growth and recolonisation, but were less contaminated than old sediments at highly eutrophic sites. Because the new sediments were less contaminated than the old sediments, they could help return the estuary to a noneutrophic state. However, if the new sediments, which are less favourable for microalgal growth, disperse over the old sediments at highly eutrophic sites, they could become contaminated and interfere with estuarine recovery. Therefore, recovery of microalgal communities and the estuary was expected to be generally long, but variable and site-specific, with the least eutrophic sites recovering quickly, and the most eutrophic sites taking years to return to a pre-earthquake and non-eutrophied state. changes in channels and water flow, and a huge influx of liquefied sediments that covered up to 65% of the estuary floor. Water nitrogen increased due to damage to sewage infrastructure and the diversion pipeline being turned off. Together, these drastically altered the estuarine ecosystem. My study involves three laboratory and five in situ experiments that investigate the base of the food chain and responses of benthic microalgae to earthquake-driven sedimen tand nutrient changes. It was predicted that the new sediments would be coarser and less contaminated with organic matter and nutrients than the old sediments, would have decreased microalgal biomass, and would prevent invertebrate grazing and bioturbation activities. It was believed that microalgal biomass would become similar across new and old sediments types as the unstable new sediments were resuspended and distributed over the old sediments. Contact cores of the sediment were taken at three sites, across a eutrophication gradient, monthly from September 2011 to March 2012. Extracted chlorophyll a pigments showed that microalgal biomass was generally lower on new liquefied sediments compared to old sediments, although there was considerable site to site variation, with the highly eutrophic sites being the most affected by the emergence of the new sediments. Grazer experiments showed that invertebrates had both positive and negative site-specific effects on microalgal biomass depending on their identity. At one site, new sediments facilitated grazing by Amphibola crenata, whereas at another site, new sediments did not alter the direct and indirect effects of invertebrates (Nicon aestuariensis, Macropthalmus hirtipes, and A. crenata) on microalgae. From nutrient addition experiments it was clear that benthic microalgae were able to use nutrients from within both old and new sediments equally. This implied that microalgae were reducing legacy nutrients in both sediments, and that they are

The sea anemone Bartholomea annulata, is an ecologically important member of Caribbean coral reefs. This anemone serves as symbiotic host to crustacean associates, some of which may control parasite loads by "cleaning" reef fishes. Associates may gain protection from predation by dwelling with anemones. B. annulata was the most abundant anemone documented on three reefs, with 52% host to crustacean symbionts. Of those occupied by multi-species groups, 92% included Alpheus armatus shrimp. A. armatus is an important anemone associate providing protection to the anemone from predators such as Hermodice carunculata, in laboratory and field trials. H. carunculata can completely devour or severely damage prey anemones. Here I show that anemones hosting symbiotic alpheid shrimp are extremely less likely to sustain damage by predators than solitary anemones. The role of protector may be reciprocally provided by anemone and decapod associates. / by Amber McCammon. / Thesis (M.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

Hypoxia and sulfide exposure, increased using glucose, are considered major environmental stressors in seagrass communities. Quantum efficiency, total soluble protein and catalase activity were quantified to evaluate the applicability of each of these bioindicators to detect environmental stress in three tropical seagrass species, Thalassia testudinum (Banks ex Kèoenig), Halodule wrightii (Ascherson) and Syringodium filiforme (Kuetz). Hypoxia + sulfide treatments significantly decreased the quantum efficiency of all three species, but showed no response in protein and catalase activity. Although no treatment effect was found, catalase activity was enhanced in T. testudinum leaves and H. wrightii roots relative to other tissues, while S. filiforme showed no location-specific catalase activity. These results indicate that quantum efficiency is a more sensitive indicator than protein and catalase activity to hypoxia and sulfide stress in seagrasses. / by Connor Irwin. / Title on signature page (p. ii) : Environmental stress biomonitoring in sub-tropical seagrasses. / Thesis (M.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

In natural systems, it has been observed that plankton exist in patches rather than in an even distribution across a body of water. However, the mechanisms behind this patchiness are not fully understood. Several previous modeling studies have examined the effects of abiotic and biotic factors on patch structure. Yet these models ignore a key point: zooplankton often undergo diel vertical migration. I have formulated a model that incorporates vertical movement into the Rosezweig-MacArthur (R-M) predator-prey model. The R-M model is stable only at a carrying capacity below a critical value. I found that adding vertical movement stabilizes the system even at a high carrying capacity. By analyzing temporal stability and spatial structure, my results show that vertical movement interacts with carrying capacity to determine patch structure. / by Simantha Ather. / Thesis (M.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

A primary goal of marine ecology is to understand the physical and biological mechanisms that drive patterns of larval dispersal and population connectivity. The larvae of many marine organisms develop in the pelagic environment before settling on benthic habitat. Early efforts to predict dispersal patterns assumed that larvae are passive particles dispersed by currents for 10s to 100s of kilometers (km). However, recent studies using parentage analyses to observe dispersal patterns reveal that peak dispersal occurs within 1 – 2 km, and declines exponentially with increasing distance from the natal reef. This gap between predicted and observed dispersal patterns suggests that other factors, such as larval behavior, may play an important role in shaping patterns of dispersal. However, due to challenges associated with obtaining larvae early in development, there is little information on the ontogeny of behavior from hatching through settlement. In this dissertation, I begin to address these challenges by developing a protocol for rearing the larvae of two species of sponge-dwelling neon gobies, Elacatinus lori and E. colini. Using lab-reared specimens, I provide the first description of larval development for both species. Then, I investigate the ontogeny of swimming ability in larvae of E. lori, E. colini and the model species Amphiprion percula. Remarkably, A. percula were capable of swimming twice as fast and three orders of magnitude longer than E. lori near settlement. Relating swimming speed to published dispersal patterns for E. lori, A. percula and another species Plectropomus leopardus, I show there is a positive association between swimming speed and the median and maximum dispersal distance. This finding suggests that swimming abilities may influence the extent of long distance dispersal. Finally, I investigate the role of habitat preferences and post-settlement persistence in establishing the distribution of E. lori settlers on sponge habitat. I demonstrate that E. lori settlers are more abundant, persist longer, and prefer to settle on large Aplysina fistularis, suggesting that settling E. lori choose sponge habitats that confer the highest relative fitness. This dissertation indicates the importance of larval and settler behaviors in determining the dispersal patterns and distribution of fishes on coral reefs.

The resilience of coral reefs depends, among others, upon local physical and biological characteristics. This dissertation focused on how herbivory, structural complexity, and sedimentation can impact the structure, function, and, ultimately, resilience of Caribbean coral reefs. We filled an important knowledge gap related to trophic niche and ecological roles of surgeonfishes (A. coeruleus and A. tractus), two of the most important herbivorous fishes in the Caribbean. We showed that both species feed primarily on turf algae preventing further progression of algal succession while A. tractus may also help reduce macroalgal abundance by targeting common macroalgal species such as Dictyota spp. We used a factorial experiment to analyze the interactive effects of herbivory (exclosure vs. open plots) and reef structural complexity (vertical vs. horizontal substrate orientation), on the development of benthic communities. We found that vertical substrates were quickly dominated by crustose algae regardless of herbivory treatment while succession of horizontal substrates was determined by herbivory. Our results suggest that at small scale, reef complexity is a major factor determining algal community structure. We investigated why, despite high levels of herbivory, coral cover in South Florida has failed to recover. We surveyed benthic composition, grazing and abiotic characteristics along six spur and groove reefs in the Florida Keys. Using boosted regression tree analyses, we found that sediment abundance was the best predictor of both juvenile and adult corals, which could explain the failure of coral recovery. We studied spatial and temporal changes of reef communities of reefs in Havana, Cuba where global and local stressors have affected coral communities while overfishing and nutrient enrichment has led to low herbivory levels. Our surveys revealed a region-wide high abundance of algae (~60%) as a consequence of heavy overfishing with likely negative consequences on coral recovery. In summary, my dissertation showed context-depend effects of herbivory, structural complexity, and sediment on Caribbean coral reefs. While reduction of herbivory can often suppress coral recovery, on coral reefs with robust herbivore populations, physical factors such as structural complexity and sediment may still limit coral recovery and fundamentally impact reef resilience.

In some continental shelf sediments integrated benthic microalgal biomass is greater than the integrated phytoplankton biomass in the overlying water column. In addition, benthic microalgae may account for up to 10% of the primary production responsible for the coastal fishery yield of the eastern United States. A three-dimensional model of the eastern Gulf of Mexico examines the effects of water-column nutrient sources on the growth of benthic microalgae. To parameterize the exchange of nutrients across the sediment/water interface in these permeable sediments, a non-local exchange submodel was constructed and tested within the framework of the model's grid. Based on the results of the three dimensional simulations, the growth of benthic microalgae from water-column nutrients is highly dependent on the light limitation of overlying phytoplankton. When light is available to phytoplankton in high enough quantities, water-column nutrients are used up before reaching the sediments. When the overlying phytoplankton are light limited, nutrients are able to reach the sediments where the shade adapted benthic microalgae can grow.

The breeding success of the Little Penguin was significantly higher in northern populations compared with documented southern colonies. Several southern colonies including Phillip Island in Victoria and colonies in Tasmania, have been characterised by poor breeding success, increasingly later commencement of breeding, and declining populations. This study aimed to compare and contrast the ecological attributes of a thriving northern population with other documented colonies. I collected long term data on breeding success (1987 to 1997) of the Little Penguin on Bowen Island, and related variability in breeding success to ocean currents and climate patterns, foraging behaviour and diet, nesting habitat, and inter-specific and fisheries competition. The benefits of successional changes to nesting habitat on Bowen Island since active habitat management commenced in 1989 were examined, including the importance of burrow depth, aspect, distance to water from the burrow, and vegetation type on breeding success of the Little Penguin. Morphological measurements of east coast penguins indicated a north-south cline, similar to that described in New Zealand. The Little Penguin was larger at higher latitudes. Whilst adults were sedentary and displayed a high degree of nest site fidelity, juveniles dispersed widely in their first three years, but then returned to the colony, sometimes to their natal burrow, to breed. This appears to be an adaptive mechanism, which selects for high quality nesting habitat. The study confirmed earlier findings that mature vegetation assemblages, namely woodland and forest, support higher breeding success than structurally simpler grassland and herbland habitat. This may contribute to observed differences in breeding success between northern and southern colonies, because many of the southern colonies have degraded nesting habitat. Most important to the diet of the Little Penguin were clupeoids, which dominated the fish species of Jervis Bay. The substantial clupeoid resources were targeted by the tuna fishery for bait, in the same areas and coinciding with maximum demands (chick raising and fledging), as penguins. The potential quantity of baitfish taken from Jervis Bay was over 10, 000 tonnes per year, which was well beyond the quantities raising concerns in other regions, although the fishery remains unregulated. Nevertheless, the foraging range of Bowen Island penguins was smaller than has previously been described Little Penguins on Bowen Island had a heavy reliance on relatively shallow waters of the Bay, within 5 km of the island. Daily foraging distances exceeding 20 km coincided with low breeding success, sometimes below that required for population replacement. Greater daily foraging range during the breeding season in southern Victoria may explain in part why these populations are declining. The principal mechanism for nutrient enrichment of Jervis Bay waters was the East Australia Current (EAC). This is a large and powerful, warm water boundary current of 250 km diameter and 1000 feet depth, which promoted slope water intrusion through upwelling along the New South Wales coast during the study, particularly during the penguin breeding season. The EAC effects northern colonies, but less so southern colonies. The Bowen Island colony was prone to periodic breeding failure, which was related to the El Nino Southern Oscillation (ENSO) phenomenon, indicated in Australia by the Southern Oscillation Index (SOI). ENSO warm events, corresponding with negative values of the SOI, depressed the EAC and caused downwelling, leading in some seasons to increased breeding failure. There was a correlation between both fledging success and adult mortality, and the SOI. The mean breeding success of the Bowen Island colony, at 1.46 chicks per pair over the ten-year study, was the highest recorded for the Little Penguin, and the population was increasing.

Target species in some Australian shark fisheries are adequately managed, but there has been little attention given to non - target shark species and there is limited information on the biology of their local populations. Among this group of non-target species, the piked spurdog - Squalus megalops ) is of special interest because it is a dominant and ecologically important species with high natural abundance. Hence, the main purpose of the present research was to improve knowledge of the basic biology of this species and to provide essential data for its management, sustainable use and conservation. Squalus megalops had a complex population structure, segregating by sex, size and breeding condition. The sex ratio was biased towards females and there was sexual size dimorphism with females attaining a larger maximum size than males. Conversion factors from partial lengths to total length and from partial masses to total mass were determined due to the common commercial fishing practice of eviscerating, beheading and finning sharks. Comparisons of total and partial length - length and mass - length relationships between males and females using different ranges of size showed that there was no effect of size range on measurements reflecting only somatic growth ( fork and carcass lengths ; carcass, pectoral fin and caudal fin masses ). However, for variables reflecting somatic and reproductive growth ( total and liver masses ), different outcomes can be expected when different ranges of size are compared. Examination of dietary composition revealed that S. megalops is an opportunistic predator that consumes a wide range of prey items. High variability was found when overall importance of prey items was estimated. Dietary composition varied in space and time, exhibiting differences among regions, seasons and size classes. Therefore, the intrinsic natural variability in the dietary composition of S. megalops and its spatial and temporal variation in diet suggest that information on the ecological relationships among species is likely to be missed when predator - prey interactions are only inferred from overall diet. Reproductive parameters were determined for population assessment. For both sexes, length - at - maturity differed depending on the criterion adopted for defining maturity. Mature males are capable of mating throughout the year. Females have a continuous asynchronous reproductive cycle. The sex ratio of embryos is 1 : 1 and litter size and nearterm embryo size increase with maternal length. Females have an ovarian cycle and gestation period of two years. Although all females are mature at 600 mm, only 50 % of them are in maternal condition, contributing to annual recruitment each year. Hence, for chondrichthyan species with reproductive cycles of two, three or more years, if maturity ogives are used in population assessments instead of maternity ogives, the models will over - estimate recruitment rates. Age and growth information was also determined for population assessment. Precision estimates, the relationship between spine total length and body length, edge analysis, and agreement between counts on the inner dentine layer and the enameled surface support the use of the first dorsal fin spine for the age estimation of S. megalops. Based on goodness - of - fit criterion, the best growth model for males and females was a two - phase von Bertalanffy function. However, model selection cannot be based on quality of statistical fit only and results should be interpreted with caution. Regardless of the model used, the growth rate of S. megalops, particularly of females, is very low, even within the range of growth rates reported for shark species. A three - levelled hierarchical risk assessment approach was trialed to evaluate the suitability of the approach for S. megalops. Integration of qualitative, semi - quantitative, and quantitative biological and fishing impact data showed that S. megalops is potentially highly susceptible to the effects of fishing. A qualitative assessment indicated that the only fishing related activities to have moderate or high impact on S. megalops were those associated with ' capture fishing ' of the otter trawl, Danish seine, gillnet and automatic longline methods. A semi - quantitative assessment ranked S. megalops at risk because of its low biological productivity and, possibly, its catch susceptibility from cumulative effects across the separate fishing methods. Finally, a quantitative assessment showed that population growth is slow even under the assumption of density - dependent compensation where the fishing mortality rate equals the natural mortality rate. Therefore, conservation and management for sustainable use of S. megalops will require a close control of fishing mortality due to the low capacity of this species to withstand fishing pressure. / Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2006.