Generalist herbivores profoundly influence the biomass and species composition of macroalgae assemblages. In subtidal ecosystems of temperate latitudes, large invertebrates are usually the most influential herbivores. I tested the prediction that exclusion of invertebrate herbivores would lead to changes in the biomass and species composition of the macroalgae assemblages that are a prominent feature of the reefs in south-western Australia. The most abundant invertebrate herbivores were sea urchins (Heliocidaris erythrogramma, Phyllacanthus irregularis and Centrostephanus tenuispinus), and these occupied different trophic positions. Heliocidaris was present at virtually all reefs surveyed, and was particularly abundant in the Fremantle region. Analyses of stable isotopes and direct observations of gut contents revealed that it was almost exclusively herbivorous, and that it mainly ate foliose brown algae. In contrast, Phyllacanthus and Centrostephanus were omnivorous; while they consumed large proportions of algae, a substantial proportion of the diet of both species was animal tissue. Because Heliocidaris is a generalist herbivore that occurs at high densities, it could exert a large influence on the macroalgae assemblage. This prediction was tested by a series of press experiments. Contrary to the prediction, Heliocidaris exerted a very minor influence on the biomass, and no detectable influence on the species composition, of attached macroalgae. However, it exerted a major influence on the retention of drift macroalgae and seagrass by trapping and feeding on drift. It exerted a particularly strong influence on retention of the kelp Ecklonia radiata. This kelp was not abundant in the attached algae assemblage (when all plots were pooled it ranked 35th in biomass), but was abundant as drift (ranking 1st). Most of the drift Ecklonia was retained by sea urchins, rather than freely drifting.Herbivorous fish may also influence macroalgae assemblages. To compare the effects of sea urchins versus fish on recruiting and adult macroalgae a 13-month exclusion experiment was conducted. There were no detectable effects of sea urchins (mainly Heliocidaris) on either recruiting or adult macroalgae. There were some patterns in the biomass of recruiting algae consistent with an influence by herbivorous fish; however, these patterns were also consistent with the presence of artefacts (shading and reduced water flow) by fish exclusion devices. I began with the prediction that large invertebrate herbivores were a major influence on the macroalgae assemblages of subtidal reefs in south-western Australia. Overall, there was little evidence to support this prediction: within spatial extents of tens of square metres and over periods of 1-2 years, only minor effects were detected. However, it remains plausible that herbivores exert an influence over long time periods across large spatial extents in south-western Australia. I propose that trophic subsidies support the comparatively high densities of Heliocidaris that exist at some reefs. I further propose that these subsidies mediate the effects of sea urchins on the attached macroalgae assemblage, and that they might play an important role in energy and nutrient cycling in these nearshore ecosystems.

[Truncated abstract] Selection of priority areas for Marine Park conservation is often compromised by the lack of comprehensive biodiversity data and the resources and expertise necessary to gain this information directly by sampling. One cost effective alternative is the use of species groups or indicator species as surrogates for total biodiversity. However use of these surrogates requires an ecological understanding of how they reflect biodiversity gradients. A framework for unravelling these relationships has been suggested that involves relating species biodiversity to different and competing ecological models using appropriate statistical analysis. I use this framework to explore coral species biodiversity over a range of environmental gradients encompassing the North West Shelf of Australia and the Great Barrier Reef in North East Australia. ... I assessed physiological responses of corals to physical factors to corroborate crossshelf patterns in species biodiversity. Finally, I investigated to what extent coral cooccurrence based species groups (or guilds) can be used as surrogates for total coral biodiversity. The major findings of this thesis were: i) coral biodiversity along cross-shelf environments was highly correlated to specific gradients of abiotic reef conditions; ii) larval modelling indicates the potential for significant connectivity across continentalshelf environments such that differences in species distribution are not simply as a result of self seeding. iii) similar correlative patterns were demonstrated for coral species that occur along comparable abiotic gradients in reef areas of both Eastern and Western Australia, suggesting a causal relationship between the physical environment and coral biodiversity; iv) coral physiological parameters measured using lipid fractions independently corroborated the hypothesis that there is a biological basis for observed coral distributions; v) reef coral communities are not highly structured across abiotic physical gradients and biodiversity across the shelf increases as conditions become suitable for a wider range of species; vi) total coral biodiversity can be estimated very accurately (within r2 values ranging from 0.75 to 0.90) using a small number (15-30) of optimally chosen indictor species using the randomForest statistical method. These results suggest coral biodiversity over cross-shelf environments conforms most closely to the

Thesis (doctoral)--Universität Bremen, 2003. / Includes bibliographical references.

Reef habitats built by the tubiculous polychaete Sabellaria spinulosa have been identified as a habitat with significant conservation importance, based on their historic decline across Europe and the assumption that, like many other biogenic reef systems, S. spinulosa reefs enhance biodiversity. Despite the high conservation status of this habitat very little work has been undertaken to explore the role that S. spinulosa reefs play in marine ecosystems, or their sensitivity to anthropogenic disturbance. Observations of the reproductive ecology and population dynamics of the reef building organism indicate that S. spinulosa exhibit life-history traits typically associated with r-strategists, indicating that this species is likely to have the ability to recover quickly following most anthropogenic disturbance events. A series of surveys on S. spinulosa reefs identified at the Thanet Offshore Wind Farm site, where the extent of the reef habitat was found to have increased between the pre-construction and post construction survey despite extensive cable laying and turbine installation, corroborates these findings. Detailed investigations into the macrofauna associated with S. spinulosa reefs in the eastern English Channel revealed that S. spinulosa reefs support macrofaunal communities that are comparable to those associated with adjacent muddy sandy gravel and gravelly muddy sand in terms of species composition, taxonomic breadth and beta-diversity. A consistent enhancement in species richness, abundance and biomass was identified in samples collected from S. spinulosa reefs when compared with adjacent sedimentary deposits, as well as a corresponding reduction in the equitability of species, indicating that some macrofauna are able to exist in higher densities within this habitat. The increase in macrofaunal biomass associated with S. spinulosa reefs was found to influence the diet of demersal fish species, with some species feeding on the reef organism itself while others feed on species found in high densities on the reefs. The high abundance of juvenile flatfish associated with this habitat also suggests that S. spinulosa reefs may provide an important nursery habitat.

Marine ranching has been identified as an alternative to traditional aquacultural rearing and growing organisms for consumption. In the Eastern Cape, abalone ranching is a new and experimental industry. The aims of the research were to: first develop a GIS model to assist management in site selection for abalone seeding; and secondly to develop and standardize the sampling methodology in order to ground truth the sites, and assist in the monitoring and habitat identification of abalone. The GIS model developed in Chapter 3 was created using an unsupervised classification and fuzzy logic approach. Both vector and raster datasets were utilized to represent 7 different layers. Predominantly satellite imagery was used to classify the different substrate groups according to pixel colour signatures. The basic process was to apply a fuzzy rule set (membership) to rasters which gave an output raster (Fuzzification). The membership output rasters were overlaid which creates a single model output. It was found that model accuracy increased significantly as more layers were overlaid, due to the high variability within each of the individual layers. Model ground-truthing showed a strong and significant correlation (r2 = 0.91; p < 0.001) between the model outputs and actual site suitability based on in situ evaluation. Chapter 4 describes the investigation towards the optimal sampling methods for abalone ranching habitat assessments. Both destructive sampling methods and imagery methods were considered as methods of data collection. The study also evaluated whether quadrat and transects were going to be suitable methods to assess sites, and what size or length respectively they should be to collect the appropriate data. Transect length showed great variation according to the factor assessed. A transect of 15 metres was found to be optimal. Abalone counts showed no significant (p = 0.1) change in the Coefficent of Variance (CV) for transect lengths greater than 15m, and had a mean of 0.2 abalone per metre. Quadrat size showed a significant difference in functional group richness between quadrat sizes of 0.0625m2, and 0.25m2 but no difference between 0.25m2 and 1m2 quadrats for both scape and photographic quadrats. It was also found that between 5 and 10 replicates (p = 0.08) represents the functional groups appropriately using quadrats and that a 0.25m2 quadrat is most suitable for sampling. Chapter 5 describes the benthic community structure of Cape Recife shallow water reefs. Using the standardized methodology previously mentioned, 45 sites were assessed to identify the community structure. These sites were grouped into 5 different groups influenced by depth and substrate, as well as functional group composition according to a Wards classification. The community structure showed that depth and substrate play a significant role (p < 0.05) in the community type. There is also a significant relationship (p < 0.05) between complexity, rugosity, abalone presence and substrate. During this study the basic protocols for site selection and benthic community monitoring have been developed to support the abalone ranching initiative in the Cape Recife area. It has also provided a baseline of the benthic community in the ranching concession area which will be used as a benchmark for future monitoring efforts. The site selection, sampling, and monitoring methods developed during the course of this work have now been rolled out as Standard Operating Procedures for the ranching programme in this area.

Genetic variation was examined in bluehead wrasse, Thalassoma bifasciatum, populations along the Florida Keys. Interpretion of mean heterozygosity (H), percent polymorphic loci per population (P), genetic similarity, and F and G statistics demonstrated a clear division of wrasse populations into "northern" and "southern" groups. Correlation and cluster analyses indicated the six reefs can be grouped in a similar fashion based on genetic and environmental data. The conclusion from this analysis of wrasse populations in the Florida Keys is that substantial population subdivision occurs in response to differing selective pressures created by heterogeneous environments.

While ocean acidification (OA) is predicted to inhibit calcification in marine macroalgae, species whose photosynthesis is limited by current dissolved inorganic carbon (DIC) levels may benefit. Furthermore, variations in macroalgal morphology will likely give rise to a range of OA tolerance in calcifying macroalgae. One genus of calcifying macroalgae that has shown varying species’ tolerance to OA is Halimeda, a major carbonate sediment producer on tropical reefs. Species within this genus occupy a range of habitats within tropical environments (reefs and lagoons), illustrating their ability to adapt to diverse environmental conditions (e.g. carbonate chemistry, irradiance). To date it is not clear if morphological and photophysiological diversity in Halimeda will translate to different tolerances to OA conditions (elevated pCO2 and lower pH). / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Scleractinian corals extract calcium (Ca²⁺) and carbonate (CO₃²⁻) ions from seawater to construct their calcium carbonate (CaCO₃) skeletons. Key to the coral biomineralization process is the active elevation of the CO₃²⁻ concentration of the calcifying fluid to achieve rapid nucleation and growth of CaCO3 crystals. Coral skeletons contain valuable records of past climate variability and contribute to the formation of coral reefs. However, limitations in our understanding of coral biomineralization hinder the accuracy of (1) coral-based reconstructions of past climate, and (2) predictions of coral reef futures as anthropogenic CO₂ emissions drive declines in seawater CO₃²⁻ concentration. In this thesis, I investigate the mechanism of coral biomineralization and evaluate the sensitivity of coral reef CaCO₃ production to seawater carbonate chemistry. First, I conducted abiogenic CaCO₃²⁻ precipitation experiments that identified the U/Ca ratio as a proxy for fluid CO₃²⁻ concentration. Based on these experimental results, I developed a quantitative coral biomineralization model that predicts temperature can be reconstructed from coral skeletons by combining Sr/Ca - which is sensitive to both temperature and CO₃²⁻ - with U/Ca into a new proxy called "Sr-U". I tested this prediction with 14 corals from the Pacific Ocean and the Red Sea spanning mean annual temperatures of 25.7-30.1 °C and found that Sr-U has uncertainty of only 0.5 °C, twice as accurate as conventional coral-based thermometers. Second, I investigated the processes that differentiate reef-water and open-ocean carbonate chemistry, and the sensitivity of ecosystem-scale calcification to these changes. On Dongsha Atoll in the northern South China Sea, metabolic activity of resident organisms elevates reef-water CO₃²⁻ twice as high as the surrounding open ocean, driving rates of ecosystem calcification higher than any other coral reef studied to date. When high temperatures stressed the resident coral community, metabolic activity slowed, with dramatic effects on reef-water chemistry and ecosystem calcification. Overall, my thesis highlights how the modulation of CO₃²⁻, by benthic communities on the reef and individual coral polyps in the colony, controls the sensitivity of coral reefs to future ocean acidification and influences the climate records contained in the skeleton. / by Thomas Mario DeCarlo. / Ph. D.

Nitrogen (N) has traditionally been regarded as the primary limiting nutrient to algal growth in marine coastal waters, but recent studies suggest that phosphorus (P) can be limiting in carbonate-rich environments. To better understand the importance of P. alkaline phosphatase activity (APA) was measured in reef macroalgae in seven counties of south Florida ; several significant trends emerged : 1) APA decreased geographically from the highest values in Dada>Monroe>Palm Beach>St. Lucie>Broward>Martin>Lee counties 2) APA varied temporally with increasing nutrient-rich runoff in the wet season 3) APA varied due to taxonomic division Phaeophyta>Rhodophyta>Chlorophyta 4) Nutrient enrichment experiments demonstrated that increased N-enrichment enhanced P-limitation while increased P decreased P-limitation. These results suggest that high APA observed in carbonate-rich waters of Dade County and low APA in Broward County resulted from high nutrient inputs associated with anthropogenic nutrient pollution. / by Courtney Kehler. / Thesis (M.S.)--Florida Atlantic University, 2012. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

Benthic foraminifera are exceptional organisms with distinctive features that allow for interpretation of both past and present environmental conditions. Some benthic foraminifera are widely distributed while some are restricted to specific environments due to their way of life. Foraminiferal assemblages south of Biscayne Bay and north of Cape Canaveral have previously been investigated; however, a gap exists in data covering a transitional zone along the Florida coast between the tropical waters of the western Atlantic and the cooler coastal waters along the North American coast. The purpose of this study was to collect baseline data on the benthic foraminifera of the small marine environment off of Pompano Beach that falls within this zone. This environment has a very particular relict reef system that includes a near-shore ridge complex, the unique foraminiferal assemblage of which has not been documented. Thirteen rubble samples were collected from this near shore ridge complex between October 2013 and April 2015 from depths of 2.5m – 9m. Abundances and diversity indices were calculated, and multivariate analysis and SHEBI analysis carried out to summarize baseline data for the area. Substrate types and seasonal collections were compared with foraminiferal abundances to determine if benthic foraminifera diversity varied between the four substrate types found on the near-shore ridge and between wet and dry seasons in Florida. Results revealed a variation in abundances for both substrates and seasons with the dominant genera being Quinqueloculina, Laevipeneroplis, and Archaias. Multivariate analysis displayed dissimilarities between substrates colonized by corals and those that were uncolonized. Comparison of studies from surrounding areas revealed fewer, however similar, species and different dominant genera. Overall, this area has proven to be a different environment compared to surrounding coastal areas and merits further investigation. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection