Dissertations / Theses on the topic 'Marine habitats'

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environmental and Applied Science
Full Text

Dimethylsulphoniopropionate (DMSP) is a dimethylated sulphur compound that appears to be produced by most marine algae and is a major component of the marine sulphur cycle. The majority of research to date has focused on the production of DMSP and its major breakdown product, the climatically important gas dimethylsulphide (DMS) (collectively DMS/P), by phytoplankton in the open ocean. A number of functions for intracellular DMSP (DMSPi) in phytoplankton have been identified and the cycling of DMS/P appears to be critical for ecosystem function. However, mechanisms for the production and release of DMS/P in the coastal ocean are poorly understood, despite the region’s economic and ecological importance. Coralline algal habitats (e.g. maerl beds, coral reefs, seagrass meadows, kelp forests) are distributed throughout the coastal oceans worldwide. Their three-dimensional structure supports high biodiversity and provides numerous services, generating considerable economic wealth. DMSPi in coralline algae is known to be high, thus coralline algal habitats may be critical components of the coastal sulphur cycle. This research aimed to improve our understanding of the production of DMS/P by coralline algal habitats by investigating (1) natural spatiotemporal variation and (2) the influence of environmental pressures. This was achieved through a number of laboratory and field-based studies, utilising modern and well-established techniques. The first objective of this research was to better understand the photosynthesis of red coralline algae (Chapter 3), as the algal precursor to DMSPi is methionine, a product of photosynthesis. The photosynthetic characteristics of coralline algae exhibited acclimation to changing light conditions (e.g. over a diurnal cycle or between natural and static lighting conditions). Further, for the species tested, coralline algae are often subjected to light-saturating natural conditions, therefore requiring efficient photo-protective mechanisms, which may include DMSPi regulation. On a global scale, DMSPi in coralline algae may decline with latitude, reinforcing the role of DMSPi as an antioxidant (Chapter 4). At smaller spatial scales, DMS/P production, release and recycling mechanisms were apparent in a number of habitat types (Chapter 4). A strong seasonal trend in DMS/P was also observed at a Scottish maerl bed, driven by water temperature and cloud cover (Chapter 5). Annually averaged DMS and DMSP concentrations were 230% and 700% respectively higher than the open ocean, highlighting the potential importance of the coastal ocean in the marine sulphur cycle (Chapter 5). The influence of environmental pressures (decreased salinity, variable pH and grazing) on DMS/P production by coralline algal habitats was examined (Chapters 6 – 8). In agreement with the phytoplankton literature, a chronic, but not acute, reduction in salinity led to a significant decline in coralline algal DMSPi concentrations and a sinking of the surface epithelial cells but no apparent impact on photosynthesis (Chapter 6). In the naturally variable tropical reef environment, calcifying algae continually regulated DMSPi concentrations in response to the diurnal cycling of carbonate saturation state (Chapter 7), suggesting that DMSPi may be enhanced under low pH regimes to compensate for enhanced oxidant production. Under low pH conditions, cracks were observed between the surface epithelial cells of coralline algae, potentially allowing DMSPi to leak from the cells (Chapter 7). In the field, grazing by urchins appeared to facilitate the release of DMS/P from kelp in coralline algal habitats (Chapter 8). In the laboratory, DMSPi in coralline algae increased in response to chemical cues from grazers rather than direct grazing activity, as had been previously proposed. Prior to this research, little information was available on DMS/P concentrations in coralline algal habitats. The marine sulphur cycle may impact climate regulation and ecosystem function on a global scale. This research provides a comprehensive source of information on the importance of coralline algal habitats in the marine sulphur cycle by examining natural variability and potential changes in response to environmental perturbations. This work will form a baseline for continued research in this field, investigating, for example, the impact of multiple stressors on DMS/P production, release and recycling in coastal marine habitats.

La biodiversità marina regola il funzionamento ecosistemico, responsabile della produzione di beni e servizi importanti per la biosfera ed il benessere umano. I cambiamenti climatici globali e le attività umane stanno alterando la biodiversità degli oceani ed il funzionamento ecosistemico. Al momento, partendo dalla consapevolezza che le sole misure di conservazione non sono sufficienti a invertire la degradazione degli ecosistemi, è riconosciuto che il restauro ambientale è una azione di cruciale importanza per far fronte a questa minaccia. Tuttavia, è necessaria una maggiore conoscenza scientifica per rendere efficaci azioni di restauro, specialmente negli ambienti profondi che sono largamente sconosciuti. Tra le maggiori attività che avranno impatti sugli habitat marini vi sono lo sfruttamento di risorse minerarie e la pesca a strascico, le quali, risospendendo particelle polimetalliche e sedimenti, avranno effetti principalmente sulle specie bentoniche. In questa tesi, il Corallium rubrum, specie strutturante di elevata valenza ecologica, è stato esposto a questi due tipi di particolato. Dopo la rimozione della fonte di impatto, questo organismo è in grado di recuperare parzialmente tassi di alimentazione e la sua integrità tissutale. Questo esperimento fornisce utili informazioni non solo per meglio comprendere gli effetti di tali attività su organismi bentonici, ma anche per definire possibili misure di mitigazione attraverso una modulazione appropriata della loro intensità e durata. Allevare in acquario specie di corallo minacciate potrà essere utile per futuri progetti di restauro che prevedono il trapianto di colonie donatrici. Una dieta appropriata da somministrare durante l’allevamento può avere effetti benefici sulla loro crescita ed il loro successo riproduttivo. In questa tesi, è stata studiata la selezione di cibo da parte di alcuni coralli profondi (Desmophyllum pertusum, Madrepora oculata and Dendrophyllia cornigera), i quali hanno mostrato una preferenza per il crostaceo Mysis relicta. I risultati ottenuti dalle analisi condotte sugli isotopi stabili hanno inoltre fornito nuove informazioni sulle nicchie trofiche occupate nel Mar Mediterraneo da queste specie. Una volta ampliate le conoscenze sugli habitat e le specie da restaurare, è necessario valutare l’efficacia delle procedure di rispristino che si vogliono applicare. In questa tesi, sono stati studiati gli effetti di due esperimenti pilota di trapianto della fanerogama Cymodocea nodosa e della gorgonia Eunicella singularis su attributi di funzionamento ecosistemico. I risultati ottenuti indicano che il trapianto di tali organismi, se opportunamente pianificato, non solo garantisce la loro sopravvivenza, ma può anche avere effetti positivi su processi ecosistemici chiave. Tuttavia, sono necessari ulteriori studi per valutare la possibile estensione di queste azioni per affrontare l'attuale scala spaziale di perdita di specie/habitat. Questo lavoro fornisce nuovi elementi per la comprensione dei potenziali benefici ecologici derivanti dal restauro ambientale e delle sue ricadute per la conservazione del capitale naturale.
Marine biodiversity regulates ecosystem functions, which are responsible for the production of goods and services for the biosphere and human well-being. Global changes and human activities are altering ocean biodiversity and ecosystem functioning. At present, stemming from the awareness that conservation and management are often not enough to halt and revert the degradation of threatened ecosystems, it has been recognized that active restoration is crucial to cope with this issue. More knowledge is needed to make restoration actions effective, especially for the largely unknown deep ocean. Two of the main activities that will alter marine habitats are ore exploitation and bottom trawling that, resuspending polymetallic and sediment particles, will affect benthic species. In this thesis, the habitat-forming species Corallium rubrum was exposed to these types of particles. After the removal of the disturbance, its feeding rates and tissue integrity partially recovered. This experiment provides new insights on the consequences of these activities as well as on potential mitigation strategies by properly modulating their intensity and duration. Rearing endangered corals in aquaria can be useful for future projects that aim to restore degraded reefs by transplanting healthy colonies. An appropriate diet may positively impinge on their growth or reproduction success. In this perspective, I studied the food selection of cold-water corals (Desmophyllum pertusum, Madrepora oculata and Dendrophyllia cornigera) was studied and these species showed a preference for the crustacean Mysis relicta. Stable isotope analyses provided also novel information on the trophic niches occupied by these coral species in the Mediterranean Sea. After expanding the knowledge on the habitat or the species to be restored, it is necessary to evaluate the effectiveness of the restoration actions that it might be applied. In this thesis, the effects of two pilot transplantation experiments of the seagrass Cymodocea nodosa and the gorgonian Eunicella singularis on ecosystem functioning of surrounding sediments have been studied. The results showed that transplantation can be effective and that it can have also positive effects on key-ecological processes. However, further studies are needed to assess the potential of scaling-up these actions addressing the present scale of species/habitat loss. This work provides new elements for a better understanding of the potential ecological benefits that can contribute to the conservation of the natural capital.

Coastal infrastructure has replaced many vital fish nursery habitats with structures designed without fully mitigating for the loss of the natural ecosystems. This thesis details research focused on the use of small, inexpensive, artificial reef modules as replacement juvenile fish habitat within marinas. My research hypothesis was that the placement of small, structurally complex artificial reef modules would increase fish abundance and species richness relative to unmodified marina seawalls. Non-destructive visual surveys of fishes were completed monthly for 14 months for 12 artificial reef sites and 12 control (unmodified) sites within the Nova Southeastern University Guy Harvey Oceanographic Center (NSU-GHOC) marina. Divers recorded species, abundance, and size class (0-2 cm, >2-5 cm, >5-10 cm, >10-20 cm, >20-30 cm, >30-50 cm, >50 cm) for all sites. Data was statistically analyzed using analysis of variance (ANOVA) and post-hoc Student Newman-Keuls (SNK) tests to explore differences in mean abundance, mean species richness, and mean abundance and species richness by size class and month. Total mean fish abundance and mean species richness (all months and sizes combined) were both significantly higher at artificial reef sites than at control sites. Artificial reef sites were consistently higher in total abundance and species richness when analyzed by month. Analysis of mean abundance by size class found the >2-5 cm, >5-10 cm, >10-20 cm and >20-30 cm classes were significantly higher for artificial reef sites. Species richness analysis by size class found classes >2-5 cm, >5-10 cm, >10-20 cm, and >20-30 cm were significantly higher at artificial reef sites. Fishes from the grunt (Haemulidae) and snapper (Lutjanidae) families contributed the most to the total abundance for both types of sites. These results support my hypothesis and have important implications for mitigating ecological impact to coastal fish nursery areas with the use of artificial structure.

Large pieces of plastic greater than a millimetre in diameter contaminate marine habitats worldwide and the associated environmental problems are well documented. In addition tiny fragments of plastic debris less than a millimetre in size have recently been reported. This thesis examines the distribution and environmental consequences of microscopic particles of plastic within marine habitats. To quantify the relative influence of wind and depositional environment on the accumulation of plastic debris, a mensurative experiment was conducted in a macrotidal Estuary. The overall trend was that material accumulated in down-wind sites. However, the relative importance of wind as a transport agent depended on the size and density of the plastic. Natural sediments are transported according to their size; but the extent to which models of sediment dynamics could be applied to the transport of plastic debris remains untested. I examined relationships between the abundance of microplastic debris and sediment particle size, latitude and human population density using samples from sandy shores worldwide. Microplastic was found at every location, showing the global extent of this contamination and there was a significant positive correlation between human population density and microplastic abundance. Sewage sludge disposal grounds were examined as potential sources of microplastic. Replicate sediment grab samples showed that disposal grounds near Plymouth and Newcastle (UK) had greater abundance of microplastic debris compared to reference sites. To investigate the biological consequences of ingesting clean microplastic particles the mussel, Mytilus edulis (L.) was used as a model organism. The fate of ingested plastic was tracked within the body tissues using a laboratory trial. Mussels were exposed to 3.0 and 9.61µm microplastic particles in seawater for 3 hours and then transferred to clean conditions. After 3 days ingested microplastic had accumulated in the circulatory fluid of M edulis. Smaller particles 3.0 µm were present in the haemolymph in consistently higher numbers than larger particles, and both sizes were still present after 48 days. There were no measurable changes in organismal health from ingestion of this material. However, it has been frequently suggested that plastics debris may transfer chemical contaminants to marine life. To test this, the sorption-affinity of candidate environmental hydrophobic contaminants from aqueous solution onto microscopic particles of polyvinylchloride and similar sized particles of sand was compared. Chemical analysis confirmed that polyvinylchloride absorbed more contaminants than sand. A second experiment examined the bioavailability of sorbed contaminants and chemical additives that are incorporated into plastic during manufacture. Laboratory trials using Arenicola marina (L.) showed that the sorbed contaminants and additives bioconcentrated in gut tissues leading to deleterious biological effects. In conclusion, microplastic debris is a ubiquitous form of contamination and when ingested, this material can translocate from the gut to the circulatory system and haemocytes, and can transfer chemicals into animal tissues, and reduce the health of animals near the base of the food chain. The implications of these findings are discussed in relation to potential measures to improve the management of plastics in society and to reduce the amount of plastic entering the environment.

This thesis presents results obtained from the investigation of secondary metabolites through screening of marine organisms, marine-derived microbes, and microbes form under-explored habitats. The first part includes the isolation of eight cytotoxic diterpene derivatives of which four were new from the organic extract of the sponge Spongionella sp. obtained from the U.S. National Cancer Institute’s Open Repository Program, the isolation of three new antibacterial dibenzofuran derivatives and a known butyrolactone from ascomycete Super1F1-09 isolated from the Indo-Pacific sponge Acanthella cavernosa. An attempt to synthesize these compounds was conducted. This part also includes the isolation of five known pyrroloiminoquinone alkaloids, from the Fijian sponge Zyzzya sp., which showed potent antiprotozoal activity. The second part comprises the use of OSMAC approach for the isolation of four new ansamycin-type polyketides, three new macrolactones and one known siderophore from Streptomyces strain C34 isolated from Atacama Desert, Chile. These compounds showed good antibacterial activity with one of the ansamycins showed pronounced antibacterial activity against a panel of clinical isolates of methicillin-sensitive as well as methicillin-resistant S. aureus (MRSA). This part also contains the use of microbial co-culture for the induction of secondary metabolites. It comprises the isolation of ten antiprotozoal fungal metabolites, of which one was new, from Aspergillus fumigatus when co-cultured with the novel strain Streptomyces C2 isolated from Atacama Desert. In conclusion, natural products from diverse sources proved to be the major resource of drug discovery. This thesis describes the isolation and structural characterisation of 35 compounds, 15 of which were new. Extremophiles proved to be a good source for new secondary metabolites.

Marine planners need to know about ecosystems, such as Priority Marine Habitats (PMHs) in order to manage and conserve them effectively. The overarching theme of this thesis is to contribute to this knowledge through the development of “marine planning tools”. The primary focus is on the PMH, Modiolus modiolus beds, although other PMHs and Marine Protected Areas (MPAs) were also considered. Four key studies were designed and conducted, i) Species Distribution Modelling (SDM) of M. modiolus in UK waters; ii) SDM of PMHs in Europe; iii) assessment of MPA management effort; and iv) the genetic connectivity of M. modiolus beds Overall, the research provided information and knowledge to contribute to implementation of a truly ecosystem-based approach to management and effective PMH management. It is now known: i) where Modiolus modiolus beds occur; ii) where they have the potential to occur, now and in the future; iii) that there is the potential for them to be lost/ hindered or lack-viability if ocean temperatures increase; iv) that they may become more important to conservation at northern latitudes in the future; v) that European nations will have to work towards integrated marine conservation policies and protection when considering all PMHs; vi) that some MPAs may require more effort to manage than others and that it may be possible to predict which ones they will be; vii) that cumulative human impacts may not be the driving force for management effort; and viii) that some M. modiolus beds in the UK are potentially connected. The data and discussion points generated within this thesis will enable effective PMH management through the selection of appropriate management strategies.

Marine bioeroders, borers, and burrowers can have drastic effects to marine habitats and facilities. By physically altering the structure of marine habitats, these organisms may elicit ecosystem-level effects that cascade through the community. While borer damage is typically restricted to a few substratum types, burrowing isopods in the genus Sphaeroma attack a diversity of substrata in tropical and temperate systems. My dissertation examined how boring sphaeromatid isopods affect coastal habitats (saltmarshes, mangroves) and other estuarine substrata as well as marine structures. I used a combination of lab and mensurative field experiments to quantify the effects of boring by isopods and examine how select factors affect the colonization, hence burrowing damage by isopods. I explored these questions primarily using the temperate boring sphaeromatid, Sphaeroma quoianum, as a model organism. My initial lab experiments quantified the per capita erosion rates of S. quoianum in four commonly attacked estuarine substrata. I found marsh banks and Styrofoam substrata were the most affected per capita. I supplemented this lab experiment with a year-long mensurative field experiment examining how erosion rates differ between marshes infested and uninfested by boring isopods. Marshes infested with isopods eroded 300% faster than uninfested marshes. I further examined the boring effects on Styrofoam floats. I compiled surveys and observations and conducted a short experiment to describe how isopods affect Styrofoam floats used in floating docks. I observed dense colonies of isopods attacking floats and expelling millions of plastic particles in the ocean. The boring effects to simulated Styrofoam floats were also affected by seawater temperature. Burrowing effects in Styrofoam floats exhibited a curvilinear relationship with temperature and peaked around 18°C. These results suggest a 1-2°C increase in water temperature could increase boring effects 5-17% of populations of isopods in Oregon and California bays. To examine the small-scale factors that mediate colonization and boring, I conducted a series of binary choice experiments. I found the presence of conspecifics, biofilm, and shade were important factors influencing colonization. These small scale factors likely explain why isopod attack is focused in some substrata. Finally, to examine the boring effects of tropical isopods in mangroves, I examined the associations between burrowing by S. terebrans and mangrove performance and fecundity. I found negative relationships between boring effects and performance and fecundity in two mangrove species in a restored mangrove stand in Taiwan. Together, these studies elucidate the effects of bioerosive isopods on saltmarshes, mangroves, and marine structures. However, the similar mechanisms involved in bioerosion in other boring species suggest that these results can be used to infer similar effects of other borers. In addition, since many species of sphaeromatid isopods have been introduced, this research shows how the effects of a non-native bioeroder can damage marine facilities and degrade and alter marine habitats. Through biological erosion and thus changing the physical structure of a marine habitat these non-native species can have ecosystem-level effects that cascade throughout the local community.

The diet and feeding habits of the southern stingray, Dasyatis americana, were investigated through aerial surveys, land-based observations, and quantitative analysis of stomach contents. The field research was conducted in the Exuma Cays Land and Sea Park, central Bahamas. Systematic aerial surveys and the land-based observations were made to determine population density and feeding periodicity in terms of time or tidal phase. In August, 1989, systematic surveys were flown over two cays in the Park; a 12 km2 area around Waderick Wells Cay and a 21km2 area around Shroud Cay. Both survey areas were flown three times over different times of the day. Over the large area covered by the aerial surveys the population varied over time of day. A significantly higher density occurred in the morning for both grids and was lowest in the afternoon for both grids suggesting that the stingrays prefer to feed early in the day in the summer. The peak density was 2.07 stingrays per km2 for the Waderick Wells survey area and 1.87 per km2 for the Shroud survey area. A total of 117 hours of land-based observations were made over 4 months; with 28 to 31 hours of observations in April and May 1990 and January and July, 1991. The land-based observations indicated that the stingrays were actively feeding throughout the day, but showed some increase in feeding activity during the high tidal phase. The habitat utilization was recorded during the land-based observations and showed that the stingrays spent most of their time feeding in the soft sediment habitats, thus taking advantage of the soft sediment algal turf and sandy shoal habitats that dominate the shallow marine environments within the Park. Eighteen stingrays were collected in January, 1991 for stomach content analysis. Decapod crustaceans were the most important prey category, but the large number of prey types found in all of the stomachs indicates that the southern stingray is a generalist feeder. There were no empty stomachs and 77% of the stomachs had more than 20 prey items. Stomach fullness measures did not indicate any feeding periodicity. The southern stingray is a generalist feeder taking advantage of a broad range of prey types and opportunistic in its feeding habits, showing no strong feeding periodicity.

In this dissertation, I experimentally examine predation-induced mortality upon juvenile queen conch, Strombus gigas, and assess the importance of select habitat predator and conch characteristics affecting predation intensity. Experiments were conducted during the summer and early fall of 1987, 1988, 1990 and 1991 in seagrass beds and adjacent sand flats near Lee Stocking Island, Exuma Cays, Bahamas. These experiments indicate that various factors act interactively to produce habitat-specific mortality rates in queen conch due to predation. These include (1) habitat type, whereby seagrass beds offer some protection; (2) local population dynamics, such that populated seagrass beds appear to enhance conch survival; (3) population density in some seagrass beds, such that mortality is inversely density-dependent; (4) conch size, such that larger conch have higher survival rates, depending on the specific type of habitat; and (5) predation intensity and predator guilds, which likely differ across habitats, producing habitat-specific mortality rates. When integrated with complementary studies of queen conch trophodynamics, these results provide critical information regarding key ecological factors affecting conch survival. In particular, results from the hatchery-reared experiments demonstrate the potential use of hatchery-reared stocks in natural habitats, and hence a valuable option for enhancement of fishery stocks throughout the Caribbean. In general, the integration of results obtained in this dissertation, with complementary studies of queen conch trophodynamics, should provide valuable suggestions of queen conch habitats, densities and scales of patchiness producing highest survivorship and growth rates in nature.

The following four broad aims were addressed in this study. (1) To ascertain whether the characteristics of the benthic macroinvertebrate assemblages within the different nearshore marine habitat types identified by Valesini et al. (2003) on the lower west coast of Australia differ significantly, and whether the pattern of those spatial differences matches those among the environmental characteristics that were used to distinguish those habitat types; (2) To develop a quantitative approach for classifying nearshore habitats in estuarine waters that employs readily-available data for a range of enduring environmental characteristics, and to use that approach to classify the various habitat types present in nearshore waters of the Swan-Canning Estuary on the lower west coast of Australia; (3) To test the hypothesis that the characteristics of the benthic macroinvertebrate assemblages in the in the Swan-Canning Estuary differ significantly among nearshore habitat types, and that the pattern of those differences matches that among the environmental characteristics used to distinguish those habitat types and (4) To test the hypothesis that, as a result of environmental changes in the Swan-Canning Estuary, the characteristics of the benthic macroinvertebrate assemblages at various habitats in this estuary in 1986/7 differ from those in 2003/4. To address the first aim, benthic macroinvertebrates were sampled seasonally for one year in the subtidal waters and intertidal zone (upper and lower swash zones) at the six nearshore habitat types that were identified by Valesini et al. (2003) on the lower west coast of Australia. The habitat types, which differed mainly in the extent of their exposure to wave activity and whether seagrass and/or nearshore reefs were present, had been distinguished quantitatively using values for a suite of seven statistically-selected enduring environmental characteristics. The faunal samples yielded a total of 121 species representing eight phyla, among which the Polychaeta, Malacostraca and Bivalvia were the most speciose classes and contributed ~ 38, 23 and 10%, respectively, to the total number of individuals. The total number of species and mean density of macroinvertebrates was far greater at the most protected habitat type (1), which also contained dense beds of seagrass, than at any other habitat type, i.e. 70 species and 209.2 individuals 0.1 m-2, compared to 32 species and 36.9 individuals 0.1 m-2 at the most exposed habitat type (6), which had a substrate comprised only of sand. Differences among habitat type influenced the benthic macroinvertebrate species composition to a greater extent than differences among either zones or seasons. Significantly different faunal compositions were detected among those latter two factors only at the most protected habitat type. The faunal assemblage at habitat type 1 was clearly the most distinct from those at the other five habitat types, particularly in the subtidal zone (R-statistics=0.642-0.831, p=0.1%), and was typified by five abundant polychaete species that were adapted to deposit-feeding. In contrast, the fauna at habitat type 6 was typified by four crustacean species and a species of bivalve and polychaete, whose mobility and tough external surface facilitated their survival and feeding in those turbulent waters. The extents of the differences in species composition among the six habitat types was significantly matched with that among the suite of enduring environmental characteristics that distinguished those habitat types, particularly in the case of the subtidal zone (Rho=0.676). Such results indicated that the environmental variables used to distinguish the nearshore habitat types could be used to reliably predict the types of benthic macroinvertebrate species likely to occur at any site along the lower west coast of Australia. The above biological validation of the nearshore marine habitat classification scheme developed by Valesini et al. (2003) provided the justification for the approach to the second broad aim of this study, namely to develop a quantitative scheme for classifying habitat types in the Swan-Canning Estuary. This approach was similar to that employed by Valesini et al. (2003) in that it considers that differences among habitat types are well reflected by differences in a suite of enduring environmental variables. However, it improves on that earlier method by employing a completely objective and quantitative approach. Thus, a large number of environmentally-diverse nearshore sites (102) were initially selected throughout the Swan-Canning Estuary and a suite of 13 enduring environmental variables quantified at each using remotely-sensed images of the estuary in a Geographic Information System. Such variables were chosen to reflect either (i) the type of substrate and submerged vegetation present, (ii) the extent of exposure to wave action or (iii) the location of the site within the estuary with respect to its vicinity to marine and fresh water sources. These data were then subjected to the CLUSTER routine and associated SIMPROF procedure in the PRIMER v6 multivariate statistical package to quantitatively identify those groups of sites that did not differ significantly in their environmental characteristics, and thus represented habitat types. Eighteen habitat types were identified, which were shown to well reflect spatial differences in a suite of non-enduring water quality and sediment characteristics that were measured in situ at a range of estuarine sites during both summer and winter in 2005 (Rho=0.683 and 0.740, respectively, p=0.1%). However, those latter environmental characteristics required far more time in the field and laboratory to quantify than the enduring variables used to identify the habitat types. Benthic macroinvertebrates were sampled during summer and winter in 2005 in the shallow subtidal regions (~1 m depth) at sites representing eight of the habitat types identified in the Swan-Canning Estuary. These samples contained a total of 51 and 36 species during summer and winter, respectively, and, in both seasons, represented nine phyla, namely Annelida, Crustacea, Mollusca, Sipuncula, Nematoda, Platyhelminthes, Cnidaria, Uniramia and Nemertea. The compositions of the benthic macroinvertebrate assemblages differed significantly among habitat types and, to a similar extent, between seasons (Global R-statistic=0.408 and 0.409, respectively, p=0.1%). However, the spatial differences were considerable greater in winter than in summer (Global R-statistic=0.536 vs 0.280, p=0.1%), presumably due to the greater spatial variation in particular non-enduring in situ environmental characteristics, such as redox depth and salinity. While the number of species, overall density and taxonomic distinctness of benthic macroinvertebrates also differed significantly among habitats, those variables differed to a greater extent between seasons, being greater in winter than in summer. While the measures of taxonomic distinctness tended to be greater at habitat types located in the lower to middle reaches, i.e. habitat types 6, 7, 9, 10, 13 and 18, than the upper reaches i.e. habitat types 1 and 3, the number of species and overall density reflected this trend only during winter. During summer, the mean numbers of species at habitat types 1, 3, 6 and 10 (3.4-6.0) were significantly lower than those at habitat types 7, 13, and 18 (8.8-10.9), whereas the overall density of benthic macroinvertebrates was far greater at habitat type 7 (32260 individuals 0.1 m-2)than at any other habitat type in this season (3135-18552 individuals 0.1 m-2). Overall, the greatest differences in assemblage composition occurred between those at habitat types 1 and 18 (R-statistic=0.669, p=0.1%), which were located in the uppermost region of the estuary and the lower reaches of the basin, respectively, and differed to the greatest extent in their enduring environmental characteristics. The assemblage at habitat type 1, and also that at habitat type 3, located just downstream, were relatively distinct from those at all other habitat types, particularly during winter (R-statistics=0.666-0.993, p=0.1%). The fauna at the first of these habitat types was relatively depauperate, containing low numbers of species and densities, and was characterised by the polychaetes Leitoscoloplos normalis and Ceratonereis aequisetis and the bivalve Arthritica semen. The assemblage at habitat type 3 was also characterised by those three species and the amphipod Paracorophium minor and the polychaete Boccardiella limnicola. In contrast, the assemblage at habitat type 18 was characterised by a more diverse assemblage, i.e. the polychaetes Capitella capitata, C. aequisetis, L. normalis and Pseudopolydora kempi, the amphipods, Grandidierella propodentata and Corophium minor and the bivalve Sanguinolaria biradiata. The number of species was among the highest at this habitat type during both seasons, which was also reflected in the high taxonomic diversity, and the overall density was the highest in winter and second highest in summer. Despite the above faunal differences, those between assemblages at habitat types 7 and 9, which were both located in the basin of the Swan-Canning Estuary, were similar in magnitude to those that occurred between pairs of habitat types located in two different regions of the estuary. Although both habitat types 7 and 9 were characterised by a similar suite of species, i.e. Oligochaete spp., C. aequisetis, C. capitata, C. minor, G. propodentata, L. normalis, and S. biradiata, the substantial differences in assemblage composition between these habitat types in both summer and winter (R-statistics=0.570 and 0.725, respectively) was due to marked differences in the relative contributions of each of these species. Significant and strong correlations were shown to exist in both summer and winter between the pattern of differences in the benthic macroinvertebrate assemblages among habitat types and that among the enduring environmental characteristics used to identify those habitat types (Rho=0.625 and 0.825, respectively, p=0.1%). Furthermore, these correlations were greater than those obtained between the benthic macroinvertebrate fauna and any combination of the non-enduring environmental characteristics (i.e. water quality and sediment parameters) recorded in situ at each habitat type (Rho=0.508 and 0.824, in summer and winter, respectively, p=o.1%). This demonstrates the greater capacity of surrogate enduring environmental characteristics to account for differences in the range of variables that may influence the distribution of benthic invertebrate fauna. Thus, the lists of characteristic benthic macroinvertebrate taxa produced for each of the eight habitat types studied in the Swan-Canning Estuary provide a reliable benchmark by which to gauge any future changes in those fauna. Moreover, these results indicate that the above habitat classification scheme can be used to reliably predict the types of benthic macroinvertebrate fauna that are likely to occur at any nearshore site of interest in this estuarine system. The final component of this study showed that the benthic macroinvertebrate assemblages at four sites in the middle reaches of the Swan-Canning Estuary in 2003/4 differed significantly from those recorded at the same sites in 1986/7. Such differences were reflected in (1) changes in the relative densities of a suite of ten species that were responsible for distinguishing the faunas in these two periods, (2) the absence of 22 rare species in 2003/4 (i.e. 42% of the number of species recorded in 1986/7), (3) the presence of 17 new species in 2003/4, including an abundant polychaete that is likely to have been introduced and (4) a far greater extent of seasonal variation in the number of species and densities of benthic macroinvertebrates in 2003/4. Such changes are likely to be related to lower sediment oxygen levels in certain seasons in 2003/4, as well as an altered hydrological regime due to increased temperatures and decreased rainfall in that more recent period. The fact that these changes have occurred within the Swan-Canning Estuary highlights the need for effective management tools, such as the habitat classification scheme and associated faunal survey undertaken in this study. Such data will provide a sound basis by which to examine the ways in which fauna vary spatially within the system, and allow for the establishment of comprehensive benchmarks for detecting future changes.

This project investigated the fundamental principles of the Theory of Island Biogeography. How biodiversity is influenced by habitat age, size, isolation and quality was studied in two little-known ecosystems; pumice-rafted marine communities that travel through the Pacific Ocean and strand on shorelines, and Queensland's critically endangered Melaleuca irbyana forests. This research found that while habitat age, size and isolation were important for species richness; habitat quality, defined by resource availability and climate, was more influential for predicting biodiversity levels. Small pumice stones and small remnant forests can provide the conditions species need to prosper. Therefore, small and isolated habitats are also important to conserve.

Biology
Ph.D.
Chemosynthetic ecosystems are habitats whose food webs rely on chemosynthesis, a process by which bacteria fix carbon using energy from chemicals, rather than sunlight-driven photosynthesis for primary production, and they are found all over the world on the ocean floor. Although these deep-sea habitats are remote, they are increasingly being impacted by human activities such as oil and gas exploration and the imminent threat of deep-sea mining. My dissertation examines deep-sea chemosynthetic ecosystems at several ecological scales to answer basic biology questions and lay a foundation for future researchers studying these habitats. There are two major varieties of chemosynthetic ecosystems, hydrothermal vents and cold seeps, and my dissertation studies both. My first chapter begins at cold seeps and at the population level by modeling the population dynamics and lifespan of a single species of tubeworm, Escarpia laminata, found in the Gulf of Mexico. I found that this tubeworm, a foundation species that forms biogenic habitat for other seep animals, can reach ages over 300 years old, making it one of the longest-lived animals known to science. According to longevity theory, its extreme lifespan is made possible by the stable seep environment and lack of extrinsic mortality threats such as predation. My second chapter expands the scope of my research from this single species to the entire cold seep community and surrounding deep-sea animals common to the Gulf of Mexico. The chemicals released at cold seeps are necessary for chemosynthesis but toxic to non-adapted species such as cold-water corals. Community studies in this area have previously shown that seeps shape community assembly through niche processes. Using fine-scale water chemistry samples and photographic mapping of the seafloor, I found that depressed dissolved oxygen levels and the presence of hydrogen sulfide from seepage affect foundation taxa distributions, but the concentrations of hydrocarbons released from these seeps did not predict the distributions of corals or seep species. In my third chapter I examine seep community assembly drivers in the Costa Rica Margin and compare the macrofaunal composition at the family level to both hydrothermal vents and methane seeps around the world. The Costa Rica seep communities have not previously been described, and I found that depth was the primary driver behind community composition in this region. Although this margin is also home to a hybrid “hydrothermal seep” feature, this localized habitat did not have any discernible influence on the community samples analyzed. When vent and seep communities worldwide were compared at the family-level, geographic region was the greatest determinant of community similarity, accounting for more variation than depth and habitat type. Hydrothermal vent and methane seeps are two chemosynthetic ecosystems are created through completely different geological processes, leading to extremely different habitat conditions and distinct sets of related species. However, at the broadest spatial scale and family-level taxonomic resolution, neutral processes and dispersal limitation are the primary drivers behind community structure, moreso than whether the habitat is a seep or a vent. At more local spatial scales, the abiotic environment of seeps still has a significant influence on the ecology of deep-sea organisms. The millennial scale persistence of seeps in the Gulf of Mexico shapes the life history of vestimentiferan tubeworms, and the sulfide and oxygen concentrations at those seeps determine seep and non-seep species’ distributions across the deep seafloor.
Temple University--Theses

[Truncated abstract] Spatially explicit marine habitat data is required for effective resource planning and management across large areas, although mapped boundaries typically lack rigour in explaining what factors influence habitat distributions. Accurate, quantitative methods are needed. In this thesis I aimed to assess the utility of ecological models to determine what factors limit the spatial extent of marine habitats. I assessed what types of modeling methods were able to produce the most accurate predictions and what influenced model results. To achieve this, initially a broad scale marine habitat survey was undertaken in the Recherche Archipelago, on the south coast of Western Australia using video and sidescan sonar. Broad and more detailed functional habitats types were mapped for 1054km2 of the Archipelago. Broad habitats included high and low profile reefs, sand, seagrass and extensive rhodolith beds, although considerable variation could be identified from video within these broad types. Different densities of seagrass were identified and reefs were dominated by macroalgae, filter feeder communities, or a combination of both. Geophysical characteristics (depth, substrate, relief) and dominant benthic biota were recorded and then modelled using decision trees and a combination of generalised additive models (GAMs) and generalised linear models (GLMs) to determine the factors influencing broad and functional habitat variation. Models were developed for the entire Archipelago (n=2769) and a subset of data in Esperance Bay (n=797), which included exposure to wave conditions (mean maximum wave height and mean maximum shear stress) calculated from oceanographic models. Additional distance variables from the mainland and islands were also derived and used as model inputs for both datasets. Model performance varied across habitats, with no one method better than the other in terms of overall model accuracy for each habitat type, although prevalent classes (>20%) such as high profile reefs with macroalgae and dense seagrass were the most reliable (Area Under the Curve >0.7). ... This highlighted not only issues of data prevalence, but also how ecological models can be used to test the reliability of classification schemes. Care should be taken when mapping predicted habitat occurrence with broad habitat models. It should not be assumed that all habitats within the type will be defined spatially, as this may result in the distribution of distinctive and unique habitats such as filterfeeders being underestimated or not identified at all. More data is needed to improve prediction of these habitats. Despite the limitations identified, the results provide direction for future field sampling to ensure appropriate variables are sampled and classification schemes are carefully designed to improve descriptions of habitat distributions. Reliable habitat models that make ecological sense will assist future assessments of biodiversity within habitats as well as provide improved data on the probability of habitat occurrence. This data and the methods developed will be a valuable resource for reserve selection models that prioritise sites for management and planning of marine protected areas.

This study addresses the fungi of two poorly studied subtropical coastal habitats: a mangrove site and recreational sandy beaches. Little is known regarding the occurrence and distribution of the higher filamentous fungi in mangroves of South Florida. Previous studies have demonstrated that marine fungi are an important degradative component and assume an important role in nutrient recycling systems in estuarine and near-shore ecosystems. In this study over 30 species of higher filamentous fungi were identified from driftwood collected in the mangroves in J.U. Lloyd State Park over a period of one year. The drift wood collected was mainly comprised of pieces of Rhizophora mangle and Conocarpus erectus. The predominant species, by frequency of occurrence, include the Ascomycetes Hypoxylon oceanicum (8.7%), Leptosphaeria australiensis (15.6%), Lulworthia grandispora (5.2%), and Nais glitra (11.6%) as well as the Fungi Imperfecti Humicola alopallonella (5%) and Cirrenalia species (6.4%). A new record for Florida is the Ascomycete Massarina velatospora, and a new host record for Phaeosphaeria gessneri occurring on R. mangle is reported. In addition, a description of two undescribed ascomycetous species is included. Overall, the marine mycota of South Florida appears to be very similar to that reported for other tropical and subtropical regions. Another site with important overlooked fungal components is the sand of bathing beaches. The second purpose of this study was to obtain mean counts of colony forming units (CFUs) of yeasts from the wet and dry sand of three bathing beaches in South Florida. The different yeast species were also isolated and identified, using molecular methods, in order to see whether there are any pathogenic species that grow in the sand. A total of 21 yeast species were identified including 4 Basidiomycetes and 17 Ascomycetes. Several species are known to be human pathogens. The most frequently occurring species included the Ascomycete Candida tropicalis and the Basidiomycete Rhodotorula mucilaginosa. Both species diversity and total mean counts of CFUs were found to be higher in the dry sand vs the wet sand, probably as the result of a more stable habitat. Mean counts were highest at the most crowded beach, suggesting that humans and warm-blooded animals may serve as a source of contamination of the sand.

Throughout the Pacific, many species of echinoderms and molluscs have cultural value and are harvested extensively in subsistence fisheries. Many of these species are sedentary and often associated with distinct reef-top habitats. Despite the significance of reef habitats and their fauna for fisheries and biodiversity etc, little information has been available on the distribution of habitats and their influence on the reef-top fauna in the Cook Islands. This thesis developed a novel approach to assess the status of the shallow-water reef-tops of Rarotonga, Cook Islands, to provide critical information to fisheries and conservation managers. The approach used remote sensing (aerial photography with ground truthing) to map the spatial arrangement and extent of the entire reef-top habitats accurately, and historical wind data and coastline shape to determine the windward and leeward sides of the island. The benthic habitat maps and degree of wind exposure were used to design and undertake a stratified sampling programme to assess the distribution and abundance of the epibenthic macroinvertebrate fauna of the reef-top. I quantified the distribution and abundance of the epibenthic macroinvertebrates and how they varied with habitat, assessed the effectiveness of a traditional ra�ui (marine protected area) for conserving stocks of Trochus niloticus and other invertebrates, and investigated the reproductive biology and impacts of traditional gonad harvesting on Holothuria leucospilota. There were four major habitat types (rubble/rock, sand/coral matrix, algal rim and sand) identified, the most extensive being rubble/rock (45%) and sand/coral matrix (35%). The degree of exposure to winds was found to correlate with the reef development and habitat distribution. The assemblage composition of each major habitat type differed significantly from every other habitat. The rubble/rock habitat had the greatest substratum heterogeneity and structural complexity, and the highest number of species and individuals. The overall abundance of the fauna was dominated by holothurians (68%) and echinoids (30%), while Trochus niloticus and Tridacna maxima accounted for the remaining 2% of the total invertebrate assemblage. Clear habitat partitioning was also found for adult and juvenile Trochus niloticus and Tridacna maxima. In the traditional fishery for Holothuria leucospilota, the mature gonads of males are harvested by making an incision in the body-wall of the animal, removing the gonads and then returning the animal to the reef to allow regeneration. Monthly collections of H. leucospilota were used to describe the reproductive biology of this species. Gametogenesis and spawning were synchronous between the sexes and spawning occurred annually during summer, when water temperature and photoperiod were at their highest. Although the incision in the body-wall and gonad removal had no impact on the survival of H.leucospilota in experimental cages, their body weight, and general sheltering and feeding behaviors were affected. Gonads took at least 41 days to start regenerating, suggesting a considerable delay in the spawning of fished individuals. In 1998, five Rarotongan communities re-introduced the traditional ra�ui system of resource management, prohibiting all fishing and gathering from their reefs. The performance of the Nikao ra�ui, which had been put in place to allow trochus stocks to increase, was investigated. Comparisons of macroinvertebrate assemblage composition and species density were made between three fishing treatments, i.e. fished areas adjacent to the ra�ui, within the ra�ui after two years of protection, and in the ra�ui after it had been lifted for three weeks to allow a commercial trochus harvest. Analysis of variance on the count data for the twelve most abundant species, and non-metric multi-dimensional scaling indicated that there were no differences in the microhabitat or the invertebrate assemblage composition between the three fishing treatments. However, there were significant differences between the rubble/rock and sand/coral matrix habitat types. The results on the effectiveness of the Nikao ra�ui are equivocal, due to the small sample size, and the variability between samples which was highlighted by the wide confidence intervals. This study highlights the importance of habitat to the macroinvertebrate fauna of the reef-top and the need for accurate habitat maps to increase the cost-effectiveness of future resource surveys, to provide information to management, and for the design of Marine Protected Areas. The mapping and survey methods must be reliable and repeatable in terms of the limitations of time, and the availability of expertise, funding and resources. The results provide important information for fisheries and conservation managers of Rarotonga and other Pacific Islands to better design rigorous sampling programmes for monitoring the status of reef-top resources, and for evaluating and planning Marine Protected Areas.

Overall, this thesis expands on our ecological understanding of a group of biologically diverse marine fishes by investigating how they are shaped by their habitats, prey, and predators. In my first data chapter, I used the seahorse Hippocampus whitei as a case study for investigating the ecological correlates of syngnathid abundance and distributions. Expanding on research that had looked at how either their habitats, prey, or predators affected their populations, I considered all three components in a single holistic approach. I investigated these correlations at two scales: among different seagrass beds (200-6000 m apart), and within a single seagrass bed (<100 m in size). I found that habitat, prey, and predator variables all correlated with seahorse density or height distributions to varying extents, depending on the scale of the study. Total predators was negatively associated with seahorse density across seagrass beds, the only ecological variable that was correlated with seahorses across beds. Within seagrass beds, seahorse locations correlated with greater depth, denser seagrass, more prey types, and fewer predators. In my second data chapter, I reviewed the diets and feeding behaviour of syngnathids, bringing together, summarizing, and providing new insights on a large amount of fragmented information on the topic. I answered three central questions. 1. How do syngnathids eat? 2. How does feeding and diet vary across a morphogically diverse family of fishes? 3. How does feeding and diet vary across a family of fishes that lives in a three-dimensional space? I answered question 1 by summarizing a number of different studies on the morphologies and kinematics of syngnathid feeding events. I answered questions 2 and 3 using a meta-analysis on syngnathid diets found the literature. Overall, I found there to be a large amount of variation in syngnathid diets that I hypothesize is caused by large differences in prey availability. Of the explained variation, I found their diets were most strongly correlated with their relative snout lengths and gape sizes. These feeding morphologies also had high phylogenetic signal, suggesting that dietary differences across genera were largely explained by how they differed with respect to these morphologies.
Science, Faculty of
Zoology, Department of
Graduate

There is an increasing need for more detailed knowledge about the spatial distribution and structure of shallow water benthic habitats for marine conservation and planning. This, linked with improvements in hyperspectral image sensors provides an increased opportunity to develop new techniques to better utilise these data in marine mapping projects. The oligotrophic, optically-shallow waters surrounding Rottnest Island, Western Australia, provide a unique opportunity to develop and apply these new mapping techniques. The three flight lines of HyMap hyperspectral data flown for the Rottnest Island Reserve (RIR) in April 2004 were corrected for atmospheric effects, sunglint and the influence of the water column using the Modular Inversion and Processing System. A digital bathymetry model was created for the RIR using existing soundings data and used to create a range of topographic variables (e.g. slope) and other spatially relevant environmental variables (e.g. exposure to waves) that could be used to improve the ecological description of the benthic habitats identified in the hyperspectral imagery. A hierarchical habitat classification scheme was developed for Rottnest Island based on the dominant habitat components, such as Ecklonia radiata or Posidonia sinuosa. A library of 296 spectral signatures at HyMap spectral resolution (~15 nm) was created from >6000 in situ measurements of the dominant habitat components and subjected to spectral separation analysis at all levels of the habitat classification scheme. A separation analysis technique was developed using a multivariate statistical optimisation approach that utilised a genetic algorithm in concert with a range of spectral metrics to determine the optimum set of image bands to achieve maximum separation at each classification level using the entire spectral library. These results determined that many of the dominant habitat components could be separated spectrally as pure spectra, although there were almost always some overlapping samples from most classes at each split in the scheme. This led to the development of a classification algorithm that accounted for these overlaps. This algorithm was tested using mixture analysis, which attempted to identify 10 000 synthetically mixed signatures, with a known dominant component, on each run. The algorithm was applied directly to the water-corrected bottom reflectance data to classify the benthic habitats. At the broadest scale, bio-substrate regions were separated from bare substrates in the image with an overall accuracy of 95% and, at the finest scale, bare substrates, Posidonia, Amphibolis, Ecklonia radiata, Sargassum species, algal turf and coral were separated with an accuracy of 70%. The application of these habitat maps to a number of marine planning and management scenarios, such as marine conservation and the placement of boat moorings at dive sites was demonstrated.

There is an increasing need for more detailed knowledge about the spatial distribution and structure of shallow water benthic habitats for marine conservation and planning. This, linked with improvements in hyperspectral image sensors provides an increased opportunity to develop new techniques to better utilise these data in marine mapping projects. The oligotrophic, optically-shallow waters surrounding Rottnest Island, Western Australia, provide a unique opportunity to develop and apply these new mapping techniques. The three flight lines of HyMap hyperspectral data flown for the Rottnest Island Reserve (RIR) in April 2004 were corrected for atmospheric effects, sunglint and the influence of the water column using the Modular Inversion and Processing System. A digital bathymetry model was created for the RIR using existing soundings data and used to create a range of topographic variables (e.g. slope) and other spatially relevant environmental variables (e.g. exposure to waves) that could be used to improve the ecological description of the benthic habitats identified in the hyperspectral imagery. A hierarchical habitat classification scheme was developed for Rottnest Island based on the dominant habitat components, such as Ecklonia radiata or Posidonia sinuosa. A library of 296 spectral signatures at HyMap spectral resolution (~15 nm) was created from >6000 in situ measurements of the dominant habitat components and subjected to spectral separation analysis at all levels of the habitat classification scheme. A separation analysis technique was developed using a multivariate statistical optimisation approach that utilised a genetic algorithm in concert with a range of spectral metrics to determine the optimum set of image bands to achieve maximum separation at each classification level using the entire spectral library. These results determined that many of the dominant habitat components could be separated spectrally as pure spectra, although there were almost always some overlapping samples from most classes at each split in the scheme. This led to the development of a classification algorithm that accounted for these overlaps. This algorithm was tested using mixture analysis, which attempted to identify 10 000 synthetically mixed signatures, with a known dominant component, on each run. The algorithm was applied directly to the water-corrected bottom reflectance data to classify the benthic habitats. At the broadest scale, bio-substrate regions were separated from bare substrates in the image with an overall accuracy of 95% and, at the finest scale, bare substrates, Posidonia, Amphibolis, Ecklonia radiata, Sargassum species, algal turf and coral were separated with an accuracy of 70%. The application of these habitat maps to a number of marine planning and management scenarios, such as marine conservation and the placement of boat moorings at dive sites was demonstrated. Committee Information

There is an increasing need for more detailed knowledge about the spatial distribution and structure of shallow water benthic habitats for marine conservation and planning. This, linked with improvements in hyperspectral image sensors provides an increased opportunity to develop new techniques to better utilise these data in marine mapping projects. The oligotrophic, optically-shallow waters surrounding Rottnest Island, Western Australia, provide a unique opportunity to develop and apply these new mapping techniques. The three flight lines of HyMap hyperspectral data flown for the Rottnest Island Reserve (RIR) in April 2004 were corrected for atmospheric effects, sunglint and the influence of the water column using the Modular Inversion and Processing System. A digital bathymetry model was created for the RIR using existing soundings data and used to create a range of topographic variables (e.g. slope) and other spatially relevant environmental variables (e.g. exposure to waves) that could be used to improve the ecological description of the benthic habitats identified in the hyperspectral imagery. A hierarchical habitat classification scheme was developed for Rottnest Island based on the dominant habitat components, such as Ecklonia radiata or Posidonia sinuosa. A library of 296 spectral signatures at HyMap spectral resolution (~15 nm) was created from >6000 in situ measurements of the dominant habitat components and subjected to spectral separation analysis at all levels of the habitat classification scheme. A separation analysis technique was developed using a multivariate statistical optimisation approach that utilised a genetic algorithm in concert with a range of spectral metrics to determine the optimum set of image bands to achieve maximum separation at each classification level using the entire spectral library. These results determined that many of the dominant habitat components could be separated spectrally as pure spectra, although there were almost always some overlapping samples from most classes at each split in the scheme. This led to the development of a classification algorithm that accounted for these overlaps. This algorithm was tested using mixture analysis, which attempted to identify 10 000 synthetically mixed signatures, with a known dominant component, on each run. The algorithm was applied directly to the water-corrected bottom reflectance data to classify the benthic habitats. At the broadest scale, bio-substrate regions were separated from bare substrates in the image with an overall accuracy of 95% and, at the finest scale, bare substrates, Posidonia, Amphibolis, Ecklonia radiata, Sargassum species, algal turf and coral were separated with an accuracy of 70%. The application of these habitat maps to a number of marine planning and management scenarios, such as marine conservation and the placement of boat moorings at dive sites was demonstrated. Committee Information

Chapter 1 Producing thematic coral reef benthic habitat maps from single-beam acoustic backscatter has been hindered by uncertainties in interpreting the acoustic energy parameters E1 (~roughness) and E2 (~hardness), typically limiting such maps to sediment classification schemes. In this study acoustic interpretation was guided by high-resolution LIDAR (Light Detection And Ranging) bathymetry. Each acoustic record, acquired from a BioSonics DT-X echosounder and multiplexed 38 and 418 kHz transducers, was paired with a spatially-coincident value of a LIDAR-derived proxy for topographic complexity (Reef-Volume) and its membership to one of eight LIDAR-delineated benthic habitat classes. The discriminatory capabilities of the 38 and 418 kHz signals were generally similar. Individually, the E1 and E2 parameters of both frequencies differentiated between levels of LIDAR Reef-Volume and most benthic habitat classes, but could not unambiguously delineate benthic habitats. Plotted in E1:E2 Cartesian space, both frequencies formed two main groupings: uncolonized sand habitats and colonized reefal habitats. E1 and E2 were significantly correlated at both frequencies; positively over the sand habitats and negatively over the reefal habitats, where the scattering influence of epibenthic biota strengthened the E1:E2 interdependence. However, sufficient independence existed between E1 and E2 to clearly delineate habitats using the multi-echo E1/E2 Bottom Ratio method. The point-by-point calibration provided by the LIDAR data was essential for resolving the uncertainties surrounding the factors informing the acoustic parameters in a large, survey-scale dataset. The findings of this study indicate that properly interpreted single-beam acoustic data can be used to thematically categorize coral reef benthic habitats. Chapter 2 A large-scale acoustic survey was conducted in Apr-May 2008, with the objective of quantifying the abundance and distribution of seasonal drift macroalgae (DMA) in the Indian River Lagoon. Indian River was surveyed from the Sebastian Inlet to its northernmost extent in the Titusville area. Banana River was surveyed from its convergence with the Indian River northward to the Federal Manatee Zone near Cape Canaveral. The survey vessel was navigated along pre-planned lines running east-west and spaced 200 m apart. The river edges were surveyed to a minimum depth of approximately 1.3 m. Hydroacoustic data were collected with a BioSonics DT-X echosounder and two multi-plexed digital transducers operating at 38 and 418 kHz. The 38 and 418 kHz hydroacoustic data were processed with BioSonics Visual Bottom Typer (VBT) seabed classification software to obtain values of E1’ (time integral of the squared amplitude of the 1st part of the 1st echo waveform), E1 (2nd part of 1st echo), E2 (complete 2nd echo), and FD (fractal dimension characterizing the shape of the 1st echo). Following quality analysis, a training dataset was compiled from 131 hydroacoustic + video samples collected across the extent of the study area. The 38 and 418 kHz E1’, E1, E2, and FD datasets were merged and submitted to a series of three discriminant analyses (DA) to refine the training samples into three pure end-member categories; bare substrate, short SAV (typically Caluerpa prolifera, ~10cm or less), and DMA. The Fisher’s linear discriminant functions from the third and final descriptive DA were used to classify each of the 480,000+ hydroacoustic survey records as either bare, short SAV, or DMA. The classified survey records were then used to calculate the biomass of DMA as the product of average DMA cover for a block of ten records times the wet weight of DMA. The DMA biomass was found to be 69,859 metric tons (wet weight) within the 293.1 km2 study area. The acoustically-predicted mean percent cover of DMA was (i) significantly greater within the navigation channels (18.3%) than outside (12.2%), and (ii) significantly greater in the Indian River (12.9%) than in the Banana River (9.3%). The overall predictive accuracy of total SAV (i.e. short SAV plus DMA) was 78.9% (n=246) at three levels of cover (0-33, 33-66, and 66-100%). The Tau coefficient, a measure of the improvement of the classification scheme over random assignment, was 0.683 ± 0.076 (95% CI), i.e. the rate of misclassifications was 68.3% less than would be expected from random assignment of hydroacoustic records to total SAV cover. The incorporation of multi-plexed digital transducers in conjunction with new post-processing techniques realized the goal of establishing an accurate, efficient, and temporally consistent method for acoustically mapping DMA biomass. Chapter 3 This chapter presents the results of a large-scale hydroacoustic survey conducted in April-May 2008. The objective of this study was to map the distribution and vertical extent of muck in the Indian River Lagoon, utilizing the data collected during a seasonal drift macroalgae survey. Indian River was surveyed from the Sebastian Inlet to its northernmost extent in the Titusville area. Banana River was surveyed from its convergence with the Indian River northward to the Federal Manatee Zone near Cape Canaveral. The survey vessel was navigated along pre-planned lines running east-west and spaced 200 m apart, except for when muck was indicated by the oscilloscope display, at which point a meandering path was adopted to demarcate the horizontal extent of muck. Hydroacoustic data were collected with a BioSonics DT-X echosounder and two multi-plexed digital transducers operating at 38 and 420 kHz. The vertical extent of muck was derived from the 38 kHz hydroacoustic signal, which was processed with Visual Analyzer, a fish-finding software package produced by BioSonics Inc. The software was adapted to integrate echo energy below the water-sediment interface, and a set of post-processing algorithms were developed to translate the sub-bottom echo energy profile into continuous scale estimates of muck thickness. In this manner 500,000+ 38 kHz pings were translated into 88,927 geo-located estimates of muck layer thickness, down to a minimum bottom depth of 1 m. Ground-truthing was conducted in July 2008 at twenty sites within the Indian River. The predictions of muck layer thickness were found to be accurate over the ground-truthed range of 0-3m (r2 = 0.882, SE=0.52m). The vertical distribution of acoustically-predicted muck demonstrated the tendency for muck to accumulate in deeper areas of the lagoon. For the case of Indian River (excluding navigation channels), muck was not detected in depths shallower than 1.4m and rare in the range of 1.4-2.2 m (only 3.6% of records had a predicted muck thickness greater than 0.5 m). The frequency of muck plateaued between 2.2-3.4 m (9.6%) before making a sharp rise to 82% in the range of 4-5 m. As expected, the mean muck layer thickness was significantly greater within the navigation channels (0.56 m) than outside of them (0.08 m). A significant latitudinal trend of muck thickness was detected within the Indian River navigation channels. The mean muck thickness decreased from 1.38 m at its northernmost origins to 0.83 m in the Titusville area before plateauing at approximately 0.4 m for the remainder of segments. Outside of the main ICW channels, 23 individual muck deposits were identified; 22 in the Indian River and 1 in the Banana River. Factors in descending order of co-occurrence were proximity to causeways or jetties, riverbed depressions, and proximity to shore and drainage channels. In conclusion, this study establishes that a single-beam acoustic survey is a cost-effective and accurate alternative for mapping the distribution and vertical extent of muck deposits in the shallow-water environment of the Indian River Lagoon. Moreover, the temporal consistency afforded by a digital transducer allows for direct and meaningful comparisons between successive surveys. Chapter 4 A thematic map of benthic habitat was produced for a coral reef in the Republic of Palau, utilizing hydroacoustic data acquired with a BioSonics DT-X echosounder and a single-beam 418 kHz digital transducer. This paper describes and assesses a supervised classification scheme that used a series of three discriminant analyses (DA) to refine training samples into end-member structural and biological elements, utilizing E1′ (leading edge of 1st echo), E1 (trailing edge of 1st echo), E2 (complete 2nd echo), fractal dimension (1st echo shape), and depth as predictor variables. Hydroacoustic training samples were assigned to one of six predefined groups based on the plurality of benthic elements (sand, sparse SAV, rubble, pavement, rugose hardbottom, branching coral), visually estimated from spatially co-located ground-truthing videos. Records that classified incorrectly or failed to exceed a minimum probability of group membership were removed from the training dataset until only ‘pure’ end-member records remained. This refinement of ‘mixed’ training samples circumvented the dilemma typically imposed by the benthic heterogeneity of coral reefs, i.e. to either train the acoustic ground discrimination system (AGDS) on homogeneous benthos and leave the heterogeneous benthos un-classified, or attempt to capture the many ‘mixed’ classes and overwhelm the discriminatory capability of the AGDS. This was made possible by a conjunction of narrow beamwidth (6.4o) and shallow depth (1.2 to 17.5 m), which produced a sonar footprint small enough to resolve most of the microscale features used to define benthic groups. Survey data classified from the 3rd-Pass training DA were found to (i) conform to visually-apparent contours of satellite imagery, (ii) agree with the structural and biological delineations of a benthic habitat map created from visual interpretation of 2004 IKONOS imagery, and (iii) yield values of benthic cover that agreed closely with independent, contemporaneous video transects. The methodology was proven on a coral reef environment for which high quality satellite imagery existed, as an example of the potential for single-beam systems to thematically map coral reefs in deep or turbid settings where optical methods are unsatisfactory. Chapter 5 Beginning In the winter of 2003-2004, several episodes of red drift macroalgae blooms resulted in massive amounts of macroalgae washing ashore the beaches of Sanibel Island, Bonita Springs, and Ft Meyer Florida. A study conducted after the first event supported a link to increasing land-based nutrient enrichment. A large-scale program was initiated in May 2008, with the primary goal of further defining the possible roles and sources of nutrient enrichment with respect to nuisance macroalgae blooms. This study reports the results of the hydroacoustic mapping component of this program. The goal of this study was to identify areas of substrate suitable for supporting a macroalgae bloom. Areas within San Carlos Bay and offshore Sanibel Island, FL were hydroacoustically surveyed from nearshore to about 11 km offshore during the periods of October 6-10, 2008 and May 10-22, 2009. The hydroacoustic data was acquired with a BioSonics DT-X echosounder and a multiplexed single-beam digital transducers operating at 38 and 418 kHz. Eleven acoustic parameters derived from the 38 and 418 kHz signals were utilized to classify the survey data into 5 ascending categories of visually-apparent seabed roughness. Classes 1 and 2 were both primarily constituted of unconsolidated silt and sand-sized sediments, unsuitable for a bloom. Class 3 is a marginal substrate for a bloom, consisting of packed sand and large intact shell debris. Classes 4 and 5 offer the best attachment sites for a bloom, consisting of consolidated shell hash, live hardbottom, and submerged aquatic vegetation. The majority (~ 80%) of acoustic classifications were of soft bottom sediments (classes 1-2), but there were two significant expanses of rough seabed suitable for macroalgae attachment. These two areas covered a total of 19 km2, within which ~ 56% of the hydroacoustic records classified as “rough” (classes 3-5). The first was a large area of seagrass beds and live hardbottom in the mouth of San Carlos Bay, where large amounts of macroalgae were variably present during the April-May 2009 surveys. The second was offshore Lighthouse Point, near the mouth of San Carlos Bay, situated near a large sand spit that extended from the beach to approximately 6 km offshore. Along the west side of the sand spit there were substantial areas of moderate to high bottom roughness, mostly in the form of consolidated shell hash. The average depths of these two acoustically-rough areas were only 5.0 and 4.0 m, so sufficient irradiance to initiate a bloom could be assumed. These textured and shallow areas on or near the mouth of San Carlos Bay are presumably potential sources for macroalgae attachment and growth, which could easily be transported onto the beaches under some storm conditions given the close proximity to the shoreline. In contrast, the areas in open Gulf of Mexico waters were classified predominantly as soft sediments with low bottom roughness. The site offshore Redfish Pass had a moderate (~22%) proportion of “rough” classifications out to 5km offshore, but from 5-10km offshore the bottom classified as >95% soft sediments. The other two Gulf of Mexico sites classified as >95% soft sediments from nearshore to 11 km offshore. Independent, concurrent video transects indicated there were small areas with large amounts of shell and live hard bottom that occurred sporadically greater than 10km offshore, but all things considered the open Gulf waters around Sanibel Island may not be a major source of drift macroalgae. Chapter 6 This study presents the results of methods developed for acoustic remote sensing of Acropora cervicornis, a threatened species of scleractinian sporadically occurring on the nearshore hardbottom of Southeast Florida. The objective was to develop techniques for mapping isolated Acropora patches on a scale larger than what is feasible using on-the-ground methods. A time-series of A. cervicornis cover could inform resource managers about the fate of such patches, e.g. do they appear and vanish, creep by extension from a central point, or leap by colony fragmentation. The main challenge to acoustically mapping A. cervicornis was distinguishing it from gorgonians occupying the same habitat. Hydroacoustic surveys were conducted in October 2009 at two nearshore sites in Broward County, FL utilizing a BioSonics DT-X echosounder and multiplexed single-beam digital transducers operating at frequencies of 38 and 418 kHz. NCRI scientists have monitored the spatial extent and percent cover of A. cervicornis within these sites, providing an ideal background against which to calibrate the hydroacoustic predictions. Two approaches were evaluated. The first approach utilized BioSonics EcoSAV post-processing software, designed to predict areal cover and canopy height of submerged aquatic vegetation using a series of heuristic pattern-recognition algorithms. Anchored over A. cervicornis, the 38 and 418 kHz signals performed similarly well. Anchored over gorgonians, the 38 kHz signal detected the canopy roughly half as frequently as the 418 kHz signal. Undifferentiated 418 kHz EcoSAV cover was allocated to either A. cervicornis or gorgonians exploiting this frequency-dependent detection. The second approach utilized the acoustic energy (E0, E1′, E1, and E2) and shape (fractal dimension) parameters obtained from BioSonics Visual Bottom Typer software. A dual-frequency training dataset was used to classify records as sand, bare pavement, gorgonians, or A. cervicornis. Both approaches yielded promising results, based on a number of metrics, unambiguously demonstrating that single-beam AGDS are capable of reliably detecting A. cervicornis and gorgonians under controlled conditions.

Dans un contexte de changement climatique et d’érosion de la biodiversité marine, la surveillance écologique des habitats marins les plus sensibles est primordiale et nécessite des méthodes opérationnelles de suivi permettant aux décideurs et gestionnaires d’établir des mesures de conservation pertinentes et d’évaluer leur efficacité. TEMPO et RECOR sont deux réseaux de surveillance centrés sur les herbiers de posidonie et les récifs coralligènes, les deux habitats les plus riches et sensibles de Méditerranée. L’objectif de cette thèse est de répondre aux besoins de la surveillance des habitats marins par le développement de méthodes d’évaluation de leur état de santé, basées sur deux techniques d’analyses d’images clés : les réseaux de neurones convolutifs et la photogrammétrie. Les résultats montrent que les réseaux de neurones convolutifs sont capables de reconnaître les principales espèces des assemblages coralligènes sur des photos sous-marines issues de RECOR, avec une précision semblable à celle d’un expert taxonomiste. Par ailleurs, nous avons montré que la photogrammétrie permettait de reproduire en 3D un habitat marin avec une grande précision, suffisante pour un suivi de la structure de l’habitat et de la distribution d’espèces à fine échelle. À partir de ces reconstructions, nous avons mis au point une méthode de cartographie automatique des herbiers de posidonie, permettant de réaliser un suivi temporel de la qualité écologique de cet habitat sensible. Enfin, nous avons caractérisé la structure 3D des récifs coralligènes à partir de leurs reconstructions photogrammétriques et étudié les liens avec la structuration des assemblages qui les composent. Ce travail de thèse a permis de développer des méthodes opérationnelles, aujourd’hui intégrées aux réseaux de surveillance TEMPO et RECOR, et ouvre la voie à de futures recherches, notamment la caractérisation de l’activité biologique des récifs coralligènes grâce au couplage entre photogrammétrie, réseaux de neurones et acoustique sous-marine
In a context of climate change and the erosion of marine biodiversity, ecological monitoring of the most sensitive marine habitats is of paramount importance. In particular, there is a need for operational methods that enable decision-makers and managers to establish relevant conservation measures and to evaluate their effectiveness. TEMPO and RECOR are two monitoring networks focusing on Posidonia meadows and coralligenous reefs, the two richest and most sensitive habitats in the Mediterranean. The objective of this thesis is to meet the needs of effective monitoring of marine habitats by developing methods for assessing their health, based on two key image analysis methods: convolutional neural networks and photogrammetry. The results show that convolutional neural networks are capable of recognizing the main species of coralligenous assemblages in underwater photographs from RECOR, with a precision similar to that of an expert taxonomist. Furthermore, we have shown that photogrammetry can reproduce a marine habitat in three dimensions with a high degree of accuracy, sufficient for monitoring habitat structure and species distribution at a fine scale. Based on these reconstructions, we have developed a method for automatic mapping of Posidonia meadows, enabling temporal monitoring of the ecological quality of this sensitive habitat. Finally, we characterized the three-dimensional structure of coralligenous reefs based on their photogrammetric reconstructions and studied the links with the structuring of the assemblages that make them up. This PhD work has led to the development of operational methods that are now integrated into the TEMPO and RECOR monitoring networks. Results of this work paves the way for future research, in particular concerning characterization of the biological activity of coralligenous reefs thanks to the coupling of photogrammetry, neural networks and underwater acoustics

This thesis presents a study of the marine habitats of Bahrain together with details of some of the physical factors which may effect the distribution of those habitat types. Satellite remote sensing techniques were employed together with aerial photography and in-field 'ground-truthing' to locate 8 distinct habitat type. A comparison between the satellite-predicted habitat types and the actual habitats present reveals an accuracy of greater than 87%. Over 250 intertidal and subtidal study sites were surveyed for community type, key species, water quality measurements and seasonal variation. A final map of 12 habitat types was produced by expanding on the satellite characterisation using results from the detailed field surveys and the aerial reconnaissance. A set of sensitivity maps was drawn up to identify areas of commercial and scientific importance and to allocate areas in need of conservation, protection and management. The importance of each habitat type and its role in the overall ecosystem is discussed. The findings of this survey constitute the foundations for an effective national marine conservation strategy. Seagrass beds are identified as one of the most important habitat types around Bahrain and the effects of temperature, depth and salinity on the distribution and biomass of the three native species of seagrass are investigated. These three factors are identified as being the most variable physical factors likely to constrain seagrass growth and distribution. 14 sites were surveyed at different seasonal periods to collect data on the biomass, leaf length and leaf number of the different species of seagrass along with temperature, depth and salinity data. The leaf measurements and biomass data from the 3 species of seagrass show a clear relationship to physical factors. Temperature effects the growth of all 3 species to a varying extent. Water depth influences the distribution and growth patterns of Halodule uninervis and Halophila stipulacea. Salinity has no apparent effect on biomass or distribution. The possibility that salinity influences growth pattern and leaf morphology, particularly in Halophila ovalis, is inconclusive and would require further investigation.

La biodiversité englobe toute la diversité des éléments du vivant des molécules à la biosphère et différents niveaux de biodiversité peuvent être distingués. Les habitats coralligènes sont des constructions biogènes calcaires emblématiques de la mer Méditerranée principalement construits par des espèces d’algues rouges calcaires puis consolidés par les squelettes calcaires de différents invertébrés marins. La structure tridimensionnelle formée abrite de nombreuses espèces, faisant des habitats coralligènes un point chaud de biodiversité en mer Méditerranée. L’étude de la diversité génétique chez une algue rouge calcaire ingénieure a révélé la présence d’espèces cryptiques dont l’abondance relative varie en fonction de la localité et de la profondeur. Cette approche a aussi montré que la diversité génétique chez l’espèce cryptique la plus abondante est principalement structurée par des processus neutres de dérive et de migration eux-mêmes influencés par la courantologie. L’étude de la diversité en espèces des communautés, réalisée par une approche de métabarcoding, a révélé une forte diversité au sein des habitats coralligènes ainsi qu’une forte influence des variables environnementales sur la composition des communautés d’espèces. La comparaison des deux niveaux de diversité révèle que la diversité génétique et la diversité spécifique sont positivement corrélées pour la composante alpha et non corrélées pour la composante beta .Cette thèse contribue à améliorer nos connaissances de la biodiversité et du fonctionnement écologique des habitats coralligènes et a aussi permis le développement des certaines méthodes potentiellement applicable au monitoring de ces habitats
Biodiversity encompasses the diversities of all the living elements from the molecules to the biosphere and several levels of biodiversity can be distinguished. Coralligenous habitats are emblematic calcareous biogenic constructions of the Mediterranean Sea mainly built by calcareous red algae and consolidated by calcareous skeletons built by several mine invertebrates. The complex three-dimensional structure shelters for a huge variety of species, and coralligenous habitats are considered to be one of the biodiversity hotspot of the Mediterranean Sea. The study of the genetic diversity of a engineering calcareous red algae, by capture sequencing, revealed that this nominal species is actually composed of eight cryptic species which relative abundances vary among localities and depth. This approach also showed that genetic diversity in the most abundant cryptic species, is shaped by neutral processes of drift and migration strongly influenced by oceanic currents in Marseilles area. The species diversity in communities was studied using a metabarcoding approach. It revealed the high diversity found in these habitats and the important effect of environmental variables on the species communities composition. The comparison between both level of diversities established that that genetic diversity and species diversity are positively correlated for the alpha component of diversity and uncorrelated for the beta component.These work contribute to improve our knowledge of the biodiversity and ecological functioning of these habitats. Some of the methods developments and tuning implemented during this study could be used in monitoring applications of these habitats

Harbour porpoise (Phocoena phocoena) are the most abundant cetacean in UK waters, and are likely to be affected by a variety of marine industries and activities. This research uses data collected by acoustic recorders (C-PODs) and aerial video surveys to investigate patterns in porpoise detection. The findings can be split into five key themes, and are used to support the development of spatial management and survey recommendations. 1. Porpoise detection changes based on time of day in different habitats, indicating possible differences in diel habitat use and highlighting potential issues with visual or video data collection methods for assessing distribution. 2. Porpoise exhibit seasonal shifts in detection, yet year-round data are often lacking, therefore seasonal changes in distribution are often unknown. 3. The highest proportions of buzzes (associated with foraging) are not detected in areas with the highest relative density of porpoise. I propose that porpoise use different foraging strategies in different habitats which are not equally detectable by acoustic recorders. 4. Porpoise distribution may be influenced by the distribution of perceived risk from predator / competitor species (dolphins). Temporal partitioning of sites may arise either from porpoise actively avoiding times when bottlenose dolphins are expected to be present, or from porpoise and bottlenose preferences for different environmental conditions. 5. The choice of spatial modelling method can influence the fine-scale predictions of areas with the highest density. Improving our understanding of top and mesopredator ecology is informative for management strategies. Each of the points raised above should be considered when determining management strategies to minimise the impact from fisheries, offshore developments and other industrial activities on harbour porpoise.

Thesis (doctoral)--Ludwig-Maximilians-Universität München, 2006.
Title from PDF t.p. (viewed on May 14, 2006). Includes reprints of papers co-authored with others. Vita. Includes bibliographical references.

Quantitative photographs of benthic communities at two northern Miami Terrace sites, originally investigated as part of an environmental impact survey in advance of the proposed Calypso pipeline, and two Pourtalès Terrace sites, investigated as part of an exploration of deep-sea coral and sponge ecosystems (DSCEs) within the Pourtalès Terrace Deep-water Coral Habitat Area of Particular Concern (CHAPC), were reanalyzed and compared for similarities and differences. Both terraces are part of an elongated lithified platform that parallels the southeastern Florida coast at depths averaging between 250 and 450 m. Although both sites have similar geological origins and lie under the Florida Current, previous work has suggested that the two terraces support different benthic faunas. Images from 28 phototransects from the two terraces were condensed into two depth bins of 250-300 m and 450-550 m. Distributions of taxa compared among individual sites were depth driven, whereas distributions of taxa between the northern Miami Terrace and Pourtalès Terrace appeared to be driven by geological features, as sites at similar depths had different communities and densities, with the only distinguishing variables being location and geologic features. Results indicate that location is the driving factor contributing to differences in deep-water benthic communities between the two terraces. Depth bin 450-550 m was dominated on the Miami Terrace by hard substrates supporting octocorals (Pseudodrifa nigra, Primnoidae, Keratoisis sp., and Anthomastus sp.), anemones, and sponges (mainly Phakellia sp.) and on the Pourtalès Terrace by hard substrates and coral rubble supporting Paramuricea unid sp. 3, Comatonia cristata, Plumarella sp. 2, and Astrophorina unid. sp. 4. Depth bin 250-300 m on the northern Miami Terrace was dominated by sediment substrates and supported anemones, soft corals and zoanthids, and on the Pourtalès by sediment-veneered hard bottom with Stylaster miniatus, Plumarella unid sp., Hydroida unid sp., and Isididae unid sp. 2. The relationships between depth, location and geomorphology may be useful in designing future benthic mapping projects. In addition, species densities and protection statuses can aid future community assessments between protected habitats and non-protected habitats to measure the effectiveness and management strategies of deep-water marine protected areas. The relationships revealed by this study can be used to support the management of the Miami Terrace, Pourtalès Terrace, and other sites to conserve deep-water coral environments.

I Cambiamenti climatici e le attività antropiche hanno un ruolo nel determinare la composizione degli habitat bentonici ed interferiscono nel funzionamento di molti processi ecosistemici. La quantificazione dei cambiamenti a livello di habitat è ad oggi limitata da tradizionali metodi di campionamento e tecnologie impiegate.Lo scopo di questa ricerca è di ottimizzare la caratterizzazione di habitat marini bentonici utilizzando metodi fotogrammetrici basati sulla Structure for Motion (SfM). Gli obiettivi sono (i) standardizzare una metodologia per lo studio della composizione spaziale di comunità bentoniche ed individuare l’effetto della scala del campione nel determinare la sua rappresentatività; (ii) applicare e testare la metodologia sviluppata per studiare l’effetto di pressioni antropiche e naturali su comunità bentoniche di barriere coralline; e (iii) di proporre nuovi metodi per lo studio della struttura di popolazione e biomassa si organismi bentonici a portamento eretto. La ricerca è stata condotta presso la Riserva Marina Parziale di Ponta do Ouro (PPMR, Mozambico) e l’Area Marina Protetta di Portofino (Italia). Presso la PPMR è emerso che l’area ottimale di campionamento è di 25 m2. Questa superficie di campionamento permette di descrivere diversità, abbondanza, complessità strutturale e morfologica degli organismi della barriera corallina e di studiare gli effetti dei delle attività antropiche (i.e. immersioni subacquee ricreative). Siti di immersione altamente frequentati presentano una bassa densità e diversità di taxa, e sono principalmente popolati da organismi resistenti- a- impatti- di- natura- fisica (i.e. spugne ed alghe) di grandi dimensioni e forme complesse. Al contrario, siti di immersione scarsamente frequentati presentano organismi fragili- a- impatti- di- natura- fisica (i.e. Acropora spp.). Questa ricerca ha dimostrato che nuvole di punti generate da SfM possono essere utilizzate non solo per il calcolo di metriche dimensionali ed abbondanza di organismi a portamento eretto, ma anche per accurate stime della loro biomassa. Il medoto proposto quindi supporta studi di per il calcolo della produttività secondaria ed evita campionamenti distruttivi. Questa tesi sottolinea come SfM possa essere impiegata in supporto alla gestione di aree marine protette ed enfatizza sulla necessità di (i) standardizzare l’impiego di metodi basati sulla SfM a scale spaziali rilevanti per la conservazione degli habitat; (ii) migliorare gli approcci per la stima di biodiversità, biomassa di organismi bentonici e della struttura dei loro habitat, and (iii) provvedere a nuove conoscenze sulla variabilità spaziale delle comunità bentoniche come risultato di pressione antropiche.
Global environmental changes and human activities are having significant effects on the composition of marine benthic habitats, disturbing the ecological functioning of many ecosystems. Yet, quantifying ecological responses to habitat changes is challenging because of limitation of current field methods and technology. The aim of this research is to improve the characterization of benthic marine communities by using Structure for Motion (SfM)-based methods. The objectives are (i) to provide a SfM framework to assess the spatial composition of benthic communities and uncover the scale-specific effects that determine sample representativeness; (ii) to apply and test the framework to study the effects of human and environmental pressures on coral reefs; and (iii) to propose a new method for investigating the population structure and biomass of benthic tree-shaped species. The research was carried out at the Partial Marine Reserve of Ponta do Ouro (PPMR, Mozambique) and at the Marine Protected Area of Portofino (Italy). At PPMR, the findings show that the best sampling size is 25 m2. This size allowed capturing the diversity, abundance, structural complexity and morphological functions of reefs' organisms, and investigating changes driven by anthropic activities (i.e. scuba diving). Highly dove sites had low taxa diversity and density, and were characterized by mainly resistant-to-physical-impact organisms (i.e. sponges and algae) of big sizes and with complex shapes. On the contrary, low or moderately dove sites presented fragile-to physical- impact organisms (i.e. Acropora spp.). This research also demonstrated that in addition to abundance and morphological information, the use of SfM point clouds over tree-shaped organisms allows to have accurate prediction of biomass, avoiding to conduct destructive sampling and supporting the calculation of secondary production. To support marine management using SfM to investigate benthic communities, this research emphasizes the need to (i) recognise the need of standardised approaches of SfM method to identify relevant scales for conservation; (ii) develop better approaches to derive quantitative information on marine organisms biodiversity, biomass and on their structural habitat, and (iii) establish further knowledge on the spatial variation of benthic communities as a result of human pressure.

Few studies of tropical fish communities compare fish distributions across the full range of near-shore tropical marine habitats. As a result, our understanding of tropical marine fish communities is often biased towards habitats preferred by researchers. The distribution and habitat preferences of all 136 fish species occurring at 106 stations in three bays off Tortola in the British Virgin Islands were assessed. At a species level, habitat type was often the key factor influencing fish distribution. Of the 44 species occurring at more than 10 stations, 3 were sand specialists, 5 were strongly associated with mangroves, 7 were dependent on seagrass and algal beds and 14 were found only on the forereef. Eleven species were widely distributed both on the forereef and in bays, and 9 of them showed clear evidence of ontogenetic partitioning. The juveniles all preferred bay habitat types and moved onto the forereef as they approached sexual maturity. At a community level, five distinct fish assemblages were found. The assemblage types were classified according to their distribution: 1) forereef, 2) reef flat, 3) non-mangrove associated seagrass, 4) mangrove associated seagrass and 5) eutrophic areas. Forereef stations were the most species-rich with 24 species per station while eutrophic stations had the most depauperate communities with only 4 species per station. Variation in fish species richness at each station was largely explained by a simple habitat complexity index. It accounted for 70% of the variation in fish species richness and 21% of the variation in fish abundance. Rugosity and variety of growth forms were the most important predictors of species richness, but the height of the habitat architecture was the most useful predictor of fish abundance. Artificial reefs were constructed to test the effects of each habitat complexity variable experimentally. Increasing rugosity, variety of growth forms and percentage hard substrate increased the observed number of species but increasing the variety of hole-sizes, and height had no effect. The only complexity variable that had a significant effect on fish abundance was percentage hard substrate. In addition to the static substrate structure, long-spined sea urchins Diadema antillarum affected fish distribution because small fish shelter from predators in their spines. The urchins increase species richness and abundance in low complexity seagrass beds, but on artificial reefs, where shelter was not a limiting factor, the effect was less pronounced. Organic pollution is another factor that negatively affects the fish community by reducing fish species richness and abundance. Poor water quality often alters the natural habitat, confounding observations, but fish species richness was reduced in polluted areas even when artificial reefs were used as habitat controls. The applications of these findings to the management and conservation of fish in the British Virgin Islands are discussed.

Le bassin méditerranéen est reconnu comme un "point chaud" de biodiversité soumis à de fortes pressions anthropiques. En domaine marin, les habitats coralligènes participent grandement à cette biodiversité et leur situation côtière les rend accessibles aux hommes. La thèse porte sur l'identification et l'évaluation de leurs services écosystémiques. J’ai utilisé le concept de \textit{service écosystémique} à une échelle locale : la Baie de Marseille (anthropisée) et le Parc national de Port-Cros (sous pression humaine minimale). Le premier volet de la thèse porte sur l'identification et la description des services rendus par les habitats coralligènes dans les zones d’étude. Les services les plus évidents (production de ressource alimentaire, production de corail rouge et sites de plongée) font l’objet d’une étude plus approfondie. Le deuxième volet de la thèse teste le concept de cascade de service écosystémique d'Haines-Young et Potschin pour décrire les éléments et fonctions de l'écosystème impliqués dans chaque service, les bénéficiaires et les types de valeurs économiques qui en sont issus, et des indicateurs pour mesurer chaque niveau de la cascade. Le troisième volet de la thèse porte sur une analyse de l'activité de plongée sur les habitats coralligènes de la baie de Marseille. Le dernier volet de la thèse est une étude des préférences déclarées dans les secteurs de Marseille et Port-Cros concernant les services rendus par les habitats coralligènes, grâce à la méthode des choix discrets. Ce dernier volet comprend une étude de l’impact de la connaissance initiale et de l’apport d’information dans la formation des préférences
The Mediterranean basin is recognized as a "hotspot" of biodiversity subjected to strong anthropic pressures. In the marine domain, coralligenous habitats greatly contribute to the basin’s biodiversity and their coastal location makes them accessible to humans. The thesis attempts to identify and economically evaluate some of those ecosystem services. I used the concept of \textit{ecosystem service} at a local scale, focusing on the Bay of Marseille (anthropized) and the Port-Cros national park (under minimal human pressure). The first part of the thesis deals with the identification and description of the services rendered by coralligenous habitats in the study areas. The second part of the thesis describes the provisionning services through the application of the concept of ecosystem service cascade as developed by Haines-Young and Potschin. This approach helps to identify the elements and functions of the ecosystem involved in each service, the human beneficiaries and the types of economic benefits associated with the services. This chapter also proposes variables to measure each level of the cascade. The third part of the thesis deals with an analysis of the relationship between the presence of coralligenous habitat and the frequency of dives in the Bay of Marseille. The last part of the thesis employs the method of discrete choices experiment to study the declared preferences in the study areas of Marseille and Port-Cros concerning the services rendered by the coralligenous habitats. This analysis provided insight into how preferences can evolve as initial knowledge is enhanced through the provision of additional information

Les habitats de coraux d’eau froide formés par des scléractiniaires coloniaux, des gorgones, des antipathaires et des pennatules sont des hotspots de biodiversité et de biomasse. Ils fournissent des fonctions importantes, comme des refuges et des zones d’alimentation, pour d’autres organismes. Mais, ils sont également vulnérables aux activités humaines, parce qu’ils sont fragiles, croissent lentement et atteignent des records de longévité. Dans les canyons sous-marins, le relief tourmenté, l’hydrodynamisme et l’hétérogénéité des substrats offrent des conditions environnementales propices au développement des habitats coralliens. Dans le Golfe de Gascogne, les coraux d’eau froide sont connus depuis la fin du 19e siècle, mais leur distribution, leur densité et leur rôle fonctionnel avaient été très peu étudiés.Pour augmenter cette connaissance, 24 canyons sous-marins et 3 sites sur l’interfluve/haut de pente contiguë aux canyons adjacents ont été visités par un ROV et une caméra tractée pendant 46 plongées au cours de 7 campagnes océanographiques. Les habitats coralliens définis par le système de classification CoralFISH ont été cartographiés à partir des images prises par les engins sous-marins puis la faune associée, les types de substrat et les déchets ont été annotés.Onze habitats coralliens et 62 morphotypes de coraux ont été observés dans les canyons sous-marins du Golfe de Gascogne hébergeant 191 morphotypes de faune associée, dont 160 morphotypes uniques. Les patrons de distribution à l’échelle locale et à l’échelle régionale pourraient être liés aux régimes hydrodynamiques et sédimentaires. Le type de substrat était important pour les assemblages de coraux et leurs faunes associées, distinguant les habitats biogéniques, sur substrat dur et sur substrat meuble. Les assemblages de coraux étaient similaires entre habitats biogéniques et habitats sur substrat dur, mais la faune associées était plus abondante et diversifiée sur les habitats biogéniques. La diversité-alpha, -beta et –gamma étaient étonnement élevée sur les habitats coralliens sur substrat meuble, égalant ou dépassant la diversité des habitats biogéniques.Les déchets marins étaient abondants et principalement composés de plastiques et de matériels de pêche. Ces déchets pourraient impacter les habitats coralliens : ils ont été trouvés à des profondeurs similaires et les déchets étaient piégés par des reliefs créés par des structures biologiques et géologiques. L’ocurrence des récifs de coraux préférentiellement sur les pentes plus abruptes des canyons sous-marins tandis que les débris de coraux sont plus fréquents sur des aires plus plates de l’interfluve ou du haut de pente, pourraient indiquer un impact de la pêche.Cette étude a contribué à l’initiative en cours de création d’un réseau Natura 2000 qui protégera à terme l’habitat « récif » dont les habitats coralliens biogéniques et sur substrat dur, mais pas les habitats coralliens sur substrat meuble. Pour ces derniers, un complément d’étude et d’autres stratégies de préservation seront nécessaires
Cold-water coral (CWC) habitats formed by colonial scleractinians, gorgonians, antipatharians and sea pens are biodiversity and biomass hotspots that provide important functions, such as shelter and feeding grounds, to other organisms. But, they are also vulnerable to human activities, because they are long-lived, grow slowly and have a low resistance. Submarine canyons may offer the environmental conditions needed for CWC habitat development, due to their steep topography, complex hydrodynamics and substrate heterogeneity. In the Bay of Biscay, which margin is incised by hundreds of canyons, CWCs are known to exist since the late 19th century, but their distribution, density and functional role remained largely unknown, which impaired their preservation.To increase this knowledge, 24 canyons and three locations between adjacent canyons were visited with an ROV and a towed camera system during 46 dives on 7 cruises. Images were analysed for CWC habitats using the CoralFISH classification system. Within these habitats, corals, associated fauna were identified and substrate cover measured. Litter was identified in 15 out of 24 canyons.Eleven coral habitats constructed by 62 coral morphotypes were observed in the canyons of the Bay of Biscay hosting 191 associated megafaunal morphotypes, including 160 unique morphotypes. The distribution patterns at regional and local scales could be linked to hydrodynamics and sedimentary regimes. Substrate type was an important driver for coral and associated faunal assemblages, distinguishing biogenic, hard substrate and soft substrate habitats. Coral assemblages were similar between biogenic and hard substrate habitats, but the associated fauna was more abundant and diverse on biogenic habitats. The alpha, beta and gamma diversity was surprisingly high on soft substrate habitats, equalling or exceeding that of biogenic habitats.Marine litter was abundant and was mainly composed of plastic items and fishing gear. Litter could co-occur with CWCs and impact them: litter and most CWC habitats were observed at similar water depths and litter was more abundant in areas with a seafloor relief created by biological or geological features. Observations of coral reefs on steeper areas in the canyons and coral debris on flatter areas on the interfluve/upper slope may indicate a potential impact of the fishing industry. This study supports the ongoing effort to create a Natura 2000 network that will protect biogenic and hard substrate habitats, but also points out the need to develop a framework for the preservation of coral habitats on soft substrate

The concept of temperature dependent sex determination (TSD) has been somewhat of an evolutionary enigma for many decades and has had increased attention with the growing predictions of a changing climate, particularly in species that are already threatened or endangered. TSD taxa of concern include marine turtles, which go through various life stages covering a range of regions. This, in turn, creates difficulties in addressing basic demographic questions. Secondary sex ratios (from life stages post-hatchling) were investigated by capturing juvenile green turtles (Chelonia mydas), 22.6-60.9 cm in straight carapace length (SCL), from three developmental areas along the east coast of Florida (a region known to have important juvenile aggregations) by analyzing circulating testosterone levels. All three aggregations exhibited significant female biases with an overall ratio of 3.2:1 (female: male). The probability of a turtle being female increased as the size of the individual decreased. Ratios obtained in this study were slightly less female-biased, but not significantly different, than those observed in the late 1990s. However, they were significantly more biased than those found in a late 1980s pilot study. The shift to significantly female-biased ratios may be beneficial to a recovering population, an evolutionary adaptation, and is common among juvenile aggregations. A more skewed female bias in smaller size classes may be indicative of recent, warmer periods during incubation on the nesting beaches. This female bias could become more exaggerated if temperatures meet future climate warming predictions.
M.S.
Masters
Biology
Sciences
Biology

This study investigates a way to characterize the geology and biology of the seafloor in two Marine Protected Areas on the West Florida Shelf. Characterization of benthic habitats needs to include sufficient detail to represent the complex and heterogeneous bottom types. Characterizations can be interpreted from multiple data sets and displayed as benthic habitat maps. Multibeam sonar bathymetry and backscatter provide full spatial data coverage, but interpretation of such data requires some form of ground truth (to characterize the habitat). Imagery from towed underwater video provides continuous transects of seafloor data, which provide a more efficient method than data from sediment grabs, stationary cameras, or video from slow-moving remotely-operated vehicles while a ship is on station. Two Marine Protected Areas, Steamboat Lumps and Madison-Swanson, were previously mapped by the USGS using a 95 kHz multibeam sonar system. Researchers at the University of South Florida, using a 300 kHz high-resolution multibeam sonar in 2002 and a 400 kHz high-resolution multibeam sonar in 2016, filled in the northeast triangular portion of Madison-Swanson. Bathymetry and backscatter data were compared to towed underwater-video observations. A modified version of the Coastal and Marine Ecological Classification Standard (CMECS), utilizing a scale-based hierarchy, was used for habitat characterization of video images. Identifiers from the geoform and substrate components of CMECS, as well as substrate-influencing biologic components, were characterized using still images at 15-second intervals from towed underwater video collected using the Camera-Based Assessment Survey System (C-BASS). These characterizations were then georeferenced (located in three-dimensional space) for comparison with bathymetry and backscatter data. In Steamboat Lumps, eight substrate variations were identified from video, while in Madison-Swanson 27 substrate variations were identified, including many combinations of hard and soft substrate types. Four new hard-bottom textures are identified from video in Madison-Swanson: exposed high-relief, moderate-relief, and low-relief hard bottom, as well as covered low-relief hard bottom identified by the presence of attached biota. Hard- and mixed-bottom substrate types identified from video are more heterogeneous than can be resolved from 95 kHz Kongsberg EM 1002 multibeam sonar bathymetry and beam-averaged backscatter. However, in soft bottom areas, more changes are evident in beam-averaged backscatter than are visible in video, though this may be attributed to changes in sonar settings. This does not appear to be the case with high-resolution and ultra-high resolution multibeam sonars, such as the 300 kHz Kongsberg EM 3000 and the 400 kHz Reson SeaBat 7125, which can use time-series rather than beam-averaged backscatter. Analyses of the multibeam bathymetry data indicate that 94.5% of Steamboat Lumps is “flat” (slope < 5°) versus “sloping” for the remaining area (5° < slope < 30°). Only 87% of Madison-Swanson is “flat” versus “sloping”. Both marine protected areas have very low rugosity, i.e., the surface of the seafloor is nearly planar.

The Florida Reef Tract (FRT) extends from the tropical Caribbean northward along the Florida coast into a warm temperate environment where tropical reef communities diminish with increasing latitude. This study was designed to map the nearshore benthic habitats including coral reefs and evaluate how the benthic communities differ between habitats and along the coast. Benthic communities across the northern FRT from Key Biscayne to Hillsboro Inlet (25.5°-26.3° N) were digitized from aerial photography taken in 2013 at a 1:1,000 scale. Three main hard-bottom habitat types were identified that ran parallel to shore and consecutively further away from shore: Colonized Pavement, Ridge, and Inner Reef. Five 1-km wide cross-shelf corridors (numbered 1-5, south to north) were designated and spaced as evenly as possible throughout the region. Five sites per habitat per corridor (70 total) were randomly selected and quantitative data collected within 4,200 m2. Significant differences in percent benthic cover among habitats were found in all corridors and within habitat types between corridors, indicating cross-shelf and latitudinal variation. Mean stony coral density increased with depth, with the Inner Reef habitat being significantly higher than both the Colonized Pavement and Ridge. Mean stony coral species richness also increased with depth, with all habitats significantly different from one another. A total of 22 stony coral species were identified within the mapped region, the three most abundant being Porites astreoides, Siderastrea siderea, and Acropora cervicornis. Results from this study support the ecosystem regions denoted in the Walker (2012) study. Corridor 1, located in the Biscayne Region, was the only corridor to contain any seagrass. In addition, Corridor 1 Inner Reef had significantly higher values for mean stony coral density, mean stony coral species richness, mean gorgonian density of the plume morphotype, and mean density of stony corals infected with Cliona spp. Corridors 2-4, located in the Broward-Miami Region, had some variability associated with them, but were generally similar in benthic composition. Corridor 5, likewise located in the Broward-Miami Region but in close proximity to the Deerfield Region, also had differences associated with it. Both the Colonized Pavement and Ridge habitats in Corridor 5 had the lowest mean coral species richness, as well as total absence of both sponge species noted in this study. Corridor 5 Inner Reef also had significantly lower mean stony coral densities compared to Corridors 1, 2, and 4. As such, these results support the idea of different biogeographic regions occurring off the southeastern Florida coast. This study produced two key findings. It discovered over 110 large (>2 m) resilient coral colonies, of which 50 were alive in various conditions. This study also found 38 acres of dense Acropora cervicornis patches, tripling the previously known area within the study region. These are the largest dense patches in the continental United States.

Inshore tropical and subtropical estuaries harbor a relatively high abundance and diversity of organisms. Specifically within estuaries, mangrove and seagrass habitats provide shelter and food for a plethora of organisms, through some or all their life histories. Given the biological connection between offshore coral reefs and coastal estuaries, there is a critical need to understand the underlying processes that determine distribution and abundance patterns within mangrove-seagrass habitats. The predatory fish assemblage within the mangrove and seagrass beds of Biscayne Bay, Florida (USA), was examined over 24-hr. time periods along a distance and habitat gradient from the mangrove edge and nearshore environment (0–300 m) to farshore (301–700 m) seagrass beds. This thesis also investigated the occurrence, distribution and timing of reef fish movement between offshore coral reef habitat and inshore seagrass beds over 24-hr periods. Results indicate that fish predators differed over both the sampling period and with distance from mangrove edge. The results also demonstrated reef fishes move into Biscayne Bay at dusk and exit at dawn by utilizing Broad Creek Channel as a passageway. This work supports the idea of diel migration of selected reef fishes to inshore seagrass beds and highlights the importance of connective channels between habitats. The results suggest that the degradation or loss of seagrass habitat could differentially impact the life-history stages of reef fish species.