In the Arctic, shallow sea-floor communities have been documented to shift abruptly from an invertebrate-dominated state to a state with high macroalgal abundance. Climate warming, resulting in increased water temperatures and decreased sea ice cover, could trigger such regime shifts in benthic ecosystems, but the underlying mechanisms are not clear. To gain a better understanding, a mechanistic model of algal growth and interspecific competition was applied in two marine ecosystems in northwestern Svalbard. Unravelling the effects of light and temperature on the model parameters, the current study showed that light is a key factor determining the algal dominance in the two ecosystems. Changes in sea-ice cover, which alters the underwater light regime, is therefore considered the most likely trigger for invertebratealgae regime shifts. A continued prolonging of the ice-free season in the Arctic is likely to occur in the upcoming years, considering the current climatic development. Thus, it is expected that macroalgal cover in shallow rocky-bottom communities will continue to increase, altering species composition and function in seasonally ice-covered arctic ecosystems. / I ekosystem på grunda havsbottnar i Arktis har snabba, kraftiga förändringar i artsammansättning och ekosystemstruktur dokumenterats. Organismsamhällen som tidigare främst utgjorts av ryggradslösa organismer och hårda kalkalger har plötsligt blivit dominerade av olika tångarter. Den globala uppvärmningen medför högre ytvattentemperatur och minskat havsistäcke i Arktis, vilket i sin tur innebär förbättrade ljusförhållanden. Dessa förändringar tros kunna utlösa regimskiften där de ekosystemen övergår från ett stadium dominerat av ryggradslösa djur, till ett stadium dominerat av tång. Mekanismerna bakom sådana regimskiften är emellertid inte kartlagda. Denna studie syftade därför till en bättre förståelse för regimskiften i Arktiska havsbottenekosystem. En mekanistisk modell för algtillväxt och konkurrens tillämpades på två marina organismsamhällen i nordvästra Svalbard, som genomgått sådana regimskiften. Temperatur- och ljusberoendet hos modellens parametrar uppskattades först utifrån kunskap från ett antal tidigare studier. Med hjälp av modellen testades sedan hur fördelningen av alger påverkades av temperatur- och ljusförändringar. Modelleringen indikerade att ljusförhållanden var avgörande för expansionen av tång i de två studerade organismsamhällena på Svalbard, och att ljusförändringar således kan vara en huvudsaklig orsak till regimskiften i Arktis. Med tanke på den nuvarande klimatutvecklingen är en fortsatt förlängning av den isfria säsongen mycket sannolik. Detta kommer troligen innebära en vidare expansion av tång samt förändrad artsammansättning och ekosystemfunktion i grunda, arktiska havsbottenekosystem.

Regulation of transcription is an important molecular mechanism through which organisms can respond to environmental change. Environmentally-related transcriptional variation can play a significant role in evolution, potentially acting as a mechanism for the formation of new adaptive phenotypes. Organisms are most sensitive to the influence of external environmental variation during development, yet very few studies have explored environmentally-related transcriptional variation in early life history stages. Marine invertebrate metamorphosis, where intimate larval-environment interactions trigger settlement onto the benthos and a drastic morphological shift from larval to adult form, exemplifies the influence of environment on development. Variation in both the timing of metamorphosis and the form of specific metamorphic inductive cues, even at an intraspecific level, suggests that larvae have molecular mechanisms for surviving settlement and metamorphosis in a range of environmental conditions. The extent of transcriptional variation at metamorphosis remains largely unknown due to limited information on both the natural inductive cues and the molecular mechanisms directing metamorphosis in marine invertebrates. Contributing to current understanding of the interplay between genes, environment and phenotype during development, I explored molecular and ecological aspects of metamorphosis in a marine invertebrate, the tropical abalone Haliotis asinina. First, I employed cDNA microarray methods to identify candidate genes and document widespread transcriptional changes occurring in Haliotis asinina larvae during larval development and metamorphosis. Microarray results reveal that as the abalone veliger larva matures, it requires coordinated regulation of temporally different gene batteries involved in a wide range of physiological and developmental processes associated with the transition to a new, benthic habitat. All candidate genes showed changes in expression following exposure of larvae to coralline algae, an external inductive cue, demonstrating the remarkable effect of environment on transcription during marine invertebrate metamorphosis. 144 genes, ~40% of which are novel, were identified as candidates for a role in H. asinina metamorphosis. This high proportion of novel genes indicates that the conserved signaling pathways operating in marine invertebrate metamorphosis likely regulate the expression of taxon-specific genes. The relationship between abalone larvae and their natural inductive cue, coralline algae, is species-specific. To characterize the metamorphic cue preferences of Haliotis asinina larvae from Heron Island Reef, Australia, I documented larval induction response to a number of different coralline algae species commonly found in adult H. asinina habitat. H. asinina larvae exhibit highly specific responses to induction of metamorphosis by different coralline algae species, with 0 – 100% metamorphosis by 48 hours post induction depending on algae species. Unlike any other abalone species studied, the most effective inducers of Heron Island Reef H. asinina are articulated corallines of the genus Amphiroa. Comparing the response of different larval families to select species of coralline algae indicated that coralline algae community composition is likely to significantly impact H. asinina population structure. Additionally, I compared larval response to dead and live coralline algae to show that induction specificity is driven by chemical, not physical, properties. Characterization of the surface cell biomarkers of three different coralline algae species indicates that algal biomolecular composition relates to variations in H. asinina induction response. To explore the influence of variation in larval induction environment, I compared transcription patterns of 17 metamorphosis-related genes in Haliotis asinina larvae induced by three different species of coralline algae. H. asinina post-induction gene expression profiles vary according to the species of coralline algae inducer. This transcriptional variation occurs in genes with diverse functions and spatial expression patterns, highlighting the global nature of the impact of benthic microhabitat on gene expression. The environment-specific modulation of gene expression in H. asinina post-induction may be a means for marine invertebrates to cope with changes in their settlement environment at metamorphosis. Genes expressed in the larval sensory structures acting to detect external metamorphic cues may be particularly good candidates for studying environmentally-related transcriptional variation. I identified three novel genes expressed in putative sensory structures of Haliotis asinina larvae just prior to metamorphosis. The spatial and temporal expression patterns of these genes correlate with changes in larval ciliation patterns throughout metamorphosis, strongly suggestive of a role in metamorphic initiation. The three genes exhibit significant overlap in spatial expression profiles, indicative of genetic crosstalk between different sensory systems at metamorphosis. Transcriptional variation in gastropod sensory system genes may have assisted the evolution of different metamorphic inductive cues for different species. The results presented here establish an important role for transcriptional variation during marine invertebrate metamorphosis. Transcriptional variation underlies the morphological change from larval to adult body plan and also appears to assist larval recruitment in variable benthic habitats. Modulation of gene expression at metamorphosis in response to the environment may ultimately influence marine invertebrate species biogeography and evolution.

<p>To further investigate the strength of the association and the relative advantages of the association to both organisms, several manipulation experiments were set up. A cage experiment set up in the shallow subtidal zone showed that the coralline survived equally well without the winkle and did therefore not require the winkle or its empty shell for survival. A second controlled laboratory aquarium experiment was designed under both fluorescent (rich in blue light) and incandescent light (rich in red light) to ascertain whether the coralline had a preference for O. sinensis over the similar O. tigrina. This experiment was inconclusive as no recruitment was obtained under either of the light regimes. A third laboratory experiment was designed to determine whether the extra coralline weight had any possible advantage to the winkle, particularly against predation from the rock lobster Jasus lalandii. Results suggested that there were no apparent advantages to the winkle bearing the extra coralline load as adult O. sinensis bearing the coralline alga (3.7 &plusmn / 2.2 winkles 24hr-1) were equally prone to predation than those lacking the coralline (2.3 &plusmn / 1.9 winkles 24hr-1) (p = 0.184). Observations suggested instead that the convoluted nature of the coralline may indeed have promoted predation. We ultimately deduced that the high occurrence of the coralline on the shells of O. sinensis was probably due to the substantial overlap in the niches of the two organisms. This conclusion was supported by the high densities of juvenile O. sinensis combined with the high percent cover abundance of the coralline in intertidal rockpools. Understanding sexual reproduction in coralline algae as well as the life cycle of the winkle, ultimately provided insight into the postulated life cycle of this coralline-winkle association...</p>

The Miocene Nullarbor Limestone is the most recent formation in the Cenozoic Eucla Group and was deposited in the Eucla Basin, southern Australia, at ~38°S paleolatitude during the early to middle Miocene. The rocks form the modern surface of the vast, karsted Nullarbor Plain. Older Eucla Group marine carbonates (Eocene-earliest Miocene) are cool-water in nature and dominated by bryozoans and echinoderms. The Nullarbor Limestone is subtropical in composition and rich in coralline algae (rhodoliths and articulated types), large and small benthic foraminifera and molluscs. Diverse zooxanthellate corals are also present but not numerous. Deposition is interpreted to have taken place in three main paleoenvironments: rhodolith gravels, seagrass banks, and open seafloors. The Southern Ocean extended inboard ~450 km from the shelf edge during Nullarbor Limestone deposition. Interpreted paleodepths ranged from the top to the base of the photic zone, implying a small slope over a wide shelf. The Miocene Eucla platform is therefore interpreted to have been epeiric in nature. Paleoenvironment distribution is explained using epeiric platform sedimentation patterns and comparisons with modern environments. Open seafloor environments, the deepest settings, are thought to have been below fair-weather wave base. Rhodolith gravels accumulated at intermediate depths, where waves frequently swept the seafloor. Seagrass banks developed in the shallowest waters farthest inboard, where wave energy had been largely dissipated. Diverse corals, large benthic foraminifera and micrite envelopes inboard and in the western part of the basin support the notion of paleotemperatures generally above 20°C, the upper limit of subtropical carbonate accumulation. Although deposition occurred during the Miocene Climatic Optimum, a simple overall temperature increase cannot completely account for the subtropical nature of these sediments at mid-latitudes. Tropical components decrease from west to east, implying a temperature gradient, probably due to the warm proto-Leeuwin Current. Thus, these subtropical carbonates were deposited at mid-latitudes and their presence did not simply reflect a change in global climate. / Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2010-12-23 16:05:47.981

<p>To further investigate the strength of the association and the relative advantages of the association to both organisms, several manipulation experiments were set up. A cage experiment set up in the shallow subtidal zone showed that the coralline survived equally well without the winkle and did therefore not require the winkle or its empty shell for survival. A second controlled laboratory aquarium experiment was designed under both fluorescent (rich in blue light) and incandescent light (rich in red light) to ascertain whether the coralline had a preference for O. sinensis over the similar O. tigrina. This experiment was inconclusive as no recruitment was obtained under either of the light regimes. A third laboratory experiment was designed to determine whether the extra coralline weight had any possible advantage to the winkle, particularly against predation from the rock lobster Jasus lalandii. Results suggested that there were no apparent advantages to the winkle bearing the extra coralline load as adult O. sinensis bearing the coralline alga (3.7 &plusmn / 2.2 winkles 24hr-1) were equally prone to predation than those lacking the coralline (2.3 &plusmn / 1.9 winkles 24hr-1) (p = 0.184). Observations suggested instead that the convoluted nature of the coralline may indeed have promoted predation. We ultimately deduced that the high occurrence of the coralline on the shells of O. sinensis was probably due to the substantial overlap in the niches of the two organisms. This conclusion was supported by the high densities of juvenile O. sinensis combined with the high percent cover abundance of the coralline in intertidal rockpools. Understanding sexual reproduction in coralline algae as well as the life cycle of the winkle, ultimately provided insight into the postulated life cycle of this coralline-winkle association...</p>

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / CoordenaÃÃo de AperfeÃoamento de Pessoal de NÃvel Superior / Neste trabalho foram analisadas as caracterÃsticas geoquÃmicas das algas calcÃrias do nordeste brasileiro, situadas em diversas profundidades, coletadas na plataforma continental e em bancos oceÃnicos em diversos programas de geologia marinha. As determinaÃÃes realizadas nesta pesquisa foram a difratometria de raios X (DRX), fluorescÃncia de raios X (FRX), Infravermelho (IV), Microscopia EletrÃnica de Varredura (MEV), a determinaÃÃo de elementos quÃmicos, do teor de carbonato de cÃlcio e assinaturas isotÃpicas de carbono e oxigÃnio. Foram selecionadas 66 amostras entre Lithothamnion sp. e Halimeda sp., mas apenas em 11 amostras foram realizadas a difratometria de raios X (DRX), fluorescÃncia de raios X (FRX), Infravermelho (IV), Microscopia EletrÃnica de Varredura (MEV), e anÃlises de elementos quÃmicos e em 23 amostras foi determinada a composiÃÃo isotÃpica da crosta e do nÃcleo perfazendo 46 determinaÃÃes. As determinaÃÃes das tÃcnicas DRX, FRX, MEV identificaram os minerais aragonita e calcita; assim como o IV constatou estas formaÃÃes e hà presenÃa de polissacarÃdeos nestas algas calcÃrias. Quanto aos teores de carbonatos de cÃlcio estas algas apresentaram altos teores e no que diz os elementos quÃmicos, os metais traÃos apresentam valores de elementos traÃos primordiais para nutriÃÃo animal e vegetal entre outros fins. Jà para os macronutrientes os valores estÃo compatÃveis com a mesma utilizaÃÃo. As variaÃÃes do 13CPDB guardam grande correlaÃÃo com as variaÃÃes de suprimento CO2 atmosfÃrico para dentro das cÃlulas que formam o CID (carbono inorgÃnico dissolvido) que interagem com o pH interno das membranas formando o carbonato de cÃlcio atravÃs de mecanismos ainda nÃo bem elucidados, assim tambÃm o oxigÃnio onde as variaÃÃes de &#61540;18OVPDB de valores negativos indicam perÃodos onde houve um incremento cinÃtico da hidrataÃÃo do gÃs carbÃnico molecular. Jà os valores positivos de 18OVPDB indicam a precipitaÃÃo de Ãons Ca2+ na forma de aragonita e calcita como foi identificado pela caracterizaÃÃo das outras anÃlises. Os cÃlculos de temperatura pelas assinaturas de 18OVPDB indicam valores bastante heterogÃneos dessas temperaturas de precipitaÃÃo dos carbonatos nas crostas e nÃcleos dos carbonatos que nÃo segue um padrÃo nÃo identificado. Foram identificadas temperaturas elevadas nos bancos oceÃnicos que à de origem vulcÃnica; mas somente a determinaÃÃo da composiÃÃo isotÃpica de oxigÃnio nÃo indica mudanÃas climÃticas nos oceanos. / This study analyzed the geochemical characteristics of calcareous algae in northeastern Brazil, located at various depths, collected on the continental shelf and oceanic banks in several programs of marine geology. The analyzes performed in this study were X-ray diffraction (XRD), X-ray fluorescence (XRF), infrared spectroscpy(IR), Scanning Electron Microscopy (SEM), chemicals, calcium carbonate content and isotopic signatures of carbon and Oxygen. We selected 66 samples between Lithothamnion sp. and Halimeda sp., but on only 11 samples were performed at X-ray diffraction (XRD), X-ray fluorescence (XRF), infrared (IR), Scanning Electron Microscopy (SEM), chemical elements and on 23 samples was determined composition isotopic of crust and core totaling 46 determinations. Techniques XRD, XRF, SEM identified the minerals aragonite and calcite; IV also indicated these formations but also the presence of these polysaccharides in calcareous algae. As to the levels of calcium carbonates these algae showed high levels and metals present values of trace elements essential for plant and animal nutrition among other purposes. The macronutrient values are compatible with the same use. Variations of &#61540;13CPDB keep high correlation with changes in atmospheric CO2 supply into the cells that form the CID (dissolved inorganic carbon) that interact with the internal pH of the membranes forming calcium carbonate through mechanisms not yet elucidated, and also where oxygen variations &#61540; 18OVPDB negative values indicate periods where there was an increase of kinetic molecular hydration of carbon dioxide. Positive values of &#61540;18OPDB are associated with the precipitation of Ca+2 ions in the form of aragonite and calcite as identified by the characterization of other analyzes. The calculations of temperature predicted by the signatures of &#61540;18OPDB indicate values of these temperatures quite heterogeneous from in carbonate crust and core that does not follow an identified pattern. Elevated temperature was identified in banks of volcanic origin, but with isotopic composition of oxygen only an indication of climate change in the oceans is not possible.

Magister Scientiae (Biodiversity and Conservation Biology) / To further investigate the strength of the association and the relative advantages of the association to both organisms, several manipulation experiments were set up. A cage experiment set up in the shallow subtidal zone showed that the coralline survived equally well without the winkle and did therefore not require the winkle or its empty shell for survival. A second controlled laboratory aquarium experiment was designed under both fluorescent (rich in blue light) and incandescent light (rich in red light) to ascertain whether the coralline had a preference for O. sinensis over the similar O. tigrina. This experiment was inconclusive as no recruitment was obtained under either of the light regimes. A third laboratory experiment was designed to determine whether the extra coralline weight had any possible advantage to the winkle, particularly against predation from the rock lobster Jasus lalandii. Results suggested that there were no apparent advantages to the winkle bearing the extra coralline load as adult O. sinensis bearing the coralline alga (3.7 &plusmn; 2.2 winkles 24hr-1) were equally prone to predation than those lacking the coralline (2.3 &plusmn; 1.9 winkles 24hr-1) (p = 0.184). Observations suggested instead that the convoluted nature of the coralline may indeed have promoted predation. We ultimately deduced that the high occurrence of the coralline on the shells of O. sinensis was probably due to the substantial overlap in the niches of the two organisms. This conclusion was supported by the high densities of juvenile O. sinensis combined with the high percent cover abundance of the coralline in intertidal rockpools. Understanding sexual reproduction in coralline algae as well as the life cycle of the winkle, ultimately provided insight into the postulated life cycle of this coralline-winkle association. / South Africa

Over the past few decades, coral cover has declined worldwide due to overfishing, disease, and storms, and these effects have been exacerbated by ocean warming and acidification. Corals are extremely susceptible to these changes because they are already living close to their thermal and aragonite saturation thresholds. Ocean warming and acidification (OAW) may also impact coral survival and growth by impacting their settlement cues. Coral larvae use crustose coralline algae (CCA) and their associated biofilms as cues for settlement, i.e., habitat selection. Settlement cues can also be negatively affected by increased water temperature and acidity. It was hypothesized that the impacts of OAW on settlement substrate can further threaten coral persistence by altering/inhibiting larval settlement and potentially decreasing the post-settlement survival and growth of coral recruits. In this study, we 1) assessed the effect of substrate quality (substrate conditioned in ambient or OAW conditions) on settlement of A. agaricites larvae, 2) determined the effect of substrate quality on post-settlement survival and growth of A. agaricites recruits, and 3) determined the effect of ocean warming and acidification on the post-settlement survival and growth of A. agaricites recruits. Aragonite settlement tiles were placed offshore for one month to accrue CCA and associated biofilms, and were then conditioned in either ambient (29°C, 8.2 pH) or predicted future oceanic conditions (31°C, 7.9 pH) conditions for 7 – 10 days. Agaricia agaricites larvae were then introduced to the settlement tiles, and their settlement percentage was calculated. Once a week for 12 weeks after larval settlement, the size, survival, and pigmentation of A. agaricites recruits was recorded. Larvae settled marginally more on optimally conditioned tiles than on tiles previously exposed to OAW conditions (p=0.053). The survival of coral recruits in OAW conditions was greatly reduced, their growth was very limited, and they became paler over time. When reared in ambient conditions, recruits on OAW treated substrate initially displayed higher survival rates than recruits on ambient treated substrate. After 3 weeks in ambient conditions, however, survival rates were similar for recruits on ambient and OAW treated substrate; their growth curves were very similar, and coral recruits became more pigmented over time. Ocean warming and acidification conditions not only directly impacted the growth, survival, and pigmentation of A. agaricites recruits, but it also indirectly affected larval 5 settlement by likely altering microbial composition in bacterial biofilms on the settlement tiles. These results indicate that future conditions of ocean warming and acidification can be deleterious for A. agaricites, particularly after settlement. If the early life stages of scleractinian corals are negatively affected by OAW conditions, successful recruitment throughout the Caribbean and Florida Reef Tract could decrease. As a result, recovery from disturbances could be hindered, thus compromising the sustainability of many coral species and other marine ecosystems that depend on coral reefs for protection, habitat, and food.

Η παρούσα μεταπτυχιακή διατριβή επικεντρώνεται στην μελέτη της παράκτιας ζώνης της νήσου Λέρου στο Νοτιοανατολικό Αιγαίο, παρουσιάζοντας τα αποτελέσματα της ερμηνείας των γεωφυσικών στοιχείων που συλλέχθηκαν από το Εργαστήριο Θαλάσσιας Γεωλογίας και Φυσικής Ωκεανογραφίας (Ε.ΘΑ.ΓΕ.Φ.Ω.) τον Ιούνιο του 2011. Η έρευνα φιλοδοξεί να συνεισφέρει στην ανάδειξη της υποθαλάσσιας πολιτιστικής και φυσικής κληρονομιάς του νησιού, καθώς η συλλογή, επεξεργασία και ερμηνεία του συνόλου των δεδομένων επέτρεψε την αναγνώριση και την λεπτομερή χαρτογράφηση υποθαλάσσιων στόχων μεγάλης ιστορικής και περιβαλλοντικής σημασίας. Ως εκ τούτου, η διατριβή κινείται σε δύο κατευθύνσεις. Η πρώτη κατεύθυνση αφορά στον εντοπισμό στόχων πιθανής ιστορικής σπουδαιότητας που εντοπίστηκαν στην επιφάνεια του πυθμένα ενώ η δεύτερη κατεύθυνση αφορά στον εντοπισμό και την αποτύπωση βιογενών σχηματισμών και συγκεκριμένα λειμώνων P. Oceanica και ασβεστιτικών ροδοφυκών (corallegene formations). Οι θαλάσσιες έρευνες πραγματοποιήθηκαν σε δύο διακριτά στάδια, στην συστηματική αποτύπωση του πυθμένα με ηχοβολιστή πλευρικής σάρωσης (EG&G 272 TD) και την οπτική επιβεβαίωση των αποτελεσμάτων της ηχοβολιστικής αποτύπωσης με σύστημα συρόμενης υποβρύχιας κάμερας. Η ανάλυση και επεξεργασία των ηχογραφιών οδήγησε στον εντοπισμό ναυαγίων που συνδέονται με τη Μάχη της Λέρου (9-10/1943), ένα από τα σημαντικότερα πολεμικά γεγονότα που έλαβαν χώρα κατά τη διάρκεια του Δευτέρου Παγκοσμίου πολέμου, στην ανατολική Μεσόγειο και τα οποία αποτελούν πολύτιμα ιστορικά στοιχεία σε παγκόσμια κλίμακα, μεταξύ των οποίων το βυθισμένο ελληνικό αντιτορπιλικό Βασίλισσα ‘Ολγα (D15). Στο πλαίσιο της δεύτερης κατεύθυνσης εντοπίστηκαν και χαρτογραφήθηκαν οι λειμώνες P. Oceanica και οι σχηματισμοί των ασβεστιτικών ροδοφυκών σχεδόν ανά όρμο περιμετρικά της νήσου. Η σχεδίαση των αντιστοίχων υποθαλάσσιων θεματικών χαρτών της παράκτιας ζώνης της Λέρου αναμένεται να αποτελέσουν ένα σημαντικό εργαλείο στην προστασία και στην ανάδειξη της σημαντικής υποθαλάσσιας ιστορικής και φυσικής κληρονομιάς του νησιού / The present study describes the submarine geophysical survey which was carried out in Leros Island, Aegean Sea and presents the results of the geophysical data analysis. The data were collected by the Laboratory of Marine Geology & Physical Oceanography, department of Geology, University of Patras during the period 11-17 June 2011. The research aims to contribute to the enhancement of underwater cultural and natural heritage of the island, as the collection, processing and interpretation of all of the data has allowed the identification of underwater targets of great historic and environmental importance. Geophysical survey in Leros Island, using a side scan sonar (EG&G 272 TD), coupled with ground-truthing by deploying a Towing Camera System of historic shipwrecks from World War II and of the major seabed habitats, namely Posidonia oceanica and coralligène formations. The survey revealed a great number of shipwrecks associated with the Battle of Leros (9-10/1943), one of the most important military events that took place during the World War II, in the Eastern Mediterranean which are considered as valuable historic data on a global scale, including the sunken Greek destroyer Queen Olga (D15). The design of the thematic maps of the coastal zone of Leros is expected to become an important tool in both protecting and promoting the significant underwater cultural and natural heritage of the island.

Η παρούσα διδακτορική διατριβή αποτελεί ένα συνδυαστικό ερευνητικό προϊόν που στοιχειοθετείται από την ανάπτυξη υπολογιστικών εργαλείων επεξεργασίας και ανάλυσης θαλάσσιων γεωφυσικών δεδομένων και την εφαρμογή τους σε πρωτογενή δεδομένα, συλλεγμένα από το Εργαστήριο Θαλάσσιας Γεωλογίας και Φυσικής Ωκεανογραφίας (Ε.ΘΑ.ΓΕ.Φ.Ω) του πανεπιστημίου Πατρών, κατά το διάστημα 2005 – 2011. Τα πεδία στα οποία συγκεντρώνεται το κέντρο βάρους της διατριβής είναι: 1) τα συστήματα ακουστικής ταξινόμησης πυθμένα και 2) η χαρτογράφηση και παραμετροποίηση εμφανίσεων των πολύ σημαντικών θαλάσσιων ενδιαιτημάτων της Ποσειδώνιας και των κοραλλιογενών σχηματισμών στο Ιόνιο και στο Αιγαίο πέλαγος. Έτσι αναπτύχθηκαν και παρουσιάστηκαν εκτενώς τα λογισμικά εργαλεία SonarClass και TargAn, που αναφέρονται αντίστοιχα στην αυτόματη ακουστική ταξινόμηση πυθμένα και την παραμετροποίηση περιοχών ενδιαφέροντος σε εικόνες ηχοβολιστών ευρείας σάρωσης και εφαρμόστηκαν για την χαρτογράφηση λειμώνων ποσειδώνιας στη Ζάκυνθο και κοραλλιογενών σχηματισμών (τραγάνας) στις Κυκλάδες νήσους. Παράλληλα και επεκτείνοντας το εύρος των ερευνητικών προϊόντων αυτής της διατριβής, αναπτύχθηκαν επίσης: 1) το λογισμικό SBP-Im-An για τη γεωαναφορά και ψηφιοποίηση παλαιών αναλογικών καταγραφών τομογράφων υποδομής πυθμένα, 2) το λογισμικό χωροστάθμησης θαλάσσιων γεωμαγνητικών δεδομένων MagLevel και 3) το λογισμικό ποσοτικοποίησης αλιευτικών ιχνών σε δεδομένα ηχοβολιστών ευρείας σάρωσης PgStat, με αντίστοιχες σημαντικές εφαρμογές σε πρωτογενή δεδομένα. Η παρούσα διατριβή επιδεικνύει πρωτοτυπία τόσο σε επίπεδο ανάπτυξης νέων μεθόδων ανάλυσης και επεξεργασίας γεωφυσικών δεδομένων όσο και σε επίπεδο παρουσίασης εφαρμογών τους σε περιοχές μελέτης με ιδιαίτερο περιβαλλοντικό ενδιαφέρον αλλά και σε πεδία έρευνας για τα οποία το ενδιαφέρον της σύγχρονης θαλάσσιας επιστημονικής κοινότητας βρίσκεται στο απόγειό του. / The present PhD thesis is a combinational research product concerning the development of software tools for the processing and analysis of marine geophysical data and their application to original data, collected by the Laboratory of Marine Geology and Physical Oceanography (L.M.G.P.O), university of Patras, Greece, during the period 2005-2011. The fields that this thesis focuses on are: 1) the Acoustic Seabed Classification Systems and 2) the mapping and quantification of very important marine habitats that specifically are the Posidonia Oceanica Prairies and the Coralline formations in the Aegean and Ionian seas. The software tools SonarClass and TargAn, that respectively refer to the Acoustic Seabed Classification and the quantification of Regions Of Interest in swath sonar imagery are presented and applied to the cases of Posidonia Oceanica in Zakinthos Isl. (Ionian Sea) and Coralline formations in Cyclades Isl. (Aegean Sea). Additionally and extending the range of the research products of this thesis, other software tools that are presented are: 1) the SBP-Im-An for the recreation (georeferencing and digitization) of old analog Sub Bottom Profiler recordings, 2) the MagLevel for the tie line leveling of marine geomagnetic data and 3) the PGStat for the quantification of trawl marks in swath sonar imagery, all of them with significant applications to original data. This thesis demonstrates originality due to both the development of new methods for the analysis and processing of marine geophysical data and the applications to study areas with particular environmental interest and research fields for which the attention of the marine scientists is at its peak.