Dissertations / Theses on the topic 'Marine biodiversity'

Marine biodiversity is changing in response to numerous, mounting anthropogenic impacts, and effective conservation and management in the face of these threats requires a robust understanding of spatial and temporal patterns and trends in marine biodiversity. Achieving such an understanding is possible with the vast amounts of data present in aggregated online repositories, such as the Ocean Biogeographic Information System (OBIS), however overcoming incomparability between constituent datasets, and issues of variable methodology, detectability, and effort, requires that we employ statistical methods that ensure derived trends are robust to bias from "unstructured data". In this thesis, I explore how one of these methods, occupancy modelling, can be used to overcome issues of detectability and variable surveyor effort in OBIS data, while employing data management and analysis techniques to minimise the effects of variable methodologies. I use this combination of methods and aggregated data to assess temporal trends in the lesser-studied molluscs, expanding our understanding of molluscs in the Celtic Sea, and assessing the utility of multispecies models on a global scale for the genus Conus. I then go on to address more fundamental macroecological questions by deriving inter- and intraspecific abundance-occupancy relationships in European cetaceans, to then demonstrate how occupancy modelled unstructured data can be used to robustly estimate relative abundance of species within this group. Finally, I apply occupancy modelling to an Atlantic wide dataset of marine fauna, to attempt to address recent debate surrounding the marine latitudinal diversity gradient. I find throughout this thesis that occupancy modelling and unstructured data are useful in determining robust but coarse scale trends when sufficient data are available, and end by suggesting future avenues of research to both further test the methodology, and improve our knowledge of changes in marine biodiversity.

Investigations on the biodiversity in relation to conservative and non-conservative parameters in the Mangalavanam mangrove ecosystem, located in the northern fringes of Cochin City have been carried out from January to June 2002. The mangrove ecosystem is regularly under tidal influence and hence submergence and emergence of land takes place depending on the tidal amplitude. The average dissolved oxygen of the water was found to be 3.5ml/l despite the fact, phytoplankton was abundant in the ecosystem. It reveals that respiratory demand of the aquatic biota has exceeded the photosynthetic oxygen production. The indirect relationship exhibited by the quantity of phytoplankton and oxygen is attributed to anthropogenic activities, which resulted in to the eutrophication of the mangrove ecosystem. The general nutrient load was at a higher level. The macrophytic vegetation was dominated by A^icennia marina, Rhizdphora mucronata and Acanthus ilicifolius. The presence of Avicennia and Acanthus in majority of the area that showed decrease in salinity and more freshwater influx. The phytoplankton community was dominated by djatoms represented Naviculaceae followed by Coscinodisceae, which Is evidenced by the presence of high quantity of silicate. The Zooplankton was dominated by copepods. Benthic community is dominated by the infauna such as polychaetes and decapods. Juveniles of common brackish water fishes. Chanos spp., Liza spp., Etroplus spp., Silago spp., Lethrinus spp. and Lutjanus spp., and species of crustaceans like Penaeus spp., Metapenaeus spp., Macrobrachium spp., Acetes spp., Metaplex spp., Sesarma spp., Uca spp., and Scylla spp., have been found to be the residents of the mangrove ecosystem. Avian fauna comprises mostly little cormorants (Phalactocorax niger) and black crowned night heron (Nycticorax nycticorax). Other arboreal fauna is dominated by Indian flying fox (Pteropus giganteus). An evaluation on the biodiversity of the mangrove ecosystem in the light of the present investigations reveals that species diversity Is less, but moderate population density of available species could be observed. To put It In a nutshell, human interventions on the environment has been detrimental and a general degradation of the ecosystem has been evidenced by the emergence of terrestrial vegetation and shrinking of the true mangrove areas.

Les communautés de poissons marins, essentielles au bon fonctionnement des écosystèmes, sont de plus en plus menacées par les pressions humaines : surpêche, dégradation des habitats, pollutions et changement climatique. Dans ce contexte, des réserves marines sont mises en place pour tenter de les protéger. Afin de mieux orienter la protection des espèces, notamment les plus vulnérables, il faut mieux connaître leur répartition spatiale et bathymétrique, mais aussi leur niveau de coexistence avec les pressions humaines. L’obtention de ces données est difficile avec les outils classiques tels que la plongée, cantonnée aux zones superficielles ou la pêche qui reste destructive et sélective sur les espèces. En alternative, le metabarcoding de l’ADN environnemental (ADNe), permet une meilleure détection des espèces, même les plus rares ou les plus furtives, et semble particulièrement adapté aux communautés des zones mésophotiques (30-150 mètres de profondeur) qui restent mal connues car relativement inaccessibles. Cette méthode consiste à collecter et amplifier l’ADN laissé par les organismes dans leur environnement, puis à l’assigner à des espèces connues par comparaison aux séquences d’une base de référence génétique. Dans quelle mesure un échantillonnage de l’ADNe le long de gradients spatiaux, bathymétriques et anthropiques va-t-il pouvoir alimenter des modèles prédictifs d’occurrence des espèces et renseigner des plans de conservation pour la biodiversité ichtyologique côtière ? Telle est la question centrale de la thèse.Le premier chapitre synthétise les connaissances actuelles sur la répartition spatiale et bathymétrique des poissons marins à l’échelle mondiale, ainsi que la disponibilité des séquences dans les bases de référence génétiques publiques. Seules 19% des 11 786 espèces marines étudiées sont couvertes par le marqueur teleo couramment utilisé pour la détection des poissons. De ce fait, les possibilités d’utilisation des données ADNe restent limitées, car 81% des espèces ne peuvent pas être identifiées. De plus, les espèces ne vivant qu’au-delà de 30m de profondeur sont moins couvertes par les bases de référence.Le deuxième chapitre présente une modélisation visant à évaluer et comparer les effets relatifs des réserves et du confinement sur les probabilités d’occurrence de 87 espèces de poissons. Pour cela, un important travail de séquençage des espèces a été réalisé pour compléter la base de référence des espèces présentes en mer Méditerranée française. Au cours des campagnes d’échantillonnage d’ADNe menées entre 2018 et 2022, des échantillons ont été récoltés à l’intérieur et à l’extérieur de 11 réserves marines où la pêche est interdite, dont 160 pendant le confinement du printemps 2020 lié à l’épidémie de COVID-19. Les résultats montrent une augmentation de la probabilité d’occurrence dans les réserves pour 59% des espèces. La probabilité d’occurrence a augmenté lors du confinement pour 62% des espèces. La réponse à l’effet des réserves et du confinement est différente en fonction des espèces, suggérant que la mise en place de grandes réserves avec moins de présence humaine, en sus des réserves actuelles, sont nécessaires pour protéger l’ensemble de la biodiversité ichtyologique.Le troisième chapitre présente des modèles de distribution d’espèces prenant en compte les co-occurrences et les habitats côtiers méditerranéens. À partir de la distribution estimée de 120 espèces, des zones à protéger en priorité le long des côtes méditerranéennes françaises ont pu être identifiées pour atteindre les 30% de couverture en AMP préconisée d’ici 2030 et optimiser la conservation de la biodiversité ichtyologique.Dans cette thèse, le couplage entre les données issues du metabarcoding de l’ADNe et la modélisation a permis de décrire la répartition spatiale et bathymétrique des espèces, évaluer l’efficacité des mesures de protection et informer les futurs plans de conservation
Marine fish communities, which are essential to the proper functioning of ecosystems, are under increasing threat from human pressures: overfishing, habitat degradation, pollutions and climate change. In this context, marine reserves are set up to try to protect them. In order to better guide the protection of species, particularly the most vulnerable, we need to know their spatial and bathymetric distribution, but also their level of coexistence with human pressures. Obtaining this data is difficult with conventional tools such as diving, which is limited to superficial areas, or fishing, which is destructive and selective for species. Alternatively, the metabarcoding of environmental DNA (eDNA) allows better detection of species, even the rarest or most elusive ones, and seems particularly suited to study communities in mesophotic zones (30-150 meters deep) which remain poorly known because of their relative inaccessibility. This method consists of collecting and amplifying the DNA left by organisms in their environment, then assigning it to known species by comparison with sequences in a genetic reference database. To what extent will eDNA sampling along spatial, bathymetric and anthropogenic gradients be able to feed predictive models of species occurrence and inform conservation plans for coastal ichthyological biodiversity? This is the central question of the thesis.The first chapter summarizes current knowledge of the spatial and bathymetric distribution of marine fish at the global scale, as well as the availability of sequences in the public genetic reference databases. Only 19% of the 11,786 marine species studied are covered by the teleo marker commonly used for fish detection. As a result, the possibilities for using eDNA data remain limited, as 81% of species cannot be identified. In addition, species living only at depths greater than 30m are less well covered by reference databases.The second chapter presents modeling aimed at evaluating and comparing the relative effects of reserves and lockdown on the probabilities of occurrence of 87 fish species. To do this, a major species sequencing project was carried out to complete the reference database of species present in the French Mediterranean Sea. During the eDNA sampling campaigns carried out between 2018 and 2022, samples were collected inside and outside 11 marine reserves where fishing is banned, including 160 during the spring 2020 lockdown period linked to the COVID-19 epidemic. The results show an increase in the probability of occurrence in reserves for 59% of species. The probability of occurrence increased during lockdown for 62% of species. The response to the effect of reserves and lockdown is different depending on the species, suggesting that the establishment of large reserves with less human presence, in addition to current reserves, are necessary to protect all species.The third chapter presents species distribution models considering co-occurrences and Mediterranean coastal habitats. Based on the estimated distribution of 120 species, priority areas for conservation along the French Mediterranean coast have been identified to achieve the recommended 30% MPA coverage by 2030 and optimize the conservation of ichthyological biodiversity.In this thesis, the combination of data from eDNA metabarcoding and modeling was used to describe the spatial and bathymetric distribution of species, assess the effectiveness of protection measures and inform future conservation plans

Dissolved organic nitrogen (DON) represents a major pool of fixed, reactive nitrogen in marine systems. It is now recognized that this pool can support primary production and the ability of some algal species to exploit DON compounds as sources of Nitrogen (N) may indicate that specific DON components can exert selective pressure on the composition of the phytoplankton community. In this study the ability of monocultures of ecologically-relevant algal species from the English Channel (Emiliania huxleyi, Micromonas pusilla, Alexandrium minutum and Chaetoceros peruvianus) to grow with DON as the only N source was examined using different artificial media. Among the two tested artificial seawater recipes, Aquil* was preferred as it contained lower micronutrient concentrations, and gave better growth results for all used species. In order to constrain the DON uptake to algae alone, a method for bacterial removal was tested using antibiotic additions. Both Slocombe antibiotic mixture (Cefotaxime-Carbenicillin-Kanamycin-AugmentinTM) and Penicillin-Streptomycin-Neomycin used were effective and not toxic to the algae. Incubation with the antibiotic up to 48 hours and a transfer period into antibiotic-free medium after 72 hours proved to be effective. However, the treatment removed bacteria in A. minutum cultures only; further treatment would be required for the other species to be cultured axenically. The ability to use DON was tested for the above mentioned species using the amino acid L-Arginine (ARG) as the sole N source, and growth was compared with nitrate-containing cultures of the same species. All the selected species grew in both NOᴈ‾ and in ARG, reaching lower final densities when incubated with ARG, although these were not significant. This study has shown that E. huxleyi, A. minutum, M. pusilla and C. peruvianus can grow on organic N, either by direct or indirect uptake, and develop comparable biomasses to species using inorganic N. Both C. peruvianus and M. pusilla cultures contained dissolved ammonium at the end of the experimental period, indicating potential indirect use by the algae of organic N converted to inorganic N by bacteria. A. minutum grew in the presence of ARG along with the cosmopolitan E. huxleyi; N-demand estimates, based on the molar concentration of N-ARG consumed, correlated with the final cell density, indicating that the species did not develop on inorganic N produced from ARG mineralisation, but directly on the ON substrate. Since A. minimum has been linked to harmful algal blooms, and E. huxleyi contributes significantly to oceanic CaCOᴈ deposition, their ability to utilise DON has environmental consequences in addition to the oceanic N-budget. Climate change scenarios predict both episodic conditions of elevated rainfall and extended periods of dry conditions leading to variable riverine inputs to coastal areas, altered nitrogen to phosphorus (N:P) ratios, and changes in the inorganic to organic balance of the nutrient pools. Organic N can constitute up to 69 % of the total N pools, respectively, making it crucial, to understand the cycling of this fraction in coastal waters, and how changes in the composition of nutrient pools could impact on marine ecosystem function and health.

The decline in biodiversity over the last decade has motivated researchers to investigate the relationship between species richness (biodiversity) and ecosystem function. Empirical approaches are becoming more realistic as more factors have been included. Spatial heterogeneity is an example. Heterogeneity is an inherent part of the environment and apparent in all habitat types creating a patchy, mosaic of natural landscape. Researchers have reported the extent of heterogeneity in the landscape, but surprisingly not yet included heterogeneity into biodiversity and ecosystem function (BEF) studies. In recent years, empirical studies of marine systems have enhanced the BEF debate. Depauperate estuarine systems are ideal candidates for establishing model systems. In this study, estuarine microphytobenthos (MPB) were used as a response variable since the relationship between MPB and primary productivity is well-known. This relationship was exploited to employ MPB biomass as a proxy for primary productivity. Benthic chambers were used to assess the effect of macrofauna in single species and multi-species treatments on both ecosystem function and net macrofaunal movement. Heterogeneity was created through enriching sediment ‘patches’ with Enteromorpha intestinalis, providing areas of high and low nutrient. Heterogeneity, macrofaunal biomass, species richness, species diversity and flow were all varied in order to assess combined effects on the functioning of the system. Heterogeneity was found to have a significant influence on ecosystem functioning and on macrofaunal movement, however, patch arrangement did not. MPB biomass was highest in patches containing organic enrichment suggesting that nutrients were obtained locally from the sediment/water interface rather than the water column. There was variation in MPB biomass with macrofaunal species, probably resulting from differences in behavioural traits. It was also evident that flow altered species behaviour, as there was a significant difference between static and flow treatments. This work shows the importance of heterogeneity for BEF relationships.

This study focuses on the seaweed biodiversity around the Antarctic Convergence in the South Atlantic. It integrates field work in the Falkland Islands and surrounding regions with algal culturing, molecular techniques, microscopy and morphological identification. Chapter 2 explores the diversity of seaweeds of the south-western Antarctic Peninsula which is poorly studied, contrasting with the substantial knowledge available for the northern parts of the Peninsula. A baseline seaweed species checklist for the southern Adelaide Island and northern Marguerite Bay region is presented here, combining data obtained during a small number of surveys in 1973-5 and a six week intensive diving-based field campaign in 2010-2011. Subantarctic and Antarctic regions remain little studied in their seaweed diversity. Chapter 3 is based upon field collections in the early 1970s and 2007-2013. It is supported by sequencing COI and reports new records of several macroalgal species and an oomycete. Chapter 4 revisits the enigmatic Subantarctic brown alga Cladochroa chnoosporiformis, which had been collected only on one occasion by Carl Skottsberg in 1907 from Port Philomel, West Falkland, resulting in its formal taxonomic description. Within the framework of this study, Cladochroa was rediscovered after 106 years at its type locality, confirming its existence and morphological features as described by Skottsberg. The recollection enabled molecular studies of its phylogenetic placement by DNA sequencing, suggesting that C. chnoosporiformis is conspecific with Utriculidium durvillei. In Chapter 5, DNA barcoding was applied to both seaweed tissue samples taken while preparing herbarium specimens during 2 expeditions to the Falkland Islands, and to live macroalgal isolates obtained from substratum samples using the Germling Emergence Method. In several cases, this enabled detection of previously unsequenced or undescribed taxa, respectively. The potential and challenges of applying DNA barcoding for cataloguing the biodiversity of remote bioregions such as the Falklands are discussed.

Free-living nematodes are abundant in all marine habitats, highly diverse and can be important ecological indicators for monitoring anthropogenic impacts on the environment. Despite such attributes, nematode diagnostics has traditionally relied on detailed comparison of morphological characters which is often difficult and laborious, and as a result there is an increasing 'black hole' in faunal inventories where the biodiversity of groups such as nematodes is typically underestimated. Molecular methods offer a potentially efficient alternative approach to studying the biodiversity of marine nematode communities, and the main focus of this thesis was to apply molecular ecological tools for improved understanding of nematode diversity in marine and estuarine environments. Denaturing gradient gel electrophoresis (DGGE) has been evaluated as a novel tool for the identification of marine nematodes and for rapid assessment of their diversity based on amplification of the nuclear 18S rRNA gene. This approach successfully identified nematode taxa based on banding pattern and was also able to detect the most abundant taxa in samples from marine and estuarine environments. A DNA barcoding approach based on the 18S rRNA gene was applied for the first time in marine nematology, in an attempt to speed up the identification process. The success rate of this approach, across a range of nematode groups, was found to be close to 97%. A combined morphometrics and molecular approach was also undertaken to investigate cosmopolitanism and cryptic speciation by analysing populations of a cosmopolitan marine nematode, Terschellingia longicaudata, from different geographical regions. Results suggest that Terschellingia longicaudata is indeed truly cosmopolitan, with a wide geographic distribution. Two haplotypes that were divergent from most T. longicaudata were also identified in this study, indicating possible novel cryptic lineages or previously undescribed species of the genus. The final focus of this thesis was to develop methods for the molecular investigation of nematodes stored in formalin and other organic compounds. The effectiveness of formalin as a short term preservative was first evaluated, since this would allow morphological and molecular work to be conducted on the same specimen. Amplifiable DNA could be routinely obtained from specimens stored in formalin for periods of up to nine days. In addition the effectiveness of other organic solvents for the preservation of both molecular and morphological integrity of marine nematodes was investigated. The final part of this study developed and optimized a novel DNA extraction technique that could be employed to recover DNA from archived formalin fixed marine nematode specimens so as to carry out subsequent molecular analysis such as PCR amplification and sequencing.

Marine biodiversity is of significance to the existence of humankind but has been experiencing globally continuous deterioration due to anthropogenic activities in the past decades. It has been generally accepted that damage to marine biodiversity is mainly caused by marine pollution, alien invasive species, unsustainable use and overexploitation of resources such as overfishing, destructive fishing operation and illegal, unreported and unregulated fishing, habitat loss, and climate change. Due to its importance, marine biodiversity must be protected and when damaged there should be liability imposed on the polluter. This thesis assesses the extent to which existing international law covers damage to marine biodiversity, permits actions and ensures recovery. To answer these questions, this thesis comprehensively examines the relevant international legal instruments on prevention and protection of marine biodiversity. It finds that protection of marine biodiversity under the current regulatory framework is piecemeal and no comprehensive liability regime exists. The factors hindering the development of an international liability regime for such damage include conceptual problems of the concept of marine biodiversity and the definition of damage to marine biodiversity, and the lack of baseline conditions as reference for the damage. Because of the gaps and inadequacy of the existing regimes which concern liability for damage to marine biodiversity, the thesis advocates that a liability regime for such damage shall be established and several important elements of such a regime are analysed. For this regime, the thesis discusses the theoretical basis first and then suggests a structure that will include relevant national legislation to be developed or refined, changes of the current multilateral liability regimes, and the creation of a new international legal instrument comprehensively addressing liability for damage to marine biodiversity within and beyond the areas of national jurisdiction. Significant obstacles in developing such a regime are identified and discussed.

The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower Keys). The objective was to describe changes in reef fish community responses through time and space in the Florida Keys, and to determine whether patterns in reef fish diversity indices were attributable to levels of protection, benthic habitat strata, or geographic subregion. The goal was to develop a framework for reef fish biodiversity assessments that can inform management and policy in the FKNMS, and support updates to the periodic Condition Reports generated by the Sanctuary. Diversity indices (with the exception of evenness) were significantly higher in no-take marine zones compared to areas open to fishing. All indices were significantly different by strata type. High Relief Reef habitats had the highest abundance, biomass, richness, Simpson diversity, Shannon diversity, and functional diversity, but had moderate evenness values. The biodiversity metrics for the Upper Keys and Lower Keys were not significantly different, but both of these areas were significantly different from the Middle Keys for all indices except species richness, which did not vary by subregion. Generalized additive models revealed that the principal driver across indices was habitat structure (strata and depth). Time (year), space (latitude, longitude), and no-take marine zones (0, unprotected and 1, protected) explained roughly similar proportions of deviance across all indices. Simpson diversity, Shannon diversity, and functional diversity showed similar trends in no-take marine zones, strata, and subregion through time. The Florida Keys is characterized as having relatively low functional diversity due to a few common traits shared by many individuals and many rare traits shared by a few individuals. This suggests that the Florida Keys reef fish are less vulnerable to functional loss due to high functional redundancy among species. However, functionally rare traits, those possessed by few individuals, are vulnerable to functional loss and will have a larger impact on ecosystem functioning than species that share similar traits. Low functional diversity also suggests lower adaptability to environmental perturbations. Given the minimal robustness of traits, the ecosystem is less likely to possess functions that can withstand disturbances. The impacts of two types of perturbations were examined in a qualitative manner: hurricanes and cold-temperature events. Disturbance by hurricanes in 2004 and 2005 and the extreme cold event of January 2010 had a high impact on reef fish community composition. Between 2004 and 2006, following two consecutive years of hurricanes, abundance of reef fish declined 31%, biomass declined 53%, species richness declined 18%, Simpson diversity declined 12%, Shannon diversity declined 14%, and functional diversity declined 8%. Following a year without hurricanes in 2007 abundance of reef fish increased 11%, biomass increased 13%, richness increased 14%, Simpson and Shannon diversity increased 10%, and functional diversity increased 6%. After the January 2010 extreme cold event, reef fish abundance and biomass also declined 17%, richness declined 10%, Simpson diversity and Shannon diversity declined 5% and 6%, and functional diversity declined 2%. All matrices increased the following year, where abundance increased 13%, biomass increased 31%, richness increased 13%, Simpson diversity increased 7%, Shannon diversity increased 10%, and functional diversity increased 8%. Based on my findings and literature review, to better preserve biodiversity and enhance ecosystem functioning, I recommend prioritizing conservation efforts in source habitats (e.g., High Relief Reefs) and habitats with varying complexity by implementing corridor reserves that facilitate the natural migration of organisms between different habitat types. I also recommend prioritizing preservation of species that possess functionally rare traits with few individuals (e.g., cleaner species) by preserving areas with greater functional diversity (e.g., Higher Relief Reefs and Forereef Deep Linear Reefs).

La biodiversità marina regola il funzionamento ecosistemico, responsabile della produzione di beni e servizi importanti per la biosfera e il benessere umano. La stima della biodiversità è uno degli obiettivi fondamentali della scienza. I cambiamenti globali e le attività antropiche stanno avendo un impatto crescente sugli ecosistemi. Le valutazioni d'impatto e i programmi di monitoraggio si basano su specie di grandi dimensioni, trascurando gli organismi di piccola taglia come la meiofauna (20-500 µm), a causa delle difficoltà connesse con la tradizionale identificazione morfologica. L’obiettivo di questo lavoro è quello di implementare i metodi per lo studio della meiofauna, combinando l’approccio morfologico e molecolare. Al fine di rispondere alle esigenze della Direttiva Quadro sulla Strategia Marina sono stati testati, in diversi ecosistemi marini, uno strumento per la valutazione dello stato ambientale e varie metodologie innovative di campionamento. Gli strumenti molecolari, come il metabarcoding, insieme ai nuovi sistemi di campionamento, mostrano un grande potenziale per lo studio della biodiversità marina. Il protocollo molecolare qui messo a punto, permette di analizzare la diversità di organismi di piccola taglia in modo rapido ed economicamente efficiente, migliorando la capacità di studiare la biodiversità della meiofauna anche in ecosistemi marini profondi. Nonostante i numerosi vantaggi, l'applicazione del metabarcoding al monitoraggio richiede il superamento di alcuni limiti. L'incompletezza delle banche dati e la presenza di copie multiple di geni in individui della stessa specie ostacolano l'interpretazione dei dati e non consentono di effettuare stime quantitative di biodiversità. Per garantire che le analisi di metabarcoding possano essere ulteriormente convalidate, risulta cruciale conservare la competenza nell’identificazione morfologica. L’approccio tradizionale e quello molecolare forniscono informazioni diverse, quindi dovrebbero essere usati entrambi per ottenere stime accurate di biodiversità.
Marine biodiversity regulates ecosystem functions that are responsible for the production of goods and services for the entire biosphere and human wellbeing. Censusing species inhabit oceans is among the most fundamental questions in science. Global changes and human activities are having an increasing impact on ocean biodiversity and ecosystem functioning. Impact assessments and monitoring programmes are almost based on large and conspicuous species. Small and cryptic organisms including eukaryotic meiobenthic fauna (20-500 µm) remain overlooked due to the difficulties associated with the traditional, morphology-based identification. We here aim to implement methods for the study of meiofaunal biodiversity, combining classical morphological and molecular approaches. In order to answer to the needs of the Marine Strategy Framework Directive, an environmental status assessment tool and a variety of innovative sampling methodologies have been tested in different ecosystems. Along with new sampling approaches, molecular tools, as metabarcoding, have a great potential in innovating the analysis of marine biodiversity. Molecular protocol set up in this work allows to analyse the diversity of tiny organisms in a rapid and cost-effective way, thus increasing our ability to investigate meiofaunal biodiversity, also in the deep sea. Beyond its many advantages, the routine application of metabarcoding for monitoring requires overcoming some limitations. The incompleteness of public databases and the presence of multi-copy genes within meiofaunal species hamper the interpretation of metabarcoding data and do not allow to infer biodiversity quantitative estimates. It is thus critically important to maintain expertise in morphological identification to ensure that metabarcoding analyses can be further validated. Morphological- and molecular-based approaches provide different information, thus they should be combined to obtain better evaluations of the actual marine biodiversity.

There are more than 1029 bacteria on our planet which represent the most abundant living form and that act as key players within biogeochemical cycles and in the ecosystem functioning. The photo-/autotrophic prokaryotes are one of the major primary producers in the oceans fueling pelagic food webs especially in oligotrophic conditions, while the heterotrophic fraction represents the principal consumers of the dissolved organic matter (that represent 14 to 20 times the amount of terrestrial organic carbon) contributing to the remineralization of nutrients. Inside the microbial loop, biomass of prokaryotes is continuously recycled via viral lysis while grazing of heterotrophic nanoflagellates and small ciliates channel it towards upper trophic levels. The relevance of prokaryotic biomass as principal source of carbon supporting pelagic food webs in the Mediterranean Sea have been demonstrated among different trophic conditions. The ingestion of prokaryotes by grazers was assessed according with the dilution technique that allows to determine whenever prey communities are efficiently controlled by predators. Bacterivory resulted to be the major pathway for carbon flux in oligo-, meso- and eutrophic conditions although even in eutrophicated situations, when herbivory prevailed, the carbon flux generated by ingestion on prokaryotes was still relevant. Also at the meso- bathypelagic layers the prokaryotes’ consumption still represented an efficient pathway for carbon transfer. Prokaryote communities have been demonstrated to change in abundance and composition over time due to modification of environmental conditions (such as temperature, salinity, resource availability) - bottom-up control - and to mortality mediated by viruses and/or grazers. Predation activity – top-down control – was often identified as the main cause of prokaryotic loss. Some experimental evidences support that feeding process tends to be more selective in regard to more active cells although selection might depend on the composition of grazers’ community. Bacterivores are mainly protists and different taxa display different feeding strategies (e.g. filter-feeding, sedimentation, interception feeding, raptorial, hosmotroph). Several protist communities have been analyzed from water samples taken during the XXIX Italian expedition in Antarctica - Ross Sea; the analysis of their biodiversity was based on molecular approach though Next Generation Sequencing (NGS) technique and samples were sequenced with Ion Torrent PGM platform. The results highlighted as protist communities were shaped accordingly with the history of the water masses: young-newly formed high salinity shelf waters (HSSW) presented protist communities characterized by high relative abundance of autotrophic organisms - which typically bloom at the surface - down at several hundred meters of depths. On the contrary, older circumpolar deep waters (CDW) shown higher abundance of taxa as Radiolaria, Discoba and Diplonema (the latter two belong to the Supergroup of Excavata, typically bacterivore). The same NGS approach was adopted in the experimental design to test the consequences of Aurelia aurita ephyrae appearance in a pelagic community of the Gulf of Trieste. Both protist and prokaryote community compositions were analyzed and the study provides a new insight in jellyfish-microbes interactions; it underlines how jellyfish tend to selectively prey on more motile groups of protists while they impact on prokaryote community and favors the blooming of copiotrophic taxa.

La valeur esthétique des paysages et des espèces est un élément central de la conservation de la biodiversité, puisqu’elle fait intervenir les dimensions affectives et émotionnelles de notre rapport à la nature. Le lien entre biodiversité et perception esthétique demeure cependant peu étudié dans le cadre des services écosystémiques.Suite à un premier travail de synthèse ayant permis de poser les bases conceptuelles et méthodologiques de l’esthétique des paysages, trois études menées sur des systèmes sous-marins à différentes échelles ont permis de mieux comprendre et de quantifier le lien entre les différentes facettes de la biodiversité et la perception esthétique.Les résultats ont permis de mettre en évidence que la nature du lien entre biodiversité et préférences esthétique est dépendante de l’échelle de perception : à une échelle multi-spécifique, la biodiversité et la composition en espèces ont un effet positif sur les préférences esthétiques, tandis que les préférences à l’échelle spécifiques sont déconnectées du fonctionnement écologique des écosystèmes.Ces résultats confirment l’importance de la valeur esthétique dans notre perception de la biodiversité, qui pourrait avoir des conséquences majeures sur la façon dont nous protégeons notre environnement. L’approche fonctionnaliste de l’expérience esthétique est proposée et décrite afin de promouvoir une perception esthétique basée sur la compréhension et la reconnaissance des processus écologiques. Des pistes d’éducation à la biodiversité basée sur une expérience esthétique engagée sont également proposées afin de reconnecter les besoins écologiques et les préférences esthétiques
The aesthetic value of landscapes and species is a central element for the conservation of biodiversity, since it involves the emotional and emotional dimensions of our relationship to nature. However, the links between biodiversity and aesthetic perception remains poorly studied and recognized within the ecosystem services framework.Following a first critical review, that described the conceptual and methodological bases of landscape aesthetics, three studies on underwater systems at different scales have been computed in order to better understand the link between the different facets of biodiversity and aesthetic perception.The results revealed that the link between biodiversity and aesthetic preferences is dependent on the scale of perception: at a multi-specific scale, biodiversity and species composition have a positive effect on aesthetic preferences, while preferences at a specific scale are disconnected to the ecological functioning of ecosystems.These results confirm the importance of aesthetic value in our perception of biodiversity, which could have major consequences in the way we protect our environment. The aesthetic experience based on the understanding of ecological functioning is proposed and described in order to promote an aesthetic perception relevant to ecological processes. Education to biodiversity based on engaged aesthetic is also proposed, in order to reconnect ecological needs and aesthetic preferences

Word processed copy.
Includes bibliographical references (p. 80-89).
The aims of this thesis are to estimate how many marine species remain to be described in this region and which areas are most in need of additional sampling effort.

Wetlands contain both aquatic and terrestrial environments which generates high biodiversity. However, they are commonly associated with mosquitoes (Diptera: Culicidae), and mosquitoes are usually regarded as negative by humans because they can cause nuisance and transmit diseases. This thesis aimed to clarify the association between mosquitoes and wetlands and to achieve a more balanced view of biodiversity in wetlands by including mosquito diversity. Studies on adult mosquito diversity and assemblages were performed in 18 wetlands spread over Sweden. The Swedish mosquito species were organized in ten functional groups based on four life-history characteristics. This classification was used as an additional diversity measurement and as a tool for presentation of mosquito data. Mosquito diversity showed several of the well-established diversity patterns such as a latitudinal gradient, a species-area relationship and a distribution-abundance relationship. In a landscape perspective, diversity of both mosquitoes and dytiscids (Coleoptera: Dytiscidae) were positively influenced by a high proportion of permanent water and a high amount of open areas, indicating co-varying diversity patterns. Mosquito assemblages in the Nedre Dalälven region were mainly structured by the extent of flooded areas and wetland type (wet meadow, swamp and bog). In addition to the influence of the proportion of temporary wetlands at a local scale, the proportion of forest gained importance at larger spatial scales and in relation to dispersal distances of species. In southern Sweden, mosquito faunas differed between natural and constructed wetlands, partly reflecting differences in wetland size. In an experiment, different responses of two co-occurring mosquito species to rapid larval habitat desiccation indicate that weather conditions after a flood could influence mosquito assemblages. The conclusions of this thesis provide suggestions on how to construct and position wetlands for increased insect diversity, and indicate that low abundance of major nuisance species might be crucial for acceptance of wetlands near human settlements.

Momentum behind the economic valuation of ecosystems, after a decade of hopeful support from researchers and policymakers, is currently petering out and decision-makers still do not consider biodiversity conservation to be a political priority. Surprisingly, the economic benefits provided by the conservation of ecosystems have been poorly investigated, unlike the ecosystems themselves. Furthermore, is the valuation of conservation (the valuation of the “interest rate” made on the natural capital saved, instead of the valuation of the natural capital itself) an efficient means to better serve decision-making? The research presented here addresses this question, in proposing a more effective approach to the valuation of conservation. It also investigates how such economic valuation exercises could best serve the decision-making process. The research method for measuring conservation value relies on a comparison of Total Economic Values for analogous ecosystems both within a protected area and in outside adjacent areas. This methodology is tested in a sample of five marine protected areas in West Africa. For the estimation of the Total Economic Values in these sites, the research has applied most of the available valuation tools and includes all values for which data are available, including non-use values. The results indicate a predominance of benefits linked to indirect use values over direct use values and non-use values. The marine protected areas display substantial benefits when compared to unprotected sites. These benefits are thought to derive primarily from the better marine health status associated with protected areas, and subsequent higher indirect use values which compensate for the decrease in direct use values caused by the conservation policy and the subsequent limitations imposed as a result. The ‘paper areas’ (i.e. those protected areas with no management plan) show, however, a deficit even when compared to unprotected sites. The research discusses and highlights the shortcomings of such an approach within the West African context (data-poor situation, non-monetised economies, value transfer to developing countries, difficulties in communicating non-use values of biodiversity) and associated time and space considerations. It also underlines the importance of considering the socio-cultural context in any economic valuation, which provides key information for valuation interpretation. Furthering the approach within the ‘economics of protection’ stream (after the ‘economics of degradation’ and the ‘economics of welfare’), this research delivers a new approach for valuing biodiversity conservation. The extensions of this research for policy purposes may include management support (comparison of conservation benefits with costs of management, increased consideration of indirect use values), advocacy information (through the calculation of the costs of policy inaction), and mechanisms for sustainable financing (through the development of payment for ecosystem services).

Marine species are highly susceptible to climate change as demonstrated by several studies. However, most of these studies focus on few species or on restricted geographical areas. Within this context, the main goal of my dissertation is to characterize global patterns and forecast the effects of climate change on marine biodiversity. This work is the first macroecological approach to investigate the effects of climate change in the marine realm on key commercial marine groups, namely coastal lobsters (125 species), cephalopods (161 species) and small pelagic fish (103 species). Here I aimed to improve our understanding of how projected changes in species distribution might affect key marine species diversity, body size, assemblage composition, variations in catch, and finally infer on the potential impacts for fisheries worldwide. Using Ecological Niche Models (ENMs) the projected global diversity patterns of the analyzed species generally showed higher values in tropical areas and lower values in higher latitudes. Nonetheless, these patterns were projected to change significantly by the end of the century, with a general tendency of species tracking adequate habitat suitability to higher latitudes. The results obtained provide critical information to anticipate negative impacts of climate change on marine biodiversity and should be considered in future studies, as they highlight climate hot-spot areas or with highly vulnerable species. Ultimately, it is crucial to evaluate species adaptation potential and develop hybrid models that better can guide future political decisions on conservation and management measures; RESUMO: Padrões globais da biodiversidade marinha e o potencial impacto das alterações climáticas As espécies marinhas são altamente suscetíveis às alterações climáticas, como demonstrado em numerosos estudos. Porém muitos desses estudos focam-se num número reduzido de espécies ou numa determinada área geográfica (local ou regional). Neste contexto, a presente dissertação tem como objetivo investigar os padrões globais de biodiversidade marinha e projetar como estes poderão estar modificados no final do século. Este trabalho constitui a primeira abordagem macroecológica que investiga, numa escala global, os impactos das alterações climáticas em taxa marinhos com alto interesse económico, como lagostas (125 espécies), cefalópodes (161 espécies) e pequenos peixes pelágicos (103 espécies). Os padrões globais de biodiversidade marinha para todos os taxa analisados mostram maior riqueza na zona dos trópicos e menor número de espécies nas maiores latitudes. No entanto, estes padrões podem sofrer modificações significativas até ao final do século verificando-se uma tendência generalizada das espécies migrarem para latitudes maiores de forma a encontrarem refúgio em áreas com boa adequação ambiental. Os modelos usados nesta tese (modelos de nicho ecológico) projetam alterações significativas na distribuição das espécies analisadas, com impactos profundos na riqueza e abundância em áreas vitais para a saúde dos oceanos e para as pescas, a longo prazo. Esta dissertação representa um contributo importante para o conhecimento dos padrões globais da biodiversidade nos oceanos futuros. Servindo os seus resultados para orientar estudos pormenorizados em áreas de risco elevado ou com espécies mais vulneráveis e informar a tomada de decisões com vista a proteção de espécies marinhas com elevado valor económico e ambiental. Contudo, atendendo aos efeitos das alterações climáticas já sentidos nos oceanos, é crucial avaliar a capacidade de adaptação destas espécies e encontrar modelos híbridos que melhor nos permitam orientar medidas de gestão e conservação futuras.

The present work focuses on different aspects related to the Antarctic seaweed. As the main primary producers of the coastal areas of Antarctica, this group of organisms play a key role in shaping the biological communities and the ecological dynamics of Antarctic shores. However, compared to other groups of Antarctic organisms or the seaweed communities of other regions of the world, Antarctic macroalgae remain less studied. This is especially true in several areas of knowledge as their actual biodiversity, their evolutionary history and patterns, some aspects of their ecology or the total extent of their relations with other Antarctic organisms and their environment. Aiming to address the lack of knowledge of these areas, we aimed to extend it by focusing our work in several key aspects of Antarctic seaweed biology. As so, we tried to respond several specific questions regarding the topics above mentioned. In this context, we studied biodiversity of seaweed communities that are present in the South Shetland Islands. For that, we tried to identify the composition and influencing factors of the seaweed assemblages present in Deception Island. We also studied how seaweed biodiversity affects Antarctic epiphytic diatoms richness, studying the composition of them, both from Deception and Livingston islands. Moreover, we tried to expand the data with evolutionary relevance by analysing the nuclear DNA content and ploidy levels (C values), as well as the nuclear developmental patterning of some common Antarctic seaweed species with no previous data for those characters. This was achieved by using a fluorimetry technique that sets a reference for comparison for future studies on those parameters. Additionally, we condensed the latest knowledge on the chemical ecology of seaweeds and other organisms from Antarctica, and tried to expand it by investigating the potential antimicrobial activity of these seaweeds. For this, we tested their natural extracts against several Antarctic microorganisms and identified several species that were active chemically. Also, we tested the same extracts for antimicrobial action against several microorganisms that are common human pathogenic surrogates and identified potential human interest in these seaweeds on the search for new sources of antibiotics. Finally, we reported our findings on the role seaweed have in the context of climate change in the Antarctic region. Those findings include the identification of non-native kelp rafts that arrived to the maritime Antarctica, and presented several passenger species that have potential invasiveness in the Antarctic. Regarding that, we classified and explored the possible roles that the rafts themselves and the species travelling with them may play in futures scenarios of climate change in Antarctica.

This thesis presents the first seasonal study in the Antarctic of shallow water hard rock communities, including surveys to quantify biodiversity and biomass (Ash Free Dry Mass, AFDM). In addition temporal changes in biodiversity since 1998 were evaluated in the same location. To do this all benthic organisms greater than 3mm in size were collected at 6m, 12m and 20m depth from three transects near Rothera Point, Adelaide Island (67° 34’ S, 68° 07’ W) in the summer and winter of 2015. Organisms were identified and their wet, dry and ash free dry masses obtained. Benthic community structure did not vary seasonally, low metabolic costs due to slowed growth rates, reproduction, development with the ability to cease feeding for the winter months may explain the lack of change between season. Community structure did, however, vary with depth, which agrees with previous studies of shallow water Antarctic hard substratum communities. Comparisons between the 2015 and 1998 survey showed reductions of both biodiversity and organic biomass at all three depths over the intervening 17 years. The greatest change was at 12m where faunal density, diversity, richness and biomass all declined significantly between 1998 and 2015. Ice scour is thought to be the main driver of this change as previous studies have shown an increase in ice scour frequency around 10m depth. The effects of seasonality on metabolism were also investigated using the five most common marine invertebrates and significant energy transformers Odontaster validus, Sterechinus neumayeri, Nacella concinna, Heterocucumis steineni and Ophionotus victoriae. Measurements of metabolic rates using closed circuit respirometry were carried out across a size range (juveniles to fully reproductive adults), to represent the population of five locally abundant species during the austral summer and winter. Oxygen consumption of Sterechinus neumayeri and Odontaster validus was significantly higher (by 39% & 44% respectively) in summer than winter. However, metabolic rates showed no consistent seasonal trends in Nacella concinna, and in Ophionotus victoriae and Heterocucumis IV steineni were higher in summer than winter, but only in large individuals which could be due to feeding and reproducing during the summer months. Seasonal metabolic changes were in line with previous studies on Antarctic marine invertebrates. Having established the metabolic rates of these species, identifying how much organic carbon there is in each and what they eat (diet), it is possible to estimate the energy required within the ecosystem to meet their metabolic demands long term. Molecular methods were employed to advance our understanding of diet. Gut contents from the same five species were analysed using DNA extraction and molecular techniques. This project forms a baseline to understand future changes in Antarctic benthic biodiversity and to analyse energy flows in these communities.

The current thesis covers two important and poorly known aspects of Antarctic bryozoans: biodiversity and chemical ecology. The comparative analyses of diversity carried out here (Chapters 1 and 2) between Antarctica and the last separated fragments of Gondwana support the hypothesis of the sequential separation of Gondwana. We discuss that the high number of species from the Argentine Patagonian (AP) region shared with Antarctica found in our study question the real extent of Antarctic isolation for cheilostome bryozoans. The presence of shared common bryozoan species between these two regions may also be explained by the free migration of marine organisms in and out of the Polar Front, via the deep abyssal plains and the potential passive northwards transport of larvae (or perhaps even adults) to considerable distances, via the branch of the Antarctic Circumpolar Current (ACC) flowing northward along the continental shelf of Argentina, the Falkland/Malvinas Current. The role of the Scotia Arc and other dispersal pathways, like eddies of ACC, and human dispersal mechanisms, may increase the bryozoan connection found between the Antarctica and the AP region. Also, our studies (Chapters 1 and 2) are among the first characterizations of the bryozoan communities, mainly at the slope, from the AP region, and from the Southern Ocean (SO), specially the Weddell Sea. The bathymetric distribution from the AP region and the SO found in our studies fits well with the limits of the continental shelf, the slope and the deep sea. Interestingly, our research also shows an expansion in the known distribution of diverse bryozoan species from the AP region and the SO. Our results stress the importance of taxonomical studies in these scarcely explored regions, reporting a high number of new genera and species, and new records too. Among the new species found in our study, a bryozoan of the genus of Reteporella characterized by rare giant spherical avicularia is described in Chapter 3, leading us to discuss which are the potential roles of the avicularia. Since the studied bryozoan communities, below areas affected by local disturbances (iceberg scours and anchor ice), are mainly subject to biotic factors such as competence and predation, the evolution has favoured the development of chemical mechanisms in benthic organisms, which have also been investigated here (Chapters 4 and 5). Our studies are among the first reports on chemical ecology of Antarctic bryozoans. In order to study these chemical interactions, new adapted protocols were designed using sympatric and abundant predators. Our findings demonstrate the importance of diverse chemical ecology mechanisms against competence and predation in Antarctic bryozoans. Most bryozoan species tested here display cytotoxicity and/or repellent activity against the sea urchin Sterechinus neumayeri and the amphipod Cheirimedon femoratus, respectively (Chapter 4). In Chapter 5, our results demonstrate that bryozoans seem to be readily defended against at least one of the two abundant predators, Odontaster validus and C. femoratus. The intra- and interspecific variability in bioactivity suggest an adaptive response to diverse abiotic and biotic factors, presence of microorganisms and/or genetic variability. The general trend in our study indicates the presence of a combination of both chemical and physical defensive mechanisms in most bryozoan species, suggesting complementary traits. In general, these results lead to the conclusion that this phylum is very active with extended repellent activities.
Aquesta tesi cobreix dos aspectes importants i poc coneguts dels briozous antàrtics: la biodiversitat i l'ecologia química. L'anàlisi comparatiu de diversitat realitzat aquí (Capítol 1 i 2) entre l'Antàrtida i altres zones geogràficament properes recolzen la hipòtesi de la separació seqüencial de Gondwana. Es discuteix que l'elevat nombre d'espècies de la regió de la Patagònia argentina (PA) compartides amb l'Antàrtida qüestiona el grau real d'aïllament de l'Antàrtida en briozous queilostòmats. Els nostres estudis (Capítols 1 i 2) són també una de les primeres caracteritzacions de les comunitats de briozous, principalment del talús, de la regió de la PA, i de l' Oceà Austral, especialment el Mar de Weddell. Els nostres resultats remarquen la importància dels estudis taxonòmics en aquestes regions escassament explorades, incloent un gran nombre de nous gèneres i espècies, i noves cites. Entre les noves espècies trobades en el nostre estudi, es descriu un briozou del gènere Reteporella caracteritzat per una rara aviculària esfèrica i gegant, portant-nos a reconsiderar quines són les possibles funcions de l'aviculària (Capítol 3). Com les comunitats estudiades de briozous, per sota de les zones afectades per pertorbacions locals (erosió per icebergs), estan subjectes principalment a factors biòtics com la competència i la depredació, l'evolució ha afavorit el desenvolupament de mecanismes químics de protecció (Capítols 4 i 5). Els nostres estudis són dels primers en ecologia química de briozous antàrtics. Els nostres resultats demostren la importància de diversos mecanismes d'ecologia química contra la competència i la depredació en briozous antàrtics. La majoria de les espècies de briozous mostraven activitat citotòxica i/o repel•lent contra l'eriçó de mar Sterechinus neumayeri i l'amfípode Cheirimedon femoratus, respectivament (Capítol 4). En el capítol 5, totes les espècies de briozous estudiats mostraven activitat de repel•lència alimentària contra almenys un dels dos depredadors abundants considerats, l'estrella de mar Odontaster validus i l'amfípode Cheirimedon femoratus. La tendència general en el nostre estudi indica la possessió d'una combinació de mecanismes físics i químics en la majoria de les espècies, fet que suggereix estratègies complementàries.

La biodiversité est de plus en plus modifiée par les activités humaines, ce qui a conduit à des recherches considérables sur l'effet de la biodiversité sur le fonctionnement des écosystèmes. Ces recherches ont cependant rarement inclu le stress anthropogénique qui cause la perte de biodiversité. Cette thèse analyse l'impact du stress (pesticides et métaux lourds) sur la relation entre la biodiversité et le fonctionnement des écosystèmes à la base de la chaîne alimentaire marine, avec des producteurs marins primaires (diatomées) et leurs principaux consommateurs (copépodes). Le premier résultat est que la pollution chimique altère la régularité plutôt que la richesse des espèces, avec un effet disproportionné sur le fonctionnement si un stress sélectif provoque la domination par des espèces tolérantes avec une faible contribution fonctionnelle. L'effet du stress sur le fonctionnement est prévisible sur la base d'une corrélation des traits biologiques prédisant l'abondance des espèces et des traits prédisant leur effet sur le fonctionnement. L'effet de la biodiversité sur le fonctionnement augmente sous l'effet du stress dû à une augmentation d'interactions facilitatrices entre les espèces (effet de complémentarité). L'effet du stress sur la qualité alimentaire des producteurs primaires réduit le transfert d'énergie au niveau des consommateurs, soulignant la pertinence du changement de biodiversité dans un contexte trophique. La thèse se termine par un cadre synthétique présentant les trois principaux effets (stress sélectif, stress physiologique, complémentarité) déterminant l'effet du stress sur la relation entre la biodiversité et le fonctionnement des écosystèmes
Biodiversity is increasingly altered by human activities, which has led to considerable research on the consequences of biodiversity loss for ecosystem functioning. The anthropogenic stressors driving the ongoing biodiversity loss are however rarely included into biodiversity-ecosystem functioning experiments. The present thesis analyses the impact of anthropogenic stressors (pesticides, heavy metals) on the biodiversity-ecosystem functioning relation in marine primary producers (diatoms) and consumers (copepods). It was shown that chemical stress alters species evenness rather richness, with a disproportionate effect on functioning if stress causes dominance by tolerant species with a low functional contribution. Stress tolerance and the functional contribution were predictable based on the species’ biological traits, and the effects of stress on ecosystem functioning depended on the correlation of traits predicting species abundance and traits predicting the species’ effect on ecosystem functioning. The biodiversity effect on primary producer biomass production increased under stress due to facilitative interactions (complementarity effect). Stressor-induced biodiversity loss reduced the food quality of primary producers and impaired the energy transfer to the consumer level, highlighting the relevance of stressor-induced biodiversity changers in a trophic context. The thesis ends with a synthetic framework which puts forward the three main effects (selective stress, physiological stress, complementarity) through which anthropogenic stress affects biodiversity-ecosystem functioning relations at the basis of marine food webs

Marine environmental resource managers and consultants require comprehensive, accurate and current data on the status of marine biodiversity in order to fully evaluate resource consent applications that involve development, impact or encroachment within the marine environment, and for identifying areas of coast appropriate for conservation. The role and efficacy of existing global, national and regional marine biodiversity databases in delivering these types of data are evaluated. Consultation with environmental consultants revealed that none regularly, if ever used any existing marine biodiversity database during their routine consulting activities. Moreover, no existing biodiversity database had appropriate data-mining tools, although each was determined to provide information of value to resource managers and environmental consultants operating at national and regional scales; none was deemed to provide the sort of information required to manage marine resources at a local scale. To achieve the objectives of this research programme, resource managers, data users and data compilers were consulted to determine their ideal data and database requirements. Existing biodiversity data sets that included New Zealand marine biodiversity then were searched or procured, and these data and that of a novel data set of species occurring at 296 intertidal and 25 fringe-saline (effectively freshwater) sites within and proximal to the Hauraki Gulf Marine Park (from Mimiwhangata Bay in the north to Tauranga Harbour in the south) were compared with species inventories from environmental consultants operating in this region. Biodiversity data from the 296 saline, comprising presence/absence data for 713 taxa recorded from the survey region were analysed in detail. Significantly different species assemblages were identified amongst these 296 sites, five intertidal habitats being recognised, each with characteristic species assemblages: marine-hard shores, marine-soft shores, brackish-hard shores, brackish-soft shores, and mangrove shores. Species richness and diversity were consistently higher in marine habitats, and greatest on hard substrata. Most sites host unique assemblages of species. A novel index of species richness is proposed, and although the spatial distribution of richness isn’t particularly revealing, as obvious patterns in the distribution of richness are not apparent, this index has value in that the richness of any shore can be compared and contrasted with that of others throughout the region. Augmenting this richness index is a novel index of species rarity. Based on the frequency of occurrence of taxa on shores throughout the survey region, very rare through to ubiquitous taxa are recognised to routinely occur on almost all shores, regardless of the total species richness. Moreover, very rare to uncommon taxa often comprise a disproportionately high percentage of the total species occurring on any given intertidal shore, in any habitat. Accordingly, alarm bells should ring for reviewers of resource consent applications wherein environmental consultants state that an area subject to development ‘hosts no rare, unique or otherwise remarkable species or ecology.’ Two applications of these novel biodiversity data are demonstrated: the relationship between species richness and regional council consented activities is described, with a negative correlation reported for the intensity of disturbance (using the number of consented activities as a proxy for disturbance) and species richness on marine hard shores; and an appraisal of four selection criteria for marine reserves (naturalness, representativeness, uniqueness and complementarities), wherein the intertidal fauna and flora of no existing or proposed marine reserve appears to be natural, unique or representative, and effort seems to have been spent duplicating certain assemblages of species in reserve networks. The former is intuitively obvious, but the latter is alarming, and the ramifications of it far reaching in terms of conservation of the marine environment. Protocols for conducting biodiversity surveys must be established and implemented to elevate the standards of environmental consultants, resulting value judgements on the composition of species, and the likely and actual effects of these developments on the marine environment to ensure that statements made in reports are based on current data rather than perceptions and client expectations. It is possible that resource consents have been issued based on spurious appraisals of the immediate and cumulative effect of discharge on the environment, or of the relative rarity (or appreciation of this) of species that occur within it. Prior to development of the novel Monalisa data set, no existing database or data set existed that provided the information routinely required by managers and consultants to make informed judgements that affect coastal development throughout the survey region. Recommendations for additional research to build on findings detailed herein are made.

The irreversibility and global ubiquity of marine litter pollution and plastic, in particular, make this material a potential planetary boundary threat. Although the growing attention from the scientific community and the increasing number of peer-reviewed papers, the occurrence and distribution of plastic litter in the Mediterranean Marine Protected Areas (MPAs) and its impacts and effects on marine wildlife remain still poorly investigated. Within the Plastic Busters MPAs project, this PhD thesis provided a comprehensive assessment of marine litter pollution in the sea surface waters and beaches of the Pelagos Sanctuary and the Tuscan Archipelago National Park and the potential physical and chemical impacts related to plastic ingestion on several Mediterannean bioindicators. The experimental designs planned ad-hoc for the selected study areas (Chapter 3), harmonised and implemented the current methods for sampling marine litter in the different environments and defined a new simultaneous multilevel approach reflecting the strong pressure that marine litter, and in particular plastics, exert on organisms inhabiting the protected areas. A total of 273 monitoring transects of floating macrolitter, 141 manta trawl and 14 beaches were sampled and monitored evaluating the occurrence, abundances and composition of marine litter according to the characterization protocols implementing the Marine Strategy Framework Directive (MSFD) (Chapter 4). Particular attention was applied to investigate the potential influences of environmental and anthropic variables affecting the litter distribution and to identify potential hotspot accumulation areas representing a major hazard for marine organisms. Several species were collected, starting from invertebrates to cetaceans, to evaluate the frequency of ingestion and confirm/validate their potential role as marine litter bioindicators (Chapter 5). For the first time, an exhaustive analysis of phthalate acid esters (PAEs) presence was assessed on different organisms and biological tissues through the GC-MS analysis (Chapter 5). Strong litter inputs were identified to originate from the mainland and accumulate in coastal waters within about 10-15 nautical miles. Harbours and riverine outfalls may contribute significantly to plastic pollution representing the main sources of inputs as well as areas with warmer waters and weak oceanographic features could facilitate the accumulation of litter. The high concentrations of plastics floating on the sea surface (399 items/km2 for macrolitter and 259,490 items/km2 for MPs) and stranded on beaches (up to 1,033 ± 915 items/100m) indicate a potentially threatening trend of particle accumulation that may pose a serious risk to organisms living in the Pelagos Sanctuary. The twofold monitoring approach, simultaneously investigating plastic and MP ingestion in several species and concentrations of plasticizers has allowed gaining information on the direct link between synthetic particle ingestion and its additive substances release. Microplastic ingestion was assessed for the first time in the Mediterranean Sea in Velella velella organisms (0.71 items/ind), filter-feeding organisms such as the Mobula mobular (23 items/ind.) and Balaenoptera physalus (35 items/ind.), as well as in poorly investigated species i.e. seabirds, lanternfishes and odontocete cetaceans. Phthalate acid ester loads (mainly DIBP, DBP and DEHP compound) and their pattern of accumulation were evaluated in several species and different biological tissues respectively, according to their feeding behaviour, long life span and spatial distribution. Finally, the spatial risk assessment (Chapter 6) indicated the Gulf of La Spezia and the National Park of the Tuscan Archipelago as the most affected by the accumulation of plastic waste and at higher risk of exposure to organisms as well as the Genova canyon and the seamount area. The results obtained here provide further indications for dealing with plastic pollution in MPAs and could facilitate future recommendations for the management and use of the marine and coastal environment of these protected areas.

This doctoral dissertation was produced in a cooperation between Halmstad University (Wetland Research Centre, School of Business and Engineering) and Lund University (Limnology & Marine Biology, Department of Ecology). Abstract . Wetland creation at large, regional scales is implemented as a measure to abate the biodiversity loss in agricultural landscapes and the eutrophication of watersheds and coastal areas by non-point source nutrient pollution (mainly nitrogen). The consequences of creating many new wetlands for biodiversity conservation and nutrient reten- tion (ecosystem functioning) in agricultural landscapes are still relatively unknown, both on local (per wetland) and regional (per landscape) scales. In Sweden, wetland creation has progressed already since the 1990s, and by now larger numbers of created wetlands are present, mainly in the intensively farmed landscapes of southwestern Sweden. This thesis aimed to investigate the following aspects in these systems: (i) their large-scale effects on biodiversity, (ii) their functional diversity of bacterial denitrifiers, (iii) the abiotic and biotic influences on wetland ecosystem functioning, (iv) the potential for biodiversity-function links, and (v) the potential for functional links and joint functioning.(i) Created wetlands hosted diverse assemblages of macroinvertebrates and plants. They maintained a similar com- position and diversity as natural ponds in agricultural landscapes. The environmental conditions per wetland did hardly affect macroinvertebrate and plant assemblages, and the prerequisites for nutrient retention did neither. In landscapes were wetland creation efforts had increased the total density of small water bodies by more than 30%, macroinver- tebrate diversity of created wetlands was facilitated on both local and regional scales. (ii) Diverse communities of denitrifying bacteria with the capacity for conducting different denitrification steps (functional types) were present in all investigated wetlands. The richness of denitrifying bacteria communities was affected by nitrate concentration and hydraulic loading rate, which may potentially be relevant for the nitrogen retention function of created wetlands. The diversity across different functional types of bacterial denitrifiers increased with nitrate concentration. (iii) Both abiotic and biotic factors influenced ecosystem functions of created wetlands. Variation in nitrogen retention was associated to nitrate load, but even to vegetation parameters. In wetlands with constant nitrate load, planted emergent vegetation facilitated nitrogen retention compared to other vegetation types. In wetlands with variable loads, nitrogen retention was facilitated if nitrate load was high and many different vegetation types were present; nitrogen load could explain the majority of the variation in nitrogen retention compared to vegetation parameters. Phosporus retention of created wetlands was best explained by vegetation parameters. Litter decomposition was inhibited at high nitrate to phosphorus ratios. Methane production increased with age and decreased with plant cover. (iv) Biodiversity may facilitate wetland ecosystem functions, particularly in dynamic wetland ecosystems. Nitrogen retention increased with vegetation type diversity, phosphorus retention capacity with plant richness, and litter decomposition with macroinvertebrate diversity. (v) Created wetlands have the capacity of sustaining several parallel ecosystem services. Some wetland functions were coupled; nitrogen retention increased with fast litter decomposition. On the other hand, methane emission and nitro- gen retention were independent of each other, as were nitrogen and phosphorus retention.In conclusion, created wetlands have the potential to at least partly abate the lost biodiversity and multifunctionality caused by the past extensive destruction of natural wetlands in agricultural landscapes.

[Paper II] Milenkovski S., Thiere G., Weisner S.E.B., Berglund O. & Lindgren P.-E. Variation of eubacterial and denitrifying bacterial biofilm communities among constructed wetlands. Submitted manuscript. [Paper V] Thiere G. & Weisner S.E.B. Influence of biotic and abiotic parameters on ecosystem functioning of created wetlands. Manuscript.

The degradation of natural diversity results in the erosion of key systemic properties such as resilience, or the capacity to recover from disturbances. Resilience loss leads to an increase in the fragility and vulnerability of natural communities, fearfully approaching, if not surpassing, the tipping point that turns them into degraded communities with fewer ecosystem services. A potential pathway to avoid the continuous decline of resilience is to generate biodiversity- inclusive resilience metrics that can be broadly applied, monitored, and taken into consideration before conservation decision making. It is hard to manage what cannot be measured. This thesis contributed to our understanding of the resilience of marine temperate rocky reefs, integrating biodiversity metrics with environmental variables and management actions. To do so, this thesis put forward multiple community metrics that allowed a global and integrative vision of the actual situation of the temperate rocky reefs of the Iberian Peninsula, the Spanish territories in Northern Africa, the Balearic Islands, and the Canary Islands. In particular, the thesis investigated the impact of artificial substrates on diversity, quantified the resistance of marine communities to recover a more pristine stage, analyzed the efficiency of marine protection on fish communities, and developed a new integrative tool that allowed the quantification of marine resilience by harmonizing numerous biological, environmental, and management factors that regulate the resilience of temperate marine systems. The results obtained in this thesis showed the negative impact of artificial substrates on diversity, mainly in sessile organisms or species with reduced mobility. This thesis provided evidence that unprotected marine areas were more resistant than partially protected areas to recover their diversity. Furthermore, marine protection had greater benefits on the biomass than on the diversity of the marine fish community. This thesis also laid the foundations to quantify resilience and to detect priority areas to preserve, reflecting the importance of adequate marine management. This thesis is, therefore, a compendium of studies that reflects my commitment to advance our understanding of marine biodiversity. The research carried out in this thesis evaluated the current status of our littoral rocky reefs and promoted its conservation using emerging ecological concepts with strong implications for management. In particular, my thesis set the basis for an improved understanding of the resilience of temperate rocky reefs providing widely-spread, georeferenced empirical estimates of resilience, a particularly elusive topic in the scientific literature to date. Overall, this thesis actively sought to promote a healthier, more diverse marine environment through the study of biodiversity-based resilience and its potential to improve management.
La acentuada degradación que están sufriendo los ecosistemas naturales promueve la erosión de propiedades comunitarias vitales como la resiliencia, o la capacidad de recuperación. La pérdida de resiliencia conlleva un aumento de la fragilidad y vulnerabilidad de las comunidades naturales, haciendo que estas comunidades naturales se aproximen temerosamente al punto de inflexión que las conduce a convertirse en comunidades degradadas, disminuyendo los servicios ecosistémicos proporcionados. Una potencial vía para evitar la continua degradación de resiliencia es estudiar esta métrica a través de la diversidad biológica, de tal forma que se puedan aplicar, supervisar y, considerar esta información antes de la toma de decisiones en conservación. Es difícil gestionar lo que no se puede medir. La presente tesis contribuye a conocer el estado de la diversidad y resiliencia marina en diferentes contextos de los arrecifes rocosos templados marinos. Para ello, la tesis elaboró métricas comunitarias que permitieron crear una visión global e integradora de la situación real de los arrecifes rocosos de la Península Ibérica, archipiélago Canario y Balear y, el norte de África. En concreto, la tesis investigó el impacto que tienen los substratos artificiales sobre la diversidad, cuantificó la resistencia de las comunidades marinas a recuperar un estado más prístino, estudió la eficiencia que tienen las figuras de protección sobre la comunidad de peces marinos. Y, desarrolló una nueva herramienta integradora que permitió cuantificar la resiliencia marina mediante la armonización de numerosos factores biológicos, ambientales y de gestión que regulan la resiliencia de los sistemas marinos de las zonas templadas. Los resultados obtenidos en la tesis ponen de manifiesto el impacto negativo que tienen los substratos artificiales en la diversidad de los organismos marinos, principalmente en la comunidad sésil o con movilidad reducida. La tesis aportó pruebas de que las zonas marinas no protegidas son más resistentes que las zonas parcialmente protegidas para recuperar su diversidad. También se ha reflejado que la protección marina presenta mayores beneficios en la biomasa que en la diversidad de la comunidad de peces marinos. Y por último, esta tesis siesta las bases para cuantificación de la resiliencia y detección de zonas prioritarias a conservar, lo que refleja la importancia de una ordenación marina adecuada. Por todo ello, esta tesis es un compendio de estudios que reflejan mi compromiso de avanzar en nuestra comprensión de la biodiversidad marina, evaluar el estado actual de nuestros arrecifes rocosos templados y promover su conservación utilizando conceptos ecológicos emergentes con fuertes implicaciones para la ordenación. En particular, mi tesis ha sentado las bases para una mejor comprensión de la capacidad de recuperación de los arrecifes rocosos de las zonas templadas, proporcionando estimaciones empíricas de resiliencia georreferenciadas y sobre una gran área geográfica, un tema particularmente elusivo en la literatura científica hasta la fecha. En definitiva, esta tesis promueve activamente un medio ambiente marino más saludable y más diverso mediante el estudio de la resiliencia basado en la biodiversidad y su potencial para mejorar la gestión.

2012/2013
Heterotrophic nanoflagellate (HNF) grazing is one of the major source of prokaryotic mortality in marine ecosystems, acting as a strong selection pressure on communities. Protozoans may thus affect prokaryotic abundance and alter the diversity and the taxonomic composition of the prey community, as individual prokaryotes can develop distinct grazing-resistant mechanisms. Moreover, the microbial loop is well known to regulate carbon fluxes in surface marine environments but few studies have quantified the impact of HNF predation on prokaryotes in the dark ocean. The present work was aimed to: (1) quantify the impact of HNF predation on the deep prokaryotes biomass; (2) investigate if and how prey diversity varies in response to different predation pressure; (3) define taxonomic community composition in studied areas and identify most affected prokaryotic phylotypes by HNF grazing (4) evaluate the effects of small HNF (<3 µm), which are known to dominate nano-sized compartment and represent the main bacterivores in aquatic ecosystems, being an important link between bacteria and larger protists; (5) evidence differences in community sensitivity to grazing between surface and mesopelagic ecosystems (6) identify the main environmental drivers shaping microbial community diversity. Predation experiments were performed with surface and mesopelagic water samples collected from the Southern Adriatic and Northern Ionian basins. An additional predation experiment was set up in the North-eastern Adriatic Sea. We coupled the traditional ‘dilution method’ with high-throughput molecular analysis (ARISA and Ion Torrent/454 sequencing) to provide a quantitatively and qualitatively evaluation of the grazing process occurring in marine microbial communities. The present work is structured by four manuscripts in preparation and one manuscript already submitted. 1. Heterotrophic nanoflagellate grazing on picoplankton in deep waters (manuscript in preparation) 2. Effects of heterotrophic flagellate predation on bacterial community diversity (manuscript in preparation) 3. HNF grazing impact on taxonomic composition of marine prokaryotic community (manuscript in preparation) 4. Environmental drivers structuring surface and deep bacterial communities in Adriatic and Ionian Seas (manuscript in preparation) 5. Biodiversity changes of bacterial community under predation pressure analyzed by 16S rRNA pyrosequencing (manuscript submitted) My PhD research led to important progresses in the comprehension of microbial dynamics regulating carbon cycles and bacterial diversity in the Adriatic and Ionian basins. Prokaryotic abundance and biomass were one order of magnitude higher in the photic than in the aphotic layers of Southern Adriatic and Ionian Seas (surface biomass 1.68 ± 1.76 µC L-1, deep biomass 9.00 ± 2.11 µC L-1). The Northern Adriatic community presented the highest biomass value (57.46 µC L-1), according to its richer trophic status. All in situ communities displayed the same evenness, being dominated by rare phylotypes. Rare taxa were confirmed to represent the major contributors of microbial communities, with only a few phylotypes dominant. Mesopelagic bacterial communities were as rich and variable as surface assemblages, despite the significant biomass decrease along the water column. Natural archaeal assemblages were characterized by very low richness as we recovered only two genera (Cenarchaeum and Nitrosopumilus), while in situ bacterial communities were composed by the six major marine phyla (Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes and Deinococcus-Thermus), whose contribution varied according to sampling depth. Flagellates were demonstrated to efficiently control their preys (ingestion rates: 7.86-22.26 µg C L-1 in surface experiments, 0.53-10.61 µg C L-1 in deep experiments), causing important losses in the potentially produced prokaryotic biomass. Despite picoplankton and HNF abundance reduction with depth contrasts with the hypothesis that at least 108 picoplanktonic cells L-1 are necessary to sustain HNF community, our data confirm that also in mesopelagic waters prey and predator concentrations are sufficient to sustain efficient microbial food webs. HNF grazing modified bacterial community diversity in both surface and deep marine systems but with different strength. Mesopelagic communities were more sensitive to grazing impact, evidencing a bell-shaped response to the increasing ingestion rates. Moderate-high top-down control preserved or enhanced bacterial diversity, that fell at low predation. In upper communities grazing did not induce wide variations of bacterial richness and evenness, revealing to be more stable. Small HNF (<3 µm) were the dominant size fraction within flagellate communities and likely constituted the main bacterivores. After the removal of large HNF, a higher fraction of prokaryotic phylotypes was affected. Larger protists partially reduced small flagellate impact on their preys. Larger HNF had a more important role in photic systems compared to mesopelagic waters. The fraction of bacterial taxa favored or affected by predation when small HNF were the only predators more markedly varied in surface experiments, while few phylotypes changes their behavior between the two size treatments in deep experiments. Some taxa were consumed mainly by larger HNF (3-10 µm), while others were grazed by smaller ones (<3 µm). Over 50% of the predated phylotypes belonged to the rare biosphere, mainly in the surface experiments. Rare bacteria are thus not only a dormant ‘seed bank’ but constitute a fundamental component of microbial food webs and actively vector the carbon transfer toward higher trophic levels, being as important as dominant organisms. Although general patterns applicable to all communities were not found, trends of selectivity over different phylotypes were highlighted within sampling layer along the water column and between different systems. While the majority of predator-prey interactions were characteristic to specific environments, some can be considered common to different systems (e.g. Burkholderiaceae and Pseudomonadaceae were exclusively selected in all mesopelagic sites, Bacterivoracaceae were subjected to small HNF predation independently from sampling site or depth). The Southern Adriatic and Ionian basins were significantly distinguished by both the physicochemical water characteristics and the prokaryotes and protists abundance distributions. Cluster analysis based on Jaccard and Bray-Curtis metrics evidenced that depth and geographical location of sampling sites influenced bacterial community similarity. The Southern Adriatic Sea was clearly distinguished from the Ionian Sea. The Northern Adriatic samples were always separated from the others, coherently with different biotic and abiotic characteristics of the sub-basin. Additionally, temperature, chl a and O2 concentration represented important environmental drivers shaping biodiversity of bacterial communities that inhabit Adriatic and Ionian basins. In conclusion, we evidenced that heterotrophic flagellates control bacterial biomass and select certain taxa among all possible preys, grazing also on the rare ones. HNF predation thus shapes bacterial community structures, which in turn influence the ecosystem functioning. Despite the cell abundance decrease of both predators and preys reduces encounter probabilities, the dark ocean hosts complex microbial food webs, structured around three trophic levels (i.e. prokaryotes, small and large heterotrophic flagellates).
I nanoflagellati eterotrofi (HNF) costituiscono una delle principali cause di mortalità dei procarioti in ambiente marino, esercitando una forte selezione sulle comunità predate. Possono modificarne l’abbondanza cellulare e alterarne la diversità e la composizione tassonomica, in quanto le diverse specie procariotiche possono sviluppare distintivi meccanismi di resistenza alla predazione. Mentre l’impatto degli HNF sui procarioti degli acque marine superficiali è ben noto, pochi studi si sono focalizzati sullo studio degli ambienti profondi. Il presenta lavoro di dottorato è stato finalizzato a: (1) quantificare l’impatto della predazione da parte degli HNF sulla biomassa procariotica profonda; (2) capire se e come la biodiversità della comunità predata vari in risposta alla diversa pressione di predazione; (3) definire la composizione tassonomica delle comunità presenti nell’area di studio e identificare i filotipi maggiormente colpiti dalla predazione da parte degli HNF; (4) valutare il contributo dei piccolo flagellati (<3 µm), i quali costituiscono la più abbondante frazione nanoplanctonica e rappresentano i principali organismi batterivori negli ambienti acquatici; (5) evidenziare possibili differenze nella risposta alla predazione tra comunità procariotiche che vivono in acque superficiali e profonde; (6) identificare i principali fattori ambientali che modulano la diversità delle comunità microbiche. Esperimenti di predazione sono stati condotti su campioni di acqua superficiale e mesopelagica raccolti nel Mar Adriatico meridionale e nel Mar Ionio settentrionale. Un ulteriore esperimento è stato condotto nel Mar Adriatico nord-orientale. Il tradizionale metodo delle diluizioni è stato abbinato ad analisi molecolari quali elettroforesi capillare (ARISA) e sequenziamento (Ion Torrent e 454) per consentire una valutazione quali-quantitativa degli effetti della predazione sulle comunità microbiche marine. La presente tesi è costituita da quattro articoli in preparazione e un articolo già sottomesso: 1. Heterotrophic nanoflagellate grazing on picoplankton in deep waters (articolo in preparazione) 2. Effects of heterotrophic flagellate predation on bacterial community diversity (articolo in preparazione) 3. HNF grazing impact on taxonomic composition of marine prokaryotic community (articolo in preparazione) 4. Environmental drivers structuring surface and deep bacterial communities in Adriatic and Ionian Seas (articolo in preparazione) 5. Biodiversity changes of bacterial community under predation pressure analyzed by 16S rRNA pyrosequencing (articolo sottomesso) La ricerca condotta durante il mio dottorato ha portato a interessanti progressi nella comprensione delle dinamiche microbiche che regolano i cicli del carbonio e la diversità batterica nei bacini adriatico e ionico. L’abbondanza e la biomassa delle comunità procariotiche superficiali è risultata un ordine di grandezza superiore rispetto alle comunità profonde in Mar Adriatico meridionale e Mar Ionio (biomassa superficiale 9.00 ± 2.11 µC L-1, biomassa profonda 1.68 ± 1.76 µC L-1). La comunità descritta nel Mar Adriatico settentrionale è caratterizzata dai valori più elevati di biomassa (57.46 µC L-1), coerentemente con l’eutrofia del bacino. I flagellati eterotrofi hanno causando perdite significative nella biomassa procariotica in tutti gli esperimenti condotti, con tassi di ingestione pari a 7.86-22.26 µgC L-1 negli esperimenti superficiali e 0.53-10.61 µgC L-1 negli esperimenti profondi. Un’abbondanza picoplanctonica di 108 cellule L-1 è stata ipotizzata come necessaria per sostenere la comunità degli flagellati. Nonostante l’aumento della profondità comporti una riduzione dell’abbondanza del picoplancton tale da non raggiungere questa soglia, i nostri dati confermano che anche negli ambienti profondi si instaurano interazione preda-predatore sufficienti a sostenere le reti trofiche microbiche. Tutte le comunità in situ hanno mostrato la medesima distribuzione, con prevalenza di filotipi rari e pochi gruppi dominanti. Le comunità mesopelagiche presentano diversità e variabilità analoghe a quelle superficiali, nonostante il decremento in biomassa lungo la colonna d’acqua. Una bassa diversità è stata osservata nelle comunità naturali di Archea, dove sono stati rilevati due soli generi (Cenarchaeum e Nitrosopumilus), mentre le comunità batteriche sono composte dai sei principali phyla marini (Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes e Deinococcus-Thermus), la cui frequenza varia in base alla profondità di campionamento. La predazione esercitata dagli HNF ha modificato la diversità delle comunità sia superficiali che profonde ma con diversi effetti. Le comunità profonde si sono dimostrate più suscettibili alla diversa intensità della predazione. Un controllo top-down medio-alto ha preservato o incrementato la diversità batterica, che invece è risultata fortemente ridotta con bassa pressione di predazione. Al contrario, le comunità superficiali hanno subito solo leggere variazioni nella biodiversità batterica in risposta ai diversi tassi di ingestione, dimostrandosi più stabili. I piccoli flagellati (<3 µm) costituiscono la frazione dominante delle comunità nanoplanctoniche. In seguito alla rimozione dei predatori >3 µm, variazione significative dell’abbondanza sono state riscontrate in una maggiore percentuale di filotipi procariotici. Flagellati di maggiori dimensioni possono quindi mitigare l’impatto dei piccoli predatori sulle prede, con una maggior influenza nei sistemi fotici. Alcuni taxa batterici sono stati consumati prevalentemente dal grandi HNF (3-10 µm), mentre altri sono stati selezionati dai piccoli flagellati (<3 µm). Oltre il 50% dei filotipi predati apparteneva alla biosfera rara, soprattutto negli esperimenti condotti in superficie. I batteri rari (0.1-1% dell’abbondanza totale) non rappresentano quindi una frazione ‘dormiente’ il cui contributo varia in seguito a cambiamenti delle condizioni ambientali, come inizialmente ipotizzato. Costituiscono invece una componente fondamentale delle reti trofiche microbiche e contribuiscono attivamente al trasferimento di carbonio verso i livelli trofici superiori, così come gli organismi dominanti. Nonostante ciascuna comunità risponda in maniera distintiva alla predazione, in funzione della composizione tassonomica delle comunità stesse e dello stato trofico del sistema, alcuni indizi di selettività sono stati individuati. Alcune interazioni preda-predatore si sono rivelate tipiche delle comunità profonde o superficiali, mentre altre erano comuni ad entrambi i sistemi (es. Burkholderiaceae e Pseudomonadaceae sono stati selezionati sono in ambiente pelagico, Bacterivoracaceae sono stati sottoposti a predazione da parte di piccolo flagellati in tutti gli esperimenti, indipendentemente dalla profondità e dal sito di campionamento). I bacini Adriatico meridionale e Ionio settentrionale sono significativamente distinti sia per le caratteristiche chimico-fisiche della colonna d’acqua, sia per l’abbondanza di pico- e nanoplancton. La cluster analisi basata sugli indici di Jaccard e Bray-Curtis ha evidenziato che profondità di campionamento e localizzazione geografica sono i principali fattori che determinano la similarità tra le comunità batteriche. Il Mar Adriatico settentrionale è risultato sempre separato dagli altri campioni, coerentemente con le diverse caratteristiche biotiche e abiotiche del bacino. Oltre a profondità e sito geografico, temperatura, concentrazione di chl a e ossigeno contribuiscono a determinare la biodiversità batterica adriatica e ionica. In conclusione, il presente lavoro ha evidenziato come i flagellati eterotrofi controllino la biomassa procariotica e mostrino preferenza per determinati taxa, selezionando anche quelli rari. La predazione influenza la struttura delle comunità e di conseguenza il funzionamento degli ecosistemi. Anche gli ambienti marini profondi ospitano complesse reti trofiche, strutturate attorno a tre livelli principali (procarioti, piccoli e grandi flagellati eterotrofi) così come le acque superficiali.
XXVI Ciclo
1986

Thesis (PhD)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: Historical vicariant processes due to glaciations, resulting from the large-scale environmental changes during the Pleistocene (0.012-2.6 million years ago, Mya), have had significant impacts on the geographic distribution of species, especially also in marine systems. The motivation for this study was to provide novel information that would enhance ongoing efforts to understand the patterns of biodiversity on the South African coast and to infer the abiotic processes that played a role in shaping the evolution of taxa confined to this region. The principal objective of this study was to explore the effect of Pleistocene climate changes on South Africa′s marine biodiversity using five intertidal gastropods (comprising four rocky shore species Turbo sarmaticus, Oxystele sinensis, Oxystele tigrina, Oxystele variegata, and one sandy shore species Bullia rhodostoma) as indicator species. Sequence data obtained from partial segments of the mitochondrial cytochrome oxidase c subunit 1 (COI), and the nuclear ribosomal DNA (encompassing part of 5.8S, second Internal Transcribed Spacer and part of 28S, hereinafter called ITS2; or comprising part of the first Internal Transcribed Spacer, 5.8S, second Internal Transcribed Spacer and part of 28S, hereinafter called ITS), were used as genetic markers to construct phylogeographic patterns and to investigate demographic histories of the taxa. Population structure was investigated using haplotype network analyses, pairwise ΦST statistics, analysis of molecular variance (AMOVA), isolation by distance analyses, Bayesian analysis of population structure (BAPS) and coalescent analysis of gene flow. Demographic history was analysed through Fu′s Fs tests, mismatch distributions, and Bayesian skyline plots. Demographic analyses suggest that all five intertidal gastropods studied experienced demographic expansions dating to the late Pleistocene. The sandy shore direct developer B. rhodostoma began expansion after the LGM (c. 15 kya) whereas for the four rocky shore broadcast spawners (T. sarmaticus, O. sinensis, O. tigrina, and O. variegata) the onset of expansion coincided with or preceded the LGM (c. 25, 60, 50, 40 kya, respectively). Consistent with recent range expansions and gene flow patterns, the population genetic structure in all species was characterised by shallow or a lack of population differentiation. Oxystele variegata was an exception as it showed a deep disjunction, of late Pleistocene origin, between individuals in the west coast Namaqua Bioregion and those in the south coast Agulhas Bioregion. These results provide strong evidence of the vital role that Pleistocene climatic changes and current regimes played in shaping the nature and distribution of biodiversity on the South African coast. In addition, gene flow in all species, except O. tigrina, was remarkably asymmetrical with the regions around Cape Infanta and Port Elizabeth acting as source populations. Considering the generally weak population genetic structure and gene flow patterns detected for most gastropod species studied here, it is recommended that T. sarmaticus, O. sinensis, O. tigrina and B. rhodostoma be managed as panmictic populations, and that the region encompassing Cape Infanta, and Port Elizabeth should be prioritised for conservation as it appears to harbour source populations. Oxystele variegata was the only species showing distinct population structure and in this instance, species specific conservation efforts should recognize this divergence by treating the two genetic assemblages as distinct management units.
AFRIKAANSE OPSOMMING: Historiese vikariante prosesse kan toegeskryf word aan glasiasie, en het tot gevolg gehad dat grootskaalse veranderinge in die omgewing plaasgevind het tydens die Pleistoseen (,012 - 2.6 miljoen jaar gelede, Mjg). Dit het 'n beduidende impak gehad op die geografiese verspreiding van spesies, veral ook in die mariene stelsels. Die motivering vir hierdie studie was om nuwe data te voorsien wat sal bydrae tot die voortgesette pogings om die patrone van biodiversiteit langs die Suid-Afrikaanse kus te verstaan. Dit sou ook help om die abiotiese prosesse af te lei wat 'n rol gespeel het in die evolusie van taksa wat in hierdie streek voorkom. Die hoofdoel van hierdie studie was om die effek van die Pleistoseen klimaatsveranderinge op Suid-Afrika se mariene biodiversiteit te bepaal deur gebruik te maak van vyf intergety slak spesies as indikatore (vier wat in rotsagtige gebiede voorkom: Turbo sarmaticus, Oxystele sinensis, Oxystele tigrina, Oxystele variegata en 'n sanderige strand spesies: Bullia rhodostoma). Volgorde data verkry vanaf gedeeltelike segmente van die mitochondriale sitochroom oksidase c subeenheid 1 (COI), en die kern ribosomale DNA (bestaande uit 'n deel van 5.8S, tweede interne getranskribeerde spasieërders en 'n deel van 28S), hierna genoem ITS2 is gebruik as genetiese merkers om filogeografiese patrone te dokumenteer en ook om die demografiese geskiedenis van die spesies te ondersoek. Bevolking struktuur is ondersoek deur gebruik te maak van haplotipe netwerk analise, paarsgewyse ΦST statistiek, analise van molekulêre variansie (AMOVA), isolasie deur afstand analise, Bayesiaanse analise van die bevolking struktuur (BAPS) en analise van gene vloei. Demografiese geskiedenis is ontleed deur Fu se Fs toetse, misparing verdelings, en Bayesiaanse luglyn kurwes. Demografiese ontleding dui daarop dat al vyf die intergety slakke wat ondersoek is demografiese uitbreidings ervaar het wat terugdateer tot die einde van die Pleistoseen. Die sanderige strand direkte ontwikkelaar, B. rhodostoma, het die uitbreiding begin na die LGM (c. 15 Kya), terwyl vir die vier rotsagtige kusbewoners wat eiers oor 'n uitgebreide gebiede versprei (T. sarmaticus, O. sinensis, O. tigrina, en O. variegata) het die aanvang van die bevolkings uitbreiding saamgeval met die laaste galsiasie of dit voorafgegaan (c. 25, 60, 50, 40 Kya, onderskeidelik). In ooreenstemming met die onlangse reeks bevolkings uitbreidings, is die bevolking genetiese struktuur in alle spesies gekenmerk deur weinig differensiasie. Oxystele variegata was 'n uitsondering en het 'n ontwrigting van laat Pleistoceen oorsprong getoon tussen individue langs die weskus Namaqua Biostreek en dié in die suid kus Agulhas biostreek. Hierdie resultate voorsien sterk bewyse van die belangrike rol wat die Pleistoseen klimaatsveranderinge gespeel het in die vorming en verspreiding van biodiversiteit langs die Suid-Afrikaanse kus. Daarbenewens, geen vloei in alle spesies, behalwe O. tigrina, was merkwaardig asimmetries. Kaap Infanta en Port Elizabeth verteenwoordig moontlik die bron bevolkings. Met inagneming van die geringe bevolking genetiese struktuur en geenvloei patrone wat waargeneem is vir die meeste slak spesies wat bestudeer is, word dit aanbeveel dat T. sarmaticus, O. sinensis, O. tigrina en B. rhodostoma bestuur word as 'n panmiktiese bevolking, en dat die streek wat Kaap Infanta en Port Elizabeth insluit geprioritiseer moet word vir bewaring. Oxystele variegata was die enigste spesie wat duidelike bevolking struktuur getoon het en in hierdie geval, moet spesie spesifieke bewaringspogings aangewend word.

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

La biodiversité est de plus en plus modifiée par les activités humaines, ce qui a conduit à des recherches considérables sur l'effet de la biodiversité sur le fonctionnement des écosystèmes. Ces recherches ont cependant rarement inclu le stress anthropogénique qui cause la perte de biodiversité. Cette thèse analyse l'impact du stress (pesticides et métaux lourds) sur la relation entre la biodiversité et le fonctionnement des écosystèmes à la base de la chaîne alimentaire marine, avec des producteurs marins primaires (diatomées) et leurs principaux consommateurs (copépodes). Le premier résultat est que la pollution chimique altère la régularité plutôt que la richesse des espèces, avec un effet disproportionné sur le fonctionnement si un stress sélectif provoque la domination par des espèces tolérantes avec une faible contribution fonctionnelle. L'effet du stress sur le fonctionnement est prévisible sur la base d'une corrélation des traits biologiques prédisant l'abondance des espèces et des traits prédisant leur effet sur le fonctionnement. L'effet de la biodiversité sur le fonctionnement augmente sous l'effet du stress dû à une augmentation d'interactions facilitatrices entre les espèces (effet de complémentarité). L'effet du stress sur la qualité alimentaire des producteurs primaires réduit le transfert d'énergie au niveau des consommateurs, soulignant la pertinence du changement de biodiversité dans un contexte trophique. La thèse se termine par un cadre synthétique présentant les trois principaux effets (stress sélectif, stress physiologique, complémentarité) déterminant l'effet du stress sur la relation entre la biodiversité et le fonctionnement des écosystèmes
Biodiversity is increasingly altered by human activities, which has led to considerable research on the consequences of biodiversity loss for ecosystem functioning. The anthropogenic stressors driving the ongoing biodiversity loss are however rarely included into biodiversity-ecosystem functioning experiments. The present thesis analyses the impact of anthropogenic stressors (pesticides, heavy metals) on the biodiversity-ecosystem functioning relation in marine primary producers (diatoms) and consumers (copepods). It was shown that chemical stress alters species evenness rather richness, with a disproportionate effect on functioning if stress causes dominance by tolerant species with a low functional contribution. Stress tolerance and the functional contribution were predictable based on the species’ biological traits, and the effects of stress on ecosystem functioning depended on the correlation of traits predicting species abundance and traits predicting the species’ effect on ecosystem functioning. The biodiversity effect on primary producer biomass production increased under stress due to facilitative interactions (complementarity effect). Stressor-induced biodiversity loss reduced the food quality of primary producers and impaired the energy transfer to the consumer level, highlighting the relevance of stressor-induced biodiversity changers in a trophic context. The thesis ends with a synthetic framework which puts forward the three main effects (selective stress, physiological stress, complementarity) through which anthropogenic stress affects biodiversity-ecosystem functioning relations at the basis of marine food webs

A one-year experimental fishery for P. delagoae was established in April 2004 to determine the frequency and magnitude at which pulse fishing may be sustainable (Government Gazette 2004). Determining the extent of recovery after fishing is one aim of the experimental fishery. Assessments of the growth rate, size at sex maturity and natural mortality of P. delagoae were performed in 2000 (Groeneveld et al) and can be supplemented by the results of this study, which assess the reproductive biology of the East Coast spiny lobster in order to address this aim. A recent study (Groeneveld in press) assessed fecundity, egg loss during gestation, relative reproductive potential and lifetime egg production per recruit for P. gilchristii from three areas along the South African south coast. A general east-west trend of increasing fecundity, size at sexual maturity, and lifetime egg production per recruit was found for P. gilchristii. Examining egg-loss through the first four ( of six) developmental stages of gestation showed significant loss of around 15 % by stage four, irrespective of lobster size (Groeneveld in press). The study of fecundity in P. gilchristii ( Groeneveld in press) was used as a framework for assessing the fecundity of P. delagoae in this study.

Coccolithoviruses are large dsDNA viruses infecting the cosmopolitan calcifying marine phytoplankton Emiliania huxleyi. Therefore they are instrumental components of algal bloom demise and thus agents contributing significantly to biogeochemical cycling in the oceans. Several coccolithovirus strains exist in culture and have been used so far to study the co-evolutionary arms-race between them and their unicellular host in naturally occurring or induced blooms in the North Atlantic Ocean and the fjords of Norway. However, little is known of their distribution in non-bloom conditions, their natural diversity in times of reduced infectivity rates, and the role of functionally important genes found in natural coccolithovirus communities. Even less is known about their genetic differences and the phenotypic consequences of these differences on their infection dynamics. Hence here a three dimensional approach was undertaken, during which the genomes of several coccolithovirus strains were analysed, their diversity in the global ocean characterised, and their phenotypic properties as seen from their infection dynamics with their host established. It was revealed that although coccolithoviruses share a common subset of core genes, they differ in a large proportion of their genomic material, as seen from the presence and/or absence of large sub-clusters of functionally unknown genes. Moreover, a gene that encodes for a phosphate scavenging mechanism (phosphate permease) was truncated from the genome of the Norwegian isolate EhV-99B1 but not from any other strain, while a gene encoding for the virulence factor sialidase was truncated only in the genomes of the English Channel strains isolated in 2001. The discovery of an additional gene that is potentially involved in the regulation of sphingosine and ceramide intermediates during the de novo virus encoded sphingolipid biosynthesis pathway was also intriguing, and the extent of gene homology to host genes (i.e. almost 13% of the analyzed genomes) highlighted the importance of horizontal gene transfer events in the co-evolution between algal hosts and their viruses. Secondly, it was established that virus competition over its resource, the host-cell, is fierce and that during host coinfection, some viruses (i.e. EhV-207) were superior to others (i.e. EhV-86) in their quicker utilisation of the host metabolic machinery and possibly shorter latency period within the infected cells. The biogeochemical and evolutionary implications of these distinct phenotypic properties are far reaching as in the environment there would be hundreds of different virus strains fighting over a few dominant hosts, with “losers” and “winners” coming and going from a particular niche, affecting the recirculation of nutrients and carbon at different rates. Finally, by community fingerprinting cococlithoviruses in the global ocean with phylogenetic markers (major capsid protein) and functional markers (serine palmitoyltransferase) it was discovered that the diversity of these viruses increase with depth, and that the 3D structure of the SPT protein (involved in the propagation of host cell death) differs among strains, dictated by a variant amino acid linker region between the two domains of the protein, LCB1 and LCB2, potentially influencing the efficiency of the virus encoded sphingolipid biosynthesis pathway. This study is an important first step in understanding the role of coccolithoviruses, their evolution, their functional characteristics, and the possible implications of the latter to biogeochemical cycling and global climate and primary production predictions. Articles: Draft genome sequence of the coccolithovirus EhV-84 / Josef I. Nissimov ... [et al.]. Standards in Genomic Sciences, v. 5 (2011), p. 1-11 and Functional inferences of environmental coccolithovirus biodiversity / Josef I. Nissimov ... [et al.]. Virologica sinica (2013), doi: 10.1007/s12250-013-3362-1 have been removed from PDF for the copyright reasons.

Deep-sea systems are understudied compared to any other ecological system on Earth, but they are important for ecosystem functioning and services. The deep sea is important in the climatic regulation of Earth, and it is a new frontier for resource provisioning for humanity. Impacts, such as increased carbon emissions and deep-sea fishing and mining will likely influence the system, but these effects are not well understood. To recognise these impacts, common patterns in community structure need to be understood. This study aims to assess community structure in the deep sea by looking at patterns in body size and biodiversity. It uses polychaetes (bristle worms) as a study group as they are the most abundant group in the benthic macrofauna in terms of density and play key roles in the food web. Body size is an important component of the community structure, as body size is correlated with many other traits of the organism, from physiological rates (e.g. heart or breathing rates) to population dynamics (e.g. production rates or population abundances) and species richness. It is thought that body size of deep-sea (endo)benthic organisms declines with increasing depth, which is often related to food availability which itself declines with increasing depth. Many contradictory results on body-size change with increasing depth, however, have been reported, including no change, increasing, or a parabolic relationship. It is demonstrated here (Chapter 2) that there is much variety in body-size estimates between different geographic regions and taxonomic groups. These differences can ultimately influence the predictions of other traits, and might hint at what might happen in changing climatic conditions. It sets the basis to argue that there should be a focus on explaining why there are differences, instead of focusing on finding a general trend for organisms in all geographical regions. Furthermore, it is unlikely that food availability alone can explain a change in body size. An alternative explanation is offered (Chapter 3), where habitat complexity is shown to influence body size. Sponge density, in the form of habitat complexity, can have a structuring effect on the community potentially through the loss of spicules that add complexity to soft-sediments, and this in turn can influence body size of organisms. Deep-sea community structure in terms of family richness has been studied at local spatial scale. Fewer studies have been performed on regional spatial scale and these studies lack extensive sampling coverage of environmental gradients. Here (Chapter 4), the first study is presented on the maintenance of deep-sea family composition on regional scale with high sampling coverage along a variety of environmental gradients. It is shown that energy (food) availability, habitat complexity, and long-term temperature are important in influencing the polychaete distribution in this region. It is shown that there is an unusual high proportion of an opportunistic group, the Capitellidae, present in the study area. Biodiversity is important for the maintenance of ecosystem functioning, but human impacts result in the restructuring of biodiversity. The first deep-sea biodiversity - ecosystem functioning relationship for macrofauna is presented (Chapter 5). It is shown that there is a positive and saturating relationship between biodiversity and ecosystem functioning. However, fishing intensity seems to influence this relationship by potentially affecting secondary biomass production, abundance and taxonomic and functional diversity measures. It is suggested that as the disturbance of fishing negatively impacts taxonomic and functional evenness, a system is created where opportunistic species are dominant, like communities found in disturbed areas such as under fish farms. This will have consequences for the state of the system and energy transfer to trophic levels higher up.

The distribution of benthic polychaetes in the Mississippi Canyon was examined to evaluate impacts of environmental variables on species assemblages. Environmental variables considered included depth, bathymetric slope, hydrographic features, sediment grain size, food availability and sediment contamination. Samples were collected using GOMEX boxcorer. Density decreased with increasing depth exponentially. Diversity exhibited a unimodal pattern with depth with a maximum value in the intermediate depth range (about 1269 m). Deposit feeders were the most abundant feeding guild. Both the feeding guilds and faunal composition could be divided into three groups along the depth gradient: shallow (300 – 800 m), intermediate (800 – 1500 m) and deep (> 1500 m). Results of statistical analyses revealed that depth was the most important determinant in organizing polychaete assemblages in the study area. The Mississippi Canyon and the Central Transect (a non-canyon area) were found not contaminated by trace metals or Polynuclear Aromatic Hydrocarbons (PAHs) in sediments, although the highest PAHs concentration occurred at the head of the Canyon, MT1. The mean density was higher in the Mississippi Canyon (1668 N/m2) than in the Central Transect (979 N/m2), while the mean diversity in the Canyon (ES(100) = 26.9 ) was lower than the Central Transect (ES(100) = 33.1). Large amounts of terrigenous input from the Mississippi River to the Canyon could enhance polychaete density and accelerate competitive exclusion, and thus lead to lower diversity. The faunal composition was significantly different between the two transects, with higher species richness in the Mississippi Canyon (301 species). This could be attributed to structure complexity in the Mississippi Canyon. The distribution of feeding guilds was similar between two transects. The differences observed in polychaete assemblages between two transects may be largely due to high terrigenous sediment and organic matter input to the Mississippi Canyon by the Mississippi River.

An estimated 500 million cases of malaria occur each year. The increasing prevalence of drug resistant strains of Plasmodium in most malaria endemic areas has significantly reduced the efficacy of current antimalarial drugs for prophylaxis and treatment of this disease. Therefore, discovery of new, inexpensive, and effective drugs are urgently needed to combat this disease. Marine biodiversity is an enormous source of novel chemical entities and has been barely investigated for antimalarial drug discovery. In an effort to discover novel therapeutics for malaria, we studied the antimalarial activities of a unique marine-derived peak fraction library provided by Harbor Branch Oceanographic Institute (HBOI). Within this unique library, we have screened 2,830 marine natural product (MNP) peak fractions through a medium throughput screening effort utilizing the SYBR Green-I fluorescence based assay, and have identified 253 fractions that exhibit antimalarial activity. From those inhibiting fractions we have identified twenty species of marine organisms that inhibit Plasmodium falciparum growth, from which thirty-five fractions were selected for further study. Among those thirty-five, eighty-three percent were also found to inhibit the chloroquine resistant strain of P. falciparum, Dd2. The most potent inhibitors were then screened for their cytotoxic properties using the MTT cell viability assay. Among the samples that exhibited potent inhibition of P. falciparum growth were fractions derived from a sponge of the genus Spongosorites sp.. This genus of sponge has been reported to contain the nortopsentin and topsentin class of bis-indole imidazole alkaloids. Nortopsentin A inhibited the parasite growth at the trophozoite stage with an IC[sub]50 value of 1.6micrometer]. This is the first report of antimalarial activity for this class of compound.
ID: 030423269; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (M.S.)--University of Central Florida, 2010.; Includes bibliographical references (p. 56-61).
M.S.
Masters
Burnett School of Biomedical Sciences
Medicine

Sea-bed benthic-invertebrate assemblages of species within and proximal to an existing mussel farm off Taniwhanui Point, eastern Waiheke Island, are reported. Substratum type, whether predominantly mud, gravels or an admixture of the two, mud/gravels, is shown to influence infaunal species assemblage composition; the bivalve Theora lubrica, ostracods, amphipods and polychaetes characterise muddy substrata; polychaetes, particularly spionids and syllids, ostracods, amphipods, bivalves and ophiuroids characterise mud/gravel substrata; and diverse assemblages of polychaetes, bivalves, pagurid crabs, gastropods, ostracods, ophiuroids and nemertean worms characterise gravel substrata. Significant differences in sea-bed assemblages are reported along one transect inside and outside the farm over the three seasons during which surveys were conducted, summer, autumn, winter of 2008. Along the northern side of the mussel farm those sediments beneath the farm are characterised by greater abundances of polychaetes and crustaceans (Malacostraca), whereas sediments outside the farm are characterised by greater abundances of bivalves and ostracods. Sediments both inside and outside the north-eastern border of the farm during summer are characterised by similar abundances of polychaetes, bivalves and ostracods. Similarly, those sediments within and outside the farm along its southern border during summer are characterised by abundances of polychaetes, bivalves, crustaceans (Malacostraca) and gastropods. Measures of relative abundance, rarity and species richness are applied to sea-bed assemblages off eastern Waiheke Island to enable an appraisal of the spatial distribution of each within and outside the farm, and throughout the eastern Waiheke Island region. One of these measures, relative abundance, is then compared with other, albeit limited abundance data from previous soft-sediment surveys conducted throughout Hauraki Gulf. The most species rich and abundant sites off eastern Waiheke Island occur in gravelly substrata between Waiheke Island and Pakatoa Island, and between Rotoroa and Ponui Islands, in addition to beneath the southern portion of the existing mussel farm. Gravel-based substrata are recognised to be the most species rich and densely populated with invertebrates for this sediment type in Hauraki Gulf. Similarly, the muddy substrata off eastern Waiheke Island region appear to host more individuals and species than any other reported muddy substratum in Hauraki Gulf. The existing mussel farm is shown to significantly affect sea-bed communities, but in a manner that has not been previously reported in New Zealand. Species richness and abundance are greater beneath the farm, as are the proportions of very rare and uncommon taxa to more common and ubiquitous taxa. Sediments beneath the farm are not characterised by elevated abundances and richness of opportunistic species; and no obvious difference in sediment grain size is apparent along a transect extending from 20 m inside the farm to at least 110 m outside it. The biological footprint of the farm is limited, appearing to extend no further than 20 metres from the northern physical boundary of the farm; the gross sedimentary characteristics (grain size) do not differ significantly within and outside the farm. Within and immediately outside the farm species richness and abundance tend to increase during colder seasons; beneath the farm, species richness (d), abundance (N), Shannon index (H’) and Simpson index (1-λ’) were higher during May (autumn) and August (winter) than during February (summer); diversity values outside the farm were similar during summer and autumn, but species richness (d), evenness (J’), Shannon index (H’) and Simpson index (1-λ’) were all greater during winter. No opportunistic taxa are considered to be appropriate indicators of organically enriched environments, at least enrichment that can be intuitively linked to any direct effect of the existing mussel farm. One species, the heart urchin Echinocardium cordatum, only rarely occurs inside the physical farm boundary, so its relative abundance renders it an appropriate indicator species of mussel-farm impacts.

Anthropogenic stressors are increasingly changing conditions in coastal areas and impacting important habitats. But, when multiple stressors act simultaneously, their effects on ecosystems become more difficult to predict. In Chesapeake Bay, USA, predictions suggest that anthropogenic stressors from climate change, such as warming temperatures, may increase the frequency and severity of storm events, leading to increased freshwater, nutrient, and sediment inputs. Coastal development, another source of anthropogenic stressors, continues to increase with growing coastal populations, and may lead to altered sediment characteristics, habitat fragmentation, altered food webs, and loss of vegetated habitats. Community processes may interact with stressors, for example, immigration of propagules between habitat patches may alter diversity, and modify community response to stressors. Changes in biodiversity might alter ecosystem functioning and services, but diverse ecosystems may be more stable especially in the face of multiple stressors. Many habitats are vulnerable to anthropogenic stressors, including seagrass systems, which provide many valuable ecosystem services. Understanding how multiple stressors and community processes interact now is key to maintaining ecosystem services in the future. Using a model seagrass (Zostera marina) system, I tested the effects of multiple stressors and their interactions with crustacean grazer immigration and diversity on ecosystem properties in a series of fully-factorial mesocosm experiments. I found that despite grazer species having varied responses to individual stressors, grazing pressure was largely maintained in spite of multiple stressors. More diverse grazer assemblages generally stabilized epiphytic algal biomass in the face of stressors, thereby increasing the resistance stability of this important component of the fouling community. Immigration of crustacean grazers did not interact significantly with stressors, and had little effect overall except to increase grazer biomass. Stressors generally reduced primary producer biomass, although in some cases they favored epiphytic algae. Generally, I did not find interactions among stressors and grazer immigration or diversity, even though diverse grazer assemblages stabilized epiphytic algal biomass. to assess potential impacts of coastal development, I surveyed twenty seagrass beds in lower Chesapeake Bay, VA and assessed local shoreline development effects on adjacent seagrass beds. I sampled primary producers, consumers, water quality, and sediment characteristics in seagrass beds, and characterized development along the adjacent shoreline. I found that development significantly affected sediment characteristics, while epifaunal and epiphytic algal biomass was significantly higher on the Western versus the Eastern side of the bay. Grazer and predator biomass did not differ with either development or bay region. Thus, in seagrass communities, various factors appear to drive sediment and biological community properties on different spatial scales. This may be an important consideration for management, because efforts that incorporate spatial scales of ecosystem processes will likely have more impact. Overall, these results suggest that stressor impacts in seagrass ecosystems generally do not interact but are sometimes context specific, while grazer diversity may have a limited but potentially important role in buffering certain ecosystem properties again stressors. Different factors appear to influence ecosystem properties at various spatial scales, an important consideration for predicting future impacts of multiple anthropogenic stressors in submerged vegetated systems.

The Cretaceous–Paleogene (K–Pg) mass extinction event occurred 66 million years ago, the most recent of the ‘Big Five’ extinction crises of the last 540 million years. This event had a profound effect on both life and the broader Earth system, with the extinction of up to 75% of life. Despite years of detailed research, debate continues as to the nature and timing of the extinction. Ideas for an abrupt crisis, triggered by bolide impact at Chicxulub in the Gulf of Mexico, contrast with those suggesting a more gradual extinction, involving volcanism from the Deccan Traps Large Igneous Province in India and/or climatic changes. Evidence from the high latitudes has been used to suggest that the fossil record from Antarctica is incompatible with models for a single, sudden event, and that extinction intensity declined at high latitudes. This thesis presents a detailed study of extensive fossil and sediment collections from the highest southern latitude onshore outcrop containing the K–Pg transition; the highly expanded and fossiliferous López de Bertodano Formation of Seymour Island, James Ross Basin, located at 65°S today, and during the Cretaceous. New biostratigraphic and diversity data for the molluscan (bivalves, gastropods, cephalopods) faunas of the López de Bertodano Formation, and geochemical datasets (seawater sulphur and pyrite sulphur isotopes) are compared to published records, and evidence for palaeoenvironmental change. They suggest a single, rapid extinction event coincident with the K–Pg boundary, with no precursor decline. The magnitude of the extinction in Antarctica is also consistent with lower latitudes, suggestive of a global, catastrophic trigger for the K–Pg extinction, such as bolide impact. Sulphur isotope data suggest the K–Pg sulphur cycle was able to respond to rapid environmental changes before, and after the K–Pg mass extinction. A decoupling of the carbon and sulphur cycle occurred during the latest Cretaceous, but productivity collapse after the K–Pg extinction also affected the sulphur cycle. The recovery to pre-extinction values was achieved on the same timescale as carbon cycle and initial ecological recovery, suggesting close geosphere-biosphere links at this time.

Establishment of marine protected areas (MPAs) has intensified in recent years, and there are now over 6800 MPAs worldwide. However, there is a prominent need to assess their effectiveness in terms of protecting biodiversity. In Chapter 1, I provide the theoretical background to this dissertation and define its central goal, i.e., to assess the effectiveness of no-take (‘restricted') sections of the Table Mountain National Park MPA (TMNP MPA), relative to zones that are designated as ‘controlled', where harvesting can take place under national regulations. Chapter 2 compares the effectiveness of no-take versus harvested areas in the TMNP MPA in protecting the biodiversity of intertidal rocky shores. Surveys were conducted to compare (1) the densities and sizes of exploited species and rarely harvested species, and (2) community composition, between these two levels of protection. Some clear patterns emerged. Firstly, notake areas had significantly greater densities of the commonly harvested limpets Cymbula granatina, C. oculus and Scutellastra argenvillei, most obviously on sandstone ledges where abundances were greatest. In contrast, densities of the rarely harvested limpets, S. cochlear, S. longicosta and S. granularis did not differ in a manner reflecting protection levels. Secondly, C. granatina and S. argenvillei were significantly larger in no-take areas, although C. oculus displayed the opposite pattern. None of the rarely harvested limpets showed differences in sizes between protection levels. Thirdly, community composition differed significantly between protection levels. No-take areas were characterised by a greater abundance of commonly harvested limpets and mussels, while harvested areas were dominated by ephemeral and corticated algae, due to their release from grazing pressure by limpets. Chapter 3 focuses on a subset of the sites, all lying on the west coast and all comprising sandstone rocks. First, in a temporal comparison, I evaluated changes in densities and sizes of limpets and in community composition between historical data from 1970 and my sampling in 2017, at two sites where harvesting has intensified since 1970. This analysis showed three kinds of changes: (1) the appearance of alien species; (2) the effects of increased harvesting; and (3) the direct and indirect effects of these changes on other species. Secondly, to disentangle the effects of harvesting from those of alien invasions, I made spatial comparisons using my 2017 data, between two harvested sites and two sites in a no-take zone. One striking result was transformation of mid-shore zones by the appearance of the invasive Mediterranean mussel Mytilus galloprovincialis, and the indirect effects of this on the demography of the granular limpet Scutellastra granularis. Adults of this limpet have been excluded by the mussel, whereas juveniles find a secondary home on the shells of the mussel. In addition, harvesting has decimated the granite limpet Cymbula granatina and Argenville's limpet Scutellastra argenvillei. This has led to the proliferation of opportunistic seaweeds, such as Ulva spp., or corticated algae, notably Pachymenia orbitosa. The dual effects of alien invasive species and over-harvesting thus have major ecosystem effects. In chapter 4, densities of the limpet Cymbula granatina were manipulated at two sites within a fully-protected no-take area to generate four density levels ranging from zero to maximum natural densities, to evaluate the effects of harvesting this limpet on the community composition. Following removal or substantial thinning of C. granatina, community composition changed, cover of corticated and ephemeral algae increased and recruitment of C. granatina decreased. These outcomes were, however, dependent on the time frame considered, as algae underwent an annual cycle, and the effects of limpet removal were evident only during cooler months when the algae proliferated. All these effects have management implications. Chapter 5 provides an overview of the findings from this dissertation and their management implications. The major limitation of the dissertation is that interpretation of results was clouded by an absence of reliable data on actual harvesting rates as reflected in the numbers and activities of people operating in the restricted and controlled portions of the MPA, and of the efficiency with which law enforcement takes place. Nevertheless, strong evidence emerged that no-take areas within the MPA are effective means of conserving biodiversity, and the effects of harvesting deduced in Chapter 2 and 3 were verified by the experiment undertaken in Chapter 4, in which depletion of a dominant and commonly harvested limpet, Cymbula granatina, did yield algal proliferations like those evident in harvested portions of the park. The fact that this outcome was observed only at certain times of the year points to the need for studies and monitoring to be undertaken over sufficient time scales to produce meaningful results.

The conservation of marine ecosystems is at least 20 years behind terrestrial and freshwater ecosystems due to the difficulties in studying and monitoring these dynamic and complex environments. Furthermore, marine environment receive less attention because human impacts are less visible in the sea, and oceans are viewed as global commons. The purpose of the present dissertation is to contribute to the knowledge of marine conservation through the development of three components in natural resources management: inventory, monitoring, and assessment of impacts. I elaborate a multi-taxa inventory, identify key species to monitor, characterize one of the key species, and assess the impacts of the most important fishery in the community-based controlled marine area of the Seri Indians along the Sonoran desert coast of Mexico. A total 657 species of mollusks, echinoderms, sharks, rays, bony fish, sea turtles, sea snake, aquatic birds and marine mammals were recorded in the Seri territory through review of 30 scientific collections housed in museums and universities, literature, and field collections. The fish information was improved through the analysis of 151 traditional Seri names. Fifty species were identified for monitoring ecosystem health. They represent species with a legal status, rare, commercially important, taxa that dominate or characterize entire communities, common taxa, and species recognized in the Seri culture. The annual eelgrass (Zostera marina atam) was selected as a key species inside the Canal de Infiernillo in the Seri territory. Coverage of the eelgrass beds was estimated using aerial photographs, field mapping, and Seri traditional ecological knowledge. The total extent of the eelgrass beds was approximately 6687 ha, which regrew in the same areas during the three-year study, maintaining the same general shapes and sizes. Twenty-six percent of the eelgrass beds overlap with the swimming crab (Callinectes bellicosus) fishing zones. Major impact on this fishery are caused by "ghost" fishing traps, which continue to capture crabs and animals and modify the substrate as they are moved around by currents and accumulate on the sea bottom. Efforts to standardize the use of traps will reduce these impacts on this fishery in the long term.

I cambiamenti climtici minacciano la biodiversità, il funzionamento degli ecosistemi e la vita umana su scala globale. Gli oceani mitigano l'impatto dei cambiamenti globali dovuti alle attività umane, ma diversi fattori di stress, come variazioni di temperatura, acidificazione, scioglimento dei ghiacci e deossigenazione, minacciano i sistemi marini. Studi recenti hanno svelato impatti negativi dovuti a singoli fattori di stress, ma gli effetti sinergici di più fattori di stress concomitanti sono largamente sconosciuti, soprattutto per i sistemi bentonici marini. Inoltre, le attuali evidenze si basano principalmente su risposte di singole specie in esperimenti a breve termine. I sistemi naturali con condizioni ambientali simili a quelle previste dai modelli di cambiamento globale possono servire a studiare i possibili effetti dei cambiamenti climatici. Nella presente tesi, sono stati condotti esperimenti di laboratorio ed in situ in sistemi naturali modello, per valutare i possibili effetti dell' acidificazione, deossigenazione, e fattori contemporanei di stress su biodiversità e funzionamento degli ecosistemi marini. Questi studi sono stati condotti su singole specie (Corallium rubrum), e su comunità (di coralligeno, meiofauna e microbiche). I risultati ottenuti evidenziano 4 messaggi chiave. Primo, livelli più elevati di biodiversità possono mitigare l'impatto dell' acidificazione oceanica sugli ecosistemi bentonici marini. Secondo, gli impatti sono evidenti sia su organismi calcificanti (coralli e alghe coralline) che non (nematodi), con significativi cambiamenti di struttura di comunità. Terzo, la deossigenazione degli oceani può alterare il funzionamento degli ecosistemi pelagici e bentonici, promuovendo processi chemioautotrofi e favorendo il controllo virale sulle comunità microbiche. Infine, i sistemi naturali mostrano che l'impatto di più fattori di stress concomitanti ma intermittenti può essere inferiore a quello di un solo, ma costante, fattore di stress.
Global climate change is threatening biodiversity, ecosystems functioning and human life. The oceans can help in moderating anthropogenic global change, but several stressors, such as temperature shifts, acidification, freshening, and hypoxia/anoxia are disrupting the good environmental status of marine systems. Scientific advances have unveiled the effects of single stressors, but the possible synergistical impacts of multiple-stressors remain largely overlooked, especially on benthic marine ecosystems. Moreover, current evidences are mostly based on the response of single species to short-term pertubation experiments. To help overcoming these limits, natural systems mimicking future climate change scenarios can be studied to understand the complex network of global change impacts. In the present work, we analyzed through laboratory experiments and in situ studies in natural model systems, the impacts of ocean acidification, deoxygenation, and multiple-stressors on the biodiversity and functioning of the marine ecosystems. Our studies were conducted from single species, such as Corallium rubrum, to complex communities such as the coralligenous, meiofauna and microbial assemblages. Our results highlight four key messages. First, higher biodiversity levels can partially mitigate ocean acidification's impact on benthic ecosystems. Second, impacts are evident either for calcifying (corals, coralline algae) and non-calcifying taxa (nematodes), with major shifts in the benthic assemblage composition. Third, seawater deoxigenation can alter the pelagic and benthic ecosystems functioning and biogeochemical cycles, by promoting chemoautotrophic processes and favouring the viral control of microbial assemblages. Fourth, the study of natural systems shows that the impact of temporary multiple stressors can be lower than that caused by one only but constant stressing factor.

Doutoramento em Biologia
In the complex and rich Northeast (NE) Atlantic and Macaronesia coasts, the superoder Peracarida (Crustacea) is one of the most abundant and commom marine invertebrate taxa with an important role in benthic communities. The study of this group is often limited to inventory lists or benthic community studies and the genetic knowledge of the group in this region is poor. The main goal of this thesis was to improve knowledge on Peracarida diversity and evolution in the NE Atlantic and Macaronesia, with particular emphasis on shallow water and rocky shore members of the orders Amphipoda, Isopoda and Tanaidacea. The thesis comprises five chapters with original research, entailing a DNA barcodebased screening of the species diversity in this group through the comparison of morphology and molecular-derived data (chapter 2), a set of two studies of the isopod genus Dynamene (chapters 3 and 4), one chapter about the amphipod family Hyalidae (chapter 5), and a multi-species analyses of the diversity and broad phylogeographic patterns of Macaronesian peracarideans (chapter 6). In the first chapter, we reported a DNA barcode reference library for the superorder Peracarida, comprising specimens from marine Atlantic coasts, mainly from Iberian Peninsula, together with additional members of the same or sister taxa from other locations. A higher number of Barcode Index Numbers (BINs) compared with the number of morphospecies was found, with some of them displaying up to six BINs. The presence of deeply divergent intraspecific lineages suggests the existence of considerable overlooked taxonomic diversity, even in one of the most well-known peracaridean faunas in the world. These findings indicate the need for a broad, comprehensive and integrated revision of the peracaridean fauna from the Southern European Atlantic coasts. In the second chapter, the commom but species-poor and controversial isopod Dynamene genus was investigated in detail by examining thousands of specimens records sampled during more than fifty years. The distribution and taxonomy of the six Dynamene species along the Northeast Atlantic-Black Sea axis was revised and updated. New distribution maps and illustrated keys to the adult males and females of the northern hemisphere species are provided. In the last three chapters, molecular delineation tools revealed extensive cryptic diversity in the genus Dynamene (3 morphospecies vs 12 molecular operational taxonomic units - MOTUs), in the amphipod family Hyalidae (7 morphospecies vs 32 MOTUs) and in twenty-five peracaridean species (25 morphospecies vs 90 MOTUs). A split between Macaronesian and continental populations was patent, and in most cases the Macaronesian populations displayed high levels of diversity. These findings suggest a much larger role of oceanic islands in the diversification of these marine invertebrates than would have been anticipated, and contributes to expose weakly explored events in the phylogeography and evolution of Macaronesia’s marine fauna. This thesis showed that marine biodiversity, as seen in peracarideans from the NE Atlantic and Macaronesia, has been considerably underestimated. The level of diversity will likely increase with the addition of different taxa, different types of habitat and distinct marine regions. It also suggests that these oceanic islands may act as drivers of evolution, diversification and endemism, just as well for marine organisms as they do for terrestrial ones.
Nas costas complexas e ricas do Nordeste (NE) Atlântico e da Macaronésia, a superordem Peracarida (Crustacea) é um dos taxa de invertebrados marinhos mais abundante e comum, com um papel importante nas comunidades bentónicas. O estudo deste grupo é muitas vezes limitado a listas de inventários ou estudos de comunidade bentónicas e o seu conhecimento genético nesta região é deficiente. O objetivo principal desta tese foi o de melhorar o conhecimento sobre a diversidade e a evolução dos peracarídeos no Atlântico Nordeste e na Macaronésia, com ênfase nos membros presentes nas zonas pouco profundas e nas zonas costeiras rochosas das ordens Amphipoda, Isopoda e Tanaidacea. Esta tese compreende cinco capítulos com pesquisa original, incluindo uma biblioteca de referência de DNA barcodes neste grupo, através da comparação de dados morfológicos e moleculares (capítulo 2), um conjunto de dois estudos dedicados ao género isopode Dynamene (capítulos 3 e 4), um capítulo dedicado à família de anfípodes Hyalidae (capítulo 5), e uma abordagem multi-espécies da diversidade e dos padrões filogeográficos dos peracarídios presentes na Macaronésia (capítulo 6). No primeiro capítulo, relatamos uma biblioteca de referência de DNA barcodes para a superordem Peracarida, que inclui espécimes de costas do Atlântico, principalmente da Península Ibérica, juntamente com membros adicionais do mesmo ou semalhantes taxa de outros locais. Um maior número de Barcode Index Numbers (BINs) em comparação com o número de morfo-espécies foi encontrado, com algumas morfo-espécies exibindo até seis BINs. A presença de linhagens profundamente divergentes sugere a existência de uma considerável diversidade taxonómica anteriormente negligenciada, mesmo numa das mais conhecidas faunas de peracarídeos do mundo. Estas descobertas indicam a necessidade de uma revisão ampla, abrangente e integrada da fauna de peracarídeos das costas do Atlântico do Sul da Europa. No segundo capítulo, o abundante mas controverso género Dynamene foi investigado em detalhe, ao examinar vários milhares de individuos amostrados durante mais de cinquenta anos. A distribuição e a taxonomia das seis espécies de Dynamene ao longo do eixo Nordeste Atlântico-Mar Negro foram revistas e actualizadas. Novos mapas de distribuição e chaves ilustradas para os machos adultos e fêmeas das espécies deste género, presentes no hemisfério norte, são fornecidas. Nos três últimos capítulos, as ferramentas de delineamento molecular revelaram uma extensa diversidade críptica no género Dynamene (3 morfoespécies vs 12 unidades taxonómicas operacionais moleculares - MOTUs), na família de anfípipodes Hyalidae (7 morfoespécies vs 32 MOTUs) e em vinte e cinco espécies de peracarídeos (25 morfoespécies vs 90 MOTUs). Uma separação entre as populações presentes na Macaronésia e as presentes no continente foi visivel e, na maioria dos casos, as populações presentes na Macaronésia apresentavam maiores níveis de diversidade. Estas descobertas sugerem um papel maior das ilhas oceânicas na diversificação destes invertebrados marinhos do que se anteciparia e contribuiram para expor eventos pouco explorados na filogeografia e evolução da fauna marinha na Macaronésia. Esta tese mostrou que a biodiversidade marinha, como se observa em peracarídeos presentes no NE Atlântico e na Macaronésia, foi consideravelmente subestimada. O nível de diversidade provavelmente aumentará com a adição de diferentes taxa, diferentes tipos de habitat e de regiões marinhas distintas. Esta tese também sugere que estas ilhas oceânicas podem atuar como impulsionadoras da evolução, da diversificação e do endemismo em organismos marinhos, como acontece nos organismos terrestres.