Dissertations / Theses on the topic 'Marine ecology'

Marine mammals comprise a paraphyletic group of species whose current abundance and distribution has been greatly shaped by past environmental changes and anthropogenic impacts. This thesis describes molecular ecological approaches to answer questions regarding habitat requirements, genetic differentiation, and life-history trade-offs in three species of marine mammals.  The annual sea-ice dynamics of the Arctic may have large effects on the abundance and distribution of Arctic species such as the pagophilic ringed seal (Pusa hispida). Paper I describes and applies a simple molecular method for isolating and characterizing a relatively large set of single nucleotide polymorphisms (SNPs) in the ringed seal. These SNPs have been genotyped in a yet-to-be-analysed dataset which will form the basis in an assessment of the micro-evolutionary effects of annual sea-ice dynamics on ringed seal.  Current management efforts directed towards the North Atlantic fin whale (Balaenoptera physalus) are hampered by an unclear understanding of population structure. Paper II investigates the DNA basis for the high levels of genetic differentiation that have been reported in allozyme studies of the North Atlantic fin whale. We find that additional processes (at the organismal level) may have contributed to shaping the phenotype of the underlying allozyme variation. Telomeres may potentially serve as markers for determining the chronological and biological age of animals where other means of inference is difficult. Paper III describes the application and evaluation of four qPCR assays for telomere length estimation in humpback whales (Megaptera novaeangliae), finding that reliable telomere length estimates require extensive quality control. Paper IV applies the best performing qPCR assay to test whether telomeres may provide a method for genetic determination of chronological age in whales and concludes that the biological and experimental variation in telomere length estimates is too large to determine age with sufficient resolution. Finally, because telomere length and rate of telomere loss also may be affected by other cellular and organismal processes, such as resource allocation among self-maintenance mechanisms, growth and reproduction, Paper V describes the correlations between individual telomere length and rate of telomere loss, and sex, maturity status and female reproductive output. We found that the costs of reproduction in terms of telomere loss are higher in mature humpback whales than in juveniles; that reproductive costs are higher in males than females; and that differences among females tend to correlate with reproductive output.
At the time of doctoral defence the following papers were unpublished and had a status as follows: Paper 2: Submitted; Paper 3:Submitted; Paper 4: Manuscript; Paper 5:Manuscript

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Marine microbes play a fundamental role in driving ocean ecosystem dynamics and biogeochemistry. While their importance is global in scale, microbial processes unfold at the level of single cells and are intimately dependent on interactions between microorganisms, their neighbors, and the surrounding physical and chemical environment. Furthermore, traditional imaging techniques often provide frozen snapshots of the marine microbial world, yet microbial interactions are inherently dynamic, as for example in the case of motility, chemotaxis, and the encounter of microbes with viruses and animal hosts. These biological processes are frequently driven by physical mechanisms, and our understanding of them can benefit from a focus on the physical ecology of marine microbes. This is the approach pursued in this thesis, by directly applying dynamic imaging and microfluidics, which offer powerful new opportunities to study microbial processes in a time resolved manner and with exquisite environmental control. Through single-cell, live imaging of three fundamental marine microbial processes - motility, chemotaxis and viral adsorption - we demonstrate how capturing previously unseen biophysical processes in microbial ecology at their natural timescales can both shed light on unexplained mechanisms and provide robust quantifications of interaction rates. We first study a newly discovered nanoscale motility adaptation in the marine bacterium Vibrio alginolyticus using high-speed imaging. We found that marine bacteria can exploit a buckling instability of their flagellum to change direction during swimming, achieving the same functionality as multi-flagellated cells, but with the cost of synthesizing and operating only one flagellum. This finding not only reveals a new role of flexibility in prokaryotic flagella, but also highlights the exquisite motility adaptations of marine microbes to the resource-poor environment of the ocean. We then determine how this motility adaptation affects the cells' ability to climb chemical gradients ('chemotaxis'). We found that, counter- to current models, chemotaxis in V. alginolyticus is speed-dependent. Faster cells exhibited not only faster chemotactic migration, but also tighter accumulation around the resource peak. This result adds a new dimension to our understanding of bacterial chemotaxis pathways, by demonstrating that swimming speed can be an important and counter-intuitive control parameter in how marine microbes encounter and exploit chemical resources. Finally, we consider an encounter process that is motility-independent - that between a nonmotile host and a virus. Using the globally abundant marine cyanobacterium Prochlorococcus and a cyanobacterial virus ('cyanophage') as a model system, we directly imaged the encounter and adsorption dynamics of the virus and the host at the level of single cells, using dual-wavelength epifluorescent microscopy. By applying this non-invasive approach to quantify thousands of encounter events using automated image acquisition and analysis, we directly measured the rate at which viruses encounter and adsorb to hosts. We found that the probability of adsorption is considerably lower than was obtained with traditional, bulk measurement approaches, suggesting the need for a revision of viral infection dynamics in marine ecosystem models and opening the door for studies of microbial individuality in the context of viral infection. In summary, this thesis demonstrates that physical processes in microbial ecology, studied by means of new approaches including microfluidics and dynamic imaging at the single-cell scale, can contribute fundamental new insights into the ecology of marine microbes.
by Kwangmin Son.
Ph. D.

Seabirds have evolved within an open and dynamic environment, the ocean. As meso-top predators, seabirds are greatly influenced by the oceanographic conditions driving marine productivity, and therefore, distribution of their prey. Consequently, seabirds’ behaviour and, ultimately, life-history traits are greatly influenced, by the ever-changing oceanographic conditions. However, oceanographic conditions are currently changing at ever-increasing rates due to global warming and human harvest impacting marine ecosystems. Thus, seabirds have become particularly vulnerable to these changes. Accordingly, in this thesis, we investigated the ecological responses of seabirds, in terms of foraging and breeding performance, to the spatio-temporal variability of environmental conditions imposed by oceans and exacerbated by climate and human stressors. In particular, we (i) identified the climate and human stressors impacting the world’s ocean, (ii) investigated the actual scale at which seabirds interact with their environment, (iii) assessed how seabirds respond to oceanographic variability by changing their foraging and reproductive strategies and (iv) proposed an integrative tool for the design of marine reserves protecting seabirds and their environment. The objectives of this thesis were accomplished through advanced procedures in the fields of satellite remote sensing and animal tracking. Our results confirmed the unprecedented changes experienced by oceans in the last decades. However, we were able to provide deepest insights on the uneven distribution of climate and human driven environmental changes. When investigating the link between such environmental variability and seabirds’ behaviour, we found that dynamic processes as ocean currents were key factors determining the scale at which seabirds interact with their environment. Environmental features driving the spatiotemporal distribution of prey (e.g. sea surface temperature, chlorophyll-a, sea fronts and persistent areas of productivity) along with industrial fisheries played a fundamental role in determining the foraging distribution of seabirds. However, seabirds’ foraging strategies were largely constrained by limitations imposed by their central-place foraging behaviour and by dynamic factors such as prevalent winds, which influenced individual decision- making in heading directions when foraging. Intra and interspecific competition for resources also modulated foraging distributions, avoiding conspecifics or segregating foraging areas among sympatric species in appropriate stages. In general, we have provided a complete picture of environmental processes affecting seabirds. We argue that this information would be extremely useful for designing suitable management and conservation strategies. Thus, we finally proposed an adaptive framework for delimitation of more meaningful marine reserves that maximises conservation targets for seabirds, while accounting for human activities, environmental and biological factors largely driven seabird performance and, remarkably, the dynamism inherent to marine systems.

Gaining an understanding of the spatial ecology of marine turtles is essential for elucidating aspects of their life history ecology and for effective conservation management. This thesis presents a collection of chapters seeking to investigate the spatial ecology of this taxon. An array of technologies and methodologies are employed to ask both ecological and spatial management questions. Work focuses on foraging and thermal ecology, spatial appropriateness of Marine Protected Areas, movement models to describe habitat utilisation, analysis of data from sightings and strandings schemes and the use of a large synoptic fisheries dataset to describe fisheries patterns and putative risks to marine megavertebrates.

In this study phytoplankton viruses were investigated from a point of view of their genotypic richness, ecology and role in controlling two microalgae species: Emiliania huxleyi and Phaeocystis pouchetii. Host specificity determined for Emiliania huxleyi-virus (EhV) isolates revealed a highly variable host range suggesting a relation between virus specificity and genetic or phenotypic variations within E. huxleyi strains and EhVs. Subsequently the dynamics and genetic richness of Emiliania huxleyi and EhVs were monitored in mesocosm experiments and during the progression of a natural bloom in the sea. The results confirmed the role of virus infection in regulating the intraspecific succession of E. huxleyi in the ocean. Furthermore, they revealed significant differences in genotypic composition and dynamics among blooms. The mesocosm setup appeared to be a very robust experimental system, which allowed reproducibility. The most important factor determining the development of the blooms in the enclosures was the experimental manipulation (i.e. nutrient addition), whereas the effect of filling of the enclosures, delay in nutrient addition and position in the raft were of minor importance. Further laboratory experiments revealed differences in the genomic content of different EhVs. EhV isolates from the English Channel carry a putative phosphate permease gene (ehv117) while the only available EhV from a Norwegian fjord has replaced ehv117 with a putative endonuclease, suggesting different propagation strategies among closely related EhVs. Culture studies using one of the English Channel isolates and E. huxleyi CCMP 1516 showed that the lack of phosphate (P) reduced the growth rate of the host and inhibited the production of viral particles. Furthermore, P availability was shown to have an effect on the level of ehv117 expression. In addition, other mesocosm studies revealed that specific viruses (PpVs) play a significant role in the termination of induced Phaeocystis pouchetii blooms. However, the role of PpVs may be significant only for the flagellated stage of P. pouchetii. Phenotypic characteristics of PpVs isolated during these studies indicate that they are probably members of the Phycodnaviridae family.

Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina), have overlapping ranges but contrasting population dynamics around the UK; whilst grey seals have generally increased, harbour seals have shown significant regional declines. A robust analytical methodology was developed to produce maps of grey and harbour seal usage estimates with corresponding uncertainty, and scales of spatial partitioning between the species were found. Throughout their range, both grey and harbour seals spend the majority of their time within 50 km of the coast. The scalability of the analytical approach was enhanced and environmental information to enable spatial predictions was included. The resultant maps have been applied to inform consent and licensing of marine renewable developments of wind farms and tidal turbines. For harbour seals around Orkney, northern Scotland, distance from haul out, proportion of sand in seabed sediment, and annual mean power were important predictors of space-use. Utilising seal usage maps, a framework was produced to allow shipping noise, an important marine anthropogenic stressor, to be explicitly incorporated into spatial planning. Potentially sensitive areas were identified through quantifying risk of exposure of shipping traffic to marine species. Individual noise exposure was predicted with associated uncertainty in an area with varying rates of co-occurrence. Across the UK, spatial overlap was highest within 50 km of the coast, close to seal haul outs. Areas identified with high risk of exposure included 11 Special Areas of Conservation (from a possible 25). Risk to harbour seal populations was highest, affecting half of all SACs associated with the species. For 20 of 28 animals in the acoustic exposure study, 95% CI for M-weighted cumulative Sound Exposure Levels had upper bounds above levels known to induce Temporary Threshold Shift. Predictions of broadband received sound pressure levels were underestimated on average by 0.7 dB re 1μPa (± 3.3). An analytical methodology was derived to allow ecological maps to be quantitatively compared. The Structural Similarity (SSIM) index was enhanced to incorporate uncertainty from underlying spatial models, and a software algorithm was developed to correct for internal edge effects so that loss of spatial information from the map comparison was limited. The application of the approach was demonstrated using a case study of sperm whales (Physeter macrocephalus, Linneaus 1758) in the Mediterranean Sea to identify areas where local-scale differences in space-use between groups and singleton whales occurred. SSIM is applicable to a broad range of spatial ecological data, providing a novel tool for map comparison.

Isoprene is an atmospheric trace gas whose emissions to the atmosphere are roughly equal to that of methane. It is highly reactive and has the potential to affect climate through a variety of interactions in the atmosphere, including the formation of ozone. In the marine environment alone, algae produce up to 11 Tg y-1 of isoprene. To date, little is known about its degradation by microbes in the marine environment. In this project, isoprene-degrading bacteria from a range of marine sites were characterised and Illumina sequencing was used to mine the genomes of isoprene-degrading strains related to Gordonia polyisoprenivorans and Mycobacterium hodleri, isolated from the Colne Estuary, Essex. From these genomes, we retrieved novel sequences encoding isoprene monooxygenase, previously identified in a terrestrial Rhodococcus species. This information allowed the design of specific PCR primer sets for the isoA gene, encoding the alpha subunit of isoprene monooxygenase, to retrieve isoprene-specific genes from environmental samples. The primers amplify isoA from a wide range of marine genera. A database of isoA sequences from extant isoprene degraders and isoA sequences retrieved by PCR from DNA from a variety of different marine environments was created. The data obtained demonstrated that isoprene monooxygenase genes are widespread in the marine environment. Other work focused on the physiology of isoprene-degrading bacteria, particularly the marine isolate Gordonia polyisoprenivorans. SDS-PAGE, oxygen electrode assays and RT-PCR were also used to investigate the regulation of soluble diiron centre monooxygenases in this organism, and showed that two separate, inducible monooxygenase enzyme systems exist in this organism and are responsible for the oxidation of isoprene and propane. DNA-Stable Isotope Probing revealed that members of the genera Rhodococcus, Mycobacterium, Gordonia and Microbacterium are active isoprene degraders in the Colne Estuary.

Protists are a taxonomic group of organisms world wild distributed with high abundance and biodiversity; their countless forms, sizes, and trophic activities constitute a continuum of species ranging from bacterial-sized cells for the smallest known species of chlorophytes to meters in length for the largest colonies of radiolaria. The enormous size range of protists, their many nutritional modes, and their rapid metabolic rates result in their pivotal ecological roles as primary producers and consumers at and near the base of marine food webs. Protists, in particular the heterotophic ones, are, with few metazoans larval stage, the major components of microzooplankton, on which this study focuses. Microzooplankton assemblage is described as a group of planktonic organisms in the size range of 10/20-200 µm; they are consumers of bacteria, cyanobacteria, other protists, viruses, and some metazoans. The quantitative importance of microzooplankton as consumers of primary production in the ocean has been recognized in the last decades; at the same time copepod predation on heterotrophic dinoflagellates and ciliates constitutes a trophic link more important than the phytoplankton–copepod link in many situations. Phagotrophic protists are the primary trophic link between minute cyanobacterial and bacterial production and higher organisms, a concept formalized more than 35 years ago in the microbial food web by Pomeroy (1974). In this study I want to provide more information on microzooplankton assemblages, describing the community composition and the role of this important component in different environments. I point out some of the factors influencing the distribution of these organisms with the aims to increase the current knowledge on microzooplankton and to contribute to the understanding of the phenomena that regulate the efficiency of the trophic web of the marine ecosystem. In the first chapter of the thesis entitled “Microzooplankton composition in the winter sea ice of the Weddell Sea” sympagic microzooplankton were studied during late winter in the northern Weddell Sea, for diversity, abundance and carbon biomass. In order to asses the role of microzooplanktonic component as food supply for the upper levels of the trophic web in this particular environment, the ice-cores were collected on an ice floe along three dive transects, and sea water was taken from under the ice through the central dive hole from which all transects were connected. The areal and vertical microzooplankton distributions in the ice and water were compared. They showed high abundance (max 1300 cells L-1) and biomass (max 28 µg C L-1) in the ice-cores, and were lower in the water, below sea ice (maxima, 19 cells L-1; 0.15 µg C L-1, respectively). The highest amounts were found in the lower 10 cm section of ice cores. The microzooplankton community within sea ice comprised mainly aloricate ciliates, foraminifers and micrometazoans. In winter, microzooplankton represent an important fraction of the sympagic community in the Antarctic sea ice. They can potentially control microalgal production and can contribute to particulate organic carbon concentrations when released into the water column due to ice melting in spring. Continued reduction of the sea ice might undermine these roles of microzooplankton, leading to reduction or completely loss in diversity, abundance and biomass of these sympagic protists. The second Chapter of this work focuses on the microbial community along the Ligurian coast in correspondence of two marine canyons. Community structures along the water column were studied using microscopic techniques, and their relationships with the environmental factors recorded along the canyons were investigated. The study considered pico-, nano- and micro-planktonic fractions, their abundances and

Seasonal occurrence and activity of heterotrophic nanoflagellates (HNANO or heteroflagellates) and bacteria were studied in a sheltered brackish water embayment of Chesapeake Bay wetlands (Virginia, USA) over a three year period (1981 - 1984). Epifluorescence direct counts and Scanning and Transmission Electron Microscopy (SEM and TEM) techniques were used for the description of organisms, enumeration, and biomass determinations. Seasonal bacterial growth rates and growth and grazing rates of bactivorous HNANO were estimated using diffusion chambers equipped with Nuclepore polycarbonate membrane filters in natural salt marsh tidal pools. Environmental monitoring of nanoplankton populations revealed a seasonal pattern of bacterial abundances with temperature while heteroflagellate abundances and growth rates showed no seasonal pattern nor correlation with fluctuations in bacterial densities. Heteroflagellate populations were dominated by 34 to 50 (mu)m('3) sized monads, choanoflagellates, bodonids, and Paraphysomonas sp., all found in varying abundances throughout the year. Blooms were concurrent with extended low tide or specific bacterial populations (i.e., cyanobacteria) typical of spring and autumn periods. Heteroflagellate growth in diffusion chambers reflected the environmental blooms and increased diversity of low water assemblages. Growth and grazing rates of heteroflagellates at ambient densities thus could account for 20 to 80% of daily bacterial carbon production. Although heteroflagellate ingestion rates did not regulate seasonal bacteria densities or vice versa, maximum growth of bacteria and heteroflagellates in chambers was closely coupled. Heteroflagellate grazing activity may regulate the rate of bacterial production by preventing substrate limitation and maintaining the population in an active growth phase. The seasonal study demonstrated the dynamic nature of nanoplankton populations during autumn and spring transitional periods. SEM photomicroscopy revealed that the dominant component of spring blooms may be composed of several members of the loricate choanoflagellate family, Acanthoecidae. Using modified EM techniques, eleven Acanthoecidae choanoflagellates species, identified from spring in situ chamber experiments, were described. In situ growth and grazing rates for the spring chamber populations ranged from 0.023 h('-1) to 0.196 h('-1) and 40 to 210 bacteria h('-1) respectively. These high rates represent an opportunistic response to optimum conditions and an expression of maximum grazing potential. (Abstract shortened with permission of author.).

Abstract

The European eel (Anguilla anguilla) migrates to the Sargasso Sea to spawn. Even though the biology of A. anguilla leptocephali in the Sargasso Sea has been studied for several decades, information regarding their diet has remained unknown until now. Previous dietary studies concerning other species of leptocephali in the Pacific Ocean have been limited to the recognition of identifiable prey remains amongst gut contents. Hence, in this study a molecular approach relying on the detection of prey DNA amongst gut contents was used to study dietary profiles of A. anguilla leptocephali in the Sargasso Sea.

 

Leptocephali were collected during the circumglobal Galathea 3 expedition in spring 2007 to the Sargasso Sea. DNA extracted from gut contents were PCR amplified using universal primers targeting the nuclear 18S rRNA gene. In order to separate eel amplicons from prey amplicons, PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE). Furthermore, clone libraries were constructed using universal primers targeting a portion of the 18S rRNA and mitochondrial COI gene, respectively. In total, the gut contents of 78 leptocephali were screened by DGGE.

 

A diverse array of eukaryotic taxa was identified, hence demonstrating the applicability of a universal PCR- DGGE approach to study gut contents of leptocephali. The results presented here show, for the first time, that young stages of A. anguilla leptocephali feed on a large variety of zooplankton of which many were gelatinous (e.g. Hydrozoa, Thaliacea and Ctenophora). Several of the identified taxa also constitute important parts of the Sargasso Sea zooplankton community and are of size ranges (adult or larval stages) that made them reasonable as leptocephali prey.

Rates of habitat alteration and degradation are increasing worldwide due to anthropogenic influence. On coral reefs, the loss of live coral reduces structural complexity while facilitating algal increase. In many coastal lagoons seagrass and corals are cleared to make room for cultivated macroalgae. This thesis deals with reef and lagoon habitat structure and how fish assemblage patterns may be related to physical and biological features of the habitat. It further examines assemblage change following habitat disturbance. Four studies on East African coral reefs concluded that both the abundance and species richness of recruit and adult coral reef fish were largely predicted by the presence of live coral cover and structural complexity (Papers I-III, VI). Typically, recruits were more selective than adults, as manifested by limited distributions to degraded sites. Paper VI compared short- and long-term responses of fish assemblages to the 1997-1998 bleaching event. The short-term response to coral mortality included the loss of coral dwelling species in favour of species which feed on algae or associated detrital resources. Counterintuitively, fish abundance and taxonomic richness increased significantly at one of two sites shortly after the bleaching. However, the initial increase was later reversed and six years after the death of the coral, only a limited number of fish remained. The influence of fleshy algae on fish assemblages was studied in algal farms (Paper IV), and examined experimentally (Paper V). The effects of algal farming in Zanzibar were significant. Meanwhile, manually clearing algal-dominated patch reefs in Belize from macroalgae resulted in short-term increases of abundance, biomass and activity of a few species, including major herbivores. The findings of this thesis demonstrate the significance of habitat as a structuring factor for tropical fish assemblages and predicts that coral death, subsequent erosion and algal overgrowth may have substantial deleterious impacts on fish assemblage composition, abundance and taxonomic richness, with recovery being slow and related to the recovery of the reef framework.

The pike (Esox lucius) is a major predator and top-down regulator in the Baltic Sea where it exists in two sympatric forms. One spawn in streams and rivers and the other one spawn in the sea. During the last decades, the habitats for both of these forms have developed in a negative way. In some freshwater systems, up to 90 % of the water areas have disappeared, mainly through drainage and straightening of watercourses for agricultural purposes. In the sea, reproduction habitats decrease due to construction of harbours and human activities that create disturbances. The perhaps largest single factor negatively affecting recruitment of pike in the sea is the eutrophication. Bottoms are overgrown with filamentous algae and shallow bays are covered with dense Phragmites belts decreasing the habitats suitable for spawning. Further on, a predator on egg and fish larvae, the three-spined stickleback (Gasterosteus aculeatus) has increased in abundance. It is difficult to restore and enhance pike production in the sea and probably the only economically viable alternative is to make restorations in freshwater. However, there is a limited knowledge about the freshwater spawning pike in the Baltic Sea. Thus in this thesis I, together with my coauthors, set out with an aim to increase the knowledge base regarding anadromous pike behaviour. We found that pike of natal freshwater origin were common in the Baltic Sea. Through Sr:Ca studies in otoliths, about 45 % of the pike were interpreted to be of freshwater origin. The majority of the pike had emigrated out of freshwater at a length below 6 cm. These results indicate that freshwater recruitment is successful, contrasting the vast areas available for spawning in the sea. This creates incitements that restoration measures in these watercourses could have a significant effect on the pike population in the Baltic Sea. Further, in four streams running out in the Baltic Sea, more than three thousand pike were marked to study spawning migration. About 30-40 % returned to the same river the subsequent year. Most of the pike used the lower parts of the stream for spawning. The homing of pike to a watercourse indicate that freshwater pike in the Baltic Sea consist of specific populations and this is crucial information when taking decisions on fish restoration measures. Three wetlands adjacent to streams were restored for pike production. The most successful restoration involved minimal digging, with flooded grasslands providing optimal conditions for spawning. The first spawning season after restoration increased the pike production hundredfold. In conclusion, the anadromous pike are numerous in the Baltic Sea. To compensate for the decline in pike populations in the sea, “pike-factories” created along the coastline are probably the most justifiable option.

Copepods have a crucial role in the pelagic marine ecosystem, for their participation in the nutrient cycling and carbon export in biogeochemical cycles, and their role as link organisms between primary producers and higher trophic levels. Historically, marine zooplankton studies have focused on large organism (> 1mm), due to the use of relatively large mesh sizes in plankton nets, which has resulted in an underestimation of the importance of small copepods such as the genus Oithona. The study of small copepods, and especiall of Oithona, has raised special interest in recent years due to its great abundance and ubiquitous presence in both coastal and oceanic regions, and with a distribution that extends from polar to tropical . Besides their numerical dominance, Oithona also makes up a significant fraction of the biomass of copepods in certain regions. Their described low metabolic rates, coupled with an ambush feeding behavior and low mortality, are considered the clue of their success and of their capacity to maintain active populations throughout the year. Although new insights on the ecology of Oithona have been acquired in the past decade, knowledge on their vital rates is still very scarce. The lack of studies on the ecophysiology of Oithona contrasts with the large amount of studies conducted on calanoid copepods on aspects related to feeding, growth, and egg production. The main objective of this thesis was to contribute to a better knowledge and understanding of some biological and ecological aspects of the genus Oithona. For that purpose, we carried out laboratory experiments with cultured specimens, and experimental lab and fieldwork with natural populations in polar and tropical regions. In the laboratory we studied the effect of food concentration on ingestion and fecundity rates of Oithona davisae. The results obtained indicate that Oithona davisae is able to feed at very low food concentrations, which indicates its ability to exploit oligotrophic environments. Oithona capacity to reproduce continuously throughout the year, even in environments or periods of low food availability, was confirmed by the relatively high fertility rates observed in laboratory experiments at low food concentrations. The trophic role of Oithona, their natural diet and ingestion rates were studied in different pelagic ecosystems; as well as the fecudity of adult females in these ecosystems, and their relationship with environmental factors. We also investigated some aspects of the population ecology Oithona in polar regions (abundance, vertical distribution and migration patterns). The results of the in situ investigations were carried out in order to compare life strategies between Oithona species of contrasting habitats. In polar environments, winter reproductive activity of the adult females was observed, which highlights the importance of small copepods in high-latitude environments, especially when large calanoid are not present in the productive zone of the water column. Moreover, the strategy of Oithona life in polar area is different from that of large calanoid, and it benefits from its independence from the spring blooms of phytoplankton to maintain active populations throughout the year. The ability of Oithona to successfully survive when unfavourable conditions are present in the water could explain the success of this genus of copepods in marine environments around the world.

Climate change threatens to disrupt biological systems around the globe, sparking debate over natural capacity for adaptation in a fragmented landscape. Marine turtles are evolutionarily ancient and have survived millions of years of prehistoric climate change, but are threatened by the rapidity of modern warming and a history of severe overexploitation that has left most populations depleted. This thesis explores a nesting aggregation of the green turtle (Chelonia mydas) in northern Cyprus, where a longitudinal programme of both intensive and extensive monitoring enables insight into individual and population level parameters and processes. Nesting on the two coastlines covered by this project is in the early stages of recovery, possibly in response to exhaustive nest protection efforts over the last twenty years. Saturation tagging at one key site allows us to confirm that recruitment of new breeders is an important driver of this trend, and that average clutch frequency has remained stable around three nests per female per year, validating nest-count derived abundance estimates at a regional scale. Concern has been raised, however, regarding recent changes in fishing practices which are impacting the local juvenile neritic phase, which may have a lagged effect on the recovery of this nesting population. A collaborative tracking effort including all other countries with major nesting in the Mediterranean allows us to identify major foraging grounds for this species, with two hotspots accounting for >50% of tracked individuals, as well as coastal and pelagic seasonal corridors of high use. Bycatch levels and mortality rates for turtles in these key areas are largely unknown and should be prioritised for investigation. Hatchling sex ratios from the main study beach are extremely female-biased (estimated 97% female for the twenty year period 1993-2012). A 1oC rise in average incubation temperatures threatens near complete hatchling feminisation on this beach, whilst a 2oC rise could reduce hatch success to less than 50%. Thermal effects on hatchling morphometrics are evident, with a 1oC rise in temperature reducing average length, width and weight by 1%, 2% and 3% respectively. More favourable incubation conditions were found early in the season, in deeper nests laid by larger females, and on beaches of lighter sand. In contrast, adult sex ratios at the main site are male-biased, posing questions regarding sex-specific survival rates and optimal hatchling sex ratios. A phenological shift towards earlier nesting is demonstrated for the first time in this species, and could potentially ameliorate warming effects. Carry-over climate forcing effects from the foraging ground influence the breeding frequency of individuals, driving population level responses in annual magnitude of nesting. This work emphasises the utility and necessity of long-term individual-based monitoring programmes in elucidating population trends and climate responses in iteroparous species with non-annual breeding.

Macrobenthic assemblages and sedimentary conditions of five areas were described and compared; the role of abiotic factors in shaping benthic distributions was also examined. Two of the study sites were actively dredged at the time of sample collection and the effects of this aggregate extraction were investigated. It was concluded that trailer dredging (at the level intensity employed at these sites) was not associated with any significant disruption to benthic community structure, despite the differences in abiotic and biotic characteristics of the two dredged areas. A meta-analysis of findings from published dredging impact studies revealed a differential response to dredging that was related to habitat type. Full recovery of the benthos following the cessation of dredging was not observed in any of the habitat types suggesting that dredging is associated with a long-term alteration of macrobenthic resources.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references.
The goal of this thesis is to understand how the functional traits of species, biotic interactions, and the environment jointly regulate the community ecology of phytoplankton. In Chapter 2, I examined Continuous Plankton Recorder observations of diatom and dinoflagellate abundance in the North Atlantic Ocean and interpreted their community ecology in terms of functional traits, as inferred from laboratory- and field-based data. A spring-to-summer ecological succession from larger to smaller cell sizes and from photoautotrophic to mixotrophic and ieterotrophic phytoplankton was apparent. No relationship between maximum net growth rate and cell size or taxonomy was found, suggesting that growth and loss processes nearly balance across a range of cell sizes and between diatoms and dinoflagellates. In Chapter 3, I examined a global ocean circulation, biogeochemistry, and ecosystem model that indicated a decrease in) phytoplankton diversity with increasing latitude, consistent with observations of many marine and terrestrial taxa. Ii the modeled subpolar oceans, seasonal variability of the environment led to the competitive exclusion of phytoplankton with slower growth rates and to lower diversity. The relatively weak seasonality of the stable subtropical and tropical oceans in the global model enabled long exclusion timescales and prolonged coexistence of multiple phytoplankton with comparable fitness. Superimposed on this meridional diversity decrease were "hot spots" of enhanced diversity in soc regions of energetic ocean circulation which reflected a strong influence of lateral dispersal. In Chapter 4, I investigated how small-scale fluid turbulence affects phytoplankton nutrient uptake rates and community structure in an idealized resource competition model. The flux of nutrients to the cell and nutrient uptake are enhanced by turbulence, particularly for big cells in turbulent conditions. Yet with a linear loss form of grazing, turbulence played little role in regulating model community structure and the smallest cell size outcompeted all others because of its significantly lower R* (the minimum nutrient requirement at equilibrium). With a quadratic loss form of grazing, however, the coexistence of many phytoplankton sizes was possible and turbulence played a role in selecting the number of coexisting size classes and the dominant size class. The impact of turbulence on community structure in the ocean may be greatest in relatively nutrient-deplete regions that experience episodic inputs of turbulence kinetic energy.
by Andrew David Barton.
Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013
Cataloged from PDF version of thesis.
Includes bibliographical references.
Iron is a cofactor of a number biochemical reactions that are essential for life. In the marine environment, this micronutrient is a scarce resource that limits processes of global importance such as photosynthesis and nitrogen fixation. Given that marine microorganisms play a central role in modulating such biogeochemical cycles, understanding how their distribution, diversity and activity may be affected by changes in iron availability is key. This thesis explores how the availability of iron affects the ecology of marine microbial populations and communities. At the population level, I characterized the prevalence and diversity of iron acquisition strategies in specific populations of marine vibrios with distinct micro-habitat preferences. Using a combination of genomics and functional screens, I showed that siderophore-based iron acquisition is not conserved at the organismlevel but represents a stable trait at the population level. This population-level trait further appears to play a role in driving the diversification of specific vibrio populations, especially of those that are thought to prefer particles as a micro-habitat. At the community level, I measured whole microbial community responses to iron addition in microcosm experiments in different regions of the Pacific Ocean. Using metagenomics, I characterized the impact of iron availability on the microbial community structure of the Central Equatorial Pacific Ocean. This study showed that addition of iron to an iron-limited ecosystem triggers a phytoplankton bloom dominated by Pseudo-nitZschia-like diatoms, which in turn stimulate a Bacteroidetes population functionally distinct from the ambient free-living population. In the North Pacific Subtropical Gyre, I explored how iron availability impacts microbial community gene expression dynamics. Using a metatranscriptomic approach I showed that in that environment, the impact of iron was tightly connected to the supply of other limiting macronutrients, and seems to mostly affect photosynthetic organisms. This initial study paves the way for more in depth and longer-term studies to further investigate the effects of iron on the dynamics of the microbial community in the North Pacific Subtropical Gyre. Taken together data and analyses presented in this thesis demonstrate how iron availability can shape the ecology of marine microorganisms at population, community and functional levels.
by Laure-Anne Ventouras.
Ph.D.

In situ measurements of the fertilization success of broadcast spawning marine invertebrates have been conducted mainly on shallow subtidal echinoderm and coral species. In this study, field fertilization success was measured for two infaunal, intertidal polychaetes Arenicola marina and Nereis virens. Both species are epidemic spawners, with populations of A. marina spawning over a few days in autumn while N. virens spawns in early spring. The fertilization success of female Arenicola marina is highly variable, ranging from 0 to 100%, and is determined by male spawning density. It is hypothesised that fertilization success over the entire spawning period is the result of an accumulation of fertilizations each day in the spawning period. Fertilization success was measured indirectly in Nereis virens by transplanting oocytes into the field. At least two spawning periods occurred for the population studied here. Fertilization success was uniformly high during the first period, and in the second fertilization success was highest among those eggs located high in the water column as opposed to those at substratum level. The fertilization strategies of these polychaetes are discussed in the light of these results. Comparative laboratory experiments were performed on factors that affect fertilization success in Arenicola marina. Nereis virens, Asterias rubens and Echinus esculentus, including sperm:egg ratio, sperm-egg contact time and sperm concentration. The extent to which each of these factors affects fertilization success varies with species, and this is explained by gamete attributes and mathematical models. Gamete longevity significantly affects fertilization success, and eggs and sperm of Arenicola marina are extraordinarily long lived compared to those of the other species studied here and elsewhere. Eggs are viable for 5 days after spawning, while dilute sperm remains capable of fertilizing eggs for more than 48 hours. The laboratory data are discussed in terms of the fertilization strategies of each of the species.

L'aqüicultura és el subsector productiu agroalimentari amb més creixement des dels anys setanta. El seu percentatge en la producció alimentària marina ha crescut de manera ininterrompuda. En un context de captures decreixents i estocs pesquers en risc, l'aqüicultura ha estat proposada com la solució a la creixent demanda de productes pesquers. Aquesta tendència ha transformat les pràctiques de producció marina, passant de la pesca a la granja, alhora que ha ofert noves fronteres per a l’entrada del capital a través del desenvolupament d'inversions i d’innovacions sociotecnològiques. Aquesta tesi tracta de contribuir a la millor comprensió d'aquesta transformació i de les relacions socials i ecològiques desiguals produïdes. Es centra en el cas europeu, i planteja la pregunta de com i per què l'aqüicultura transforma les relacions de producció en l'àmbit marí i la seva governança. S'han fet servir diverses metodologies qualitatives, en el marc de l'ecologia política, i s'han abordat tres objectius: (i) analitzar els discursos europeus aqüícoles i identificar de quina manera es relacionen amb els processos de confinament i mercantilització del medi marí; (ii) identificar els conflictes socioambientals relacionats amb les granges aqüícoles a Europa des de la perspectiva de la justícia ambiental; i (iii) explorar l'expansió geogràfica, espacial i taxonòmica de les fronteres extractives associades a l'aqüicultura marina intensiva. Els resultats de la investigació suggereixen que l'aqüicultura de peixos marins condiciona i transforma els espais i les relacions productives marines a través de l'expansió contínua del capital, l'extensió a noves fronteres extractives i el confinament de béns comuns. Un procés que és facilitat pels discursos dominants com ara l'imperatiu del creixement. A través de la recerca de vies per a una major acumulació de capital, la transformació de la pesca cap a l'aqüicultura intensiva marina canvia les relacions socials i ambientals en l'àmbit marí. La reconfiguració resultant de l'accés i el control sobre els comuns marins exclou diversos actors, i això al seu torn genera conflictes socioambientals i demandes de justícia ambiental relacionats amb les granges aqüícoles. La investigació assenyala que aquesta expansió produeix nous règims naturals, espacials i socioeconòmics amb la intenció de superar les crisis d'acumulació del capital vinculades al decreixement dels estocs i captures pesqueres, i es produeix mitjançant el confinament i la mercantilització del medi marí. A través de la investigació realitzada, aquesta tesi contribueix a la literatura d'ecologia política vinculada a l'aqüicultura així com als debats teòrics més amplis associats als confinaments, el canvi agrari i socioambiental i la governança ambiental neoliberal.
La acuicultura es el subsector productivo agroalimentario con mayor crecimiento desde los años setenta. Su porcentaje en la producción alimentaria marina ha crecido de manera ininterrumpida. En un contexto de capturas decrecientes y stocks pesqueros en riesgo, la acuicultura ha sido propuesta como la solución a la creciente demanda de productos pesqueros. Esta tendencia ha transformado las prácticas de producción marina, pasando de la pesca a la granja, al tiempo que ha ofrecido nuevas fronteras para la entrada del capital a través del desarrollo de inversiones e innovaciones socio-tecnológicas. Esta tesis trata de contribuir a una mejor comprensión de esta transformación y de las relaciones sociales y ecológicas desiguales producidas por ella. Se centra en el caso europeo, y plantea la pregunta de cómo y por qué la acuicultura transforma las relaciones de producción en el ámbito marino y su gobernanza. Se han usado diversas metodologías cualitativas, en el marco de la ecología política, y se han abordado tres objetivos: (i) analizar los discursos europeos acuícolas e identificar de qué manera se relacionan con los procesos de confinamiento y mercantilización del medio marino; (ii) identificar los conflictos socioambientales relacionados con las granjas acuícolas en Europa desde la perspectiva de la justicia ambiental; y (iii) explorar la expansión geográfica, espacial y taxonómica de las fronteras extractivas asociadas a la acuicultura marina intensiva. Los resultados de la investigación sugieren que la acuicultura de peces marinos condiciona y transforma los espacios y relaciones productivas marinas a través de la expansión continua del capital, la extensión a nuevas fronteras extractivas y el confinamiento de bienes comunes. Un proceso que es facilitado por los discursos dominantes como por ejemplo el imperativo al crecimiento. A través de la búsqueda de vías para una mayor acumulación del capital, la transformación de la pesca a la acuicultura intensiva marina cambia las relaciones sociales y ambientales en el medio marino. La reconfiguración resultante del acceso y el control sobre los comunes marinos excluye a diversos actores, y esto a su vez genera conflictos socioambientales y demandas de justicia ambiental relacionados con las granjas acuícolas. La investigación señala que esta expansión produce nuevos regímenes naturales, espaciales y socioeconómicos con la intención de superar las crisis de acumulación del capital vinculadas al decrecimiento de los stocks y capturas pesqueras, y se produce por medio del confinamiento y la mercantilización del medio marino. A través de la investigación realizada, esta tesis contribuye a la literatura de ecología política vinculada a la acuicultura así como a los debates teóricos más amplios asociados a los confinamientos, el cambio agrario y socioambiental y la gobernanza ambiental neoliberal.
Aquaculture is the fastest-growing food-production sector globally—since the 1970s, its share in total seafood production has increased uninterruptedly. In the context of falling captures and endangered fish stocks, aquaculture has been proposed as the solution for supplying the rising global seafood demand. This trend has transformed the practices of seafood production from capture to farming, while opening new frontiers for capital with new types of investments and socio-technical innovations. In this thesis, I contribute to understanding this transformation and the resulting uneven social and ecological production relations. By focusing on the case of Europe, I address the question of how and why marine finfish aquaculture transforms the relations of seafood production and marine governance. Adopting a range of qualitative methodological approaches informed by political ecology, my analysis has three objectives: (i) to analyze discourses on European aquaculture and uncover the way they relate to processes of enclosure and commodification of marine areas; (ii) to identify socio-environmental conflicts related to fish farms in Europe and examine them through the lens of environmental justice; and (iii) to explore the geographic, spatial, and taxonomic expansion of commodity frontiers associated with intensive marine aquaculture. The research findings presented in this thesis suggest that marine finfish aquaculture shapes and transforms marine spaces and production relations through the continuous expansion of capital into new commodity frontiers and the enclosure of marine commons, enabled by dominant discourses like growth imperative. By seeking further capital accumulation, the transformation from capture fisheries to intensive marine aquaculture changes social and ecological relations within marine area. The resulting reconfiguration of access to and control over marine commons excludes a variety of social actors, and leads in turn to socio-environmental conflicts related to fish farms informed by environmental justice demands. I claim that such a continuous expansion underpins how capital produces nature, space, and socio-ecological regimes with the intention of overcoming accumulation crises related to declining stocks and capture fisheries through further enclosing and commodifying marine areas. Through these findings, this thesis contributes to literatures on the political ecology of aquaculture as well as to broader theoretical debates on enclosures, agrarian and socio-environmental change and on neoliberal environmental governance.

The incubation shift length of the Ancient Murrelet ( Synthliboramphus antiquus), an exceptionally long and varied for an auk. I studied colonies of this species at East Limestone Island (1993-1995, 2002-2003: data collected by Laskeek Bay Conservation Society) and Reef Island (2007-2008), Haida Gwaii, British Columbia. Incubation shift length was correlated between pair members and my results show that maintaining incubation schedule was an essential component of reproductive success. Incubation shift length varied in response to prevailing local weather and sea conditions (e.g. wind speed, wave height), perhaps as a consequence of reduced foraging efficiency. Incubation shift length was longer in years when sea surface temperature in April was high. In years with longer shift, birds had lower reproductive success and chicks departed the nest with a lower body mass. My results explained if we assume that multi-day incubation shifts in Ancient Murrelets are the adaptively preferred strategy, through reduction in predation risk, but that actual shift lengths are modified by immediate weather and foraging constraints.

Biological N2 fixation, the reduction of dinitrogen (N2) gas to biologically available nitrogen, is a fundamental process since it represents a source of new nitrogen for marine life in areas where this important element can be limiting, supporting primary productivity and thus biological carbon export to the deep ocean. This process is performed by the nitrogen-fixing prokaryotic microorganisms (the so-called diazotrophs). However, very little is still known about the identity and ecology of diazotrophs, which largely limits our capacity to understand the global significance of this process, and to predict potential variations in nitrogen fixation upon changes in environmental conditions. In this thesis, we aimed at improving the knowledge on the diversity, ecology and evolution of the marine nitrogen-fixing microorganisms in the open ocean. Most current knowledge on diazotrophic diversity has been obtained using the nifH marker gene, which encodes for a structural protein of the enzymatic complex that performs the N2 fixation reaction. Thus, in Chapter 1 we first conducted a global exploration of the nifH gene extracted from metagenomic data derived from 68 globally distributed stations collected during the Tara Oceans expedition. This approach differs from previous studies in that it does not rely on primers to detect the nifH genes, and thus allows a more quantitative estimation of the contribution of these microorganisms and a more realistic view of their diversity. This study provides a first `primer-free¿ global map of the distribution of open ocean diazotrophic communities across ocean basins and throughout the water column, showing that diazotrophs often occurred at very low abundances, and that in general they were significantly more abundant in the mesopelagic than in photic waters. Likewise, we uncovered novel diversity that had remained unnoticed in all previous primer-based studies, since we demonstrate that more than half of the detected nifH variants cannot be captured by the primers used. This suggests that most diazotroph diversity studies may be disregarding an important fraction of the nitrogen-fixing community members. Among the diazotrophs detected in Chapter 1, the most abundant was the unicellular cyanobacterium C. Atelocyanobacterium thalassa (UCYN-A), which lives in symbiosis with a prymnesiophyte alga and has been shown to be a relevant player in nitrogen fixation. Thus, in Chapter 2 and Chapter 3, we explored aspects related to the ecology, diversity and evolution of this remarkable microorganism. We detected UCYN-A in the South Atlantic Ocean using not only metagenomic approaches but also microscopic visualization techniques (CARD-FISH). This allowed us to unveil that different UCYN-A lineages, UCYN-A1 and UCYN-A2, live in symbiosis with two distinct prymnesiophyte partners of different sizes. Both UCYN-A lineages showed a streamlined genome expression towards nitrogen fixation. We estimated that these two lineages diverged almost 100 Mya under a strong purifying selection process. Finally, in Chapter 3 we focused on the study of UCYN-A3, another lineage of which very little was known, to gain insight into its ecology. Using an array of methods (PCR, qPCR, CARD-FISH and metagenomes) we could visualize and identify for the first time UCYN-A3 and its association with an alga of different size, which suggests that different UCYN-A lineages occupy different planktonic compartments that are not always considered when nitrogen fixation of nifH diversity are studied. Finally, we manage to reconstruct a significant fraction of its genome, establishing that this lineage constitutes a new UCYN-A genomic species. Overall, this thesis has significantly contributed to expand the knowledge on marine diazotrophic organisms, unveiling new diversity and new planktonic compartments that could potentially lead to a better understanding of the marine nitrogen cycle.
La fijación biológica de nitrógeno, es decir, la reducción del nitrógeno (N2) a amonio, es un proceso fundamental ya que representa una fuente de nitrógeno para la vida marina en áreas donde este elemento es limitante, posibilitando la producción primaria y por tanto la exportación de carbono al océano profundo. Este proceso se lleva a cabo por microorganismos procariotas, los llamados diazotrofos. Sin embargo, aún sabemos muy poco sobre la identidad y la ecología de estos microorganismos, lo que limita enormemente nuestra comprensión de la importancia global de este proceso, y nuestra capacidad de predecir cambios en la fijación de N2 ligados a cambios en el ambiente. El objetivo de esta tesis, por tanto, fue ahondar en el conocimiento de la diversidad, ecología y evolución de los microorganismos diazotrofos en el océano. La mayoría del conocimiento actual sobre la diversidad de diazotrofos se deriva del gen marcador nifH, que codifica una proteína estructural del complejo enzimático responsable de la fijación de nitrógeno. Por tanto, en el Capítulo 1 realizamos una exploración global del gen nifH usando datos metagenómicos de 68 estaciones muestreadas durante la campaña oceanográfica Tara Oceans. Nuestra aproximación se diferencia de los estudios anteriores ya que no se basa en el uso de cebadores para detectar el nifH y posibilita por tanto una cuantificación más precisa de la diversidad real. Este estudio representa el primer mapa global (no basado en cebadores) de la distribución de diazotrofos en el océano desde superficie hasta el mesopelágico. Aunque la abundancia de diazotrofos fue muy baja en general, era significativamente mayor en el océano profundo. Asimismo, descubrimos nuevos diazotrofos que habían pasado desapercibidos en los estudios basados en cebadores: más de la mitad de los diazotrofos detectados no se capturan por los cebadores para el nifH. Esto sugiere que la mayoría de estudios previos pueden haber obviado una fracción importante de las comunidades de fijadores de nitrógeno. Entre los diazotrofos detectados en el Capítulo 1, el más abundante fue la cianobacteria unicelular C. Atelocyanobacterium thalassa (UCYN-A), que vive en simbiosis con un alga primnesiofita y que juega un papel importante en la fijación de nitrógeno. En los capítulos 2 y 3 nos dedicamos a estudiar en detalle los aspectos relacionados con la ecología, diversidad y evolución de este diazotrofo. Mediante el análisis de metagenomas y de técnicas de visualización microscópicas como el CARD-FISH pudimos detectar UCYN-A en el atlántico sur, revelando que UCYN-A1 y UCYN-A2, dos linajes diferentes de UCYN-A, viven en simbiosis con dos hospedadores diferentes, dos primnesiofitas de tamaños distintos. Además, el análisis del perfil de expresión del genoma de ambos linajes mostró una dedicación optimizada a la fijación de nitrógeno. La edad de divergencia de UCYN-A se estimó en unos 100 millones de años, y presumiblemente ocurrió bajo presiones evolutivas de tipo estabilizadora. Por último, en el Capítulo 3, nos centramos en el estudio de UCYN-A3, otro linaje del que se sabe muy poco. Mediante el uso de varios métodos (PCR, qPCR, CARD-FISH y metagenomas) se logró visualizar e identificar por primera vez el linaje UCYN-A3 asociado con una alga de tamaño diferente, lo que sugiere que los distintos linajes de UCYN-A ocupan diferentes compartimentos planctónicos que no siempre se consideran en estudios de diversidad de nifH o de fijación de nitrógeno. Finalmente, pudimos reconstruir una fracción importante del genoma de UCYN-A3, estableciendo que representa una especie genómica diferente a las anteriores. En definitiva, esta tesis ha contribuido significativamente al conocimiento de los diazotrofos en el océano mediante el descubrimiento de nueva diversidad como de nuevos compartimentos del plancton donde puede darse la fijación de nitrógeno y que podrían ayudar a entender mejor el ciclo marino del nitrógeno.

Any good conservation project should have at least basic elements of research which run parallel to the day to day conservation management. Current populations of sea . turtles in the Mediterranean are at seriously reduced levels. This is particularly the case for green turtles (Chelonia mydas) which suffered from serious over-exploitation during the last century. This exploitation has now largely ceased, with loggerhead turtles (Caretta caretta) now being the species most at risk from fisheries bycatch. I analysed 15 years of monitoring data from nesting beaches in Northern Cyprus. The major result obtained from this analysis was that, whilst the loggerhead turtle population appears.stable, the number of green turtle nests laid annually is declining. Conservation measures which have been put into place over the years, have significantly increased the clutch hatching success experienced at this location and it is hoped that these efforts will eventually counteract the apparent decline. Over a five year period we collected epibiont species present on the carapace of both green and loggerhead turtles nesting at Alagadi. The two most commonly occurring epibionts were the acorn barnacles Chelonibia testudinaria and Chelonibia caretta. For these two species we analysed their spatial distribution and found the larger . specimens of the former to be sited on the anterior portion of the carapace. I recorded five new species of sea turtle epibiont: Laomedea flexuosa, Caprella fretensis, Hyale nilssoni, Hyale schmidti, Parasinelobus chevreuxi; as part of a total of nine zoological epibionts present on 35 female green (Chelonia mydas) and 100 loggerhead (Caretta caretta) turtles nesting in Cyprus. Using nesting data, sexing of hatchlings and incubation temperatures enabled me to successfully establish the first pivotal temperatures and incubation durations for green and loggerhead turtles in Cyprus. From these findings I was able to estimate the extremely female biased hatchling sex ratio produced across the island and predict the potential catastrophic outcome for hatchlings in the face of global temperature rise. Part of my work in this thesis involved the triating of two different types of technologies. One involved placing geolocating light loggers on turtles, to indicate their locations in a Mediterranean context. An element of this study was to cakulate,-me respective errors when compared to satellite telemetry. I obtained very positive results from this study, giving an accuracy of c. 50km. The second study concerned the use of animal borne digital cameras, placed on green turtles to elucidate subsurface habitat utilisation and the possibility of feeding during the internesting period. Such analysishas established some of the criteria which may allow researchers to allocate likely behaviour based on dive profIles, and thus to examine dive data and imagery collected .over a longer time-series and to inform the determination of time-energy budgets. Due to their dependence on environmental temperatures, the Mediterranean :population of sea turtles must be considered one of the most vunerable to be impacted . by global climate change. Therefore we must develope a greater understanding of their biology, if we are to reduce current and future impacts on these species.

Photosynthetic picoeukaroytes (PPEs), defined here as single celled organisms <3 μm in diameter, are significant contributors to primary production. Until recently, marine PPEs had received relatively little research attention in contrast to the more numerous picocyanobacteria. Molecular studies have now started to reveal the diversity of this group, using both the nuclear 18S rRNA gene and the plastidtargeted 16S rRNA gene as taxonomic markers. The latter marker has the advantage of directly targeting the PPE community, counteracting the problem of heterotrophic sequences dominating clone libraries. As well as PCR based molecular approaches, genomic studies of PPEs are starting to reveal the metabolic capabilities of these organisms. In this thesis, taxonomic information obtained on two flow-sorted PPE populations (Euk-A and Euk-B) showed that pico-prymnesiophytes, largely representing lineages with no close cultured counterpart, dominated the Euk-A and Euk-B libraries (54 and 58%, respectively) in tropical and sub-tropical waters of the Atlantic Ocean. Radiotracer work performed elsewhere had shown these PPE groups contribute up to 19% and 38% (Euk-A and Euk-B, respectively) to total CO2 fixation, demonstrating the importance of these PPE groups in marine carbon cycling. To further assess the taxonomic composition and distribution of these Euk-A and Euk-B PPE populations at the ocean-basin scale, clone libraries were constructed along an Atlantic Meridional Transect (AMT18). Major components of these flow cytometry sorted PPE populations were Prymnesiophyceae and Chrysophyceae using plastid markers, or Prasinophyceae and Dinophyceae (nuclear markers) including several lineages with no cultured counterparts. In surface waters a latitudinal diversity gradient was observed with a peak in PPE diversity found in the equatorial region. Distribution patterns of specific PPE groups and OTUs were subsequently correlated with measured environmental parameters, although most of the variation in PPE diversity was not explained by the measured variables. Attempts were undertaken to obtain into culture novel PPEs, especially those representative of oligotropic regions. However, the majority of isolates obtained were related to Prasinoderma or Chlorella which are cosmopolitan, fast-growing genera. Even so, some isolates more relevant of open ocean environments were obtained, including a clade VIIA prasinophyte and a Pelagomonas sp. Trancriptomics was used to further assess the functional potential of specific PPE populations, firstly in cultures using both an Ochromonas sp. and a prasinophyte as being representative of organisms present along AMT18. This approach revealed a C4 carbon concentrating mechanism in the clade VIIA prasinophyte and enzymes required for a functioning urea cycle in the Ochromonas sp. A pipeline was also developed to undertake a metatranscriptomic approach on a flow cytometrically sorted PPE population from the south Atlantic gyre. This approach revealed a diatom-like C4 carbon concentrating system in the metatranscriptome. Overall, this thesis has given new insights into the diversity of specific PPE groups at the ocean basin-scale, developed a new pipeline for the transcriptomic analysis of PPEs both in culture and in the environment, and in so doing has provided new information on the functional potential of these important photosynthetic organisms.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.
Cataloged from PDF version of thesis. Each chapter with its own abstract. Each appendix with its own summary.
Includes bibliographical references.
Microbial secondary metabolites are among the most structurally and functionally complex molecules in nature. Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive post-translational modification. Most lanthipeptides are bactericidal but they are also known to act as signaling molecules or morphogenetic peptides, nevertheless the function of many lanthipeptides remains unknown. Prochlorosins are a diverse group of lanthipeptides produced by strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Unlike other lanthipeptide-producing bacteria, picocyanobacteria utilize an unprecedented mechanism of catalytic promiscuity for the production multiple structurally diverse lanthipeptides using a single biosynthetic enzyme. Also unprecedented is the production of lanthipeptides by single celled, planktonic gram-negative bacteria in a dilute nutrient-limited habitat, which suggests that they may have an unconventional biological function. The overarching goal of this thesis is to further our understanding of the ecology and evolution of the prochlorosins, and provide insights into their biological role in the marine environment. Here, we demonstrate that the prochlorosin genes are widespread in the ocean and that globally distributed populations of marine picocyanobacteria have the genetic potential of producing thousands of different lanthipeptide structures. The diversity of prochlorosin structures provides an interesting model to study the evolutionary forces that drive the creation of new lanthipeptide structures. We present evidence that there is a unique evolutionary interplay between the components of prochlorosin biosynthesis pathway; while the peptide substrates independently expand and diversify within the genome, the catalytically promiscuous biosynthetic enzyme evolves under a strong purifying selection that maintains its substrate tolerant state. This relationship indicates that the lanthipeptide production trait in marine picocyanobacteria might find its evolutionary advantage in the plasticity of the production of multiple cyclic peptides with diverse ring topologies. The remarkable diversity of prochlorosins poses many questions regarding their biological role in the marine environment. In laboratory experiments, we explore of some of the potential bioactivity of the prochlorosins, namely their potential as signaling molecules, antimicrobials and nutrient sources. The results from this exploration open new perspectives for the role of the lanthipeptides in the natural environment - more specifically the oligotrophic ocean.
by Andrés Fernando Cubillos-Ruiz.
Chapter 1. Chapter 2. Chapter 3. Chapter 4. Chapter 5. Appendix A. Appendix B. Introduction -- Evolutionary radiation of lanthipeptides in natural populations of marine picocyanobacteria / Andres Cubillos-Ruiz ; Jessica W. Berta-Thompson ; Jamie Becker ; Sallie W. Chisholm -- Exploring the biological role of prochlorosins / Andres Cubillos-Ruiz ; Jamie Becker ; Yanxiang Shi ; Wilfred van der Donk ; Sallie W. Chisholm -- Amino acid toxicity and tolerance in prochlorococcus / Andres Cubillos-Ruiz ; Audrey Olshefsky ; Sallie W. Chisholm -- Conclusion and future directions -- Proposed molecular mechanism for the expansion and diversification of prochlorosins - Hawaii Ocean experiment : prochlorosin amendment.
Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and Woods Hole Oceanographic Institution), 2000.
Includes bibliographical references.
The marine cyanobacteria Synechococcus and Prochlorococcus are important primary producers in oligotrophic oceans. The abundance and cell division rates of these cyanobacteria can be influenced by trace metals such as iron and copper. Iron is an essential trace metal that is present in the high nutrient, low chlorophyll waters of the equatorial Pacific in extremely low concentrations. When these waters were enriched with iron, Prochlorococcus chlorophyll fluorescence per cell and cell size increased. Cell division rates doubled inside the iron enriched patch and reached two divisions per day in bottle incubations with additional iron, indicating that Prochlorococcus were iron limited. However, cell numbers remained constant because mortality rates nearly doubled after the addition of iron and essentially matched the increases in cell division rate. Trace metals can also be present in toxic, rather than limiting concentrations. Copper is an essential trace element that is toxic to cyanobacteria in pM quantities. In stratified water columns in the Sargasso Sea, free Cu2+ concentrations are high in the mixed layer (up to 6pM) and most of the Prochlorococcus population is located below the thermocline where free Cu2+ concentrations are lower. The distribution of Synechococcus is more uniform with depth. Prochlorococcus isolates were more sensitive to copper than Synechococcus, but members of the low chi BIA (high light adapted) ecotype were less sensitive than strains with high chi BIA ratios (low light adapted). In the field, the in situ concentration of free Cu2+ had a strong effect on the copper sensitivity of Prochlorococcus. Net growth rates were substantially reduced when Prochlorococcus from environments where the in situ free Cu2+ was low (deep mixed layers and below the thermocline in stratified water) were exposed to copper. Prochlorococcus in shallow mixed layers where in situ Cu2 + was high were less sensitive to copper and may have been members of the copper resistant low chi B/ A ecotype. Synechococcus were relatively copper resistant across a range of environments. These data are consistent with the hypothesis that ambient copper levels may influence the relative abundance of Prochlorococcus and Synechococcus in the Sargasso Sea.
by Elizabeth Lowell Mann.
Ph.D.

All marine ecosystems in the Mediterranean Sea are highly threatened by anthropogenic stressors that can alter their structure and function, especially in rocky shores. Moreover, extreme climate events are becoming more frequent and intense in our times. To detect the potential impacts and the vulnerability of any ecosystem, the combination of experimental and observational studies in the field is vital. In addition, long-term monitoring programs carried out simultaneously on human-protected and human- impacted environments may be crucial to discern the nature of the impacts. Macroalgal beds dominate the shallow benthic Mediterranean habitats where they play a pivotal role. Among them, the canopy-forming Cystoseira sensu lato species represent the highest structural complexity level and provide unique habitats with ecological services comparable to terrestrial forests. Canopy-forming algae are in decline in many coastal areas where, among other impacts, overgrazing by herbivorous can lead to the loss of these diverse habitats shifting towards degraded sea urchin barren grounds. Conservation tools such as marine reserves or No-take zones (NTZs) have the potential to reduce some of the anthropogenic threats and to restore benthic habitats through trophic cascade effects caused by the major abundance of predator. Besides, active ecosystem restoration strategies may speed up the recovery of impacted ecosystems. Nevertheless, there is an important lack of continuous and long-term studies providing robust ecological data of the natural dynamic and vulnerability of macroalgal assemblages while integrating the role of marine conservation. In this dissertation, different methodological approaches were combined to explore the long-term dynamics of macroalgal communities and the role of different conservation strategies (NTZs and active restoration) in the Montgrí, Medes Islands, and Baix Ter (MIMBT) Natural Park (NW Mediterranean Sea). In the first two chapters, the analysis of long-term monitoring datasets provided essential information to understand how macroalgal assemblages and sea urchin populations respond to natural fluctuations and anthropogenic disturbances, mainly overfishing. In the third chapter, field monitoring and sampling were combined with genetic analyses to increase the ecological knowledge of the canopy-forming alga Treptacantha elegans as well as to describe their recent expansion. In the fourth and last chapter, active restoration actions as seeding experiments were conducted in aquaria and in the field to optimize restoration techniques to recover degraded shallow ecosystems. In addition, different restoration strategies were combined in the field inside and outside the Medes Islands NTZ to evaluate the role of marine protection on restoration activities. The results of this thesis showed that the abundance and structure of the main macroalgal assemblages in the MIMBT Natural Park were stable at large over the last fifteen years. Overall, any effect of marine protection was observed on the most representative species of this habitat but we found a higher abundance of canopy- forming algae inside the NTZ than in unprotected areas. Contrarily, sea urchin populations were deeply affected by a severe storm in 2008 which caused the almost depletion of its populations in all the studied areas. Although similar trajectories of sea urchin abundance have been observed over the years between both protection regimes due to the large stability of the sea urchin high-density state, clear differences in the recovery of sea urchin populations were found after the storm linked to marine protection. The sea urchin populations inside the NTZ recovered slowly than the populations outside the NTZ inside due to the higher predatory fish abundance inside the NTZ. In contrast to the global widespread decline of canopy-forming macroalgal assemblages across many regions during the last decades, Treptacantha elegans has increased their distributional range and has shown an extraordinary expansion along the Catalan northern coast over the last two decades. The results of this thesis contributed to explaining this geographical and depth range extension, which could be linked to some ecological attributes such as their relative fast-growing dynamics, early fertile maturity, and high turnover rate. Besides, the molecular analyses have shown that all the populations of T. elegans in the Catalan coast constitute a single genetic group that could be originated in the MIMBT Natural Park under the marine protection benefit. Given the fast and stable population dynamics of T. elegans, this species was selected as a potential species to actively restore degraded shallow rocky ecosystems (e.g., sea urchin barren grounds) turning them into productive marine forests. In this way, the effectiveness of active restoration actions combined with passive strategies such as marine protection (e.g., NTZs) was experimentally demonstrated. This thesis addressed marine vegetation changes in the shallow rocky shores of the MIMBT Natural Park integrating the macroalgal and sea urchin dynamics in front of natural and human-related impacts, and the role and effectiveness of Marine Protected Areas and restoration actions as conservation tools at lower trophic levels. Besides, since most of this thesis is based on long-term monitoring data, a valuable baseline of the algal community’s structure and functioning was provided here which could be vital to predict and detect ecological changes that could jeopardize the preservation of marine forests.
Els ecosistemes bentònics mediterranis es troben fortament amenaçats per pressions, tant a nivell local com global, que poden alterar la seva estructura i funcionament, especialment en els fons rocosos litorals. A més, els episodis climàtics extrems esdevenen cada vegada més freqüents i intensos. Per a detectar els possibles impactes sobre qualsevol ecosistema així com la seva vulnerabilitat, la combinació d’estudis observacionals i experimentals al camp és primordial. En aquest sentit, els estudis a llarg termini realitzats simultàniament en zones impactades i en zones protegides de l’acció humana, poden ser crucials per a identificar la naturalesa dels impactes. Al mar Mediterrani, les comunitats de macroalgues dominen els hàbitats bentònics soms, on tenen un paper primordial. D’entre elles, les algues de tipus arborescent del gènere Cystoseira representen el nivell més elevat de complexitat estructural i proporcionen hàbitats amb serveis comparables als boscos terrestres. Aquestes algues es troben en declivi en diverses zones costaneres. És aquí on, entre altres impactes, la sobrepastura dels herbívors pot portar a la pèrdua d’aquests hàbitats rics i diversos i la seva transició cap a fons degradats dominats pels eriçons. Les eines de conservació, així com ara les reserves marines o les àrees on està prohibida completament l’extracció (NTZs), tenen el potencial de reduir algunes de les amenaces derivades de l’acció humana i de restaurar els hàbitats bentònics gràcies als efectes dels depredadors a través de les cascades tròfiques. A més de la restauració passiva a través de la creació d’aquestes àrees protegides, la restauració activa dels ecosistemes impactats pot accelerar la seva recuperació. No obstant això, hi ha una manca important d’estudis continuats i a llarg termini que proporcionin dades ecològiques robustes sobre la dinàmica natural i la vulnerabilitat dels hàbitats de macroalgues i que alhora integrin el paper de les diferents eines de conservació marina. En aquesta tesi, s’han combinat diferents metodologies per explorar la dinàmica de les comunitats de macroalgues juntament amb el paper de diferents estratègies de conservació (NTZs i restauració activa) al Parc Natural del Montgrí, les Illes Medes i el Baix Ter (MIMBT), situat al Nord-oest del mar Mediterrani. En els primers dos capítols, les anàlisis de dades d’estudis a llarg termini han proporcionat informació essencial per millorar la nostra comprensió sobre com les comunitats de macroalgues i les poblacions d’eriçons responen a les fluctuacions naturals i a les pertorbacions d’origen antròpic, principalment, la sobrepesca. En el tercer capítol, mostrejos en el camp s’han combinat amb anàlisis genètics per augmentar el coneixement ecològic de l’alga arborescent Treptacantha elegans i per descriure la seva recent expansió. Al quart i últim capítol, s’han realitzat accions de restauració activa, com ara experiments de sembra en aquaris i al camp per optimitzar les tècniques de restauració dels ecosistemes poc profunds degradats. A més, s’han combinat diferents estratègies de restauració a camp, dins i fora de la NTZ de les Illes Medes, per avaluar el paper de la protecció en les activitats de restauració. Els resultats d’aquesta tesi mostren que la abundància i la composició de les principals comunitats algals del Parc Natural del MIMBT s’han mantingut estables al llarg dels darrers quinze anys. En general, no es va observar cap efecte de la protecció en les espècies d’algues més representatives, tot i que si que es van trobar abundàncies més elevades de l’alga T. elegans a dins de la NTZ que a les zones no protegides de l’acció humana. Al contrari, les poblacions d’eriçons es van veure profundament afectades per una forta tempesta l’any 2008, el que va provocar el declivi gairebé total d’aquestes poblacions a les zones estudiades. Tot i que s’havien observat trajectòries similars en l’abundància d’eriçons al llarg del temps, tant a dins com a fora de la NTZ, degut a la gran estabilitat de les poblacions d’eriçons quan les poblacions presenten elevades densitats, en aquesta tesi es van trobar clares diferències en la recuperació d’aquestes poblacions després de la tempesta que estarien vinculades a l’efecte de la protecció marina. Les poblacions d’eriçons a dins de la NTZ es van recuperar més lentament que les de les zones no protegides degut a la major abundància de peixos depredadors a dins de la NTZ. Davant de la davallada generalitzada de les macroalgues arborescents que s’ha pogut observar a moltes regions al llarg de les darreres dècades, l’alga Treptacantha elegans ha demostrat una extraordinària expansió a la costa nord catalana al llarg de les dues darreres dècades, augmentat considerablement la seva distribució. Els resultats d'aquesta tesi contribueixen a explicar aquesta expansió, tant en fondària com a nivell geogràfic, que podria estar relacionada amb alguns trets ecològics, com ara la seva dinàmica de creixement relativament ràpid, la maduresa reproductiva precoç i la seva elevada taxa de renovació poblacional. A més, les anàlisis moleculars mostren que totes les poblacions de T. elegans a la costa catalana constitueixen un únic grup genètic que podria tenir el seu origen al Parc Natural del MIMBT com a conseqüència de la protecció marina. Atesa la dinàmica ràpida i estable de les poblacions de T. elegans, es va seleccionar aquesta com a potencial espècie per restaurar activament els ecosistemes rocosos poc profunds degradats (els blancalls originats per la sobrepastura d’eriçons) convertint-los en productius boscos marins. Gràcies a això, també s’ha demostrat experimentalment l’èxit de combinar accions de restauració activa amb estratègies passives com la protecció marina (p.e. NTZs). Aquesta tesi aborda els canvis de vegetació marina als fons soms i rocosos del Parc Natural del MIMBT integrant la dinàmica de les macroalgues i els eriçons enfront dels impactes naturals i humans, i, el paper i l’eficàcia de les zones marines protegides i de les accions de restauració com a eines de conservació per als nivells tròfics més basals. A més, atès que la major part d’aquesta tesi es basa en dades d’estudis a llarg termini, aquesta tesi proporciona una valuosa referència de la dinàmica i de l’estat actual de les comunitats infralitorals dominades per algues, el que podria ser vital per predir i detectar canvis ecològics que puguin posar en perill la preservació dels boscos marins.

I investigated the ecological functions of halogenated secondary metabolites from the red alga Asparagopsis armata, their localisation in specialised cells and also their cost of production. A. armata produces large amounts of halogenated metabolites ( < 20 ??g / mg dry weight) that are sequestered in gland cells, as was demonstrated with light, epifluorescence and transmission electron microscopy. Cellular structures were identified that likely assist the release of metabolites from the gland cells to the algal surface. The halogenated metabolites of A. armata have multiple ecological roles, functioning as both inhibitors of bacterial fouling and as herbivore deterrents. Their activity against bacteria and herbivores was measured by a novel test in which the metabolites were manipulated in A. armata by omitting bromide ions from the culture media. This technique prevented the production of halogenated metabolites, but did not impact on other aspects of algal biology. Algae lacking halogenated metabolites (bromide [-] algae) had higher densities of epiphytic bacteria than those that continued to produce metabolites (bromide [+] algae). Bioassays with pure compounds against individual bacterial isolates further supported an inhibitory role for the halogenated metabolites against epiphytic bacteria, and also indicated an affect on bacterial community structure as well as abundance. Bromide (+) A. armata produced halogenated metabolites that also deterred feeding by two herbivores (an amphipod and an abalone), but not a third (an opisthobranch mollusc). A novel outcome from these feeding assays was the demonstration of a relationship between herbivore size and consumption of the chemically defended A. armata by the abalone Haliotis rubra. In addition to the fitness benefits gained from chemical defence, there were also costs for allocating resources to secondary metabolites. These costs were only detected under limiting light resources, consistent with predictions of the plant defence models. The integration of chemical analyses and cellular measures of chemical defence proved essential in elucidating resource allocation to chemical defence in the filamentous stage of A. armata. This thesis highlights that the simple relationships between growth and defence in filamentous algae can provide an excellent model for studies of the ecology and evolution of chemical defences in marine algae.

Silicon (Si), in its dissolved form of silicic acid (DSi), is a key nutrient in the ocean. The availability of such nutrient in marine ecosystems is regulated through its use by silica-secreting organisms, a variety of groups including protists, algae, and animals that consume DSi to build their silica (BSi) skeletons. The interest in determining how Si cycles in the ocean is high, since it interacts with the cycling of other major nutrients and ocean primary productivity. Because diatoms are the most abundant Si users, the scientific attempts to quantify the Si utilization in the ocean have been only focused on these organisms, considering negligible the role of other Si users. Over the last decades, some studies have suggested that at least another group, the siliceous sponges, are also playing a non-negligible role in the consumption of Si in marine ecosystems. Marine sponges are conspicuous animals in benthic ecosystems. They are common across the world ocean, irrespective of the latitude and depth, being able to form enormous aggregations that may extend over large areas. Both their ubiquity and their abundance make sponges good candidates to develop relevant functional roles in marine ecosystems. Regarding the use of Si, it is surprising that, despite about 80% of the sponge species require from DSi to elaborate their skeleton, almost no information is available about how sponges consume such nutrient. In fact, before the beginning of this PhD, only few studies had investigated DSi consumption in marine sponges, with kinetic models available for only four species in two genera of demosponges. This lack of knowledge sparked this PhD, which has been developed in the frame of three research grants: 1) “A research action to quantify fluxes and sinks of silicon through sponges: a neglected circuit within the marine cycle” (MEC–CTM2012-37787); 2) “Exploring the biological production of silica and its applications in science and technology” (MINECO-CTM2015-67221- R); and 3) WP4 —Ecosystem functions, services, and goods— in the EU’s project SponGES (H2020-No. 679849). The main objective of the work was to improve the general understanding on how sponges utilize DSi, to facilitate further assessment of the quantitative role of the sponges as Si users. Here we investigated the kinetics of DSi consumption in five sponge species: four temperate, shallow-water demosponges and, for the first time, a cold, deep-water hexactinellid sponge. We also examined the sources of between-species and between-individual variability in DSi consumption responses. Interestingly, we detected that DSi consumption kinetics can change seasonally in some species, what may have important implications when quantifying the role of sponges as Si users. Additionally, we determined for the first time the rate of DSi utilization by a sponge species in situ. The results significantly matched those estimated from the kinetic models obtained in the laboratory, supporting the use of long (>24h) incubations in laboratory to investigate DSi consumption kinetics in sponges, in contrast to the very short periods traditionally recommended for diatoms (< 3h). Finally, we used the empirically information gained on DSi consumption over the development of this PhD to estimate the utilization of DSi by a sponge assemblage at the ecosystem level, using as case study the bay of Brest (France). In summary, this research showed that sponges have a noticeable role as Si users, even in a shallow-water ecosystem (the bay of Brest) where diatoms largely contribute to the phytoplankton biomass. Our results also indicated that sponges increase their role in marine ecosystems with increasing availability of DSi in seawater. Thus, sponges are predicted to play a relevant role as Si users in high-latitude and deep-water habitats, characterized by high DSi availability. All together, the siliceous sponges should be considered as Si users if we aim to accurately quantify the cycling of Si in marine ecosystems.
El silicio (Si), en su forma disuelta de ácido silícico (DSi), es un nutriente clave en el océano. Su disponibilidad en los ecosistemas marinos la regulan varios grupos de organismos, los cuales consumen DSi para construir sus esqueletos de sílice (BSi). Debido a que las diatomeas son el consumidor de Si más abundante, los intentos por cuantificar el uso del Si en el océano se han centrado principalmente en estos organismos, considerando el papel de los otros usuarios de Si como irrelevante. Durante las últimas décadas, algunos estudios han sugerido que al menos otro grupo, las esponjas silíceas, también están jugando un papel no-despreciable en el consumo de Si en los ecosistemas marinos. Las esponjas marinas son animales abundantes en los ecosistemas bentónicos. Es sorprendente que, pese a que el 80% de las especies necesitan DSi para formar sus esqueletos, casi no existe información disponible sobre cómo las esponjas consume dicho nutriente. De hecho, antes del comienzo de esta tesis (inicios del 2014), solo unos pocos estudios habían investigado el consumo de DSi en esponjas marinas, con modelos cinéticos sólo disponibles para dos géneros de demosponjas. Así, el principal objetivo de este trabajo fue mejorar el conocimiento general de cómo las esponjas utilizan DSi, facilitando futuras cuantificaciones del papel de las esponjas como usuarias de Si. Primero, investigamos las cinéticas de consumo de DSi en cinco especies de esponjas, incluida, por primera vez, una especie de la Clase Hexactinellida. También examinamos las fuentes de variabilidad entre especies y entre individuos, detectando que en algunas especies pueden ocurrir cambios estacionales en las cinéticas de consumo. Además, determinamos por primera vez la tasa de uso de DSi en esponjas en su hábitat natural (in situ). Los resultados, significativamente concordantes con los estimados por modelos cinéticos obtenidos en el laboratorio, respaldan el uso de incubaciones largas (>24h) en el laboratorio para investigar las cinéticas de consumo de DSi en esponjas. Finalmente, usamos toda la información empíricamente obtenida durante esta tesis para estimar el uso de DSi por parte de una comunidad de esponjas al nivel de ecosistema: la bahía de Brest (Francia). En resumen, este trabajo muestra que las esponjas tienen un papel relevante como usuarios de Si, incluso en un ecosistema somero en donde las diatomeas contribuyen ampliamente a la biomasa fitoplanctónica. Nuestros resultados también indican que el papel de las esponjas en los ecosistemas marinos aumenta junto con la disponibilidad de DSi. Por tanto, se predice que las esponjas jueguen un papel importante como usuarios de Si en hábitats profundos y de latitudes altas, caracterizados por alta disponibilidad de DSi. Todo ello indica que las esponjas silíceas deben ser consideradas como usuarios de DSi si queremos cuantificar de forma precisa el ciclo del Si a través de los ecosistemas marinos.

Primary production was studied in Fram Sound, part of the Hell Gate-Cardigan Strait polynya, from June to August, 1982. Primary production rates, phytoplankton biomass (chlorophyll α), and water transparency were measured and used in conjunction with modelled solar radiation values to numerically model primary production during this time. The major phytoplankton nutrients were also measured. Early season chlorophyll α concentrations were low, and the increased light availability due to reduced ice cover in this area did not appear to enhance early season production. Chlorophyll concentrations peaked twice; the first peak occured on 20 July and the second on 14 August. The mean primary production rate and phytoplankton biomass were 998 mg C.m⁻² .d⁻¹ and 72 mg chl.m⁻² . This production rate is higher than that measured in other High Arctic areas. Nitrogen, phosphorus and silica were essentially homogeneously distributed during the sampling period and these concentrations varied little from June to August except during 5 days in late August, when they decreased by half then returned to previous levels.
Applied Science, Faculty of
Civil Engineering, Department of
Graduate

Policy-makers increasingly need to use scientific data that are imprecise. This problem is particularly apparent for marine mammal management issues, where practical research constraints leave scientists and managers with the problem of drawing inference from sparse data. Effective use of such data therefore places great demands on our methods of data analysis and statistical inference. In this thesis I introduce novel Bayesian methods for the analysis of data on marine mammal abundance and trends. Bayesian methods are applied to a suite of case studies to inform current management issues of importance both in the UK and overseas. These include estimating the probability of density dependence in the growth of a killer whale (Orcinus orca) population inhabiting the inshore waters of Washington State; estimating the size of a widespread population of bottlenose dolphins (Tursiops truncatus) in the Bahamas; and assessing the population status and abundance trends of bottlenose dolphins within a newly designated Special Area of Conservation in the Moray Firth, NE Scotland. Each of these case studies uses model-based analysis of individual photo- identification data to make inference about unknown population parameters of interest. Specifically, Bayesian inference, based on "posterior" probability distributions and statements, is used to facilitate scientific reporting in the face of uncertainty about these unknowns. Additional issues addressed are the selection of alternative statistical models for inference based on posterior model probabilities; incorporating model selection uncertainty into inference through the estimation of model-averaged parameter estimates; and the use of random effects prior distributions to model the relatedness between unknown parameters and increase estimate precision. The application of these methods is accomplished through the use of Markov chain Monte Carlo sampling methods, which are implemented using the WinBUGS software.

Thesis (Ph.D.)--University of Adelaide, School of Earth and Environmental Sciences, Discipline of Environmental Biology, 2005?
"July 2004" Includes bibliographical references (leaves 150-172). Also available electronically.

Biological invasions are an important issue of global change and an increased understanding of invasion processes is of crucial importance for both conservation managers and international trade. In this thesis, I have studied the invasion of the brown seaweed Fucus evanescens, to investigate the fate and effect of a perennial, habitat-forming seaweed introduced to a coastal ecosystem. A long-term study of the spread of F. evanescens in Öresund (southern Sweden) showed that the species was able to expand its range quickly during the first 20 years after the introduction, but that the expansion has been slow during the subsequent 30 years. Both in Öresund and in Skagerrak, the species is largely restricted to sites where native fucoids are scarce. Laboratory experiments showed that the restricted spread of F. evanescens cannot be explained by the investigated abiotic factors (wave exposure and salinity), although salinity restricts the species from spreading into the Baltic Sea. Neither did I find evidence for that herbivores or epibiota provide biotic resistance to the invader. On the contrary, F. evanescens was less consumed by native herbivores, both compared to the native fucoids and to F. evanescens populations in its native range, and little overgrown by epiphytes. Instead, the restricted spread may be due to competition from native seaweeds, probably by pre-occupation of space, and the establishment has probably been facilitated by disturbance. The studies provided little support for a general enemy release in introduced seaweeds. The low herbivore consumption of F. evanescens in Sweden could not be explained by release from specialist herbivores. Instead, high levels of chemical anti-herbivore defence metabolites (phlorotannins) could explain the pattern of herbivore preference for different fucoids. Likewise, the low epibiotic colonisation of F. evanescens plants could be explained by high resistance to epibiotic survival. This shows that colonisation of invading seaweeds by native herbivores and epibionts depends on properties of the invading species. The large differences between fucoid species in their quality as food and habitat for epibionts and herbivores imply that invasions of such habitat-forming species may have a considerable effect on a number of other species in shallow coastal areas. However, since F. evanescens did not exclude other fucoids in its new range, its effect on the recipient biota is probably small.