Benthic algal ecology and primary pathways of energy flow were considered on the Squamish River delta at the head of Howe Sound, a fjord-type estuary. The study elucidated the structure and function of major autotrophic components of the estuarine ecosystem. Benthic algae were investigated with regard to species composition and distribution and the capacity for energy conversion, input to the system and storage. Comparisons were made with existing information on the vascular plant component of the ecosystem. The benthic algal community was studied by regular field sampling of major macroalgae and microalgal associations with a monitoring of physical-chemical environmental factors. Presence of an alga in the estuary was a function of its osmoregulatory capabilities. Establishment and temporal-spatial distribution patterns were controlled by substrate-habitat preference and availability and the interaction of light, interspecies competition, desiccation, temperature and salinity, light being of greatest importance. Carex lyngbyei Hornem., the dominant vascular plant, had a significant effect on distribution of benthic algae through light restriction during Its summer growth period and action as a substrate during the winter. Total species diversity, biomass and distributional area of benthic algae were greatest at the latter period. The effect of ecosystem structure on function was investigated by analysis of energy flux through major benthic algal producers. Comparisons were made of the total amount of energy input attributable to benthic algae and vascular plants. The importance of an algal producer to energy flux•m⁻² was a function of either high primary productivity, photosynthetic efficiency and caloric content, or in the case of diatom dominated micro-algal associations, high caloric content alone. Distribution, reflecting the presence of suitable substrate-habitat, modified this pattern. Macroalgae having high energy input•m⁻² (Monoetroma oxyapermum (Kutz.) Doty, Pylaiella littoral-is (Lyngb.) Kjell.) were of minimum importance to total energy input. Two microalgal associations (Association E, diatom dominated, Association G, Ulothrix flaoca (Dill.) Thur. dominated), each with low energy input-m but with wide distribution and high photosynthetic efficiency and caloric content contributed a total of 8H% of available energy attributable to benthic algae. Benthic algae account for a maximum of ca. 7% of total energy input to the delta ecosystem compared to ca. 90$ by vascular plants and 3% by addition of organic matter. The majority of energy for the detrital based ecosystem comes from vascular plants and becomes available after a lag period allowing decomposition. Benthic algae are significant to the ecosystem as a readily available, continually present energy source requiring little or no breakdown for utilization and not for total energy input. Energy is available as either dissolved or particulate organic matter. Of the latter, ca. 49$ is removed to the estuary, 33% incorporated into the sediments of the delta and 18$ used by consumers in the delta ecosystem. / Science, Faculty of / Botany, Department of / Graduate

Unicellular, eukaryotic organisms - known as protists - form the base of all aquatic food webs. Frequently, marine protists are divided into either phytoplankton or (proto)zooplankton. Phytoplankton use phototrophy to acquire their energy from light to fix carbon dioxide into organic carbon, while protozooplankton use phagotrophy to directly acquire organic carbon from their prey. Mixoplankton that employ mixotrophy, i.e. the combination of phototrophy and phagotrophy within one cell, are often neglected. However, many marine protists are mixoplankton and they are ubiquitous in the worlds’ oceans. In oligotrophic oceans, mixoplankton are the base of food webs and many harmful algal blooms are formed by mixoplankton. Yet, the concept of mixoplankton is slow to mature within coastal water management. This thesis hypothesizes that the whole protist community, including mixoplankton, needs to be taken into account to understand and predict the effect of anthropogenic pressures on coastal systems. This thesis is a cumulative summary of three papers that employ data analysis, model developments and modelling scenarios to test this hypothesis. As a study area the Southern North Sea was chosen as it is an exceptionally well sampled coastal sea that is forecast to be heavily modified in the future. In a first step, routine monitoring data from the Southern North Sea were analyzed. The data analysis showed that the relative occurrence of mixoplankton was highest in seasonally stratified, clear, dissolved inorganic nutrient depleted environments. In a second step, a mathematical model, called PROTIST, was developed with the aim to reproduce the trophic composition of protist communities across abiotic gradients. Not only was PROTIST capable of reproducing the trophic composition of protist communities in the Southern North Sea, a sensitivity analysis conducted on the model results also showed that the occurrence of mixoplankton in the Southern North Sea is driven mainly by the availability of dissolved inorganic phosphate and silica and not by the availability of light. In a third step, PROTIST was used in a 3D model scenario of the North Sea to research whether the planned intensification of seaweed aquaculture affects the composition of protist communities. Preliminary 3Dmodel results show that seaweed aquaculture in the Southern North Sea could decrease nutrient concentrations in winter and lead to an increase in mixoplankton biomass. Pooling the information gained from the different approaches, this thesis concludes that coastal zone management should take mixoplankton into account to understand and predict the effect of future anthropogenic pressures on coastalecosystems. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Biological invasions are a leading cause of biodiversity loss and cause extensive economic losses. Since its introduction to Europe, the invasive Pacific oyster (Magallana gigas) has successfully established far-reaching populations in Scandinavia. This achievement can in part be attributed to the species’ high tolerance to a wide range of environmental conditions. However, the temperature range for survival and reproduction of this species has not been fully evaluated and is poorly understood. The relatively cold climate of northern Europe was initially deemed unsuitable for Pacific oyster populations as potential habitat. This would prove to be a vast underestimation of the species’ adaptability, however, since populations are now widely distributed in the region and their range still expanding. Nevertheless, exposure to severe winter conditions has been demonstrated to cause mortality events and change the contemporary distribution of oyster populations. Such conditions are common in Scandinavia and their effects on the oyster population are yet to be assessed. The purpose of this study was to estimate the extent to which mortality occurred among the Swedish Pacific oyster populations as a consequence of the relatively severe conditions during the 2020/2021 winter. Additionally, these surveys sought to investigate the relationship between winter mortality and the oyster settlement depth distribution. Our observations showed that survival probability generally increased with greater settlement depth. This was in accordance with previous findings. Furthermore, we found that there was considerable variation between geographical locations, with survival rates ranging between 63-98%. The average survival rate across all sampling sites was calculated to 87%. This suggested that the mortality of Pacific oysters in the winter 2020/2021 was influenced by other environmental factors in addition to depth. This project primarily aimed to provide an estimate of the relationship between the settlement depth of oysters and survival probability in a year with medium cold winter temperatures in Sweden. Additionally, a secondary purpose of this project was to develop standard procedures for analysing the survival probability of oysters in Scandinavia using generalised linear mixed models.

Most of the reef's biodiversity remains undiscovered due to its complex tridimensional structure and the small size of the organisms that compose most of its biodiversity. To better understand the biodiversity of the major biological component of the reef environment (the cryptobiome), artificial cubic-like tools called Autonomous Reef Monitoring Structures (ARMS) were created to mimic the tridimensional nature of coral reefs. Here, I deployed 16 ARMS within four distinct benthic habitats on Tahla reef in the Red Sea (Saudi Arabia) to investigate how changes in reef habitats reflect changes in associated biodiversity of the cryptobiome. The following habitat types were selected after reef surveys and based on benthic coverage prevalence: i) Algae Pavement; ii) Rubble; iii) Plating corals; and iv) Branching corals. Habitats were located at the same depth contour (~10m), under similar exposure conditions and separated by at least 35m. The rugosity of the habitats was estimated based on the chain method, whereas monthly measurements of the physicochemical characteristics of the water were assessed by water collections (nutrients and chlorophyll a) and Conductivity-Temperature-Depth (CTD) instrument deployments (temperature, salinity). A fixed quadrat of approximately 15m2 was marked within each habitat type and four ARMS were deployed randomly within it. Units were retrieved after a period of approximately seven months for analysis of pioneer eukaryotic assemblages through traditional taxonomy identification of organisms larger than 2000μm, and through molecular metabarcoding using COI and 18S markers for the remaining ARMS fractions: sessile, 500μm-2000μm, and 106μm-500μm. To compare two distinct current methodologies to assess cryptobenthic taxa, water collections next to each ARMS unit were conducted right before retrieval. These samples were used to investigate the environmental DNA using the same COI and 18S markers. The biodiversity of the pioneer cryptobiome assemblage was analyzed through a combination of univariate and multivariate statistical methods. Overall, the habitats that showed greatest significantly distinct cryptobenthic community composition were Algae Pavement and Plating Corals, the ARMS and eDNA were defined as complementary techniques to assess the cryptofauna, and the use of a multi-marker approach increased the resolution of the cryptofauna characterization across different reef habitats.

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The global climate is strongly regulated by the oceans, which store carbon away from the atmosphere for long periods. In an effort to understand the role of the oceans in the carbon cycle, it is necessary to understand the nuances of specific regional and functional marine ecosystems. The continental shelf of the West Antarctic Peninsula (WAP) is one particularly important regional ecosystem that plays a vital role in the Southern Ocean carbon export. Within the seasonally productive marginal ice zone of the WAP, I sought to identify the long-term drivers of particulate organic carbon (POC) flux. The vast majority of exported POC on the WAP was previously found to be made up of krill fecal pellets. I provide evidence that supports the hypothesis that the inherent life cycle of krill drives the observed 5-year oscillation in POC export. At the end of their life cycle, when krill are at their largest body size, the WAP experiences anomalously high POC export events through the production and sinking of large, carbon-rich krill fecal pellets. Conversely, when krill are young and small, POC export is anomalously low. This pattern shows that ecology exerts a first-order control on the the biogeochemical cycles of the WAP. Upon identifying the source and driver of POC export on the WAP, I set out to determine the role heterotrophic bacteria play in POC flux attenuation. I collected krill fecal pellets on the WAP over three years and measured bacterial metabolic activity in terms of bacterial production and respiration, thereby identifying the amount of organic carbon within the sinking fecal pellets that is lost due to bacteria. Overall, fecal pellet POC turnover rate by bacteria is very low. The relationship between bacteria and POC is complex with each having an affect on the other. Despite varied reactions of the free-living bacterial populations to the presence of krill fecal pellets, a consistent pattern emerged in the concentration of nucleic acid within each bacterial cell. Access to fecal pellets increased the metabolic activity of the free-living bacterial population. This finding shows that the egestion of krill fecal pellets metabolically stimulates the surrounding bacterial community, even though bacteria play a minor role in fecal pellet POC flux attenuation. Though bacteria were found to play a minimal role in organic carbon uptake on krill fecal pellets, they are still vital members of the WAP ecosystem and biological pump. I next sought to identify which bacteria in particular were responsible for colonizing and consuming the fecal pellet POC. Krill fecal pellets were genetically sequenced after timed exposure to the free-living water column bacterial community. I found that there is an endemic population of bacteria that are associated with each population of krill and their fecal pellets. This community of fecal pellet-associated bacteria does not change over time, indicating little colonization by free-living bacteria. Krill fecal pellets, aside from being good agents of POC export, seem to be selective environments for certain specialized copiotrophic bacteria. Further, I find that only a small subset of these endemic copiotrophs actively partake in carbon consumption on krill fecal pellets. Overall, these results show that a small endemic, specialized bacterial community play an outsized role in krill fecal pellet POC degradation and flux attenuation, but that krill fecal pellets remain efficient agents of carbon export to the deep ocean.

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

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