Doctoral Theses / Doktorsavhandlingar Institutionen för marina vetenskaper

Permanent URI for this collectionhttps://gupea-staging.ub.gu.se/handle/2077/40511

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Ventilation of the Arabian Sea Oxygen Minimum Zone
(2025-09-23) Font Félez, Estel
Ocean deoxygenation, driven by climate-induced warming, stratification, and circulation changes, threatens marine ecosystems globally. The Arabian Sea hosts the thickest and most intense oxygen minimum zone (OMZ), maintained by an interplay between physical oxygen supply and biological consumption. This thesis combines observations from ocean gliders, autonomous floats, and numerical models to quantify how surface, mode, and dense marginal-sea waters ventilate the upper OMZ boundary across spatiotemporal scales. The surface mixed layer forms the interface between the ocean and atmosphere and plays a central role in oxygen ventilation through wind-driven and buoyancy-driven mixing. In the Sea of Oman, intraseasonal surface mixed layer variability is forced by Shamal-driven latent heat loss and submesoscale fronts, with the latter accounting for nearly 70% of the wintertime restratifying buoyancy flux and contributing to the timing of spring restratification. Mode waters (MWs) mediate the vertical transport of oxygen between the surface and ocean interior, acting as an oxygen reservoir and a buffer for oxygen demand in the OMZ. MW formation occurs annually in the northern Arabian Sea and biannually in the south, linked to the summer and winter monsoons, with regional variability shaped by advection and bio-optical modulation of heating absorption. Seasonal MW transformation is predominantly isopycnal, but diapycnal transformation becomes important at shorter timescales. We find that physical mixing - split nearly equally between isopycnal and diapycnal processes - accounts for about half of the observed oxygen variability in MW, while biological consumption contributes roughly one-fourth. Mesoscale eddies further amplify the physically mediated oxygen fluxes, nearly doubling them relative to non-eddy conditions. The estimated physical fluxes, together with high biological respiration within MW, underscore MW's central role in supplying oxygen to the OMZ and mitigating the biological oxygen demand that drives OMZ intensification. Dense water formation from marginal seas, such as the Persian Gulf Water (PGW) outflow, is another important pathway in supplying oxygen to the Arabian Sea OMZ. Intermittent shear-driven mixing enhances dissipation from double-diffusive processes below PGW. These conditions are co-located with large oxygen gradients at the upper OMZ oxycline, resulting in increased oxygen ventilation towards the ocean interior on short timescales. Altogether, this work demonstrates that small-scale processes are critical in controlling upper OMZ oxycline variability. These findings advance our understanding of key processes influencing oxygen dynamics within the OMZ, providing insights for estimates of water mass transformation and oxygen exchange, which can ultimately improve modeling and prediction efforts.
Clonality, connectivity, and conservation: Genomic insights into eelgrass (Zostera marina) across the Baltic and Scandinavian Seas
(2025-09-12) Ries, Stefanie R.
We are currently facing an extreme loss of biodiversity on a global scale, affecting many species. A critical aspect of this crisis is the erosion of genetic diversity, as it provides insight into a species adaptive potential in a changing environment. Investigating the genetic variation, particularly of foundation species (species that provide a habitat for many other species), is therefore important. The marine flowering plant eelgrass (Zostera marina, Linnaeus 1753) is a habitat provider in the Northern Hemisphere, sustaining a large number of associated species, and plays a significant role in sediment stabilization and carbon sequestration. This thesis aims to explore genetic variation, clonality, connectivity, and aspects of conservation of eelgrass along the Scandinavian coastlines. To achieve this, population genomic analyses were conducted at local, countrywide, and across- country levels covering wide areas of the eelgrass distribution in Norway, Sweden, Germany, Estonia, and Finland. Patterns of genetic variation and differentiation were examined, along with the environmental factors driving this variation. On a local scale (1s - 10s km) within Sweden, we found genetic differences between eelgrass meadows in sheltered compared to exposed sampling sites. Expanding to a regional scale (10s - 1,000s km), eelgrass meadows in the Skagerrak and Kattegat exhibit higher genetic diversity and lower clonality compared to those in the Baltic Sea, and at the species northern distribution limit in Norway. This pattern appears to be driven by the extreme environment of the Arctic and the Baltic Sea, with cold temperatures and short summers in the Arctic and the salinity gradient in the Öresund acting as a barrier to gene flow into the Baltic Sea. While the increased clonal reproduction can be a strategy for surviving in extreme environments, it can also lower genetic diversity and increase vulnerability. The thesis therefore further addresses how clones from facultative reproductive organisms influence population dynamics, genetic diversity, and the adaptive potential. Across the study area, genetic diversity within meadows increased when clones were included, suggesting that somatic mutations may contribute to adaptation, particularly within the isolated Baltic and northern Norway eelgrass meadows. Based on these results, more frequent application of direct comparisons between clone-included and clone-removed datasets is required. For conservation, meadows with high genetic diversity should be prioritized and monitored for shifts towards dominant clonal reproduction, which can signal environmental stress and a loss of adaptive potential.
Antarctic Winter Water: its role in Southern Ocean dynamics and sea ice variability
(2025-09-04) Spira, Theo
The Southern Ocean is central to the global climate system, connecting the world's major ocean basins and regulating intense exchange of carbon and heat between the atmosphere and deep ocean. Antarctic sea ice is a critical component to this system, influencing planetary albedo, modulating air--sea exchanges, and regulating the vertical structure of the upper ocean. In recent years, Antarctic sea ice has undergone an unprecedented and rapid change, shifting from a multi-decadal state of gradual sea ice expansion to a regime of low and variable coverage---proposed as a new sea ice state. The processes driving this transition, particularly the vertical ocean--ice interactions, remain poorly understood and models fail to reproduce the sea ice conditions. This thesis examines the role of Antarctic Winter Water---the remnant cold wintertime mixed layer sandwiched between the warm and fresh summertime mixed layer and the warm and salty subsurface ocean interior. I investigate Winter Water's role in the overturning circulation system, how it modulates vertical fluxes, and its contribution in shaping Antarctic sea ice variability, hypothesising that it acts as a stratification barrier. Using a circumpolar dataset of quality-controlled multi-platform \textit{in-situ} observations (including Argo, SOCCOM, MEOP seal-borne sensors, gliders and ship-based CTDs) spanning from 2004 to 2022, combined with satellite records of sea ice concentration and re-analysis output of various other parameters, I characterise Winter Water properties, quantify their role in recent sea ice changes, and assess regional variations in ocean--ice coupling. Four main studies underpin this thesis. First, I describe the seasonal cycle, spatial distribution, and export pathways of Winter Water, highlighting its role within the overturning circulation. Second, I show that from 2005–2015, Winter Water shoaled across much of the Southern Ocean, preconditioning the ocean for enhanced vertical ocean heat fluxes that contributed to the 2015 transition to a new sea ice regime. Third, I reveal that this transition was not circumpolarly uniform: contrasting hydrographic structures across sectors led to opposing regional sea ice responses. Finally, I demonstrate that giant iceberg melt in the Weddell Sea modifies Winter Water properties, increasing stratification and altering upper-ocean heat content. The findings identify Winter Water as a critical component of the Southern Ocean system. By regulating vertical heat exchange, Winter Water regionally influences sea ice distribution and ocean density structure. Improving the representation of Winter Water in climate models is essential for better projections of Antarctic sea ice and the Southern Ocean under continued climate change.
Tracking fjord biodiversity through space and time: exploring methods to define reference conditions with benthic foraminifera
(2025-08-19) O'Brien, Phoebe
This thesis aims to develop new methods to establish in situ reference conditions in nearshore marine environments, using morphospecies and sedimentary environmental DNA (eDNA and sedaDNA) metabarcoding analysis of the benthic foraminifera assemblages. The study focuses on well-studied fjord systems along the Skagerrak coast, to address “the estuarine quality paradox”, by delineating the anthropogenically produced environmental stress from that which is naturally a feature of transitional environments. Ecological Quality Status (EcoQs) assessment in environments that are most proximal to, and therefore disproportionally effected by, human activities is essential to preserve ecosystem services and mitigate further damage. Some key fundings of this thesis show that a) SedaDNA preservation is increased in low-oxygen environments that lack bioturbation, meaning this methodology could be particularly effective in areas effected by both natural and human enduced eutrophication B) Diversity indices calculated from morpho-taxonomic and genetic assemblages show coherent response to both contemporary and historical variation in environmental conditions C) SedaDNA analysis can help to resolve the ecological preferences of otherwise under studied taxonomic groups, such as monothalamids. Taxa consistently found to be associated with polluted, or stressed environmental conditions could represent novel indicator species for future biomonitoring studies. The ultimate goal of this thesis is to demonstrate that by integrating benthic foraminiferal morphospecies and genetic diversity, sensitivity and multimeric indices for use in biomonitoring; benthic foraminifera hold a high potential as a ‘biological quality element’ (BQE) in anoxic or polluted coastal environments, in which traditional monitoring strategies such as macrofaunal community analysis are not applicable.
Oysters in Scandinavia: Status and Threats
(2025-04-24) Robert, Chloé
Flat oysters, Ostrea edulis, are native to European waters. Wild populations have declined in the past decades, mainly due to overfishing and the introduction of parasites. Oyster farms have been extensively developed, with regular translocations of stocks between countries resulting in the homogenisation of genetic diversity. However, Swedish populations in the Skagerrak and Kattegat are exceptions, as fishing laws have historically protected them from overharvesting, and Swedish waters have been free from the parasites found in other European stocks. However, oysters in this geographic area have not been well-studied and although largely protected from external threats, they will face challenges in the future, including ocean warming and the proliferation of the invasive Pacific oyster, Crassostrea gigas. This thesis aimed to assess the status of the Scandinavian oyster populations with a particular focus on the Swedish populations. In this process, I investigated four distinct but related aspects of oyster biology to evaluate the effects of potential threats to their resilience and persistence. First, I investigated the current population structure of Scandinavian flat oysters to assess genetic diversity in northern Europe (Paper I). Using genomic tools, I found that the populations in the Skagerrak are genetically homogeneous and form a single panmictic population. This indicates that individuals may be translocated among sites within this water body without risk of genetic change. I also assessed how projected environmental change, specifically increased temperature, affect flat oysters from the Skagerrak (Paper II). During experiments, I monitored physiological responses (feeding and respiration rates) and gene expression. Surprisingly, flat oysters survived short-term (3 day) exposure to temperatures up to 32 °C, suggesting that flat oysters in Sweden may tolerate acute exposure to marine heatwaves, though not necessarily long-term warming. Given that flat oysters are widely cultivated in hatcheries, I investigated the genetic impacts of domestication to assess whether this leads to predictable genomic changes (Paper III). The study included both wild and cultivated oysters from Sweden and from Scotland/Ireland. I found significant genomic divergence between cultivated and wild populations after only three generations, stressing the importance of regularly supplementing hatchery stocks with wild individuals. Finally, as the Pacific oyster has rapidly colonised the Skagerrak, I investigated its adaptive potential to new salinity conditions through crossing experiments (Paper IV). Results showed that this invasive species has become capable of reproducing in low-salinity waters, suggesting a potential to colonise the brackish waters of the Baltic Sea in the future. This thesis contributes to a better understanding of population dynamics, genetic variation, and environmental responses of flat and Pacific oysters in Scandinavia, with direct implications for conservation and aquaculture management.
Spatial distributions and temporal changes of coastal bivalve populations
(2025-03-21) Greeve, Youk
Bivalves are common animals in coastal ecosystems that alter energy flows and the characteristics of their surroundings, which contributes to ecosystem functions and services. Most bivalve species are suspension-feeders, clearing the water from organic particles and phytoplankton and thereby lowering water turbidity and exert top-down control on phytoplankton communities. Faeces are deposited on the sea floor, coupling the pelagic and benthic ecosystem components and enhancing the long-term storage and remineralization of nutrients which is important for mitigating negative effects of eutrophication. The infaunal species’ burrowing behaviour reworks the sediment which increases the flux of oxygen and other solutes between sediments and water, while epifaunal species create complex reef structures that can be utilized by other species promoting biodiversity. Globally, much of the epifaunal bivalve reefs have been greatly diminished, resulting in a loss of function and services, while invasive species have been introduced in many areas causing shifts in ecosystems. The aim of this thesis was to describe the coastal bivalve communities on the Skagerrak coast in terms of species composition, distribution, abundances and biomass. This was done in order to identify key species, functional groups and habitat types that contribute to ecosystem functions and services. Recently collected data was contrasted against older records to access temporal changes in the structure of the bivalve populations. The possible underlying mechanisms to these changed and the potential consequences for ecosystem functioning was also explored. The results showed that populations are shaped by a combination of environmental factors, species habitat preference and the availability of those habitats. While epifaunal species are overall more ecologically relevant than infaunal species, the later can be locally more impactful. Since the invasive Pacific oyster arrived it has become the dominant species in terms of biomass which has, together with a general decline of infaunal bivalves, likely caused shifts in bivalve ecosystem functions and services. The methods and analyses described provide an important current baseline for the bivalve populations in this area and to compare further changes to in the future.
Tiny titans: Impact of Meiofauna diversity and activity on coastal sediment biogeochemistry
(2024-11-11) Maciute, Adele
Chemical reactions in marine sediments and the resulting fluxes across the sediment-water interface influence ecosystem functioning, global carbon cycling, and ultimately global habitability. Although previous research has recognized the major role of microorganisms and macrofauna (invertebrates > 1 mm), it still debated whether meiofauna (invertebrates < 1 mm) can make significant contributions to ecosystem functioning due to their small size. This motivated me to estimate meiofauna contribution to total oxygen uptake and methane release from the sediment, and further investigate meiofauna activity and diversity under environmental perturbations, such as microplastic pollution and climate change. In this thesis, I described a microsensor-based method for respiration measurements, with ability to induce desired experimental conditions (paper I). This method revealed that traditional theoretical estimates of respiration can lead to a four-fold overestimation of measured rates. Although respiration rates were highly variable within each meiofauna group, rates were lower (and thus contribution to ecosystem processes was smaller) under hypoxic compared to oxic conditions (paper II). Macrofaunal bioturbation significantly enhanced methane release from coastal sediments, but this effect was somewhat offset by meiofauna due to interactions with microorganisms (paper III). Bioturbation depth, however, was reduced when communities were exposed to microplastic pollution (paper IV) which may affect organic matter mineralization and nutrient fluxes over longer periods. Lastly, climate change is intensifying environmental stressors such as river discharge and coastal erosion, which were shown to affect meiofauna community, but not nematode diversity (paper V). In addition, nearshore habitats, which are particularly impacted by these stressors, favored colonizer-dominated nematode communities, whose future dominance may reduce ecosystem stability as river discharge and coastal erosion increase. Overall, the results provide new insights into meiofauna’s role in sediment biogeochemistry by quantifying its contribution to essential ecosystem processes. This thesis presents the first direct measurements of respiration rates for specific meiofauna, the first investigation of macrofauna-meiofauna-microorganism interaction effects on methane release, impact of microplastics on bioturbation, and the application of molecular tools to study metazoan diversity in Siberian Arctic. The presented findings are especially relevant as growing oxygen-deprived bottoms, intensifying microplastic pollution, and accelerating climate change increasingly threaten marine ecosystems. Such ecosystem-level changes may negatively impact meiofauna and could potentially lead to previously overlooked cascading effects on sediment biogeochemistry.
Methane offsets to carbon sequestration in coastal ecosystems
(2024-11-08) Yau, Yu Yan Yvonne; Yau, Yvonne
Mangroves, saltmarshes, and seagrasses are known as blue carbon ecosystems because of their high rates of productivity and efficiency in sequestering carbon. Carbon can be stored in sediments, biomass, exported laterally to the coastal ocean, or returned to the atmosphere as carbon dioxide (CO2) and methane (CH4). CH4 is a greenhouse gas with global warming potential 34-86 times higher than CO2 on a mass basis. CH4 is often produced in anoxic, carbon-rich sediments during carbon degradation. CH4 emissions to the atmosphere potentially offset some of the carbon sequestration in blue carbon ecosystems. A broad literature compilation showed that aquatic CH4 fluxes may reduce their net sediment carbon sequestration by up to 7000% in saltmarshes, 3500% in mangroves, and 900% in seagrass meadows. These earlier observations have great spatial variability and large uncertainties, and often do not separate local methane from upstream freshwater sources. In this thesis, I performed high resolution continuous dissolved CH4 measurements in surface water from various coastal marine ecosystems in Brazil, Spain, China, and Iceland. I estimated sea-air CH4 fluxes and evaluated the biogeochemical processes driving the production and oxidation of CH4. The investigated coastal vegetated ecosystems inputs acted as a net CH4 source (mangroves: 75 ± 190 µmol m-2 d-1; saltmarsh: 3.0 ± 2.0 µmol m-2 d-1; seagrass: 0.1 ± 0.1 µmol m-2 d-1). Tidally-driven porewater exchange was an important source of CH4 in mangroves and saltmarshes, but not in seagrasses. The lack of major external freshwater inputs led to relatively small methane fluxes in the investigated blue carbon ecosystems. Overall, my observations revealed that water-air CH4 emissions offset only 1 to 8% of the sediment carbon sequestration rates in these marine ecosystems, underscoring the important role of coastal vegetated ecosystem as a carbon sink.
Drivers affecting seagrass meadows: An approach for conservation and restoration in Mozambique
(2024-09-30) Cossa, Damboia
Seagrasses and other shallow-water vegetation are important coastal habitat because they provide many ecosystem services, including food, shelter and nursery areas of shellfish and finfish as well as marine endangered species such as dugongs and sea turtles. However, following a worldwide trend, seagrass meadows in Mozambique are experiencing a reduction in area due to a combination of natural disturbances and anthropogenic impacts. The aim of this thesis was to assess two relevant drivers affecting seagrass ecosystem services, while contributing to developing innovative management tools for conservation, restoration and sustainable use of this ecosystem in Maputo Bay, Mozambique. The thesis focuses on the impacts from both global (ocean acidification, OA) and local (fishing) stressors on marine invertebrates and dugongs. The thesis also aims to develop innovative methods for shallow-water monitoring using drones and machine learning as well as developing appropriate seagrass restoration techniques. Paper I evaluates the biological response (growth rate and net calcification) of a marine calcifier (sea urchin), to different levels of variability of pCO2/pH imposed in the absence or presence of seagrass in the context of OA as a global stressor. The results showed that larvae growth rates significantly decreased with decreasing average pH in both absence and presence of seagrass. Moreover, larvae raised in presence of seagrass, maximized calcification during the day, and lowering their calcification during the night. These results have implications to better understand the mechanisms behind the sensitivity of organisms to OA in variable coastal ecosystems. Paper II shows the influence of gillnet fishing activities as a local stressor on dugong feeding grounds. A drone survey revealed overlap between dugong foraging areas and fishing grounds, increasing the risk of dugong entanglement when the gillnets are deployed at Inhaca Island, Mozambique. Thus, management initiatives to control gillnet fishing activity with involvement of the local community were highlighted to support future conservation efforts. A survey on local ecological knowledge was used in paper III to assess community perceptions at Inhaca Island on both global and local stressors in seagrass meadows, while evaluating how fishing communities are adapting to face potential future changes of seagrass habitats and associated services. Results showed that the fishing community at Inhaca Island depends on fishing activities for their basic livelihood, and they perceived sedimentation associated with floods as the leading cause of seagrass changes, followed by destructive fishing practices. A decrease in coastal protection and loss of habitats (and associated invertebrates and fish) are perceived as the main threats to their livelihood and wellbeing. Paper IV presents a field experiment to restore seagrass (Halodule uninervis), which is used as food by dugongs, with the aim to assess infauna biodiversity and colonization after planting. Two planting methods were tested, including a plug method and a single shoot method applied with two seagrass shoot densities. Results showed that the both methods influenced the transplants growth with consequences for the infauna abundance and composition. The results of this thesis are discussed in an integrated approach to understand both global and local drivers of changes in seagrass meadows in Maputo Bay, Mozambique, while proposing an effective conservation and management strategies, which include the use of innovative technologies such as drones, involvement of local communities and restoration approaches to enhance the role of seagrass as an important coastal ecosystem.
Carbon outwelling and greenhouse gas exchange across mangrove seascapes
(2024-08-09) Cabral, Alex
Mangroves, renowned for their high primary productivity and carbon burial rates, play a crucial role in the ocean carbon cycle. However, uncertainties persist regarding the fate of mangrove-derived carbon across seascapes. This doctoral thesis addresses these uncertainties by quantifying mangrove vertical water-atmosphere and horizontal mangrove-ocean exchange, an often-overlooked pathway for carbon sequestration and greenhouse gas exchange. I combine new regional-scale observations with comprehensive global-scale reviews to better understand mangrove carbon fluxes. I used radium isotopes to quantify carbon outwelling across several spatial scales, from porewater to the continental shelf. My results demonstrated that the mangrove-derived carbon is rapidly exported to the continental shelf mostly as bicarbonate, increasing the perceived carbon sequestration capacity of mangroves when compared to soil carbon burial alone. My findings also revealed that mangroves not only act as sources of carbon dioxide (CO2) and methane (CH4) but also as sinks for nitrous oxide (N2O). A global mangrove N2O sink can offset 18% of global mangrove CH4 emissions over a 20-year time horizon. Furthermore, neglecting lateral exports could underestimate CH4 emissions by up to 50% in relation to water-atmosphere fluxes. Global porewater-derived CO2 emissions represents 25% of the mangrove net primary production and are twice the estimated global sediment carbon burial rates. Overall, my thesis revels complex carbon flux pathways in diverse mangrove seascapes and emphasizes the importance of incorporating lateral transport and multiple greenhouse gases to resolve the net climate change mitigation potential of blue carbon ecosystems. The significant role of outwelling, particularly as bicarbonate, highlights the need for further research on the long-term fate of mangrove-derived carbon in the ocean. Moreover, my findings shift our perception of mangroves as N2O sources to N2O sinks that partially offset their methane emissions. Integrating multi-scale observations and diverse geochemical tracers was essential to build a more comprehensive understanding of mangrove carbon cycling and its implications for climate change mitigation strategies.
The role of chromosomal inversions in rough periwinkle snails (Littorina saxatilis)
(2024-04-15) Reeve, James
Chromosomal inversions are genomic rearrangements that may have a major role in local adaptation, facilitating ecotype formation and speciation. Recombination can hinder these processes as it breaks apart beneficial combinations of alleles, mixing them with alleles brought in by gene flow. Inversions suppress recombination, preventing the breakdown of beneficial allele combinations. Thus, they are expected to harbour loci influenced by habitat-driven selection. Sharp habitat transitions between boulder fields and rocky shores have been used to study the genetic basis of habitat-driven selection in the intertidal snail Littorina saxatilis. Snail populations are adapted to different environmental pressures on each side of these habitat transitions. A Crab ecotype that is resistant to predation in boulder fields, and a Wave ecotype that is present in rocky shores and has adapted to resist being swept away by strong waves. Hybrid zones join these ecotypes, where strong changes in phenotype and shifts in allele frequencies have been observed. Eighteen inversions have been found with shifts in arrangement frequencies across the L. saxatilis hybrid zones. Three of them have a strong association to Crab-Wave ecotype formation, two are related to shore height adaptation, and three are linked with sex determination. However, much of our understanding of L. saxatilis inversions comes from sampling across hybrid zones, from a handful of sites in Sweden. This sampling may not reflect the role of inversions across the species’ range. I investigated the broader roles that these inversions have in adaptation across a range of Swedish habitats, and their broader role across the species range and in other Littorina species. I show that most inversions have links to local environmental variation, not just at the major habitat boundary between the Crab and Wave ecotypes (Chapter 1). Extensive local sampling showed that ecotypes are the extreme ends of a continuum of phenotypic diversity, and all inversions have roles in local adaptation across multiple environmental gradients (Chapter 2). At the broader taxonomic scale, I found the inversions are distributed across the species range and across species boundaries, suggesting they are ancient (Chapter 3). This suggests inversions contribute to the parallel evolution of ecotypes across European coasts. Inversions are, however, not linked to the different reproductive modes of L. arcana and L. saxatilis, demonstrating that speciation can proceed without ecological divergence (Chapter 4). The key findings of this thesis are that inversions are widespread in their geographic and taxonomic distributions, and that most of them have roles in local adaptation. Littorina is a good system for studying the roles of inversions throughout speciation, as each inversion tells a separate, yet linked story over a long process of divergence.
On the generation of Maud Rise polynyas in the Weddell Sea
(2024-04-12) Gülk, Birte
The Weddell Sea is a region prone to the formation of open-ocean polynyas. Open-ocean polynyas are offshore openings of sea ice in the winter season, often accompanied by deep convection. Deep convection allows for the homogenization of the water column and the intense exchange of heat and gasses between the deep ocean and the atmosphere making them important for the forma- tion of deep waters. In the 1970s, large polynyas were observed in the central Weddell Sea, called Weddell Sea polynyas. The Weddell Sea polynya has not reoccurred since, sparking questions about their frequency and climate relevance. Instead smaller and short-lived polynyas have irregularly occurred in the vicinity of Maud Rise, a seamount in the eastern Weddell Sea, most recently in 2016 and 2017. The interaction of Maud Rise with the large-scale ocean circulation in the Weddell Sea, the Weddell Gyre, forms two prominent hydrographic features: a warm-water Halo and a Taylor Cap. The Taylor Cap sits above Maud Rise and the warm-water Halo encircles it. Our knowledge of the processes and dynamics in the region of Maud Rise is based on a scarce number of observations. Various processes for the generation of the Maud Rise polynya have been proposed, and the adequate representation of Maud Rise polynyas in ocean models remains a challenge. This thesis proposes to investigate the mechanisms leading to the generation of the 2016 and 2017 polynyas, and provides a modeling approach for the adequate representation of these events in ocean models. In this thesis, publicly available observations and newly gained SO-CHIC observations from 2022 are used, as well as two reanalyses and two new regional ocean model configurations. This thesis revealed large interannual variability of the Halo and Taylor Cap with a period of a near-vanishing Taylor Cap in the years preceding the polynya opening. The variability is largely controlled remotely through the advection of anomalous water masses from the Weddell Gyre. The flow-topography interaction of the Weddell Gyre and Maud Rise enhances the chances of polynya opening by generating anomalies in the stratification. These anomalies are found to be related to the Taylor Cap and depend on the strength of the impinging flow. Further, the role of thermobaric effects on ambient stratification is important in triggering the 2016 polynya. The numerical simulation highlighted that the 2016 polynya preconditioned the region for the 2017 polynya. The 2017 polynya was enabled by an Ekman transport of salinity from the Taylor Cap to the Halo destratifying the region immediately north of the rise. In summary, this thesis highlights the complexity of processes at play in the most recent polynya events at Maud Rise and emphasizes the role of the ocean. Moreover, it shows the importance of improving the available convection parameterizations to improve deep convection and polynyas in ocean models.
From alpha to beta ocean: Exploring the role of surface buoyancy fluxes and seawater thermal expansion in setting the upper ocean stratification
(2023-12-05) Caneill, Romain
The ocean plays a central role in the climate system by absorbing excess anthropogenic heat and carbon dioxide. Moreover, the ocean circulation distributes heat from the tropics towards the poles. Due to the large ocean stratification, vertical exchanges between the ocean interior and the surface are limited. Subduction links the ocean surface and its interior and occurs in winter at mid- or high-latitudes, where the mixed layers (MLs) are deep. In subtropical regions, temperature and salinity decrease below the ML. Temperature has thus a stabilising effect, while salinity has a destabilising effect, a stratification regime called alpha ocean. Opposite, in polar regions, temperature and salinity increase below the ML, and salinity is the stabilising factor, a regime called beta ocean. In between these two regimes lies the polar transition zone (PTZ), where both temperature and salinity are stabilising. Despite the importance of the alpha-beta distinction, the underlying mechanisms controlling these regimes remain unclear. This thesis investigates the factors influencing the upper ocean stratification and the deep MLs adjacent to the PTZs. From observational profiles, we produce novel climatologies of the upper ocean properties. These climatologies confirm that MLs are deep on the poleward flanks of the alpha oceans. Deep MLs are also present in the beta ocean along the coast of Antarctica. In winter, the transition between the different regimes is abrupt. In summer, both temperature and salinity stratify almost the entire ocean. Based on idealised numerical simulations and observations, we find that the buoyancy fluxes largely determine the position of the PTZ. By stabilising the water column poleward of the PTZ, buoyancy fluxes inhibit convection, permitting beta-ocean formation. The exact position of the PTZ and the adjacent deep MLs are determined by the competition between the winter buoyancy loss and the strength of the existing stratification. Importantly, the impact of heat flux on buoyancy is scaled by the thermal expansion coefficient (TEC). The TEC is a strong function of the temperature, a property unique to water. This diminishes the buoyancy fluxes over cold waters. We find that the local value of the TEC in the subpolar region is of paramount importance in controlling the winter buoyancy loss and stratification, and thus the position of the PTZ. A larger TEC value would cause the alpha ocean to extend poleward, inhibiting beta-ocean formation. Considering the importance of the beta ocean in sea-ice formation, the Earth’s climate is influenced by the TEC values, which are directly linked to the ocean surface temperature. In summary, this thesis enlightens the central role of the TEC in modulating buoyancy fluxes and thereby controlling the alpha-beta ocean distinction.
Connections between biodiversity and ecosystem functioning in large-scale natural ecosystems
(2023-11-21) Hagan, James
Billions of years of evolution have given us a planet that supports a remarkable diversity of life. Estimates for the number of Eukaryotic species frequently number in the millions and the Prokaryotes are much more diverse than that. This biodiversity makes up the ecosystems that we, as humans, rely on to sustain almost every aspect of our lives. But, despite our reliance on these biodiverse ecosystems, we are eroding them at an alarming rate through habitat destruction, overexploitation and our transformation of the climate. Indeed, some estimates suggest that the rate at which species are going extinct is as high as previous mass extinction events that have sporadically occurred throughout earth’s history. How will this loss of biodiversity affect the functioning of ecosystems that we rely on? How much biodiversity do we need for healthy ecosystems? These are some of the questions that researchers began to address in the early 1990’s. Based on hundreds of experimental manipulations of biodiversity, there is a general scientific consensus that biodiverse ecosystems tend to be more stable and more productive than depauperate ones. However, much of this work has taken place in artificial, experimental systems and at small scales of space and time. Thus, several questions remain. For example, if small-scale experiments show that biodiversity is important for ecosystem functioning, will the effects be the same at large scales? If ten species are required to maximise ecosystem functioning in a one square meter experimental grass patch, how many are required in a whole meadow, or in a landscape with many meadows? In my thesis, I attempt to extend our knowledge so we can better understand the consequences of biodiversity loss in natural systems and at larger scales of space and time. In Paper I, I re-examined experimental work on biodiversity and ecosystem functioning from the last 30 years through the lens of community assembly theory. The aim was to understand what these experiments may tell us about how biodiversity loss will impact ecosystem functioning in natural ecosystems. My analysis showed that there are probably many cases where the results of experiments will not easily transfer to natural ecosystems. Rather than studying the community of species present in a local place, as is done in the experiments, I argue that we should instead focus on the pool of species present in the whole landscape, and the processes that govern the composition of local communities. Many experiments performed over the last 30 years have shown that a high-diversity community of species is only rarely higher functioning than the highest functioning single species (i.e. monoculture). In Paper II, I used a set of theoretical simulations, an experiment in a bacteria-based model system, and a synthesis of previously published experiments to show that this may be because experiments have been performed in relatively homogeneous environments. When environmental heterogeneity increased, we found that the functioning of diverse species mixtures increased relative to the highest functioning monocultures. But, despite the general trend observed in Paper II, there were many experiments in the synthesis where a single species in monoculture was highest functioning across the range of environmental conditions. This contradicted many theoretical models for the effect of biodiversity on ecosystem functioning. Thus, in Paper III, I wanted to study species along an environmental gradient to see if we would obtain similar results. I did this using a transplant experiment with four common species of marine seaweeds on Swedish rocky shores. These species occupy relatively distinct depth zones on the shores, which are characterised by different environmental conditions. I thus hypothesised that the four species would grow best at the depth where they are most common. Counter to my predictions, the experiment showed that only one species responded strongly to being transplanted to a different depth zone. For Paper IV, I took the results obtained from Paper III and attempted to model what would happen to the biomass production of the seaweed communities if each of the four species went extinct. I found that the biomass production of these rocky shore communities would probably only be strongly affected if one of the seaweed species (Fucus vesiculosus) went extinct. This is because the four species showed high productivity outside of the depth zones where they are naturally found and, therefore, may be able to compensate for the loss of any of the other species. Arguably the most direct way to calculate an effect of biodiversity on ecosystem functioning is to compare a mixture of interacting species to a null expectation where species do not interact based on species’ functioning in monoculture. However, in natural systems, this is generally not possible because we rarely have natural monocultures. In Paper V, I developed a Bayesian analytical pipeline to impute missing monoculture data which enables comparisons of mixtures and monocultures in natural ecosystems. Combined with a previously developed statistical partition, I was able to show that a combination of local-scale species interactions, local-scale dominance by a few high functioning species and spatial niche partitioning all contributed to a positive effect of biodiversity on ecosystem functioning in two, natural marine ecosystems. Based on these five papers, I conclude that the hundreds of experiments that have been done to date provide useful but imprecise information about how biodiversity loss may affect the functioning of natural ecosystems. To understand the ecosystem-level effects of biodiversity loss more thoroughly, we will need to carefully study how biodiversity is changing across multiple scales of space and time and use methods that can detect the consequences of these changes. Papers IV and V suggest avenues for how this may be done.
Seaweeds as a future protein source: innovative cultivation methods for protein production
(2023-10-20) Stedt, Kristoffer
As the global population is projected to reach approximately 10 billion people by 2050, it is estimated that we will need to produce up to 60% more food compared to 2010. Although the current food production system contributes to 25% of greenhouse gas emissions worldwide, accounts for 70-80% of eutrophication and freshwater usage, and occupies half of all ice- and desert-free land, it fails to meet the global nutritional needs. Furthermore, with extreme weather events and heat waves affecting terrestrial food production systems, it is evident that we need to look elsewhere to produce sustainable, protein-rich, and nutritious food. Recently, seaweeds have emerged as a promising part of this solution. Cultivating seaweeds requires no arable land, freshwater supply, or high nutrient input. Furthermore, seaweeds have high productivity that outperforms many terrestrial crops such as wheat, seeds, and soybeans. The protein often contains all the essential amino acids, making seaweeds a favorable protein source for human consumption. However, even though seaweeds often have protein contents in the range of some beans and pulses, it is lower than in soybeans. Therefore, their protein content needs to be increased if seaweeds are to become a competitive protein source in the future. This thesis aims to explore the potential of seaweeds as a sustainable future protein source. It specifically focuses on optimizing seaweed cultivation to boost both growth rates and protein content. To achieve this, the effects of different cultivation conditions and the potential of one kelp and three green seaweed species are investigated. A novel nutrient loop is explored, wherein industrial food production process waters (FPPWs) are used as seaweed growth media. By conducting a meta-analysis, as well as land-based experiments that combine physiological, biochemical, chemical, and sensory analyses, the thesis aims to establish the potential for seaweed cultivation in nutrient-rich process waters. The findings from this thesis show that seaweeds can become a promising alternative food source in the ongoing dietary protein shift. The results show that all groups of seaweeds (brown, green, and red) can be cultivated in various nutrient-rich process waters; but green seaweeds have the highest potential. After identifying the green seaweed species Ulva fenestrata, which usually has a crude protein content of 10-20% dry weight, as a promising candidate, its cultivation in FPPWs yielded protein content of up to 37% dry weight. Furthermore, the biomass yield was up to six times higher compared to when grown in seawater. The safety aspects of consuming the biomass were confirmed by showing that large quantities of the biomass can be consumed every day without exceeding health-based reference points for heavy metals. Also, no sensory attributes regarded as negative were found after cultivation in the FPPWs. In conclusion, this thesis illustrates a novel nutrient loop, where the disposal of industrial food production process waters can be turned into nutrient-rich and valuable biomass through seaweed cultivation.
Survivors of the Sea: Investigating the genomics and survival strategies of the diatom Skeletonema marinoi
(2023-09-14) Pinder, Matthew
Diatoms are an ecologically important group of phytoplankton, responsible for around 20% of global primary production. One of the features contributing to their success is their ability to form resting stages, a response to adverse conditions in which they enter a dormant state and sink to the sediment. While some resting stages may germinate upon the return of favourable conditions and become resuspended, others can become buried in the dark, anoxic sediment for long periods, retaining their viability. Resting stages of some species have been revived in the lab after over a century, yet the precise mechanisms behind this ability to survive so long in this state is not well understood. One such species capable of forming long-lived resting stages is Skeletonema marinoi. The draft reference genome of this marine diatom was recently assembled and annotated, and thus my thesis has involved using this genome as a tool to explore the species and investigate its resting stage survival. In paper I, the use of ancient diatom DNA (i.e. DNA obtained from revived diatom resting stages) in research was reviewed, with particular attention to S. marinoi. While much insight has already been gained using this resource, developments in several fields have led to exciting prospects for future research. In papers II and III, I compared gene expression between vegetative cells of S. marinoi, and resting stages induced by exposure to darkness, anoxia, and nitrogen starvation. After re-exposure to nitrate, the resting stages’ gene expression was measured using RNA sequencing over the course of six months. In paper II, I performed a differential expression analysis to determine which processes were active in this ‘dormant’ life stage. Much of the resting stages’ central metabolism has undergone shifts in expression, and genes involved in protein synthesis were upregulated throughout the resting stage. In paper III, I examined the RNA sequencing results from the perspective of allelic expression bias, and identified a handful of genes showing significant shifts in expression bias between alleles between vegetative and resting cells. Of these, I noted several that formed complete pathways related to the formation of diatoms’ silica cell walls. Lastly, in paper IV, I developed a bioinformatic tool – Bamboozle – to identify novel, intraspecific genomic barcoding loci, capable of tracking the relative abundance of multiple strains of S. marinoi in co-culture over time. This tool was initially applied to 54 strains of S. marinoi, revealing loci that enabled subsequent tracking of strains during an artificial evolution experiment. Bamboozle has been further developed to accommodate haploid organisms, and was used to identify intraspecific barcoding loci in the model green alga Chlamydomonas reinhardtii. The results of this thesis provide insights and highlight further questions regarding diatom resting stages, as well as providing a novel tool for studying these fascinating phytoplankton. Application of additional omics methods to diatom resting stages in future, and testing of Bamboozle on natural diatom populations, should both lead to further understanding of this taxon.
Single cell carbon and nitrogen dynamics in chain forming diatoms, including their resting stage
(2023-08-10) Stenow, Rickard
The oceans are a fundamental part of all life on earth, accounting for more than half of Earth’s oxygen production. The ocean is also key to long term carbon dioxide sequestration. Diatoms are a group of phytoplankton differentiated by their silica shell/frustule and account for ~20% of global primary production. Some of these diatoms form colonies/chains which are viewed as a way to reduce grazing pressure, but also effect aggregation, sedimentation, and nutrient assimilation. Exponential growth conditions during algae blooms have been well studied. Less is known about how they survive between blooms when conditions are no longer optimal. In nature, high nutrient availability in the photic zone and subsequent blooms only last a few weeks. Growth limited conditions persist for most of the year. In chapter I and II, shifts in carbon and nitrogen assimilation dynamics were investigated in two chain forming diatoms: Chaetoceros affinis (I) and Skeletonema marinoi (II) at the beginning of nitrate limitation. C. affnis which are often larger than S. marinoi and are relatively more abundant during summer conditions with low nitrate availability. Skeletonema produce smaller cells and dominate at the beginning of blooms, where they thrive and assimilate excess nitrogen. C. affinis produced exudates of sugars and was colonized by attached bacteria that assimilated both carbon and nitrogen derived from their host. Later, diatoms were remineralised by bacteria, releasing ammonium. This ammonium could balance carbon assimilation for active diatoms. I speculate that cells in chains could benefit from remineralization of other cells in the chain and supply active cells with ammonium. S. marinoi showed no difference in carbon and nitrogen assimilation depending on chain length. The cells assimilated nitrate at a rate 25-65 times lower than the diffusive supply could provide, when compared to modelled diffusive supply from the ambient water. This indicated that cells were limited by biological uptake rates rather than diffusive supply. In chapter I and II, I demonstrated that C. affinis and S. marinoi had different ways of dealing with nitrate limitation, corresponding to the niches they fill. C. affinis recirculate the nitrogen with help of bacteria, which would allow them to keep a standing population in low nitrogen availability between blooms. S. marinoi on the other hand assimilated an excess of nitrogen during high availability, where they usually dominate. In addition to playing a key role in primary production and nutrient turnover, diatoms also contribute to particle transport from the photic zone to the sediment. Diatoms form resting stages which can survive decades to centuries in dark and anoxic sediments. Mechanism of survival is unknown, and they have previously been considered as “dormant” in the sediment. Basic mechanisms for cell maintenance in resting stages of S. marinoi were investigated in chapter III. I showed that they were able to assimilate both nitrate and ammonium in dark and anoxic conditions. The nitrogen specific generation time varied between 23-500 years which may be enough to maintain viable cells, but not for growth. In chapter IV, I investigated if resting stages could use nitrate as an electron acceptor and assimilate organic molecules available in the sediment (acetate and urea). The resting stages performed dissimilatory nitrate reduction to ammonium (DNRA) and assimilated N from urea. They could not assimilate carbon from urea but assimilated carbon from acetate. Hence, the sediment provides resting stages with both carbon and nitrogen for assimilation and respiration. I have shown that diatom resting stages are not as dormant as previously assumed. I also showed that two common chain forming diatoms have different mechanisms of circumventing reliance on nitrate diffusion from the ambient water. The next step is to connect this to marine monitoring and prediction models taking chain formation into account. This thesis has only scratched the surface on chain forming diatoms responses to adverse conditions. Considering the large diversity of chain forming diatoms, the responses to such conditions may be equally diverse.
Nutrient Transfer in Aquaponic Systems – Optimizing microbial processes for greater circularity and economic viability
(2023-04-18) Lobanov, Victor
The trend towards sustainable process design in modern industries combines the goal of improving process efficiency with a conscientious shift towards resource conservation. Aquaponics, a system that involves co-cultivating fish and plants, is a waste-conscious food production system. The primary system inputs - water and fish feed - are supplied to the aquaculture component and then transferred downstream to an area of plant cultivation. The upstream aquaculture component is organized in the form of a recirculating aquaculture system (RAS), while the downstream portion is most often a hydroponic greenhouse and as such takes the form of two recirculating loops that have a variable degree of connectivity. Aquaponics, just as its parent fields of aquaculture and hydroponics, falls under the umbrella of closed environment agriculture (CEA) systems. Unlike aquaculture and hydroponic cultivation systems, aquaponics relies heavily on endogenous microbial communities to remineralize nutrients and eliminate fish-toxic waste products. To date, efforts to improve nutrient use efficiency in aquaponic systems have primarily focused on nitrogen metabolism within the biofilter, with research around the utilization of other nutrient streams (solid waste) relegated to waste disposal. This dissertation addresses this shortcoming by investigating the processes underlying microbial colonization and nutrient remineralization in aquaponics, along with an analysis of the potential to improve system efficiency and sustainability through solids revalorization. These efforts demonstrate the capacity of bioprocess innovation to bridge the commercialization gap that has thus far limited widespread adoption of this type of high intensity, yet sustainable, food production systems. While there are already hundreds of aquaponics operations developing globally, achieving industrial scale production at similar scales to land-based aquaculture and hydroponic facilities has yet to be accomplished. Therefore, this dissertation aims to better understand nutrient flows and remineralization and how they can be utilized to improve food production and resource-use efficiency. Chapter 2 discusses how plants can guide microbial colonization in aquaponic systems, Chapter 3 reviews the advent of ecosystem-specific microbiota and microbiome databases, Chapter 4 introduces a novel nutrient remineralization system that converts fish solids into a fertilizer for CEA, and finally, Chapter 5 expands this technology to include the generation of methane from fish solids. In conclusion to these four chapters, a discussion section contextualizes the experiments within the larger umbrella of microbial and nutrient flow and how this relates to sustainable process design.
Evolutionary and Ecological Effects of Metal Pollution on Coastal Diatoms
(2022-10-21) Andersson, Björn
Oceans are changing rapidly in response to human activities, such as toxic pollution, eutrophication, and climate change. Diatoms are major primary producers in the oceans with short generation times, flexible reproductive strategies, and high standing genetic diversity. These traits should facilitate rapid evolution, potentially increasing the resilience of individual species and buffer against the effects of global change. In my thesis, I use the Baltic Sea and metal pollution as a model system to study the evolution of diatoms in response to global change. I use two native species, Skeletonema marinoi and Thalassiosira baltica, to investigate evolutionary and ecological responses to metal pollution at a mining-exposed inlet. The mine, Solstads gruva, has been active for 400 years, and the ore was deposited on the shore of a five km2 large inlet, Gåsfjärden. I first attempted to use a resurrection approach to study evolutionary processes backward through time. However, cross-contamination from contemporary cells at the sediment surface made age determination inconclusive. As previous studies have not quantified contamination directly, this finding suggests that phytoplankton survival in sediment may have been overestimated, and evolutionary interpretations possibly confounded. I re-directed focus on the contemporary diatom population present on the sediment surface. I found noticeable species differences between S. marinoi and T. baltica in tolerance towards non-essential metals (silver, cadmium, and lead) and indications that S. marinoi had evolved elevated tolerance towards copper and cobalt at the mining-polluted inlet. Moreover, I showed that metal pollution modifies competitive interactions between S. marinoi and T. baltica. Specifically, both species had large and overlapping, intraspecific variability in tolerance to copper, and evolution through selection on standing strain diversity modified the competitive outcome between them. To better understand selection and other evolutionary processes, we collect and analyze whole genome sequencing data from 55 strains of S. marinoi. We developed a bioinformatic tool that can identify the most allele-rich loci across a species genome and used it to localize three hypervariable loci in S. marinoi with at least 100 unique alleles amongst the 55 diploid genomes. I used the barcode loci to track selection in an artificial evolution experiment with a relatively high diversity consisting of 58 strains. The barcodes enabled me to enumerate and quantify fitness of individual strains under co-cultivation. I showed that under intense copper stress, and within 42 days [or 50 generations], one or two strains outcompeted the other conspecific strains. Future studies utilizing the barcode loci should be able to track evolution in more complex ecological settings and with much higher genetic diversity than what was possible with existing technologies. Finally, I link the copper tolerance phenotypes with genomic changes in copy number variance of metal detoxifying and transporting genes. Although I found copy number variance to be prevalent in genes encoding metal binding proteins, this did not correlate with copper tolerance in strains, suggesting that other genetic mechanisms were responsible for the evolved copper tolerance in the population. In summary, my thesis enhances our understanding of the evolutionary potential of phytoplankton in general, and metal tolerance in diatoms specifically. This evolution can be rapid; genetic diversity can be created within centuries, and selection on this diversity provides populations with the capacity to adapt to environmental change on timescales relevant for seasonal blooms.
Modelling the Evolution of Species’ Ranges
(2022-09-16) Eriksson, Martin
The fact that species have limited ranges is often due to a limited ability to adapt to the environmental conditions that occur outside their geographic ranges. However, due to ongoing climate change, the environmental conditions within species’ geographic ranges may change in the near-future. To avoid extinction, many populations therefore need to migrate to new areas and/or adapt to the new conditions. Migration to new areas may be problematic, however, because adaptation to new environmental factors, such as predation/grazing, competition, or parasitism from new species, or new physical factors besides temperature, may be necessary even though the temperature is the same in the new area as in the native habitat. In addition, migration to new areas is associated with a considerable loss of genetic diversity, which may severely reduce the ability to adapt to new conditions. To understand if and how populations may adapt to new environments, or if their ranges will contract when the environmental conditions change, it is necessary to understand which evolutionary mechanisms underly the geographic range limits of species. In my dissertation, I am using mathematical and computer-based modelling to study the limits to evolution at range margins. I find, among other things, that the ability to self-fertilise often is favourable at range margins, despite the depletion of genetic diversity that is typically associated with self-fertilisation. Likewise, I find that it is often favourable for range expansions if combinations of genes that are under selection tend to be inherited together (rather than being mixed up under so-called genetic recombination), in part because locally adapted combinations of genes are partially protected from being mixed up with less well-adapted genes. It is known that another factor that facilitates range expansions is phenotypic plasticity: that is, the ability of an organism to change its characteristics (phenotype) as a response to the environment it is exposed to. I find that evolution favours increased plasticity only as long as the cost of plasticity is not too high. To interpret empirical experiments involving plasticity correctly it is important to know if the observed change in phenotype improves the local fitness or if it is just a consequence of physiological stress, which I illustrate with simulations. Finally, I find that the effects of multiple environmental gradients (gradual changes in the environmental conditions across geographical space) are added to each other in such a way that the total environmental gradient may become steep enough to prevent further range expansion, even when each individual gradient is shallow and easy to miss in field studies. To conclude, the new insights from my thesis contribute to improving the understanding of why limits to species’ ranges form.

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