Förslag till Marina exjobb 2019 Suggestions for exam projects 2019

Maringeologi Disciplinen är den gren av geologin som omfattar läran om kusternas, havssträndernas och havsbottnarnas ytformer, uppbyggnad, bildning och utveckling liksom därtill relaterade marina, biologiska, kemiska, fysiska och klimatiska processer. För att finna ett lämpligt och spännande ex-arbete, kontakta Kjell Nordberg ([email protected]) eller Lennart Bornmalm ([email protected]) Examensarbeten på Bachelor och Masternivå Marinmikropaleontologi

Deprojektsomvanligenerbjudsinomämnetmaringeologiärstudieravmikroskopiskamarinaorganismersk.foraminiferer,vilkaanvändssomverktygförattundersökamiljöförändringarihavetsåvälSenkvartäraochHolocenasedimentlagerföljdersomiheltrecentamiljöer.LängsSkagerrakkustenerbjudsunikamöjligheterattnyttjabottenlevandeforaminiferersomverktyg/indikatorerförmiljö-ochklimatvariationer.DemarinaförhållandenaochavsaknadenavextremsyrebristsomärvanligtförekommandeiÖstersjönochinorskafjordar,påträffasrikafaunorisedimenten.Marinmikropaleontologiharennärakopplingtillfysiskoceanografiförattbelysahurhydrografinvarieratellerförändratsövertid(paleoceanografi).MarinmiljögeologiMänskligpåverkanpåhavsmiljönavspeglasoftasomsyrebristihavetmedlamineradeochförorenadesediment,liksomallvarligpåverkanpåmarinafaunorochfloror(marinmikropaleontologiellerålgräsbottnar).Ävenhärutgörackumulationsbottnarmedkontinuerligdepositionavsediment,föroreningarochmikrofossilettanvändbartmiljöarkivochettvärdefulltverktygförattspåraförekomstochspridningavföroreningarochmiljöförändringarövertid.Tungmetaller,miljögifter,sedimentstrukturerochmikrofossilbevarasisedimentenochkanpåsåsättanvändasbådetemporaltochspatialt.Denmarinamiljögeologinmedstudieravhistorisksyrebristochföroreningarharmångagångermycketstarkafördelardåvimedstratigrafiskteknikkanarbetamedäldresedimentdärinteregelbundnamiljöundersökningargenomförtstidigare.Marinmiljögeologiharocksåennärakopplingtillfysiskoceanografiförattbelysaspridningsmekanismerihavsmiljön.

Title: Development of a short-term ecotoxicology screen for microalgae

Supervisor: Björn Andersson PhD student, ([email protected])

Main supervisor: Anna Godhe ([email protected]) Department of Marine Sciences,

Focus of the project: Marine Biology or Chemistry

Location: Göteborg

Electron microscope image of S. marinoi

Background: Microalgae are routinely used as in aquatic ecotoxicology tests due to the relative ease robustness of cultivation (compared with for example fish larvae or invertebrates). Standardized method is based om how growth is inhibited over the course of 72 to 96 h. One problem with these assays is that they require the cells to be able to propagate at relatively dense cultures during this time, which require artificial growth media to be used. Due to its chemical composition this growth media may interfere with compound being toxicologically tested. For example, EDTA or other chelators are used in most medias to stabilize essential trace metals, and this causes great reduction in toxicity to for example heavy metals

Problem: To work around this problem, we have started using a method that does not require cellular growth and can be done in the course of a few hours. Consequently, microalgae could in theory be tested in various natural water, which would be more informative when predicting potential ecological effects of heavy metal pollution. This method probes photosynthetic capacity, rather than monitor growth per se, uses a Pulse Amplitude Modulated chl a (PAM) Fluorometer.

Method: The object of this theses would be to optimize the method in terms of exposure length, concentrations, variance in different natural waters etc. The next step will be to calibrate the new method against the old for proof-of-concept and also to determine if it is possible to determine a calibration factor between the two methods for sub-sequential translation between the two.

Suitable level and length: Bachelor (15 hp)

Suitable time period: project can be performed all year round.

Title: Nickel toxicity and metabolism of diatoms

Supervisor: Björn Andersson PhD student, ([email protected])

Main supervisor: Anna Godhe ([email protected]) Department of Marine Sciences,

Focus of the project: Marine Biology

Location: Göteborg

Electron microscope image of S. marinoi

Background: Nickel (Ni) is an essential trace metal for most bacteria species but it is not required in higher eukaryotes, such as plants and mammals. Microalgae are a diverse group of single celled eukaryotes whom also have complex, and often mutualistic, relationship with surrounding aquatic bacteria. Based on recent genomic data many genes and metabolic functions have also been transferred between bacteria and algae, through horizontal gene transfer. Relatively little is known about the relationship of microalgae to Ni.

Problem: While doing ecotoxicological screens, we recently discovered a Ni hypersensitive individual of the diatom species Skeletonema marinoi. One current hypothesis is that this individual has developed Ni sensitivity through laboratory evolution since we have kept it in culture for almost 15 years, corresponding to several 1000’s of generations. If true, this indicates that the species has some form of relationship with Ni in its natural environment, either through toxic encounters or it may require Ni as a cofactor for proper metabolism. Separately we are having issues growing this species in completely artificial media, which does not contain Ni, and have pinpointed this down to the lack of one (or more) trace mineral/compound present in normal seawater. We have determined that the missing compound is not organic, which indicates that it is an element(s) and could potentially be Ni. Method: The main objective of this Bachelors project would be to design an experimental strategy to determine if Ni is an essential compound for S. marinoi. Based on the students interest it may also be possible to further describe the Ni sensitive individual in our culture collection through an ecotoxicological approach. We also have an in-house genome available of S. marinoi and a more bioinformatically interested student may be able to look for marker genes of Ni metabolic pathways.

Suitable level and length: e.g. Bachelor (15 hp)

Suitable time period: project can be performed all year round.

Title: Development of an intraspecific barcoding method for the chain-forming model diatom Skeletonema marinoi

Main supervisor: Mats Töpel ([email protected]) Co-supervisor: Björn Andersson, PhD student ([email protected])

Focus of the project: Marine Biology/Bioinformatics

Location: Göteborg, Department of Marine Sciences Electron microscope image of S. marinoi

Background: The evolutionary capacity of phytoplankton has profound impacts on long-term responses to anthropogenic stressors, such as climate change and pollution. The majority of manipulator studies on phytoplankton so far does not incorporate evolutionary responses either because the experiments have been too short to permit selection or that only one or a few individual genotypes was investigated. We have performed selection experiments to test the evolutionary capacity of a cosmopolitan diatom species, Skeletonema marinoi, in response to copper mining activity. Our results show that amongst 60 individual genotypes from two locales, the mining exposed site has more variability in Cu tolerance and about 10-20% of the genotypes have higher Cu tolerant than any one from the reference locale. This indicates that local populations have evolved Cu tolerance. In long-term selection experiments (for 45 day which corresponds to ~50 generations) on artificially assembled populations (30 genotypes) we were able to rapidly raise the Cu tolerance through selection for more tolerant genotypes.

Problem: Based on morphology or other phenotypic traits we cannot distinguish which S. marinoi genotypes have increased in frequency during the selection period. Traditional molecular methods used to quantify this (e.g. microsatellites) are impractical to use due to the large initial genotype diversity. The aim of this project is to develop a molecular method that is able to identify which individual strains have been selected for during this experiment, based on bulk DNA samples and Next-Generation-Sequencing techniques.

Method: In this project you will analyze whole genome sequence data from ~100 strains of S. marinoi with the aim of identifying genomic regions that can be used to discriminate between unique strains. Likely this will be an inter-genetic region flanked by conserved genes for which PCR-primers can be designed. We will then use the PacBio Sequel platform to generate circular consensus sequences (CCS) of this region from the strains used for the selection experiment to identify shifts in the population structure due to the Cu treatment. Whole genome sequencing and annotation of the successful strains will shed light on the underlying genetic and physiological mechanism conferring the tolerance.

Suitable level and length: Masters (45-60 hp)

Suitable time period: The project can be performed all year around and is suitable for a student interested in bioinformatics and genomics.

Entangled genomes - changes in host- microbiome diversity over a steep salinity gradient Supervisors: Mats Töpel [email protected] & Ricardo Pereyra [email protected] Background Dittami et al. (2015) has shown that microbial communities may have had an impact on acclimation and physiological response of brown algae to different environments, and further proposed the microbiome as a possible facilitator of speciation. The same research group has also shown interesting results where metabolic pathways of Ectocarpus siliculosus and associated bacteria overlap and complement each other. The project You will use bioinformatics methods to analyse the microbial species composition associated with brown algae of the genus Fucus along a salinity gradient of the Swedish cost with the aim to (1) identify differences in the microbiome of F. vesiculosus and F. radicans and (2) analyse shifts in microbial species composition from the marine conditions of the west coast to the brackish water of the Baltic sea. In this project you will identify microbiome components specific to the two Fucus species, and analyse shifts in the microbiome composition along the salinity gradient. Future prospects involve isolating some of these bacteria and further sequencing and generation of reference genomes in order to characterise them. Expected results This project will add an additional dimension to the analysis of the differentiation of the two Fucus species currently being sequenced in the IMAGO initiative. Furthermore:

• The results will shed light on the relative importance of biotic vs. abiotic mechanisms governing the algal-bacterial interactions.

• We will learn how bacteria have played a role in algal evolution and by which processes they have interacted and influenced the algal acclimation to a new environment.

• Finally, the outcome will reveal potential patterns of coevolution relative to the bacteria-algal interaction and environmental clines.

References Dittami et al. (2014) Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae. Frontiers in genetics. Vol5, Article 241. Dittami et al. (2015) Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures. The ISME Journal, 1–13. Hartman et al. (2010). V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J Microbiol Methods. Nov;83(2): 250-3. Li and Godzik (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. Jul 1;22(13): 1658-9. Zang et al. (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 30(5): 614-620.

Projects related to analytical chemistry methods for measuring aggregation rates of particles

Title: Method development for measuring aggregation rates of nanoparticles using nanoparticle tracking analysis

Main supervisor: Julián Gallego, [email protected]

Focus of the project: marine chemistry

Location: Kristineberg

Background: Nanoparticles, NP, are defined as particles with at least one dimension under 100 nm. NP in the aquatic environment can have multiple origins including i) anthropogenic, as those used in consumer products intended for direct release, ii) unintentional released, as those coming from degradation/erosion of litter and iii) naturally occurring, such as precipitates of inorganic species, biologically produced macromolecules or those coming from natural events. The widespread use of NP in consumer products and the release of nanoparticles from macro-litter, will eventually lead to increase amounts of these particulates in natural waters. Under certain conditions NP tend to aggregate, either with particles of their own type or other naturally available particles, leading to an increase in size and, therefore, their settling velocities. One technique for measuring particle size is nanoparticle tracking analysis, NTA. In this technique, individual particles are illuminated with a laser beam and the 90 degrees scattered light is tracked with help of a CCD camera mounted on a light microscope. The particles trajectories are tracked for a period of time and their hydrodynamic diameters obtained with help of the Stokes-Einstein relation.

Problem: Several techniques have been used in the past to follow and monitor NP aggregation rates leading to the determination of attachement efficiencies, a parameter that can be used to model and predict the final fate of NP in natural environments. A technique that has been overlooked for this purpose is NTA.

Method: This project involves acquisition and analyze of aggregation rates of selected NP, aquatic media and suspended particulate matter using nanoparticle tracking analysis.

Suitable level and length: project can be adapted to suitable education level

Suitable time period: project can be performed all year round

Reference:

Gallego-Urrea, J. A, et al (2011). Applications of particle-tracking analysis to the determination of size distributions and concentrations of nanoparticles in environmental, biological and food samples. TrAC Trends in Analytical Chemistry, 30(3), 473–483. https://doi.org/10.1016/j.trac.2011.01.005

Title: Genetic patterns of facultative sex in Skeletonema marinoi

Main supervisor: Marina Rafajlović ([email protected])

Co-supervisors: Anna Godhe ([email protected]) & Mats Töpel ([email protected])

Focus of the project: Evolutionary Biology

Location: Gothenburg

Background: Individuals of Skeletonema marinoi (a marine planktonic diatom) are known to reproduce by both sexual and asexual means (cloning). Sexual reproduction in this species has been suggested to play a key role in avoiding local and global extinction of the species, not only because sexual reproduction is likely to allow for faster adaptation by, for example, pruning the genome from deleterious mutations, but also because of purely mechanistic reasons, such as restoring the size of individuals. Indeed, individuals reproduced by cloning in this species (cell division) are progressively smaller in size than their parent before the division, causing the individuals to inevitably reach a critical size below which they cannot divide further; at this point, sexual reproduction is a necessary means by which individuals may restore their maximum size. Still, earlier laboratory tests suggest that in this species cloning is much more prevalent than sex.

Problem: The rate of sexual reproduction in Skeletonema marinoi is unknown to date. Earlier analyses of individuals sampled at 8 microsatellite loci showed high genotype diversity among individuals and no evident signatures of clonal reproduction. This may be because the rate of sexual reproduction in the species is higher than the theoretically derived critical threshold above which signatures of clonality are hidden by sex, or because the power to detect any such signatures was poor with the data set used. Now we aim to re-test a population of this species for genetic signatures of cloning using a subset of whole-genome sequences of samples from three different periods in the past (samples are taken from individuals originating from different sediment layers) particularly focusing on SNPs found at pairs of large contigs that are likely to represent different chromosomes. By comparing patterns found within and between contigs, as opposed to comparing patterns at a small number of randomly sampled microsatellite loci, we expect larger power for detecting signatures of clonal reproduction.

Method: The empirical data will be analysed by means of several statistics frequently used to detect signatures of cloning, such as !"# and LD patterns. In addition, we may test for correlations between site-frequency spectra (SFS) found within and between contigs and use this as an informative statistic contrasting fully sexual as opposed to fully asexual populations. The latter will require further development of existing theory on SFS either analytically or using individual-based computer simulations (or both), particularly to contrast fully asexual to fully sexual populations. An extension to facultative sexual populations would be beneficial for the project.

Suitable level and length: Master 30, 45 or 60 hp. If the student is to develop the existing theory further, then 60 hp project is most suitable.

Suitable time period: The project can be performed all year round.

Title: Life cycle specific modulations of cell division rates in diatom cultures Background: Diatoms are among the most important primary producers on earth. They inhabit soils, lakes, rivers, sea ice, and probably most importantly, the oceans. Because of their prominent appearance and wide distribution, researchers have investigated diatoms for more than two centuries. A common approach to study diatoms and other unicellular algae is to grow clonal populations under well-controlled laboratory conditions. By this means we can measure cell division rates and other phenotypic traits to study treatment effects and build hypotheses about potential fitness consequences in natural populations facing environmental change. Although the story is usually much more complex, and the relationship between culture experiments and what happens in nature is not all that straight forward, this approach may also suffer from a very basic problem, which is intrinsic the diatom life cycle. Diatoms are covered by a silicate shell, which consists of a larger and a smaller part. This rigid shell may provide protection from grazing and other threats. During cell division the smaller part of each shell is re-built and consequently, dividing cells become smaller and smaller until they reach a critical size. That is when the cells usually undergo sexual reproduction and become large and start over again. Problem: Earlier studies have shown that cell division rates in diatom cultures are affected by cell size. Larger cells divide slower than smaller cells. Consequently, a clonal diatom lineage will show variation in cell division rates, depending on the respective life-cycle stage. Methods: This project aims to use laboratory cultures of different strains of the common diatom Skeletonema marinoi to investigate life cycle specific modulations of cell division rates and other phenotypic traits, such as cell size. It will involve a range of techniques, including single cell isolation under the light microscope and microscopy in general, algal culturing techniques, preparation of seawater media, counting and measuring cells using the microscope as well as automated high-throughput cell counting techniques, and chlorophyll fluorescence measurements. The results are supposed to help evaluating potential consequences of life cycle depended growth rate modulations in diatoms and may allow developing new methods to improve future experiments.

Skeletonema marinoi in the light microscope

Contact: Anna Godhe or Olga Kourtchenko [email protected] [email protected] Location: Göteborg (Anna Godhe lab, Botan building) Time period: 2019 Level: BSc level (15 hec)

Title: Hybrid shell deformation - What's the problem?

Main supervisor: Kerstin Johannesson, [email protected]

Focus of the project: Marine Ecology

Location: Tjärnö

Background: Snails of Littorina saxatilis form ecotypes that differ remarkably in morphology, but ecotypes still hybridize in contact zones. However, cross-mating ecotypes in the lab result in hybrid snails with weird morphologies (see Figure). Such snails are never observed in the field. This suggests that there is selection against hybrids in the wild, and this will constitute a reproductive barrier between ecotypes supporting a speciation process.

Problem: Why are these malformed hybrids never observed in the lab? Two possibilities have been suggested: (1) Crabs are more successful in attacking them and the shell deformation makes the shell less robust against crab attacks. (2) Wave action removing them from the shore, as the shell deformation make snails less able to attach to the rock. The aim with the project is to test these two (and possibly) other hypotheses that may explain why malformed snails do not survive in the field.

Method: Snails with malformed shells, and control snails, are available from an existing snail culture at Tjärnö. Crab attacks can be experimentally tested with shore crabs as predators, in tanks. Snails' resistance to waves can be tested in the "snail flume" at Tjärnö.

Suitable level and length: "Master (30-60 hp)", depending on the ambition and design of the project. It is, for example, possible to restrict the test to either wave action or crab attacks, or include both.

Suitable time period: Project can be performed all year round. Snails are available from approximately April 2019.

Figure. Maldeformed snail (extreme deformation) (left) and normal crab and wave ecotype (right).

Title: Effect of pH-stress on macroalgal resistance to wave action

Main supervisor: Alexandra Kinnby / Gunilla Toth / Kerstin Johannesson

Focus of the project: Marine Ecology

Location: Tjärnö

Background: Preliminary results show that the macroalgae Fucus vesiculosus increase growth rate under pH stress but the new grown tissue is thinner than for non-stress individuals. The mechanism may simply be increased capacity for photosynthesis when the supply of carbonate is slightly increased. However, the thinner thallus may have a negative effect on the robustness of the Fucus, for example, wave action may risk to ripe of parts of the thallus.

Problem: This project will experimentally test potential consequences of morphological changes in the Fucus thallus under pH stress, such as, decreased resistance to wave action.

Method: Culture thalli of Fucus under controlled and pH stressed conditions. Test the new tissue for resistance to high water flow in our "snail/seaweed flume".

Suitable level and length: "Bachelor (15 hp)" or "Master (30-45 hp)", depending on the exact design of the project, for example, it is easy to include more than one species, and additional interacting stress factors may be added such as grazing from snails or isopods.

Suitable time period: Project can be performed all year round.

Title: Effects of pollutants on the feeding behavior in marine mesoherbivores

Main supervisor: Gunilla Toth ([email protected])

Focus of the project: Marine biology

Location: Tjärnö marine laboratory

Background: Marine mesoherbivores are small herbivores that live and feed on their seaweed hosts. Some herbivores (e.g. Littorina sp. and Idotea sp.) are selective and prefer to feed on seaweed species or individuals that contain low levels of chemical defense compounds. The mechanisms that allow the herbivores to choose different food types are relatively unknown for many species, but may include taste/smell receptors that could be affected by different pollutants.

Problem: This project aims at investigating if different pollutants (e.g. heavy metals, petroleum, herbicides, pesticides, and personal care products) affect the feeding preference of common marine mesoherbivores at the Swedish west coast.

Method: Projects could include a review and meta-analysis of the present status of the research field, field observations, and/or manipulative field- and laboratory experiments. The student will gain insight in experimental design, chemical ecology working skills (e.g. extraction and quantification of chemical defenses and feeding bioassays), statistical analysis of the results, and scientific writing.

Suitable level and length: Project can be adapted to suitable education level

Suitable time period: Project can be performed all year round

Title: Seaweed aquaculture Main supervisor: Gunilla Toth ([email protected]) Focus of the project: Marine biology Location: Tjärnö marine laboratory

Background: Aquaculture is rapidly growing on a global scale but is still very minor in Sweden, in spite of our long coast. This is especially true for the cultivation of aquatic macrophytes. Marine seaweeds offer a highly interesting complement to crop cultivation on land, without the negative environmental consequences associated with the use of fertilizers, pesticides and freshwater irrigation. On the contrary, and in strong contrast to marine fish farms, seaweed farms can significantly contribute to the remediation of eutrophicated coastal waters. Furthermore, culture of seaweeds can be combined with aquaculture of other species in order to increase and diversify yield and to extract dissolved nutrients from the water (also called integrated multitrophic aquaculture or IMTA). Problem: At Tjärnö marine laboratory we have several projects focused on different aspects of seaweed aquaculture, both in the field and in tanks in the laboratory. Our aims are to optimize cultivation techniques and to integrate seaweed cultivation with cultivation of other aquatic species. Method: Projects can include a mix of field and laboratory observations and experiments. Examples of projects include (but are not limited to) studies on factors that optimize different life cycle transitions (growth, reproduction), field cultivation techniques, cultivation of “new” species, IMTA etc. Suitable level and length: Project can be adapted to suitable education level Suitable time period: Project can be performed all year round

Photo: Gunilla Toth and Maria Tjernström

Title: Consequences of changes in biodiversity

Main supervisor: Lars Gamfeldt, [email protected]

Focus of the project: This project is about experimentally studying the role of species diversity for ecosystem function. Laboratory experiments can be done with either (i) marine macroalgal assemblages (macroalgae and grazers), marine- and freshwater rock pool communities, or (iii) bacterial strains in the lab. Experiments with bacteria will be performed in collaboration with scientists at the Department of Chemistry and Molecular Biology.

Location: Tjärnö or Gothenburg.

Background: Threats to species and ecosystems are greater today than ever before in human history. While the loss of biological diversity is a tradegy in itself, it may also feed back on how nature functions. Over the last two decades we have learned through hundreds of experiments and theoretical studies that impoverished biodiversity generally results in lower ecosystem function, such as primary production and nutrient uptake. However, our knowledge is mainly based on relatively small-scale studies in homogeneous environments.

One crucial issue in biodiversity-functioning research remains unresolved: What is the role of spatial scale and environmental heterogeneity in mediating the biodiversity-ecosystem functioning relationship? This student project aims at partly filling this knowledge gap.

Problem: To set up an experiment to test the role of spatial scale and spatial heterogeneity for how changes in species diversity affect ecosystem function.

Method: Depends on the exact question and study system. (i) Experiments in which the diversity of macroalgae and small grazers (such as amphipods and isopods) are manipulated outdoors in aquaria of different sizes on the Ecotron at Tjärnö. (ii) Experiments in which we test how simulated rock pool communities (crustaceans mainly) are affected by predation on different spatial scales. (iii) Bacterial communities of different diversity and how they perform under different environmental conditions (for example, different antibiotics).

Suitable level and length: Master (30, 45 or 60 hp)

Suitable time period: Late spring and summer 2019. Experiments with bacteria can be performed all year round.

Title: Copepodamides -the scent of fear under water

Main supervisor: Erik Selander [email protected]

Focus of the project: Marine biology/Marine chemistry master or bachelor

Location: Gothenburg (mainly fieldwork may be performed elsewhere

Background:Copepodamides are a group of polar lipids released by copepods. Marine algae, and microzooplankton respond to the compounds and launch defensive strategies to avoid predation. We have discovered around 20 copepodamides from marine copepods but recently discovered that freshwater copepods also produce significant amounts of these compounds. This is new to science, and we would like to pursue this topic by sample several species of fresh water copepods and analyse their content of copepodamides. This is a suitable project for both bachelor and master thesis. You will learn how to work with zooplankton, how to extract and analysze copepodamides using liquid chromatography coupled to a triple quadrupole mass spectrometer. The project can also potentially be more ecologically oriented and focus on the effects of copepodamides in fresh water. It is known that fresh water algae respond to the presence of copepods, but the cueing compounds are still unknown.

Problem: Extracting and analyzing signaling lipids from new sources of limnic zooplankton

Method: Field work in lakes collecting copepods, analytical chemistry, extraction and analysis of polar lipids with LC-MS. Potentially ecological experiments with copepodamides and limnic organisms.

Suitable level and length: “project can be adapted to suitable education level”

Suitable time period: e.g. "spring and summer 2019”

Figure 1: Copepods (A) release the copepodamides (B) that induce e.g. amnesic shellfish toxin production in some phytoplankton, and colonysize changes in others. Copepodamide also induce bioluminescens in marine dinoflagellates

Title: Experimental assessment of cost of plasticity in Fucus vesiculosus

Main supervisor: Kerstin Johannesson ([email protected])


Location: Tjärnö

Background: Most species are partly plastic in their phenotypic traits, and plasticity is considered very important for survival in variable environments, and for establishing new individuals in a new environment. Fucus vesiculosus (bladderwrack) seems to be very plastic with respect to salinity, and individuals from the Swedish west coast can survive and grow in salinities down to 4 permille (corresponding to salinity outside Umeå).

Problem: It is assumed that plasticity comes with a cost - but rarely this cost has been estimated. In Fucus vesiculosus, it should be possible to estimate the cost by experimentally grow small adventitious branches from the same individual of Fucus in different salinities, to assess the plasticity of this individual, and repeat this for a couple of different individuals. This experiment will inform us about which individuals are most plastic. Simultaneously, the same individuals (or rather adventitious branches of them) can be grown in a stable environment to study their performance and survival. If there is a cost of plasticity, it is expected that the more plastic individuals do worse in a constant environment, than the more plastic ones.

Method: Use adventitious branches from Fucus vesiculosus and grow these in several different salinities to assess plasticity. In addition, grow additional adventitious branches from the same individuals in an environment that is constant and close to the population's optimum environment. Growth can be assessed after 2-3 weeks.

Suitable level and length: Master 30, 45 or 60 hp, depending on the ambition of the student. Plasticity may be tested for one physical factors, e.g. salinity, or for two or more physical factors, which will extend the experimental part of the project but also make it more interesting.


Photograph illustrating adventitious branches that grow from a thalli of Fucus vesiculosus

Title: Assessing the power of reciprocal-transplant experiments for inferring plasticity in Fucus vesiculosus using modelling

Main supervisor: Marina Rafajlović ([email protected])

Co-supervisor: Martin Eriksson ([email protected])

Focus of the project: Evolutionary Biology


Background: Plasticity may be a major evolutionary factor allowing a species to inhabit and persist in highly variable environments. This view seems consistent with a large number of studies suggesting that many species exhibit plasticity in traits relevant to the key environmental variables. For example, Fucus vesiculosus (bladderwrack) has successfully expanded its range from the North Sea into the Baltic Sea, despite being faced with a steep salinity gradient throughout. This, together with earlier reciprocal-transplant experiments involving adventitious branches from the same individual (identical clones), suggests that F. vesiculosus may be highly plastic with respect to salinity.

Problem: The results of reciprocal-transplant experiments depend on many underlying factors, including the joint effect of selection, plasticity and the underlying reaction norm for plasticity. In particular, if realized differential selection in contrasting environments is weak (despite the gradient of the environmental variable being steep), the fitness of an individual lacking plasticity in the relevant trait will be very similar between these environments. Importantly, it is the performance of individuals that is measured in reciprocal-transplant experiments, and the performance may be either negatively or positively correlated to the actual fitness of individuals. However, an experimental finding suggesting similar performance of individuals in different environments would be traditionally interpreted as ‘evidence’ of plasticity, specifically of ‘phenotypic buffering’. The aim of this project is to use modelling to evaluate the power of differently designed reciprocal-transplant experiments to infer plasticity when it is present. The model will be specifically used to suggest a suitable experimental design to infer plastic response of Fucus vesiculosus with respect to salinity.

Method: Build a simple individual-based model with selection and plasticity, assuming different selection strengths and reaction norms. Mimic various reciprocal-transplant experimental designs in the model and assess the distribution of fitness and the resulting performance in control and transplanted individuals of the same and different clones. Estimate the power of each experimental design in inferring plasticity (i.e. estimate the proportion of false negatives and false positives based on the standard inference methods).

Suitable level and length: Master 30, 45 or 60 hp. If new experimental designs are suggested and evaluated by the student, then 60 hp project is most suitable.

Suitable time period: The project can be performed all year round.

Using next-generation sequencing for conservation of eelgrass Supervisor: Marlene Jahnke ([email protected]) Focus: population genomics of eelgrass Location: Tjärnö Marine Lab Background The marine benthos is one of the most sensitive and most impacted communities on earth. In order to investigate and predict population viability and connectivity, we need to gain some understanding of population and meta-population demography. This is a complicated endeavour in any organism, but particularly when a species has different and mixed reproduction strategies. The project focuses on the seagrass Zostera marina (eelgrass), which is a priority species in conservation because of its large-scale decline and important role as foundation species. Eelgrass is a monoecious (male and female functions are separated on spadices within the same flower) flowering plant, which is mainly outcrossing, but also exhibits selfing as well as partial clonality as a potential reproduction strategy. Both selfing and clonality have important impacts on the evolution of genetic diversity at the population level and consequently may impact evolvability.

Aims and Methods

In a previous study we have shown that eelgrass is relatively well connected, but that there are also some strong barriers to dispersal (Jahnke et al, 2018) and in this project we will now take a genomic approach to understand local dynamics better. In order to investigate the impacts of clonality and selfing on evolvability, high-resolution markers generated by high-throughput sequencing are necessary. In this project, the use of thousands of single nucleotide polymorphisms (SNPs) markers for the eelgrass Z. marina, will make it possible to study the impact of partial clonality on populations dynamics and use evolutionary simulation frameworks to model the effect of partial clonality and selfing (e.g. SLiM, simuPOP and fastsimcoal) on population dynamics and evolution.

Application for conservation Population genomic approaches that harness the power of high-throughput sequencing can provide information that is useful and necessary for improved conservation and management of benthic species, in particular for modelling past, present and future population dynamics. In particular, the results of this proposal can be used for highlighting vulnerable sites (with low connectivity and high levels of clonality and selfing, leading to reduced effective population size and decreased efficacy of selection) and for understanding and modelling past and future changes.

Level This project is ideal for a 60hp MSc thesis and previous knowledge in molecular lab techniques and basic bioinformatic and/or population genetic methods is an advantage.

Title: Biomass and nutritional content of seaweed flies raised on different seaweed diets

Main supervisor: Gunilla Toth ([email protected]), Swantje Enge ([email protected]), Emma Berdan ([email protected])


Location: Tjärnö marine laboratory

Background: Seaweed flies are very common on seashores and are immensely important for the decomposition of beach-cast seaweeds. The flies breed in the beached seaweed beds, and it is the larval feeding, in combination with microbial activity, that is responsible for the rapid decomposition of the seaweeds. The larvae contain high amounts of nutrients and fat and are important as food for seashore birds.

Problem: Seaweed fly larvae raised on cultivated seaweeds (Ulva lactuca and Saccharina latissima) have been suggested to be a good nutritional source for cultivated fish. However, the species composition of beached seaweeds is diverse and the aim of this project is to study and compare the biomass and nutritional composition of seaweed fly larvae raised on other seaweed species naturally found in beached seaweed beds.

Method: A mixture of field and laboratory work. Species inventory of beach-cast seaweeds as well as collection of fresh seaweeds and fly larvae. Larval growth experiments with different seaweed species in laboratory cultures, as well as chemical analyses of the nutritional content of the larvae.

Suitable level and length: Project can be adapted to suitable education level


Adaption to wave exposure in bladder wrack

The bladder wrack, Fucus vesiculosus is a common brown seaweed on the rocky shores of the Northern Atlantic. The morphology of the plants varies with the grade of wave exposure; in sheltered areas the plants are larger, more bushy-like and have bladders whereas on more wave exposed sites they are smaller, have a flatter structure and lack bladders. The variation in morphology is hypothesised to be an adaption to the hydrodynamic climate where the morph found on exposed sites is expected to better withstand stronger water currents without braking or become detached. This hypothesis is however not previously tested. This project aims at quantifying the differences in morphology among plants from sites with various hydrodynamic exposure and to test the plants performance in a high-speed laboratory flow channel. By measuring the force imposed on the plants by flowing water and compare this drag to the morphological differences, we hope to find out how much the morphology affects the flow induced forces and which aspects of the morphology that is most important to the observed drag. Since the algae are flexible in their structure, we will also monitor the change in shape with increasing flow velocity and investigate how this affect the drag coefficient. This work will except mapping differences in morphology and shape, and measuring drag forces in the flow channel also involve measurements of flow exposure in the field using gypsum erosion. Master project starting summer or autumn at the Sven Lovén Centre Tjärnö Supervisor: Ann Larsson ([email protected])

www.alamy.com www.aphotomarine.com

Eider duck (Somateria mollisima) predation in blue mussel cultivations: Behaviour of eiders related to deterrence/boat chasing Background The blue mussel (Mytilus edulis) is the main prey for the already threatened and now red listed eider duck. However, the natural blue mussel population on the Swedish west coast has been in great decline during recent years, indicating that mussel cultivations currently have an essential role for the eiders food intake. Concurrently, eider predation in blue mussel cultivations results in extensive financial losses and increased environmental effects due to ingestion and knock-off of mussels from cultivation ropes. So far, the best bird deterrent method is boat chasing. However, it is a short-term solution which is expensive in labour and fuel, hence not a sustainable method. Furthermore, boat chasing of eider ducks may not be considered ethical, and it is not yet known how the deterrent method affects the eiders. The student project will be included as a part of the main project “Development of methods and knowledge to reduce eider predation in blue mussel cultivations”. The project is in collaboration with the largest mussel farm in Sweden, Scanfjord AB, and with scientists at SLU as well as ornithologists at Naturcentrum and Bohusläns museum. Possible fieldwork will take place nearby Scanfjord’s mussel cultivations around Orust whilst video analyses and observations from surveillance cameras, positioned at some cultivations, will take place in lab. As the main project take place throughout 2018, it is preferable that the student project will be conducted in autumn 2018. The duration of the project is flexible, however, the length of the project determines the extent of fieldwork and collection of data material. The aim of the project can be approached in many different ways and can be discussed in more detail with the supervisor. Following is a short description of applicable questions that can be combined depending on the duration of the project. Potential field studies

- How does the presence of eiders in a mussel cultivation differ over time (day, season)? - Study the behaviour of eiders (and other birds) related to deterrence/boat chasing. How does

the escape behaviour look like and how long time does it take for the eiders to return after deterring?

- Are there any differences between females and males? Flock behaviour or individual behaviour?

Potential video analyses

- How does the presence of eiders in a mussel cultivation/between cultivations differ over time (day, season)?

- To what extent can you observe that the cultivation buoys becomes lighter due to eider predations in the mussel cultivation?

- Is there any difference in distribution of females and males in the cultivations? - To what extent does other birds than eiders appear in the cultivations?

Contacts Karl Lundström, Sveriges lantbruksuniversitet Epost: [email protected] Tel: 010-478 4138 Mats Lindegarth, Göteborgs Universitet Epost: [email protected] Tel : 031-786 9672 Per Bergström, Göteborgs Universitet Epost: [email protected]

Wind-front interactions as measured by Wave Gliders and Seagliders, simultaneously

Suggested Masters project by Sebastiaan Swart (contact: [email protected])

Scientific background

The interaction between the ocean and atmosphere are extremely important to the processes that govern the upper ocean. These processes drive air-sea fluxes or heat and carbon that are critical to the global climate. One way in which these air-sea fluxes are moderated is through the interaction between surface winds and ocean flow fields, such as fronts and eddies. The energetics of the ocean flow field are particularly amplified at submesoscales (1-10 km) where they manifest in regions of large horizontal density gradients. We have valuable datasets of high frequency Wave Glider winds together with high-resolution temperature and salinity profiles of ocean from Seagliders that can be directly compared to each other to assess the interaction between the surface wind stress and the fronts of the Southern Ocean.

Objectives and approach of project

• - Search of any relevant literature on this topic, specifically on air-sea interaction and wind- front interactions

• - Analyze available datasets from Wave Glider and Seaglider multi-month deployments in the Southern Ocean

• - Provide simple analysis and interpretation of the wind data with horizontal density gradients of the ocean

Some competency in Matlab/Python or alternate code is needed. If it does not clash with course work, the student may have the opportunity to join a research cruise to the Southern Ocean/Antarctica. The project has prospects to lead into a PhD thesis.

The impact of the 2015-2016 Weddell polynya on the Southern Ocean circulation Master student project (30-60 credits). Possibility to carry out a bachelor project on a related topic. Contact: Fabien Roquet ([email protected])

Scientific background: The Weddell Polynya is a large sensible heat polynya infrequently observed in the Weddell Sea. The opening of a Weddell Polynya has a far-reaching impact on the physical and biogeochemical conditions of the Southern Ocean. Deep convection is associated with the release of large quantities of heat into the atmosphere, leading to a large cooling and freshening of the central Weddell Sea, likely associated with a spin-up of the Weddell Gyre and an acceleration of the ACC. In turn, these large-scale circulation changes should modify the structure and strength of the Southern Ocean overturning circulation, which regulates the vertical exchange of heat, carbon dioxide and other tracers.

Major Weddell Polynyas occurred between 1974 and

1976, but since then only very minor polynyas have been observed a few years and it has been hypothesized that climate change would prevent it to occur again in the future. Yet, in 2015 and 2016, the Weddell polynya re-opened again, and while its size was small compared to the ones in the 70s, it raises the questions of 1) why did it open this time, 2) what impact have the recent polynyas had on the ocean and atmosphere circulations in the Southern Ocean, and 3) is it likely that a major polynya would open in a near future. The H2020-funded major project SO-CHIC (Southern Ocean Carbon and Heat Impact on Climate) has recently been granted to study the Southern Ocean impact on climate, including the effect of polynyas and the proposed Master project would be a direct contribution to the SO-CHIC work plan.

General methodology: The CMEMS GLORYS reanalysis at 1/12° resolution (Glorys12) will be analyzed and validated in the region of the Weddell Sea to study the impact of the recent Weddell polynyas on the large-scale circulation. Glorys12 is based on the numerical model NEMO and discretized on the ORCA12 horizontal grid. In situ hydrographic profiles, satellite SST, and sea-level anomalies obtained from along-track satellite altimetry are assimilated in the Glorys12 reanalysis using a reduced-order Kalman filter approach. Glorys12 will in particular be analyzed to identify newly formed water masses following the emergence of Polynyas in 2015 and 2016, and to assess how the Weddell Gyre’s deep-ocean stratification and circulation react to Polynya development. The response of the Southern Ocean overturning circulation to the Polynyas will also be quantified. This analysis will provide a synthesis of the large-scale impacts of the recent Polynyas.

Some experience in scientific programming is desirable (Matlab, Python or similar). The ability to process and analyze large datasets (numerical simulations or observational datasets) will be developed as part of this Master thesis.

Sea surface signature of the Atlantic meridional overturning circulation Master student project (30-60 credits). Possibility to carry out a bachelor project on a related topic. Contact: Fabien Roquet ([email protected])

Scientific background: The sea surface height of the ocean is a key dynamical property, whose gradient determines the intensity and direction of surface geostrophic currents. Since the advent of satellite altimetry in the early 90’s, it has become possible to measure both its temporal and spatial variability with sufficient accuracy, revealing all the richness of the eddy turbulence and the complexity of major current systems.

Knowledge of sea surface height not only gives precious information on the near-surface ocean circulation, but it also tells a lot about the deeper ocean circulation if carefully analyzed. The sea surface height is indeed dependent on the interior thermohaline stratification through the hydrostatic balance.

In a recent study, a close match was noted between the position of the mean sea level contour (i.e. the places where the sea level exactly equals the global mean sea level) and the zero-wind stress curl (i.e. the places where the Ekman pumping is on average zero). This was interpreted as a clear indication that Ekman pumping is a major driver of the global ocean circulation. However, these two contours diverge greatly in one particular oceanic sector, namely the Atlantic subtropical area. In this project, we want to explore the possibility that this discrepancy would be generated by the Atlantic meridional overturning circulation (AMOC), which carries surface waters northward across the Atlantic and deeper waters southward.

General methodology: In this project, we propose to analyze the position of the global-

mean sea level contour. If the ocean were at rest, the sea surface would be perfectly flat. Deviations from the global-mean sea level thus reflect the integrated effect of applied forces. The global-mean sea level contour can thus be seen as the fulcrum of the large-scale circulation. We will analyze the temporal variability of its position, at both seasonal and interannual time scales, and analyze how it is correlated with the AMOC variability. The analysis will be carried out on the CMEMS GLORYS reanalysis at 1/4° resolution, an advanced product that optimally combines state-of-the-art ocean general circulation models with the nearly complete global ocean data sets for 1992 to present. Some experience in scientific programming is desirable (Matlab, Python or similar). The proposed work will develop the student’s skills in physical oceanography, model data analysis and large-scale ocean dynamics.

Figure 1: (a) Mean sea surface topography. The color scale is centered on the global-mean SSH (thick black line contour). (b) Mean vertical Ekman velocity. The global-mean sea level contour is repeated (thick black line) to highlight the spatial correlations between the two fields. From Roquetet al. (2011), J Phys Oceano, 41:2328-2342.

Title: DNA barcode species determination of canned tuna Main supervisors: Thomas Dahlgren, [email protected] Sara Hornborg, [email protected] Focus of the project: Marine Biology Location: Göteborg Background: Seafood is the most traded food commodity, with long and complex supply chains. In the EU, tuna is the top consumed seafood product, with canned tuna being one of the most popular tuna products. Today, a range of tuna species are fished around the world, and products from the global tuna fishing industry has world-wide spread. Producers are in general required to label the cans with what species it contain, if it is cultured or from fisheries and what area the content was fished or from which country it was cultured. This is important so that the aware consumer can make informed choices and avoid vulnerable species. The meat of some species of tuna is also more likely than others to contain high levels of mercury, due to bioaccumulation by higher trophic level species. Problem: Miss-labeling occurs in the seafood industry, in many cases found to be around 30% of the products. The reasons are many-facetted: long and complex supply chains, illegal fisheries, market less-popular species as more-popular ones, etc. Miss-labeling cause problems in many ways, such as illegally fished products can enter the market and contribute to overfishing of stocks, and some seafood products may pose health risks to certain consumer groups and must thus be correctly labelled. Most recently, a study of canned tuna reported in Swedish newspapers showed interesting results on mercury content, which may indicate mislabeling and would be interesting to follow up on. Method: A sample of tuna cans will be purchased from local stores. The contents will be DNA extracted. To determine the species composition of the content DNA barcode genes (the CO1 marker) will be sequenced and resulting data compared with publicly available databases (GenBank). Suitable level and length: project can be adapted to suitable education level Suitable time period: project can be performed all year round

The genetic basis of plasticity and resilience to climate change in Baltic Sea Isopods Ecosystems with more species tend to be more resilient to change. This importance of species-level biodiversity is well-understood. The effects of within-species genetic diversity on ecosystems are far less well known, and yet it is at this level that human activities are having the most impact – reducing the size, and genetic diversity, of populations. This is being accelerated by ocean global change which is happening at rates unprecedeted in tens of millions of years. This project aims to quantify the effects of genetic diversity on species functioning under different climate regimes. Specifically, we will breed distinct families of Idotea and determine differential phenotypic plasticity of growth, respiration, feeding and/or reproductive rates of these families to varying environments (heatwaves, freshening shocks, or some other disturbance – precisely what factors to investigate is open at present). The resulting family groups of Idotea will feed into a larger Internationally coordinated project to investigate the impacts of intraspecific (genetic) diversity of seagrass mesocosms on resilience to future fluctuating climates, to be run in summer of 2020. That project will be run in collaboration with Christian Pansch (Kiel) and Paul Renaud / Iris Hendriks (Tromsø). Suitable level and length: Master (60 hp). Time and place: Starting in the Fall of 2019 at the Tjärnö Marine Lab. Contact: Pierre De Wit [email protected]

Jon Havenhand [email protected]

The outdoor aquarium system at the A pregnant isopod with juveniles in a Tjärnö Marine Lab. brood pouch.

Does genetic (within-species) diversity confer resilience to climate change in Seagrass Ecosystems? Ecosystems with more species tend to be more resilient to change. This importance of species-level biodiversity is well-understood. The effects of within-species genetic diversity on ecosystems are far less well known, and yet it is at this level that human activities are having the most impact – reducing the size, and genetic diversity, of populations. This is being accelerated by ocean global change which is happening at rates unprecedented in tens of millions of years. This project aims to quantify the effects of genetic diversity on the functioning of seagrass ecosystems under different climate regimes. Specifically, we will create seagrass mesocosms with low, or high, genetic diversity and expose these to a variety of different climate scenarios (warming, acidification, fluctuations in heat and pH simulating heatwaves, or upwelling events). We will measure the overall productivity of each component of the ecosystem (seagrass, algae, isopods). This project is closely linked to one suggested by Pierre De Wit on Isopods, and feeds into a larger internationally coordinated project investigating the impacts of genetic diversity of seagrass mesocosms on resilience to future fluctuating climates. That project will run in spring/summer of 2020 in collaboration with researchers from Kiel and Tromsø. Suitable level and length: Master (60 hp). Time and place: Starting in the Fall of 2019 or Spring 2020 at the Tjärnö Marine Lab. Contact: Jon Havenhand [email protected]

Pierre De Wit [email protected]

Seagrass mesocosms with CO2 control systems. We will control seawater pH and temperature to create “current” and “future” climates in the mesocosms

Seagrass have many shoots per plant / genotype. This lets us pick whether we have many shoots of one genotype or one shoot each of many genotypes in each mesocosm

Seagrass, algae, and isopods in a mesocosm. We will use multiple trophic levels to simulate natural seagrass beds

Title: Wind farm wakes and the induced ocean circulation.

Main supervisor: Göran Broström, [email protected]

Focus of the project: Physical Oceanography

Location: Göteborg

Background: Offshore wind farms become more and more abundant, they also becomes larger and larger with ever increasing size of the wind mills. Behind a wind farm, the wind speeds will be lower, and thus also the wind stress on the sea surface. This creates a strong artificially curl of the wind stress, which in turn create up- and down-welling patterns. There have not been any study of the oceanic response on time scales longer than a few days, and the aim of the project is to carry out such analysis.

Problem: se above.

Method: The student will setup and use an ocean General Circulation Model (GCM), and outline a design to study how the wind curl behind a wind farm will impact on the upper ocean. Some preliminary numerical experiments using MITgcm are available. The student will carry out a suite of numerical experiment and analyze results. The project also includes a theoretical part to describe results at least in some detail, and vertical integration of e.g. vorticity should be a part of the project. Simplified reduced gravity models may also be considered for increasing clarity on dynamics.

Suitable level and length: MSc (45-60 hp).

Suitable time period: “project can be performed all year round"

Title: Seiches in Lake Vättern.



Location: Göteborg

Background: Lake Vättern is the second largest lake in Sweden. It is quite deep and has a simple geometry. It is well known that there are some seiche-oscillations in the lake. The present project aims at studying those in some greater detail.

Problem: Some new measurements of water level have been taken by the supervisor. The student will analyze this observation e.g. with respect to dominating frequencies in the spectral analysis of the time series. The data analysis will consider how accounting for atmospheric pressure influences analysis of seiche amplitude and frequencies. Role of sampling interval should also be considered. The work aims at suggesting new measurement strategies for further and improved studies of these seiches. New measurements will be taken in 2019, and this work is a pre-study for these observations.

Method: The method will be analytical and numerical analysis of time series that is available. Some simple laboratory work to determine response time of device may be included. Furthermore, some simple eigenmode analysis using COMSOL multhipysics can be included.

Suitable level and length: Bachelor (15 hp) but project can be extended to suitable education level. At MSc level, designing and carrying out field measurements should be considered.

Suitable time period: spring 2019

Title: Near inertial oscillations in Lake Vänern.



Location: Göteborg

Background: Lake Vänern is the largest lake in Sweden. It is quite deep at parts but has a complex geometry. Some new observations on thermal structure (moorings) shows presence/strong indication of large internal waves having frequencies close to the rotational frequency. It was a somewhat surprising result from a recent observational study. The present project aims at studying those observations in greater details. For instance, will existing Ocean General Circulation (GCM) models for lake Vänern display similar waves.

Problem: The student will analyze newly taken observations from lake Vänern e.g. with respect to dominating frequencies in the spectral analysis of the time series. The student should also make literature studies for putting measurement into a broader perspective. There exist a high-resolution ocean model for lake Vänern, and part of the investigation is to seek for similar waves in the Vänern GCM runs. New measurements will be taken in 2019, and this work is a pre-study for these observations.

Method: The method will be analytical and numerical analysis of time series that is available. Literature studies will be required, as well as analysis from a GCM output.

Suitable level and length: Bachelor (15 hp) but project can be extended to suitable education level. At MSc level, designing and carrying out GCM experiments should be considered.

Suitable time period: “project can be performed all year round"

Parametrisering av primärproduktionens ljusberoende i svenska marina områden. Bakgrund: Fytoplanktons upptag av koldioxid genom fotosyntesen är en av de viktigaste processerna inte bara för att det är grunden för de marina näringskedjorna utan även för att det är en av de största omsättningarna av växthusgaser på jorden. Att kunna uppskatta och beskriva denna är därför av fundamental betydelse både för den marina ekologin och för klimatforskningen. Den metod som generellt används är att man, vid en station, tar vatten på olika djup, fyller det på flaskor, som sedan inkuberas under ett antal timmar varefter men tar upp dem läser av hur stor fotosyntes som skett. Detta kan mätas antingen som producerad syrgas eller upptag av radioaktivt märkt koldioxid. Från dessa mätningar kan man göra integreringar över hur stor den sammanlagda fotosyntesen är i hela vattenpelaren eller man kan (om man har ljusdata tillgängligt) parametrisera det hela en ljusmättnadskurva som exv enligt ekvation av Jassby and Platt (1976):

$ = $&(1 − *+,-./)

P är där produktion; Pm (maximala produktionen); α lutningen vid origo i en ljusmättnadskurva; E är ljusstyrkan. För långsiktiga och globala uppskattningar så krävs det att man kan generalisera dessa parametriseringar till att vara giltiga för flera tider och positioner än just då de är mätta. Det är så man har gått till väga för uppskattning av den globala produktionen. Man identifierar ett antal olika biogeokemiska domäner där man antar att man kan använda samma ljusmättnadskurva och då ljuset och biomassa kan uppskattas med hög upplösningen från satellitdata så ger det globala uppskattningar av produktionen. Dessa uppskattningar blir dok, med nödvändighet, väldigt grova och för en mer tillförlitlig beskrivning av omsättningarna på lokal nivå krävs större upplösningar i både tid och rum. Projektets målsättning Det har inom den marina övervakningen gjorts regelbundna mätningar av primärproduktionen på ett antal platser. Dessa har i viss mån bearbetats till integrerade produktioner men har systematiskt parametriseras enligt ljusmättnadskurvor så att man kan uppskatta möjligheter till att göra generella uppskattningar av hur homogen produktionskapaciteten är och om det finns vissa perioder/lokaler som avviker. Projektets målsättningar skall därför vara att genomföra sådana parametriseringar med samma teknik för tillgängliga data och utifrån det göra utsagor om möjligheter till generaliseringar. De data som kommer i första hand är den serie med mätningar i Gullmarsfjorden som sträcker sig 30 år tillbaka med minst en mätning per månad. Andra serier finns inom den generella övervakningen och från fältstationer i Östersjön. Framtid Detta arbete kommer att vara en del av den utbyggnad av kompetenser då det gäller användningen av satelitdata för uppskattning av fytoplantonsammansättning och produktion som vi planerar att bygga upp på marina institutionen. Omfattning Arbetet lämpar sig väl som ett kandidatarbete inom marin vetenskap (15 hp). Skulle kunna expanderas till ett masterarbete eller längre kandidatarbete (30hp) om fler aspekter tas upp. Förkunskapskrav Det krävs att man har viss känsla för och kunnighet då det gäller fytoplanktons fotosyntes. Vad som mera krävs är beredskap att hantera databaser och kunnighet att hantera data med exv Matlab eller R. Handledare Sten-Åke Wängberg (samverkan med Peter Tiselius), [email protected]

Title: Nitrogen and phosphorus in the Baltic Sea – variations in benthic fluxes between basins

Main supervisor: Astrid Hylén ([email protected])

Co-supervisor: Per Hall ([email protected])

Focus of the project: Marine chemistry


Background: Eutrophication and spreading of oxygen-depleted zones are increasing around the world. These problems are expected to be enhanced by climate change and a growing population on earth. It is therefore crucial that we understand the mechanisms behind these problems, so that we can counteract and mitigate their effects. The Baltic Sea, the world’s largest continental brackish water sea, comprises several basins that differ significantly in several aspects. The Gulf of Bothnia in the north is relatively pristine, while the Baltic Proper and Gulf of Finland in the south are heavily affected by human activities and suffer from increased nutrient concentrations, eutrophication and oxygen depletion in the bottom water. Since problems experienced here now are observed in many parts of the world, it has been suggested that the Baltic Sea could be seen as a “time machine” for the future coastal ocean. Combined with some of the world’s longest oceanographic observation time-series, the difference between basins make the Baltic Sea suitable for studies of mechanisms behind eutrophication and spreading of oxygen-depleted zones. Problem: For almost two decennia, the group for benthic biogeochemistry at the University of Gothenburg has sampled the Baltic Sea in situ with benthic chamber landers. This has resulted in a large set of published and unpublished sediment-water nutrient fluxes. The purpose of this project is to compile and analyse these data and with the help of environmental parameters draw a picture of how and why fluxes of nitrogen and phosphorus vary between basins.

Method: Literature studies, statistical analysis in the software R (no previous knowledge in R required)

Suitable level and length: Bachelor (15 hp)

Suitable time period: Spring or summer 2019

Exam projects within the OPTIMUS (Optimization of mussel farming cultures for fish feed in in the Baltic Sea) project Background OPTIMUS is a 3-year project with the focus on various aspects of mussel farming and its environmental impacts. The overall goal of the project is to provide scientific documentation for the potential and impact on the coastal environment of mussel aquaculture. Harnessing the full potential of the “blue economy” is seen today as one of the most promising means to boost growth, employment opportunities and competiveness. In marine systems like the Baltic Sea that already are heavily exploited and subject to multiple anthropogenic pressures, it is of key importance for the long-term sustainability of the blue growth that it does not add to the pressure factors. Aquaculture of extractive species like mussels and seaweed is an example of a blue growth potential that will not add to the pressure on the Baltic ecosystem but in contrast has the potential to mitigate some of the effects of excess load of nutrients. Before mussel farming can be accepted as a mitigation tool by the public, stakeholders and managers, there is a need for a robust demonstration of the ecological feasibility of using the tool in different types of environments in the Baltic Sea. Mussel farms not only remove nutrients by harvesting, but in addition have positive effects on the environment by improving water clarity and reducing Chl. a and seston concentrations. There may on the other hand be negative effects through increased sedimentation of biodeposits below the farms increasing the oxygen consumption and changing the sediment chemistry and benthic fauna. The impact is known to depend on mussel density and environmental conditions such as hydrography, water exchange, sediment type, and eutrophication status.

As OPTIMUS is a project that deals with a wide range of aspects of mussel farming, there are many different questions that can be performed and evaluated as an exam project. Below are some different suggestions but we are open for discussion about any suggestions from students regarding potential projects related to bivalve aquaculture. Potential projects Project A: Growth and survival

This project focuses on experimental studies on the survival and growth of potential mitigative species under mussel farms and their utilization of the biodeposition of faeces and pseudofaeces. These studies will allow for identification of species likely to survive and growth well under the conditions present at mussel farm sites and thus might have a potential to function as species mitigating the effects of biodeposition from the farms on the sediment surface.

Project B: Mitigative effects Here the focus is on the effects of different potentially mitigative species on biogeochemical fluxes across the sediment-water interface. By studying how a specific species affects the fluxes of nutrient in environment affects by biodeposits from mussel farms vs environments that are unaffected an idea of the effect the species will have on sediment below mussel farms if used in remediation efforts.

Project C: Environmental impacts of mussel shells One potentially big impact on the sediment below mussel farms is deposition of shells from the farm. This project includes studies on how the accumulation of shells on the sediment surface influence the fluxes of nutrients across the sediment-water surface and the potential of different bioturbating species to

Figure 2. The Mussel mitigation concept

survive, grow and thrive in sediment affected by high organic load, such as under a mussel farm.

Project D: Impact on the benthic organism community By studies of the macrofauna below mussel farms located in areas with different environmental conditions the environmental parameters, influencing the effect of mussel farms on the macrofaunal communities can be evaluated. This study is preferably conducted during 2018 when a more extensive sampling is planned for the most mussel farming intensive area on the Swedish west coast.

Project E: Caging Before any mitigative efforts can be performed in field, methods for caging of species need to be tested. This project focuses on development and testing of caging methods for different potentially interesting mitigative species.

Length of projects Preferably, master level (30-60 hp) but shorter projects can also be discussed depending on the preferred research question.

Time frame Depending on the specific research question(s) selected for the projects.

Location Experimental part:

Tjärnö Marine Field Station and depending on the project potentially partly also at collaborating mussel farms.

Analysis and writing: Preferably at Tjärnö but can be partly done elsewhere depending on the student.

Contacts Mats Lindegarth Epost: [email protected] Tel : 031-786 9672 Per Bergström Epost: [email protected]

MSC project: “Investigation of molecular clock genes of the European shore crab Carcinus maenas” Contact: Marlene Jahnke, [email protected] This project is part of a VR-financed project of Prof. Per Jonsson and Associate Prof. Per-Olav Moksnes and you will be directly supervised by the PostDoc Dr. Marlene Jahnke. You will investigate molecular clock genes, a topic that won the Nobel Prize in 2017! The big topic of the project is “Local adaptation driven by evolution of dispersal traits in marine larvae”. Most marine invertebrate disperse during a planktonic larval stage that may last for many weeks while drifting with the ocean circulation. A challenge for larvae of coastal species is to stay close to the coastline or return at the time of recruitment. Most larvae may control their vertical position in the water column and can perhaps exploit depth-dependent variations in water transport to modify their net dispersal. Carcinus maenas shows a cline in larval behavior (vertical migration) along a gradient in tidal influence from the English Channel to the Kattegat. In areas where tides are significant, shore crab larvae display an inherited endogenous vertical migration rhythm with local tides, which is believed to facilitate cross-shelf transport and recruitment. In areas where the tide is insignificant, larvae show instead migration to deeper waters during the day, possibly reducing predation. Oceanographic modelling and behavioural data collection is ongoing and we have collected samples from the English Channel up to the Baltic for genetic analyses (SNP genotyping). We will therefore have a good knowledge of population genetic structure and want to add RNA-based studies on genes that may be involved in the regulation of the above described larval behaviour. Recently, it was found that a family of neuropeptides in crabs (pigment-dispersing hormones, PDHs) likely is involved in the molecular clock that controls circatidal rhythm. We will use published sequences of shore crab PDHs and other potential clock genes to screen for differences in expression of these genes among tidal and a-tidal crabs. Additionally we will also investigate potential changes in DNA sequences of these candidate genes and will investigate differences in methylation patterns, to also investigate the potential role of epigenetics in driving larval behaviour. Lab techniques that will be used include RNA- and DNA- extraction, qPCR, PCR, gel electrophoresis and enzyme digestions. The project will also involve bioinformatics for screening available transcriptomes, genomes and sequence data-bases for potentially interesting candidate genes and for analysing DNA and RNA-based results. The position is based on Tjärnö.

Title: Exploring aquaculture of the seaweed fly (Coelopa frigida)

Main supervisor: Emma Berdan ([email protected])

Focus of the project: marine biology

Location: Göteborg/Tjärnö

Background: Fishmeal and fish oil production cannot sustain the growing aquaculture industry, which is growing at fast pace. Alternative feeds are necessary but common animal feeds such as soybeans do not contain the vital fatty acids necessary for fish growth. Coelopa frigida, the seaweed fly, grows at a fast rate on rotten seaweed, and its larvae are potentially suitable for fish feed.

Problem: We are exploring the best methods of culturing C. frigida as well as working towards tests of fish growth.

Method: The project would be on determining the best methods for culturing C. frigida and doing some analysis of the amino and fatty acid content. It is possible that the student could also be involved in feeding trials at a later date.

Suitable level and length: project can be adapted to suitable education level

Suitable time period: spring and summer 2019

Title: Small-scale transport of microplastics: the role of hydrodynamics on particle dispersal and trapping

Main supervisor: Dr. Eduardo Infantes, [email protected]

Focus of the project: Interdisciplinary project; oceanography, marine biology and marine chemistry.

Location: Kristineberg marine station.

Background: Pollution of the marine environment with plastic is an increasing worldwide problem with a challenging solution. Plastics in the environment can decompose in small fragments or particles called micro-plastics. These particles are hazardous in the environment because they can be ingested by a wide variety of different marine organisms (eg. fish, turtles, mammals, birds). Microplastics have a long degradation time and during this time they can travel and disperse over large-scales by currents. On a small-scale less is known about the transportation patterns of different types of microplastics (eg. particles size, buoyancy, density).

Problem: The west coast of Sweden is affected microplastics that are transported from other coastal regions and accumulated in the area, but also by local point-sources. Little is known of the local small-scale transport of microplastic in our area and the effects that these pollutant particles can have on the local environment. Coastal habitats have different levels of hydrodynamic exposition and bottom complexity, for example, particles could be easily transported in shallow coastal areas with higher waves and currents than deeper areas. In the same way, eelgrass beds have higher bottom roughness than sandy bottoms which increase the trapping of small particles. Information about these processes could be useful to increase general knowledge about plastic transport and trapping, but also provide some empirical parameters that can be used for oceanographic and coastal dispersion models. The aim of the Master project is to 1) quantify the hydrodynamic conditions to disperse floating and submerge microplastics in the marine environment and 2) determine the level of bottom complexity or substrate type that will experience higher accumulation or trapping of particles.

Method: A hydraulic flume at Kristineberg that simulates currents and waves will be used to quantify small-scale transport of microplastics. Environmental substrates will be reproduced in the flume representing common Swedish coastal habitats (eg. sandy bottom, rocky bottom, macroalgae, oyster/mussel beds and eelgrass meadows).

Suitable level and length: Master (30, 45 or 60 hp)


Student project: Genetic assessments of biodiversity in the Koster National Park Time effort: 15-60 HP Earliest possible start: April 2019 In this project you will use different genetic monitoring devices to assess status and changes of biodiversity in the coastal environment of the Koster National Park. To this end you will be able to deploy Artificial Reef Monitoring Structures, so-called ARMS (http://arms.biocodellc.com/), as well as take sediment, plankton, and microbial samples. The samples will be processed further for genetic analysis. Sampling will take place between May and June and you will be able to analyse genetic sequence data from samples collected in 2018. The initial scientific purpose of the project is to identify newly arrived Non-Indigenous Species (NIS) and track the migration of already known NIS. If appropriate you can also focus on alternative or additional scientific questions, such as e.g. compare communities across different environmental gradients, habitats and locations. The project is part of an international network (http://www.assembleplus.eu/research/ocean-sampling-day-2018), which has similar deployments across Europe and in the Polar Regions. For more information on the activity, please contact Matthias Obst ([email protected]) at the University of Gothenburg, Sweden.

Självständiga arbeten (examensarbeten) för: kandidat, magister och masternivå

Biogeokemisk struktur och funktion hos kustnära marina ekosystem

Kontakt: Prof. Stefan Hulth [email protected] 031-786 9024

Övergripande bakgrund Om du har för avsikt att utföra ditt självständiga arbete (examensarbete) på kandidat-, magister-, eller masternivå utgör nedanstående beskrivning ett axplock av exempel på möjliga inriktningar inom det övergripande området ”Biogeokemisk struktur och funktion hos kustnära marina ekosystem”. Tillsammans med mig eller någon av mina medarbetare försöker vi gemensamt, utifrån intresse och individuella förutsättningarna, utforma ett lämpligt projekt för respektive nivå. Exempel på delområden där vi bedriver forskning är:

• Mikrobiell biogeokemi och betydelsen av funktionell biodiversitet för viktiga ekosystemfunktioner (hastighet och reaktionsvägar i kretsloppen av C, N och P under mineralisering av organiskt material) i bentiska system.

• Utveckling av state-of-the-art analytiska tekniker att bestämma lösta ämnen med hög riktighet och precision (t.ex. kemiska och biologiska sensorer)

• Användande av molekylära diagnostiska verktyg (genomik och proteomik) för att identifiera och karakterisera mikrobiella samhällen (struktur och funktion)

Ytterligare exempel på mer specifika projekt är: • Kemiska och biologiska sensorer för högupplöst (tid och rum) detektion av lösta

ämnen

• Alternativa reaktionsvägar i kvävets kretslopp (t.ex. anammox)

• Mikrobiell biodiversitet och ekosystemfunktioner

• Funktionell biodiversitet av sedimentlevande makrofauna och nedbrytning av organiskt material

Dynamics and kineticsof surface-catalyzed

vesicle formation

Cell and organelle intra-communication throughlipid-nanotube networksMolecular biology,

physiology and ecology

Microbial functional characterization and biodiversity

Structure and function of marine ecosystems

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Dynamic, high-resolution solute detection

Macrofaunal functionalbiodiversity

Biotechnology

In situ molecularbiomarkers

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vesicle formation

Cell and organelle intra-communication throughlipid-nanotube networks

Cell and organelle intra-communication throughlipid-nanotube networksMolecular biology,

physiology and ecology

Microbial functional characterization and biodiversity

Structure and function of marine ecosystems

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• Betydelsen av sedimentlevande mikroalger för filterfunktionen i solbelysta kustnära ekosystem

Intresseanmälan Är du intresserad av att veta mer om vilka möjligheter som finns till självständiga arbeten inom ramen för forskningsområdet ”Biogeokemisk struktur och funktion hos kustnära marina ekosystem” är du välkommen att höra av dig till [email protected] för en fördjupad dialog. I normalfallet är det möjligt att starta arbetet (15, 30, 45 eller 60 hp) närhelst under året även om begränsningar kan förekomma beroende på praktiska orsaker. Arbetet kan skrivas både på svenska och engelska, även om det krävs särskilda språkfärdigheter att skriva kandidatarbetet på engelska.

Tidigare arbeten Exempel på tidigare självständiga arbeten är:

• Östersjön: En fråga om fosfor eller kväve ?

• The presence of anammox (Anaerobic AMMonium OXidation) bacteria in the Baltic Sea

• Betydelse av ytsedimentets reaktivitet för absoluta och relativa hastigheter av ANaerob AMMonium OXidation (anammox) i kustnära marina sediment

• Benthic oxygen and nutrient fluxes beneath long-line mussel farms

• Benthic Macrofauna and Biogeochemistry in Highly Reducing Sediments – An Experimental Approach

• Effects of different oxygen conditions and density of bioturbating macrofauna on nutrient cycling in benthic sediments of the Swedish west coast

• Identifiering och karaktärisering av bakterier i sediment - tipsonikering som metod vid provupparbetning

• Fluorescent Dissolved Organic Matter in Shallow Water Embayments

• Kovalent inbindning av 3,6,8 hydroxypyren trisulfonsyra till cellulosa

• On-line bestämning av 14NO3- och 15NO3

- i havsvatten med LC-MS

• Potentialkänsliga färgämnen och optiska sensorer för ammonium

• Fluorosensors for the detection of O2 and NH4+ in natural waters

• Imaging NH4+ concentration and diffusion transport using a ratiometric fluorosensor

• Distributions of solutes and particle associated compounds in marine sediments: a 2-D approach

Benthic oxygen and nutrient fluxes in illuminated shallow-water sediment systems: organic matter input and trophic status

Grunda och solbelysta sedimentsystem är betydelsefulla för kustzonens filterfunktion, dvs. möjligheten att omvandla och kvarhålla biotillgängliga närsalter (t.ex. N, Si och P) från transport till havet. De grunda systemen har genom sin fotosyntetiska aktivitet potential att agera källor eller sänkor för syre, koldioxid och närsalter. Förmågan att agera filter beror bland annat på systemets trofiska status (balansen mellan primärproduktion och respiration) där den heterotrofa komponenten också påverkas av kvalitet och kvantitet av reaktivt organiskt material i sedimentet. Det här föreslagna självständiga arbetet syftar till att genom sediment-vatten inkubationer kvantifiera trofistatus och flöden av DIC/alkalinitet och närsalter på två kontrasterande lokaler med avseende på organiskt innehåll i sedimentet. Inkubationerna bör upprepas med visst mellanrum för att relatera till betydelsen av organiskt material som brutits ner för de uppmätta flödeshastigheterna. I arbetet kommer du bland annat att:

• Genom litteratursökning hitta lämpliga referensartiklar

• Kartlägga mekanismer som styr syre och närsaltsflöden samt flöden av DIC och alkalinitet i solbelysta kustområden på dygnsbasis

• Kvantifiera trofisk status, NPP, GPP samt bentiska flöden av DIC och alkalinitet under dag och natt

• Bestämma porvattenfördelning av syre, DIC, alkalinitet och närsalter

• Bestämma koncentrationen av organiskt kol i sedimentet

Arbetet har en inriktning mot biogeokemi och är framförallt lämpligt på magister- eller master nivå (30 – 60 hp). Del av det experimentella arbetet kommer att bedrivas på Kristineberg.

Kontaktperson: Prof. Stefan Hulth ([email protected]), 031-786 9024

Characterization of anammox bacteria in marine sediments using linear epitopes and subdiffractional immunofluorescence

spectroscopy Anammoxbakterier är betydelsefulla i kvävets kretslopp och spelar en viktig roll i omvandlingen av biotillgängligt kväve (ammonium, nitrit och nitrat) till mer inert kvävgas i marina system. Genom molekylära tekniker (t.ex. FISH) och fylogenetisk analys påvisas en stor närvaro av anammoxbakterier i många olika typer av marina system. Emellertid tycks diversiteten starkt begränsad där bakterien i marina system exklusivt tillhör släktet Candidatus ‘Scalindua’. I det föreslagna självständiga arbetet kommer hastigheter av anammox och denitrifikation i sediment bestämmas genom 15N-inmärkning. Absoluta och relativa hastigheter kommer sedan relateras till funktionell karakterisering av anammoxbakterierna (Scalindua) genom linjära epitoper och immunofluorescens med extremhög upplösning. I arbetet kommer du bland annat att:

• Genom litteratursökning hitta lämpliga referensartiklar

• Extrahera bakterier från sedimentpartiklar med tipsonikering

• Utföra 15N-inmärkningar för att bestämma processhastigheter för anammox och denitrifikation

• Använda linjära epitoper för specifik immunofluorescens av marina anammoxbakterier (Scalindua)

• Använda STED som teknik för extremhög upplösning av fluorescens

Arbetet har en inriktning mot analytisk kemi/biogeokemi och är framförallt lämpligt på magister- eller master nivå (30 – 60 hp). En mindre del av det experimentella arbetet kommer att bedrivas på Kristineberg.


Optiska sensorer för kvantifiering av lösta ämnen i marina system

Under den senaste 25-årsperioden har optiska sensorer blivit ett allt vanligare analytiskt verktyg att med hög riktighet och precision kunna bestämma koncentrationen av lösta ämnen i havet. En rad olika tekniker har utvecklats för att optiskt kvantifiera ett flertal av de biogeokemiskt intressanta ämnena. Exempel på ämnen som kan bestämmas med optiska sensorer är O2, pH, CO2, NO2-/NO3-, NH4+ och Mn2+. Det här föreslagna kandidatarbetet i marin vetenskap (15 hp) är ett teoretiskt arbete som syftar till att utifrån vetenskaplig litteratur:

• Kartlägga vilka ämnen som hittills kan bestämmas genom optiska sensorer

• Lära känna och analytiskt kunna beskriva ett antal olika optiska tekniker samt eventuella för- och nackdelar/begränsningar med deras användning

• Exemplifiera några användningsområden där optiska sensorer har en tydlig fördel jämfört med traditionella metoder relaterade till diskret provtagning och efterföljande våtkemisk analys

• Skissera och föreslå princip för att optiskt bestämma koncentrationen av (minst) ett ämne för vilket en optisk sensor ännu inte utvecklats (alt. föreslå princip att signifikant förbättra en existerande sensor)

Arbetet har en inriktning mot kemi/biogeokemi och är ett litteraturarbete framförallt lämpligt på kandidatnivå (15 hp).


Visualisering och kvantifiering av bakterier i marina sediment Att visualisera och kvantitativt bestämma abundans och sammansättning (taxonomiska nivåer) av mikroorganismer utgör ett betydelsefullt verktyg att uppskatta biogeokemisk status och kunna förutsäga hur olika marina system svarar på miljöpåverkan. I takt med utvecklingen av molekylära metoder och tekniker för genomsekvensiering finns idag möjligheten att visualisera och kvantifiera också vissa marina bakterier ner till artnivå. Det här föreslagna kandidatarbetet i marin vetenskap (15 hp) är ett teoretiskt arbete som syftar till att utifrån vetenskaplig litteratur:

• Beskriva grundläggande principer för hur sedimentlevande bakterier genom molekylära tekniker kan visualiseras och kvantifieras ner till artnivå

• Exemplifiera funktionen av några typer av bakterier som har bestämts (identifierats och kvantifierats) med hjälp av molekylära tekniker i marina system

• Beskriva begränsningar med nuvarande tekniker och skissera principer för eventuella förbättringar i tillvägagångssätt.

Arbetet har en inriktning mot biogeokemi och är ett litteraturarbete framförallt lämpligt på kandidatnivå (15 hp). Kontaktperson: Prof. Stefan Hulth ([email protected]), 031-786 9024

Marine pelagic food web structure The lower trophic levels of the marine pelagic environment are a highly dynamic part of the coastal ecosystem. My research focus on clarifying the ecological function of the smallest plants and animals in this system. A lot is known about the zooplankton larger than 1 mm and also of the phytoplankton smaller than this size. But there is a general lack of understanding of what controls the trophic levels of these small organisms. I can supervise projects involving experiments, observations and field studies of the plankton in the Gullmar fjord and work based at Kristineberg. Recently, we have discovered potential trophic structure among the microzooplankton and we would like to study this in more detail. Correlation studies indicate an intermediate grazing level between ciliates and small autotrophic phytoplankton. Student projects can be developed to suit your interest in this field. Interested? Contact: [email protected] For more background info, see: http://plankt.oxfordjournals.org/cgi/reprint/fbw096? ijkey=m22pNm0OJQAfz9z&keytype=ref

A suggested scenario how copepods and Mnemiopsis leidyi may affect the lower trophic levels of the food web. A. In years without M. leidyi the copepods are abundant controlling the ciliate biomass and reducing the larger phytoplankton. This creates a flagellate dominated base for the food web. B. When M. leidyi removes the copepods, ciliates thrive and reduce flagellates while supporting M. leidyi larval growth. In order to start the rapid reproduction of M. leidyi, a sufficient fraction the copepod biomass needs to be removed to relieve ciliates from their predation pressure. Green arrows indicate changes in phytoplankton biomass, blue arrows indicate changes in zooplankton biomass.

Effects of ocean acidification on shell shape/morphometrics and implications for aquaculture Supervisor Kirti Ramesh ([email protected]) Co-supervisor Sam Dupont Focus Climate change and aquaculture Location Kristineberg Background

Understanding the effects of ocean acidification (OA) on key aquaculture species such as oysters is an important challenge and defines our ability to predict the ecological and economic challenges of anthropogenic climate change. In Sweden, the native flat oyster (Ostrea edulis) faces threats in the form of competition (invasive Pacific oyster) and sensitivity to climate change. However, limited information is available o n how this species will be affected OA. Specifically, there is no information regarding the plasticity of shell shape and shell traits in O. edulis. To remedy this knowledge deficit, we are currently running a long-term experiment under control (current day) and simulated OA conditions

using juvenile O. edulis. Aim The main aim of this project will be to evaluate the effects of simulated ocean acidification on shell morphometrics of the native European flat oyster (Ostrea edulis). A supplementary goal of this project will be to examine what effects (if any) alterations in shell shape will have for the oyster aquaculture industry. Method Shell shape and morphometrics (traits) will be analysed using packages designed for R. The experiment is already 4 months underway and the main challenges for the student will be fine tuning scripts and analyses for the species at hand (Ostrea edulis). These will be based on previously established techniques (see Telesca et al 2018: https://www.nature.com/articles/s41598-018-20122-9). There is scope to implement additional techniques (eg: SEM imaging) depending on the students’ interests. Level This project is ideally for a 60hp Masters’ thesis and we are looking for candidates with a basic knowledge of R.

Miljöeffekter av utsläpp från konstgräsplaner: hur påverkas fiskar av partiklarna som hamnar i våra vattendrag? Fotbollsplaner med konstgräs blir vanligare allt eftersom naturligt gräs ersätts med dessa produkter, som är gjorda av nyproducerad och återvunnen gummi. Studier har visat att konstgräs släpper ifrån sig en del farliga kemikalier som tex PAHer och metaller. Kemikalierna är kända mutagener och cancerogena ämnen. Vi vet inte exakt vilka mängder gummi som hamnar i miljön och en del av projektet gäller undersökningar av dagvatten samt dess utlopp i Göteborgs hamn. Vi vill också använda gummipartiklarna i toxicitets tester för att mäta effekter av dessa på magtarmkanelens fysiologi och barriäregenskaper hos fisk. Studenten kommer att få möjlighet att arbeta delvis med fältprovtagningar samt laborativt. Projektet är baserat på fysiologiska samt ekotoxikologiska frågeställningar. Projektet bäst lämpad för masters nivå. Kan göras vilken tid på året som helst. Plats: Zoologen i Göteborg. Kontakta [email protected] eller [email protected]

Round goby thesis projects (Bachelor/Master, 15-45 ECTS) Invasive species pose a serious threat to biodiversity in aquatic ecosystems. The round goby is native to the Black Sea and Caspian Sea and was probably transported to the Baltic Sea in ballast water. First found in the Gulf of Gdansk in 1990, it has rapidly expanded its range:

in 2008 it was found in in the Karlskrona archipelago in Sweden, in 2010 it was reported from Visby and Gothenburg, in 2013 from Muskö in the southern Stockholm archipelago, and in 2014 it was found in the Kalmar strait. The round goby is an invasive species with high reproductive turnover rate and high tolerance to various environmental factors. It may compete with other Baltic Sea bottom-dwelling species such as black goby, eelpout and flounder. Negative effects of the species’ invasion have been reported from the Great Lakes (U.S.) but it is still unclear which impact it may have on Swedish coastal ecosystems. Basic information about round goby traits and food web impact is lacking, and the thesis proposals listed below will help filling these knowledge gaps.

1. Variation in life history characters between round goby populations in Sweden. Monitory fishing for sampling of otoliths (age determination), length, weight and sex (including gonadal

status) of fish from an area within Sweden where the species is abundant, e.g. Gothenburg, Karlskrona, Kalmar or Visby. The results are compared with data from other areas where the species is indigenous or well-established.

2. Round goby diet plasticity. Sampling of fish in the field and/or laboratory experiments of gut content in order to study how round goby food consumption varies spatially and temporally. The study is carried out in an area where the species is

abundant, e.g. Gothenburg, Karlskrona, Kalmar or Visby. 3. Utilization of round goby as prey. To which extent do native predators (seals, cormorants

and/or predatory fish) feed on round goby? Predator gut content from the Karlskrona area is analyzed in order to answer this question.

The thesis projects could include field work between May-September and/or experimental work, but there is also data available for analyses, meaning that the projects could be carried out at any time during the year. Depending on the student’s knowledge and interest the projects could be carried out either within the field of Ecology or Environmental analysis. The size and scope of the projects is flexible and would be suitable for students at both bachelor and master levels. For further information, please contact Ann-Britt Florin, Institute of Coastal Research, Swedish University of Agricultural Sciences (SLU): [email protected]; 010-478 41 22 or Isa Wallin: [email protected]; 010-478 41 62. Internal contact person at University of Gothenburg is Carl André: [email protected]

Examensarbeten om svartmunnad smörbult (kandidat/master, 15-45 hp) Invasiva arter är ett allvarligt hot mot den biologiska mångfalden i akvatiska ekosystem. Den svartmunnade smörbulten är en fisk med ursprung från Svarta havet och Kaspiska havet och har sannolikt kommit via barlastvatten till Östersjön. Den rapporterades första gången 1990 i Gdanskbukten där den nu är den vanligast

förekommande kustnära fiskarten. År 2008 observerades arten för första gången i Sverige, i Karlskrona skärgård, och under 2010 kom rapporter om fynd både i Göteborgs och Visby hamn. 2013 kom nya rapporter av arten ifrån Torhamn i Blekinge, Muskö vid Nynäshamn och inre Bråviken, och 2014 observerades den i Kalmarsund. Den svartmunnade smörbulten är en invasiv art med hög reproduktionstakt och hög tolerans för olika miljöfaktorer. Det finns risk för att den kan komma att konkurrera med andra bottenlevande arter som svart smörbult, tånglake och skrubbskädda. I de stora sjöarna i Nordamerika finns negativa effekter rapporterade men vi vet ännu inte vilken påverkan svartmunnad smörbult kan ha i svenska vatten. Grundläggande information om hur arten beter sig i våra kustekosystem saknas, och nedanstående projektförslag bidrar på olika sätt till

denna kunskapsuppbyggnad. 1. Livshistoriekaraktärer hos

populationer av svartmunnad smörbult i Sverige. Provfiske för insamling av data om ålder (otoliter), längd, vikt, kön och könsstatus i något område där arten förekommer i stor mängd i Sverige, t.ex. Göteborg, Karlskrona, Kalmar eller Visby. Jämförelse av resultat med data från andra områden där arten är naturligt förekommande eller etablerad sedan en längre tid.

2. Födoval hos svartmunnad smörbult. Insamling av fisk i fält och/eller experiment på lab för att studera vad smörbulten äter i olika områden och över säsonger. Görs i något område där arten förekommer i stor mängd i Sverige, t.ex. Göteborg, Karlskrona, Kalmar eller Visby.

3. Svartmunnad smörbult som bytesart. I vilken utsträckning utnyttjar inhemska predatorer (säl, skarv och/eller rovfisk) svartmunnad smörbult som byte? Maginnehåll från predatorer från Karlskrona analyseras på lab för att besvara denna frågeställning.

Projekten kan inkludera fältverksamhet under sommarhalvåret (maj-september) och/eller laboratorieexperiment, men det finns även redan insamlat material att använda så de kan göras när som helst under året. Beroende på bakgrundskunskaper och intresse kan examensarbetet göras antingen inom ekologi eller miljöanalys. Omfattningen är flexibel och projekten kan göras på både kandidat- och masternivå. För mer information, kontakta Ann-Britt Florin, Kustlaboratoriet, Sveriges Lantbruksuniversitet: [email protected]; 010-478 41 22 eller Isa Wallin: [email protected]; 010-478 41 62. Intern kontaktperson vid Göteborgs Universitet är Carl André: [email protected]

Scandinavian bivalves — conservation status and interactions with invasive Pacific oysters Ane Timenes Laugen, University of Agder & Åsa Strand, IVL Swedish Environmental Institute

Our bivalve research group can offer several types of projects in conservation biology for GU-students, both at BSc- and MSc-level,

Possible topics (a non-exhaustive list) 1. Population control and management of Pacific oysters through commercial activities such as

harvest of wild populations and population modeling 2. Efficiency of the Norwegian efforts to remove Pacific oysters from popular beaches 3. Interactions between Pacific oysters and native bivalves and restoration trials to enhance

native bivalve populations 4. Literature studies to determine the baselines for determining conservation status and future

management actions to protect native blue mussels and European oysters 5. The geographic range expansion of the invasive Pacific oyster and its effects on local

communities along a salinity gradient 6. Development of new culture protocols for both native bivalves and Pacific oysters using

submerged culture systems 7. Alternative methods for stock enhancement of flat oysters

Work place Some of the projects can be computer-based (e.g. 4) and can thus take place anywhere with frequent contact with supervisors through email and Skype. Other projects can be based entirely at Sven Lovén Centre for Marine Science at Kristineberg or Tjärnö (e.g. 3, 6, 7). A substantial part of the field-based projects (e.g. 1 and 2), 7 takes place around the Oslo fjord (Bohuslän, Østfold, Vestfold, Agder), but some of the projects (e.g. 5) will venture further south along the Swedish west coast and the Danish archipelago. We have funds to cover field work expenses, but we encourage prospective students to apply for scholarships.

Our study organisms — Pacific oysters (Magallana gigas), European oyster (Ostrea edulis) and blue mussel (Mytilus edulis)

The group We have a long-standing collaboration on Scandinavian bivalve communities and have a long track-record on supervising students with different backgrounds and interests. Don’t hesitate to contact us for an informal discussion about what we can offer and to tailor a project that suits your interests.

Contact Professor Ane Timenes Laugen Centre for Coastal Research University of Agder, Kristiansand, Norway [email protected] Dr. Åsa Strand IVL Swedish Environmental Institute Sven Lovén Centre for Marine Science Kristineberg, Fiskebäckskil, Sweden [email protected]

Left: European oyster (Ostrea edulis) spat for population restoration trials. Right: Experimental setup for blue mussel (Mytilus edulis) restoration trials

Left: Looking for Pacific oysters in Skåne. Right: Pacific oyster reef in Bohuslän

Förslag till Marina exjobb 2019 Suggestions for exam projects 2019 · 2019-04-26 ·...

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