On-going Research Projects

Energy-efficient cultivation of marine microalgae for biomass production


Society faces major challenges in the production of sufficient amounts of biomass for energy and material production. Biomass from microalgae that are rich in oil has great potential as a complement to biomass from forests and agriculture. The success of microalgae as feedstock depends on achieving high yield with minimum energy input. In this project we want to further develop a system shown to be energy-efficient, for outdoor cultivation of marine microalgae. This entails identifying algal strains that are productive and can cope with the dynamic climate of the Swedish west coast. The objectives are to:
• Identify suitable algal strains for a rotation model, where different strains are cultivated during three growth seasons
• Further develop and optimize an energy-efficient cultivation process for marine environment
An energy-efficient annual rotation model for cultivation of marine microalgae could provide an extended growth season and higher total production of biomass for industry.

Project members and collaborators: PI Cornelia Spetae-Wiklund,  Co-PIs Anna Godhe, Susanne Ekendal, Rise

Funding: Energimyndigheten


Adaptation to warming in natural phytoplankton populations


Global warming imposes rapid environmental shifts on all species and it is therefore important to investigate the capacity of biological systems to adapt to changed conditions. We will study adaptation by using phytoplankton populations revived from sediment cores from two areas affected by cooling water discharges from nuclear
power plants. Resting stages of the diatom Skeletonema marinoi, from before and after the thermal perturbation began, have be germinated. Each strain has then been phenotyped in a lab-experiment at 18°C (low) and 23°C (high temperature conditions), to recreate the temperature regimes of pre- and post-power plant summer conditions. We have found that under high temperature conditions, post-power plant populations have
higher fitness than pre-power plant populations and vice versa, indicating that adaptation to warmer water conditions has occurred. We will in this project do whole genome sequencing of these adapted strains to identify genomic changes that can explain the differences in phenotype. The sequence reads will be aligned to the reference genome of S. marinoi and the degree of polymorphism and large-scale structural rearrangements will be identified. By comparing the frequency of warm water genotypes in pre- versus post-power plant populations we can determine if the changes is due to selection on standing genetic variation or if the changes are due to a new mutation favored by selection under thermal stress.

Project members and collaborators: PI Mats Töpel,  Co-PI Anna Godhe

Funding: Swedish Research Council FORMAS


Live to tell: Have phytoplankton evolved in response to environmental                pollution during the last centuries?


In perturbated environments some species will be resilient. We will study the underlying mechanisms of resilience (genetic adaptation or phenotypic plasticity) by studying two diatom species from a cupper contaminated inlet. One species is a permanent resident of the area whereas the other disappeared when [Cu2+] increased but recolonized when water quality improved. We will sample undisturbed sediment cores, date them by isotopes, and revive populations from before, during and after the perturbation. The populations are between 0 and 150 years old. In an ecotoxicological experiment we will compare the populations’ tolerance to cupper. Our hypotheses are that the capacity of a resilient population to tolerate pollution exposure can be quantified in a selection experiment, and this capacity is larger than for a non-resilient population. Experimentally induced cupper tolerance is negligible in an adapted population if all individuals share a gene for Cu tolerance that has spread through natural selection in the past. If tolerance to high Cu is due to plasticity the experimental evolution of pollution tolerance is associated with a cost, and if selection pressure is relaxed it will lead to lower tolerance than the original population had. We will use NGS sequencing to determine populations’ genetic diversity through space and time, and patterns of migration. Additionally, we will look for candidate genes for Cu-tolerance correlating with the phenotypic trait of cupper tolerance.

Project members and collaborators: PI Anna Godhe, PhD student Björn Andersson, Co-PIs Karin Rengefors, Helena Filipsson, Olof Berglund, Lund University.

Funding: Swedish Research Council FORMAS


Investigating the driving forces and spread of antibiotic resistance: the case of marine aquaculture in Asia and sub-Saharan Africa


The use of antibiotics in aquaculture is a hazard associated with the development and spread of antibiotic resistance genes (ARG) in marine environments. Bacteria are carriers of ARGs and associated with planktonic organisms, and studies of plankton and oceanic circulation may provide new insight into the spread of resistance. However, to establish fair and effective governance of antibiotic use, especially in developing countries where aquaculture production is an important source of livelihood and revenue, it is also necessary to know the driving forces behind the usage. Our aim is to produce a synthesis, based on biophysical and socioeconomic factors, for policy recommendations for Asia and East Africa. The synthesis will be based on empirical results and we will address where and on which level remedies to prevent antibiotic resistance spread are most effective. More specifically, we will investigate the local economic role of, and need for antibiotics and produce a cost-benefit analysis. We will map the flow of antibiotics from production to use in order to identify points in the value chain where restrictions would be fair and effective. Further, we will use metagenomics to identify genetic fingerprints of the ARG pool from four aquaculture sites. The spread of specific ARG patterns are hypothesised to be linked to the dispersal of phytoplankton and will be projected by oceanographic connectivity models and verified with repeated sampling at different geographic scales.

Project members and collaborators: PI Anna Godhe, Post-doc Josefin Sefbom, Co-PIs Per Knutsson University of Gothenburg, Indrani Karunasagar Nitte University India, Ramchandra Bhat Indian Council of Agricultural Research, Arvind Singh Physical Research Laboratory India, Rashmi Narayana TA Pai Management Institute.

Funding: Swedish Research Council


Functional Genomics of the Marine Diatom Skeletonema marinoi

The main goal of this proposal is to continue developing Skeletonema marinoi as a new genetic model for marine diatoms. S. marinoi possesses many of the diverse characteristics of this ecologically important group of phytoplankton.

The model S. marinoi strain chosen for this project (RO5A) was only recently isolated from an experimental field site on the Swedish west coast in 2010, and thus has not been in continuous laboratory culture for many years as for other diatom model species. RO5A grows well under our laboratory culturing conditions, and was the S. marinoi strain for which the reference genome sequence was recently completed (http://cemeb.science.gu.se/research/target-species-imago%20/skeletonema-marinoi). The project therefore leverages the new genetic transformation method for S. marinoi and the available reference genome sequence both undertaken by our research group. As such, we have got continued support from the MMI to further develop the various genetic methods necessary to establish this project. Our specific aims are:

  • To continue refining the methods for identifying the genomic insertion site in marinoi transformants;
  • To develop other genetic tools such as complementation, over-expression, and the CRISPR/Cas9 system necessary for fully exploiting marinoi as a genetic model organism for marine, chain-forming diatoms;
  • To increase the number of stable transformants to prepare a genome-wide collection of randomly inserted, but identifiably tagged mutants;
  • To use this marinoi mutant collection (SMMC) to launch an interdisciplinary, multi-group research theme studying the causal links between an important diatom genotype and its phenotypic responses;

Project members PI Dr Adrian Clarke GU, Co-PIs Dr Anna Godhe, Dr Anders Blomberg and Dr Mats Töpel.
Dr Oskar Johansson (post-doc), Dr Olga Kourtchenko.

Financed by Gordon and Betty Moore Foundation Marine Microbiology Initiative (MMI) 2017-2019.


Lessons for the future: Qualifying and quantifying South Asia’s first widespread ciguatera poisoning outbreak


South Asia has long had a fish eating tradition as well as a growing domestic and export fishing industry. However, recently there have been sporadic reports of ciguatera fish poisoning (CFP) from this region. This is a circumtropical disease transmitted by eating carnivorous fishes that contain toxins accumulated from their food and is characterised by
gastrointestinal and neurological symptoms which may result in disablement and/or death. Despite the known presence ofthe dinoflagellate Gambierdiscus spp., one of the most common causative agents of CFP, in the region (Indian Ocean and Arabian Sea) there has been no previously recorded large-scale CFP incident in this area until now. On 1st October 2016 South Asia’s first widespread CFP outbreak occurred in the city of Mangalore, Karnataka, on the coast of SW India, resulting in several hundred hospital attendances and admissions. This is believed to be as a result of the consumption of locally caught carnivorous fish, such as the red snapper, Lutjanus bohar, contaminated with ciguatera toxins. These fish were originally intended for a fish processing plant in the city but were also sold at the Mangalore fish market. This recent outbreak presents a unique opportunity to qualify and quantify the presence of the causative algal species, whilst at the same time conduct state-of-the-art toxin analysis of contaminated seafood samples in a region of the world currently underrepresented both in terms of sampling coverage and technological analysis of an algal-born toxin outbreak event. Increased seawater temperatures and lowered salinity are known to favour the regional dinoflagellate community in general, and specifically Gambierdiscus spp. The previous 12 months have seen sea surface temperatures in the Indian Ocean consistently 0.5-1.0 degrees C above average coinciding with the ongoing El Niño Southern Oscillation and this season’s monsoon has been particularly sustained, lowering coastal salinity. Data gathered during the proposed study will allow us to make predictions for the occurrence of further outbreaks of CFP along the South Asian coastline and elsewhere, including in the face of global climate change. Our aim to implement a rapid response screening and management programme in response to future CFP events will help to ensure the health and wellbeing of those who depend on fishing as a protein and/or economic resource.

Project members and collaborators: PI Lucy Turner Plymouth University UK, Co-PIs Andy Turner CEFAS, UK; Indrani Karunasagar Nitte University, India; Anna Godhe University of Gothenburg, Sweden; Lars Edler WEAQ Sweden.

Funding: NERC, UK


Biofuel production in microalgae on the Swedish West Coast


There is an urgent need to develop highly productive and sustainable energy systems under an environment that is changing from seconds to seasons, and biofuel production in microalgae has great potential to be part of the solution in Sweden.

Our specific aim is to provide a rotation model for algae strains suitable for the four seasons on the Swedish West Coast, which widely vary in both temperature and light conditions. Our focus will be on the benthic diatom Skeletonema marinoi (S. marinoi), which displays a wide genetic and physiological variability in the West Coast region. Recent work showed that this species could accumulate high neutral lipids (up to 30% of dry weight), making it promising for biofuel production.

Project members and collaborators: PI Cornelia Spetea Wiklund, Co-PIs Anna Godhe, Mats Andersson

Funding: Carl Tryggers Stiftelse


Identification of specialized bacteria that break down ship wrecks in the Baltic Sea


In marine environment archaeological wood including shipwrecks are slowly degraded by bacteria. Since the early 1980s several attempts to identify the so called erosion bacteria has been given by researchers around the world. This pilot study will investigate a new possibility using the latest DNA sequencing techniques and metagenomic tools. When their identity and their enzymatic tools for decay is known, it is possible develop efficient preservation methods for protection of unique archaeological wooden remains in situ. The work is carried out by a cross-disciplinary team at the Dept. of MarineSciences, University of Gothenburg.

Project members and collaborators: PI Charlotte Björdal, Co-PIs Marina Panova, Anna Godhe

Funding: Riksantikvarieämbetet


Exploring human-induced evolution using genomics of revived diatoms from natural archives
In this project our aim is to study genetic changes of diatoms in eutrophicated environments over time. From fjords with well-documented hydrographic history, we establish Skeletonema marinoi (a common diatom) populations spanning the age from 0-120 years old. We are in the process of sequence the genome of this protist and we will use this as a back-bone for our analyses. We are resequencing random individuals from distinct dated sediment layers. From the resequenced genomes possible candidate genes with a high degree of polymorphism between the old and the young strains will be identified. The populations are phenotyped, and individual fitness in response to pre-industrial and ambient environmental conditions is determined. Candidate genes will be sequenced from the old and young populations, and we will with this approach likely find variation in specific genes that are correlated with phenotypic trait values, and in this way infer links between genotype and phenotype. Recent populations exposed to different degree of eutrophication will additionally be analysed to confirm the correlation between genetic divergence in specific loci and divergence in stress. This research is important for increasing the scope of ecological risk assessment to include the effects of evolutionary response, for defining a genetic baseline for eutrophication, and for identifying markers which can be used to detect diffuse signals of eutrophication.

Project members and collaborators: PhD student Susanna Gross. Dr Anders Blomberg, Dr Kerstin Johannesson, Dr Mats Töpel, Dr Sylvie Tesson, Dr Olga Kourtchenko, Dr Tuomas Rajala, Dr Marina Axelsson-Fisk, Dr Kjell Nordberg at University of Gothenburg. Dr Marianne Ellegaard and Dr Thorbjørn Joest Andersen.

Funding: Swedish Research Council Formas.

Human health and well being at risk: scenarios for climate change induced harmful microbial blooms along the Indian/Sri Lankan coasts
The project aims to understand how climate-induced changes in sea surface temperature (SST), salinity, pH, and sources of macronutrients may affect the phytoplankton community structure, and to identify environmental drivers of harmful algal bloom (HAB) species. Such knowledge will enable us to foresee effects in the marine food web affecting e.g. fisheries, and assess the risks HABs pose to human health under present and future environmental conditions. Many of the harmful algal species have a cosmopolitan distribution, and therefore the theoretical models and the validation can be applicable on wide geographical scales. The rational for executing this project in Arabian Sea/north Indian Ocean is that IPCC has identified areas of regional tropical precipitation maxima as particularly vulnerable. Upwelling currents along SW coast of India are the main inorganic nutrient source for the entire marine food web. Hydrographic settings of coastal Arabian Sea may therefore display increase of SST, higher freshwater runoff and decreased surface salinity, stronger stratification, altered carbon speciation, and changed ratios of macronutrients with auto- respectively allochthonous origins. All these scenarios are potent to change the phytoplankton community structure, in terms of species, abundances, primary production, and the quality of carbon utilized by higher trophic levels. These changes will invariably influence the marine food web with impact on fisheries, the carbon sink of the oceans, CO2 fixation properties, and the occurrence of marine bacterial pathogens. Partly, the future conditions describe settings considered beneficial for dinoflagellates and flagellates in competition with other phytoplankton, e.g. diatoms, but also for marine pathogenic bacteria.

Project members and collaborators: Dr. Lucy Turner, Dr Per Knutsson, PhD students Gurpreet Kahlon and Alin Kadfak (University of Gothenburg), Dr Ann-Sofi Rehnstam-Holm (Kristianstad University/Sahlgrenska Akademien, University of Gothenburg), Dr Lars Edler (WEAQ), Dr Iddya Karunasagar, Dr Indrani Karunasagar (Nitte University, India), Dr Ashwin Rai, Dr HRV Reddy, Dr MN Venugopal and Dr Chetan Reddy (Karnataka Veterinary Animal and Fisheries Sciences University, India), Dr R Ramesh, Dr Sanjeev Kumar, Dr Arvind Singh, Dr Bhavya (Physical Research Laboratory, Ahmedabad, India), Dr Darshanee Ruwandeepika (Sabaragamuwa University of Sri Lanka)

Funding: Swedish Research Council, Swedish Research Council Formas, Sida, Gothenburg Centre for Marine Research, University of Gothenburg

Evolutionary adaptation to warming in natural phytoplankton populations
The main objectives of the proposed project are to address adaptive responses to increased seawater temperature in natural phytoplankton populations by tracing genotypic selection.
In particular, we plan to investigate adaptation to increased seawater temperatures in revived resting stages from undisturbed sediment cores of the common diatom species S. marinoi that have been affected by cooling water discharges from nuclear power plants. This approach will be complemented by laboratory temperature experiments using isolates from pre- and post-power plant populations.

Project members: PI Dr Kai Lohbeck (DFG post-doc fellow), Dr Anna Godhe, University of Gothenburg.

Funding: DFG (Deutsche Forschungsgemeinschaft), SciLifeLab

Genetic Transformation of the Diatom Skeletonema marinoi.
Note Press release
The aim of this project is to develop a reliable method for genetic transformation of S. marinoi that can be used for future forward and reverse genetics. S. marinoi has several characteristics that make it attractive for such approach. Although typically forming colonial chains, S. marinoi is unicellular with no obvious crosstalk between cells. The vegetative cells are diploid and predominantly reproduce asexually by binary fission. As such, transformants once obtained should segregate quickly under selection to produce homozygous mutant lines. We have also established reliable culturing conditions both in liquid and on plates, as well as developed long-term storage conditions by cryopreservation10. Moreover, we are currently in the process of assembling the reference genome and transcriptome sequences for S. marinoi, using the Illumina and PacBio sequencing platforms (http://cemeb.science.gu.se/research/target-species-imago+/skeletonema-marinoi), which will be completed in Autumn 2015. It should also be noted that six S. marinoi de novo transcriptomes (i.e., MMETSP0918, 0920, 1039-40, 0319-20) are available within the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) database at http://data.imicrobe.us/project/view/104.

Project members PI Dr Adrian Clarke GU, Co-PIs Dr Anna Godhe, Dr Anders Blomberg and Dr Mats Töpel.
Dr Oskar Johansson (post-doc), Dr Olga Kourtchenko.

Financed by Gordon and Betty Moore Foundation Marine Microbiology Initiative (MMI) 2015-2016.

A natural phenomenon turned nasty: Where, when, and why will cyanobacterial blooms be toxic?
Aquatic environments are of enormous importance as natural resources of drinking water, fish production, and recreation. However, surface waters worldwide are threatened by toxic cyanobacterial algal blooms, which have detrimental effects on human health and aquatic biota. One of the most important toxic cyanobacteria in Swedish freshwater is the genus Microcystis. We know which species may be harmful, but cannot predict where and when blooms will be toxic due to interpopulation and strain variation. Using a new population genomic approach along with novel single-colony technology we will address this issue with the aim to understand temporal and spatial prevalence, and the underlying function of toxicity. Our overarching hypothesis is that toxic and non-toxic populations have emerged as a result of ecological differentiation. By using genome sequencing we will identify SNPs and determine the population genetic structure of toxic and non-toxic strains. Genomic data will be paired with toxin analyses from single colonies to determine the composition and distribution of toxic strains. We will determine whether toxic and non-toxic populations have undergone ecological differentiation by exploring the pattern of genomic differences for signs of positive ecological selection Additionally, using the collected data we will develop
and optimize an early-warning detection tool of toxic Microcystis strains for Swedish conditions for future implementation in management and monitoring.

Project members: PI Dr Karin Rengefors Lund University, Co-PIs Dr Anna Godhe, Dr Catherine Legrand Linneaus University

Funded by the Swedish Scientific Council Formas

Marine microalgae enriched in carbohydrates for concomitant nutrient recycling and green chemicals production.
For displacement of fossil resources in a bio-based society there is a need for carbon-neutral raw material in the production of chemicals for biofuels, bulk, and high-value products. This project aims at using marine Chlorella algae to provide starchcontaining biomass as substrate for bio-based production of chemicals. Biomass will be obtained by microalgal cultivation using nutrients from waste material, like wastewater as macronutrient support and flue gas as source of carbon dioxide, allowing for nutrient recycling. The work will be divided into four parts by identification of suitable microalgal strains and waste material, by studying the influence of cultivation parameters on algal growth and cellular content, and by evaluating fermentability of hydrolysed algal biomass. Effects of process conditions (temperature, pH and illumination) and nutrient and CO2 supply by waste material on cellular response and composition will be evaluated. Assessments will be done at well defined conditions in bioreactors by thoroughly following the response of algae with measurements of growth, gas exchange, cellular composition, and metabolomics. The development of optimized starch-containing algal biomass as a base for biotechnological production will contribute to fulfill the need of sustainable bio-production with the reuse and recycling of material, cleaning of waste, reduction in demand on the world?s freshwater reservoirs, and simultaneous production of usable raw material.

Project members: PI Dr Eva Albers Chalmers Technical University, Co-PIs Dr Anna Godhe GU, Dr Susanne Ekendahl SP, PhD student Sigita Vaiciulyte

Funded by the Swedish Scientific Council Formas