Reconstructing plankton food web interactions with DNA metabarcoding

This study is published in Molecular Ecology and shows for the first time the natural diet of zooplankton under temporal variation of food resources.

Knowledge of zooplankton in situ diet is critical for accurate assessment of marine ecosystem function and structure, but due to methodological constraints, there is still a limited understanding of ecological networks in marine ecosystems. Several target consumers, including copepods and cladocerans, were investigated by sequencing 16S rRNA and 18S rRNA genes to identify prokaryote and eukaryote potential prey present in their guts. During the spring phytoplankton bloom, we found a dominance of diatom and dinoflagellate trophic links to copepods. During the summer period, zooplankton including cladocerans showed a more diverse diet dominated by cyanobacteria and heterotrophic prey. Our study suggests that copepods present trophic plasticity, changing their natural diet over seasons, and adapting their feeding strategies to the available prey spectrum, with some species being more selective. We did not find a large overlap of prey consumed by copepods and cladocerans, based on prey diversity found in their guts, suggesting that they occupy different roles in the trophic web. This study represents the first molecular approach to investigate several zooplankton–prey associations under seasonal variation, and highlights how, unlike other techniques, the diversity coverage is high when using DNA, allowing the possibility to detect a wide range of trophic interactions in plankton communities.

Spring (March, April) and summer (June, July, August) zooplankton trophic interactions for (a) 16S and (b) 18S rRNA gene reads represented as coloured segments in circos plots. Zooplankton consumers are shown at the top and associated prey on the bottom of the plot. The width of the connection ribbons represents the relative abundance of a particular prey of that consumer and the width of each
prey taxon segment is proportional to the relative abundance of each prey considering all samples. Copepod (i.e., Maxillopoda) and parasitic (i.e., order Syndiniales) sequences are excluded in the plots.

New study shows that some populations of the copepod Eurytemora affinis can adapt to a future warmer Baltic Sea

To predict effects of global change on zooplankton populations, it is important to understand how present species adapt to temperature and how they respond to stressors interacting with temperature. Here, we ask if the calanoid copepod Eurytemora affinis from the Baltic Sea can adapt to future climate warming. Populations were sampled at sites with different temperatures. Full sibling families were reared in the laboratory and used in two common garden experiments (a) populations crossed over three temperature treatments 12, 17, and 22.5°C and (b) populations crossed over temperature in interaction with salinity and algae of different food quality. Genetic correlations of the full siblings’ development time were not different from zero between 12°C and the two higher temperatures 17 and 22.5°C, but positively correlated between 17 and 22.5°C. Hence, a population at 12°C is unlikely to adapt to warmer temperature, while a population at ≥17°C can adapt to an even higher temperature, that is, 22.5°C. In agreement with the genetic correlations, the population from the warmest site of origin had comparably shorter development time at high temperature than the populations from colder sites, that is, a cogradient variation. The population with the shortest development time at 22.5°C had in comparison lower survival on low quality food, illustrating a cost of short development time. Our results suggest that populations from warmer environments can at present indirectly adapt to a future warmer Baltic Sea, whereas populations from colder areas show reduced adaptation potential to high temperatures, simply because they experience an environment that is too cold.

Karlsson, K,  Winder, M.  Adaptation potential of the copepod Eurytemora affinis to a future warmer Baltic Sea. Ecol Evol.  2020; 00: 1– 17.

The copepod Eurytemora affinis. Foto credit: Konrad Karlsson

New study shows limited evidence for common interannual trends in Baltic Sea summer phytoplankton biomass

We used dynamic factor analysis to study if there are common patterns of interannual
variation that are shared (“common trends”) among summer phytoplankton total and class-level biomass time series observed across Baltic Sea latitudinal gradients in salinity and temperature. We evaluated alternative hypotheses regarding common trends among summer phytoplankton biomass: Baltic Sea-wide common trends; common trends by geography (latitude and basin); common trends differing among functional groups (phytoplankton classes); or common trends driven by both geography and functional group.

Summer phytoplankton blooms in the Gulf of Finland.

Summer phytoplankton blooms in the Gulf of Finland. Credit: NASA Earth Observatory image by Joshua Stevens and Lauren Dauphin, using Landsat data from the U.S. Geological Survey and MODIS data from LANCE/EOSDIS Rapid Response

Our results indicated little support for a common trend in total summer phytoplankton biomass. At a finer resolution, classes had common trends that were most closely associated with the cryptophyte and cyanobacteria time series with patterns that differed between northern and southern sampling stations. These common trends were also very sensitive to two anomalous years (1990, 2008) of cryptophyte biomass. The Baltic Sea Index, a regional climate index, was correlated with two common class trends that shifted in mean state around the mid-1990s. The limited coherence in phytoplankton biomass variation over time despite known, large-scale, ecosystem shifts suggests that stochastic dynamics at local scales limits the ability to observe common trends at the scale of monitoring data collection.


Griffiths JR, Lehtinen S, Suikkanen S, Winder M (2020) Limited evidence for common interannual trends in Baltic Sea summer phytoplankton biomass. PLoS ONE 15(4): e0231690.

Shifting spring phytoplankton blooms in the Baltic Sea

A new publication shows that spring phytoplankton blooms occur 1-2 weeks earlier over the last 20 years in the central Baltic Sea. Warmer temperature advance timing of diatom and dinoflagellates, the two dominant taxonomic groups of the spring bloom, and decrease bloom magnitude. Bloom timing of the entire species composition was, however, buffered by a temperature and ice related shift in composition from early blooming diatoms to later blooming dinoflagellates and the autotrophic ciliate Mesodinium rubrum.

A shift from early blooming and fast sedimenting diatoms to later blooming flagellated groups at higher temperature is expected to increase energy transfers to pelagic secondary production and decrease spring bloom inputs to the benthic system.

Spring phytoplankton blooms contribute a substantial part to annual production, support pelagic and benthic secondary production and influence biogeochemical cycles. Understanding environmental effects on spring bloom dynamics is important for predicting future climate responses for managing aquatic systems.

The full publication is available at:

Hjerne O, Hajdu S, Larsson U, Downing A, Winder M (2019) Climate Driven Changes in Timing, Composition and Magnitude of the Baltic Sea Phytoplankton Spring Bloom. Frontiers in Marine Science. 6.

Seasonal biomass dynamics of major phytoplankton groups in the Baltic Sea



We started a new MASMA project on fish larvae distribution in coastal East Africa in collaboration with the Kenya Marine and Fisheries Research Institute, Mombasa, Kenya, and the Institute of Marine Sciences, Zanzibar, Tanzania.

This project aims to understand to what extent food-provisioning services in the form of fish larval production are threatened by habitat degradation and fragmentation, and how production of this natural resource is related to climate change and development in the coastal Western Indian Ocean region. We will identify sensitive seagrass habitats that need to be protected and threshold values for healthy productive seagrass habitats, and estimate the socio-economic costs of seagrass beds loss to fisheries. Specifically, this will be done by identification of habitat conditions critical for fish recruitment and key drivers for fish larvae production, which will provide scientific information that can lead to improved management and protection strategies in coastal East Africa.


Foto: Dr. Jacob Ochiewo, Prof. Monika Winder, Dr. James Mwaluma at a meeting in Nairobi.

Open PhD position in Marine Biology focusing on ecological network modelling

We have an open PhD position in ‘Ecological network modelling of plankton food webs’ in our group.

This is a 4-yr position with the goal to use existing environmental, species and sequencing data gathered in extensive monitoring and metabarcoding studies to describe patterns of biotic interaction strength and explore their implications for food web dynamics. We will quantify the strength of diverse biotic interactions – trophic, symbiotic and parasitic – and how these interactions affect community dynamics, food web functioning and stability. We expect that outcomes of this project will provide essential understanding of how communities are organized and respond to changes.

We are looking for a highly motivated and self-directed student with an excellent diploma or master degree in biology, ecology, and/or aquatic science. We expect a strong interest in general ecological questions and great enthusiasm for scientific work. Ideally, the student will have experience in ecological and statistical modelling, knowledge of plankton ecology or molecular ecology analysis. Good analytical  skills, excellent interpersonal and communication skills, a strong sense of determination to succeed, and the ability to express his or her ideas in English is further expected.

The student will conduct the research at Stockholm University within the Department of Ecology, Environment and Plant Sciences. This is a collaborative project with other PhD students and researchers from Stockholm University.

The position will be based within a dynamic and active group working on current topics in aquatic ecology. We use a multi-disciplinary research approach, combining descriptive field studies, experimental and long-term ecological research to understand the consequences of environmental dynamics for food web processes and ecosystem functions. We offer state-of-the-art experimental and analytical facilities that allow properly addressing current ecological questions.

For mor information and link to the application site, please visit the Stockholm University website.

For more information, please contact project leader Prof. Monika Winder, telephone: +46 8 16 1741,

New paper on: Life-history responses to changing temperature and salinity of the Baltic Sea copepod Eurytemora affinis by Konrad Karlsson et al.

To understand the effects of predicted warming and changing salinity of marine ecosystems, it is important to have a good knowledge of their capacity to adapt to environmental changes. In this study we investigated how different populations of the copepod Eurytemora affinis from the Baltic Sea respond to varying temperatures and salinity conditions. We collected copepods in the Stockholm archipelago, Bothnian Bay, and Gulf of Riga and conducted common garden experiments.

Our main finding was that low salinity has a detrimental effect on development time, the additive effects of high temperature and low salinity have a negative effect on survival, and their interaction has a negative effect on hatching success. We observed no variation in survival and development within populations, and all genotypes had similar reaction norms with higher survival and faster development in higher salinities.

This suggests that there is no single genotype that performs better in low salinity or high salinity; instead, the best genotype in any given salinity is best in all salinities. Our results suggest that E. affinis can tolerate close to freshwater conditions also in high temperatures, but with a significant reduction in fitness.


Female of Eurytemora affinis with an egg sack from the Baltic Sea. Foto credit: Simona Puiac.


Nauplia life stage of Eurytemora affinis. Foto credit: Simona Puiac.

New project on the Galapagos Archipelago

We started an exciting collaboration with José Marin at the Charles Darwin Foundation and Rafael Bermudez at Universidad San Francisco de Quito (USFQ) on research in the Galapagos Archipelago and visited the islands in January.

The Galapagos are famous for their large number of endemic species with beautiful and interesting ecosystems. Planktonic organisms are however largely understudied. Stefan Eiler, a master student from Stockholm University started to work on a joint project to investigate spatial and temporal dynamics of crustacean plankton and population genetics for key crustacean species. He stays Charles Darwin station for some months. More on this later as the project evolves.

Thanks to José and Rafael for hosting us.

IMG_6407 (1)

View to the Charles Darwin station on Santa Cruz island, Galapagos.

IMG_6387 (1)

Stefan Eiler, Santa Cruz, Galapagos Island

NEW: Open PhD position in ‘Molecular analysis of plankton food web interactions’

There is a 4 year PhD position in Marine Biology open in my group. Please find more information below and here:

PhD student in Marine Biology

at the Department of Ecology, Environment and Plant SciencesClosing date: 23 February 2018.

At the Department of Ecology, Environment and Plant Sciences at Stockholm University, research and education is conducted in an international environment. The subject areas are Ecology and Evolution, Ecotoxicology, Marine Biology, Plant Physiology and Plant Systematics. Some of the research has direct environmental and societal relevance and the approach is often broad and interdisciplinary. About 140 people are working at the Department, of which ca. 35 are teachers and researchers and 50 are PhD students.

Project description
The Department of Ecology, Environment and Plant Sciences invites applications for a four-year PhD position part of the project Molecular analysis of plankton food web interactions. The aim of this project is to understand how environmental factors affect the structure and function of planktonic food webs by using DNA sequencing. This project will focus on zooplankton interactions through in situ identification of dietary uptake using novel methods of metabarcoding and metagenomics. This knowledge will be used to investigate the response of food web structure and function to global and local environmental gradients in temperature, salinity, eutrophication, or others. The outcome of this research is expected to yield transformative insight on the dynamics of plankton food web interactions under environmental change. The student will conduct field surveys, laboratory experiments, molecular analysis, including DNA sequencing, bioinformatics and network modelling. The student will conduct the research at Stockholm University within the Department of Ecology, Environment and Plant Sciences and has the opportunity to collaborate with other PhD students and participate in international collaborations within other projects.

The position will be based within a dynamic and active group working on current topics in aquatic ecology. We use a multi-disciplinary research approach, combining descriptive field studies, experimental and long-term ecological research to understand the consequences of environmental dynamics for food web processes and ecosystem functions. We offer state-of-the-art experimental and analytical facilities that allow properly addressing current ecological questions.

We are looking for a highly motivated and self-directed student with a strong interest in general ecological questions and great enthusiasm for scientific work. Ideally, the student will have knowledge in plankton ecology and experience in molecular analysis, culturing organisms, and field sampling. Good data analysis skills, excellent interpersonal and communication skills, a strong sense of determination to succeed, and the ability to express his or her ideas in English is further expected. The applicants should be willing to travel and spend periods in the field.

Qualification requirements
In order to meet the general entry requirements, the applicant must have completed a second-cycle degree, completed courses equivalent to at least 240 higher education credits, of which 60 credits must be in the second cycle, or have otherwise acquired equivalent knowledge in Sweden or elsewhere.

In order to meet the specific entry requirements, the general syllabus for doctoral studies in the field of Marine Biology stipulates, that applicants must have completed at least 60 higher education credits in the second cycle of which 15 credits must be from a course in Marine Biology, and 30 credits from a project in Marine Biology. Applicants may also have otherwise acquired equivalent knowledge in Sweden or elsewhere.

The qualification requirements must be met by the deadline for applications.

The criteria used in the selection for admittance to research training in Marine Biology are knowledge of theory and applications in the research field, knowledge with relevance for the research project; ability to communicate orally and in writing, knowledge of English, creativity, analytic competence, initiative, independence and collaboration ability. The assessment will be based on previous experience and grades, the quality of the degree project, references, relevant experience, interviews, and the candidate’s written motivation for seeking the position.

Admission Regulations for Doctoral Studies at Stockholm University are available at:

Terms of employment
Only a person who will be or has already been admitted to a third-cycle programme may be appointed to a doctoral studentship.

The term of the initial contract may not exceed one year. The employment may be extended for a maximum of two years at a time. However, the total period of employment may not exceed the equivalent of four years of full-time study.

Doctoral students should primarily devote themselves to their own education, but may engage in teaching, research, and administration corresponding to a maximum of 20 % of a full-time position.

Please note that admission decisions cannot be appealed.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

For more information, please contact project leader, Professor Monika Winder, telephone: +46 8 16 17 41,

Further information about the position can be obtained from the Subject Representative Professor Jonas Gunnarsson, telephone: +46 8 16 42 53,

Union representatives
Ingrid Lander (Saco-S) and Lisbeth Häggberg (Fackförbundet ST and Lärarförbundet), telephone: +46 8 16 20 00 (operator), (SEKO), and PhD student representative,

Apply for the PhD student position at Stockholm University’s recruitment system by clicking the “Apply” button. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline. We recommend that you hand in your application, including necessary documents, in English.

Please include the following information with your application

  • Your contact details and personal data
  • Your highest university degree
  • Your language skills
  • Contact details for 2–3 reference persons

and, in addition, please include the following documents

  • Cover letter (2-3 pages), containing
    – Your expectations from, and intentions with the education
    – Why you are interested in the specific project
    – What makes you suitable for the specific project
  • CV – degrees and other completed courses, work experience and a list of degree projects/theses
  • Degree certificates and grades confirming that you meet the general and specific entry requirements (no more than 6 files)
  • Degree projects/theses (no more than 6 files).

The instructions for applicants are available at: Instructions – Applicants.

You are welcome to apply!

We are one of Europe’s leading universities in one of the world’s most dynamic capitals. A relationship with Stockholm University delivers quality outcomes whether you are an employee, student, researcher or stakeholder. Our education and research produce results.

Closing date: 23/02/2018