DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species

Alternative pathways of energy transfer guarantee the functionality and productivity in marine food webs that experience strong seasonality. Nevertheless, the complexity of zooplankton interactions is rarely considered in trophic studies because of the lack of detailed information about feeding interactions in nature.

In this study, we used DNA metabarcoding to highlight the diversity of trophic niches in a wide range of micro- and mesozooplankton, including ciliates, rotifers, cladocerans, copepods and their prey, by sequencing 16- and 18S rRNA genes. Our study demonstrates that the zooplankton trophic niche partitioning goes beyond both phylogeny and size and reinforces the importance of diversity in resource use for stabilizing food web efficiency by allowing for several different pathways of energy transfer. We further highlight that small, rarely studied zooplankton (rotifers and ciliates) fill an important role in the Baltic Sea pelagic primary production pathways and the potential of ciliates, rotifers and crustaceans in the utilization of filamentous and picocyanobacteria within the pelagic food web. The approach used in this study is a suitable entry point to ecosystem-wide food web modelling considering species-specific resource use of key consumers.

Read the full article here


and a related news report here


A large rotifer of the genus Asplanchna, surounded by three cladocerans, Bosmina. Top: A copepodite (juvenile copepode). Right: two rotifers, Keratella. The background is scattered with diatoms. Photo: Andreas Novotny.

We have an open PhD position in plankton ecology

The Department of Ecology, Environment and Plant Sciences invites applications for a four-year PhD position part of the project ‘Plankton-fish interactions: An understudied link in Baltic Sea food webs and fisheries management’. The goal of this PhD project is to investigate prey preference of small pelagic fish including the entire prey spectrum using novel molecular tools that amplify and sequence low levels of DNA combined with network models to project trophic coupling under changing climate, nutrient and fisheries scenarios. Small-sized pelagic fish have a central role in marine food webs as they control production of predatory fish and at the same time feed on zooplankton and thereby indirectly control algal blooms. Understanding variation in plankton-fish feeding interactions are key for developing management strategies that promote fish stocks and enhance control on algal blooms, which requires detailed knowledge about feeding interactions from primary producers to upper trophic levels. Results of this project will be of relevance to better understand temporal and spatial dynamics of fish feeding, growth and recruitment, which is important to advice ecosystem management for sustainable fisheries and prevention of algal blooms.

The student will conduct field surveys in the Baltic Sea, laboratory experiments, molecular analysis, including DNA sequencing, bioinformatics and network modelling. The research will be performed at Stockholm University within the Department of Ecology, Environment and Plant Sciences with opportunities to collaborate with other PhD students and to participate in international collaborations.

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 or fish ecology, experience in molecular analysis, organism culturing and field sampling. Good data analysis skills or modelling, 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.

For more information and submission of your application, please see


Congratulations to two successful master thesis presentations

Two master students finished their projects in Dec 2020:

Calum Young: Examination of plankton communities, invaders and harmful algal species within mangrove areas of the Galápagos Islands using eDNA metabarcoding

Phytoplankton are critical components of the marine environment but their understanding within the Galápagos Marine Reserve (GMR) remains largely underexplored with research focused within mangrove systems being further limited. Between November and December, the Galápagos Islands transition from the dry, milder season to the wet, warmer season. By examining the dominant phytoplankton genera within mangrove communities during this time, inference can be made on the communities’ responsiveness to seasonal change. This study utilised environmental DNA (eDNA) metabarcoding of the 18S ribosomal RNA (rRNA) molecular marker to survey the micro-eukaryotic community in surface waters collected from six mangrove sites. Compositions were shown to be influenced by both spatial conditions and seasonality. Diatoms represented a significant proportion of the community and were shown to undergo a strong seasonal shift to dominance by smaller sized taxa, possibly due to their efficient nutrient acquisitional traits. Dominance within dinoflagellates appeared dependent on several eco-physiological strategies; with parasitism and endosymbiosis appearing most advantageous for community dominance. 

Mangrove communities were also examined for invasive and toxic algae species. These groups represent an area of growing concern within the region and exploration of their distribution within the GMR has not previously been conducted using metabarcode sequencing. Here, several new observations of invasive species for the GMR are reported. Additionally, a range of toxin-producing algal species was also detected. However, for both groups, the respective relative abundance of individual species within mangroves communities was minimal. Sites located closer to human activity did not appear to be more impacted by problem species than more isolated areas. The low proportion held by harmful groups is encouraging, but the diversity of species detected warrants improved monitoring to ensure populations and their associated negative impacts remain negligible. 

Vivien Holub: Connectivity through larval dispersal in Kenya and Tanzania: A hydrodynamic connectivity model of marine protected areas   

Marine protected areas (MPAs) are considered as major conservation tools and have been implemented globally to protect marine biodiversity and to support the sustainability of coastal fisheries. Following scientific guidelines, conservation efforts also aim to establish representative MPA networks at various spatial scale, which is expected to enhance the efficiency of individual areas. Yet, degree at which MPA populations are potentially connected by the dispersal of marine organisms remain largely unknown. To address this knowledge gap, the present study investigates connectivity patterns among Kenyan and Tanzanian MPAs (between 0  – 10  and 38 – 47 ) in the Western Indian Ocean, a region where food and livelihood security are highly dependent on coastal fisheries. Interconnectedness is evaluated through a hydrodynamic larval dispersal model parameterized for the seagrass parrotfish Leptoscarus vaigiensis, a heavily targeted fish species by small-scale fisheries in the region. Applying graph theory and various connectivity metrics, this study shows that the Kenyan-Tanzanian MPAs form a weakly connected network where connections are the strongest in the Tanzanian Tanga and Zanzibar region and weakest in the northmost Kenyan MPAs. Poor coherency is likely the result of the predominantly northwardly flow of the regional East African Coastal Current which generates and imbalance of larval migration rate between MPAs on a latitudinal scale. Although connectivity patterns are significantly stronger when the dominant current is temporarily weakened and deflected in North Kenya during NEM season, on average the strength of connectivity remains low. Therefore, the present investigation demonstrates that the regional hydrodynamic patterns poses a challenge for achieving effective MPA network. Continued studies with more conservative model conditions is recommended. However, based on its findings, this study suggest that local governments further increase MPA surface coverage and consider a cross-boundary management of MPAs to improve connectivity.   

New article on evidence of host-parasite interactions in zooplankton

Although parasitism is one of the most prevalent interactions in nature, studies of aquatic food webs rarely include parasites. Syndiniales (Dinophyceae, Alveolata) is a diverse parasitic group of dinoflagellates, common in all marine environments, and are described as dominant components of pelagic ecosystems. However, their temporal dynamics, prevalence, and host-specificity are poorly known. Using DNA metabarcoding to explore trophic interactions of zooplankton, we found a high proportion of Syndiniales sequence reads associated with the targeted consumers. We observed the occurrence of Syndiniales in copepods, cladocerans, appendicularians, and polychaete larvae, ranging between 11 and 36% relative read abundance, encompassing 11 main putative clades. Zooplankton–Syndiniales interactions showed variability in occurrence across the taxa, but also certain host-specificity. The study suggests that the observed copepod–Syndiniales interactions can be both direct parasitic infections and the result of trophic transmission through potentially infected prey by Syndiniales. Our findings emphasize that their interactions should be recognized as key players in the structure and connectivity of plankton food webs.

Zamora-Terol, S., Novotny, A. & Winder, M. Molecular evidence of host-parasite interactions between zooplankton and SyndinialesAquat Ecol (2020). https://doi.org/10.1007/s10452-020-09816-3

Schematic representation of potential host-parasite interactions between copepods and Syndiniales based on results from this study and literature information. *Lima-Méndez et al. 2015 and Sassenhagen et al. 2020; **Clarke et al. 2019; ***Cachon 1964 and Sassenhagen et al. 2020

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. https://doi.org/10.1002/ece3.6267

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. https://doi.org/10.1371/journal.pone.0231690

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. https://doi.org/10.3389/fmars.2019.00482

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.