Fjords are deep-water estuaries that support a wide range of marine habitats for pelagic fish. Yet, knowledge gaps in fish distribution and habitat use limit the implementation of efficient marine conservation strategies within fjords. Using five British Columbia fjords as a case study, we demonstrated that eDNA metabarcoding combined with species traits can enhance the detection and monitoring of conservation priority species (CPS) within systematic conservation planning frameworks. Spatiotemporal eDNA patterns confirmed the presence of endangered eulachon (Thaleichthys pacificus) across three fjords and identified deep fjord habitats as conservation priorities for mesopelagic species, including sensitive elasmobranchs and diel vertical migrators such as northern lampfish (Stenobrachius leucopsarus). eDNA peaks for several CPS during winter and spring matched documented spawning windows, underscoring the importance of fjords as seasonal spawning habitat. This globally transferable approach can supplement local stewardship initiatives and long-term monitoring efforts, contributing to more effective marine conservation area design and management.

In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.

Models that estimate rates of energy flow in complex food webs often fail to account for species-specific prey selectivity of diverse consumer guilds. While DNA metabarcoding is increasingly used for dietary studies, methodological biases have limited its application for food web modeling. Here, we used data from dietary metabarcoding studies of zooplankton to calculate prey selectivity indices and assess energy fluxes in a pelagic resource-consumer network. We show that food web dynamics are influenced by prey selectivity and temporal match-mismatch in growth cycles and that cyanobacteria are the main source of primary production in the investigated coastal pelagic food web. The latter challenges the common assumption that cyanobacteria are not supporting food web productivity, a result that is increasingly relevant as global warming promotes cyanobacteria dominance. While this study provides a method for how DNA metabarcoding can be used to quantify energy fluxes in a marine food web, the approach presented here can easily be extended to other ecosystems. 

The plankton community consists of diverse interacting species. The estimation of species interactions in nature is challenging. There is limited knowledge on how plankton interactions are influenced by environmental conditions because of limited understanding of zooplankton feeding strategies and factors affecting trophic interactions. In this study, we used DNA-metabarcoding to investigate trophic interactions in mesozooplankton predators and the influence of prey availability on their feeding behavior. We found that mesozooplankton feeding strategies vary within species across an environmental gradient. Some species, such as Temora longicornis consistently used a selective strategy, while diets of Centropages hamatus and Acartia spp. varied between stations, showing a trophic plasticity with the prey community. We found a dominance of Synechococcales reads in Temora’s gut content and a high prey diversity for the cladoceran Evadne nordmanni. Our study shows the wide range of prey species that supports mesozooplankton community and helps to understand the spatial and temporal complexity of plankton species interactions and discriminate the selectivity ability of four zooplankton key species. Due to the central role of plankton in marine waters, a better comprehension of the spatiotemporal variability in species interactions helps to estimate fluxes to benthic and pelagic predators. 

Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.

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.

The oceans are important regulators of the Earth’s climate system by sequestering carbon from the atmosphere taken up by primary producers. Zooplankton, including protozoans and metazoans of different phyla and size classes, occupies several trophic niches and regulates energy flow between primary producers and fish. The structural configuration of the food web determines the rates at which primary production is either enriched to sustain organisms at higher trophic levels or exported to the ocean floor. However, limited knowledge about plankton interactions causes uncertainty of how the oceans will respond to climate changes. This thesis presents a framework for studying and modeling pelagic food webs using novel implementations of DNA metabarcoding. Study I shows that DNA metabarcoding of zooplankton sampled in their natural environment reveals a broader and more complex diet than zooplankton in classic grazing observations. We also show that differential feeding strategies facilitate species coexistence and that the zooplankton diet is largely dependent on prey availability. The approach was extended in Study II, where we include the smaller fraction of zooplankton that is often overseen in food web studies to broaden the perspective of functional diversity in pelagic food webs. We show that different populations have unique functions in channeling the primary production of different sources and especially highlight the role of filter-feeders in making detrital nutrients available for other organisms in the food web. In Study III, we shifted focus to trophic links between zooplankton and fish by comparing niche overlap between the three main planktivorous fish in the Baltic Sea - stickleback, sprat, and herring. The results from the three first studies were finally used to calculate selectivity indices between each predator and prey. This information was implemented in Study IV in a network model quantifying fluxes of energy through the food web. The model revealed cyanobacteria as the primary contributor to secondary production in the Baltic Sea food web and that the spring bloom of diatoms and dinoflagellates remains largely unutilized by the zooplankton. This is the first time DNA metabarcoding is used to compare niche differences of several zooplankton species in a pelagic guild and to quantify fluxes in a food web model. The thesis refines our knowledge of pelagic community and food web structure, and the framework presented here is a suitable entry point for food web modeling in other ecosystems.

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. Given the quantitative importance of Syndiniales and zooplankton in marine environments, our findings emphasize that their interactions should be recognized as key players in the structure and connectivity of plankton food webs.

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. Here, we used DNA-metabarcoding to study trophic interactions, with the aim to unveil the natural diet of zooplankton species under temporal variation of food resources. 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.

In boreal forests, N₂-fixation by filamentous heterocystous cyanobacteria in symbiosis with pleurocarpous feathermosses represent the main biological input of new nitrogen (N), and greatly support the surrounding forest productivity. In these ecosystems, climate change is expected to result in 2-8°C increase in temperature and two times greater carbon dioxide (CO₂) over the next century, yet little is known about the effects of these factors on the community composition of cyanobacteria in symbiosis with feathermosses. In particular, it is unknown how N₂-fixation activity will change and the resulting impact on the moss growth rate (MGR). Here, we reconstructed the symbiosis between the common feathermoss Pleurozium schreberi and different cyanobacteria isolated from feathermosses. Feathermosses were inoculated with different strains of cyanobacteria and exposed to different temperature (11°C and 19°C) and CO₂ (500 ppm and 1000 ppm) conditions. Changes in MGR, N₂-fixation rate, and cyanobacterial community structure and composition were measured at distinct time points: 5, 10, 20, and 30 weeks of exposure. Our results indicate that both elevated temperature and CO₂ levels can individually and combined have positive effects on the N₂-fixation activities, and consequently on MGR. The underlying biotic mechanisms for increased N₂-fixation and MGR were changes in the cyanobacterial community diversity and composition.  In general, we observed a reduction in cyanobacterial diversity and an increase in cyanobacterial strain abundance that have adapted and dominated under the elevated temperature and CO₂ levels.