Small pelagic fish have a central position in pelagic food webs, linking plankton production to higher trophic levels. They often favour crustacean mesozooplankton and are thought to compete for the same resource, an assumption that relies on microscopy diet identification that neglects digested and soft-bodied prey. Here, we aimed to systematically identify the entire resource use and overlap among the dominant small pelagic fish in the central Baltic Sea at high taxonomy resolution. The diet composition of two clupeid species, herring (Clupea harengus) and sprat (Sprattus sprattus), and the three-spined stickleback (Gasterosteus aculeatus) was assessed in May and October using DNA metabarcoding, stable isotopes, and microscopy. All three methods gave consistent results. The clupeids shared a similar diet in May when prey diversity was low, composed mainly of the copepods Pseudocalanus and Acartia, whereas three-spined stickleback favoured different copepod species and the rotifer Synchaeta, which was confirmed by a different isotopic value as compared to the two clupeids. In October, all forage fish preyed on diverse zooplankton species, mainly composed of the copepods Acartia, Eurytemora, and Temora, while Pseudocalanus was only important for herring. The observed resource use partitioning between sprat and herring was confirmed by the stable isotope values from October, suggesting that different prey species were targeted during the summer period. Our study highlights that resource use overlaps among small pelagic fish were limited and varied with prey availability. This suggests that shifts in zooplankton dynamics, rather than competition for resources, have the potential to drive small pelagic fish population fluctuations.

Understanding species phenology and temporal co-occurrence across trophic levels is essential to assess anthropogenic impacts on ecological interactions. We analyzed 15 yr of monitoring data to identify trends and drivers of timing and magnitude of bloom-forming phytoplankton and diverse zooplankton taxa in the central Baltic Sea. We show that the timings of phytoplankton blooms advance, whereas crustacean zooplankton seasonal timings remain constant. This increasing offset with the spring bloom is linked to the decline of Pseudocalanus, a key copepod sustaining pelagic fish production. The majority of copepod and cladoceran taxa, however, are co-occurring with summer blooms. We also find new developing fall blooms, fueling secondary production later in the season. Our study highlights that response to climate change differs within and between functional groups, stressing the importance of investigating plankton phenologies over the entire annual cycle in pelagic systems.

Environmental changes reshape biological communities, inducing cascading effects throughout the food webs. These changes pressure species either to adapt or to track favorable habitats. Estuaries represent an interesting case study to investigate such responses as species will rapidly reach physical boundaries if they cannot adapt fast enough and need to track suitable conditions. One such estuary is the Baltic Sea, characterized by a salinity and temperature gradient that shapes species distribution and imposes physiological stress on organisms. The Baltic Sea is projected to be affected by substantial modifications in environmental conditions by the end of the 21st century, which could have major consequences for species distribution and community composition. However, despite the impending changes and their potential impact, there is a gap in understanding the potential consequences on pelagic species of the Baltic Sea. This study employs long-term observations of primary zooplankton species in the pelagic food web to model changes in their distribution under future climate projections. We found that the parameters having the largest influence on habitat suitability varied across species, although maximal temperature was the most important for six out of seven species. In addition, there was a shrinkage of suitable area for several key species driven by a decrease in salinity and a rise in water temperature. We discuss the complex interplay between environmental changes and the spatial distribution of pelagic species in the Baltic Sea, highlighting the need for proactive management strategies to mitigate potential ecological impacts in the face of future climate scenarios.

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.

 Zooplankton and bacteria are two critical groups of aquatic organisms and their associations play important roles in contributing to ecological processes. However, the taxonomy patterns and dynamics of zooplankton-associated bacterial communities across different hosts over temporal and spatial gradients are seldom described in nature[KJ1] . Here, 16s rRNA sequencing and functional annotation were implemented on the bacterial communities of 12 zooplankton genera sampled across the Baltic Sea salinity gradient in two seasons. Our results suggest that functional grouping of the zooplankton-associated bacteria captures host and environment specific patterns better than bacteria taxonomic composition. The distribution of functional clusters of bacteria identified by K-medoid did not strictly follow host taxonomy, temporal and spatial gradients. But certain clusters, such as clusters of higher potential for unsaturated fatty acid synthesis showed host and temporal specificity. These specificities were further analyzed by random forest, suggesting that the dynamics of zooplankton-associated bacteria were related to environmental parameters such as temperature and phosphorus, and host diet composition. These results implied the co-effects of abiotic factors and biotic host lifestyles shaping the dynamics of zooplankton bacterial communities.

 The marine alveolates consist of a group of protist parasitic dinoflagellates belonging to the order Syndiniales, which infect other planktonic taxa, including other dinoflagellates, copepods, and cladocerans. The ecological roles of Syndiniales linked to zooplankton remain poorly understood, though some Syndiniales Groups (SGs) are known to consistently kill their hosts. We identified the associated Syndiniales-zooplankton interactions of selected taxa using DNA metabarcoding across the environmental gradient of the Baltic Sea. We determined the abiotic drivers of these interactions and the infection pathways through the prey consumed by the hosts. We found variations in Amplicon Sequence Variants (ASVs) of different Syndiniales groups associated with zooplankton. The Syndiniales associations with zooplankton were driven highly by low-oxygen water conditions. The environmental variables create unique niches for both the hosts and the parasites, driving niche-specific associations. These interactions demonstrate species specificity shaped by host feeding behaviour and the surrounding abiotic environments. These findings indicate that niche-specific interactions occur along the environmental gradients of the Baltic Sea.