The trophic mode is one of the most important functional traits of organisms, determining their position in the food web and their role in the ecosystem. Under the classical concept, phytoplankton was considered to consist exclusively of phototrophic and microzooplankton exclusively of heterotrophic organisms. However, it is now increasingly recognized that mixotrophy (e.g. combining photo- and phagotrophy) occurs among both photo- and microzooplankton species, and that in extension, trophic diversity and relationships among plankton are expected to be more extensive and complex than previously thought. To enhance understanding of plankton trophic modes, diversity and relationships during spring bloom period in Bornholm Basin, central Baltic Sea, we categorized here the temporal succession in (1) the aquatic protist community by trophic modes, and (2) the community composition in terms of taxonomic groups and feeding mode, and its correlation with environmental factors and available prey-size. Our results show that the trophic mode composition of the community changed drastically over the course of the spring season, representing a high trophic complexity and more complex dynamics than previously suggested. The heterotrophic community was characterized by a high diversity of species and groups, with heterotrophic ciliates showing a clear seasonal succession in body size-classes, switching from the smallest sized-fraction (10-20 & micro;m) in winter to an increasingly amount of larger-sized species of 30-55 & micro;m and >55 & micro;m with progression of the spring period. Changes in ciliate community composition were correlated with sea surface temperature, shifting from a cold-associated to a warm-associated community over the course of the spring season. Results further suggest that in communities including a larger mixotrophic component, size trait-based trophic relations between heterotrophic groups and their prey are complex, potentially due to similar prey-size preferences among heterotrophic and mixotrophic species. Overall, our findings emphasize the importance of accounting for the trophic modes of species to enhance the understanding of trophic relations and dynamics within bloom events.

Many species have demonstrated persistence through past climate phases, but the recent accelerated anthropogenic climate change severely impacts species composition, altering aquatic biodiversity and phytoplankton communities. Uncovering how species have responded to natural climate variability in the past is of great value for understanding adaptive dynamics and predicting future adaptations. Here, we investigated the Holocene adaptation dynamics of the cosmopolitan diatom species Skeletonema marinoi by reviving dormant phytoplankton cells that have accumulated in the sediment of the Baltic Sea. The Baltic Sea is strongly affected by current climate change and has undergone fundamental environmental changes throughout its Holocene history, including glacial rebound, alternating warmer and cooler periods, and changes in salinity and nutrient availability. Using resurrected temporal cohorts from up to 6800-year-old sediment horizons, we studied past adaptation dynamics by performing growth experiments and morphological measurements under different temperature and salinity conditions. Our results demonstrate that S. marinoi temporal cohorts exhibit differences in their morphological trait values and environmental optima, partially reflecting past ambient environments. Moreover, divergences from expected adaptation patterns demonstrate the complexity of evolution in natural ecosystems. Based on our findings, we expect S. marinoi to cope well with projected environmental changes for the Baltic Sea. These findings highlight the resilience of phytoplankton and emphasize their capacity for phenotypic adaptation to changing conditions. Furthermore, this research underscores the importance of understanding past adaptation processes in predicting phytoplankton responses to future climate change.

Coastal zones and estuaries are highly dynamic marine systems subject to anthropogenic pressure and to climaterelated changes. The coastal zone of the Baltic Sea, shaped by extreme seasonality, strong bentho-pelagic coupling, and intense human use, represents a unique model system to study these interactions under accelerating climate change. While extensive research has been conducted on warming, eutrophication, and large scale hypoxia in the region, critical gaps remain in understanding how physical forcing, sediment type, and benthic-pelagic coupling control nutrient turnover, primary production, seed and egg bank dynamics, and the emission of climate-relevant gases under rapidly changing dynamic conditions. The Baltic Sea, with 26 % of its area shallower than 15 m, harbor mostly sandy sediments along the southern coast, but the coastal nutrient filter remains poorly investigated because element fluxes are mostly controlled by advection. Sediments are home for phytoplankton resting stages, but the contribution of seed germination to the development of phytoplankton blooms is unknown. The resting eggs of zooplankton are also deposited in the sediment, but the timing of zooplankton and fish development in spring and the impact of progressive warming are poorly understood. Decreases in salinity strongly influence macrobenthos in the Baltic Sea, whereas increased eutrophication favors the growth of opportunistic species. Finally, coastal darkening is discussed, as it affects marine life in ways that are difficult to assess. Future studies of coastal zones will benefit from technical innovations like mooring systems that transmits data immediately to the shore and uses drones to aid in sampling along coastlines. This review synthesizes current knowledge on the state and functioning of the Baltic coastal zone, highlighting novel insights into the role of permeable sandy sediments as nutrient cycling hotspots. We identify key uncertainties arising from the high spatio-temporal variability of these systems, which limit the predictive capacity of existing models. Only by combining novel approaches we can improve projections of climate-change impacts, and provide a robust scientific basis for the management and protection of vulnerable coastal ecosystems. Accordingly, the measures that will enable stakeholders and politicians to improve the protection of coastal areas remain to be developed.

Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8000 years in one of the world's largest brackish water bodies: the colonisation of the Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To this end, we combined target capture of the entire nuclear genome with pooled shotgun sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified > 1000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient supply. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient contributes to local adaptation of S. marinoi. Taken together, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterised by a multitude of environmental gradients, is driven by widespread changes in diverse metabolic pathways and functions.

Little is known about the genetic diversity and stability of natural populations over millennial time scales, although the current biodiversity crisis calls for heightened understanding. Marine phytoplankton, the primary producers forming the basis of food webs in the oceans, play a pivotal role in maintaining marine ecosystems health and serve as indicators of environmental change. This study examines the genetic diversity and shifts in allelic composition in the diatom species Skeletonema marinoi over ~8000 years in the Baltic Sea by analyzing chloroplast and mitochondrial genomes. Sedimentary ancient DNA (sedaDNA) demonstrates the stability and resilience of genetic composition and diversity of this species across millennia in the context of major climate events. Accelerated change in allelic composition is observed from historical periods onwards, coinciding with times of intensifying human activity, like the Roman Empire, the Viking Age, and the Hanseatic Age, suggesting that anthropogenic stressors have profoundly impacted this species for the last two millennia. The data indicate a very high natural stability and resilience of the genomic composition of the species and underscore the importance of uncovering genomic disruptions caused by human impact on organisms, even those not directly exploited, to better predict and manage future biodiversity.

Germination from plankton resting stages is often inhibited by burial and anoxic conditions in the sediment. Resuspension of surface sediments by storms might, therefore, represent an important mechanism that facilitates germination. We investigated the impact of sediment resuspension on the composition of planktonic microbial eukaryote community, assessed through 18S rRNA gene metabarcoding, by incubating sediment cores from Greifswald Bay (Baltic Sea) either undisturbed or with regular resuspension events for 4 months at rising temperatures. In this experiment, the planktonic eukaryotic community composition was mostly characterized by temporal species succession likely driven by the gradual increase in water temperature. Furthermore, NO3− concentrations and sediment resuspension were identified as important factors shaping the eukaryotic community composition. Nitrate concentrations were significantly higher in the control than in the mixed sediment cores, as resuspension likely caused a significant loss of nitrate to the sediment. Unexpectedly, eukaryotic alpha diversity was not significantly altered by mixing, but the community composition changed due to the germination of previously buried species. These results highlight the importance of sediment resuspension for the activation of buried resting stages and for altering nutrient concentrations in the water column impacting planktonic microbial community composition.

Zoosporic parasites significantly influence aquatic ecosystems by infecting various phytoplankton taxa, but their interactions in brackish ecosystems remain largely unexplored. This study explores microbial communities and parasitic interactions with summer phytoplankton communities at six brackish coastal sites in the northern Baltic Sea. We hypothesized that small-scale spatial heterogeneity in environmental conditions would lead to distinct assemblages of microbial communities and phytoplankton-parasite interactions. By combining DNA metabarcoding, single-cell sequencing, and microscopy, we provide the first community-level qualitative and quantitative assessment of zoosporic parasites infecting summer phytoplankton in the Baltic Sea. Microbial communities varied significantly across sites, with salinity as primary driver of eukaryotic diversity. Chytrid fungi were the dominant parasites, infecting green algae, diatoms, and filamentous cyanobacteria, with infection rates up to 5.8% of phytoplankton biomass. Sequences from brackish chytrids clustered with those from freshwater environments, reflecting polyphyletic patterns linked to host taxa. Phytoplankton-parasite interactions were influenced by host abundance and site-specific conditions with correlation analysis suggesting broader host ranges and potential generalist behavior in some chytrid species. Additionally, an unidentified oomycete infected up to 85% of the toxic bloom-forming cyanobacterium Nodularia spp. This study highlights the ecological relevance of zoosporic parasites in the Baltic Sea and emphasizes the need for further research into their role in phytoplankton bloom dynamics.

Global warming is a major threat to marine biodiversity and ecosystem functioning, with consequences that are yet largely unknown. To frame these consequences, we need to understand how marine ecosystems respond to warming and related environmental changes. Ecosystem models have proven to be a valuable tool in this respect, but their projections vary considerably. A major limitation in current ecosystem models may be that they largely ignore evolutionary processes, which nonetheless can be relevant on the simulated timescales. In addition, ecosystem models are usually fit to contemporary data and used predictively afterwards, without further validation that they are equally applicable to past (and, by inference, future) scenarios. A promising approach to validate evolutionary ecosystem models is the use of biological archives such as natural sediments, which record long-term ecosystem changes. Since the ecosystem changes present in sediment records are affected by evolution, evolution needs to be represented in ecosystem models not only to realistically simulate the future, but also the sediment record itself. The sediment record, in turn, can provide the required constraints on long-term evolutionary changes, along with information on past environmental conditions, biodiversity, and relative abundances of taxa. Here, we present a framework to make use of such information to validate evolutionary ecosystem models and improve model projections of future ecosystem changes. Using the example of phytoplankton, key players in marine systems, we review the existing literature and discuss (I) which data can be derived from ancient sedimentary archives, (II) how we can integrate these data into evolutionary ecosystem models to improve their projections of climate-driven ecosystem changes, and (III) future perspectives and aspects that remain challenging.

Dormancy is a widespread key life history trait observed across the tree of life. Many plankton species form dormant cell stages that accumulate in aquatic sediments and, under anoxic conditions, form chronological records of past species and population dynamics under changing environmental conditions. Here we report on the germination of a microscopic alga, the abundant marine diatom Skeletonema marinoi Sarno et Zigone, that had remained dormant for up to 6871 +/- 140 years in anoxic sediments of the Baltic Sea and resumed growth when exposed to oxygen and light. Resurrected diatom strains, representing cohorts from six different time points of the past 6871 +/- 140 years, are genetically differentiated, and fundamental physiological functions such as growth and photosynthesis have remained stable through time despite distinct environmental dynamics. Showing that resurrection and full functional recovery, in comparison to 3 +/- 2 years of dormancy, is possible after millennial resting, we emphasize the relevance of dormancy and living sediment archives. For the future, sediment archives, together with the resurrection approach, would offer a powerful tool to trace adaptive traits over millennia under distinct climatic conditions and elucidate the underlying mechanisms.

AbstractSedimentary ancient DNA (sedaDNA) offers an important opportunity for investigating long‐term community dynamics. Nevertheless, sedaDNA is challenging since DNA is degraded and fragmented over time. Of particular interest for such sedaDNA studies are phytoplankton communities, which are sensitive environmental indicators and important producers in aquatic systems. So far, only a few suitable metabarcoding primers for sedaDNA targeting phytoplankton exist. In this study, we introduce new metabarcoding primers targeting cyanobacteria and dinoflagellates. They amplify short, ~200‐bp ribosomal 16S and 18S DNA fragments. We compared these primers against published ones, uncovering distinct communities captured by different primer sets. The newly designed dinoflagellate and cyanobacterial primers revealed unique sets of amplicon sequence variants (ASVs) compared to published primers, highlighting the impact of primer choice on describing community composition. We also explored the effect of amplicon length on metabarcoding success over a sample age. Observed trends suggest that amplification success decreases with longer amplicons, probably as a result of DNA degradation in older sediment samples. Lastly, strong DNA preservation challenges emerged in sediment samples older than 7000 BP, corresponding with oxic phases of the Baltic Sea bottom water. This emphasizes the importance of age, sediment type, and preservation conditions when interpreting sedaDNA results. Despite limitations in temporal resolution, the study shows that sedaDNA‐based fluctuations in the phytoplankton community are consistent with well‐known environmental stages. More research is necessary to understand (1) DNA preservation and its impact on reconstructed communities and (2) impact of abiotic conditions on phytoplankton communities.

In the Baltic Sea, the dinoflagellates Apocalathium malmogiense, Biecheleria baltica, and Gymnodinium corollarium are important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to a lack of resolution of distinctive morphological features of the three species. Here, we describe a molecular approach based on a quantitative real-time polymerase chain reaction (qPCR) primer and probe system, targeting the ITS1 and ITS2 regions of the rRNA gene for all three species and enabling their quantification. The specificity of the method was demonstrated using monocultures of A. malmogiense, B. baltica, G. corollarium as well as three other dinoflagellate species co-occurring in the Baltic Sea during spring and validated using field-collected phytoplankton samples.

Marginal sea ecosystems, such as the Baltic Sea, are severely affected by anthropogenic pressures, such as climate warming, pollution, and eutrophication, which increased in the course of the past century. Biodiversity monitoring data and assessment of environmental status in such systems have typically been carried out only for the past few decades, if at all, and knowledge on pre-impact stability and good ecological status is limited. An extension of monitoring time series can potentially be achieved through analyses of paleoecological records, e.g. for phytoplankton, which form the base of the food web and are highly susceptible to environmental changes. Within the phytoplankton community, dinoflagellates and diatoms play a significant role as primary producers, and their relative dominance in the spring bloom, calculated as Dia/Dino index, is used as an indicator for the environmental status of the Baltic Sea. To extend time series on the dominance patterns and include non-fossilized dinoflagellates, we here establish a simple droplet digital PCR (ddPCR) reaction on ancient DNA from sediment cores that decodes phytoplankton dynamics. We focus on two common spring bloom species, the diatom Skeletonema marinoi and the dinoflagellate Apocalathium malmogiense, for which we evaluate a DNA based dominance index. It performs very well in comparison to DNA metabarcoding and modern monitoring and can elucidate past species dominance across the past century and across millennia in different basins of the Baltic. For the past century, we see a dominance shift already starting before the mid-20th century in two of the Baltic Sea basins, thus substantially predating current monitoring programs. Shifts are only partly coeval among the cores and the index shows different degrees of stability. This pattern is confirmed across millennia, where a long-term stable relationship between the diatom and the dinoflagellate is observed in the Eastern Gotland Basin, while data from the Gulf of Finland bear testimony to a much more unstable relationship. This confirms that good ecological status based on the dominance pattern of diatoms and dinoflagellates must be established locally and exemplifies how sediment core DNA can be employed to extend monitoring data.

Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.

Cyanobacterial blooms in the Baltic Sea proliferated in recent decades due to rising sea surface temperatures, resulting in significant ecological impacts. To elucidate their current success, we examined ecophysiological, biochemical, and morphological traits of recent and similar to 33-year-old strains of Nodularia spumigena using a resurrection approach. The ability of many cyanobacteria to form dormant stages that can persist in anoxic sediments for decades provides a unique opportunity to study adaptive traits to past environmental conditions. A short sediment core from the Eastern Gotland Basin was processed to isolate strains of N. spumigena buried in 1987 +/- 2 and 2020 +/- 0.5 Common Era. Sequencing was used for species identification, followed by characterization of cell morphometry, carbon, nitrogen, and chlorophyll a content. Photosynthetic performance was evaluated by using pulse-amplitude modulated fluorimetry and oxygen optodes to assess light and temperature requirements. Our results revealed trait changes in N. spumigena over the past 3 decades: Temperature optimum for photosynthesis shifted from 15.3-21.1 degrees C, which is consistent with the past and present local SST. Recent strains exhibited increased carbon, nitrogen, and chlorophyll a content despite decreased cell volume. The demonstrated adaptability of N. spumigena to increasing temperature suggests that this species will thrive in a warmer climate in the future. These insights will aid modeling efforts aimed at understanding and managing consequences of future cyanobacterial blooms in the Baltic Sea ecosystem.

ABSTRACT Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics data with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8,000 years in one of the world’s largest brackish water bodies: the colonization of the Baltic Sea by the marine diatom Skeletonema marinoi . To this end, we used a novel approach for protist population genomics, combining target capture of the entire nuclear genome with pooled sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified >3,000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient availability. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation, and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient is a major factor driving local adaptation of S. marinoi . Altogether, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterized by a multitude of environmental gradients, is driven by intricate changes in diverse metabolic pathways and functions.

The installation of marine energy systems may affect marine environments, and by extension, marine fish communities.Therefore, biomonitoring is an integral part of assessing impacts on species.Environmental DNA (eDNA) provides a noninvasive alternative to conventional monitoring surveys and the possibility of a more accurate assessment of species richness.Yet, its cost efficiency compared to traditional methods of monitoring is relatively unknown, especially when applied to monitoring around tidal, wave, and offshore wind energy installations.For this study, 202 peer-reviewed journal articles were dissected to inventory the diversity of supplies used for collecting and processing eDNA samples and to compile the average cost of eDNA surveys.Information collected included the type, volume, and brand of containers used in sampling; material, size, and brand of filters; and extraction methods.Cost information was gathered for the most common supplies, and a total cost was estimated for a hypothetical eDNA survey in Sequim Bay, WA, to compare with traditional methods of surveying such as beach seining and scuba surveys.

In the Baltic Sea, cold-water adapted dinoflagellates and diatoms dominate the phytoplankton spring bloom of the Northern and Eastern Basins of the Baltic Sea. In the Central and Southern parts, where such species are less prominent, they cause occasional biomass peaks. We hypothesized that these dynamics correlate with ice cover, sea surface temperature (SST), and water transport processes, as the large Basins of the Central Baltic Sea are too deep to build-up blooms from their own seed banks. Long-term monitoring data from the past 40 and 20 years in the central and southern Baltic Sea, respectively, were analyzed here for biomass development of five cold-adapted taxa: the diatoms Pauliella taeniata, Thalassiosira baltica, Thalassiosira levanderi and Melosira spp. and the dinoflagellate Peridinella catenata. Results show that diatoms generally reached high biomass peaks in the 1980s and in shorter periods from 1995-1997, 2003- 2006, and 2010-2013 in all areas. We detected good correlations with the length of the ice cover period as well as low minimum and mean winter and spring SSTs. In contrast, biomass dynamics of the dinoflagellate P. catenata are more independent from these factors but have decreased strongly since the beginning of the 21st century. A numerical ocean model analysis confirmed the hypothesis that large blooms in the deep basins are seeded through water transport from adjacent shallow, ice-covered coastal areas such as the Gulf of Finland and the Gulf of Riga. Our results show that under ongoing climate warming, the common cold-water species may disappear from spring blooms in southern and central areas with unknown consequences for the ecosystem.

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.