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Factors influencing variance of DNA methylation in vegetatively reproducing plants, both terrestrial plants and aquatic seagrasses, is just beginning to be understood. Improving our knowledge of these mechanisms will increase understanding of transgenerational epigenetics in plant clones, of the relationship between DNA methylation and seagrass development, and of the drivers of epigenetic variation, which may underly acclimation in clonally reproducing plants. Here, we sampled leaves, rhizomes and roots of three physically and spatially separated ramet sections from a clonally propagated field of the seagrass Zostera marina. Using reduced methylome sequencing, we studied variations in the methylome of seagrass Zostera marina between the sampled tissue types and across age groups. Our analysis of ramets of different ages showed variations in methylation between older and younger samples in both specific methylation patterns and global methylation levels. Our analysis of tissue types showed a marked differentiation of the roots from the rhizomes and leaves, which showed more similar methylation patterns. These findings are in agreement with the strong connection of DNA methylation and plant development and tissue differentiation. We also suggest an effect of differential environmental exposures on the methylome of the younger versus the older ramets due to the forming of molecular stress memories., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Galice Hoarau reports financial support was provided by Research Council of Norway., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Contaminants of emerging concern (CECs) are ubiquitous in aquatic environments and pose a range of biological effects including endocrine disruption. Yet, knowledge of their occurrence in wildlife including seabirds remains scarce. We investigated the occurrence of selected bisphenols, benzophenones, phthalate metabolites, benzotriazoles, benzothiazoles, parabens, triclosan, and triclocarban in plasma of 18 breeding female common eiders (Somateria mollissima) from an endangered population in the Baltic Sea as most of these CECs have never before been examined in eiders. We sampled blood at the start (T1) and end (T2) of incubation to investigate concentration changes during incubation. As early- and late-breeding eiders tend to differ in how they finance reproduction (local vs stored nutrient reserves), we compared early and late breeders to assess whether CEC concentrations differed by breeding phenology. Of the 58 targeted CECs, 21 were detected in at least one female, with bisphenol A (BPA) and benzophenone-3 (BzP-3) occurring most frequently (T1: 78% and 61%; T2: 61% and 67%, respectively), while mono(2-ethyl-1-hexyl) phthalate (mEHP), BPA, and monoethyl phthalate (mEP) were detected in the highest concentrations (median concentrations 27.1, 12.7, and 11.2 ng/g wet weight, respectively, at T1). No CEC concentrations differed between early and late incubation. Late breeders had significantly higher concentrations of BzP-3, monomethyl phthalate (mMP), and mEP during early incubation (4.55 vs 1.24 ng/g ww, 7.05 vs 3.52, and 11.2 vs < limit of detection (LOD), respectively) and significantly higher concentrations of mMP and mEP during late incubation (6.16 vs 

Background: Zostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions. Changes in salinity generally have a strong impact on the biota, especially at the salty divide between salinity 6 and 9. To better understand the impact of the salty divide on the interaction between Z. marina and the surrounding sediment and water microbiota, we investigated the effects of Z. marina meadows on the surrounding microbiota across a salinity range of 6-15 in the Baltic Sea during the summer using 16S and 18S rRNA gene amplicon sequencing., Results: Salinity was the most important factor for structuring the microbiota within both water and sediment. The presence of Z. marina affected the composition of the bacterial and eukaryotic community and bacterial alpha diversity in the sediment. However, this effect was confined to alpha-mesohaline conditions (salinity 9-15). The impact of Z. marina below salinity 9 on water and sediment microbiota was insignificant., Conclusions: Increasing salinity was associated with a longer leaf length of Z. marina, causing an increased canopy height, which affects the sediment microbiota through reduced water velocity. Hence, we propose that the canopy effect may be the major predictor explaining Z. marina's interactions with the surrounding microbiota at salinity 9-15. These findings emphasize the importance of the physical effects of Z. marina meadow ecosystem services and have important implications for Z. marina management under brackish conditions in a changing climate., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: All authors have approved the final manuscript. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.

The number of Vibrio -related infections in humans, e.g., by Vibrio vulnificus , has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic Vibrio spp., like V. vulnificus . To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of Vibrio spp. and V. vulnificus in water were compared to environmental conditions, including the presence of the eelgrass Zostera marina , which has been suggested to reduce pathogenic Vibrio species abundance. In the water column, V. vulnificus only occurred at the German station between July and August at salinity 8.1-11.2. Temperature and phosphate (PO 4 3- spp. and Vibrio spp. and V. vulnificus spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to Vibrio spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to V. vulnificus abundance. Interestingly, V. vulnificus co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in Vibrio associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO V. vulnificus associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO 4 3- , for Vibrio species levels at intermediate salinities in the Baltic Sea., Importance: Elevated sea surface temperatures are increasing the prevalence of pathogenic Vibrio at higher latitudes. The recent increase in Vibrio -related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on Vibrio vulnificus , and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of V. vulnificus at intermediate salinities in the coastal Baltic Sea., Competing Interests: The authors declare no conflict of interest.

Parental care is regulated by multiple endocrine mechanisms. Among these hormones, prolactin (PRL) is involved in the expression of parental behaviors. Despite the consensus that PRL mediates variation in parental effort with age and body condition, its role in the adjustment of parental effort to fluctuating environmental conditions, including changing predation pressure, still awaits further investigation. To shed light on this knowledge gap, we relied on a long-term monitoring of female common eiders Somateria mollissima (n = 1277 breeding attempts, 2012-2022) incubating under fluctuating predation risk to investigate the link between baseline PRL levels and female minimum age, body condition, clutch size, environmental parameters (predation pressure, climate, nest microhabitat) and hatching success. We predicted that PRL would be higher in older females, those in better condition or incubating larger clutches. We also predicted that females would reduce parental effort when nesting under challenging environmental conditions (high predation pressure or poor climatic conditions), translated into reduced baseline PRL levels. We also explored how variation in PRL levels, female characteristics and environmental parameters were related to hatching success. Following our predictions, PRL levels were positively associated with body condition and female age (before showing a senescent decline in the oldest breeders). However, we did not observe any population-level or individual-level reduction in PRL levels in response to increasing predation pressure. Population-level baseline PRL levels instead increased over the study period, coincident with rising predation threat, but also increasing female body condition and age. While we did not provide evidence for a direct association between baseline PRL levels and predation risk, our results support the idea that elevated baseline PRL levels promote hatching success under internal constraints (in young, inexperienced, breeders or those incubating a large clutch) or constraining environmental conditions (during years of high predation pressure or poor climatic and foraging conditions). Finally, the low repeatability of baseline PRL levels and high interannual variability highlight considerable within-individual flexibility in baseline PRL levels. Further research should explore flexibility in parental effort to changing environmental conditions, focusing on both baseline and stress-induced PRL levels., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

The Finnish Archipelago Sea (AS) has long been subject to intensive anthropogenic phosphorus (P) loading. The area suffers from seasonal hypoxia and cyanobacterial blooms despite reductions in nutrient discharge from the catchment and point sources. Internal loading may even dominate the P budget. Previous estimates of internal P loading have limitations (e.g., in spatial coverage and infrequent measurements). We present the first area-wide estimates of the magnitude of internal P loading based on the long-term release of P stored in the sediments. Modelling the internal P loading in the AS is challenging due to the complexity of biogeochemical processes in the sediment-water interface, as well as the heterogenic topography of the seafloor. Instead, we calculated estimates of internal P loading based on data from previous studies on sequential chemical extraction of sediment P, sediment physical characteristics (e.g., organic content, location of muddy seabed substrates), and near-bottom oxygen (O 2 ) conditions. The estimates in three scenarios of contrasting O 2 conditions were based on potentially mobile P pools in the sediments, recycled from sediment to water (i.e., loosely-bound or exchangeable P, P bound to reducible iron oxy(hydr)oxides, and labile organic P). The potentially mobile P pools were determined by chemical extraction methods (modified from Psenner et al., 1984 and Ruttenberg, 1992). The internal P loading under presumable O 2 conditions was estimated to be fivefold that of waterborne P input to the AS; comparable to previous estimates for hypoxic areas in the Baltic Sea. Our estimates revealed wide spatial variability in the internal P loading, depending on O 2 conditions and seabed sediment substrate. The site-specific P release estimates are included in a water quality model used by regional authorities, which increases the model's reliability for estimating the impact of human activities on the water quality across the AS., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Marine heatwaves have caused massive mortality in coastal benthic ecosystems, altering community composition. Here, we aim to understand the effects of single and sequential sublethal heatwaves in a temperate benthic ecosystem, investigating their disturbance on various levels of ecological hierarchy, i.e. individual physiology, trophic groups' biomass and ecosystem carbon fluxes. To do so, we performed a near-natural experiment using outdoor benthic mesocosms along spring/summer, where communities were exposed to different thermal regimes: without heatwaves (0HW), with one heatwave (1HW) and with three heatwaves (3HWs). Gastropods were negatively impacted by one single heatwave treatment, but the exposure to three sequential heatwaves caused no response, indicating ecological stress memory. The magnitude of ecosystem carbon fluxes mostly decreased after 1HW, with a marked negative impact on mesograzers' feeding, while the overall intensity of carbon fluxes increased after 3HWs. Consumers' acclimation after the exposure to sequential heatwaves increased grazing activity, representing a threat for the macroalgae biomass. The evaluation of physiological responses and ecological interactions is crucial to interpret variations in community composition and to detect early signs of stress. Our results reveal the spread of heatwave effects along the ecological hierarchical levels, helping to predict the trajectories of ecosystem development.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

BackgroundThe Vibrio genus comprises several bacterial species present in the Baltic Sea region (BSR), which are known to cause human infections.AimTo provide a comprehensive retrospective analysis of Vibrio -induced infections in the BSR from 1994 to 2021, focusing on the 'big four' Vibrio species - V. alginolyticus , V. cholerae non-O1/O139, V. parahaemolyticus and V. vulnificus - in eight European countries (Denmark, Estonia, Finland, Germany, Latvia, Lithuania, Poland and Sweden) bordering the Baltic Sea.MethodsOur analysis includes data on infections, Vibrio species distribution in coastal waters and environmental data received from national health agencies or extracted from scientific literature and online databases. A redundancy analysis was performed to determine the potential impact of several independent variables, such as sea surface temperature, salinity, the number of designated coastal beaches and year, on the Vibrio infection rate.ResultsFor BSR countries conducting surveillance, we observed an exponential increase in total Vibrio infections (n = 1,553) across the region over time. In Sweden and Germany, total numbers of Vibrio spp. and infections caused by V. alginolyticus and V. parahaemolyticus positively correlate with increasing sea surface temperature. Salinity emerged as a critical driver of Vibrio spp. distribution and abundance. Furthermore, our proposed statistical model reveals 12 to 20 unreported cases in Lithuania and Poland, respectively, countries with no surveillance.ConclusionsThere are discrepancies in Vibrio surveillance and monitoring among countries, emphasising the need for comprehensive monitoring programmes of these pathogens to protect human health, particularly in the context of climate change.

Rising global temperatures are often identified as the key driver impacting ecosystems and the services they provide by affecting biodiversity structure and function. A disproportionate amount of our understanding of biodiversity and function is from short-term experimental studies and static values of biodiversity indices, lacking the ability to monitor long-term trends and capture community dynamics. Here, we analyse a biennial dataset spanning 32 years of macroinvertebrate benthic communities and their functional response to increasing temperatures. We monitored changes in species' thermal affinities to examine warming-related shifts by selecting their mid-point global temperature distribution range and linking them to species' traits. We employed a novel weighted metric using Biological Trait Analysis (BTA) to gain better insights into the ecological potential of each species by incorporating species abundance and body size and selecting a subset of traits that represent five ecosystem functions: bioturbation activity, sediment stability, nutrient recycling and higher and lower trophic production. Using biodiversity indices (richness, Simpson's diversity and vulnerability) and functional indices (richness, Rao's Q and redundancy), the community structure showed no significant change over time with a narrow range of variation. However, we show shifts in species composition with warming and increases in the abundance of individuals, which altered ecosystem functioning positively and/or non-linearly. Yet, when higher taxonomic groupings than species were excluded from the analysis, there was only a weak increase in the measured change in community-weighted average thermal affinities, suggesting changes in ecosystem functions over time occur independently of temperature increase-related shifts in community composition. Other environmental factors driving species composition and abundance may be more important in these subtidal macrobenthic communities. This challenges the prevailing emphasis on temperature as the primary driver of ecological response to climate change and emphasises the necessity for a comprehensive understanding of the temporal dynamics of complex systems., (© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)

Biological trait analysis (BTA) is a valuable tool for evaluating changes in community diversity and its link to ecosystem processes as well as environmental and anthropogenic perturbations. Trait-based analytical techniques like BTA rely on standardised datasets of species traits. However, there are currently only a limited number of datasets available for marine macrobenthos that contain trait data across multiple taxonomic groups. Here, we present an open-access dataset of 16 traits for 235 macrozoobenthic species recorded throughout multiple sampling campaigns of the Dutch Wadden Sea; a dynamic soft bottom system where humans have long played a substantial role in shaping the coastal environment. The trait categories included in this dataset cover a variety of life history strategies that are tightly linked to ecosystem functioning and the resilience of communities to (anthropogenic) perturbations and can advance our understanding of environmental changes and human impacts on the functioning of soft bottom systems., (© 2023. The Author(s).)

Our understanding of the community assembly processes acting on non-indigenous species (NIS), as well as the relationship with native species is limited, especially in marine ecosystems. To overcome this knowledge gap we here develop a trait-based approach based on the functional distinctiveness metric to assess niche overlap between NIS and native species, using high-resolution data on benthic invertebrate communities in the Baltic Sea. Our results show that NIS retain a certain degree of similarity with native species, but display one or a few singular unique traits (e.g., bioturbation ability). Furthermore, we demonstrate that community assembly processes, including both environmental filtering and limiting similarity affect NIS establishment, but that their effects may be highly context dependent, as illustrated by pronounced spatial patterns in distinctiveness. Finally, our trait-based approach provides a generic framework applicable to other areas and organisms, to better understand and address biological invasions., (© 2023 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Oomycete infections in farmed fish are one of the most significant disease issues in salmonid aquaculture worldwide. In the present study, Saprolegnia spp. in different farmed fish species in Finland were identified, and the molecular epidemiology of especially Saprolegnia parasitica was examined. We analysed tissue samples from suspected oomycete-infected salmonids of different life stages from a number of fish farms, as well as three wild salmonids. From collected oomycete isolates, the ITS1, 5.8S and ITS2 genomic regions were amplified, analysed phylogenetically and compared with corresponding sequences deposited in GenBank. Of the sequenced isolates, 91% were identified as S. parasitica. Isolates of yolk sac fry were identified as different Saprolegnia spp. Among the isolates from rainbow trout eggs Saprolegnia diclina dominated. In order to determine potential dominating clones among the S. parasitica, isolates were analysed using Multi Locus Sequence Typing (MLST). The results showed that one main clone contained the majority of the isolates. The MLST analysis showed four main sequence types (ST1-ST4) and 13 unique STs. This suggests that the Saprolegnia infections in farmed fish in Finland are not caused by different strains originating in the farm environment. Instead, one main clone of S. parasitica is present in Finnish fish farms., (© 2023 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

The authors assessed the importance of the round goby Neogobius melanostomus as prey for three native predatory fish species, Atlantic cod Gadus morhua, European perch Perca fluviatilis and northern pike Esox lucius, in a northern and southern area of the Baltic Proper, using a combination of visual analysis and DNA metabarcoding of predator stomach contents. To explore the influence of environmental abundances of N. melanostomus on predation, they related the occurrence of N. melanostomus in predator diets to its abundance in survey fishing. Gadus morhua and E. lucius in the southern area showed the highest tendency to feed on N. melanostomus when it was abundant, as N. melanostomus occurred in up to 100% of stomachs and constituted up to 88% of the total diet volume proportion. The diet contribution of N. melanostomus was associated with N. melanostomus abundances for G. morhua and E. lucius, and when N. melanostomus was abundant, these predators exhibited lower prey richness and a higher degree of piscivory. G. morhua and P. fluviatilis also fed less on crustacean prey when N. melanostomus was abundant. The high importance of N. melanostomus in diets of native fish predators may modify indirect interactions between N. melanostomus and native prey species in invaded coastal communities., (© 2023 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Climate change affects timing of reproduction in many bird species, but few studies have investigated its influence on annual reproductive output. Here, we assess changes in the annual production of young by female breeders in 201 populations of 104 bird species (N = 745,962 clutches) covering all continents between 1970 and 2019. Overall, average offspring production has declined in recent decades, but considerable differences were found among species and populations. A total of 56.7% of populations showed a declining trend in offspring production (significant in 17.4%), whereas 43.3% exhibited an increase (significant in 10.4%). The results show that climatic changes affect offspring production through compounded effects on ecological and life history traits of species. Migratory and larger-bodied species experienced reduced offspring production with increasing temperatures during the chick-rearing period, whereas smaller-bodied, sedentary species tended to produce more offspring. Likewise, multi-brooded species showed increased breeding success with increasing temperatures, whereas rising temperatures were unrelated to reproductive success in single-brooded species. Our study suggests that rapid declines in size of bird populations reported by many studies from different parts of the world are driven only to a small degree by changes in the production of young.

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.

In the last three decades, quantitative approaches that rely on organism traits instead of taxonomy have advanced different fields of ecological research through establishing the mechanistic links between environmental drivers, functional traits, and ecosystem functions. A research subfield where trait-based approaches have been frequently used but poorly synthesized is the ecology of seagrasses; marine angiosperms that colonized the ocean 100M YA and today make up productive yet threatened coastal ecosystems globally. Here, we compiled a comprehensive trait-based response-effect framework (TBF) which builds on previous concepts and ideas, including the use of traits for the study of community assembly processes, from dispersal and response to abiotic and biotic factors, to ecosystem function and service provision. We then apply this framework to the global seagrass literature, using a systematic review to identify the strengths, gaps, and opportunities of the field. Seagrass trait research has mostly focused on the effect of environmental drivers on traits, i.e., "environmental filtering" (72%), whereas links between traits and functions are less common (26.9%). Despite the richness of trait-based data available, concepts related to TBFs are rare in the seagrass literature (15% of studies), including the relative importance of neutral and niche assembly processes, or the influence of trait dominance or complementarity in ecosystem function provision. These knowledge gaps indicate ample potential for further research, highlighting the need to understand the links between the unique traits of seagrasses and the ecosystem services they provide., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Moreira-Saporiti, Teichberg, Garnier, Cornelissen, Alcoverro, Björk, Boström, Dattolo, Eklöf, Hasler-Sheetal, Marbà, Marín-Guirao, Meysick, Olivé, Reusch, Ruocco, Silva, Sousa, Procaccini and Santos.)

In this study, radio telemetry was used to examine the upstream spawning migration behaviour of anadromous brown trout (sea trout), Salmo trutta L., in a boreal river system, the River Isojoki, western Finland. The aim was to study the movement activity and migration characteristics of trout during the upstream spawning migration, as well as to locate the important spawning habitats and study the spawning characteristics. Furthermore, the authors analysed how flow conditions and a hydropower dam, with adjacent fishways, affected the upstream spawning migration. Tagged trout spawned in both the main stem and four tributaries, with spawning taking place from early October to November. The movement activity of radio-tagged trout was influenced by a hydropower dam (Perus dam), with spring migrators spending prolonged periods at the dam area, postponing the migration upstream. Flow conditions affected the total time spent at the dam area, as well as the movement activity in the free-flowing sections above the dam, with increasing flow stimulating activity. In addition, time of river ascent and location of spawning area had a significant effect on the movement activity of tagged trout. These results are further evidence that synergistic effects of flow and migratory obstacles can negatively influence migrations of anadromous fish, regardless of constructed fishways. The management of flow regimes and the efficiency of fishways are vital, as climate change will likely influence the flow and increase the water temperature of boreal river systems, further aggravating issues caused by obstacles., (© 2022 Fisheries Society of the British Isles.)

Climate change increases the frequency and intensifies the magnitude and duration of extreme events in the sea, particularly so in coastal habitats. However, the interplay of multiple extremes and the consequences for species and ecosystems remain unknown. We experimentally tested the impacts of summer heatwaves of differing intensities and durations, and a subsequent upwelling event on a temperate keystone predator, the starfish Asterias rubens. We recorded mussel consumption throughout the experiment and assessed activity and growth at strategically chosen time points. The upwelling event overall impaired starfish feeding and activity, likely driven by the acidification and low oxygen concentrations in the upwelled seawater. Prior exposure to a present-day heatwave (+5°C above climatology) alleviated upwelling-induced stress, indicating cross-stress tolerance. Heatwaves of present-day intensity decreased starfish feeding and growth. While the imposed heatwaves of limited duration (9 days) caused slight impacts but allowed for recovery, the prolonged (13 days) heatwave impaired overall growth. Projected future heatwaves (+8°C above climatology) caused 100% mortality of starfish. Our findings indicate a positive ecological memory imposed by successive stress events. Yet, starfish populations may still suffer extensive mortality during intensified end-of-century heatwave conditions.

Spatial self-organization of ecosystems into large-scale (from micron to meters) patterns is an important phenomenon in ecology, enabling organisms to cope with harsh environmental conditions and buffering ecosystem degradation. Scale-dependent feedbacks provide the predominant conceptual framework for self-organized spatial patterns, explaining regular patterns observed in, e.g., arid ecosystems or mussel beds. Here, we highlight an alternative mechanism for self-organized patterns, based on the aggregation of a biotic or abiotic species, such as herbivores, sediment, or nutrients. Using a generalized mathematical model, we demonstrate that ecosystems with aggregation-driven patterns have fundamentally different dynamics and resilience properties than ecosystems with patterns that formed through scale-dependent feedbacks. Building on the physics theory for phase-separation dynamics, we show that patchy ecosystems with aggregation patterns are more vulnerable than systems with patterns formed through scale-dependent feedbacks, especially at small spatial scales. This is because local disturbances can trigger large-scale redistribution of resources, amplifying local degradation. Finally, we show that insights from physics, by providing mechanistic understanding of the initiation of aggregation patterns and their tendency to coarsen, provide a new indicator framework to signal proximity to ecological tipping points and subsequent ecosystem degradation for this class of patchy ecosystems.

Azoles represent the most used family of organic fungicides worldwide and they are used in agriculture to circumvent the detrimental impact of fungi on yields. Although it is known that these triazoles can contaminate the air, the soil, and the water, field data are currently and dramatically lacking to assess if, and to what extent, the use of triazoles could contaminate non-target wild vertebrate species, notably in agroecosystems. In this study, we aimed to document for the first time the degree of blood contamination of a generalist wild bird species by multiple azoles which are used for plant protection and fungi pest control in various habitats. We deployed passive air samplers and captured 118 Common blackbirds (Turdus merula) in an agroecosystem (vineyard), a protected forest, and a city in western France. We collected blood and analyzed the plasma levels of 13 triazoles and 2 imidazoles. We found that a significant percentage of blackbirds living in vineyards have extremely high plasma levels of multiple azoles (means (pg.g -1 ); tebuconazole: 149.23, difenoconazole: 44.27, fenbuconazole: 239.38, tetraconazole: 1194.16), while contamination was very limited in the blackbirds from the protected forest and absent in urban blackbirds. Interestingly, we also report that the contamination of blackbirds living in vineyard was especially high at the end of Spring and the beginning of Summer and this matches perfectly with the results from the passive air samplers (i.e., high levels of azoles in the air of vineyards during June and July). However, we did not find any correlation between the levels of plasma contamination by azoles and two simple integrative biomarkers of health (feather density and body condition) in this sentinel species. Future experimental studies are now needed to assess the potential sub-lethal effects of such levels of contamination on the physiology of non-target vertebrate species., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

The Northeast Greenland shelf (NEGS) is a recipient of Polar Water (PW) from the Arctic Ocean, Greenland Ice Sheet melt, and Atlantic Water (AW). Here, we compile hydrographical measurements to quantify long-term changes in fjords and coastal waters. We find a profound change in the vertical distribution of water masses, with AW shoaling >60 m and PW thinning >50 m since early 2000's. The properties of these waters have also changed. AW is now 1 °C warmer and the salinity of surface waters and PW are 1.8 and 0.68 lower, respectively. The AW changes have substantially weakened stratification south of ~74°N, indicating increased accessibility of heat and potentially nutrients associated with AW. The Atlantification earlier reported for the eastern Fram Strait and Barents Sea region has also propagated to the NEGS. The increased presence of AW, is an important driver for regional change leading to a likely shift in ecosystem structure and function., (© 2022. The Author(s).)

Saprolegnia parasitica induces heavy mortality in aquaculture. The detection of S. parasitica is often time consuming and uncertain, making it difficult to manage the disease. We validated a previously published real-time quantitative PCR (qPCR) assay to confirm the presence of S. parasitica in fish and in water using environmental DNA (eDNA) quantification. Analytical sensitivity and specificity of the assay was assessed in silico, in vitro and the qPCR assay was compared with microbiological cultivation methods to detect and quantify S. parasitica in water samples from a controlled fish exposure experiment and from fish farms. Furthermore, we compared the use of an agar cultivation method and the qPCR assay to detect S. parasitica directly from mucus samples taken from the fish surface. The analytical sensitivity and specificity of the qPCR assay were high. The qPCR assay detected 100% of S. parasitica -positive water samples. In a field study, the qPCR assay and a microwell plate (MWP) enumeration method correlated significantly. Furthermore, the qPCR assay could be used to confirm the presence of S. parasitica in skin mucus. Thus, the qPCR assay could complement diagnostic methods in specifically detecting saprolegniosis in fish and used as a surveillance method for S. parasitica pathogen in aquaculture environments.

Plastic and selective mechanisms govern parental investment adjustments to predation threat. We investigated the relative importance of plasticity and selection in risk-taking propensity of incubating female common eiders Somateria mollissima facing unprecedented predation in SW Finland, Baltic Sea. Using a 12-year individual-based dataset, we examined within- and among-individual variation in flight initiation distance (FID), in relation to predation risk, nest detectability, individual traits and reproductive investment ( N FID = 559). We expected females nesting in riskier environments (higher predation risk, lower nest concealment) to mitigate environmentally imposed risk by exhibiting longer FIDs, and females investing more in current reproduction (older, in better condition or laying larger clutches) to display shorter FIDs. The target of predation-adult or offspring-affected the mechanisms adapting risk-taking propensity; females plastically increased their FID under higher adult predation risk, while risk-avoiding breeders were predominant on islands with higher nest predation risk. Risk-taking females selected thicker nest cover, consistent with personality-matching habitat choice. Females plastically attenuated their anti-predator response (shorter FIDs) with advancing age, and females in better body condition were more risk-taking, a result explained by selection processes. Future research should consider predator type when investigating the fitness consequences of risk-taking strategies.N individual = 559). We expected females nesting in riskier environments (higher predation risk, lower nest concealment) to mitigate environmentally imposed risk by exhibiting longer FIDs, and females investing more in current reproduction (older, in better condition or laying larger clutches) to display shorter FIDs. The target of predation-adult or offspring-affected the mechanisms adapting risk-taking propensity; females plastically increased their FID under higher adult predation risk, while risk-avoiding breeders were predominant on islands with higher nest predation risk. Risk-taking females selected thicker nest cover, consistent with personality-matching habitat choice. Females plastically attenuated their anti-predator response (shorter FIDs) with advancing age, and females in better body condition were more risk-taking, a result explained by selection processes. Future research should consider predator type when investigating the fitness consequences of risk-taking strategies.

Distribution of Earth's biomes is structured by the match between climate and plant traits, which in turn shape associated communities and ecosystem processes and services. However, that climate-trait match can be disrupted by historical events, with lasting ecosystem impacts. As Earth's environment changes faster than at any time in human history, critical questions are whether and how organismal traits and ecosystems can adjust to altered conditions. We quantified the relative importance of current environmental forcing versus evolutionary history in shaping the growth form (stature and biomass) and associated community of eelgrass ( Zostera marina ), a widespread foundation plant of marine ecosystems along Northern Hemisphere coastlines, which experienced major shifts in distribution and genetic composition during the Pleistocene. We found that eelgrass stature and biomass retain a legacy of the Pleistocene colonization of the Atlantic from the ancestral Pacific range and of more recent within-basin bottlenecks and genetic differentiation. This evolutionary legacy in turn influences the biomass of associated algae and invertebrates that fuel coastal food webs, with effects comparable to or stronger than effects of current environmental forcing. Such historical lags in phenotypic acclimatization may constrain ecosystem adjustments to rapid anthropogenic climate change, thus altering predictions about the future functioning of ecosystems.

The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (<5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field., (© The Author(s) 2022. Published by Oxford University Press.)

In species with alternative reproductive tactics, there is much empirical support that parasitically spawning males have larger testes and greater sperm numbers as an evolved response to a higher degree of sperm competition, but support for higher sperm performance (motility, longevity and speed) by such males is inconsistent. We used the sand goby ( Pomatoschistus minutus ) to test whether sperm performance differed between breeding-coloured males (small testes, large mucus-filled sperm-duct glands; build nests lined with sperm-containing mucus, provide care) and parasitic sneaker-morph males (no breeding colouration, large testes, rudimentary sperm-duct glands; no nest, no care). We compared motility (per cent motile sperm), velocity, longevity of sperm, gene expression of testes and sperm morphometrics between the two morphs. We also tested if sperm-duct gland contents affected sperm performance. We found a clear difference in gene expression of testes between the male morphs with 109 transcripts differentially expressed between the morphs. Notably, several mucin genes were upregulated in breeding-coloured males and two ATP-related genes were upregulated in sneaker-morph males. There was a partial evidence of higher sperm velocity in sneaker-morph males, but no difference in sperm motility. Presence of sperm-duct gland contents significantly increased sperm velocity, and nonsignificantly tended to increase sperm motility, but equally so for the two morphs. The sand goby has remarkably long-lived sperm, with only small or no decline in motility and velocity over time (5 min vs. 22 h), but again, this was equally true for both morphs. Sperm length (head, flagella, total and flagella-to-head ratio) did not differ between morphs and did not correlate with sperm velocity for either morph. Thus, other than a clear difference in testes gene expression, we found only modest differences between the two male morphs, confirming previous findings that increased sperm performance as an adaptation to sperm competition is not a primary target of evolution., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

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., (© 2022. The Author(s).)

Species interactions underlie most ecosystem functions and are important for understanding ecosystem changes. Representing one type of species interaction, trophic networks were constructed from biodiversity monitoring data and known trophic links to assess how ecosystems have changed over time. The Baltic Sea is subject to many anthropogenic pressures, and low species diversity makes it an ideal candidate for determining how pressures change food webs. In this study, we used benthic monitoring data for 20 years (1980-1989 and 2010-2019) from the Swedish coast of the Baltic Sea and Skagerrak to investigate changes in benthic invertebrate trophic interactions. We constructed food webs and calculated fundamental food web metrics evaluating network horizontal and vertical diversity, as well as stability that were compared over space and time. Our results show that the west coast of Sweden (Skagerrak) suffered a reduction in benthic invertebrate biodiversity by 32% between the 1980s and 2010s, and that the number of links, generality of predators, and vulnerability of prey have been significantly reduced. The other basins (Bothnian Sea, Baltic Proper, and Bornholm Basin) do not show any significant changes in species richness or consistent significant trends in any food web metrics investigated, demonstrating resilience at a lower species diversity. The decreased complexity of the Skagerrak food webs indicates vulnerability to further perturbations and pressures should be limited as much as possible to ensure continued ecosystem functions., Competing Interests: The authors have no conflict of interest to declare., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Biological traits analysis (BTA) links community structure to both ecological functions and response to environmental drivers through species' attributes. In consequence, it has become a popular approach in marine benthic studies. However, BTA will reach a dead end if the scientific community does not acknowledge its current shortcomings and limitations: (a) uncertainties related to data origins and a lack of standardized reporting of trait information; (b) knowledge gaps on the role of multiple interacting traits on driving the organisms' responses to environmental variability; (c) knowledge gaps regarding the mechanistic links between traits and functions; (d) a weak focus on the spatial and temporal variability that is inherent to the trait expression of species; and, last but not least, (e) the large reliance on expert knowledge due to an enormous knowledge gap on the basic ecology of many benthic species. BTA will only reach its full potential if the scientific community is able to standardize and unify the reporting and storage of traits data and reconsider the importance of baseline observational and experimental studies to fill knowledge gaps on the mechanistic links between biological traits, functions, and environmental variability. This challenge could be assisted by embracing new technological advances in marine monitoring, such as underwater camera technology and artificial intelligence, and making use of advanced statistical approaches that consider the interactive nature and spatio-temporal variability of biological systems. The scientific community has to abandon some dead ends and explore new paths that will improve our understanding of individual species, traits, and the functioning of benthic ecosystems., Competing Interests: The authors declare no competing interests., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Marine coastal zones are highly productive, and dominated by engineer species (e.g. macrophytes, molluscs, corals) that modify the chemistry of their surrounding seawater via their metabolism, causing substantial fluctuations in oxygen, dissolved inorganic carbon, pH, and nutrients. The magnitude of these biologically driven chemical fluctuations is regulated by hydrodynamics, can exceed values predicted for the future open ocean, and creates chemical patchiness in subtidal areas at various spatial (µm to meters) and temporal (minutes to months) scales. Although the role of hydrodynamics is well explored for planktonic communities, its influence as a crucial driver of benthic organism and community functioning is poorly addressed, particularly in the context of ocean global change. Hydrodynamics can directly modulate organismal physiological activity or indirectly influence an organism's performance by modifying its habitat. This review addresses recent developments in (i) the influence of hydrodynamics on the biological activity of engineer species, (ii) the description of chemical habitats resulting from the interaction between hydrodynamics and biological activity, (iii) the role of these chemical habitat as refugia against ocean acidification and deoxygenation, and (iv) how species living in such chemical habitats may respond to ocean global change. Recommendations are provided to integrate the effect of hydrodynamics and environmental fluctuations in future research, to better predict the responses of coastal benthic ecosystems to ongoing ocean global change., (© 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

We conducted a short-term field sampling complemented with time integrating stable isotope analysis to holistically investigate status and ecological interactions in a remote NE Atlantic Zostera marina meadow. We found high nutrient water concentrations, large biomass of fast-growing, ephemeral macroalgae, low abundance, and biodiversity of epifauna and a food web with thornback ray (Raja clavata) as intermediate and cod (Gadus morhua) as top predator. We observed no variation with increasing depth (3.5-11 m) except for decreasing shoot density and biomass of Zostera and macroalgae. Our results indicate that the Finnøya Zostera ecosystem is eutrophicated. During the past three to four decades, nutrients from aquaculture have steadily increased to reach 75% of anthropogenic input while the coastal top predator cod has decreased by 50%. We conclude that bottom-up regulation is a predominant driver of change since top-down regulation is generally weak in low density and exposed Zostera ecosystems such as Finnøya., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Studying how the distributions of traits in communities vary along global gradients can inform how variation in interactions and other factors contribute to the process of community assembly. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass ( Zostera marina ) spanning 30° of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed while Atlantic communities were more clustered, and increasing epiphytes were associated with increased clustering. By examining how species interactions and environmental filters influence community structure across biogeographic regions, we demonstrate how both latitudinal variation in species interactions and historical contingency shape these responses. Community trait distributions have implications for ecosystem stability and functioning, and integrating large-scale observations of environmental filters, species interactions and traits can help us predict how communities may respond to environmental change.

Anthropogenically introduced invasive species represent a major threat to global biodiversity by causing population declines and extinctions of native species. The negative impacts of introduced predators are well documented, yet a fundamental knowledge gap exists regarding the efficiency of potential mitigation methods to restore the ecosystem. Other understudied aspects concern prey behavioural antipredator responses and the historical context of native predator-prey interactions, which may moderate invasion impacts on native prey. Invasion impacts of American mink (Neovison vison) and raccoon dog (Nyctereutes procyonoides) into the Baltic Sea archipelago are poorly understood, and the efficiency of removal efforts as a means to alleviate depredation pressure on native prey is debated. Here, we examine the effectiveness of invasive predator removal on ground-nesting female common eider (Somateria mollissima) mortality, breeding success and breeding propensity over a 9-year period, while controlling for predation risk imposed by the main native predator, the white-tailed eagle (Haliaeetus albicilla). Our results clearly show that intensified removal of American minks and raccoon dogs decreased the number of female eiders killed during nesting, while improving both nesting success and breeding propensity. Such obvious positive effects of invasive predator removal are particularly noteworthy against the backdrop of a soaring eagle population, indicating that the impacts of invasives may become accentuated when native predators differ taxonomically and by hunting mode. This study shows that invasive alien predator removal is an effective conservation measure clearly aiding native fauna even under severe native predation pressure. Such cost-effective conservation actions call for governmental deployment across large areas., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Although it is generally known that a combination of abiotic and biotic drivers shapes the distribution and abundance of parasites, our understanding of the interplay of these factors remains to be assessed for most marine host species. The present field survey investigated spatial patterns of richness, prevalence and abundance of parasites in Mytilus galloprovincialis along the coast of the northern Adriatic Sea. Herein, the relationships between biotic (host size, density and local parasite richness of mussel population) and abiotic (eutrophication and salinity) drivers and parasite richness of mussel individuals, prevalence and abundance were analysed. Local parasite richness was the most relevant factor driving parasite species richness in mussel individuals. Prevalence was mainly driven by eutrophication levels in three out of four parasite species analysed. Similarly, abundance was driven mainly by eutrophication in two parasite species. Mussel size, density and salinity had only minor contributions to the best fitting models. This study highlights that the influence of abiotic and biotic drivers on parasite infections in mussels can be differentially conveyed, depending on the infection measure applied, i.e. parasite richness, prevalence or abundance. Furthermore, it stresses the importance of eutrophication as a major factor influencing parasite prevalence and abundance in mussels in the Adriatic Sea.

Genetic diversity is the basis for evolutionary adaptation and selection under changing environmental conditions. Phytoplankton populations are genotypically diverse, can become genetically differentiated within small spatiotemporal scales and many species form resting stages. Resting stage accumulations in sediments (seed banks) are expected to serve as reservoirs for genetic information, but so far their role in maintaining phytoplankton diversity and in evolution has remained unclear. In this study we used the toxic dinoflagellate Alexandrium ostenfeldii (Dinophyceae) as a model organism to investigate if (i) the benthic seed bank is more diverse than the pelagic population and (ii) the pelagic population is seasonally differentiated. Resting stages (benthic) and plankton (pelagic) samples were collected at a coastal bloom site in the Baltic Sea, followed by cell isolation and genotyping using microsatellite markers (MS) and restriction site associated DNA sequencing (RAD). High clonal diversity (98%-100%) combined with intermediate to low gene diversity (0.58-0.03, depending on the marker) was found. Surprisingly, the benthic and pelagic fractions of the population were equally diverse, and the pelagic fraction was temporally homogeneous, despite seasonal fluctuation of environmental selection pressures. The results of this study suggest that continuous benthic-pelagic coupling, combined with frequent sexual reproduction, as indicated by persistent linkage equilibrium, prevent the dominance of single clonal lineages in a dynamic environment. Both processes harmonize the pelagic with the benthic population and thus prevent seasonal population differentiation. At the same time, frequent sexual reproduction and benthic-pelagic coupling maintain high clonal diversity in both habitats., (© 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

The bacterium Pseudomonas anguilliseptica has in recent years emerged as a serious threat to production of lumpfish in Norway. Little is known about the population structure of this bacterium despite its association with disease in a wide range of different fish species throughout the world. The phylogenetic relationships between 53 isolates, primarily derived from diseased lumpfish, but including a number of reference strains from diverse geographical origins and fish species, were reconstructed by Multi-Locus Sequence Analysis (MLSA) using nine housekeeping genes (rpoB, atpD, gyrB, rpoD, ileS, aroE, carA, glnS and recA). MLSA revealed a high degree of relatedness between the studied isolates, altough the seven genotypes identified formed three main phylogenetic lineages. While four genotypes were identified amongst Norwegian lumpfish isolates, a single genotype dominated, irrespective of geographic origin. This suggests the existence of a dominant genotype associated with disease in production of lumpfish in Norwegian aquaculture. Elucidation of the population structure of the bacterium has provided valuable information for potential future vaccine development., Competing Interests: The commercial affiliation of authors Dr. Felix Scholz and Andreas Riborg represents the only conflict of interests but do not alter our adherence to PLOS ONE policies on sharing data and materials.

Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species., (© 2021. The Author(s).)

The fish pathogen Flavobacterium psychrophilum is currently one of the main pathogenic bacteria hampering the productivity of salmonid farming worldwide. Although putative virulence determinants have been identified, the genetic basis for variation in virulence of F. psychrophilum is not fully understood. In this study, we analyzed whole-genome sequences of a collection of 25 F. psychrophilum isolates from Baltic Sea countries and compared genomic information with a previous determination of their virulence in juvenile rainbow trout. The results revealed a conserved population of F. psychrophilum that were consistently present across the Baltic Sea countries, with no clear association between genomic repertoire, phylogenomic, or gene distribution and virulence traits. However, analysis of the entire genome of four F. psychrophilum isolates by hybrid assembly provided an unprecedented resolution for discriminating even highly related isolates. The results showed that isolates with different virulence phenotypes harbored genetic variances on a number of consecutive leucine-rich repeat (LRR) proteins, repetitive motifs in gliding motility-associated protein, and the insertion of transposable elements into intergenic and genic regions. Thus, these findings provide novel insights into the genetic variation of these elements and their putative role in the modulation of F. psychrophilum virulence.