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The production of this report was carried out through the HELCOM Project for the development of the Third Holistic Assessment of the Baltic Sea (HOLAS 3). The work builds on the previous assessment (HOLAS II) and methodologies, evaluations and assessments included in this report have been directly contributed to by the HELCOM BLUES project, the Baltic Data Flows project, the COMPLETE project, the COMPLETE PLUS project, and the PreEMPT project.

Methylmercury (MeHg) is a potent neurotoxin commonly found in aquatic environments and primarily formed by microbial methylation of inorganic divalent mercury (Hg(II)) under anoxic conditions. Recent evidence, however, points to the production of MeHg also in oxic pelagic waters, but the magnitude and the drivers for this process remain unclear. Here, we performed a controlled experiment testing the hypothesis that inputs of terrestrial dissolved organic matter (tDOM) to coastal waters enhance MeHg formation via increased bacterial activity. Natural brackish seawater from a coastal area of the Baltic Sea was exposed to environmentally relevant levels of Hg(II) and additions of tDOM according to climate change scenarios. MeHg formation was observed to be coupled to elevated bacterial production rates, which, in turn, was linked to input levels of tDOM. The increased MeHg formation was, however, not coupled to any specific change in bacterial taxonomic composition nor to an increased abundance of known Hg(II) methylation genes. Instead, we found that the abundance of genes for the overall bacterial carbon metabolism was higher under increased tDOM additions. The findings of this study may have important ecological implications in a changing global climate by pointing to the risk of increased exposure of MeHg to pelagic biota.

The Marine Strategy Framework Directive (MSFD) requires Member States to achieve good environmental status (GES) across their marine waters. The EU have requested ICES to advise on methods for assessing adverse effects on seabed habitats, through selection of relevant indicators for the assessment of benthic habitats and seafloor integrity and associated threshold values for GES in relation to Descriptor 6 – Seabed integrity under the MFSD. Two sets of criteria were developed to evaluate indicators and thresholds respectively for evaluation of suitability for assessing GES. 16 indicator and 12 threshold criteria were compiled and weighted by importance. The criteria were designed for evaluation at a subregional or regional level. The scoring for these criteria is meant as a guidance when choosing indicators and thresholds, so failure to meet one criterion will not necessarily prevent the use of the indicator or threshold in an assessment. The framework was evaluated for 6 indicators and for 11 methods for setting thresholds. The criteria were found to be useful for evaluation both indicators and thresholds. The process works most consistently when there are experts in the group on both the criteria themselves and on the indicators and thresholds. The MFSD Descriptor 6 determination of GES needs both a quality threshold (when are seabed habitats in a good state in a specific location) and an extent threshold (proportion of the assessment area that needs to have seabed habitats in good state). Eleven different methods for setting thresholds were identified, of which more are suitable for setting quality than for extent thresholds. Preferred methods identified an ecologically-motivated difference between a good and degraded state, rather than another transition. Quality thresholds based on the lower boundary of the range of natural variation were considered most promising. This approach can be used for most, but not all, indicators. The WK co

Methylmercury (MeHg) is a potent neurotoxin commonly found in aquatic environments and primarily formed by microbial methylation of inorganic divalent mercury (Hg(II)) under anoxic conditions. Recent evidence, however, points to the production of MeHg also in oxic pelagic waters, but the magnitude and the drivers for this process remain unclear. Here, we performed a controlled experiment testing the hypothesis that inputs of terrestrial dissolved organic matter (tDOM) to coastal waters enhance MeHg formation via increased bacterial activity. Natural brackish seawater from a coastal area of the Baltic Sea was exposed to environmentally relevant levels of Hg(II) and additions of tDOM according to climate change scenarios. MeHg formation was observed to be coupled to elevated bacterial production rates, which, in turn, was linked to input levels of tDOM. The increased MeHg formation was, however, not coupled to any specific change in bacterial taxonomic composition nor to an increased abundance of known Hg(II) methylation genes. Instead, we found that the abundance of genes for the overall bacterial carbon metabolism was higher under increased tDOM additions. The findings of this study may have important ecological implications in a changing global climate by pointing to the risk of increased exposure of MeHg to pelagic biota.

Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting ~ 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.

Climate change scenarios project that precipitation will increase in northern Europe, causing amplified inflows of terrestrial matter (tM) and inorganic nutrients to coastal areas. How this will affect the plankton community is poorly understood. A mesocosm experiment was carried out to investigate the influence of two levels of tM inputs on the composition, size-structure and productivity of a natural coastal phytoplankton community from the northern Baltic Sea. The tM addition caused browning of the water and decreased underwater light levels, while the concentrations of dissolved organic carbon (DOC) and inorganic nutrients increased. Microphytoplankton were promoted by tM addition, while in the controls picophytoplankton dominated the phytoplankton community. Inorganic nutrient availability was instrumental in defining the phytoplankton community composition and size-structure. As a response to tM addition, the phytoplankton increased their chlorophyll a content. This physiological adaptation helped to maintain high primary production rates at the low tM enrichment, but at the high tM load the primary production decreased as did the biomass of mesozooplankton. The ciliate biomass was high when the mesozooplankton biomass was low, indicating that a trophic cascade occurred in the system. Structural equation modeling showed that tM borne DOC promoted ciliates, while primary and bacterial production were disfavored. Thus, DOC originating from soils had an indirect negative effect on the mesozooplankton by reducing their food availability. Although, a positive correlation between heterotrophic bacteria and phytoplankton suggested coupling between phytoplankton produced carbon and heterotrophs growth. The results from our study indicate that river-borne DOC and inorganic nutrients have a large impact on the phytoplankton community, driving the system to the dominance of large diatoms. However, since river-borne humic substances cause browning of the water, phytoplank

Coastal ecosystems are highly dynamic and can be strongly influenced by climate change, anthropogenic activities (e.g. pollution) and a combination of the two pressures. As a result of climate change, the northern hemisphere is predicted to undergo an increased precipitation regime, leading in turn to higher terrestrial runoff and increased river inflow. This increased runoff will transfer terrestrial dissolved organic matter (tDOM) and anthropogenic contaminants to coastal waters. Such changes can directly influence the resident biology, particularly at the base of the food web, and can influence the partitioning of contaminants and thus their potential impact on the food web. Bacteria have been shown to respond to high tDOM concentration and organic pollutants loads, and could represent the entry of some pollutants into coastal food webs. We carried out a mesocosm experiment to determine the effects of: 1) increased tDOM concentration, 2) organic pollutant exposure, and 3) the combined effect of these two factors, on pelagic bacterial communities. This study showed significant responses in bacterial community composition under the three environmental perturbations tested. The addition of tDOM increased bacterial activity and diversity, while the addition of organic pollutants led to an overall reduction of these parameters, particularly under concurrent elevated tDOM concentration. Furthermore, we identified 33 bacterial taxa contributing to the significant differences observed in community composition, as well as 35 bacterial taxa which responded differently to extended exposure to organic pollutants. These findings point to the potential impact of organic pollutants under future climate change conditions on the basal coastal ecosystem, as well as to the potential utility of natural bacterial communities as efficient indicators of environmental disturbance., Errata: Rodríguez, J., Gallampois, C. M. J., Timonen, S., Andersson, A., Sinkko, H., Haglund, P., et al. Corrigendum: Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios. Front. Microbiol. 2019;10:2388. DOI: 10.3389/fmicb.2019.02388, ECOCHANGE

Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.

Phytoplankton and heterotrophic bacteria are key groups at the base of aquatic food webs. In estuaries receiving riverine water with a high content of coloured allochthonous dissolved organic matter (ADOM), phytoplankton primary production may be reduced, while bacterial production is favoured. We tested this hypothesis by performing a field study in a northerly estuary receiving nutrient-poor, ADOM-rich riverine water, and analyzing results using multivariate statistics. Throughout the productive season, and especially during the spring river flush, the production and growth rate of heterotrophic bacteria were stimulated by the riverine inflow of dissolved organic carbon (DOC). In contrast, primary production and photosynthetic efficiency (i.e. phytoplankton growth rate) were negatively affected by DOC. Primary production related positively to phosphorus, which is the limiting nutrient in the area. In the upper estuary where DOC concentrations were the highest, the heterotrophic bacterial production constituted almost 100% of the basal production (sum of primary and bacterial production) during spring, while during summer the primary and bacterial production were approximately equal. Our study shows that riverine DOC had a strong negative influence on coastal phytoplankton production, likely due to light attenuation. On the other hand DOC showed a positive influence on bacterial production since it represents a supplementary food source. Thus, in boreal regions where climate change will cause increased river inflow to coastal waters, the balance between phytoplankton and bacterial production is likely to be changed, favouring bacteria. The pelagic food web structure and overall productivity will in turn be altered.

Increased river loads are projected as one of the major consequences of climate change in the northern hemisphere, leading to elevated inputs of riverine dissolved organic matter (DOM) and inorganic nutrients to coastal ecosystems. The objective of this study was to investigate the effects of elevated DOM on a coastal pelagic food web from the coastal northern Baltic Sea, in a 32-day mesocosm experiment. In particular, the study addresses the response of bacterioplankton to differences in character and composition of supplied DOM. The supplied DOM differed in stoichiometry and quality and had pronounced effects on the recipient bacterioplankton, driving compositional changes in response to DOM type. The shifts in bacterioplankton community composition were especially driven by the proliferation of Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Alpha-and Betaproteobacteria populations. The DOM additions stimulated protease activity and a release of inorganic nutrients, suggesting that DOM was actively processed. However, no difference between DOM types was detected in these functions despite different community compositions. Extensive release of re-mineralized carbon, nitrogen and phosphorus was associated with the bacterial processing, corresponding to 25-85% of the supplied DOM. The DOM additions had a negative effect on phytoplankton with decreased Chl a and biomass, particularly during the first half of the experiment. However, the accumulating nutrients likely stimulated phytoplankton biomass which was observed to increase towards the end of the experiment. This suggests that the nutrient access partially outweighed the negative effect of increased light attenuation by accumulating DOM. Taken together, our experimental data suggest that parts of the future elevated riverine DOM supply to the Baltic Sea will be efficiently mineralized by microbes. This will have consequences for bacterioplankton and phytoplankton community composition and function, and sign

It is well-known that nutrients shape phytoplankton communities in marine systems, but in coastal waters allochthonous dissolved organic matter (ADOM) may also be of central importance. We studied how humic substances (proxy of ADOM) and other variables influenced the nutritional strategies, size structure and pigment content of the phytoplankton community along a south-north gradient in the Baltic Sea. During the summer, the proportion of mixotrophs increased gradually from the phosphorus-rich south to the ADOM-rich north, probably due to ADOM-fueled microbes. The opposite trend was observed for autotrophs. The chlorophyll a (Chl a): carbon (C) ratio increased while the levels of photoprotective pigments decreased from south to north, indicating adaptation to the darker humic-rich water in the north. Picocyanobacteria dominated in phosphorusrich areas while nanoplankton increased in ADOM- rich areas. During the winter-spring the phytoplankton biomass and concentrations of photoprotective pigments were low, and no trends with respect to autotrophs and mixotrophs were observed. Microplankton was the dominant size group in the entire study area. We conclude that changes in the size structure of the phytoplankton community, the Chl a: C ratio and the concentrations of photoprotective pigments are indicative of changes in ADOM, a factor of particular importance in a changing climate., Originally published in manuscript form.

Heterotrophic bacteria are, in many aquatic systems, reliant on autochthonous organic carbon as their energy source. One exception is low-productive humic lakes, where allochthonous dissolved organic matter (ADOM) is the major driver. We hypothesized that bacterial production (BP) is similarly regulated in subarctic estuaries that receive large amounts of riverine material. BP and potential explanatory factors were measured during May–August 2011 in the subarctic Råne Estuary, northern Sweden. The highest BP was observed in spring, concomitant with the spring river-flush and the lowest rates occurred during summer when primary production (PP) peaked. PLS correlations showed that ∼60 % of the BP variation was explained by different ADOM components, measured as humic substances, dissolved organic carbon (DOC) and coloured dissolved organic matter (CDOM). On average, BP was threefold higher than PP. The bioavailability of allochthonous dissolved organic carbon (ADOC) exhibited large spatial and temporal variation; however, the average value was low, ∼2 %. Bioassay analysis showed that BP in the near-shore area was potentially carbon limited early in the season, while BP at seaward stations was more commonly limited by nitrogen-phosphorus. Nevertheless, the bioassay indicated that ADOC could contribute significantly to the in situ BP, ∼60 %. We conclude that ADOM is a regulator of BP in the studied estuary. Thus, projected climate-induced increases in river discharge suggest that BP will increase in subarctic coastal areas during the coming century.

Heavy rainfall events causing significant terrestrial runoff into coastal marine ecosystems are predicted to become more frequent with climate change in the Mediterranean. To simulate the effects of soil runoff on the pelagic food web of an oligotrophic Mediterranean coastal lagoon, we crossed soil extract addition (increasing nutrient availability and turbidity) and fish presence in a full factorial design to coastal mesocosms containing a natural pelagic community. Soil extract addition increased both bacteria and phytoplankton biomass. Diatoms however profited most from soil extract addition, especially in the absence of fish. In contrast zooplankton and fish did not profit from soil extract addition. Furthermore, our data indicate that nutrients (instead of light or carbon) limited basal production. Presumed changes in carbon availability are relatively unimportant to primary and secondary production in strongly nutrient limited systems like the Thau Lagoon. We conclude that in shallow Mediterranean coastal ecosystems, heavy rainfall events causing soil runoff will (1) increase the relative abundance of phytoplankton in relation to bacteria and zooplankton, especially in the absence of fish (2) not lead to higher biomass of zooplankton and fish, possibly due to the brevity of the phytoplankton bloom and the slow biomass response of higher trophic levels.

Terrestrial runoff into aquatic ecosystems may have both stimulatory and inhibitory effects, due to nutrient subsidies and increased light attenuation. To disentangle the effects of runoff on microbenthos, we added soil to coastal mesocosms and manipulated substrate depth. To test if fish interacted with runoff effects, we manipulated fish presence. Soil decreased microphytobenthic chlorophyll-a per area and per carbon (C) unit, increased microbenthic phosphorous (P), and reduced microbenthic nitrogen (N) content. Depth had a strong effect on the microbenthos, with shallow substrates exhibiting greater microbenthic net ecosystem production, gross primary production, and community respiration than deep substrates. Over time, micobenthic algae compensated for deeper substrate depth through increased chlorophyll-a synthesis, but despite algal shade compensation, the soil treatment still appeared to reduce the depth where microbenthos switched from net autotrophy to net heterotrophy. Fish interacted with soil in affecting microbenthic nutrient composition. Fish presence reduced microbenthic C/P ratios only in the no soil treatment, probably since soil nutrients masked the positive effects of fish excreta on microbenthos. Soil reduced microbenthic N/P ratios only in the absence of fish. Our study demonstrates the importance of light for the composition and productivity of microbenthos but finds little evidence for positive runoff subsidy effects.

A common and established view is that increased inputs of nutrients to the sea, for example via river flooding, will cause eutrophication and phytoplankton blooms in coastal areas. We here show that this concept may be questioned in certain scenarios. Climate change has been predicted to cause increased inflow of freshwater to coastal areas in northern Europe. River waters in these areas are often brown from the presence of high concentrations of allochthonous dissolved organic carbon ( humic carbon), in addition to nitrogen and phosphorus. In this study we investigated whether increased inputs of humic carbon can change the structure and production of the pelagic food web in the recipient seawater. In a mesocosm experiment unfiltered seawater from the northern Baltic Sea was fertilized with inorganic nutrients and humic carbon (CNP), and only with inorganic nutrients (NP). The system responded differently to the humic carbon addition. In NP treatments bacterial, phytoplankton and zooplankton production increased and the systems turned net autotrophic, whereas the CNP-treatment only bacterial and zooplankton production increased driving the system to net heterotrophy. The size-structure of the food web showed large variations in the different treatments. In the enriched NP treatments the phytoplankton community was dominated by filamentous >20 mu m algae, while in the CNP treatments the phytoplankton was dominated by picocyanobacteria <5 mu m. Our results suggest that climate change scenarios, resulting in increased humic-rich river inflow, may counteract eutrophication in coastal waters, leading to a promotion of the microbial food web and other heterotrophic organisms, driving the recipient coastal waters to net-heterotrophy.

A nine year study was carried out on the evolution of macroscopic “acid streamer” growths in acidic, metal-rich mine water from the point of construction of a new channel to drain an abandoned underground copper mine. The new channel became rapidly colonized by acidophilic bacteria: two species of autotrophic iron-oxidizers (Acidithiobacillus ferrivorans and “Ferrovum myxofaciens”) and a heterotrophic iron-oxidizer (a novel genus/species with the proposed name “Acidithrix ferrooxidans”). The same bacteria dominated the acid streamer communities for the entire nine year period, with the autotrophic species accounting for ~80% of the micro-organisms in the streamer growths (as determined by terminal restriction enzyme fragment length polymorphism (T-RFLP) analysis). Biodiversity of the acid streamers became somewhat greater in time, and included species of heterotrophic acidophiles that reduce ferric iron (Acidiphilium, Acidobacterium, Acidocella and gammaproteobacterium WJ2) and other autotrophic iron-oxidizers (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans). The diversity of archaea in the acid streamers was far more limited; relatively few clones were obtained, all of which were very distantly related to known species of euryarchaeotes. Some differences were apparent between the acid streamer community and planktonic-phase bacteria. This study has provided unique insights into the evolution of an extremophilic microbial community, and identified several novel species of acidophilic prokaryotes., This article belongs to the Special Issue Extremophiles and Extreme Environments

A field-scale experiment was conducted to evaluate organic carbon amendment of mine tailings as a technique for pore water and drainage treatment. Six test cells were constructed by amending sulfide- and carbonate- rich tailings with varied mixtures of peat, spent-brewing grain and municipal biosolids. Samples were collected for microbial, geochemical and mineralogical analysis approximately three years after commencing this experiment. Test cells amended with spent-brewing grain promoted sulfate reduction and effective removal of sulfate and metal(loid)s. The addition of municipal biosolids did not sustain enhanced sulfidogenesis after three years, and peat was an ineffective source of organic carbon. Terminal-restriction fragment length polymorphism revealed that test cells which supported sulfidogenesis exhibited the greatest microbial diversity. Indigenous bacteria identified using molecular and cultivation analyses were found to be related to Cellulomonas, Thiobacillus, Bacteroides, Paludibacter and Desulfovibrio, which was the only sulfate-reducing bacterial (SRB) isolated. The results demonstrate that mixtures of solid organic materials which supported complex anaerobic microbial communities, including sulfate- reducing bacteria, were most effective in promoting pore-water treatment.