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Coastal seas receive large amounts of terrestrially derived organic carbon (OC). The fate of this carbon, and its impact on the marine environment, is however poorly understood. Here we combine underway CO2 partial pressure (pCO2) measurements with coupled 3-D hydrodynamical–biogeochemical modelling to investigate whether remineralization of terrestrial dissolved organic carbon (tDOC) can explain CO2 supersaturated surface waters in the Gulf of Bothnia, a subarctic estuary. We find that a substantial remineralization of tDOC and a strong tDOC-induced light attenuation dampening the primary production are required to reproduce the observed CO2 supersaturated waters in the nearshore areas. A removal rate of tDOC of the order of 1 year, estimated in a previous modelling study in the same area, gives a good agreement between modelled and observed pCO2. The remineralization rate is on the same order as bacterial degradation rates calculated from published incubation experiments, suggesting that bacteria has the potential to cause this degradation. Furthermore, the observed high pCO2 values during the ice-covered season argue against photochemical degradation as the main removal mechanism. All of the remineralized tDOC is outgassed to the atmosphere in the model, turning the northernmost part of the Gulf of Bothnia into a source of CO2 to the atmosphere.

Marine ecosystems are changing in response to multiple stressors such as global warming, increasing carbon dioxide (CO2) and decreasing oxygen (O2) concentrations and eutrophication of coastal waters, among others. The direct effects of these changes on plankton physiology have been studied for decades; less are known about possible effects these changes might have on the composition of plankton communities, and even less about what effects any such shift in plankton community composition will have on marine ecosystems. The plankton community makes up the base of the marine food web (i.e., primary producers, decomposers, and primary consumers) and plays a pivotal role in global biogeochemical cycles (e.g., Falkowski and Raven, 2013). Any change of the plankton community structure, driven by natural or human induced changes, may consequently have indirect effects on marine ecosystem functioning. This Research Topic focused on causes, effects and consequences of changing composition of plankton communities. The 12 contributions to this volume include seven original research papers, one method paper, and four reviews; all touching the state-of-the-art in current plankton research, and each from a complementary angle. Several of the original research papers deal with changing phytoplankton communities, environmental drivers and ecosystem effects. Fernández-Méndez et al. analyzed sea-ice ridges and the snow-ice interface, which are algal hotspots in the Arctic Ocean. Both sea-ice ridges and the snow-ice interface are projected to increase due to thinning of the ice, and Fernández-Méndez et al. described the algal communities, mostly dominated by different diatoms, in these habitats in the Arctic. von Scheibner et al. examined the phytoplankton and bacterioplankton response to short-term warming. Warming increased carbon availability for the bacterial community, but the ratio between bacterial and primary production was still relatively low, suggesting it is not much changed by short-term warming events. Cohen et al. described diatom transcriptional and physiological responses to changes in iron availability in the open Northeast Pacific Ocean and in the California upwelling system. They found species specific differences in gene expression to changes in nutrient availability and taxa specific strategies for coping with Fe stress. Ajani et al. investigated the realized niches of phytoplankton using a long-term data set collected off Eastern Australia. They demonstrated that the ecological niches can be dynamic and that climate change models cannot use fixed niches when forecasting the phytoplankton community composition. There are three original research papers on zooplankton dynamics. Lips and Lips investigated the increasing importance of the mixotrophic ciliate Mesodinium rubrum in the Baltic Sea. The abundance of this species was higher in years of earlier warming and the authors suggest that it plays an important role in shaping the inorganic nutrient pools at the start of the summer (Lips and Lips). Haraguchi et al. studied the coupling between phytoplankton and ciliates in Danish waters over 2 years, and demonstrated a close coupling between these communities, suggesting top down control of the phytoplankton community by the ciliates. Karlsson and Winder examined ecosystem effects of two locally adapted populations of the filter feeding copepod Eurytemora affinis that differed in size. They demonstrated that morphologically divergent populations of the same species can perform different ecosystem functions through differences in quantitative and qualitative feeding, and by having different population response to changes in resource supply and the phytoplankton community composition. In the method paper by Engel et al., they tested three different ways to manipulate species loss in natural phytoplankton communities. Dilution, filtration, and heat stress was used to remove rare, large and sensitive species, respectively, and this can be used as a method for non-random species manipulation in experiments. The majority of research on species loss has used the approach of random species removal, which may not be a suitable approach for studies of fragile species. The method development and standardization of approaches suggested by Engel et al. are essential for more realistic species loss modeling. The review papers covered different aspects of plankton dynamics and trait-based approaches. Lindh and Pinhassi presented a comprehensive review of bacterioplankton communities in the Baltic Sea and environmental drivers for community changes based on field and experimental studies. Bartoli et al. reviewed the drivers of cyanobacterial blooms in the Curonian Lagoon (Baltic Sea), where cyanobacteria has benefitted from long term increase in the temperature and reduction in the inorganic N:P ratio. A comparison of the differences between freshwater and marine studies of phytoplankton traits and community assembly is presented by Weithoff and Beisner. Finally, Spilling et al. reviewed and synthesize state-of-the-art knowledge on the observed, long-term increase in dinoflagellate abundance in the Baltic Sea during spring bloom and the consequences the shift from diatom to dinoflagellate dominance has for biogeochemical cycles. The topics of the papers published in this Research Topic ranged from heterotrophic bacteria, phytoplankton to zooplankton and covered different marine ecosystems. The potential shift in community composition may have dramatic effects on ecosystem functioning, for example on trophic transfer, and on biogeochemical fluxes through changes in export of organic material, i.e., the biological pump. One of the key challenges for predicting changes to the plankton community is to understand the various functional groups and their niche separation in combination with individual taxa’s ability to acclimate, adapt and compete in a changing environment. This trait-based community ecology of plankton has started to gain traction (Litchman and Klausmeier, 2008; Litchman et al., 2013), and is a useful framework to investigate potential effects of environmental change on plankton community structure. In order to disentangle the potential consequences of shifts in plankton communities, more empirical studies of ecological interactions and export are needed. Hence, we consider the research papers in this Research Topic will be a valuable addition to the accumulating empirical evidence of how plankton communities are modulated by natural and human induced changes and the indirect effect this has on marine ecosystems. This editorial is a result of funding from the Academy of Finland (decisions no 259164, KS and LT), the Estonian Research Council (no 1574P, KO) and the EU BONUS program (grant agreement 2112932-1, LT). This editorial is a result of funding from the Academy of Finland (decisions no 259164, KS and LT), the Estonian Research Council (no 1574P, KO) and the EU BONUS program (grant agreement 2112932-1, LT).

Sea ice is one the largest biomes on earth, yet it is poorly described by biogeochemical and climate models. In this paper, published and unpublished data on sympagic (ice-associated) algal biodiversity and productivity have been compiled from more than 300 sea-ice cores and organized into a systematic framework. Significant patterns in microalgal community structure emerged from this framework. Autotrophic flagellates characterize surface communities, interior communities consist of mixed microalgal populations and pennate diatoms dominate bottom communities. There is overlap between landfast and pack-ice communities, which supports the hypothesis that sympagic microalgae originate from the pelagic environment. Distribution in the Arctic is sometimes quite different compared to the Antarctic. This difference may be related to the time of sampling or lack of dedicated studies. Seasonality has a significant impact on species distribution, with a potentially greater role for flagellates and centric diatoms in early spring. The role of sea-ice algae in seeding pelagic blooms remains uncertain. Photosynthesis in sea ice is mainly controlled by environmental factors on a small scale and therefore cannot be linked to specific ice types. Overall, sea-ice communities show a high capacity for photoacclimation but low maximum productivity compared to pelagic phytoplankton. Low carbon assimilation rates probably result from adaptation to extreme conditions of reduced light and temperature in winter. We hypothesize that in the near future, bottom communities will develop earlier in the season and develop more biomass over a shorter period of time as light penetration increases due to the thinning of sea ice. The Arctic is already witnessing changes. The shift forward in time of the algal bloom can result in a mismatch in trophic relations, but the biogeochemical consequences are still hard to predict. With this paper we provide a number of parameters required to improve the reliability of sea-ice biogeochemical models.

High inputs of nutrients and organic matter make coastal seas places of intense air-sea CO2 exchange. Due to their complexity, the role of coastal seas in the global air-sea CO2 exchange is, however, still uncertain. Here, we investigate the role of phytoplankton stoichiometric flexibility and extracellular DOC production for the seasonal nutrient and CO2 partial pressure (pCO(2)) dynamics in the Gulf of Bothnia, Northern Baltic Sea. A 3-D ocean biogeochemical-physical model with variable phytoplankton stoichiometry is for the first time implemented in the area and validated against observations. By simulating non-Redfieldian internal phytoplankton stoichiometry, and a relatively large production of extracellular dissolved organic carbon (DOC), the model adequately reproduces observed seasonal cycles in macronutrients and pCO(2). The uptake of atmospheric CO2 is underestimated by 50% if instead using the Redfield ratio to determine the carbon assimilation, as in other Baltic Sea models currently in use. The model further suggests, based on the observed drawdown of pCO(2), that observational estimates of organic carbon production in the Gulf of Bothnia, derived with the 14C method, may be heavily underestimated. We conclude that stoichiometric variability and uncoupling of carbon and nutrient assimilation have to be considered in order to better understand the carbon cycle in coastal seas.

COCOA will investigate physical, biogeochemical and biological processes in a combined and coordinated fashion to improve the understanding of the interaction of these processes on the removal of nutrients along the land-sea interface. The results from the project will be used to estimate nutrient retention capacity in the coastal zone of the entire Baltic Sea coast. An ensemble of biogeochemical models will be used in combination with field studies at seven different coastal study sites around the Baltic Sea. The present report is a deliverable of COCOA work package 5 (WP5). Within the objective of WP5 process understanding and process descriptions will be improved in state-of-the-art biogeochemical models of the Baltic Sea coastal zone. This report presents brief information about the models available for the COCOA project and defines the needed input to the models that will be set-up at severallearning sites. The aim is to perform ensemble modelling at several sites, using at least two different models at each site. A pilot study to estimate nutrient retention capacity in the Stockholm Archipelago with the existing Swedish model system is ongoing and first results are presented and the concept of nutrient retention is briefly discussed.The existing models for different learning sites presented in the report are;1) The Swedish model system SCM (Öre river estuary and the Stockholm archipelago)- A multi-box-model approach2) The Danish model system FLEXSEM (Roskilde fjord)- A combined box-model and 3-D model approach3) The Finnish model system ESIM-BFMSI (Tvärminne Archipelago)- A 1D box-model approach4) The Polish model system M3D UG/ProDeMo (Puck Bay)- A 3-D model approach. Operational model.5) The Lithuanian model system SYFEM/AQUABC (Curonian Lagoon)- A combined box-model and 3-D model approach 6) The Swedish open Baltic model system RCO-SCOBI (for the open Baltic Sea and the Gulfof Gdansk/Vistula).- A 3-D model approachIn addition a biogeochemical model (Boudreau, 1996) for the Gulf of Finland (Russian StateHydrometeorological University model) is used to study the quantitative effect ofMarenzelleria on the Gulf of Finland ecosystem.Process studies at selected sites will be performed with a reactive transport model developedat Utrecht University. Focus will be on the role of iron and phosphorus cycling. Processstudies with the Danish model system will support the development of new parameterizationsof nutrient fluxes taking benthic habitat into account. The new parameterizations of thenutrient fluxes will in addition also be implemented into SCM and the models will be used toestimate nutrient fluxes, retention times and the filter capacity of the coastal zones.The In Kind contributions from previously (in the literature) well described open Baltic Seamodels RCO-SCOBI, BALTSEM, ERGOM and SPBEM that will be used for the descriptionof open sea conditions are also briefly mentioned in the report with references to the relevantliterature.6) The Swedish open Baltic model system RCO-SCOBI (for the open Baltic Sea and the Gulf of Gdansk/Vistula).- A 3-D model approachIn addition a biogeochemical model (Boudreau, 1996) for the Gulf of Finland (Russian State Hydrometeorological University model) is used to study the quantitative effect of Marenzelleria on the Gulf of Finland ecosystem.Process studies at selected sites will be performed with a reactive transport model developed at Utrecht University. Focus will be on the role of iron and phosphorus cycling. Process studies with the Danish model system will support the development of new parameterizations of nutrient fluxes taking benthic habitat into account. The new parameterizations of the nutrient fluxes will in addition also be implemented into SCM and the models will be used to estimate nutrient fluxes, retention times and the filter capacity of the coastal zones.The In Kind contributions from previously (in the literature) well described open Baltic Sea models RCO-SCOBI, BALTSEM, ERGOM and SPBEM that will be used for the description of open sea conditions are also briefly mentioned in the report with references to the relevant literature.

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.