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Despite being an abundant group of significant ecological importance the phylogenetic relationships of the Octocorallia remain poorly understood and very much understudied. We used 1132 bp of two mitochondrial protein-coding genes, nad2 and mtMutS (previously referred to as msh1), to construct a phylogeny for 161 octocoral specimens from the Atlantic, including both Isididae and non-Isididae species. We found that four clades were supported using a concatenated alignment. Two of these (A and B) were in general agreement with the of Holaxonia–Alcyoniina and Anthomastus–Corallium clades identified by previous work. The third and fourth clades represent a split of the Calcaxonia–Pennatulacea clade resulting in a clade containing the Pennatulacea and a small number of Isididae specimens and a second clade containing the remaining Calcaxonia. When individual genes were considered nad2 largely agreed with previous work with MtMutS also producing a fourth clade corresponding to a split of Isididae species from the Calcaxonia–Pennatulacea clade. It is expected these difference are a consequence of the inclusion of Isisdae species that have undergone a gene inversion in the mtMutS gene causing their separation in the MtMutS only tree. The fourth clade in the concatenated tree is also suspected to be a result of this gene inversion, as there were very few Isidiae species included in previous work tree and thus this separation would not be clearly resolved. A~larger phylogeny including both Isididae and non Isididae species is required to further resolve these clades.

Recent observations and modelling studies suggest that biogeochemical changes can mask atmospheric CO2-induced pH decreases. Data collected by the Dutch monitoring authorities in different coastal systems (North Sea, Wadden Sea, Ems-Dollard, Eastern Scheldt and Scheldt estuary) since 1975 provide an excellent opportunity to test whether this is the case in the Dutch coastal zone. The time-series were analysed using Multi-Resolution Analysis (MRA) which resulted in the identification of system-dependent patterns on both seasonal and intra-annual time scales. The observed rates of pH change greatly exceed those expected from enhanced CO2 uptake, thus suggesting that other biogeochemical processes, possibly related to changes in nutrient loading, can play a dominant role in ocean acidification.

Coastal systems can act as filters for anthropogenic nutrient input into marine environments. Here, we assess the processes controlling the removal of phosphorus (P) and nitrogen (N) for four sites in the eutrophic Stockholm Archipelago. Bottom water concentrations of oxygen and P are inversely correlated. This is attributed to the seasonal release of P from iron (Fe)-oxide-bound P in surface sediments and from degrading organic matter. The abundant presence of sulfide in the pore water, linked to prior deposition of organic-rich sediments in a low oxygen setting (legacy of hypoxia), hinders the formation of a larger Fe-oxide-bound P pool in winter. Burial rates of P are high at all sites (0.03–0.3 mol m−2 y−1), a combined result of high sedimentation rates (0.5 to 3.5 cm yr−1) and high sedimentary P at depth (~ 30 to 50 μmol g−1). Organic P accounts for 30–50 % of reactive P burial. Apart from one site in the inner archipelago, where a vivianite-type Fe(II)-P mineral is likely present at depth, there is little evidence for sink-switching of organic or Fe-oxide bound P to authigenic P minerals. Denitrification is the major benthic nitrate-reducing process at all sites (0.09 to 1.7 mmol m−2 d−1), efficiently removing N as N2. Denitrification rates decrease seaward following the decline in bottom water nitrate and sediment organic carbon. Our results explain how sediments in this eutrophic coastal system can efficiently remove land-derived P and N, regardless of whether the bottom waters are oxic or frequently hypoxic. Hence, management strategies involving artificial reoxygenation are not expected to be successful in removing P and N, emphasizing a need for a focus on nutrient load reductions.

The impacts of changes in ozone precursor emissions as well as climate change on the future ozone exposure of the vegetation in Europe were investigated. The ozone exposure is expressed as AOT40 (Accumulated exposure Over a Threshold of 40 ppb O3) as well as PODY (Phytotoxic Ozone Dose above a threshold Y). A new method is suggested to express how the length of the period during the year when coniferous and evergreen trees are sensitive to ozone might be affected by climate change. Ozone precursor emission changes from the RCP4.5 scenario were combined with climate simulations based on the IPCC SRES A1B scenario and used as input to the Eulerian Chemistry Transport Model MATCH from which projections of ozone concentrations were derived. The ozone exposure of vegetation over Europe expressed as AOT40 was projected to be substantially reduced between the periods 1990–2009 and 2040–2059 to levels which are well below critical levels used for vegetation in the EU directive 2008/50/EC as well as for crops and forests used in the LRTAP convention, despite that the future climate resulted in prolonged yearly ozone sensitive periods. The reduction in AOT40 was mainly driven by the emission reductions, not changes in the climate. For the toxicologically more relevant POD1 index the projected reductions were smaller, but still significant. The values for POD1 for the time period 2040–2059 were not projected to decrease to levels which are below critical levels for forest trees, represented by Norway spruce. This study shows that substantial reductions of ozone precursor emissions have the potential to strongly reduce the future risk for ozone effects on the European vegetation, even if concurrent climate change promotes ozone formation.

Atmospheric CO2 and climate projections for the next century vary widely across current Earth system models (ESMs), owing to different representations of the interactions between the marine and land carbon cycle on the one hand, and climate change and increasing atmospheric CO2 on the other hand. Several efforts have been made in the last years to analyse these differences in detail in order to suggest model improvements. Here we review these efforts and analyse their successes, but also the associated uncertainties that hamper the best use of the available observations to constrain and improve the ESMs models. The aim of this paper is to highlight challenges in improving the ESMs that result from: (i) uncertainty about important processes in terrestrial and marine ecosystems and their response to climate change and increasing atmospheric CO2; (ii) structural and parameter-related uncertainties in current land and marine models; (iii) uncertainties related to observations and the formulations of model performance metrics. We discuss the implications of these uncertainties for reducing the spread in future projections of ESMs and suggest future directions of work to overcome these uncertainties.

Monoterpene emissions from Scots pine have traditionally been assumed to originate as evaporation from specialized storage pools. More recently, the significance of de novo emissions, originating directly from monoterpene biosynthesis, has been recognized. To study the role of biosynthesis at the ecosystem scale, we measured monoterpene emissions from a Scots pine dominated forest in southern Finland using the disjunct eddy covariance method combined with proton transfer reaction mass spectrometry. The interpretation of the measurements was based on a correlation analysis and a hybrid emission algorithm describing both de novo and pool emissions. During the measurement period May–August 2007, the monthly medians of daytime emissions were 200, 290, 180, and 200 μg m−2 h−1. The emissions were partly light dependent, probably due to de novo biosynthesis. The emission potential for both de novo and pool emissions exhibited a decreasing summertime trend. The ratio of the de novo emission potential to the total emission potential varied between 30 % and 46 %. Although the monthly changes were not significant, the ratio always differed statistically from zero, suggesting that the role of de novo biosynthesis was observable. Given the uncertainties in this study, we conclude that more accurate estimates of the contribution of de novo emissions are required for improving monoterpene emission algorithms for Scots pine dominated forests.

Coastal areas are impacted by multiple natural and anthropogenic processes and experience stronger pH fluctuations than the open ocean. These variations can weaken or intensify the ocean acidification signal induced by increasing atmospheric pCO2. The development of eutrophication-induced hypoxia intensifies coastal acidification, since the CO2 produced during respiration decreases the buffering capacity in any hypoxic bottom water. To assess the combined ecosystem impacts of acidification and hypoxia, we quantified the seasonal variation in pH and oxygen dynamics in the water column of a seasonally stratified coastal basin (Lake Grevelingen, the Netherlands). Monthly water-column chemistry measurements were complemented with estimates of primary production and respiration using O2 light–dark incubations, in addition to sediment–water fluxes of dissolved inorganic carbon (DIC) and total alkalinity (TA). The resulting data set was used to set up a proton budget on a seasonal scale. Temperature-induced seasonal stratification combined with a high community respiration was responsible for the depletion of oxygen in the bottom water in summer. The surface water showed strong seasonal variation in process rates (primary production, CO2 air–sea exchange), but relatively small seasonal pH fluctuations (0.46 units on the total hydrogen ion scale). In contrast, the bottom water showed less seasonality in biogeochemical rates (respiration, sediment–water exchange), but stronger pH fluctuations (0.60 units). This marked difference in pH dynamics could be attributed to a substantial reduction in the acid–base buffering capacity of the hypoxic bottom water in the summer period. Our results highlight the importance of acid–base buffering in the pH dynamics of coastal systems and illustrate the increasing vulnerability of hypoxic, CO2-rich waters to any acidifying process.

Ocean acidification from the uptake of anthropogenic carbon is simulated for the industrial period and IPCC SRES emission scenarios A2 and B1 with a global coupled carbon cycle-climate model. Earlier studies identified seawater saturation state with respect to aragonite, a mineral phase of calcium carbonate, as a key variable governing impacts on corals and other shell-forming organisms. Globally in the A2 scenario, water saturated by more than 300%, considered suitable for coral growth, vanishes by 2070 AD (CO2≈630 ppm), and the ocean volume fraction occupied by saturated water decreases from 42% to 25% over this century. The largest simulated pH changes worldwide occur in Arctic surface waters, where hydrogen ion concentration increases by up to 185% (ΔpH=−0.45). Projected climate change amplifies the decrease in Arctic surface mean saturation and pH by more than 20%, mainly due to freshening and increased carbon uptake in response to sea ice retreat. Modeled saturation compares well with observation-based estimates along an Arctic transect and simulated changes have been corrected for remaining model-data differences in this region. Aragonite undersaturation in Arctic surface waters is projected to occur locally within a decade and to become more widespread as atmospheric CO2 continues to grow. The results imply that surface waters in the Arctic Ocean will become corrosive to aragonite, with potentially large implications for the marine ecosystem, if anthropogenic carbon emissions are not reduced and atmospheric CO2 not kept below 450 ppm.

Cable bacteria are multicellular, filamentous microorganisms that are capable of transporting electrons over centimeter-scale distances. Although recently discovered, these bacteria appear to be widely present in the seafloor, and when active they exert a strong imprint on the local geochemistry. In particular, their electrogenic metabolism induces unusually strong pH excursions in aquatic sediments, which induces considerable mineral dissolution, and subsequent mineral reprecipitation. However, at present, it is unknown whether and how cable bacteria play an active or direct role in the mineral reprecipitation process. To this end we present an explorative study of the formation of sedimentary minerals in and near filamentous cable bacteria using a combined approach of electron microscopy and spectroscopic techniques. Our observations reveal the formation of polyphosphate granules within the cells and two different types of biomineral formation directly associated with multicellular filaments of these cable bacteria: (i) the attachment and incorporation of clay particles in a coating surrounding the bacteria and (ii) encrustation of the cell envelope by iron minerals. These findings suggest a complex interaction between cable bacteria and the surrounding sediment matrix, and a substantial imprint of the electrogenic metabolism on mineral diagenesis and sedimentary biogeochemical cycling. In particular, the encrustation process leaves many open questions for further research. For example, we hypothesize that the complete encrustation of filaments might create a diffusion barrier and negatively impact the metabolism of the cable bacteria.

Instrumental records from the Norwegian Sea and the Trondheimsfjord show evidence that changes of bottom water temperature and salinity in the fjord are linked to the salinity and temperature variability of the North Atlantic Current (NAC). Changes in primary productivity and salinity in the surface and intermediate water masses in the Trondheimsfjord as well as the fjord sedimentary budget are mainly driven by changes in riverine input. In this study we use 59 surface sediment samples that are evenly distributed in the fjord to examine whether dinocyst assemblages and stable isotope ratios of benthic foraminifera reflect the present-day hydrology and can be used as palaeoceanographic proxies. In general, modern benthic δ18O and δ13C values decrease from the fjord entrance towards the fjord head with lowest values close to river inlets. This is essentially explained by gradients in the amounts of fresh water and terrigenous organic matter delivered from the hinterland. The distribution of benthic δ13C ratios across the fjord is controlled by the origin (terrigenous vs. marine) of organic matter, local topography-induced variability in organic matter flux at the water–sediment interface, and organic matter degradation. The dinocyst assemblages display the variations in hydrography with respect to the prevailing currents, the topography, and the freshwater and nutrient supply from rivers. The strength and depth of the pycnocline in the fjord strongly vary seasonally and thereby affect water mass characteristics as well as nutrient availability, temporally creating local conditions that explain the observed species distribution. Our results prove that dinocyst assemblages and benthic foraminiferal isotopes reliably mirror the complex fjord hydrology and can be used as proxies of Holocene climatic variability.