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Permafrost ground is one of the largest repositories of terrestrial organic carbon and might become or already is a carbon source in response to ongoing global warming. With this study of syngenetically frozen, ice-rich and organic carbon (OC)-bearing Yedoma and associated alas deposits in central Yakutia (Republic of Sakha), we aimed to assess the local sediment deposition regime and its impact on permafrost carbon storage. For this purpose, we investigated the Yukechi alas area (61.76495∘ N, 130.46664∘ E), which is a thermokarst landscape degrading into Yedoma in central Yakutia. We retrieved two sediment cores (Yedoma upland, 22.35 m deep, and alas basin, 19.80 m deep) in 2015 and analyzed the biogeochemistry, sedimentology, radiocarbon dates and stable isotope geochemistry. The laboratory analyses of both cores revealed very low total OC (TOC) contents (<0.1 wt %) for a 12 m section in each core, whereas the remaining sections ranged from 0.1 wt % to 2.4 wt % TOC. The core sections holding very little to no detectable OC consisted of coarser sandy material were estimated to be between 39 000 and 18 000 BP (years before present) in age. For this period, we assume the deposition of organic-poor material. Pore water stable isotope data from the Yedoma core indicated a continuously frozen state except for the surface sample, thereby ruling out Holocene reworking. In consequence, we see evidence that no strong organic matter (OM) decomposition took place in the sediments of the Yedoma core until today. The alas core from an adjacent thermokarst basin was strongly disturbed by lake development and permafrost thaw. Similar to the Yedoma core, some sections of the alas core were also OC poor (<0.1 wt %) in 17 out of 28 samples. The Yedoma deposition was likely influenced by fluvial regimes in nearby streams and the Lena River shifting with climate. With its coarse sediments with low OC content (OC mean of 5.27 kg m−3), the Yedoma deposits in the Yukechi area differ from other Yedoma sites in North Yakutia that were generally characterized by silty sediments with higher OC contents (OC mean of 19 kg m−3 for the non-ice wedge sediment). Therefore, we conclude that sedimentary composition and deposition regimes of Yedoma may differ considerably within the Yedoma domain. The resulting heterogeneity should be taken into account for future upscaling approaches on the Yedoma carbon stock. The alas core, strongly affected by extensive thawing processes during the Holocene, indicates a possible future pathway of ground subsidence and further OC decomposition for thawing central Yakutian Yedoma deposits.

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 (O2) and P are inversely correlated. This is attributed to the seasonal release of P from iron-oxide-bound (Fe-oxide-bound) P in surface sediments and from degrading organic matter. The abundant presence of sulfide in the pore water and its high upward flux towards the sediment surface (∼4 to 8 mmol m−2 d−1), linked to prior deposition of organic-rich sediments in a low-O2 setting (“legacy of hypoxia”), hinder the formation of a larger Fe-oxide-bound P pool in winter. This is most pronounced at sites where water column mixing is naturally relatively low and where low bottom water O2 concentrations prevail in summer. Burial rates of P are high at all sites (0.03–0.3 mol m−2 yr−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). Sedimentary P is dominated by Fe-bound P and organic P at the sediment surface and by organic P, authigenic Ca-P and detrital P at depth. 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) with rates decreasing seaward from the inner to outer archipelago. Our results explain how sediments in this eutrophic coastal system can remove P through burial at a relatively high rate, regardless of whether the bottom waters are oxic or (frequently) hypoxic. Our results suggest that benthic N processes undergo annual cycles of removal and recycling in response to hypoxic conditions. Further nutrient load reductions are expected to contribute to the recovery of the eutrophic Stockholm archipelago from hypoxia. Based on the dominant pathways of P and N removal identified in this study, it is expected that the sediments will continue to remove part of the P and N loads.

The extracellular concentration of H2O2 in surface aquatic environments is controlled by a balance between photochemical production and the microbial synthesis of catalase and peroxidase enzymes to remove H2O2 from solution. In any kind of incubation experiment, the formation rates and equilibrium concentrations of reactive oxygen species (ROSs) such as H2O2 may be sensitive to both the experiment design, particularly to the regulation of incident light, and the abundance of different microbial groups, as both cellular H2O2 production and catalase–peroxidase enzyme production rates differ between species. Whilst there are extensive measurements of photochemical H2O2 formation rates and the distribution of H2O2 in the marine environment, it is poorly constrained how different microbial groups affect extracellular H2O2 concentrations, how comparable extracellular H2O2 concentrations within large-scale incubation experiments are to those observed in the surface-mixed layer, and to what extent a mismatch with environmentally relevant concentrations of ROS in incubations could influence biological processes differently to what would be observed in nature. Here we show that both experiment design and bacterial abundance consistently exert control on extracellular H2O2 concentrations across a range of incubation experiments in diverse marine environments. During four large-scale (>1000 L) mesocosm experiments (in Gran Canaria, the Mediterranean, Patagonia and Svalbard) most experimental factors appeared to exert only minor, or no, direct effect on H2O2 concentrations. For example, in three of four experiments where pH was manipulated to 0.4–0.5 below ambient pH, no significant change was evident in extracellular H2O2 concentrations relative to controls. An influence was sometimes inferred from zooplankton density, but not consistently between different incubation experiments, and no change in H2O2 was evident in controlled experiments using different densities of the copepod Calanus finmarchicus grazing on the diatom Skeletonema costatum (<1 % change in [H2O2] comparing copepod densities from 1 to 10 L−1). Instead, the changes in H2O2 concentration contrasting high- and low-zooplankton incubations appeared to arise from the resulting changes in bacterial activity. The correlation between bacterial abundance and extracellular H2O2 was stronger in some incubations than others (R2 range 0.09 to 0.55), yet high bacterial densities were consistently associated with low H2O2. Nonetheless, the main control on H2O2 concentrations during incubation experiments relative to those in ambient, unenclosed waters was the regulation of incident light. In an open (lidless) mesocosm experiment in Gran Canaria, H2O2 was persistently elevated (2–6-fold) above ambient concentrations; whereas using closed high-density polyethylene mesocosms in Crete, Svalbard and Patagonia H2O2 within incubations was always reduced (median 10 %–90 %) relative to ambient waters.

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.

Enhanced release of alkalinity from the seafloor, principally driven by anaerobic degradation of organic matter under low-oxygen conditions and associated secondary redox reactions, can increase the carbon dioxide (CO2) buffering capacity of seawater and therefore oceanic CO2 uptake. The Baltic Sea has undergone severe changes in oxygenation state and total alkalinity (TA) over the past decades. The link between these concurrent changes has not yet been investigated in detail. A recent system-wide TA budget constructed for the past 50 years using BALTSEM, a coupled physical–biogeochemical model for the whole Baltic Sea area revealed an unknown TA source. Here we use BALTSEM in combination with observational data and one-dimensional reactive-transport modeling of sedimentary processes in the Fårö Deep, a deep Baltic Sea basin, to test whether sulfate (SO42-) reduction coupled to iron (Fe) sulfide burial can explain the missing TA source in the Baltic Proper. We calculated that this burial can account for up to 26 % of the missing source in this basin, with the remaining TA possibly originating from unknown river inputs or submarine groundwater discharge. We also show that temporal variability in the input of Fe to the sediments since the 1970s drives changes in sulfur (S) burial in the Fårö Deep, suggesting that Fe availability is the ultimate limiting factor for TA generation under anoxic conditions. The implementation of projected climate change and two nutrient load scenarios for the 21st century in BALTSEM shows that reducing nutrient loads will improve deep water oxygen conditions, but at the expense of lower surface water TA concentrations, CO2 buffering capacities and faster acidification. When these changes additionally lead to a decrease in Fe inputs to the sediment of the deep basins, anaerobic TA generation will be reduced even further, thus exacerbating acidification. This work highlights that Fe dynamics plays a key role in the release of TA from sediments where Fe sulfide formation is limited by Fe availability, as exemplified by the Baltic Sea. Moreover, it demonstrates that burial of Fe sulfides should be included in TA budgets of low-oxygen basins.

In this paper we provide an overview of new knowledge on oxygen depletion (hypoxia) and related phenomena in aquatic systems resulting from the EU-FP7 project HYPOX ("In situ monitoring of oxygen depletion in hypoxic ecosystems of coastal and open seas, and landlocked water bodies", http://www.hypox.net). In view of the anticipated oxygen loss in aquatic systems due to eutrophication and climate change, HYPOX was set up to improve capacities to monitor hypoxia as well as to understand its causes and consequences. Temporal dynamics and spatial patterns of hypoxia were analyzed in field studies in various aquatic environments, including the Baltic Sea, the Black Sea, Scottish and Scandinavian fjords, Ionian Sea lagoons and embayments, and Swiss lakes. Examples of episodic and rapid (hours) occurrences of hypoxia, as well as seasonal changes in bottom-water oxygenation in stratified systems, are discussed. Geologically driven hypoxia caused by gas seepage is demonstrated. Using novel technologies, temporal and spatial patterns of water-column oxygenation, from basin-scale seasonal patterns to meter-scale sub-micromolar oxygen distributions, were resolved. Existing multidecadal monitoring data were used to demonstrate the imprint of climate change and eutrophication on long-term oxygen distributions. Organic and inorganic proxies were used to extend investigations on past oxygen conditions to centennial and even longer timescales that cannot be resolved by monitoring. The effects of hypoxia on faunal communities and biogeochemical processes were also addressed in the project. An investigation of benthic fauna is presented as an example of hypoxia-devastated benthic communities that slowly recover upon a reduction in eutrophication in a system where naturally occurring hypoxia overlaps with anthropogenic hypoxia. Biogeochemical investigations reveal that oxygen intrusions have a strong effect on the microbially mediated redox cycling of elements. Observations and modeling studies of the sediments demonstrate the effect of seasonally changing oxygen conditions on benthic mineralization pathways and fluxes. Data quality and access are crucial in hypoxia research. Technical issues are therefore also addressed, including the availability of suitable sensor technology to resolve the gradual changes in bottom-water oxygen in marine systems that can be expected as a result of climate change. Using cabled observatories as examples, we show how the benefit of continuous oxygen monitoring can be maximized by adopting proper quality control. Finally, we discuss strategies for state-of-the-art data archiving and dissemination in compliance with global standards, and how ocean observations can contribute to global earth observation attempts.

Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements.

Ice-rich yedoma-dominated landscapes store considerable amounts of organic carbon (C) and nitrogen (N) and are vulnerable to degradation under climate warming. We investigate the C and N pools in two thermokarst-affected yedoma landscapes – on Sobo-Sise Island and on Bykovsky Peninsula in the north of eastern Siberia. Soil cores up to 3 m depth were collected along geomorphic gradients and analysed for organic C and N contents. A high vertical sampling density in the profiles allowed the calculation of C and N stocks for short soil column intervals and enhanced understanding of within-core parameter variability. Profile-level C and N stocks were scaled to the landscape level based on landform classifications from 5 m resolution, multispectral RapidEye satellite imagery. Mean landscape C and N storage in the first metre of soil for Sobo-Sise Island is estimated to be 20.2 kg C m−2 and 1.8 kg N m−2 and for Bykovsky Peninsula 25.9 kg C m−2 and 2.2 kg N m−2. Radiocarbon dating demonstrates the Holocene age of thermokarst basin deposits but also suggests the presence of thick Holocene-age cover layers which can reach up to 2 m on top of intact yedoma landforms. Reconstructed sedimentation rates of 0.10–0.57 mm yr−1 suggest sustained mineral soil accumulation across all investigated landforms. Both yedoma and thermokarst landforms are characterized by limited accumulation of organic soil layers (peat). We further estimate that an active layer deepening of about 100 cm will increase organic C availability in a seasonally thawed state in the two study areas by ∼ 5.8 Tg (13.2 kg C m−2). Our study demonstrates the importance of increasing the number of C and N storage inventories in ice-rich yedoma and thermokarst environments in order to account for high variability of permafrost and thermokarst environments in pan-permafrost soil C and N pool estimates.

Future ocean acidification has the potential to adversely affect many marine organisms. A growing body of evidence suggests that many species could suffer from reduced fertilization success, decreases in larval- and adult growth rates, reduced calcification rates, and even mortality when being exposed to near-future levels (year 2100 scenarios) of ocean acidification. Little research focus is currently placed on those organisms/taxa that might be less vulnerable to the anticipated changes in ocean chemistry; this is unfortunate, as the comparison of more vulnerable to more tolerant physiotypes could provide us with those physiological traits that are crucial for ecological success in a future ocean. Here, we attempt to summarize some ontogenetic and lifestyle traits that lead to an increased tolerance towards high environmental pCO2. In general, marine ectothermic metazoans with an extensive extracellular fluid volume may be less vulnerable to future acidification as their cells are already exposed to much higher pCO2 values (0.1 to 0.4 kPa, ca. 1000 to 3900 μatm) than those of unicellular organisms and gametes, for which the ocean (0.04 kPa, ca. 400 μatm) is the extracellular space. A doubling in environmental pCO2 therefore only represents a 10% change in extracellular pCO2 in some marine teleosts. High extracellular pCO2 values are to some degree related to high metabolic rates, as diffusion gradients need to be high in order to excrete an amount of CO2 that is directly proportional to the amount of O2 consumed. In active metazoans, such as teleost fish, cephalopods and many brachyuran crustaceans, exercise induced increases in metabolic rate require an efficient ion-regulatory machinery for CO2 excretion and acid-base regulation, especially when anaerobic metabolism is involved and metabolic protons leak into the extracellular space. These ion-transport systems, which are located in highly developed gill epithelia, form the basis for efficient compensation of pH disturbances during exposure to elevated environmental pCO2. Compensation of extracellular acid-base status in turn may be important in avoiding metabolic depression. So far, maintained "performance" at higher seawater pCO2 (>0.3 to 0.6 kPa) has only been observed in adults/juveniles of active, high metabolic species with a powerful ion regulatory apparatus. However, while some of these taxa are adapted to cope with elevated pCO2 during their regular embryonic development, gametes, zygotes and early embryonic stages, which lack specialized ion-regulatory epithelia, may be the true bottleneck for ecological success – even of the more tolerant taxa. Our current understanding of which marine animal taxa will be affected adversely in their physiological and ecological fitness by projected scenarios of anthropogenic ocean acidification is quite incomplete. While a growing amount of empirical evidence from CO2 perturbation experiments suggests that several taxa might react quite sensitively to ocean acidification, others seem to be surprisingly tolerant. However, there is little mechanistic understanding on what physiological traits are responsible for the observed differential sensitivities (see reviews of Seibel and Walsh, 2003; Pörtner et al., 2004; Fabry et al., 2008; Pörtner, 2008). This leads us to the first very basic question of how to define general CO2 tolerance on the species level.

The composition of perennially frozen deposits holds information on the palaeo-environment during and following deposition. In this study, we investigate late Pleistocene permafrost at the western coast of the Buor Khaya Peninsula in the south-central Laptev Sea (Siberia), namely the prominent eastern Siberian Yedoma Ice Complex (IC). Two Yedoma IC exposures and one drill core were studied for cryolithological (i.e. ice and sediment features), geochemical, and geochronological parameters. Borehole temperatures were measured for 3 years to capture the current thermal state of permafrost. The studied sequences were composed of ice-oversaturated silts and fine-grained sands with considerable amounts of organic matter (0.2 to 24 wt %). Syngenetic ice wedges intersect the frozen deposits. The deposition of the Yedoma IC, as revealed by radiocarbon dates of sedimentary organic matter, took place between 54.1 and 30.1 kyr BP. Continued Yedoma IC deposition until about 14.7 kyr BP is shown by dates from organic matter preserved in ice-wedge ice. For the lowermost and oldest Yedoma IC part, infrared-stimulated luminescence dates on feldspar show deposition ages between 51.1 ± 4.9 and 44.2 ± 3.6 kyr BP. End-member modelling was applied to grain-size-distribution data to determined sedimentation processes during Yedoma IC formation. Three to five robust end-members were detected within Yedoma IC deposits, which we interpret as different modes of primary and reworked unconfined alluvial slope and fan deposition as well as of localized eolian and fluvial sediment, which is overprinted by in situ frost weathering. The cryolithological inventory of the Yedoma IC preserved on the Buor Khaya Peninsula is closely related to the results of other IC studies, for example, to the west on the Bykovsky Peninsula, where formation time (mainly during the late Pleistocene marine isotope stages (MIS) 3 interstadial) and formation conditions were similar. Local freezing conditions on Buor Khaya, however, differed and created solute-enriched (salty) and isotopically light pore water pointing to a small talik layer and thaw-bulb freezing after deposition. Due to intense coastal erosion, the biogeochemical signature of the studied Yedoma IC represents the terrestrial end-member, and is closely related to organic matter currently being deposited in the marine realm of the Laptev Sea shelf.