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Coccolithophores are globally important marine calcifying phytoplankton that utilize a haplo-diplontic life cycle. The haplo-diplontic life cycle allows coccolithophores to divide in both life cycle phases and potentially expands coccolithophore niche volume. Research has, however, to date largely overlooked the life cycle of coccolithophores and has instead focused on the diploid life cycle phase of coccolithophores. Through the synthesis and analysis of global scanning electron microscopy (SEM) coccolithophore abundance data (n=2534), we find that calcified haploid coccolithophores generally constitute a minor component of the total coccolithophore abundance (≈ 2 %–15 % depending on season). However, using case studies in the Atlantic Ocean and Mediterranean Sea, we show that, depending on environmental conditions, calcifying haploid coccolithophores can be significant contributors to the coccolithophore standing stock (up to ≈30 %). Furthermore, using hypervolumes to quantify the niche of coccolithophores, we illustrate that the haploid and diploid life cycle phases inhabit contrasting niches and that on average this allows coccolithophores to expand their niche by ≈18.8 %, with a range of 3 %–76 % for individual species. Our results highlight that future coccolithophore research should consider both life cycle stages, as omission of the haploid life cycle phase in current research limits our understanding of coccolithophore ecology. Our results furthermore suggest a different response to nutrient limitation and stratification, which may be of relevance for further climate scenarios. Our compilation highlights the spatial and temporal sparsity of SEM measurements and the need for new molecular techniques to identify uncalcified haploid coccolithophores. Our work also emphasizes the need for further work on the carbonate chemistry niche of the coccolithophore life cycle.

The marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate choanoflagellates, a group of protists closely related to animals. We cultured two species of choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately −5 ‰ to −7 ‰) than cultured diatoms (−0.5 ‰ to −2.1 ‰). Instead, choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar dissolved silica concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.

Bottom trawling in the deep sea is one of the main drivers of sediment resuspension, eroding the seafloor and altering the content and composition of sedimentary organic matter (OM). The physical and biogeochemical impacts of bottom trawling were studied on the continental slope of the Gulf of Castellammare, Sicily (southwestern Mediterranean), through the analysis of two triplicate sediment cores collected at trawled and untrawled sites (∼550 m water depth) during the summer of 2016. Geochemical and sedimentological parameters (excess 210Pb, excess 234Th, 137Cs, dry bulk density, and grain size), elemental (organic carbon and nitrogen) and biochemical composition of sedimentary OM (proteins, carbohydrates, lipids), as well as its freshness (phytopigments) and degradation rates were determined in both coring locations. The untrawled site had a sedimentation rate of 0.15 cm yr−1 and presented a 6 cm thick surface mixed layer that contained siltier sediment with low excess 210Pb concentrations, possibly resulting from the resuspension, posterior advection, and eventual deposition of coarser and older sediment from adjacent trawling grounds. In contrast, the trawled site was eroded and presented compacted century-old sediment highly depleted in OM components, which were between 20 % and 60 % lower than those in the untrawled site. However, the upper 2 cm of the trawled site consisted of recently accumulated sediments enriched in excess 234Th, excess 210Pb, and phytopigments, while OM contents were similar to those from the untrawled core. This fresh sediment supported protein turnover rates of 0.025 d−1, which doubled those quantified in surface sediments of the untrawled site. The enhancement of remineralization rates in surface sediment of the trawled site was associated with the arrival of fresh particles on a chronically trawled deep-sea region that is generally deprived of OM. We conclude that the detrimental effects of bottom trawling can be temporarily and partially abated by the arrival of fresh and nutritionally rich OM, which stimulate the response of benthic communities. However, these ephemeral deposits are likely to be swiftly eroded due to the high trawling frequency over fishing grounds, highlighting the importance of establishing science-based management strategies to mitigate the impacts of bottom trawling.

The concentration of CO2 in the atmosphere is sensitive to changes in the depth at which sinking particulate organic matter is remineralized: often described as a change in the exponent “b” of the Martin curve. Sediment trap observations from deep and intermediate depths suggest there is a spatially heterogeneous pattern of b, particularly varying with latitude, but disagree over the exact spatial patterns. Here we use a biogeochemical model of the phosphorus cycle coupled with a steady-state representation of ocean circulation to explore the sensitivity of preformed phosphate and atmospheric CO2 to spatial variability in remineralization depths. A Latin hypercube sampling method is used to simultaneously vary the Martin curve independently within 15 different regions, as a basis for a regression-based analysis used to derive a quantitative measure of sensitivity. Approximately 30 % of the sensitivity of atmospheric CO2 to changes in remineralization depths is driven by changes in the subantarctic region (36 to 60∘ S) similar in magnitude to the Pacific basin despite the much smaller area and lower export production. Overall, the absolute magnitude of sensitivity is controlled by export production, but the relative spatial patterns in sensitivity are predominantly constrained by ocean circulation pathways. The high sensitivity in the subantarctic regions is driven by a combination of high export production and the high connectivity of these regions to regions important for the export of preformed nutrients such as the Southern Ocean and North Atlantic. Overall, regionally varying remineralization depths contribute to variability in CO2 of between around 5 and 15 ppm, relative to a global mean change in remineralization depth. Future changes in the environmental and ecological drivers of remineralization, such as temperature and ocean acidification, are expected to be most significant in the high latitudes where CO2 sensitivity to remineralization is also highest. The importance of ocean circulation pathways to the high sensitivity in subantarctic regions also has significance for past climates given the importance of circulation changes in the Southern Ocean.

Future deep-sea mining for polymetallic nodules in abyssal plains will negatively impact the benthic ecosystem, but it is largely unclear whether this ecosystem will be able to recover from mining disturbance and if so, to what extent and at what timescale. During the “DISturbance and reCOLonization” (DISCOL) experiment, a total of 22 % of the seafloor within a 10.8 km2 circular area of the nodule-rich seafloor in the Peru Basin (SE Pacific) was ploughed in 1989 to bury nodules and mix the surface sediment. This area was revisited 0.1, 0.5, 3, 7, and 26 years after the disturbance to assess macrofauna, invertebrate megafauna and fish density and diversity. We used this unique abyssal faunal time series to develop carbon-based food web models for each point in the time series using the linear inverse modeling approach for sediments subjected to two disturbance levels: (1) outside the plough tracks; not directly disturbed by plough, but probably suffered from additional sedimentation; and (2) inside the plough tracks. Total faunal carbon stock was always higher outside plough tracks compared with inside plough tracks. After 26 years, the carbon stock inside the plough tracks was 54 % of the carbon stock outside plough tracks. Deposit feeders were least affected by the disturbance, with modeled respiration, external predation, and excretion rates being reduced by only 2.6 % inside plough tracks compared with outside plough tracks after 26 years. In contrast, the respiration rate of filter and suspension feeders was 79.5 % lower in the plough tracks after 26 years. The “total system throughput” (T..), i.e., the total sum of modeled carbon flows in the food web, was higher throughout the time series outside plough tracks compared with the corresponding inside plough tracks area and was lowest inside plough tracks directly after the disturbance (8.63 × 10−3 ± 1.58 × 10−5 mmol C m−2 d−1). Even 26 years after the DISCOL disturbance, the discrepancy of T.. between outside and inside plough tracks was still 56 %. Hence, C cycling within the faunal compartments of an abyssal plain ecosystem remains reduced 26 years after physical disturbance, and a longer period is required for the system to recover from such a small-scale sediment disturbance experiment.

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.

Interest in seamount research has gathered momentum over the past five years in an effort to understand the physical, geochemical and biological characteristics as well as the interconnectedness of seamount ecosystems. The majority of biological seamount research has concentrated upon the rich and diverse suspension feeding organisms that dominate the megafauna, such as gorgonians and antipatharian corals; by comparison there have been few studies that have investigated the no less enigmatic, but possibly just as important infauna. To help fill this knowledge gap, the macrofaunal community was sampled from a total of five stations along a northerly transect (capturing water depths from ∼130 m to ∼3300 m), on Senghor Seamount (NE Atlantic). The focus of this study is on the polychaete communities. Polychaete abundance peaked at the summit and a mid-slope station (∼1500 m), a pattern mirrored by the biomass values. The polychaete community along the transect appeared to be particularly diverse, with 135 species nominally identified to putative species from a total of 954 individuals. A diversity maximum was identified on the upper slope at ∼800 m depth, with species diversity, richness and evenness also all peaking at this station. Depth is likely to be a significant factor in determining levels of similarity between stations.

It is important that climate models can accurately simulate the terrestrial carbon cycle in the Arctic due to the large and potentially labile carbon stocks found in permafrost-affected environments, which can lead to a positive climate feedback, along with the possibility of future carbon sinks from northward expansion of vegetation under climate warming. Here we evaluate the simulation of tundra carbon stocks and fluxes in three land surface schemes that each form part of major Earth system models (JSBACH, Germany; JULES, UK; ORCHIDEE, France). We use a site-level approach in which comprehensive, high-frequency datasets allow us to disentangle the importance of different processes. The models have improved physical permafrost processes and there is a reasonable correspondence between the simulated and measured physical variables, including soil temperature, soil moisture and snow. We show that if the models simulate the correct leaf area index (LAI), the standard C3 photosynthesis schemes produce the correct order of magnitude of carbon fluxes. Therefore, simulating the correct LAI is one of the first priorities. LAI depends quite strongly on climatic variables alone, as we see by the fact that the dynamic vegetation model can simulate most of the differences in LAI between sites, based almost entirely on climate inputs. However, we also identify an influence from nutrient limitation as the LAI becomes too large at some of the more nutrient-limited sites. We conclude that including moss as well as vascular plants is of primary importance to the carbon budget, as moss contributes a large fraction to the seasonal CO2 flux in nutrient-limited conditions. Moss photosynthetic activity can be strongly influenced by the moisture content of moss, and the carbon uptake can be significantly different from vascular plants with a similar LAI. The soil carbon stocks depend strongly on the rate of input of carbon from the vegetation to the soil, and our analysis suggests that an improved simulation of photosynthesis would also lead to an improved simulation of soil carbon stocks. However, the stocks are also influenced by soil carbon burial (e.g. through cryoturbation) and the rate of heterotrophic respiration, which depends on the soil physical state. More detailed below-ground measurements are needed to fully evaluate biological and physical soil processes. Furthermore, even if these processes are well modelled, the soil carbon profiles cannot resemble peat layers as peat accumulation processes are not represented in the models. Thus, we identify three priority areas for model development: (1) dynamic vegetation including (a) climate and (b) nutrient limitation effects; (2) adding moss as a plant functional type; and an (3) improved vertical profile of soil carbon including peat processes.

In this study, we investigate phosphorus (P) and iron (Fe) cycling in sediments along a depth transect from within to well below the oxygen minimum zone (OMZ) in the northern Arabian Sea (Murray Ridge). Pore-water and solid-phase analyses show that authigenic formation of calcium phosphate minerals (Ca-P) is largely restricted to where the OMZ intersects the seafloor topography, likely due to higher depositional fluxes of reactive P. Nonetheless, increased ratios of organic carbon to organic P (Corg/Porg) and to total reactive P (Corg/Preactive) in surface sediments indicate that the overall burial efficiency of P relative to Corg decreases under the low bottom water oxygen concentrations (BWO) in the OMZ. The relatively constant Fe/Al ratio in surface sediments along the depth transect suggest that corresponding changes in Fe burial are limited. Sedimentary pyrite contents are low throughout the ~25 cm sediment cores at most stations, as commonly observed in the Arabian Sea OMZ. However, pyrite is an important sink for reactive Fe at one station in the OMZ. A reactive transport model (RTM) was applied to quantitatively investigate P and Fe diagenesis at an intermediate station at the lower boundary of the OMZ (bottom water O2: ~14 μmol L−1). The RTM results contrast with earlier findings in showing that Fe redox cycling can control authigenic apatite formation and P burial in Arabian Sea sediment. In addition, results suggest that a large fraction of the sedimentary Ca-P is not authigenic, but is instead deposited from the water column and buried. Dust is likely a major source of this Ca-P. Inclusion of the unreactive Ca-P pool in the Corg/P ratio leads to an overestimation of the burial efficiency of reactive P relative to Corg along the depth transect. Moreover, the unreactive Ca-P accounts for ~85% of total Ca-P burial. In general, our results reveal large differences in P and Fe chemistry between stations in the OMZ, indicating dynamic sedimentary conditions under these oxygen-depleted waters.

Biological communities populating the Mediterranean Sea, which is situated at the northern boundary of the subtropics, are often claimed to be particularly affected by global warming. This is indicated, for instance, by the introduction of (sub)tropical species of fish or invertebrates that can displace local species. This raises the question of whether microbial communities are similarly affected, especially in the Levantine basin where sea surface temperatures have significantly risen over the last 25 years (0.50 ± 0.11 °C in average per decade, P Prochlorococcus and Synechococcus, was examined during two cruises through both eastern and western Mediterranean Sea basins held in September 1999 (PROSOPE cruise) and in June–July 2008 (BOUM cruise). Diversity was studied using dot blot hybridization with clade-specific 16S rRNA oligonucleotide probes and/or clone libraries of the 16S-23S ribosomal DNA Internal Transcribed Spacer (ITS) region, with a focus on the abundance of clades that may constitute bioindicators of warm waters. During both cruises, the dominant Prochlorococcus clade in the upper mixed layer at all stations was HLI, a clade typical of temperate waters, whereas the HLII clade, the dominant group in (sub)tropical waters, was only present at very low concentrations. The Synechococcus community was dominated by clades I, III and IV in the northwestern waters of the Gulf of Lions and by clade III and groups genetically related to clades WPC1 and VI in the rest of the Mediterranean Sea. In contrast, only a few sequences of clade II, a group typical of warm waters, were observed. These data indicate that local cyanobacterial populations have not yet been displaced by their (sub)tropical counterparts.