• European Marine Science
• Journal of Marine Systems close

In the context of climate change, understanding the ecological processes controlling the functioning and the efficiency of the biological pump is of primary importance. Plankton community structure and species-specific properties are often invoked as likely to affect biogeochemistry and the export of organic and biogenic mate- rial to the ocean interior. Although a major player in this respect, diatoms are still viewed as a single functional type whose diversity is generally overlooked. Here we examine that question, building on the results achieved during the MOBYDICK expedition, which occurred in the vicinity of the Kerguelen Islands (Southern Ocean) in late summer, a time window corresponding to the demise of the annually recurrent phytoplankton blooms already known to be controlled by iron availability. The Si/C/N stoichiometry of the particulate matter was studied in conjunction with the different diatom community structures, their physiological states, as well as their species-specific carbon contents and silicification degrees. Our results show that diatoms outside the iron- fertilized plateau were more heavily silicified, due to the combined effects of both taxonomic composition of the resident community and a direct physiological response to iron stress, resulting in higher Si:C elemental ratios in diatoms as well as in the bulk particulate matter. Despite low silicic acid concentrations, large chains of weakly silicified Corethron inerme were able to grow in the upper mixed layer above the plateau, while in adjacent high nutrient low chlorophyll (HNLC) waters, communities were dominated by Fragilariopsis spp., Cylindrotheca closterium and the centric genera Actinocyclus/Thalassiosira spp. Depth was also an important factor shaping diatom communities, with the presence of a deep and inactive assemblage located within the pycnocline gradient, both on- and off-plateau, which likely resulted from the differential sinking and accumulation of species previously grown at the surface. In HNLC waters, below the mixed layer, detrital frustules of the heavily silicified species Fragilariopsis kerguelensis carried mostly Si, while above the plateau, Eucampia antarctica and Chaetoceros spp. (resting spores and vegetative stages) were efficient vectors of both Si and C to the deeper layers. Our study shows that the stoichiometry of the biological pump cannot be considered solely as a simple response to a single limiting factor (here iron) highlighting the importance of a species-centered approach in order to finely resolve biogeochemical fluxes and improve our understanding of the biological pump. International audience

The general trend in ecosystem modelling is to improve the spatial resolution by shifting from rough box-models to fine 3D models. Despite the continuous speeding-up of computing, 3D models involving numerous state variables may remain intractable, especially for parameter calibration, when processes with long half-life periods (i.e, from years to decades) are introduced, such as the behaviour of organic matter in sediment and population dynamics of benthic species. In these cases, a first approach can be provided by fast-running box-models, if they take into account the most crucial hydrodynamic properties of the system. In a macrotidal shelf sea such as the English Channel, the long-term horizontal transport can be summarized by the tidal residual circulation, and the vertical stratification can be sketched by a two- or three-layered integral model. This paper compares the results obtained in the English Channel area by the same biogeochemical equations of pelagic primary production, coupled to 1) a two-layered box-model 2) a three-layered box-model (i.e., with an intermediate cline layer between surface and bottom ones) and 3) a fine-gridded 3D model. Comparison is focused firstly on thermal stratification and summer dinoflagellate blooms in the north-western Channel and secondly on the haline stratification and the sequence of blooms obtained in the eutrophicated Seine river plume. Comparison shows that box-models act as low-pass filters which reproduce correctly the weekly mean time-course, but greatly reduce the variance locally observed in a tide-oscillating plume region. As far as global characteristics are concerned, such as the annual primary production, or the percentage of variation in annual production after reducing the nutrient loadings, the box and 3D models gave very similar results. This conclusion reinforces the usefulness of using box-models as a first approach in long-term processes, for which a long transient phase is expected before reaching the annual periodic solution. (c) 2006 Elsevier B.V. All rights reserved.

The Ensemble Kalman filter (EnKF) has been applied to a 1-D complex ecosystem model coupled with a hydrodynamic model of the Ligurian Sea. In order to improve the performance of the EnKF, an ensemble subsampling strategy has been used to better represent the covariance matrices and a pre-analysis step for correcting the non-normality of the members distribution has been implemented. Twin experiments have been realized to assess the performance of the developed tool and a real data assimilation experiment has been conducted to hindcast the ecosystem at the Dyfamed site during the year 2000. Finally the performance of the EnKF has been compared with a Singular Evolutive Extended Kalman (SEEK) filter with a fixed basis. We conclude that, on one hand, there is a benefit in using the subsampling strategy and the lognormal transformation with the EnKF, and on the other hand, this filter presents better performance than the fixed basis version of the SEEK filter. However, it also incurs a large computational cost.

This is the accepted manuscript of the paper "Phyto-VFP: a new bio-optical model of pelagic primary production based onvariable fluorescence measures", published as final paper in "Journal of Marine Systems" Volume 204, April 2020, 103304 https://doi.org/10.1016/j.jmarsys.2019.103304 Marine primary production (PP) is a key factor in the regulation of the global carbon cycle, with important potential feedback on climate. Seventy percent of marine PP is generated by phytoplankton photosynthesis. However, the phytoplankton productivity rate is dependent on the photo-physiological state of phytoplankton cells, as well as other environmental conditions. To consider these variables appropriately, refine the current estimates of PP, and reduce the laboursome and lengthy methodologies of radiocarbon estimates, we have created “Phyto-VFP” (Variable Fluorescence Phytoplankton Production), a new bio-optical model classified as a Wavelength and Depth-resolved (WDR) model. The model integrates the effect of the photo-acclimation processes on the “active” fraction of the phytoplankton population with the dynamic of the water column, parametrised through a series of laboratory experiments based on in vivo variable fluorescence measures on the marine diatom Skeletonema costatum (Greville) Cleve. The performance of Phyto-VFP was compared with concurrent estimates of radiocarbon (14C) uptakes, under different dynamic and optical conditions, during two oceanographic cruises (SAMCA3 and SAMCA4) in the Mediterranean Sea. The low Root Mean Square Differences (RMSDs) show that Phyto-VFP performs well when estimating phytoplankton PP. When compared to other biooptical models, Phyto-VFP estimates of PP in coastal waters were closer to radiocarbon measurements than other models could predict [e.g., the Morel model (MM)]. The application of Phyto-VFP to the SAMCA dataset and its comparison to MM allowed the assessment of model performance under three different physical and biological conditions, in which it was possible to analyse how photo-physiological responses of phytoplankton influence PP.

International audience; With climate change, the strong seasonality and tight pelagic-benthic coupling in the Arctic is expected to change in the next few decades. It is currently unclear how the benthos will be affected by changes of environmental conditions such as supplies of organic matter (OM) from the water column. In the last decade, Kongsfjorden (79°N), a high Arctic fjord in Svalbard influenced by several glaciers and Atlantic water inflow, has been a site of great interest owing to its high sensitivity to climate change, evidenced by a reduction in ice cover and an increase in melting freshwater. To investigate how spatial and seasonal changes in vertical fluxes can impact the benthic compartment of Kongsfjorden, we studied the organic matter characteristics (in terms of quantity and quality) and prokaryotic distribution in sediments from 3 stations along a transect extending from the glacier into the outer fjord in 4 different seasons (spring, summer, autumn and winter) in 2012–2013. The biochemical parameters used to describe the sedimentary organic matter were organic carbon (OC), total nitrogen, bulk stable isotope ratios, pigments (chorophyll-a and phaeopigments) and biopolymeric carbon (BPC), which is the sum of the main macromolecules, i.e. lipids, proteins and carbohydrates. Prokaryotic abundance and distribution were estimated by 4′,6-diamidino-2-phenylindole (DAPI) staining. This study identifies a well-marked quantitative gradient of biogenic compounds throughout all seasons and also highlights a discrepancy between the quantity and quality of sedimentary organic matter within the fjord. The sediments near the glacier were organic-poor (< 0.3%OC), however the high primary productivity in the water column displayed during spring was reflected in summer sediments, and exhibited higher freshness of material at the inner station compared to the outer basin (means C-chlorophyll-a/OC ~ 5 and 1.5%, respectively). However, sediments at the glacier front were depleted in BPC (~ 0.2–0.3 mg C g− 1 DW) by 4.5 and 9 times compared to sediments from the inner and outer stations. δ13C values in sedimentary organic matter of Kongsfjorden varied between − 23.8 and − 19.3‰ and reflected distinct sources of organic matter between basins. Bacterial total cell numbers in sediments of Kongsfjorden were < 2 × 108 cells ml− 1 and the prokaryotic community structure was strongly influenced by the marked environmental biogenic gradients. Overall, the spatial variability prevailed over the seasonal variability in sediments of Kongsfjorden suggesting that glacier inputs prominently control the functioning of this benthic ecosystem and its communities.

AbstractIn August 2002, new hydrochemical and hydrophysical data were collected in the Aral Sea. The survey includes cross-sections in three locations: within the Small Aral close to Tastubek Bay, in the Large Aral at the northern tip that is Tschebas Bay and within the western basin at Chernishov Bay. All three locations represent different stages in the hydrochemical evolution of the Aral Sea.Depth profiles of pressure, temperature, conductivity, pH and dissolved oxygen were measured with a YSI 6600 profiler. Water samples were taken with a Niskin bottle and analyzed for dissolved oxygen and nutrients by standard photometric methods. Major anions and cations were analyzed by ion chromatography and ICP-OES, respectively. Benthic flux experiments were carried out with sediment cores in a batch mode assay on-site.In the Small Aral, the changes in the hydrochemical properties are not as dramatic as in the Large Aral. The Small Aral represents a brackish inland water body with salinities of 1718 g kg−1. The wind-mixed layer reached 8 m during the survey. The salinity is vertically and horizontally almost uniform. Below 8 m, a temporally hypoxic layer forms during summer. Salt redissolution was found to be an important source of salt in the water. About 33.5 g SO42− m−2 day−1 and about 30.7 g Cl− m−2 day−1 are released from the sediment in summer.In the Large Aral, the salinity distribution is uniform in shallow waters (less than 5 m) but varies strongly in deeper water. Tschebas Bay at the northern tip of the large Aral represents a shallow lagoon with a maximum depth of about 6 m. The water column was well mixed down to the bottom (~6 m) having salt concentrations of 82 g kg−1 on average. Almost no gradients in dissolved substances were observed. It is suspected that salinity is balanced by fresher water inflow originating from the Syr Darya flowing south and by groundwater exfiltration. Chernishov Bay in the north of the western basin is meromictic. Below a wind-mixed layer, a very strong pycnocline of 20 g kg−1 per m at 5 m depth isolates the water below from exchanges with the water above and led to the formation of huge anoxic water body down to the bottom at about 25 m depth. Below 10 m, the water contains hydrogen sulphide. The salt concentration increases from 82 g kg−1 in the surface water to 110 g kg−1 at depth. The salt release from the sediment is as high as 1143 g SO42− m−2 day−1 and 1626 g Cl− m−2 day−1. Benthic release of salt is considered as an important source for salt in the bottom water of the western basin and in sustaining the stable density stratification.Author Keywords: Saline lake; Hydrochemistry; Desiccation; Anoxia; Benthic flux; Asia; Kazakhstan; Aral Sea

Major advances in analytical chemistry and instrumentation have prompted major advances in our understanding of trace metal biogeochemistry. However, the deep-water concentration of most trace elements has not been yet assessed across broad regions of the oceans. A synthesis of data on trace metals (i.e. Cd, Co, Cu, Mo, Ni, Pb and Zn) measured and reported for depths 1000m or deeper, between 1976 and 2009 revealed major gaps in our coverage of this key property. Cadmium and Cu have been the elements more extensively measured with 264 and 210 deep profiles reported in 64 and 57 articles, respectively, while Mo and Co have been reported only at 17 and 60 ocean sites, respectively. Globally 68.1% (216.1 10 6km 2) of deep oceans (1000m or deeper) have not been sampled. The bulk of depth profiles published in peer reviewed scientific literature are from the Northern hemisphere (69.7% of the total reported profiles) rendering the Southern hemisphere as a poorly explored region for these important properties (mainly in the South and Eastern Pacific Ocean and in the Tropical Indian Ocean). Vertical profiles of dissolved elements plotted with data compiled during the last 34years indicate that, in addition to the variation of concentrations, vertical distributions differs per ocean basin. © 2012 Elsevier B.V.. This is a contribution to the “Malaspina 2010 Expedition” CONSOLIDER project funded by the Spanish Ministry of Science and Innovation (ref. CSD2008-00077). Peer Reviewed

Models of the marine carbon cycle assume that virtually all heterotrophic production in the open ocean is derived from near-surface carbon fixation (primary production) by phytoplankton. However, current carbon budget estimates show that respiration throughout the ocean far exceeds surface primary production. This disconnect can be grouped into two categories: Inaccurate estimates of water column respiration and carbon transport from metazoans; and missing primary production sources and. heterotrophic processing in the dark ocean. In this review, we examine the contribution to the ocean carbon cycle of chemoautotrophic production, as well as secondary production and respiration from meso-zooplankton and micro-nekton below 400 m depth. About one-third of epipelagic biomass in the ocean migrates diurnally, distributing dissolved organic carbon (DOC) and total nitrogen (TN), along with about 30–80% of the particulate organic carbon (POC) flux, from the upper ocean. Although mostly this occurs in the upper 400 m, migration depths can extend to 3000 m. In addition, up to 80% of the biomass of secondary consumers in the open ocean live part of their life cycle at depths up to 2000 m, contributing significantly to deep-sea respiration and particle flux, particularly over fall/winter in temperate-subarctic oceans, submarine canyons, and deep seas such as the Mediterranean. This active flux provides fresh organic input to the deep ocean at a time of year when surface primary productivity, and thus organic carbon (OC) flux to the deep ocean, is low. The complex spatial, temporal and depth scales of horizontal and vertical migration make modelling of the global oceanic carbon cycle extremely complex, requiring consideration of biomass movements throughout the entire water column over diurnal, lunar and seasonal cycles over broad geographic regions. An additional 10 to 50% of surface primary production occurs within mid-depth oxygen minimum zones (OMZs), fuelled by ammonia excreted from vertically migrating zooplankton concentrated near OMZ boundaries. Crustal sources such as gas and methane seeps, hydrothermal vents and submarine volcanoes support active deep-sea food webs, as well as contributing to upper ocean productivity. Crustal sources are conservatively estimated to provide >30%, and probably up to 50%, of oceanic OC flux to the dark ocean. These estimates are still poorly constrained but can no longer be ignored in global oceanic carbon cycles.