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Herndl G.J.,University of Vienna | Herndl G.J.,Netherlands Institute for Sea Research | Reinthaler T.,University of Vienna
Nature Geoscience | Year: 2013

A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the atmosphere to the ocean interior is termed the biological pump. In recent decades it has become clear that the composition of the phytoplankton community in the surface ocean largely determines the quantity and quality of organic matter that sinks to depth. This settling organic matter, however, is not sufficient to meet the energy demands of microbes in the dark ocean. Two additional sources of organic matter have been identified: non-sinking organic particles of debated origin that escape capture by sediment traps and exhibit stable concentrations throughout the dark ocean, and microbes that convert inorganic carbon into organic matter. Whether these two sources can together account for the significant mismatch between organic matter consumption and supply in the dark ocean remains to be seen. It is clear, however, that the microbial community of the deep ocean works in a fundamentally different way from surface water communities. © 2013 Macmillan Publishers Limited. All rights reserved.

Booij K.,Netherlands Institute for Sea Research | Smedes F.,Deltares
Environmental Science and Technology | Year: 2010

The quality of passive sampling methods for measuring concentrations of dissolved hydrophobic contaminants relies on accurate knowledge of in situ sampling rates. In currently used methods for estimating these sampling rates from the dissipation rates of performance reference compounds (PRCs), the PRCs that show either insignificant or complete dissipation are ignored. We explored the merits of nonlinear least-squares (NLS) methods for estimating sampling rates, aiming to retain the information stored in PRC data that is neglected in the traditional methods. To this end, we examined the error structure of weighted NLS, unweighted NLS, and the traditional methods, using model simulations. The results show that sampling rates are best estimated using unweighted NLS. Uncertainties in the sampler-water partition coefficients may result in biased estimates that only weakly depend on the number of PRCs being used. The major advantage of unweighted NLS over the traditional method is that sampling rate estimates and uncertainties are available where the traditional method fails, and that the variability of sampling rate estimates is smaller. © 2010 American Chemical Society.

Van Haren H.,Netherlands Institute for Sea Research
Geophysical Research Letters | Year: 2010

Large vertical temperature differences up to 3°C m-1 are observed very near (<0.5 m from) the 2-m sand-waves bottom in a 20-25 m deep sea strait dominated by tidal flows >1 m s-1. The upper sensor at 0.42 m above the bottom (mab) follows typical temperature variations higher up in the water column, being-90° out-of-phase with the main along-channel current. In contrast, the lower sensor at 0.08 mab is approximately +30-50° more in-phase with the free-stream current. The data confirm the mechanism of "tidal straining", but much closer to the bottom than previously observed and in a 3-D version with cross-flow influences. In this mechanism, turbulent shear flow and horizontal density gradients create stable stratification during ebb and unstable conditions during flood. Here, stratification provides a slippery boundary flow-condition and periodic support of short-scale internal waves with periods down to 50 s. © 2010 by the American Geophysical Union.

Cadee G.C.,Netherlands Institute for Sea Research
Palaios | Year: 2011

In the Wadden Sea, shell repair frequency in the small gastropod Hydrobia ulvae varied from 2.8% to 11.2%. On tidal flats of the Mok, a small bay on the island of Texel, The Netherlands, in the Wadden Sea, higher repair frequencies varying from 11.8% to 41.8% were measured. The shelduck, Tadorna tadorna, a predator of Hydrobia, occurs here in densities far above average densities for the Wadden Sea. Shelducks ingest their prey whole and crush the shells of H. ulvae internally. Live specimens of H. ulvae were collected from shelduck feces. Those with intact operculum and only a damaged outer aperture rim of the shell were kept in aquaria and repaired their shell rapidly. This indicates that predators that ingest shelled prey can also leave repair scars on shells. Such scars, however, are indistinguishable from those resulting from failed predation by predators using such pre-ingestive shell breakage as decapod crustaceans. Copyright © 2011, SEPM (Society for Sedimentary Geology).

Van Haren H.,Netherlands Institute for Sea Research
Journal of Geophysical Research: Oceans | Year: 2011

An accurate bottom pressure sensor has been moored at different sites varying from a shallow sea strait via open ocean guyots to a 1900 m deep Gulf of Mexico. All sites show more or less sloping bottom topography. Focusing on frequencies (σ) higher than tidal, the pressure records are remarkably similar, to within the 95% statistical significance bounds, in the internal gravity wave continuum (IWC) band up to buoyancy frequency N. The IWC has a relatively uniform spectral slope: log(P(σ)) = -αlog(σ), α= 2 ± 1/3. The spectral collapse is confirmed from independent internal hydrostatic pressure estimate, which suggests a saturated IWC. For σ > N, all pressure-spectra transit to a bulge that differs in magnitude. This bulge is commonly attributed to long surface waves. For the present data it is suggested to be due to stratified turbulence-internal wave coupling, which is typically large over sloping topography. The bulge drops off at a more or less common frequency of 2-3 × 10-2 Hz, which is probably related with typical turbulent overturning scales. Copyright 2011 by the American Geophysical Union.

van Aken H.M.,Netherlands Institute for Sea Research
Journal of Sea Research | Year: 2010

Time series of observations of the sea surface temperature (SST) at 12 stations in the Dutch coastal zone are analyzed to establish whether an earlier published nearly 150 year long SST time series from the Marsdiep tidal inlet is representative for the whole Dutch coastal zone. The annual cycles (SST range and phase) as well as the long-term SST trends at decadal scales from other estuaries agree with the Marsdiep time series. An increasing SST trend since 1982 is a phenomenon of the whole Dutch coastal zone. In order to increase the understanding of the causes of the observed SST variability, a multiple linear regression model is constructed, which links locally determined seasonal meteorological and oceanographic forcing factors to the seasonal mean SST. The oceanographic forcing factor is the SST value from the preceding season, representing persistence due to thermal inertia of the sea. Season to season changes of the atmospheric circulation, connected with SST variability, are represented by seasonal mean wind components as forcing factors, e.g. the western winds in winter which bring relatively warm air masses to Western Europe. For the seasons where shortwave solar radiation is the dominant term in the local heat budget (spring and summer), the number of bright sun hours is used as forcing factor, roughly representing the effects of changing cloudiness. The annual mean SST, derived from the regression models for the four seasons, applied to 4 locations along the Dutch coast, correlates quite well, not only for the year to year variability (R = 0.88) but also for the longer-term SST trends (R = 0.95). An explicit local greenhouse effect is not required as separate forcing factor to explain the recent warming trend of Dutch coastal waters starting in the early 1980s; coincident variations in wind statistics and cloudiness are a sufficient explanation. © 2009 Elsevier B.V. All rights reserved.

van Gils J.A.,Netherlands Institute for Sea Research
Proceedings. Biological sciences / The Royal Society | Year: 2013

Recent insights suggest that predators should include (mildly) toxic prey when non-toxic food is scarce. However, the assumption that toxic prey is energetically as profitable as non-toxic prey misses the possibility that non-toxic prey have other ways to avoid being eaten, such as the formation of an indigestible armature. In that case, predators face a trade-off between avoiding toxins and minimizing indigestible ballast intake. Here, we report on the trophic interactions between a shorebird (red knot, Calidris canutus canutus) and its two main bivalve prey, one being mildly toxic but easily digestible, and the other being non-toxic but harder to digest. A novel toxin-based optimal diet model is developed and tested against an existing one that ignores toxin constraints on the basis of data on prey abundance, diet choice, local survival and numbers of red knots at Banc d'Arguin (Mauritania) over 8 years. Observed diet and annual survival rates closely fit the predictions of the toxin-based model, with survival and population size being highest in years when the non-toxic prey is abundant. In the 6 of 8 years when the non-toxic prey is not abundant enough to satisfy the energy requirements, red knots must rely on the toxic alternative.

Villanueva L.,Netherlands Institute for Sea Research | Damste J.S.S.,Netherlands Institute for Sea Research | Schouten S.,Netherlands Institute for Sea Research
Nature Reviews Microbiology | Year: 2014

Archaea produce unique membrane lipids in which isoprenoid alkyl chains are bound to glycerol moieties via ether linkages. As cultured representatives of the Archaea have become increasingly available throughout the past decade, archaeal genomic and membrane lipid-composition data have also become available. In this Analysis article, we compare the amino acid sequences of the key enzymes of the archaeal ether-lipid biosynthesis pathway and critically evaluate past studies on the biochemical functions of these enzymes. We propose an alternative archaeal lipid biosynthetic pathway that is based on a 'multiple-key, multiple-lock' mechanism. © 2014 Macmillan Publishers Limited. All rights reserved.

Agency: GTR | Branch: NERC | Program: | Phase: Research Grant | Award Amount: 42.91K | Year: 2012

For the last approximately 200 years since the Industrial Revolution, human activity, primarily by burning of fossil fuels, has added carbon dioxide to planet Earths atmosphere. Carbon dioxide is an important greenhouse gas and increasing concentrations of this chemical compound in the atmosphere causes climate warming. Understanding the temporal and spatial response of Earths climate system to changing atmospheric carbon dioxide concentrations is a pressing issue for all of human society across the planet. One way to make such an assessment is to look back into the past and to reconstruct past temperature changes and to relate such variability to records of past atmospheric composition. Despite the significance of global warming, long instrumental records of changing seawater temperature in the past are not available for all of the geographical regions which interest climate scientists, or such instrumental records do not extend far enough back in time. Therefore, in order to place the most recent instrumental records of seawater temperature change in a longer temporal context, as well as to enable reconstruction of past seawater temperature where instrumental records do not exist, it is important to delve deeper into history by application of what is called a proxy-based temperature reconstruction approach. Elements and isotope ratios of some elements, when incorporated into calcium carbonate biominerals (including corals, mollusc shells and some plankton), have demonstrated potential to be used as the proxy means of reconstructing the magnitude and rates of change of seawater temperatures, for those time periods before the existence of instrumental records and for geographical regions where such instrumental records do not exist. Such an approach has long been applied to low latitude warm-water corals, since they form easily dated annual growth increments, but these organisms are restricted in distribution to the warm low latitudes. Arctica islandica is a marine bivalve mollusc that inhabits those middle to high latitude shelf seas that border the North Atlantic Ocean and individuals of this species have been shown to live for up to ~400 years. Furthermore, this organism (like a warm-water coral) deposits easily identified and dated annual shell growth increments, the composition of which has the potential to enable reconstruction of proxy-based records of past seawater temperature, on a calendar timescale (by counting annual growth increments from a known date of death), for the last few centuries and even for the last millennium (when shells of individuals are cross-correlated using the same approach as is applied to tree rings). However, to be able to generate these proxy-based records of past seawater temperature it is critically important that robust calibrations are derived, which document the strength of the relationship between the proxy measurement and seawater temperature, as well as identifying any limitations with any proxy. This detailed and systematic study will be the first use of specimens of A. islandica, which have already been cultured at constant seawater temperatures in laboratory aquaria, under controlled conditions, to derive calibrations for three novel temperature proxies. Such laboratory experiments are fundamental to the development of proxies for reconstructing past seawater temperatures, because such experiments allow for shell growth under controlled conditions. Once these calibrations have been determined the next step, in a follow-up project, will be to generate long time-series records of past seawater temperature change in different parts of the North Atlantic Ocean. Such records then will further climate scientists understanding of the past and future evolution of climate in a geographical region which is of direct relevance to the UK and western Europe.

de Jager M.,Netherlands Institute for Sea Research
Proceedings. Biological sciences / The Royal Society | Year: 2014

Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein's original theory of collision-induced Brownian motion in physics provides a parsimonious, mechanistic explanation for these observations. Here, Brownian motion results from frequent encounters between organisms in dense environments. In density-controlled experiments, movement patterns of mussels shifted from Lévy towards Brownian motion with increasing density. When the analysis was restricted to moves not truncated by encounters, this shift did not occur. Using a theoretical argument, we explain that any movement pattern approximates Brownian motion at high-resource densities, provided that movement is interrupted upon encounters. Hence, the observed shift to Brownian motion does not indicate a density-dependent change in movement strategy but rather results from frequent collisions. Our results emphasize the need for a more mechanistic use of Brownian motion in ecology, highlighting that especially in rich environments, Brownian motion emerges from ecological interactions, rather than being a default movement pattern.

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