bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of phytoplankton production by physical forcing in a strongly tidal, well-mixed estuary
Authors: Desmit X. , Vanderborght J. P. , Regnier P. , Wollast R.
Published: April 2010

Abstract. A zero-dimensional model for phytoplanktonic production in turbid, macro-tidal, well-mixed estuaries is proposed. It is based on the description of light-dependent algal growth, phytoplankton respiration and mortality. The model is forced by simple time-functions for solar irradiance, water depth and light penetration. The extinction coefficient is directly related to the dynamics of suspended particulate matter. Model results show that the description of phytoplankton growth must operate at a time resolution sufficiently high to describe the interference between solarly and tidally driven physical forcing functions. They also demonstrate that in shallow to moderately deep systems, simulations using averaged, instead of time-varying, forcing functions lead to significant errors in the estimation of phytoplankton productivity. The highest errors are observed when the temporal pattern of light penetration, linked to the tidal cycle of solids settling and resuspension, is neglected. The model has also been applied using realistic forcing functions typical of two locations in the Scheldt estuary. Model results are consistent with the typical phytoplankton decay observed along the longitudinal, seaward axis in the tidal river and oligohaline part of this estuary.
Whole-system metabolism and CO2 fluxes in a Mediterranean Bay dominated by seagrass beds (Palma Bay, NW Mediterranean)
Authors: Gazeau F. , Duarte C. M. , Gattuso J.-P. , Barrón C. , Navarro N. , Ruiz S. , Prairie Y. T. , Calleja M. , Delille B. , Frankignoulle M. , Borges A. V.
Published: April 2010

Abstract. Planktonic and benthic incubations (bare and Posidonia oceanica vegetated sediments) were performed at monthly intervals from March 2001 to October 2002 in a seagrass vegetated area of the Bay of Palma (Mallorca, Spain). Results showed a contrast between the planktonic compartment, which was on average near metabolic balance (−4.6±5.9 mmol O2 m-2 d-1) and the benthic compartment, which was autotrophic (17.6±8.5 mmol O2 m-2 d-1). During two cruises in March and June 2002, planktonic and benthic incubations were performed at several stations in the bay to estimate the whole-system metabolism and to examine its relationship with partial pressure of CO2 (pCO2) and apparent oxygen utilisation (AOU) spatial patterns. Moreover, during the second cruise, when the residence time of water was long enough, net ecosystem production (NEP) estimates based on incubations were compared, over the Posidonia oceanica meadow, to rates derived from dissolved inorganic carbon (DIC) and oxygen (O2) mass balance budgets. These budgets provided NEP estimates in fair agreement with those derived from direct metabolic estimates based on incubated samples over the Posidonia oceanica meadow. Whereas the seagrass community was autotrophic, the excess organic carbon production therein could only balance the planktonic heterotrophy in shallow waters relative to the maximum depth of the bay (55 m). This generated a horizontal gradient from autotrophic or balanced communities in the shallow seagrass-covered areas, to strongly heterotrophic communities in deeper areas of the bay. It seems therefore that, on an annual scale in the whole bay, the organic matter production by the Posidonia oceanica may not be sufficient to fully compensate the heterotrophy of the planktonic compartment, which may require external organic carbon inputs, most likely from land.
The Environment Recording Unit in coral skeletons – a synthesis of structural and chemical evidences for a biochemically driven, stepping-growth process in fibres
Authors: Cuif J. P. , Dauphin Y.
Published: April 2010

Abstract. This paper gathers a series of structural and biochemical in situ characterizations carried out to improve our knowledge of the fine scale growth patterns of fibres in coral skeletons. The resulting data show a clear correspondence between the mineral subunits of fibres and the spatial distribution of organic macromolecules. New observations using atomic force microscope confirm the close relationship between mineral and organic phases at the nanometre scale. Synthesis of these data results in a significant change in our concept of the mineralization process in coral skeletons. In contrast to the usual view of an aggregate of purely mineral units independently growing by simple chemical precipitation, coral fibres appear to be fully controlled structures. Their growth process is based on cyclic secretion of mineralizing compounds by the polyp basal ectoderm. These biochemical components of the coral fibres, in which sulfated acidic proteoglycans probably play a major role, are repeatedly produced (proteoglycans are those glycoproteins whose carbohydrate moieties consist of long unbranched chains of sulfated amino sugars). This results in a stepping growth mode of fibres and a layered global organization of coral skeletons. Therefore, in contrast to the widely accepted geochemical interpretation, we propose a fibre growth model that places coral skeletons among the typical ''matrix mediated'' structures. The crystal-like fibres are built by superimposition of few micron-thick growth layers. A biomineralization cycle starts by the secretion of a mineralizing matrix and the final step is the crystallization phase, during which mineral material grows onto the organic framework. Thus, each growth layer is the actual Environment Recording Unit. From a practical standpoint, these results may contribute to develop a new high resolution approach of the environment recording by coral skeletons.
Measurements of hydrocarbon emissions from a boreal fen using the REA technique
Authors: Haapanala S. , Rinne J. , Pystynen K.-H. , Hellén H. , Hakola H. , Riutta T.
Published: April 2010

Abstract. Fluxes of biogenic volatile organic compounds (VOC) and methane were measured above a boreal fen. Vegetation on the fen is dominated by Sphagnum mosses and sedges. A relaxed eddy accumulation (REA) system with dynamic deadband was designed and constructed for the measurements. Methane, C2-C6 hydrocarbons and some halogenated hydrocarbons were analysed from the samples by gas chromatographs equipped with FID and ECD. A significant flux of isoprene and methane was detected during the growing seasons. Isoprene emission was found to follow the common isoprene emission algorithm. Average standard emission potential of isoprene was 680 µg m-2 h-1. Fluxes of other non-methane hydrocarbons were below detection limit.
Sources of nitrous oxide emitted from European forest soils
Authors: Ambus P. , Zechmeister-Boltenstern S. , Butterbach-Bahl K.
Published: April 2010

Abstract. Forest ecosystems may provide strong sources of nitrous oxide (N2O), which is important for atmospheric chemical and radiative properties. Nonetheless, our understanding of controls on forest N2O emissions is insufficient to narrow current flux estimates, which still are associated with great uncertainties. In this study, we have investigated the quantitative and qualitative relationships between N-cycling and N2O production in European forests in order to evaluate the importance of nitrification and denitrification for N2O production. Soil samples were collected in 11 different sites characterized by variable climatic regimes and forest types. Soil N-cycling and associated production of N2O was assessed following application of 15N-labeled nitrogen. The N2O emission varied significantly among the different forest soils, and was inversely correlated to the soil C:N ratio. The N2O emissions were significantly higher from the deciduous soils (13 ng N2O-N cm-3 d-1) than from the coniferous soils (4 ng N2O-N cm-3 d-1). Nitrate (NO3-) was the dominant substrate for N2O with an average contribution of 62% and exceeding 50% at least once for all sites. The average contribution of ammonium (NH4+) to N2O averaged 34%. The N2O emissions were correlated with gross nitrification activities, and as for N2O, gross nitrification was also higher in deciduous soils (3.4 µg N cm-3 d-1) than in coniferous soils (1.1 µg N cm-3 d-1). The ratio between N2O production and gross nitrification averaged 0.67% (deciduous) and 0.44% (coniferous). Our study suggests that changes in forest composition in response to land use activities and global change may have implications for regional budgets of greenhouse gases. From the study it also became clear that N2O emissions were driven by the nitrification activity, although the N2O was produced per se mainly from denitrification. Increased nitrification in response to accelerated N inputs predicted for forest ecosystems in Europe may thus lead to increased greenhouse gas emissions from forest ecosystems.
Towards an unbiased estimate of fluctuations in reef abundance and volume during the Phanerozoic
Authors: Kiessling W.
Published: April 2010

Abstract. The globally preserved number and volume of ancient biogenic reefs is strongly biased by two factors: geological history and research intensity. These biases are sufficiently strong to cast doubts on the biological meaning of the recorded raw pattern. Without adjustment, it is hard to reliably identify factors potentially controlling the waxing and waning of this important ecosystem through time. Although it is currently impossible to completely compensate for the biases, I demonstrate here, based on a comprehensive database of ancient reefs, that spatiotemporal heterogeneities of the biases can largely be evened out by: (1) omitting oceanic reef sites and reef sites only known from subsurface exploration; (2) standardizing for economic factors known to affect research intensity; and (3) adjusting for sedimentary cycling processes. The resulting curves of fossil reef abundance and volume appear quite different from the original ones but the patterns of waxing and waning of the time series are not significantly altered and the overall volatility is not reduced. This suggests that both the raw curves and the adjusted curves correctly depict the basic timing of major reef blooms and declines. Nevertheless, the general pattern of the new curves (maximum proliferation in the middle Paleozoic, decline thereafter) is more in line with patterns of global cratonic carbonate sedimentation than the original curves. The adjusted curves should thus be preferred over the original ones for future tests of potential extrinsic controls of Phanerozoic reef development.
Bacterial carbon sources in coastal sediments: a cross-system analysis based on stable isotope data of biomarkers
Authors: Bouillon S. , Boschker H. T. S.
Published: April 2010

Abstract. Coastal ecosystems are typically highly productive, and the sediments in these systems receive organic matter from a variety of local and imported sources. To assess if general patterns are present in the origin of carbon sources for sedimentary bacteria and their relation to the origin of the sediment organic carbon pool, we compiled both literature and new data on δ13C of bacterial biomarkers (the phospholipid derived fatty acids i+a15:0), along with δ13C data on sediment organic carbon (δ13CTOC) and macrophyte biomass from a variety of typical near-coastal systems. These systems included mangroves, salt marshes (both C3 and C4-dominated sites), seagrass beds, and macroalgae-based systems, as well as unvegetated sediments. First, our δ13Ci+a15:0 data showed large variability over the entire range of δ13CTOC, indicating that in many settings, bacteria may depend on carbon derived from various origins. Secondly, systems where local macrophyte production is the major supplier of organic carbon for in situ decomposition are generally limited to organic carbon-rich, peaty sites (TOC>10 wt%), which are likely to make up only a small part of the global area of vegetated coastal systems. These carbon-rich sediments also provided a field based estimate of isotopic fractionation between bacterial carbon sources and biomarkers (-3.7±2.1), which is similar to the expected value of about -3 associated with the biosynthesis of fatty acids. Thirdly, only in systems with low TOC (below ~1 wt%), we consistently found that bacteria were selectively utilizing an isotopically enriched carbon source, which may be root exudates but more likely is derived from microphytobenthos. In other systems with between ~1 and 10 wt% TOC, bacteria appear to show on average little selectivity and δ13Ci+a15:0 data generally follow the δ13CTOC, even in systems where the TOC is a mixture of algal and macrophyte sources that generally are believed to have a very different degradability.
Global prediction of planktic foraminiferal fluxes from hydrographic and productivity data
Authors: Žarić S. , Schulz M. , Mulitza S.
Published: April 2010

Abstract. Understanding and quantifying the seasonal and spatial distribution of planktic foraminiferal fluxes reflected in sedimentary assemblages is key to interpret foraminifera-based proxies in paleoceanography. Towards this goal we present an empirical model to predict foraminiferal fluxes on a global scale. A compilation of planktic foraminiferal flux and export production data from globally distributed sediment traps together with environmental data of sea-surface temperature and mixed-layer depth from online databases is used to calibrate the model that calculates monthly foraminiferal fluxes for the 18 most common species. The calibrated model is then forced with a global data set of hydrographic and productivity data to predict monthly foraminiferal fluxes worldwide. The predictive skills of the model are assessed by comparing the model output with planktic foraminiferal assemblages from globally distributed surface sediments as well as with measured foraminiferal fluxes of sediment traps not included in the calibration data set. Many general distribution patterns of foraminiferal species recognized from the model output compare favorably with observations from coretops or sediment traps, even though the model still produces problematic results in some places. Among others, meridional gradients in species richness and diversity, increased relative abundances of Neogloboquadrina pachyderma (dex.) in upwelling areas, and peak abundances of Globigerinella siphonifera in oligotrophic subtropical gyres show good agreement between model and coretops. Absolute foraminiferal fluxes are significantly underestimated in most cases, while seasonal variations can be reproduced for some species. Interannual differences in foraminiferal fluxes are not reflected by the model which might partly be due to a lack of actual environmental data for the calibration and model experiments. The limited predictive skills of the model suggest that additional parameters should be considered. Export production should probably be replaced by a more realistic representation of food availability for planktic foraminifera. This could be achieved by adding a dynamic component to the model and linking it to an ecosystem model.
Land-surface modelling in hydrological perspective – a review
Authors: Overgaard J. , Rosbjerg D. , Butts M. B.
Published: April 2010

Abstract. The purpose of this paper is to provide a review of the different types of energy-based land-surface models (LSMs) and discuss some of the new possibilities that will arise when energy-based LSMs are combined with distributed hydrological modelling. We choose to focus on energy-based approaches, because in comparison to the traditional potential evapotranspiration models, these approaches allow for a stronger link to remote sensing and atmospheric modelling. New opportunities for evaluation of distributed land-surface models through application of remote sensing are discussed in detail, and the difficulties inherent in various evaluation procedures are presented. Finally, the dynamic coupling of hydrological and atmospheric models is explored, and the perspectives of such efforts are discussed.
The nonenzymatic template-directed ligation of oligonucleotides
Authors: Lutay A. V. , Chernolovskaya E. L. , Zenkova M. A. , Vlassov V. V.
Published: April 2010

Abstract. The nonenzymatic template-directed ligation of oligonucleotides containing 2', 3'-cyclic phosphate was investigated in the presence of divalent cations. Ligation of the oligonucleotides readily occurred in the presence of Mg2+, Mn2+, Co2+, Zn2+, Pb2+. Efficacy of the metal ion catalysts inversely correlated with pKa values of the metal-bound water molecules. The intermolecular transesterification reaction yielded at least 95metal ion. Relatively high reaction yields (up to 15fragmentation to oligonucleotides with 2',3'-cyclic phosphates, followed by reactions of those oligonucleotides could provide a source of new RNA molecules under prebiotic conditions.
The definition of life in the context of its origin
Authors: Zhuravlev Y. N. , Avetisov V. A.
Published: April 2010

Abstract. Current life is a complex, multi-level phenomenon that is so diverse in its manifestations that a short and exhaustive definition of life is hardly possible. The high complexity of life, as well as a poor understanding of what life is in essence, are the obstacles to the elaboration of such a definition. Important characteristics of life, such as whole system-, ecosystem-, and information-defined characteristics, have been included in the definition of life only recently. Ecosystem-defined characteristics have been absent in models of the pre-biotic state for a long time. However, without an ecosystem context, the concept of the emergence of life cannot be complete. Interconnections between living and non-living components of a primordial evolving system are decisive for the period of transition from chemical to biological evolution. Information-defined characteristics of life are often reduced to storage and the expression of genetic information, yet the operation of such perfect processes in prebiotic and transitional systems is unlikely. Genetic information, as defined in terms of the Shannon theory of communication, represents only a certain "informational channel" specified with respect to the expression of the structural genes. However, recent findings concerning the molecular mechanisms of the differential regulation of gene activity, and in the genomics, postgenomics and proteomics control mechanisms, suppose a richer diversity of informational flows in the organism. Moreover, considering life in a more general context, other types of related, informational channels, in particular, regarding the differentiation of higher taxa, hiatus, and expansion processes, should be kept in mind. In many publications devoted to the origin of life, the terms "living", "life", and "living organism" are freely interchanged which proves the vagueness of insights about the different levels of the living system. This report considers some variants of the definition of life that have been recently suggested and are based on present-day knowledge of the structures and functions of life. The contradictory demands of a definition, which needs to be complete and short at the same time, are emphasized. A definition characterizing life as a state, a structure, and a process, is proposed.
Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins
Authors: Dick J. M. , LaRowe D. E. , Helgeson H. C.
Published: April 2010

Abstract. Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from Pyrococcus furiosus and Bacillus subtilis was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive chemical potential constraints on the interactions of microbes with their environment.
The relationship between NH3 emissions from a poultry farm and soil NO and N2O fluxes from a downwind forest
Authors: Skiba U. , Dick J. , Storeton-West R. , Lopez-Fernandez S. , Woods C. , Tang S. , vanDijk N.
Published: April 2010

Abstract. Intensive livestock farms emit large concentrations of NH3, most of which is deposited very close to the source. The presence of trees enhances the deposition. Rates to downwind forests can exceed 40 kg N ha−1 y−1. The steep gradient in large NH3 concentrations of 34.3±20.4, 47.6±24.9, 21.7±16.8 µg NH3 m3 at the edge of a forest 15, 30 and 45 m downwind of the farm to near background concentrations within 270 m downwind (1.15±0.7 µg NH3 m3) provides an ideal site to study the effect of different rates of atmospheric NH3 concentrations and inferred deposition on biological and chemical processes under similar environmental conditions. We have investigated the effect of different NH3 concentrations and implied deposition rates on the flux of NO and N2O from soil in a mixed woodland downwind of a large poultry farm (160 000 birds) in Scotland, which has been operating for about 40 years. Measurements were carried out for a 6 month period, with hourly NO flux measurements, daily N2O fluxes close to the farm and monthly at all sites, and monthly cumulative wet and dry N deposition. The increased NH3 and NH4+ deposition to the woodland increased emissions of NO and N2O and soil available NH4+ and NO3− concentrations. Average NO and N2O fluxes measured 15, 25 and 45 m downwind of the farm were 111.2±41.1, 123.3±40.7, 38.3±28.8 µg NO-N m−2 h−1 and 9.9±7.5, 34.3±33.3 and 21.2±6.1 µg N2O-N m−2 h−1, respectively. At the background site 270 m downwind the N2O flux was reduced to 1.75±2.1 µg N2O-N m−2 h−1. NO emissions were significantly influenced by seasonal and daily changes in soil temperature and followed a diurnal pattern with maximum emissions approximately 3 h after noon. For N2O no consistent diurnal pattern was observed. Changes in soil moisture content had a less clear effect on the NO and N2O flux. In spite of the large NO and N2O emissions accounting for >3% of the N deposited to the woodland downwind of the farm, extrapolation to the entire British poultry flock suggests that these NH3 emissions contribute to less than 0.5% and 0.02%, respectively of the total annual UK NOx and N2O emissions.
Modeling impacts of management alternatives on soil carbon storage of farmland in Northwest China
Authors: Zhang F. , Li C. , Wang Z. , Wu H.
Published: April 2010

Abstract. Long-term losses of soil organic carbon (SOC) have been observed in many agriculture lands in Northwest China, one of the regions with the longest cultivation history in the world. The decline of SOC contents not only impaired the soil fertility but also increased the amount of carbon dioxide (CO2) emitted from terrestrial ecosystems into the atmosphere. However, quantifying the SOC losses at regional scale has long been remaining unsolved. A process-based model, Denitrification-Decomposition or DNDC, was adopted in the study to quantify impacts of farming management practices on SOC dynamics for a selected region, Shaanxi Province. The selected domain, with 3 million hectares of cropland across different climatic and farming management regimes, is representative for the major agricultural areas in Northwest China. The DNDC model was tested against long-term SOC dynamics observed at five agricultural sites in China. The agreement between the observed and modeled results indicate that DNDC was capable of capturing patterns and magnitudes of SOC changes across the climate zones, soil types, and management regimes in China. To quantify SOC dynamics for Shaanxi, we constructed a GIS database to hold all of the DNDC-required input information (e.g., weather, soil properties, crop acreage, and farming practices) for all the farmland in the studied domain. Sensitivity tests indicated the spatial heterogeneity of soil properties, especially initial SOC content, was the major source of uncertainty for the modeled SOC dynamics at regional scale. The Most Sensitive Factor (MSF) method was employed in the study to quantify the uncertainties produced from the upscaling process. The results from the regional simulations for Shaanxi indicated that (1) the overall 3 million hectares of farmland in the province was a source of atmospheric CO2 with 0.5 Tg C yr−1 lost in 2000 under the current farming management conditions, (2) an increase in the rate of crop residue incorporation from 15% to 50% or 90% converted the farmland from the C source to a C sink with 0.7 or 2.1 Tg C yr−1 sequestered, respectively, and (3) applying farmyard manure at a rate of 500 kg C ha−1 also converted the cropland into a weak C sink with 0.2 Tg C sequestered in the farmland in Shaanxi. In the studied domain, crop residue and farmyard manure used to be the major sources of soil nutrients during the centuries-long cultivation history but were gradually abandoned since 1950s when synthetic fertilizers became available. The results from this modeling study suggest that recovery of the traditional farming practices (i.e., residue incorporation and manure amendment) be a feasible approach to substantially improve the soil C status in the farmland of Shaanxi. The values of C gain or loss from this study for Shaanxi could vary if the modeled domain shifts to other provinces in Northwest China although the general conclusion may remain.
The importance of diazotrophic cyanobacteria as primary producers during Cretaceous Oceanic Anoxic Event 2
Authors: Ohkouchi N. , Kashiyama Y. , Kuroda J. , Ogawa N O. , Kitazato H.
Published: April 2010

Abstract. In Livello Bonarelli black shale deposited during Cretaceous Oceanic Anoxic Event 2 (OAE-2, ca. 94 Ma), nitrogen isotopic compositions of bulk sediments are mostly in a narrow range from –2.7 to –0.7‰. We also determined molecular distribution and nitrogen isotopic compositions of geoporphyrins extracted from the black shale. The nitrogen isotopic compositions of C32 Ni deoxophylloerythroetioporphyrin (DPEP) and total Ni porphyrins are –3.5 and –3.3‰, respectively, leading us to the estimation that the mean nitrogen isotopic composition of photoautotrophic cells were around +1‰ during the formation of Bonarelli black shale. This value is suggestive of N2-fixation, a dominant process for these photoautotrophs when assimilating nitrogen. Furthermore, Ni-chelated C32 DPEP, derived mainly from chlorophyll a had the highest concentration. Based on this evidence, we conclude that diazotrophic cyanobacteria were major primary producers during that time. Cyanobacteria may be key photoautotrophs during the formation of black shale type sediments intermittently observed throughout the later half of the Earth's history, and hence may have played a crucial role in the evolution of geochemical cycles even in the later half of the Earth's history.
Halogens in pore water of peat bogs – the role of peat decomposition and dissolved organic matter
Authors: Biester H. , Selimović D. , Hemmerich S. , Petri M.
Published: April 2010

Abstract. Halogens are strongly enriched in peat and peatlands and such they are one of their largest active terrestrial reservoir. The enrichment of halogens in peat is mainly attributed to the formation of organohalogens and climatically controlled humification processes. However, little is known about release of halogens from the peat substrate and the distribution of halogens in the peat pore water. In this study we have investigated the distribution of chlorine, bromine and iodine in pore water of three pristine peat bogs located in the Magellanic Moorlands, southern Chile. Peat pore waters were collected using a sipping technique, which allows in situ sampling down to a depth greater than 6m. Halogens and halogen species in pore water were determined by ion-chromatography (IC) (chlorine) and IC-ICP-MS (bromine and iodine). Results show that halogen concentrations in pore water are 15–30 times higher than in rainwater. Mean concentrations of chlorine, bromine and iodine in pore water were 7–15 mg l−1, 56–123 μg l−1, and 10–20 μg l−1, which correspond to mean proportions of 10–15%, 1–2.3% and 0.5–2.2% of total concentrations in peat, respectively. Organobromine and organoiodine were the predominant species in pore waters, whereas chlorine in pore water was mostly chloride. Advection and diffusion of halogens were found to be generally low and halogen concentrations appear to reflect release from the peat substrate. Release of bromine and iodine from peat depend on the degree of peat degradation, whereas this relationship is weak for chlorine. Relatively higher release of bromine and iodine was observed in less degraded peat sections, where the release of dissolved organic carbon (DOC) was also the most intensive. It has been concluded that the release of halogenated dissolved organic matter (DOM) is the predominant mechanism of iodine and bromine release from peat.
Multi-nutrient, multi-group model of present and future oceanic phytoplankton communities
Authors: Litchman E. , Klausmeier C. A. , Miller J. R. , Schofield O. M. , Falkowski P. G.
Published: April 2010

Abstract. Phytoplankton community composition profoundly affects patterns of nutrient cycling and the dynamics of marine food webs; therefore predicting present and future phytoplankton community structure is crucial to understand how ocean ecosystems respond to physical forcing and nutrient limitations. We develop a mechanistic model of phytoplankton communities that includes multiple taxonomic groups (diatoms, coccolithophores and prasinophytes), nutrients (nitrate, ammonium, phosphate, silicate and iron), light, and a generalist zooplankton grazer. Each taxonomic group was parameterized based on an extensive literature survey. We test the model at two contrasting sites in the modern ocean, the North Atlantic (North Atlantic Bloom Experiment, NABE) and subarctic North Pacific (ocean station Papa, OSP). The model successfully predicts general patterns of community composition and succession at both sites: In the North Atlantic, the model predicts a spring diatom bloom, followed by coccolithophore and prasinophyte blooms later in the season. In the North Pacific, the model reproduces the low chlorophyll community dominated by prasinophytes and coccolithophores, with low total biomass variability and high nutrient concentrations throughout the year. Sensitivity analysis revealed that the identity of the most sensitive parameters and the range of acceptable parameters differed between the two sites. We then use the model to predict community reorganization under different global change scenarios: a later onset and extended duration of stratification, with shallower mixed layer depths due to increased greenhouse gas concentrations; increase in deep water nitrogen; decrease in deep water phosphorus and increase or decrease in iron concentration. To estimate uncertainty in our predictions, we used a Monte Carlo sampling of the parameter space where future scenarios were run using parameter combinations that produced acceptable modern day outcomes and the robustness of the predictions was determined. Change in the onset and duration of stratification altered the timing and the magnitude of the spring diatom bloom in the North Atlantic and increased total phytoplankton and zooplankton biomass in the North Pacific. Changes in nutrient concentrations in some cases changed dominance patterns of major groups, as well as total chlorophyll and zooplankton biomass. Based on these scenarios, our model suggests that global environmental change will inevitably alter phytoplankton community structure and potentially impact global biogeochemical cycles.
Is resistant soil organic matter more sensitive to temperature than the labile organic matter?
Authors: Fang C. , Smith P. , Smith J. U.
Published: April 2010

Abstract. A recent paper by Knorr et al. (2005a) suggested that the decomposition of resistant soil organic matter is more temperature sensitive than labile organic matter. In Knorr et al.'s (2005a) model, the reference decay rate was presumed to be same for all pools of soil carbon. We refit Knorr et al.'s (2005a) model but allow both the activation energy and the reference decay rate to vary among soil C pools. Under these conditions, a similar fit to measured data can be obtained without invoking the assumption that the resistant C pool is more temperature sensitive than the labile pool. Other published evidence does not unequivocally support Knorr et al.'s (2005a) hypothesis of increased temperature sensitivity of resistant pools of soil carbon. Because of the lack of experimental data, Knorr et al.'s (2005a) conclusion that the decomposition of the resistant SOM is more temperature sensitive than the labile pool is premature.
Atmospheric CO2 modeling at the regional scale: an intercomparison of 5 meso-scale atmospheric models
Authors: Sarrat C. , Noilhan J. , Dolman A. J. , Gerbig C. , Ahmadov R. , Tolk L. F. , Meesters A. G. C. A. , Hutjes R. W. A. , Ter Maat H. W. , Pérez-Landa G. , Donier S.
Published: April 2010

Abstract. Atmospheric CO2 modeling in interaction with the surface fluxes, at the regional scale is developed within the frame of the European project CarboEurope-IP and its Regional Experiment component. In this context, five meso-scale meteorological models at 2 km resolution participate in an intercomparison exercise. Using a common experimental protocol that imposes a large number of rules, two days of the CarboEurope Regional Experiment Strategy (CERES) campaign are simulated. A systematic evaluation of the models is done in confrontation with the observations, using statistical tools and direct comparisons. Thus, temperature and relative humidity at 2 m, wind direction, surface energy and CO2 fluxes, vertical profiles of potential temperature as well as in-situ CO2 concentrations comparisons between observations and simulations are examined. These comparisons reveal a cold bias in the simulated temperature at 2 m, the latent heat flux is often underestimated. Nevertheless, the CO2 concentrations heterogeneities are well captured by most of the models. This intercomparison exercise shows also the models ability to represent the meteorology and carbon cycling at the synoptic and regional scale in the boundary layer, but also points out some of the major shortcomings of the models.
Fluorescent pseudomonads isolated from Hebridean cloud and rain water produce biosurfactants but do not cause ice nucleation
Authors: Ahern H. E. , Walsh K. A. , Hill T. C. J. , Moffett B. F.
Published: April 2010

Abstract. Microorganisms were discovered in clouds over 100 years ago but information on bacterial community structure and function is limited. Clouds may not only be a niche within which bacteria could thrive but they might also influence dynamic processes using ice nucleating and cloud condensing abilities. Cloud and rain samples were collected from two mountains in the Outer Hebrides, NW Scotland, UK. Community composition was determined using a combination of amplified 16S ribosomal DNA restriction analysis and sequencing. 256 clones yielded 100 operational taxonomic units (OTUs) of which half were related to bacteria from terrestrial psychrophilic environments. Cloud samples were dominated by a mixture of fluorescent Pseudomonas spp., some of which have been reported to be ice nucleators. It was therefore possible that these bacteria were using the ice nucleation (IN) gene to trigger the Bergeron-Findeisen process of raindrop formation as a mechanism for dispersal. In this study the IN gene was not detected in any of the isolates using both polymerase chain reaction (PCR) and differential scanning calorimetry (DSC). Instead 55% of the total isolates from both cloud and rain samples displayed significant biosurfactant activity when analyzed using the drop-collapse technique. All isolates were characterised as fluorescent pseudomonads. Surfactants have been found to be very important in lowering atmospheric critical supersaturations required for the activation of aerosols into cloud condensation nuclei (CCN). It is also known that surfactants influence cloud droplet size and increase cloud lifetime and albedo. Some bacteria are known to act as CCN and so it is conceivable that these fluorescent pseudomonads are using surfactants to facilitate their activation from aerosols into CCN. This would allow water scavenging,~countering desiccation, and assist in their widespread dispersal.
Topography induced spatial variations in diurnal cycles of assimilation and latent heat of Mediterranean forest
Authors: van der Tol C. , Dolman A. J. , Waterloo M. J. , Raspor K.
Published: April 2010

Abstract. The aim of this study is to explain topography induced spatial variations in the diurnal cycles of assimilation and latent heat of Mediterranean forest. Spatial variations of the fluxes are caused by variations in weather conditions and in vegetation characteristics. Weather conditions reflect short-term effects of climate, whereas vegetation characteristics, through adaptation and acclimation, long-term effects of climate. In this study measurements of plant physiology and weather conditions are used to explain observed differences in the fluxes. A model is used to study which part of the differences in the fluxes is caused by weather conditions and which part by vegetation characteristics. Data were collected at four experimental sub-Mediterranean deciduous forest plots in a heterogeneous terrain with contrasting aspect, soil water availability, humidity and temperature. We used a sun-shade model to scale fluxes from leaf to canopy, and calculated the canopy energy balance. Parameter values were derived from measurements of light interception, leaf chamber photosynthesis, leaf nitrogen content and 13C isotope discrimination in leaf material. Leaf nitrogen content is a measure of photosynthetic capacity, and 13C isotope discrimination of water use efficiency. For validation, sap-flux based measurements of transpiration were used. The model predicted diurnal cycles of transpiration and stomatal conductance, both their magnitudes and differences in afternoon stomatal closure between slopes of different aspect within the confidence interval of the validation data. Weather conditions mainly responsible for the shape of the diurnal cycles, and vegetation parameters for the magnitude of the fluxes. Although the data do not allow for a quantification of the two effects, the differences in vegetation parameters and weather among the plots and the sensitivity of the fluxes to them suggest that the diurnal cycles were more strongly affected by spatial variations in vegetation parameters than by meteorological variables. This indicates that topography induced variations in vegetation parameters are of equal importance to the fluxes as topography induced variations in radiation, humidity and temperature.
Sources and transport of dissolved iron and manganese along the continental margin of the Bay of Biscay
Authors: Laës A. , Blain S. , Laan P. , Ussher S. J. , Achterberg E. P. , Tréguer P. , de Baar H. J. W.
Published: April 2010

Abstract. Dissolved iron (DFe; <0.2 µm) and dissolved manganese (DMn; <0.2 µm) concentrations were determined in the water column of the Bay of Biscay (eastern North Atlantic Ocean) in March 2002. The samples were collected along a transect traversing from the European continental shelf over the continental slope. The highest DFe and DMn concentrations (2.39 nM and 6.10 nM, respectively) were observed in the bottom waters on the shelf at stations closest to the coast. The release of trace metal from resuspended particles and the diffusion from pore waters were probably at the origin of elevated DFe and DMn concentrations in the Bottom Boundary Layer (BBL). In the slope region, the highest total dissolvable iron (TDFe), DFe and DMn values (24.6 nM, 1.58 nM and 2.12 nM, respectively) were observed close to the bottom at depth of ca.~600–700 m. Internal wave activity and slope circulation are thought to be at the origin of this phenomenon. These processes were also very likely the cause of elevated concentrations (DFe: 1.27 nM, DMn: 2.34 nM) measured in surface waters of stations located in the same area. At stations off the continental slope, the vertical distribution of both metals were typical of open ocean conditions, indicating that inputs from the continental margin did not impact the metal distributions in the offshore waters.
Manganese content records seasonal upwelling in Lake Tanganyika mussels
Authors: Langlet D. , Alleman L. Y. , Plisnier P.-D. , Hughes H. , André L.
Published: April 2010

Abstract. Biogenic productivity of Lake Tanganyika is highly dependent on seasonal upwellings of cold, oxygen-depleted, nutrient-rich deep waters. We investigated the shell of freshwater bivalve Pleiodon spekii as a geochemical archive of these periodic hydrological changes tuned by the monsoon regime. The results of a three-year-long limnological and geochemical survey of the coastal waters performed on the dissolved and particulate fractions were compared to LA-ICP-MS profiles of Mn in five aragonitic shells from the same lake location. Three shells present very similar Mn/Ca profiles dominated by a peak that matched the concomitant increase of Mn and chlorophyll a in surface waters during the 2002 upwelling, while a shell collected during 2003 dry season detect both 2002 and 2003 upwelling events. Larger shells showing an extremely reduced growth display more than 8 Mn/Ca peaks suggesting at least an 8-year-record of seasonal changes in water composition. We postulate that Mn/Ca in shells record the conjunction of an increase of biological activity with supplied of dissolved Mn and nutriments in coastal waters, resulting in an enhanced assimilation of biogenic Mn-rich particles. By combining the most recent generation of laser ablation system and the powerful High Resolution ICP-MS, the spatial resolution could be improved down to 5 to 10 µm crater size and end up in a better constrain of the relative variations of the annual Mn peaks. Such an approach on P. spekii from Lake Tanganyika has definitively a great potential to provide recent and past records on primary productivity associated with the monsoon climate system.
Structure of mass and momentum fields over a model aggregation of benthic filter feeders
Authors: Crimaldi J. P. , Koseff J. R. , Monismith S. G.
Published: April 2010

Abstract. The structure of momentum and concentration boundary layers developing over a bed of Potamocorbula amurensis clam mimics was studied. Laser Doppler velocimetry (LDV) and laser-induced fluorescence (LIF) probes were used to quantify velocity and concentration profiles in a laboratory flume containing 3969 model clams. Model clams incorporated passive roughness, active siphon pumping, and the ability to filter a phytoplankton surrogate from the flow. Measurements were made for two crossflow velocities, four clam pumping rates, and two siphon heights. Simultaneous use of LDV and LIF probes permited direct calculation of scalar flux of phytoplankton to the bed. Results show that clam pumping rates have a pronounced effect on a wide range of turbulent quantities in the boundary layer. In particular, the vertical turbulent flux of scalar mass to the bed was approximately proportional to the rate of clam pumping.
A model for the benthic-pelagic coupling of silica in estuarine ecosystems: sensitivity analysis and system scale simulation
Authors: Arndt S. , Regnier P.
Published: April 2010

Abstract. A transient, vertically resolved, analytical model for the early diagenesis of silica has been developed to quantify the importance of benthic-pelagic coupling in estuarine biogeochemical silica cycling. A sensitivity analysis based on Monte-Carlo simulations is carried out to assess the intensity and timing of benthic diffusive fluxes in response to a pelagic diatom bloom. The diffusive flux dynamics are analyzed over a realistic range of dissolution rate constants (max kSi ε [6×10−3–3.6×10−1 d−1]), diffusion coefficients of dissolved silica (DSi ε [35×10−6–35×10−5 m2 d−1]) and duration of dissolved silica depletion in the water column (wPDSI ε [1–3 month]). Results show that the diffusive silica flux responds with a time delay of 20 to 120 days to the biogenic silica deposition pulse. For high max kSi, simulated time lags are shortest and completely determined by the dissolution kinetics. However, decreasing max kSi leads to a slower benthic flux response. In addition, the variability increases due to the increasing importance of transport processes. The sensitivity study also allows us to constrain the uncertainties of a system-scale simulation, where a large number of benthic compartments (>50 000) are coupled to a high-resolution (100×100 m) pelagic model of a macrotidal river and estuary (Western Scheldt, B/NL). The model is applied to a diatom bloom event recorded in 2003, characterized by pelagic silica depletion in August. Benthic processes are mainly modulated by the combined influence of local hydrodynamic conditions and pelagic primary production dynamics, and show therefore a high degree of spatial heterogeneity over short distances. Spatially integrated deposition fluxes and dissolution rates of biogenic silica are high throughout the growth period, with maxima of 1.3×105 mol d−1 (=8.0 mmol m2 d−1) and 7.8×104 mol d−1 (=4.8 mmol m2 d−1) in mid-August. The spatially integrated diffusive flux reaches a maximum of 1.5×104 mol d−1 at the end of a pelagic silica depletion period in September. However, the total amount of dissolved silica released from the estuarine sediments between June and December 2003 is small (2×106 mol) compared to the much higher riverine influx of dissolved silica (5.9×107 mol) and plays a minor role in the pelagic primary production dynamics.