bluuebunny/crossref_metadata_2025 huggingface dataset:
The nonenzymatic template-directed ligation of oligonucleotides
Authors: Lutay A.V. , Chernolovskaya E. L. , Zenkova M. A. , Vlasso 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 95% of 2',5'-phosphodiester bonds independently on the nature of the metal ion. Relatively high reaction yields (up to 15%) suggest, that RNA fragmentation to oligonucleotides with 2',3'-cyclic phosphates, followed by reactions of those oligonucleotides could provide a source of new RNA molecules under prebiotic conditions.
Constraints on oceanic N balance/imbalance from sedimentary 15N records
Authors: Altabet M. A.
Published: April 2010

Abstract. According to current best estimates, the modern ocean's N cycle is in severe deficit. N isotope budgeting provides an independent geochemical constraint in this regard as well as the only means for past reconstruction. Overall, it is the relative proportion of N2 fixation consumed by water column denitrification that sets average oceanic δ15N under steady-state conditions. Several factors (conversion of organic N to N2, Rayleigh closed and open system effects) likely reduce the effective fractionation factor (ε) for water column denitrification to about half the inherent microbial value for εden. If so, the average oceanic δ15N of ~5 is consistent with a canonical contribution from water column denitrification of 50% of the source flux from N2 fixation. If an imbalance in oceanic N sources and sinks changes this proportion then a transient in average oceanic δ15N would occur. Using a simple model, changing water column denitrification ±30% or N2 fixation by ±15% produces detectable (>1) changes in average oceanic δ15N over one residence time period or more with corresponding changes in oceanic N inventory. Changing sedimentary denitrification produces no change in δ15N but does change N inventory. Sediment δ15N records from sites thought to be sensitive to oceanic average δ15N all show no detectible change over the last 3 kyr or so implying a balanced marine N budget over the latest Holocene. A mismatch in time scales is the most likely meaningful interpretation of the apparent conflict with modern flux estimates. Decadal to centennial scale oscillations between net N deficit and net surplus may occur but on the N residence timescale of several thousand years, net balance is achieved in sum. However, sediment δ15N records from the literature covering the period since the last glacial maximum show excursions of up to several that are consistent with sustained N deficit during the deglaciation followed by readjustment and establishment of balance in the early Holocene. Since imbalance was sustained for one N residence time period or longer, excursions in ocean N inventory of 10 to 30% likely occurred. The climatic and oceanographic changes that occurred over this period evidently overcame, for a time, the capacity of ocean biogeochemistry to maintain N balance.
An oceanic fixed nitrogen sink exceeding 400 Tg N a−1 vs the concept of homeostasis in the fixed-nitrogen inventory
Authors: Codispoti L. A.
Published: April 2010

Abstract. Measurements of the N2 produced by denitrification, a better understanding of non-canonical pathways for N2 production such as the anammox reaction, better appreciation of the multiple environments in which denitrification can occur (e.g. brine pockets in ice), etc. suggest that it is unlikely that the oceanic denitrification rate is less than 400 Tg N a−1. The total oceanic sink for fixed-N is, therefore, more than 400 Tg N a−1. Because this sink term far exceeds present estimates for nitrogen fixation, the main source for oceanic fixed-N, there is a large apparent deficit (~200 Tg N a−1) in the oceanic fixed-N budget. The size of the deficit appears to conflict with apparent constraints of the atmospheric carbon dioxide and sedimentary δ15N records that suggest homeostasis during the Holocene. In addition, the oceanic nitrate/phosphate ratio tends to be close to the canonical Redfield biological uptake ratio of 16 (by N and P atoms) which can be interpreted to indicate the existence of a powerful feed-back mechanism that forces the system towards a balance. The main point of this paper is that one cannot solve this conundrum by reducing the oceanic sink term without violating an avalanche of recent data. A solution to this problem may be as simple as an upwards revision of the oceanic nitrogen fixation rate, and it is noted that most direct estimates for this term have concentrated on nitrogen fixation by autotrophs in the photic zone, even though the gene for nitrogen fixation is widespread amongst heterotrophs. Another simple explanation may be that we are simply no longer in the Holocene and one might expect to see temporary imbalances in the oceanic fixed-N budget as we transition from the Holocene to the Anthropocene in line with an apparent denitrification maximum during the Glacial-Holocene transition. Other possible full or partial explanations involve plausible changes in the oceanic nitrate/phosphate and N/C ratios, an oceanic phosphorus budget that may also be in deficit, and oscillations in the source and sink terms that are short enough to be averaged out in the atmospheric and geologic records.
CO2−3 concentration and pCO2 thresholds for calcification and dissolution on the Molokai reef flat, Hawaii
Authors: K. K. Yates  , R. B. Halley
Published: April 2010

Abstract. The severity of the impact of elevated atmospheric pCO2 to coral reef ecosystems depends, in part, on how seawater pCO2 affects the balance between calcification and dissolution of carbonate sediments. Presently, there are insufficient published data that relate concentrations of pCO2 and CO32− to in situ rates of reef calcification in natural settings to accurately predict the impact of elevated atmospheric pCO2 on calcification and dissolution processes. Rates of net calcification and dissolution, CO32− concentrations, and pCO2 were measured, in situ, on patch reefs, bare sand, and coral rubble on the Molokai reef flat in Hawaii. Rates of calcification ranged from 0.003 to 0.23 g CaCO3 m−2 h−1 and dissolution ranged from −0.005 to −0.33 g CaCO3 m−2 h−1. Calcification and dissolution varied diurnally with net calcification primarily occurring during the day and net dissolution occurring at night. These data were used to calculate threshold values for pCO2 and CO32− at which rates of calcification and dissolution are equivalent. Results indicate that calcification and dissolution are linearly correlated with both CO32− and pCO2. Threshold pCO2 and CO32− values for individual substrate types showed considerable variation. The average pCO2 threshold value for all substrate types was 654±195 µatm and ranged from 467 to 1003 µatm. The average CO3−- threshold value was 152±24 µmol kg-1, ranging from 113 to 184 µmol kg−1. Ambient seawater measurements of pCO2 and CO32− indicate that CO32− and pCO2 threshold values for all substrate types were both exceeded, simultaneously, 13% of the time at present day atmospheric pCO2 concentrations. It is predicted that atmospheric pCO2 will exceed the average pCO2 threshold value for calcification and dissolution on the Molokai reef flat by the year 2100.
Marine geochemical data assimilation in an efficient Earth System Model of global biogeochemical cycling
Authors: Ridgwell A. , Hargreaves J. C. , Edwards N. R. , Annan J. D. , Lenton T. M. , Marsh R. , Yool A. , Watson A.
Published: April 2010

Abstract. We have extended the 3-D ocean based "Grid ENabled Integrated Earth system model'' (GENIE-1) to help understand the role of ocean biogeochemistry and marine sediments in the "long-term'' (~100 to 100 000 year) regulation of atmospheric CO2, and the importance of feedbacks between CO2 and climate. Here we describe the ocean carbon cycle, which is based around a simple single nutrient (phosphate) control on biological productivity. The addition of ocean-sediment interactions is presented elsewhere (Ridgwell and Hargreaves, 2006). We have calibrated the model parameters controlling ocean carbon cycling in GENIE-1 by assimilating 3-D observational datasets of phosphate and alkalinity using an ensemble Kalman filter method. The calibrated (mean) model predicts a global export production of particulate organic carbon (POC) of 8.9 PgC yr−1, and reproduces the main features of dissolved oxygen distributions in the ocean. For estimating biogenic calcium carbonate (CaCO3 production, we have devised a parameterization in which the CaCO3:POC export ratio is related directly to ambient saturation state. Calibrated global CaCO3 export production (1.2 PgC yr−1 is close to recent marine carbonate budget estimates. The GENIE-1 Earth system model is capable of simulating a wide variety of dissolved and isotopic species of relevance to the study of modern global biogeochemical cycles as well as past global environmental changes recorded in paleoceanographic proxies. Importantly, even with 12 active biogeochemical tracers in the ocean and including the calculation of feedbacks between atmospheric CO2 and climate, we achieve better than 1000 years per (2.4 GHz) CPU hour on a desktop PC. The GENIE-1 model thus provides a viable alternative to box and zonally-averaged models for studying global biogeochemical cycling over all but the very longest (>1 000 000 years) time-scales.
Ice-nucleation negative fluorescent pseudomonads isolated from Hebridean cloud and rain water produce biosurfactants
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 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 variations in the 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 slopes and aspect, soil water availability, humidity and temperature. We used a two leaf layer 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 accurately predicted diurnal cycles of transpiration and stomatal conductance, both their magnitudes and differences in afternoon stomatal closure between slopes of different aspect. 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 at least equal importance to the fluxes as topography induced variations in radiation, humidity and temperature. Weather conditions mainly affect the shape of the diurnal cycles, and vegetation parameters the magnitude of the fluxes.
Dissolution of calcium carbonate: observations and model results in the North Atlantic
Authors: Friis K. , Najjar R. G. , Follows M. J. , Dutkiewicz S. , Körtzinger A. , Johnson K. M.
Published: April 2010

Abstract. We investigate the significance of in situ dissolution of calcium carbonate above its saturation horizons. The study relies on observations from the open subpolar North Atlantic [sNA] and on a 3-D biogeochemical model. The sNA is particularly well suited for observation-based detections of in situ, i.e. shallow depth CaCO3 dissolution [SDCCD] as it is a region of high CaCO3 production, deep CaCO3 saturation horizons, and precisely-defined pre-formed alkalinity. Based on the analysis of a comprehensive alkalinity data set we find that SDCCD does not appear to be a significant process in the open sNA. The results from the model support the observational findings and do not indicate a significant need of SDCCD to explain observed patterns of alkalinity in the North Atlantic. Instead our investigation points to the importance of mixing processes for the redistribution of alkalinity from dissolution of CaCO3 from below its saturation horizons. However, mixing has recently been neglected for a number of studies that called for SDCCD in the sNA and on global scale.
Photochemical production of ammonium in the oligotrophic Cyprus Gyre (Eastern Mediterranean)
Authors: Kitidis V. , Uher G. , Upstill-Goddard R. C. , Mantoura R. F. C. , Spyres G. , Woodward E. M. S.
Published: April 2010

Abstract. We investigated the photoproduction of ammonium (NH4+) in surface waters of the Cyprus gyre in the central Eastern Mediterranean in May 2002, in 8 on deck irradiations with freshly collected, filtered samples. NH4+ photoproduction (photoammonification) increased with time-integrated irradiance during the course of irradiations. Photoammonification rates around local noon were 0.4–2.9 nmol L−1 h−1. Normalised to time integrated irradiance, these rates were 0.9–3.8 pmol L−1 h−1/(W m−2) and were significantly correlated with Chromophoric Dissolved Organic Matter (CDOM) absorbance at 300 nm normalised to Dissolved Organic Carbon (DOC). These results are consistent with the notion that successive CDOM photobleaching in the surface mixed layer results in decreased DOC-normalised light absorbance concurrent with decreased dissolved organic matter reactivity with regard to photochemical NH4+ release. Combining our experimental data with estimates of annual solar irradiance and water column light attenuation yields an annual photoammonification rate for the Cyprus Gyre of 40±17 mmol m−2 a−1, equivalent to ~12±5% of the previously estimated annual nitrogen requirement of new production in this region. Based on this analysis, NH4+ photoproduction makes a small, but significant contribution to the nitrogen budget of the euphotic zone in the oligotrophic Cyprus Gyre.
Reconciling surface ocean productivity, export fluxes and sediment composition in a global biogeochemical ocean model
Authors: Gehlen M. , Bopp L. , Emprin N. , Aumont O. , Heinze C. , Ragueneau O.
Published: April 2010

Abstract. This study focuses on an improved representation of the biological soft tissue pump in the global three-dimensional biogeochemical ocean model PISCES. We compare three parameterizations of particle dynamics: (1) the model standard version including two particle size classes, aggregation-disaggregation and prescribed sinking speed; (2) an aggregation-disaggregation model with a particle size spectrum and prognostic sinking speed; (3) a mineral ballast parameterization with no size classes, but prognostic sinking speed. In addition, the model includes a description of surface sediments and organic carbon early diagenesis. The integrated representation of material fluxes from the productive surface ocean down to the sediment-water interface allows taking advantage of surface ocean observations, sediment trap data and exchange fluxes at the sediment-water interface. The capability of the model to reproduce yearly averaged particulate organic carbon fluxes and benthic oxygen demand does at first order not dependent on the resolution of the particle size spectrum. Model results obtained with the standard version and with the one including a particle size spectrum and prognostic sinking speed are not significantly different. Both model versions overestimate particulate organic carbon between 1000 and 2000 m, while deep fluxes are of the correct order of magnitude. Predicted benthic oxygen fluxes correspond with respect to their large scale distribution and magnitude to data based estimates. Modeled particulate organic C fluxes across the mesopelagos are most sensitive to the intensity of zooplankton flux feeding. An increase of the intensity of flux feeding in the standard version results in lower mid- and deep-water particulate organic carbon fluxes, shifting model results to an underestimation of particulate organic carbon fluxes in the deep. The corresponding benthic oxygen fluxes are too low. The model version including the mineral ballast parameterization yields an improved fit between modeled and observed particulate organic carbon fluxes below 2000 m and down to the sediment-water interface. Our results suggest that aggregate formation alone might not be sufficient to drive an intense biological pump. The later is most likely driven by the combined effect of aggregate formation and mineral ballasting.
Nitrogen load and forest type determine the soil emission of nitrogen oxides (NO and N2O)
Authors: Pilegaard K. , Skiba U. , Ambus P. , Beier C. , Brüggemann N. , Butterbach-Bahl K. , Dick J. , Dorsey J. , Duyzer J. , Gallagher M. , Gasche R. , Horvath L. , Kitzler B. , Leip A. , Pihlatie M. K. , Rosenkranz P. , Seufert G. , Vesala T. , Westrate H. , Zechmeister-Boltenstern S.
Published: April 2010

Abstract. Soil emissions of NO and N2O were measured continuously at high frequency for more than one year at 15 European forest sites as part of the EU-funded project NOFRETETE. The locations represent different forest types (coniferous/deciduous) and different nitrogen loads. Geographically they range from Finland in the north to Italy in the south and from Hungary in the east to Scotland in the west. The highest NO emissions were observed from coniferous forests, whereas the lowest NO emissions were observed from deciduous forests. The NO emissions from coniferous forests were highly correlated with N-deposition. The site with the highest average annual emission (82 μg NO-Nm−2 h−1) was a spruce forest in South-Germany (Höglwald) receiving an annual N-deposition of 2.9 gm−2. NO emissions close to the detection limit were observed from a pine forest in Finland where the N-deposition was 0.2 g N m−2 y−1. No significant correlation between N2O emission and N-deposition was found. The highest average annual N2O emission (20 μg N2O-Nm−2 h−1) was found in an oak forest in the Mátra mountains (Hungary) receiving an annual N-deposition of 1.6 gm−2. N2O emission was significantly negatively correlated with the C/N ratio. The difference in N-oxide emissions from soils of coniferous and deciduous forests may partly be explained by differences in N-deposition rates and partly by difference in characteristics of the litter layer and soil. NO was mainly derived from nitrification whereas N2O was mainly derived from denitrification. In general, soil moisture is lower at coniferous sites (at least during spring time) and the litter layer of coniferous forests is thick and well aerated favouring nitrification and thus release of NO. Conversely, the higher rates of denitrification in deciduous forests due to a compact and moist litter layer lead to N2O production and NO consumption in the soil. The two factors soil moisture and soil temperature are often explaining most of the temporal variation within a site. When comparing annual emissions on a regional scale, however, factors such as nitrogen deposition and forest and soil type become much more important.
Increased physical protection of soil carbon in the mineral soil of a poplar plantation after five years of free atmospheric CO2 enrichment (FACE)
Authors: Hoosbeek M. R. , Vos J. M. , Scarascia-Mugnozza G. E.
Published: April 2010

Abstract. Free air CO2 enrichment (FACE) experiments in aggrading forests and plantations have demonstrated significant increases in net primary production (NPP) and C storage in forest vegetation. The extra C uptake may also be stored in forest floor litter and in forest soil. After five years of FACE treatment at the EuroFACE short rotation poplar plantation, the increase of total soil C% was larger under elevated than under ambient CO2. However, the fate of this additional C allocated belowground remains unclear. The stability of soil organic matter is controlled by the chemical structure of the organic matter and the existence of protection offered by the soil matrix and minerals. Fresh litter entering the soil enhances microbial activity which induces the binding of organic matter and soil particles into macro-aggregates. As the enclosed organic matter is decomposed, microbial and decomposition products become associated with mineral particles. This association results in the formation of micro-aggregates (within macro-aggregates) in which organic matter is stabilized and protected. FACE and N-fertilization treatment did not affect the micro- and macro-aggregate weight, C or N fractions obtained by wet sieving. However, Populus euramericana increased the micro- and small macro-aggregates weight and C fractions. The obtained macro-aggregates were broken up in order to isolate recently formed micro-aggregates within macro-aggregates (iM-micro-aggregates). FACE increased the iM-micro-aggregate weight and C fractions. This study reveals that: 1) Species has an effect on the formation of macro-aggregates. The choice of species in a plantation or the effect of global change on species diversity, may therefore affect the stabilization and protection of soil C in aggregates. And 2) Increased atmospheric CO2 concentration increases the stabilization and protection of soil C in micro-aggregates formed within macro-aggregates. This mechanism increases the C sink of forest soils under increasing atmospheric CO2 concentration.
Light availability in the coastal ocean: impact on the distribution of benthic photosynthetic organisms and contribution to primary production
Authors: Gattuso J.-P. , Gentili B. , Duarte C. M. , Kleypas J. A. , Middelburg J. J. , Antoine D.
Published: April 2010

Abstract. One of the major features of the coastal zone is that part of its sea floor receives a significant amount of sunlight and can therefore sustain benthic primary production by seagrasses, macroalgae, microphytobenthos and corals. However, the contribution of benthic communities to the primary production of the global coastal ocean is not known, partly because the surface area where benthic primary production can proceed is poorly quantified. Here, we use a new analysis of satellite (SeaWiFS) data collected between 1998 and 2003 to estimate, for the first time at a nearly global scale, the irradiance reaching the bottom of the coastal ocean. The following cumulative functions provide the percentage of the surface of the coastal zone receiving an irradiance greater than Ez: PaNon-polar=28.80−16.69 log10(Ez)+0.84 log102(Ez)+0.83 log103(Ez) PaArctic=16.01−15.67 log10(Ez)+2.03 log102(Ez)+1.00 log103(Ez) Data on the constraint of light availability on the major benthic primary producers and net primary production are reviewed. Some photosynthetic organisms can grow deeper than the nominal bottom limit of the coastal ocean (200 m). The minimum irradiance required varies from 0.4 to 5.1 mol photons m−2 d−1 depending on the group considered. The daily compensation irradiance of benthic communities ranges from 0.24 to 4.4 mol photons m−2 d−1. Data on benthic irradiance and light requirements are combined to estimate the surface area of the coastal ocean where (1) light does not limit the distribution of primary producers and (2) net community production (NCP, the balance between gross primary production and respiration) is positive. Positive benthic NCP can occur over 37% of the global shelf area. The limitations of this approach, related to the spatial resolution of the satellite data, the parameterization used to convert reflectance data to irradiance, and the relatively limited biological information available, are discussed.
Algal constraints on the Cenozoic history of atmospheric CO2?
Authors: Henderiks J. , Rickaby R. E. M.
Published: April 2010

Abstract. An urgent question for future climate, in light of increased burning of fossil fuels, is the temperature sensitivity of the climate system to atmospheric carbon dioxide (pCO2). To date, no direct proxy for past levels of pCO2 exists beyond the reach of the polar ice core records. We propose a new methodology for placing an upper constraint on pCO2 over the Cenozoic based on the living geological record. Specifically, our premise is that the contrasting calcification tolerance of various extant species of coccolithophore to raised pCO2 reflects an "evolutionary memory" of past atmospheric composition. The different times of first emergence of each morphospecies allows an upper constraint of past pCO2 to be placed on Cenozoic timeslices. Further, our hypothesis has implications for the response of marine calcifiers to ocean acidification. Geologically "ancient" species, which have survived large changes in ocean chemistry, are likely more resilient to predicted acidification.
Observations of dissolved iron concentrations in the World Ocean: implications and constraints for ocean biogeochemical models
Authors: Moore J. K. , Braucher O.
Published: April 2010

Abstract. Analysis of a global compilation of dissolved iron observations provides insights into the controlling processes for iron distributions and some constraints for ocean biogeochemical models. The distribution of dissolved iron is consistent with the conceptual model developed for the scavenging of Th isotopes, whereby particle scavenging is a two-step process of scavenging mainly by colloidal and small particulates followed by aggregation and removal on larger sinking particles. Much of the dissolved iron (<0.4 μm) is present as small colloids (>~0.02 μm) and, thus, likely subject to aggregation and scavenging removal. Only the iron bound to soluble ligands (<~0.02 μm) is likely protected from scavenging removal. This implies distinct scavenging regimes for dissolved iron that appear consistent with the observational data: 1) high scavenging regime – where dissolved iron concentrations exceed the concentrations of strongly binding organic ligands; and 2) moderate scavenging regime – where dissolved iron is bound to both colloidal and soluble ligands. The removal rates for dissolved iron will be a function of biological uptake, number and size distributions of the colloidal and small particulate material, ligand dynamics, and the aggregation processes that lead to removal on larger particles. Inputs from dust deposition and continental sediments are key drivers of dissolved iron distributions. The observations provide several strong constraints for ocean biogeochemical models: 1) similar deep ocean concentrations in the North Atlantic and North Pacific (~0.6–0.8 nM), and much lower deep ocean dissolved iron concentrations in the Southern Ocean (~0.3–0.4 nM); 2) strong depletion of iron in the upper ocean away from the high dust deposition regions, with significant scavenging removal of dissolved iron below the euphotic zone; and 3) a bimodal distribution in surface waters with peaks less than 0.2 nM and between 0.6–0.8 nM. We compare the dissolved iron observations with output from the Biogeochemical Elemental Cycling (BEC) ocean model. The model output was in general agreement with the field data (r=0.76, for depths 103–502 m), but at lower iron concentrations (<0.3 nM) the model is consistently biased high relative to the observations.
Variability of annual CO2 exchange from Dutch Grasslands
Authors: Jacobs C. M. J. , Jacobs A. F. G. , Bosveld F. C. , Hendriks D. M. D. , Hensen A. , Kroon P. S. , Moors E. J. , Nol L. , Schrier-Uijl A. , Veenendaal E. M.
Published: April 2010

Abstract. An intercomparison is made of the Net Ecosystem Exchange of CO2, NEE, for eight Dutch grassland sites; four natural grasslands, two production grasslands and two meteorological stations within a rotational grassland region. At all sites the NEE was determined during at least 10 months per site, using the eddy-covariance (EC) technique, but in different years. The photosynthesis-light response analysis technique is used along with the respiration-temperature response technique to partition NEE among Gross Primary Production (GPP) and Ecosystem Respiration (Re) and to obtain the eco-physiological characteristics of the sites at the field scale. Annual sums of NEE, GPP and Re are then estimated using the fitted response curves with observed radiation and air temperature from a meteorological site in the centre of The Netherlands as drivers. These calculations are carried out for four years (2002–2005). The estimated annual Re for all individual sites is more or less constant per site and the average for all sites amounts to 1390±30 gC m−2 a−1. The narrow uncertainty band (±2%) reflects the small differences in the mean annual air temperature. The mean annual GPP was estimated to be 1325 g C m−2 a−1, and displays a much higher standard deviation, of ±100 gC m−2 a−1 (8%), which reflects the relatively large variation in annual solar radiation. The mean annual NEE amounts to –65±85 gC m−2 a−1, which implies that on average the grasslands act as a source, with a relatively large standard deviation. From two sites, four-year records of CO2 flux were available and analyzed (2002–2005). Using the weather record of 2005 with optimizations from the other years, standard deviation of annual GPP was estimated to be 171–206 gC m−2 a−1 (8–14%), of annual Re 227–247 gC m−2 a−1 (14–16%) and of annual NEE 176–276 gC m−2 a−1. The inter-site standard deviation was higher for GPP and Re, 534 gC m−2 a−1 (37.3%) and 486 gC m−2 a−1 (34.8%), respectively. However, the inter-site standard deviation of NEE was similar to the interannual one, amounting to 207 gC m−2 a−1. Large differences occur due to soil type. The grasslands on organic (peat) soils show a mean net release of CO2 of 220±90 g C m−2 a−1 while the grasslands on mineral (clay and sand) soils show a mean net uptake of CO2 of 90±90 g C m−2 a−1. If a weighing with the fraction of grassland on organic (20%) and mineral soils (80%) is applied, an average NEE of 28±90 g C m−2 a−1 is found, which means that on average the Dutch grasslands behave like a small sink for CO2. The results from the analysis illustrate the need for regionally specific and spatially explicit CO2 emission estimates from grassland.
Variation of phytoplankton absorption coefficients in the northern South China Sea during spring and autumn
Authors: Wu J. , Hong H. , Shang S. , Dai M. , Lee Z.
Published: April 2010

Abstract. We examined the temporal and spatial variabilities of phytoplankton absorption coefficients (αphλ)) and their relationships with physical processes in the northern South China Sea from two cruise surveys during spring (May 2001) and late autumn (November 2002). A large river plume induced by heavy precipitation in May stimulated a phytoplankton bloom on the inner shelf, causing significant changes in the surface water in αph values and B/R ratios (αph(440)/αph(675)). This was consistent with the observed one order of magnitude elevation of chlorophyll α and a shift from a pico/nano dominated phytoplankton community to one dominated by micro-algae. At the seasonal level, enhanced vertical mixing due to strengthened northeast monsoon in November has been observed to result in higher surface αph(675) (0.002–0.006 m−1 higher) and less pronounced subsurface maximum on the outer shelf/slope in November as compared that in May. Measurements of αph and B/R ratios from three transects in November revealed a highest surface αph(675) immediately outside the mouth of the Pearl River Estuary, whereas lower αph(675) and higher B/R ratios were featured in the outer shelf/slope waters, demonstrating the respective influence of the Pearl River plume and the oligotrophic nature of South China Sea water. The difference in spectral shapes of phytoplankton absorption (measured by B/R ratios and bathochromic shifts) on these three transects infers that picoprocaryotes are the major component of the phytoplankton community on the outer shelf/slope rather than on the inner shelf. In addition, a regional tuning of the phytoplankton absorption spectral model (Carder et al., 1999) demonstrated a greater spatial variation than seasonal variation in the lead parameter a0(λ). These results suggest that phytoplankton absorption properties in a coastal region such as the northern South China Sea are complex and region-based parameterization is mandatory in order for remote sensing algorithms.
Carbon balance assessment of a natural steppe of southern Siberia by multiple constraint approach
Authors: Belelli Marchesini L. , Papale D. , Reichstein M. , Vuichard N. , Tchebakova N. , Valentini R.
Published: April 2010

Abstract. Steppe ecosystems represent an interesting case in which the assessment of carbon balance may be performed through a cross validation of the eddy covariance measurements against ecological inventory estimates of carbon exchanges (Ehman, 2002; Curtis, 2002). Indeed, the widespread presence of ideal conditions for the applicability of the eddy covariance technique, as vast and homogeneous grass vegetation cover over flat terrains (Baldocchi, 2003), make steppes a suitable ground to ensure a constrain to flux estimates with independent methodological approaches. We report about the analysis of the carbon cycle of a true steppe ecosystem in southern Siberia during the growing season of 2004 in the framework of the TCOS-Siberia project activities performed by continuous monitoring of CO2 fluxes at ecosystem scale by the eddy covariance method, fortnightly samplings of phytomass, and ingrowth cores extractions for NPP assessment, and weekly measurements of heterotrophic component of soil CO2 effluxes obtained by an experiment of root exclusion. The carbon balance of the monitored natural steppe was, according to micrometeorological measurements, a sink of carbon of 151.7± 30.1 gC m−2, cumulated during the growing season from May to September. This result was in agreement with the independent estimate through ecological inventory which yielded a sink of 150.1 gC m−2 although this method was characterized by a large uncertainty (±130%) considering the 95% confidence interval of the estimate. Uncertainties in belowground process estimates account for a large part of the error. Thus, in particular efforts to better quantify the dynamics of root biomass (growth and turnover) have to be undertaken in order to reduce the uncertainties in the assessment of NPP. This assessment should be preferably based on the application of multiple methods, each one characterized by its own merits and flaws.
CO2 flux determination by closed-chamber methods can be seriously biased by inappropriate application of linear regression
Authors: Kutzbach L. , Schneider J. , Sachs T. , Giebels M. , Nykänen H. , Shurpali N. J. , Martikainen P. J. , Alm J. , Wilmking M.
Published: April 2010

Abstract. Closed (non-steady state) chambers are widely used for quantifying carbon dioxide (CO2) fluxes between soils or low-stature canopies and the atmosphere. It is well recognised that covering a soil or vegetation by a closed chamber inherently disturbs the natural CO2 fluxes by altering the concentration gradients between the soil, the vegetation and the overlying air. Thus, the driving factors of CO2 fluxes are not constant during the closed chamber experiment, and no linear increase or decrease of CO2 concentration over time within the chamber headspace can be expected. Nevertheless, linear regression has been applied for calculating CO2 fluxes in many recent, partly influential, studies. This approach was justified by keeping the closure time short and assuming the concentration change over time to be in the linear range. Here, we test if the application of linear regression is really appropriate for estimating CO2 fluxes using closed chambers over short closure times and if the application of nonlinear regression is necessary. We developed a nonlinear exponential regression model from diffusion and photosynthesis theory. This exponential model was tested with four different datasets of CO2 flux measurements (total number: 1764) conducted at three peatland sites in Finland and a tundra site in Siberia. The flux measurements were performed using transparent chambers on vegetated surfaces and opaque chambers on bare peat surfaces. Thorough analyses of residuals demonstrated that linear regression was frequently not appropriate for the determination of CO2 fluxes by closed-chamber methods, even if closure times were kept short. The developed exponential model was well suited for nonlinear regression of the concentration over time c(t) evolution in the chamber headspace and estimation of the initial CO2 fluxes at closure time for the majority of experiments. CO2 flux estimates by linear regression can be as low as 40% of the flux estimates of exponential regression for closure times of only two minutes and even lower for longer closure times. The degree of underestimation increased with increasing CO2 flux strength and is dependent on soil and vegetation conditions which can disturb not only the quantitative but also the qualitative evaluation of CO2 flux dynamics. The underestimation effect by linear regression was observed to be different for CO2 uptake and release situations which can lead to stronger bias in the daily, seasonal and annual CO2 balances than in the individual fluxes. To avoid serious bias of CO2 flux estimates based on closed chamber experiments, we suggest further tests using published datasets and recommend the use of nonlinear regression models for future closed chamber studies.
Effects of iron on the elemental stoichiometry during EIFEX and in the diatoms Fragilariopsis kerguelensis and Chaetoceros dichaeta
Authors: Hoffmann L. J. , Peeken I. , Lochte K.
Published: April 2010

Abstract. The interaction between iron availability and the phytoplankton elemental composition was investigated during the in situ iron fertilization experiment EIFEX and in laboratory experiments with the Southern Ocean diatom species Fragilariopsis kerguelensis and Chaetoceros dichaeta. Contrary to other in situ iron fertilization experiments we observed an increase in the bPSi : POC, bPSi : PON, and bPSi : POP ratios within the iron fertilized patch during EIFEX. This is possibly caused by a relatively stronger increase in diatom abundance compared to other phytoplankton groups and does not necessarily represent the amount of silicification of single diatom cells. In laboratory experiments with F. kerguelensis and C. dichaeta no changes in the POC : PON, PON : POP, and POC : POP ratios were found with changing iron availability in both species. BPSi : POC, bPSi : PON, and bPSi : POP ratios were significantly lower in the high iron treatments compared to the controls. In F. kerguelensis this is caused by a decrease in cellular bPSi concentrations and therefore possibly less silicification. In C. dichaeta no change in cellular bPSi concentration was found. Here lower bPSi : POC, bPSi : PON, and bPSi : POP ratios were caused by an increase in cellular C, N, and P under high iron conditions. We therefore assume that iron limitation does not generally increase silicification of diatoms and that changes in the bPSi : POC, bPSi : PON, and bPSi : POP ratios under iron fertilization in the field are caused by a variety of different mechanisms. These results imply that the effect of iron on nutrient uptake is more complex than hitherto assumed.
Nitrogen retention patterns and their controlling factors in an alpine meadow: implications for carbon sequestration
Authors: Xu X. L. , Ouyang H. , Cao G. M.
Published: April 2010

Abstract. We hypothesized that the patterns of NO3− and NH4+ retention are different over short-term scales while they are similar over long-term scales in alpine meadows and that abiotic and biotic factors might be responsible for their different patterns over short-term scales. In order to test the hypotheses, a 15N-labeled experiment was conducted in an alpine meadow in the Qinghai-Tibet Plateau over four years. Our results showed that 15NO3− and 15NH4+ retention was distinctly different within two months, and even one year after tracer additions. The long-term retention of 15N at the whole-plot level did not differ significantly between 15NH4+ and 15NO3− treatments, and averaged 50% after four years. Higher soil temperature or soil organic carbon concentration enhanced 15NH4+ retention, but significantly reduced 15NO3− retention in the soil within two months following tracer additions. Soil moisture significantly affected 15N recovered in soil organic matter and microbial biomass as well as aboveground parts, but had no significant effects on 15N recovered in roots. These findings have important ecological implications with regard to the consequences of deposited nitrogen because of the possible difference in the fate of NH4+ vs. NO3− in alpine meadow ecosystems.
Carbon and nutrient mixed layer dynamics in the Norwegian Sea
Authors: Findlay H. S. , Tyrrell T. , Bellerby R. G. J. , Merico A. , Skjelvan I.
Published: April 2010

Abstract. A coupled carbon-ecosystem model is compared to recent data from Ocean Weather Ship M (66° N, 02° E) and used to investigate nutrient and carbon processes within the Norwegian Sea. Nitrate is consumed by phytoplankton in the surface layers over the summer; however the data show that silicate does not become rapidly limiting for diatoms, in contrast to the model prediction and in contrast to data from other temperate locations. The model estimates atmosphere-ocean CO2 flux to be 37 g C m−2 yr−1. A detailed comparison of the carbonate system at other ocean locations reveals that although coccolithophore blooms occur at OWS M, they are not as prevalent here as other areas. The seasonal cycles of calcite saturation state and [CO32−] are similar in the model and in data: values range from ~3 and ~120 μmol kg−1 respectively in winter, to ~4 and ~170 μmol kg−1 respectively in summer. The timing of coccolithophore blooms within the year therefore coincides with a time of high calcite saturation state, as predicted by previous modelling work.
Calcium isotopic composition of high-latitude proxy carrier Neogloboquadrina pachyderma (sin.)
Authors: Hippler D. , Kozdon R. , Darling K. F. , Eisenhauer A. , Nägler T. F.
Published: April 2010

Abstract. The accurate reconstruction of sea surface temperature (SST) history in climate-sensitive regions (e.g. tropical and polar oceans) became a challenging task in palaeoceanographic research. However, biogenic shell carbonate SST proxies successfully developed for tropical regions often fail in cool water environments. Their major regional shortcomings and the cryptic diversity now found within the major high latitude proxy carrier Neogloboquadrina pachyderma (sin.) highlight an urgent need to develop complementary SST proxies for these cool water regions. Here we incorporate the genetic component into a calibration study of a new SST proxy for the high latitudes. We found that the calcium isotopic composition (δ44/40Ca) of calcite from genotyped net catches and core-top samples of the planktonic foraminifera Neogloboquadrina pachyderma (sin) is strongly related to temperature and unaffected by genetic variations. The temperature sensitivity has been found to be 0.17 (±0.04)‰ per 1°C highlighting its potential for downcore applications in open marine cool-water environments. Our results further indicate that however in extreme polar environments, below a critical threshold temperature of 2.0 (±0.5)°C and salinity of 33.0 (±0.5)‰ a prominent shift in biomineralization affect the Ca isotope composition of N. pachyderma (sin.) becoming insensitive to temperature. These findings highlight the need of systematic calibration studies to unravel the influencing factors on Ca isotope fractionation and to validate the proxies' applicability.