bluuebunny/crossref_metadata_2025 huggingface dataset:
The global marine phosphorus cycle: sensitivity to oceanic circulation
Authors: Slomp C. P. , Van Cappellen P.
Published: April 2010

Abstract. A new mass balance model for the coupled marine cycles of phosphorus (P) and carbon (C) is used to examine the relationships between oceanic circulation, primary productivity, and sedimentary burial of reactive P and particulate organic C (POC), on geological time scales. The model explicitly represents the exchanges of water and particulate matter between the continental shelves and the open ocean, and it accounts for the redox-dependent burial of POC and the various forms of reactive P (iron(III)-bound P, particulate organic P (POP), authigenic calcium phosphate, and fish debris). Steady state and transient simulations indicate that a slowing down of global ocean circulation decreases primary production in the open ocean, but increases that in the coastal ocean. The latter is due to increased transfer of soluble P from deep ocean water to the shelves, where it fuels primary production and causes increased reactive P burial. While authigenic calcium phosphate accounts for most reactive P burial ocean-wide, enhanced preservation of fish debris may become an important reactive P sink in deep-sea sediments during periods of ocean anoxia. Slower ocean circulation globally increases POC burial, because of enhanced POC preservation under anoxia in deep-sea depositional environments and higher primary productivity along the continental margins. In accordance with geological evidence, the model predicts increased accumulation of reactive P on the continental shelves during and following periods of ocean anoxia.
Dissolution of calcium carbonate: observations and model results in the subpolar 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 using observations from the open subpolar North Atlantic [sNA] and to a lesser extent 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 by indicating that there is not 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.
Direct and indirect metabolic CO2 release by humanity
Authors: Prairie Y. T. , Duarte C. M.
Published: April 2010

Abstract. The direct CO2 released by respiration of humans and domesticated animals, as well as CO2 derived from the decomposition of their resulting wastes was calculated in order to ascertain the direct and indirect metabolic contribution of humanity to CO2 release. Human respiration was estimated to release 0.6 Gt C year−1 and that of their associated domestic animals was estimated to release 1.5 Gt C year−1, to which an indirect release of 1.0 Gt C year−1, derived from decomposition of the organic waste and garbage produced by humans and their domestic animals, must be added. These combined direct and indirect metabolic sources, estimated at 3.1 Gt C year−1, have increased 7 fold since pre-industrial times and are predicted to continue to rise over the 21st century.
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, within particles outside of suboxic water, etc.) suggest that it is unlikely that the oceanic denitrification rate is less 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. To do so would violate an avalanche of recent data on oceanic denitrification. 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 nitrogen fixing genes are widespread. 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, but which could, perhaps, last long enough to have significant impacts.
The "neutral" community structure of planktonic herbivores, tintinnid ciliates of the microzooplankton, across the SE Tropical Pacific Ocean
Authors: Dolan J. R. , Ritchie M. E. , Ras J.
Published: April 2010

Abstract. We assessed the community characteristics of a group of planktonic herbivores across a species-rich area, the SE Pacific Ocean. A series of 22 stations between the Marquise Islands (7° S 142° W) and the coast of Chile (35° S 73° W) was sampled during the BIOSOPE cruise in 2004. We examined the relationships between taxonomic diversity, morphological diversity, patterns of tintinnid species assemblage, and phytoplankton abundance. Tintinnid community characteristics were estimated from large volume (20–60 l) discrete depth sampling and phytoplankton were characterized based on HPLC pigment signatures. Across the transect, average water column concentrations of tintinnids ranged from 2–40 cells l−1 or 8–40 ng C l−1, and were positively related to chlorophyll a concentrations which varied between 0.07–2 µg l−1. Large numbers of tintinnid taxa were found, 18–41 species per station, yielding a total of 149 species. Among stations, morphological and taxonomic diversity metrics co-varied but were not significantly related to phytoplankton diversity estimated using a pigment-based size-diversity metric. Taxonomic diversity of tintinnids, as H' or Fishers' alpha, was inversely related to chlorophyll concentration and positively to the depth of the chlorophyll maximum layer. Species abundance distributions were compared to geometric, log-series and log-normal distributions. For most stations, the observed distribution most closely matched log-series, coherent with the neutral theory of random colonization from a large species pool. Occurrence rates of species were correlated with average abundance rather than specific characteristics of biomass or lorica oral diameter (mouth) size. Among stations, species richness was correlated with both the variety of mouth sizes (lorica oral diameters) as well as numbers of species per mouth size, also consistent with random colonization.
A coccolithophore concept for constraining the Cenozoic carbon cycle
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 (pCO>sub>2). 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 a constraint on pCO2 over the Cenozoic based on the physiological plasticity of extant coccolithophores. 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 evolution of certain 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.
Assessing the potential long-term increase of oceanic fossil fuel CO2 uptake due to CO2-calcification feedback
Authors: Ridgwell A. , Zondervan I. , Hargreaves J. C. , Bijma J. , Lenton T. M.
Published: April 2010

Abstract. Plankton manipulation experiments exhibit a wide range of sensitivities of biogenic calcification to simulated anthropogenic acidification of the ocean, with the "lab rat" of planktic calcifiers, Emiliania huxleyi apparently not representative of calcification generally. We assess the implications of this observational uncertainty by creating an ensemble of realizations of an Earth system model that encapsulates a comparable range of uncertainty in calcification response to ocean acidification. We predict that a substantial reduction in marine carbonate production is possible in the future, with enhanced ocean CO2 sequestration across the model ensemble driving a 4–13% reduction in the year 3000 atmospheric fossil fuel CO2 burden. Concurrent changes in ocean circulation and surface temperatures in the model contribute about one third to the increase in CO2 uptake. We find that uncertainty in the predicted strength of CO2-calcification feedback seems to be dominated by the assumption as to which species of calcifier contribute most to carbonate production in the open ocean.
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 BSi:POC, BSi:PON, and BSi: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. BSi:POC, BSi:PON, and BSi:POP ratios were significantly lower in the high iron treatments compared to the controls. In F. kerguelensis this was caused by a decrease in cellular BSi concentrations and therefore possibly less silicification. In C. dichaeta no change in cellular BSi concentration was found. Here lower BSi:POC, BSi:PON, and BSi:POP ratios were caused by an increase in cellular C, N, and P under high iron conditions. These results indicate that iron limitation does not always increase silicification in diatoms and that changes in the BSi:POC, BSi:PON, and BSi:POP ratios under iron fertilization in the field are caused by a variety of different mechanisms. Our results therefore imply that simple cause-and-effect relationships are not always applicable for modeling of elemental ratios.
Different carbon isotope fractionation patterns during the development of phototrophic freshwater and marine biofilms
Authors: Staal M. , Thar R. , Kühl M. , van Loosdrecht M. C. M. , Wolf G. , de Brouwer J. F. C. , Rijstenbil J. W.
Published: April 2010

Abstract. Natural phototrophic biofilms are influenced by a broad array of abiotic and biotic factors and vary over temporal and spatial scales. Different developmental stages can be distinguished and growth rates will vary due to the thickening of the biofilm, which is expected to lead to a limitation of light or mass transport. This study shows that variation in CO2(aq) availability leads to a fractionation shift and thereby affects δ13C signatures during biofilm development. For phototrophic freshwater biofilms it was found that the δ13C value became less negative with the thickening of the biofilm, while the opposite trend was found in marine biofilms. Modeling and pH profiling indicated that the trend in the freshwater system was caused by an increase in CO2(aq) limitation resulting in an increase of HCO3− as C-source. The opposite trend in the marine system could be explained by a higher heterotrophic biomass and activity causing a higher carbon recycling and thereby lower δ13C values. We conclude that δ13C was more related to the net areal photosynthesis rate and carbon recycling, rather than to the growth rate of the biofilms.
Assessing the ability of three land ecosystem models to simulate gross carbon uptake of forests from boreal to Mediterranean climate in Europe
Authors: Jung M. , Le Maire G. , Zaehle S. , Luyssaert S. , Vetter M. , Churkina G. , Ciais P. , Viovy N. , Reichstein M.
Published: April 2010

Abstract. Three terrestrial biosphere models (LPJ, Orchidee, Biome-BGC) were evaluated with respect to their ability to simulate large-scale climate related trends in gross primary production (GPP) across European forests. Simulated GPP and leaf area index (LAI) were compared with GPP estimates based on flux separated eddy covariance measurements of net ecosystem exchange and LAI measurements along a temperature gradient ranging from the boreal to the Mediterranean region. The three models capture qualitatively the pattern suggested by the site data: an increase in GPP from boreal to temperate and a subsequent decline from temperate to Mediterranean climates. The models consistently predict higher GPP for boreal and lower GPP for Mediterranean forests. Based on a decomposition of GPP into absorbed photosynthetic active radiation (APAR) and radiation use efficiency (RUE), the overestimation of GPP for the boreal coniferous forests appears to be primarily related to too high simulated LAI - and thus light absorption (APAR) – rather than too high radiation use efficiency. We cannot attribute the tendency of the models to underestimate GPP in the water limited region to model structural deficiencies with confidence. A likely dry bias of the input meteorological data in southern Europe may create this pattern. On average, the models compare similarly well to the site GPP data (RMSE of ~30% or 420 gC/m2/yr) but differences are apparent for different ecosystem types. In terms of absolute values, we find the agreement between site based GPP estimates and simulations acceptable when we consider uncertainties about the accuracy in model drivers, a potential representation bias of the eddy covariance sites, and uncertainties related to the method of deriving GPP from eddy covariance measurements data. Continental to global data-model comparison studies should be fostered in the future since they are necessary to identify consistent model bias along environmental gradients.
NW Adriatic Sea biogeochemical variability in the last 20 years (1986–2005)
Authors: Tedesco L. , Socal G. , Bianchi F. , Acri F. , Veneri D. , Vichi M.
Published: April 2010

Abstract. This paper presents a long-term time series (1986–2005) of hydrological and biogeochemical data, both published and unpublished. Data were collected in the north-western area of the Adriatic Sea, at two stations that are considered hydrodynamically and trophically different. The time series have been statistically and graphically analysed on a monthly scale in order to study the annual climatologies, links between the concentrations of chlorophyll-a and the variability in the environment, trophic differences between the two areas and chlorophyll-a trends over time. Basically, the two areas have similar hydrological features, yet they present significant differences in the amount of nutrient inputs: these are in fact higher at the coastal site, which is characterized by a prevalence of surface blooms, while they are lower at the offshore station, which is mainly affected by blooms at intermediate depths. Nonetheless, throughout the whole water column, chlorophyll-a concentrations are only slightly different. Both areas are affected by riverine discharge, though chlorophyll-a concentrations are also driven strongly by the seasonal cycle at the station closer to the coast. Results show that the two stations are not trophically different, although some controlling factors, such as zooplankton grazing in one case and light attenuation in the other, may further regulate the growth of phytoplankton. In both cases no significant trends are detected in either the average chlorophyll-a values or in dispersion of the data, in contrast with significant trends in temperature and salinity.
Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO2
Authors: Denef K. , Bubenheim H. , Lenhart K. , Vermeulen J. , Van Cleemput O. , Boeckx P. , Müller C.
Published: April 2010

Abstract. The aim of this study was to identify the microbial communities that are actively involved in the assimilation of rhizosphere-C and are most sensitive in their activity to elevated atmospheric CO2 in a temperate semi-natural low-input grassland ecosystem. For this, we analyzed 13C signatures in microbial biomarker phospholipid fatty acids (PLFA) from an in-situ 13CO2 pulse-labeling experiment in the Giessen Free Air Carbon dioxide Enrichment grasslands (GiFACE, Germany) exposed to ambient and elevated (i.e. 50% above ambient) CO2 concentrations. Short-term 13C PLFA measurements at 3 h and 10 h after the pulse-labeling revealed very little to no 13C enrichment after 3 h in biomarker PLFAs and a much greater incorporation of new plant-C into fungal compared to bacterial PLFAs after 10 h. After a period of 11 months following the pulse-labeling experiment, the 13C enrichment of fungal PLFAs was still largely present but had decreased, while bacterial PLFAs were much more enriched in 13C compared to a few hours after the pulse-labeling. These results imply that new rhizodeposit-C is rapidly processed by fungal communities and only much later by the bacterial communities, which we attributed to either a fungal-mediated translocation of rhizosphere-C from the fungal to bacterial biomass or a preferential bacterial use of dead root or fungal necromass materials as C source over the direct utilization of fresh root-exudate C in these N-limited grassland ecosystems. Elevated CO2 caused an increase in the proportional 13C enrichment (relative to the universal biomarker 16:0) of the arbuscular mycorrhizal fungal biomarker PLFA 16:1ω5 and one gram-positive bacterial biomarker PLFA i16:0, but a decrease in the proportional 13C enrichment of 18:1ω9c, a commonly used though questionable fungal biomarker PLFA. This suggests enhanced fungal rhizodeposit-C assimilation only by arbuscular mycorrhizal fungal species under elevated CO2.
Net ecosystem carbon exchange in three contrasting Mediterranean ecosystems – the effect of drought
Authors: Pereira J. S. , Mateus J. A. , Aires L. M. , Pita G. , Pio C. , David J. S. , Andrade V. , Banza J. , David T. S. , Paço T. A. , Rodrigues A.
Published: April 2010

Abstract. Droughts reduce gross primary production (GPP) and ecosystem respiration (Reco), contributing to most of the inter-annual variability in terrestrial carbon sequestration. In seasonally dry climates (Mediterranean), droughts result from reductions in annual rainfall and changes in rain seasonality. We compared carbon fluxes measured by the eddy covariance technique in three contrasting ecosystems in southern Portugal: an evergreen oak woodland (savannah-like) with ca.~21% tree crown cover, a grassland dominated by herbaceous annuals and a coppiced short-rotation eucalyptus plantation. During the experimental period (2003–2006) the eucalyptus plantation was always the strongest sink for carbon: net ecosystem exchange rate (NEE) between −861 and −399 g C m−2 year−1. The oak woodland and the grassland were much weaker sinks for carbon: NEE varied in the oak woodland between −140 and −28 g C m−2 year−1 and in the grassland between −190 and +49 g C m−2 year−1. The eucalyptus stand had higher GPP and a lower proportion of GPP spent in respiration than the other systems. The higher GPP resulted from high leaf area duration (LAD), as a surrogate for the photosynthetic photon flux density absorbed by the canopy. The eucalyptus had also higher rain use efficiency (GPP per unit of rain volume) and light use efficiency (the daily GPP per unit incident photosynthetic photon flux density) than the other two ecosystems. The effects of a severe drought could be evaluated during the hydrological-year (i.e., from October to September) of 2004–2005. Between October 2004 and June 2005 the precipitation was only 40% of the long-term average. In 2004–2005 all ecosystems had GPP lower than in wetter years and carbon sequestration was strongly restricted (less negative NEE). The grassland was a net source of carbon dioxide (+49 g C m−2 year−1). In the oak woodland a large proportion of GPP resulted from carbon assimilated by its annual vegetation component, which was strongly affected by the shortage of rain in winter. Overall, severe drought affected more GPP than Reco leading to the deterioration of NEE. Although the rain-use efficiency of the eucalyptus plantation increased in the dry year, this was not the case of evergreen oak woodland, which rain-use efficiency was not influenced by drought. Recovery after drought alleviation, i.e., beginning with heavy rain in October 2005, was fully accomplished in 2006 in the oak woodland and grassland, but slow in the eucalyptus plantation.
The value of adding optics to ecosystem models: a case study
Authors: Fujii M. , Boss E. , Chai F.
Published: April 2010

Abstract. Many ecosystem models have been developed to study the ocean's biogeochemical properties, but most of these models use simple formulations to describe light penetration and spectral quality. Here, an optical model is coupled with a previously published ecosystem model that explicitly represents two phytoplankton (picoplankton and diatoms) and two zooplankton functional groups, as well as multiple nutrients and detritus. Surface ocean color fields and subsurface light fields are calculated by coupling the ecosystem model with an optical model that relates biogeochemical standing stocks with inherent optical properties (absorption, scattering); this provides input to a commercially available radiative transfer model (Ecolight). We apply this bio-optical model to the equatorial Pacific upwelling region, and find the model to be capable of reproducing many measured optical properties and key biogeochemical processes in this region. Our model results suggest that non-algal particles largely contribute to the total scattering or attenuation (>50% at 660 nm) but have a much smaller contribution to particulate absorption (<20% at 440 nm), while picoplankton dominate the total phytoplankton absorption (>95% at 440 nm). These results are consistent with the field observations. In order to achieve such good agreement between data and model results, however, key model parameters, for which no field data are available, have to be constrained. Sensitivity analysis of the model results to optical parameters reveals a significant role played by colored dissolved organic matter through its influence on the quantity and quality of the ambient light. Coupling explicit optics to an ecosystem model provides advantages in generating: (1) a more accurate subsurface light-field, which is important for light sensitive biogeochemical processes such as photosynthesis and photo-oxidation, (2) additional constraints on model parameters that help to reduce uncertainties in ecosystem model simulations, and (3) model output which is comparable to basic remotely-sensed properties. In addition, the coupling of biogeochemical models and optics paves the road for future assimilation of ocean color and in-situ measured optical properties into the models.
Relationship between photosynthetic parameters and different proxies of phytoplankton biomass in the subtropical ocean
Authors: Huot Y. , Babin M. , Bruyant F. , Grob C. , Twardowski M. S. , Claustre H.
Published: April 2010

Abstract. Probably because it is a readily available ocean color product, almost all models of primary productivity use chlorophyll as their index of phytoplankton biomass. As other variables become more readily available, both from remote sensing and in situ autonomous platforms, we should ask if other indices of biomass might be preferable. Herein, we compare the accuracy of different proxies of phytoplankton biomass for estimating the maximum photosynthetic rate (Pmax) and the initial slope of the production versus irradiance (P vs. E) curve (α). The proxies compared are: the total chlorophyll a concentration (Tchla, the sum of chlorophyll a and divinyl chlorophyll), the phytoplankton absorption coefficient, the phytoplankton photosynthetic absorption coefficient, the active fluorescence in situ, the particulate scattering coefficient at 650 nm (bp(650)), and the particulate backscattering coefficient at 650 nm (bbp(650)). All of the data (about 170 P vs. E curves) were collected in the South Pacific Ocean. We find that when only the phytoplanktonic biomass proxies are available, bp(650) and Tchla are respectively the best estimators of Pmax and α. When additional variables are available, such as the depth of sampling, the irradiance at depth, or the temperature, Tchla is the best estimator of both Pmax and α.
Does ocean acidification induce an upward flux of marine aggregates?
Authors: Mari X.
Published: April 2010

Abstract. The absorption of anthropogenic atmospheric carbon dioxide (CO2) by the ocean provokes its acidification. This acidification may alter several oceanic processes, including the export of biogenic carbon from the upper layer of the ocean, hence providing a feedback on rising atmospheric carbon concentrations. The effect of seawater acidification on transparent exopolymeric particles (TEP) driven aggregation and sedimentation processes were investigated by studying the interactions between latex beads and TEP precursors collected in the lagoon of New Caledonia. A suspension of TEP and beads was prepared and the formation of mixed aggregates was monitored as a function of pH under increasing turbulence intensities. The pH was controlled by addition of sulfuric acid. Aggregation and sedimentation processes driven by TEP were drastically reduced when the pH of seawater decreases within the expected limits imposed by increased anthropogenic CO2 emissions. In addition to the diminution of TEP sticking properties, the diminution of seawater pH led to a significant increase of the TEP pool, most likely due to swollen structures. A diminution of seawater pH by 0.2 units or more led to a stop or a reversal of the downward flux of particles. If applicable to oceanic conditions, the sedimentation of marine aggregates may slow down or even stop as the pH decreases, and the vertical flux of organic carbon may reverse. This would enhance both rising atmospheric carbon and ocean acidification.
Nitrification and inorganic nitrogen distribution in a large perturbed river/estuarine system: the Pearl River Estuary, China
Authors: Dai M. , Wang L. , Guo X. , Zhai W. , Li Q. , He B. , Kao S.-J.
Published: April 2010

Abstract. We investigated the spatial distribution and seasonal variation of dissolved inorganic nitrogen in a large perturbed estuary, the Pearl River Estuary, based on three cruises conducted in winter (January 2005), summer (August 2005) and spring (March 2006). On-site incubation was also carried out for determining ammonium and nitrite oxidation rates (nitrification rates). We observed a year-round pattern of dramatic decrease in NH4+, increase in NO3−, but insignificant change in NO2− in the upper estuary at salinity ~0–5. However, species and concentrations of inorganic nitrogen at upper estuary significantly changed with season. In winter, with low runoff, the most upper reach of the Pearl River Estuary showed relatively low rates of ammonia oxidation (0–5.4 μmol N L−1 d−1) and nitrite oxidation (0–5.2 μmol N L−1 d−1), accompanied by extremely high concentrations of ammonia (up to >800 μmol L−1) and nitrate (up to >300 μmol L−1). In summer, the upper estuary showed higher nitrification rates (ammonia oxidation rate ~1.5–33.1 μmol N L−1 d−1, nitrite oxidation rate ~0.6–32.0 μmol N L−1 d−1) with lower concentrations of ammonia (<350 μmol L−1) and nitrate (<120 μmol L−1). The Most Probable Number test showed relatively lower nitrifier abundance in summer at most sampling stations, indicating a greater specific nitrification rate per cell in the warm season. Temperature appeared to control nitrification rates to a large degree in different seasons. Spatial variability of nitrification rates appeared to be controlled by a combination of many other factors such as nutrient concentrations, nitrifier abundance and dissolved oxygen (DO) concentrations. In addition to aerobic respiration, nitrification contributed significantly to the consumption of DO and production of free CO2 at upper estuary. Nitrification-induced consumption accounted for up to approximately one third of the total water column community DO consumption in the upper estuary during the surveyed periods, boosting environmental stress on this large estuarine ecosystem.
Influences of observation errors in eddy flux data on inverse model parameter estimation
Authors: Lasslop G. , Reichstein M. , Kattge J. , Papale D.
Published: April 2010

Abstract. Eddy covariance data are increasingly used to estimate parameters of ecosystem models. For proper maximum likelihood parameter estimates the error structure in the observed data has to be fully characterized. In this study we propose a method to characterize the random error of the eddy covariance flux data, and analyse error distribution, standard deviation, cross- and autocorrelation of CO2 and H2O flux errors at four different European eddy covariance flux sites. Moreover, we examine how the treatment of those errors and additional systematic errors influence statistical estimates of parameters and their associated uncertainties with three models of increasing complexity – a hyperbolic light response curve, a light response curve coupled to water fluxes and the SVAT scheme BETHY. In agreement with previous studies we find that the error standard deviation scales with the flux magnitude. The previously found strongly leptokurtic error distribution is revealed to be largely due to a superposition of almost Gaussian distributions with standard deviations varying by flux magnitude. The crosscorrelations of CO2 and H2O fluxes were in all cases negligible (R2 below 0.2), while the autocorrelation is usually below 0.6 at a lag of 0.5 h and decays rapidly at larger time lags. This implies that in these cases the weighted least squares criterion yields maximum likelihood estimates. To study the influence of the observation errors on model parameter estimates we used synthetic datasets, based on observations of two different sites. We first fitted the respective models to observations and then added the random error estimates described above and the systematic error, respectively, to the model output. This strategy enables us to compare the estimated parameters with true parameters. We illustrate that the correct implementation of the random error standard deviation scaling with flux magnitude significantly reduces the parameter uncertainty and often yields parameter retrievals that are closer to the true value, than by using ordinary least squares. The systematic error leads to systematically biased parameter estimates, but its impact varies by parameter. The parameter uncertainty slightly increases, but the true parameter is not within the uncertainty range of the estimate. This means that the uncertainty is underestimated with current approaches that neglect selective systematic errors in flux data. Hence, we conclude that potential systematic errors in flux data need to be addressed more thoroughly in data assimilation approaches since otherwise uncertainties will be vastly underestimated.
A rapid transition from ice covered CO2–rich waters to a biologically mediated CO2 sink in the eastern Weddell Gyre
Authors: Bakker D. C. E. , Hoppema M. , Schröder M. , Geibert W. , de Baar H. J. W.
Published: April 2010

Abstract. Circumpolar Deep Water (CDW), locally called Warm Deep Water (WDW), enters the Weddell Gyre in the southeast, roughly at 25° E to 30° E. In December 2002 and January 2003 we studied the effect of entrainment of WDW on the fugacity of carbon dioxide (fCO2) and dissolved inorganic carbon (DIC) in Weddell Sea surface waters. Ultimately the fCO2 difference across the sea surface drives air-sea fluxes of CO2. Deep CTD sections and surface transects of fCO2 were made along the Prime Meridian, a northwest-southeast section, and along 17° E to 23° E during cruise ANT XX/2 on FS Polarstern. Upward movement and entrainment of WDW into the winter mixed layer had significantly increased DIC and fCO2 below the sea ice along 0° W and 17° E to 23° E, notably in the southern Weddell Gyre. Nonetheless, the ice cover largely prevented outgassing of CO2 to the atmosphere. During and upon melting of the ice, biological activity rapidly reduced surface water fCO2 by up to 100 μatm, thus creating a sink for atmospheric CO2. Despite the tendency of the surfacing WDW to cause CO2 supersaturation, the Weddell Gyre may well be a CO2 sink on an annual basis due to this effective mechanism involving ice cover and ensuing biological fCO2 reduction. Dissolution of calcium carbonate (CaCO3) in melting sea ice may play a minor role in this rapid reduction of surface water fCO2.
Heterogeneous ice nucleation activity of bacteria: new laboratory experiments at simulated cloud conditions
Authors: Möhler O. , Georgakopoulos D. G. , Morris C. E. , Benz S. , Ebert V. , Hunsmann S. , Saathoff H. , Schnaiter M. , Wagner R.
Published: April 2010

Abstract. The ice nucleation activities of five different Pseudomonas syringae, Pseudomonas viridiflava and Erwinia herbicola bacterial species and of Snomax™ were investigated in the temperature range between −5 and −15°C. Water suspensions of these bacteria were directly sprayed into the cloud chamber of the AIDA facility of Forschungszentrum Karlsruhe at a temperature of −5.7°C. At this temperature, about 1% of the Snomax™ cells induced immersion freezing of the spray droplets before the droplets evaporated in the cloud chamber. The living cells didn't induce any detectable immersion freezing in the spray droplets at −5.7°C. After evaporation of the spray droplets the bacterial cells remained as aerosol particles in the cloud chamber and were exposed to typical cloud formation conditions in experiments with expansion cooling to about −11°C. During these experiments, the bacterial cells first acted as cloud condensation nuclei to form cloud droplets. Then, only a minor fraction of the cells acted as heterogeneous ice nuclei either in the condensation or the immersion mode. The results indicate that the bacteria investigated in the present study are mainly ice active in the temperature range between −7 and −11°C with an ice nucleation (IN) active fraction of the order of 10−4. In agreement to previous literature results, the ice nucleation efficiency of Snomax™ cells was much larger with an IN active fraction of 0.2 at temperatures around −8°C.
Microbial reduction of iron and porewater biogeochemistry in acidic peatlands
Authors: Küsel K. , Blöthe M. , Schulz D. , Reiche M. , Drake H. L.
Published: April 2010

Abstract. Temporal drying of upper soil layers of acidic methanogenic peatlands might divert the flow of reductants from CH4 formation to other electron-accepting processes due to a renewal of alternative electron acceptors. In this study, we evaluated the in situ relevance of Fe(III)-reducing microbial activities in peatlands of a forested catchment that differed in their hydrology. Intermittent seeps reduced sequentially nitrate, Fe(III), and sulfate during periods of water saturation. Due to the acidic soil conditions, released Fe(II) was transported with the groundwater flow and accumulated as Fe(III) in upper soil layers of a lowland fen apparently due to oxidation. Microbial Fe(III) reduction in the upper soil layer accounted for 26.7 and 71.6% of the anaerobic organic carbon mineralization in the intermittent seep and the lowland fen, respectively. In an upland fen not receiving exogenous Fe, Fe(III) reduction contributed only to 6.7%. Fe(II) and acetate accumulated in deeper porewater of the lowland fen with maximum concentrations of 7 and 3 mM, respectively. Both supplemental glucose and acetate stimulated the reduction of Fe(III) indicating that fermentative, incomplete, and complete oxidizers were involved in Fe(II) formation in the acidic fen. Amplification of DNA yielded PCR products specific for Acidiphilium-, Geobacter-, and Geothrix-, but not for Shewanella- or Anaeroromyxobacter-related sequences. Porewater biogeochemistry observed during a 3-year-period suggests that increased drought periods and subsequent intensive rainfalls due to global climate change will further favor Fe(III) and sulfate as alternative electron acceptors due to the storage and enhanced re-oxidation of their reduced compounds in the soil.
No detectable aerobic methane efflux from plant material, nor from adsorption/desorption processes
Authors: Kirschbaum M. U. F. , Walcroft A.
Published: April 2010

Abstract. In early 2006, Keppler et al. (Nature, 439:187–191) reported a novel finding that plant leaves, and even simple organic materials, can release methane under aerobic conditions. We investigated here whether the reported methane release might simply arise from methane desorption from sample surfaces after prior exposure to higher methane concentrations. We exposed standard cellulose filter papers (i.e. organic material with a high surface area) to atmospheric methane concentration and then transferred them to a low-methane atmosphere. Our results suggest that any desorption flux was extremely small (−0.0001±0.0019 ngCH4 kgDW−1 s−1) and would play no quantitatively significant role in modifying any measured methane fluxes. We also incubated fresh detached leaves of several species and intact Zea mays seedlings under aerobic and low-light conditions. After correcting for a small measured methane influx into empty chambers, measured rates of methane emission by plant materials were zero or, at most, very small, ranging from −0.25±1.1 ngCH4 kgDW−1 s−1 for Zea mays seedlings to 0.10±0.08 ngCH4 kgDW−1 s−1 for a mixture of freshly detached grasses. These rates were much smaller than the rates originally reported by Keppler et al. (2006).
Seasonal to hour variation scales in abundance and production of total and particle-attached bacteria in the open NW Mediterranean Sea (0–1000 m)
Authors: Mével G. , Vernet M. , Goutx M. , Ghiglione J. F.
Published: April 2010

Abstract. We present the vertical and temporal dynamics of total vs. particle-attached bacterial abundance and activity over a 5 week period under summer to autumn transition in NW Mediterranean Sea. At a weekly time scale, total bacterial biomass and production in the euphotic layers was significantly correlated with phytoplanktonic biomass. At an hourly time scale, total bacterial biomass responded very rapidly to chlorophyll a fluctuations, suggesting a tight coupling between phytoplankton and bacteria for resource partitioning during the summer-autumn transition. In contrast, no influence of diel changes on bacterial parameters was detected. Episodic events such as coastal water intrusions had a significant positive effect on total bacterial abundance and production, whereas we could not detect any influence of short wind events whatever the magnitude. Finally, we show that particle-attached bacteria can represent a large proportion (up to 49%) of the total bacterial activity in the euphotic layer but display rapid and sporadic changes at hourly time scales. In the mesopelagic layers, bacterial abundance and production linearly decreased with depth, except some production peaks at 400–750 m. This study underlines the value of large datasets covering different temporal scales to clarify the biogeochemical role of bacteria in the cycling of organic matter in open seawater.
Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions
Authors: Orcutt B. , Meile C.
Published: April 2010

Abstract. Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.
Assessing seasonality of biochemical CO2 exchange model parameters from micrometeorological flux observations at boreal coniferous forest
Authors: Thum T. , Aalto T. , Laurila T. , Aurela M. , Lindroth A. , Vesala T.
Published: April 2010

Abstract. The seasonality of the NEE of the northern boreal coniferous forests was investigated by means of inversion modelling using eddy covariance data. Eddy covariance data was used to optimize the biochemical model parameters. Our study sites consisted of three Scots pine (l. Pinus sylvestris) forests and one Norway spruce (l. Picea abies) forest that were located in Finland and Sweden. We obtained temperature and seasonal dependence for the biochemical model parameters: the maximum rate of carboxylation (Vc(max)) and the maximum rate of electron transport (Jmax). Both of the parameters were optimized without assumptions about their mutual magnitude. The values obtained for the biochemical model parameters were similar at all the sites during summer time. To describe seasonality, different temperature fits were made for the spring, summer and autumn periods. During summer, average Jmax across the sites was 54.0 μmol m−2 s−1 (variance 31.2 μmol m−2 s−1) and Vc(max) was 12.0 μmol m−2 s−1 (variance 6.6 μmol m−2 s−1) at 17°C. The sensitivity of the model to LAI and atmospheric soil water stress was also studied. The impact of seasonality on annual GPP was 17% when only summertime parameterization was used throughout the year compared to seasonally changing parameterizations.
Deposition of nitrogen and phosphorus on the Baltic Sea: seasonal patterns and nitrogen isotope composition
Authors: Rolff C. , Elmgren R. , Voss M.
Published: April 2010

Abstract. Atmospheric deposition of nitrogen and phosphorus on the central Baltic Sea (Baltic Proper) was estimated monthly at two coastal stations and two isolated islands in 2001 and 2002. Yearly nitrogen deposition ranged between 387 and 727 mg N m−2 yr−1 (average 617) and was composed of ~10% organic N and approximately equal amounts of ammonium and nitrate. Winter nitrate peaks at the isolated islands possibly indicated ship emissions. Load weighted δ15N of deposited N was 3.7‰ and 0.35‰ at the coastal stations and the isolated islands respectively. Winter δ15N was ~3‰ lighter than in summer, reflecting winter dominance of nitrate. The light isotopic composition of deposited nitrogen may cause overestimates of nitrogen fixation in basin-wide isotopic budgeting, whereas relatively heavy deposition of ammonium during summer instead may cause underestimates of fixation in budgets of the upper mixed layer. δ15N in atmospherically deposited nitrate and ammonium was estimated by regression to −7.9 and 13.5‰ respectively. Phosphorus deposition showed no clear seasonal pattern and was considerably lower at the isolated islands. Organic P constituted 20–40% of annual P deposition. P deposition is unlikely to be a major source for cyanobacterial blooms but may potentially prolong an ongoing bloom.
Unusually negative nitrogen isotopic compositions (δ15N) of mangroves and lichens in an oligotrophic, microbially-influenced ecosystem
Authors: Fogel M. L. , Wooller M. J. , Cheeseman J. , Smallwood B. J. , Roberts Q. , Romero I. , Meyers M. J.
Published: April 2010

Abstract. Extremes in δ15N values in mangrove tissues and lichens (range =+4 to −22‰) were measured from a mangrove forest ecosystem located on Twin Cays, offshore islands in Belize, Central America. The N isotopic compositions and concentrations of NH4+/NH3 in porewater, rainwater, and atmospheric ammonia, and the δ15N of lichens, mangrove leaves, roots, stems, and wood were examined to study the biogeochemical processes important for establishing these unusual N isotopic ratios. Dwarfed Rhizophora mangle trees had the most negative δ15N, whereas fringing Rhizophora trees, the most positive δ15N values. Porewater ammonium concentrations had little relationship to N isotopic fractionation in mangrove tissues. In dwarfed mangroves, the δ15N of fine and coarse roots were 6–9‰ more positive than leaf tissue from the same tree, indicating different sources of N for root and leaf tissues. When P was added to dwarfed mangrove trees without added N, δ15N increased within one year from −12‰ to −2‰, approaching the δ15N of porewater ammonium (δ15N=+4‰). Isotopically depleted ammonia in the atmosphere (δ15N=−19‰) and in rainwater (δ15N=−10‰) were found on Twin Cays. We propose that foliar uptake of these atmospheric sources by P-stressed, dwarfed mangrove trees and lichens can explain their very negative δ15N values. In environments where P is limiting for growth, uptake of atmospheric N by Rhizophora mangle may be an important adaptive strategy.