ALBERT

Description: To study the effects of ocean acidification on the physiology of phytoplankton requires that the key chemical parameters of the growth medium, pCO2, pH and Ω (the saturation state of calcium carbonate) be carefully controlled. This is made difficult by the interdependence of these parameters. Moreover, in growing batch cultures of phytoplankton, the fixation of CO2, the uptake of nutrients and, for coccolithophores, the precipitation of calcite all change the inorganic carbon and acid-base chemistry of the medium. For example, absent pH-buffering or CO2 bubbling, a sizeable decrease in pCO2 occurs at a biomass concentration as low as 50 μM C in non-calcifying cultures. Even in cultures where pCO2 or pH is maintained constant, other chemical parameters change substantially at high cell densities. The quantification of these changes is facilitated by the use of buffer capacities. Experimentally we observe that all methods of adjustment of pCO2/pH can be used, the choice of one or the other depending on the specifics of the experiments. The mechanical effect of bubbling of cultures seems to induce more variable results than other methods of pCO2/pH control. While highly convenient, the addition of pH buffers to the medium induces changes in trace metal availability and cannot be used under trace metal-limiting conditions.

Description: Effective use of ocean colour and other bio-optical observations is dependent upon an ability to understand and characterise the angular scattering properties of phytoplankton populations. The two-layered sphere appears to offer the simplest heterogeneous geometry capable of simulating the observed angular scattering of phytoplankton cells. A study is made of the twolayered spherical model for the simulation of the inherent optical properties of algal populations, with a particular focus on backscattering as causal to ocean colour. Homogenous and two-layered volume-equivalent single particle models are used to examine the effects of varying cellular geometry, chloroplast volume, and complex refractive index on optical efficiency factors. A morphology with a chloroplast layer surrounding the cytoplasm is shown to be optimal for algal cell simulation. Appropriate chloroplast volume and refractive index ranges, and means of determining complex refractive indices for cellular chloroplast and cytoplasm material, are discussed with regard to available literature. The approach is expanded to polydispersed populations using equivalent size distribution models: to demonstrate variability in simulated inherent optical properties for phytoplankton assemblages of changing dominant cell size and functional type. Finally, a preliminary validation is conducted of inherent optical properties determined for natural phytoplankton populations with the two-layered model, using the reflectance approximation. The study demonstrates the validity of the two-layered geometry and refractive index structure, and indicates that the combined use of equivalent size distributions with the heterogeneous geometry can be used to establish a quantitative formulation between single particle optics, size and assemblage-specific inherent optical properties, and ocean colour.

Description: The formation of nitrate (nitrification) in soils is an important process that influences the form of N available for plant uptake and the potential off-site N losses. Gross nitrification is one of the main sources of nitrous oxide (N2O) and nitric oxide (NO) from soils. A field experiment was designed to verify the idea that gross nitrification rates in soils can be readily predicted by a model approach where seasonal variability is described only by soil moisture and soil temperature and the magnitude of gross nitrification is controlled by the soil organic matter (SOM). Gross nitrification rates were measured by a Barometric Process Separation (BaPS), first described by Ingwersen et al. (1999). The BaPS measurements were validated with the commonly used 15N pool dilution technique measurements at six times. In general, the rates determined from both measurement approaches were in the same order of magnitude and showed a good correlation. The effects of three different fertilisations (mineral fertiliser, manure and the control) over more than 100 years on gross nitrification rates were investigated. During 2004 soil probes from the long-term "static fertilisation experiment" at Bad Lauchstädt were sampled weekly and were measured in the laboratory under field conditions and subsequently under standardised conditions (16°C soil temperature and −30 kPa matrix potential) with the Barometric Process Separation system (BaPS). Gross nitrification rates determined by the BaPS-method under field conditions showed a high temporal variability and ranged from 5 to 77 μg N h−1 kg−1 dry mass, 2 to 74 μg N h−1 kg−1 dry mass and 0 to 49 μg N h−1 kg−1 dry mass with respect to manure, mineral fertiliser and control. The annual average was 0.32, 0.26 and 0.18 g N a−1 kg−1 dry mass for the manure site, mineral fertiliser site and control site, respectively. On all sites gross nitrification revealed a strong seasonal dynamic. Three different methods (a temperature and soil moisture dependency model from Recous et al., 1998, a multiple linear regression and the method proposed in this paper) were applied for reproducing the measured results. On the manure site 78% to 80%, on the mineral fertiliser site 66% to 72% and on the control site 39% to 56% of the observed variations could be explained by the tested models. Gross nitrification rates determined under standardised conditions did not show any seasonal trends but did also however reveal high temporal variability.

Description: 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.

Description: While we now know that marine N2 fixation is a significant source of new nitrogen (N) in the marine environment, little is known about the fate of this production, despite the importance of diazotrophs to global carbon and nutrient cycles. Specifically, does new production from N2 fixation fuel autotrophic or heterotrophic growth, facilitate carbon (C) export from the euphotic zone, or contribute primarily to microbial productivity and respiration in the euphotic zone? For Trichodesmium, the diazotroph we know the most about, the transfer of recently fixed N2 (and C) appears to be primarily through dissolved pools. The release of N appears to vary among and within populations and, probably as a result of the changing physiological state of cells and populations. The net result of trophic transfers appears to depend on the complexity of the colonizing community and co-occurring organisms. In order to understand the impact of diazotrophy on carbon flow and export in marine systems, we need a better assessment of the trophic flow of elements in Trichodesmium communities dominated by different species, various free and colonial morphologies, and in various defined physiological states. Nitrogen and carbon fixation rates themselves vary by orders of magnitude within and among studies highlighting the difficulty in extrapolating global rates of N2 fixation from direct measurements. Because the stoichiometry of N2 and C fixation does not appear to be in balance with the stoichiometry of particles, and the relationship between C and N2 fixation rates is also variable, it is equally difficult to derive global rates of one from the other. A better understanding of the physiology and physiological ecology of Trichodesmium and other marine diazotrophs is necessary to understand and predict the effects of increased or decreased diazotrophy in the context of the carbon cycle and global change.

Description: We conducted two (May 2002 and September 2003) pulse additions of 15NH4+ to the flood water inundating a tidal freshwater marsh fringing the nutrient-rich Scheldt River (Belgium) and traced the fate of ammonium in the intact ecosystem. Here we report in detail the 15N uptake into the various marsh components (leaves, roots, sediment, leaf litter and invertebrate fauna), and the 15N retention on a scale of 15 days. We particularly focus on the contributions of the rooted macrophytes and the microbial community in the sediment and on plant litter. Assimilation and short term retention of 15NH4+ was low on both occasions. Only 4–9% of the added 15N trace was assimilated, corresponding to 13–22% and 8–18% of the processed 15N (i.e. not exported as 15NH4+ in May and September, respectively. In May nitrogen assimilation rate (per hour inundated) was 〉3 times faster than in September. Macrophytes (above- and below ground) were of limited importance for short term 15N retention accounting for

Description: 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.

Description: Only recently has specific attention been given to culturable bacteria in Tibetan glaciers, but their relation to atmospheric circulation is less understood yet. Here we investigate the seasonal variation of culturable bacteria preserved in a Himalayan ice core. High concentration of culturable bacteria in glacial ice deposited during the pre-monsoon season is attributed to the transportation of continental dust stirred up by the frequent dust storms in Northwest China during spring. This is also confirmed by the spatial distribution of culturable bacteria in Tibetan glaciers. Culturable bacteria deposited during monsoon season are more diverse than other seasons because they derive from both marine air masses and local or regional continental sources. We suggest that microorganisms in Himalayan ice can be used to reconstruct atmospheric circulation.

Description: The cyanobacterium Trichodesmium is an important link in the global nitrogen cycle due to its significant input of atmospheric nitrogen into the ocean. Incorporating Trichodesmium in ocean biogeochemical circulation models relies on field-based correlations between temperature and Trichodesmium abundance. The observed correlation of Trichodesmium abundance with temperature in the ocean may result in part from a direct effect on Trichodesmium growth rates through the control of cellular biochemical processes, or indirectly through its influence on mixed layer depth, light and nutrient regimes. Here we present results indicating that the observed correlation of Trichodesmium with temperature in the field reflects primarily the direct physiological effects of temperature on diazotrophic growth of Trichodesmium. Trichodesmium IMS-101 (an isolate of T. erythraeum) could acclimate and grow at temperatures ranging from 20 to 34°C. Maximum growth rates (μmax=0.25 day−1) and maximum nitrogen fixation rates (0.13 mmol N mol POC−1 h−1) were measured within 24 to 30°C. This empirical relationship and global warming scenarios derived from state-of-the-art climate models set a physiological constraint on the future distribution of Trichodesmium that could significantly affect nitrogen input into oligotrophic waters by this diazotroph.

Description: The aim of this study was to compare structural differences in the denitrifying microbial communities along the environmental gradients observed in the water column and coastal sediments of the Baltic Sea. To link community structure and environmental gradients, denitrifier communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) based on nirS as a functional marker gene for denitrification. NirS-type denitrifier community composition was further evaluated by phylogenetic analysis of nirS sequences from clone libraries. T-RFLP analysis indicated some overlap but also major differences of communities from the water column and the sediment. Shifts in community composition along the biogeochemical gradients were observed only in the water column while denitrifier communities were rather uniform within the upper 30 mm of the sediment. Specific terminal restriction fragments (T-RFs) indicative for the sulfidic zone suggest the presence of nitrate-reducing and sulfide-oxidizing microorganisms that were previously shown to be important at the suboxic-sulfidic interface in the water column of the Baltic Sea. Phylogenetic analysis of nirS genes from the Baltic Sea and of sequences from marine habitats all over the world indicated distinct denitrifier communities that grouped mostly according to their habitat. We suggest that these subgroups of denitrifiers had developed after selection through several factors, i.e. their habitats (water column or sediment), impact by prevalent environmental conditions and isolation by large geographic distances between habitats.