http://www.biogeosciences.net/Biogeosciences Latest Articlesenhttp://www.biogeosciences.net/7/2591/2010/<b>Tracing carbon assimilation in endosymbiotic deep-sea hydrothermal vent Mytilid fatty acids by ¹³C-fingerprinting</b><br /><br />Biogeosciences, 7, 2591-2600, 2010<br /><br />Author(s): V. Riou, S. Bouillon, R. Serrão Santos, F. Dehairs, and A. Colaço<br /><br /><i>Bathymodiolus azoricus</i> mussels thrive at Mid-Atlantic Ridge hydrothermal vents, where part of their energy requirements are met via an endosymbiotic association with chemolithotrophic and methanotrophic bacteria. In an effort to describe phenotypic characteristics of the two bacterial endosymbionts and to assess their ability to assimilate CO₂, CH₄ and multi-carbon compounds, we performed experiments in aquaria using ¹³C-labeled NaHCO₃ (in the presence of H₂S), CH₄ or amino-acids and traced the incorporation of ¹³C into total and phospholipid fatty acids (tFA and PLFA, respectively). 14:0; 15:0; 16:0; 16:1(<i>n</i> − 7)<i>c+t</i>; 18:1(<i>n</i> − 13)<i>c+t</i> and (<i>n</i> − 7)<i>c+t</i>; 20:1(<i>n</i> − 7); 20:2(<i>n</i> − 9,15); 18:3(<i>n</i> − 7) and (<i>n</i> − 5,10,13) PLFA were labeled in the presence of H¹³CO₃⁻ (+H₂S) and ¹³CH₄, while the 12:0 compound became labeled only in the presence of H¹³CO₃⁻ (+H₂S). In contrast, the 17:0; 18:0; 16:1(<i>n</i> − 9); 16:1(<i>n</i> − 8) and (<i>n</i> − 6); 18:1(<i>n</i> − 8); and 18:2(<i>n</i> − 7) PLFA were only labeled in the presence of ¹³CH₄. Some of these symbiont-specific fatty acids also appeared to be labeled in mussel gill tFA when incubated with ¹³C-enriched amino acids, and so were mussel-specific fatty acids such as 22:2(<i>n</i> − 7,15). Our results provide experimental evidence for the potential of specific fatty acid markers to distinguish between the two endosymbiotic bacteria, shedding new light on C₁ and multi-carbon compound metabolic pathways in <i>B. azoricus</i> and its symbionts.Thu, 02 Sep 2010 00:00:00 +0200http://www.biogeosciences.net/7/2581/2010/<b>A mechanistic account of increasing seasonal variations in the rate of ocean uptake of anthropogenic carbon</b><br /><br />Biogeosciences, 7, 2581-2589, 2010<br /><br />Author(s): T. Gorgues, O. Aumont, and K. B. Rodgers<br /><br />A three-dimensional circulation model that includes a representation of anthropogenic carbon as a passive tracer is forced with climatological buoyancy and momentum fluxes. This simulation is then used to compute offline the anthropogenic &Delta;<i>p</i>CO₂ (defined as the difference between the atmospheric CO₂ and its seawater partial pressure) trends over three decades between the years 1970 and 2000. It is shown that the mean increasing trends in &Delta;<i>p</i>CO₂ reflects an increase of the seasonal amplitude of &Delta;<i>p</i>CO₂. In particular, the ocean uptake of anthropogenic CO₂ is decreasing (negative trends in &Delta;<i>p</i>CO₂) in boreal (austral) summer in the Northern (Southern) Hemisphere in the subtropical gyres between 20° N (S) and 40° N (S). In our simulation, the increased amplitude of the seasonal trends of the &Delta;<i>p</i>CO₂ is mainly explained by the seasonal sea surface temperature (SST) acting on the anthropogenic increase of the dissolved inorganic carbon (DIC). It is also shown that the seasonality of the anthropogenic DIC has very little effect on the decadal trends. Finally, an observing system for <i>p</i>CO₂ that is biased towards summer measurements may be underestimating uptake of anthropogenic CO₂ by about 0.6 PgC yr⁻¹ globally over the period of the WOCE survey in the mid-1990s according to our simulations. This bias associated with summer measurements should be expected to grow larger in time and underscores the need for surface CO₂ measurements that resolve the seasonal cycle throughout much of the extratropical oceans.Tue, 31 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2567/2010/<b>Hypoxia and cyanobacteria blooms - are they really natural features of the late Holocene history of the Baltic Sea?</b><br /><br />Biogeosciences, 7, 2567-2580, 2010<br /><br />Author(s): L. Zillén and D. J. Conley<br /><br />During the last century (1900s) industrialized forms of agriculture and human activities have caused eutrophication of Baltic Sea waters. As a consequence, the hypoxic zone in the Baltic Sea has increased, especially during the last 50 years, and has caused severe ecosystem disturbance. Climate forcing has been proposed to be responsible for the reported trends in hypoxia (&lt; 2 mg/l O₂) both during the last c. 100 years (since c. 1900 AD) and the Medieval Period. By contrast, investigations of the degree of anthropogenic forcing on the ecosystem on long time-scales (millennial and greater) have not been thoroughly addressed. This paper examines evidence for anthropogenic disturbance of the marine environment beyond the last century through the analysis of the human population growth, technological development and land-use changes in the drainage area. Natural environmental changes, i.e. changes in the morphology and depths of the Baltic basin and the sills, were probably the main driver for large-scale hypoxia during the early Holocene (8000–4000 cal yr BP). We show that hypoxia during the last two millennia has followed the general expansion and contraction trends in Europe and that human perturbation has been an important driver for hypoxia during that time. Hypoxia occurring during the Medieval Period coincides with a doubling of the population (from c. 4.6 to 9.5 million) in the Baltic Sea watershed, a massive reclamation of land in both established and marginal cultivated areas and significant increases in soil nutrient release. The role of climate forcing on hypoxia in the Baltic Sea has yet to be demonstrated convincingly, although it could have helped to sustain hypoxia through enhanced salt water inflows or through changes in hydrological inputs. In addition, cyanobacteria blooms are not natural features of the Baltic Sea as previously deduced, but are a consequence of enhanced phosphorus release from the seabed that occurs during hypoxia.Tue, 31 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2557/2010/<b>Upscaling reflectance information of lichens and mosses using a singularity index: a case study of the Hudson Bay Lowlands, Canada</b><br /><br />Biogeosciences, 7, 2557-2565, 2010<br /><br />Author(s): T. Neta, Q. Cheng, R. L. Bello, and B. Hu<br /><br />Assessing moisture contents of lichens and mosses using ground-based high spectral resolution spectrometers (400–2500 nm) offers immense opportunities for a comprehensive monitoring of peatland moisture status by satellite/airborne imagery. This information may be valuable for present and future carbon balance modeling. Previous studies are based upon point measurements of vegetation moisture content and water table position, and therefore a detailed moisture status of entire northern peatlands is not available. Consequently, upscaling ground and remotely sensed data to the desired spatial resolutions is inevitable. This study continues our previous investigation of the impact of various moisture conditions of common sub-Arctic lichen and moss species (i.e., <i>Cladina stellaris, Cladina rangiferina, Dicranum elongatum</i>, and <i>Tomenthypnum nitens</i>) upon the spectral signatures obtained in the Hudson Bay Lowlands, Canada. Upscaling reflectance measurements of the above species were conducted in the field, and reflectance analysis using a singularity index was made, since this study serves as a basis for future aircraft/satellite research. An attempt to upscale current and new spectral reflectance indices developed in our previous studies was made as well. Our findings indicate that the spectral index <i>C. rangiferina</i> is to a lesser amount influenced by scale since it has a small <i>R</i>² values between the log of the index and the log of the resolution, reduced slopes between the log of the index and the log of the resolution, and similar slopes between log reflectance and log resolution (<i>&alpha;</i>) of two wavelengths employed by the index. Future study should focus on concurrent monitoring of moisture variations in lichens and mosses both in situ and from satellite and airborne images, as well as analysis of fractal models in relations to the upscaling experiments.Fri, 27 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2545/2010/<b>Characterization of broom fibers for PRB in the remediation of aquifers contaminated by heavy metals</b><br /><br />Biogeosciences, 7, 2545-2556, 2010<br /><br />Author(s): C. Fallico, S. Troisi, A. Molinari, and M. F. Rivera<br /><br />The present level of pollution, increasingly involving ground waters, constitutes a serious risk to the environment and also to human health. Therefore the remediation of saturated and unsaturated soils to remove pollutant materials is more and more frequently required. In the present paper, the possibility of removing heavy metals by permeable reactive barrier (PRB) from the groundwater carried out specifically with broom fibers, is investigated. <br><br> Once shown the economic benefits deriving from the use of this plant, a hydraulic characterization of the broom fiber mass was performed, determining the permeability and the porosity in correspondence to different levels of compactness of the fibers. <br><br> Having verified the effectiveness of removal of some heavy metals by these fibers, the results of some experiments, carried out in the laboratory for this purpose, are shown. These experiments were carried out utilizing broom fibers obtained in different ways and, limitedly to the considered pollutants, showed the high capability of these fibers to reduce their concentrations. The best results were obtained for the broom fibers extracted by a particular chemical-physical process. <br><br> Moreover, the behaviour of this fiber with time was investigated, determining the kinetic constant of degradation.Wed, 25 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2531/2010/<b>Towards ground-truthing of spaceborne estimates of above-ground life biomass and leaf area index in tropical rain forests</b><br /><br />Biogeosciences, 7, 2531-2543, 2010<br /><br />Author(s): P. Köhler and A. Huth<br /><br />The canopy height <i>h</i> of forests is a key variable which can be obtained using air- or spaceborne remote sensing techniques such as radar interferometry or LIDAR. If new allometric relationships between canopy height and the biomass stored in the vegetation can be established this would offer the possibility for a global monitoring of the above-ground carbon content on land. In the absence of adequate field data we use simulation results of a tropical rain forest growth model to propose what degree of information might be generated from canopy height and thus to enable ground-truthing of potential future satellite observations. We here analyse the correlation between canopy height in a tropical rain forest with other structural characteristics, such as above-ground life biomass (AGB) (and thus carbon content of vegetation) and leaf area index (LAI) and identify how correlation and uncertainty vary for two different spatial scales. The process-based forest growth model FORMIND2.0 was applied to simulate (a) undisturbed forest growth and (b) a wide range of possible disturbance regimes typically for local tree logging conditions for a tropical rain forest site on Borneo (Sabah, Malaysia) in South-East Asia. In both undisturbed and disturbed forests AGB can be expressed as a power-law function of canopy height <i>h</i> (AGB = <i>a &middot; h^b</i>) with an <i>r</i>² ~ 60% if data are analysed in a spatial resolution of 20 m × 20 m (0.04 ha, also called plot size). The correlation coefficient of the regression is becoming significant better in the disturbed forest sites (<i>r</i>² = 91%) if data are analysed hectare wide. There seems to exist no functional dependency between LAI and canopy height, but there is also a linear correlation (<i>r</i>² ~ 60%) between AGB and the area fraction of gaps in which the canopy is highly disturbed. A reasonable agreement of our results with observations is obtained from a comparison of the simulations with permanent sampling plot (PSP) data from the same region and with the large-scale forest inventory in Lambir. We conclude that the spaceborne remote sensing techniques such as LIDAR and radar interferometry have the potential to quantify the carbon contained in the vegetation, although this calculation contains due to the heterogeneity of the forest landscape structural uncertainties which restrict future applications to spatial averages of about one hectare in size. The uncertainties in AGB for a given canopy height are here 20&ndash;40% (95% confidence level) corresponding to a standard deviation of less than &plusmn; 10%. This uncertainty on the 1 ha-scale is much smaller than in the analysis of 0.04 ha-scale data. At this small scale (0.04 ha) AGB can only be calculated out of canopy height with an uncertainty which is at least of the magnitude of the signal itself due to the natural spatial heterogeneity of these forests.Wed, 25 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2509/2010/<b>Feedbacks and responses of coral calcification on the Bermuda reef system to seasonal changes in biological processes and ocean acidification</b><br /><br />Biogeosciences, 7, 2509-2530, 2010<br /><br />Author(s): N. R. Bates, A. Amat, and A. J. Andersson<br /><br />Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO₂) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species <i>Diploria labyrinthiformis</i> and the seasonal variability of [CO₃^2-] and aragonite saturation state &Omega;_aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO₃^2-] and &Omega;_aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO₂. In late summer, rates of coral calcification are suppressed by release of CO₂ from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO₃^2-] and &Omega;_aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO₃^2-] and &Omega;_aragonite thresholds of ~184 μmoles kg⁻¹ and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO₃^2-] and &Omega;_aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for <i>D. labyrinthiformis</i> have declined by >50% compared to pre-industrial times.Tue, 24 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2489/2010/<b>Fractionation of iron species and iron isotopes in the Baltic Sea euphotic zone</b><br /><br />Biogeosciences, 7, 2489-2508, 2010<br /><br />Author(s): J. Gelting, E. Breitbarth, B. Stolpe, M. Hassellöv, and J. Ingri<br /><br />To indentify sources and transport mechanisms of iron in a coastal marine environment, we conducted measurements of the physiochemical speciation of Fe in the euphotic zone at three different locations in the Baltic Sea. In addition to sampling across a salinity gradient, we conducted this study over the spring and summer season. Moving from the riverine input characterized low salinity Bothnian Sea, via the Landsort Deep near Stockholm, towards the Gotland Deep in the Baltic Proper, total Fe concentrations averaged 114, 44, and 15 nM, respectively. At all three locations, a decrease in total Fe of 80–90% from early spring to summer was observed. Particulate Fe (PFe) was the dominating phase at all stations and accounted for 75–85% of the total Fe pool on average. The Fe isotope composition (&delta;⁵⁶Fe) of the PFe showed constant positive values in the Bothnian Sea surface waters (+0.08 to +0.20&permil;). Enrichment of heavy Fe in the Bothnian Sea PFe is possibly associated to input of aggregated land derived Fe-oxyhydroxides and oxidation of dissolved Fe(II). At the Landsort Deep the isotopic fractionation of PFe changed between −0.08&permil; to +0.28&permil; over the sampling period. The negative values in early spring indicate transport of PFe from the oxic-anoxic boundary at &sim;80 m depth. The average colloidal iron fraction (CFe) showed decreasing concentrations along the salinity gradient; Bothnian Sea 15 nM; Landsort Deep 1 nM, and Gotland Deep 0.5 nM. Field Flow Fractionation data indicate that the main colloidal carrier phase for Fe in the Baltic Sea is a carbon-rich fulvic acid associated compound, likely of riverine origin. A strong positive correlation between PFe and chl-<i>a</i> indicates that cycling of suspended Fe is at least partially controlled by primary production. However, this relationship may not be dominated by active uptake of Fe into phytoplankton, but instead may reflect scavenging and removal of PFe during phytoplankton sedimentation.Mon, 23 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2477/2010/<b>Shadow analysis of soil surface roughness compared to the chain set method and direct measurement of micro-relief</b><br /><br />Biogeosciences, 7, 2477-2487, 2010<br /><br />Author(s): R. García Moreno, M. C. Díaz Álvarez, A. M. Tarquis, A. Paz González, and A. Saa Requejo<br /><br />Soil surface roughness (SSR) expresses soil susceptibility to wind and water erosion and plays an important role in the development and the maintenance of soil biota. Several methods have been developed to characterise SSR based on different methods of acquiring data. Because the main problems related to these methods involve the use and handling of equipment in the field, the present study aims to fill the need for a method for measuring SSR that is more reliable, low-cost and convenient in the field than traditional field methods. Shadow analysis, which interprets micro-topographic shadows, is based on the principle that there is a direct relationship between the soil surface roughness and the shadows cast by soil structures under fixed sunlight conditions. SSR was calculated with shadows analysis in the laboratory using hemispheres of different diameter with a diverse distribution of known altitudes and a surface area of 1 m². <br><br> Data obtained from the shadow analysis were compared to data obtained with the chain method and simulation of the micro-relief. The results show a relationship among the SSR calculated using the different methods. To further improve the method, shadow analysis was used to measure the SSR in a sandy clay loam field using different tillage tools (chisel, tiller and roller) and in a control of 4 m² surface plots divided into subplots of 1 m². The measurements were compared to the data obtained using the chain set and pin meter methods. The SSR measured was the highest when the chisel was used, followed by the tiller and the roller, and finally the control, for each of the three methods. Shadow analysis is shown to be a reliable method that does not disturb the measured surface, is easy to handle and analyse, and shortens the time involved in field operations by a factor ranging from 4 to 20 compared to well known techniques such as the chain set and pin meter methods.Wed, 18 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2461/2010/<b>Contribution of advection to the carbon budget measured by eddy covariance at a steep mountain slope forest in Switzerland</b><br /><br />Biogeosciences, 7, 2461-2475, 2010<br /><br />Author(s): S. Etzold, N. Buchmann, and W. Eugster<br /><br />We calculated the contribution of advection to the C budget measured by the eddy covariance (EC) technique for a steep and forested mountain site (CarboEurope site CH-Lae, Lägeren, Switzerland) during the growing season 2007 (May to August). Thereby we followed two approaches: (1) the physical correction of the EC data for directly measured advection terms and (2) the <i>u</i>_&lowast; filter approach that replaces periods with <i>u</i>_&lowast; below a site-specific threshold with empirically modelled fluxes. We found good agreement between the two approaches in terms of daily (linear regression slope: 0.78 ± 0.04, intercept: 0.68 ± 0.29 μmol m⁻² s⁻¹, adj. <i>R</i>²=0.78) and seasonal sums of gross fluxes (difference &le; 12%), when using a <i>u</i>_&lowast; threshold of 0.3 m s⁻¹ and correcting EC for horizontal advection only. Incorporating also vertical advection into the mass balance equation resulted in unrealistic and highly erratic fluxes. However, on a daily basis vertical advection cancelled out to nearly zero. The <i>u</i>_&lowast; filter seems to account primarily for respiration fluxes, which are mainly affected by horizontal advection. We could confirm our corrections by a cross-validation with independent approaches, such as soil respiration chamber measurements, light curves and energy budget closure. Our results show that flux measurements on steep sites with complex topography are possible. Actually, sloping sites seem to have the advantage over flat sites that advection measurements can be reduced to a simplified two-dimensional measurement approach due to the two-dimensional characteristics of the wind field at those sites.Tue, 17 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2445/2010/<b>Abrupt sea surface pH change at the end of the Younger Dryas in the central sub-equatorial Pacific inferred from boron isotope abundance in corals (<i>Porites</i>)</b><br /><br />Biogeosciences, 7, 2445-2459, 2010<br /><br />Author(s): E. Douville, M. Paterne, G. Cabioch, P. Louvat, J. Gaillardet, A. Juillet-Leclerc, and L. Ayliffe<br /><br />The "δ¹¹B-pH" technique was applied to modern and ancient corals <i>Porites</i> from the sub-equatorial Pacific areas (Tahiti and Marquesas) spanning a time interval from 0 to 20.720 calendar years to determine the amplitude of pH changes between the Last Glacial Period and the Holocene. Boron isotopes were measured by Multi-Collector – Inductively Coupled Plasma Mass Spectrometry (MC-ICPMS) with an external reproducibility of 0.25&permil;, allowing a precision of about &plusmn;0.03 pH-units for pH values between 8 and 8.3. The boron concentration [B] and isotopic composition of modern samples indicate that the temperature strongly controls the partition coefficient K_<i>D</i> for different aragonite species. Modern coral δ¹¹B values and the reconstructed sea surface pH values for different Pacific areas match the measured pH expressed on the seawater scale and confirm the calculation parameters that were previously determined by laboratory calibration exercises. Most ancient sea surface pH reconstructions near Marquesas are higher than modern values. These values range between 8.19 and 8.27 for the Holocene and reached 8.30 at the end of the last glacial period (20.7 kyr BP). At the end of the Younger Dryas (11.50&plusmn;0.1 kyr BP), the central sub-equatorial Pacific experienced a dramatic drop of up to 0.2 pH-units from the average pH of 8.2 before and after this short event. Using the marine carbonate algorithms, we recalculated the aqueous <i>p</i>CO₂ to be 440&plusmn;25 ppmV at around 11.5 kyr BP for corals at Marquesas and ~500 ppmV near Tahiti where it was assumed that <i>p</i>CO₂ in the atmosphere was 250 ppmV. Throughout the Holocene, the difference in <i>p</i>CO₂ between the ocean and the atmosphere at Marquesas (Δ<i>p</i>CO₂) indicates that the surface waters behave as a moderate CO₂ sink or source (−53 to 20 ppmV) during El Niño-like conditions. By contrast, during the last glacial/interglacial transition, this area was a marked source of CO₂ (21 to 92 ppmV) for the atmosphere, highlighting predominant La Niña-like conditions. Such conditions were particularly pronounced at the end of the Younger Dryas with a large amount of CO₂ released with Δ<i>p</i>CO₂ of +185&plusmn;25 ppmV. This last finding provides further evidence of the marked changes in the surface water pH and temperature in the equatorial Pacific at the Younger Dryas-Holocene transition and the strong impact of oceanic dynamic on the atmospheric CO₂ content.Mon, 16 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2433/2010/<b>Microbial conversion of inorganic carbon to dimethyl sulfide in anoxic lake sediment (Plußsee, Germany)</b><br /><br />Biogeosciences, 7, 2433-2444, 2010<br /><br />Author(s): Y. S. Lin, V. B. Heuer, T. G. Ferdelman, and K.-U. Hinrichs<br /><br />In anoxic environments, volatile methylated sulfides like methanethiol (MT) and dimethyl sulfide (DMS) link the pools of inorganic and organic carbon with the sulfur cycle. However, direct formation of methylated sulfides from reduction of dissolved inorganic carbon has previously not been demonstrated. When studying the effect of temperature on hydrogenotrophic microbial activity, we observed formation of DMS in anoxic sediment of Lake Plußsee at 55 °C. Subsequent experiments strongly suggested that the formation of DMS involves fixation of bicarbonate via a reductive pathway in analogy to methanogenesis and engages methylation of MT. DMS formation was enhanced by addition of bicarbonate and further increased when both bicarbonate and H₂ were supplemented. Inhibition of DMS formation by 2-bromoethanesulfonate points to the involvement of methanogens. Compared to the accumulation of DMS, MT showed the opposite trend but there was no apparent 1:1 stoichiometric ratio between both compounds. Both DMS and MT had negative &delta;¹³C values of −62&permil; and −55&permil;, respectively. Labeling with NaH¹³CO₃ showed more rapid incorporation of bicarbonate into DMS than into MT. The stable carbon isotopic evidence implies that bicarbonate was fixed via a reductive pathway of methanogenesis, and the generated methyl coenzyme M became the methyl donor for MT methylation. Neither DMS nor MT accumulation were stimulated by addition of the methyl-group donors methanol and syringic acid or by the methyl-group acceptor hydrogen sulphide. The source of MT was further investigated in a H₂³⁵S labeling experiment, which demonstrated a microbially-mediated process of hydrogen sulfide methylation to MT that accounted for only <10% of the accumulation rates of DMS. Therefore, the major source of the ¹³C-depleted MT was neither bicarbonate nor methoxylated aromatic compounds. Other possibilities for isotopically depleted MT, such as other organic precursors like methionine, are discussed. This DMS-forming pathway may be relevant for anoxic environments such as hydrothermally influenced sediments and fluids and sulfate-methane transition zones in marine sediments.Mon, 16 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2419/2010/<b>The trophic biology of the holothurian <i>Molpadia musculus</i>: implications for organic matter cycling and ecosystem functioning in a deep submarine canyon</b><br /><br />Biogeosciences, 7, 2419-2432, 2010<br /><br />Author(s): T. Amaro, S. Bianchelli, D. S. M. Billett, M. R. Cunha, A. Pusceddu, and R. Danovaro<br /><br />Megafaunal organisms play a key role in ecosystem functioning in the deep-sea through bioturbation, bioirrigation and organic matter cycling. At 3500 m water depth in the Nazaré Canyon, NE Atlantic, very high abundances of the infaunal holothurian <i>Molpadia musculus</i> were observed. To quantify the role of <i>M. musculus</i> in sediment cycling, sediment samples and holothurians were collected using an ROV and in situ experiments were conducted with incubation chambers. The biochemical composition of the sediment (in terms of proteins, carbohydrates and lipids), the holothurians' gut contents and holothurians' faecal material were analysed. In the sediments, proteins were the dominant organic compound, followed by carbohydrates and lipids. In the holothurian's gut contents, protein concentrations were higher than the other compounds, decreasing significantly as the material passed through the digestive tract. Approximately 33&plusmn;1% of the proteins were digested by the time sediment reached the mid gut, with a total digestion rate equal to 67&plusmn;1%. Carbohydrates and lipids were ingested in smaller amounts and digested with lower efficiencies (23&plusmn;11% and 50&plusmn;11%, respectively). As a result, the biopolymeric C digestion rate was on average 62&plusmn;3%. We estimated that the population of <i>M. musculus</i> could remove approximately 0.49&plusmn;0.13 g biopolymeric C and 0.13&plusmn;0.03 g N m⁻² d⁻¹ from the sediments. These results suggest that <i>M. musculus</i> plays a key role in the benthic tropho-dynamics and biogeochemical processes in the Nazaré Canyon.Mon, 16 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2397/2010/<b>Simulating carbon exchange using a regional atmospheric model coupled to an advanced land-surface model</b><br /><br />Biogeosciences, 7, 2397-2417, 2010<br /><br />Author(s): H. W. Ter Maat, R. W. A. Hutjes, F. Miglietta, B. Gioli, F. C. Bosveld, A. T. Vermeulen, and H. Fritsch<br /><br />This paper is a case study to investigate what the main controlling factors are that determine atmospheric carbon dioxide content for a region in the centre of The Netherlands. We use the Regional Atmospheric Modelling System (RAMS), coupled with a land surface scheme simulating carbon, heat and momentum fluxes (SWAPS-C), and including also submodels for urban and marine fluxes, which in principle should include the dominant mechanisms and should be able to capture the relevant dynamics of the system. To validate the model, observations are used that were taken during an intensive observational campaign in central Netherlands in summer 2002. These include flux-tower observations and aircraft observations of vertical profiles and spatial fluxes of various variables. <br><br> The simulations performed with the coupled regional model (RAMS-SWAPS-C) are in good qualitative agreement with the observations. The station validation of the model demonstrates that the incoming shortwave radiation and surface fluxes of water and CO₂ are well simulated. The comparison against aircraft data shows that the regional meteorology (i.e. wind, temperature) is captured well by the model. Comparing spatially explicitly simulated fluxes with aircraft observed fluxes we conclude that in general latent heat fluxes are underestimated by the model compared to the observations but that the latter exhibit large variability within all flights. Sensitivity experiments demonstrate the relevance of the urban emissions of carbon dioxide for the carbon balance in this particular region. The same tests also show the relation between uncertainties in surface fluxes and those in atmospheric concentrations.Mon, 16 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2379/2010/<b>Temperate carbonate cycling and water mass properties from intertidal to bathyal depths (Azores)</b><br /><br />Biogeosciences, 7, 2379-2396, 2010<br /><br />Author(s): M. Wisshak, A. Form, J. Jakobsen, and A. Freiwald<br /><br />The rugged submarine topography of the Azores supports a diverse heterozoan association resulting in intense biotically-controlled carbonate-production and accumulation. In order to characterise this cold-water (C) factory a 2-year experiment was carried out in the southern Faial Channel to study the biodiversity of hardground communities and for budgeting carbonate production and degradation along a bathymetrical transect from the intertidal to bathyal 500 m depth. <br><br> Seasonal temperatures peak in September (above a thermocline) and bottom in March (stratification diminishes) with a decrease in amplitude and absolute values with depth, and tidal-driven short-term fluctuations. Measured seawater stable isotope ratios and levels of dissolved nutrients decrease with depth, as do the calcium carbonate saturation states. The photosynthetic active radiation shows a base of the euphotic zone in ~70 m and a dysphotic limit in ~150 m depth. <br><br> Bioerosion, being primarily a function of light availability for phototrophic endoliths and grazers feeding upon them, is ~10 times stronger on the illuminated upside versus the shaded underside of substrates in the photic zone, with maximum rates in the intertidal (−631 g/m²/yr). Rates rapidly decline towards deeper waters where bioerosion and carbonate accretion are slow and epibenthic/endolithic communities take years to mature. Accretion rates are highest in the lower euphotic zone (955 g/m²/yr), where the substrate is less prone to hydrodynamic force. Highest rates are found – inversely to bioerosion – on down-facing substrates, suggesting that bioerosion may be a key factor governing the preferential settlement and growth of calcareous epilithobionts on down-facing substrates. <br><br> In context of a latitudinal gradient, the Azores carbonate cycling rates plot between known values from the cold-temperate Swedish Kosterfjord and the tropical Bahamas, with a total range of two orders in magnitude. Carbonate budget calculations for the bathymetrical transect yield a mean 266.9 kg of epilithic carbonate production, −54.6 kg of bioerosion, and 212.3 kg of annual net carbonate production per metre of coastline in the Azores C factory.Fri, 13 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2369/2010/<b>Determination of total N ₂ fixation rates in the ocean taking into account both the particulate and filtrate fractions</b><br /><br />Biogeosciences, 7, 2369-2377, 2010<br /><br />Author(s): U. Konno, U. Tsunogai, D. D. Komatsu, S. Daita, F. Nakagawa, A. Tsuda, T. Matsui, Y.-J. Eum, and K. Suzuki<br /><br />Using the ¹⁵N₂ tracer method and high-sensitivity &delta;¹⁵N analytical systems, we determined N₂ fixation rates for ocean samples by dividing them into particulate (>0.7 μm) and filtrate (<0.7 μm) fractions. While N₂ fixation in the filtrate fraction had been ignored in previous studies, we found a significant N₂ fixation rates in the filtrate fraction in our study. The areal N₂ fixation rates in the western North Pacific Ocean estimated from the particulate fraction varied from <1 to 160 μmol N m^-2 d⁻¹, and those rates estimated from the filtrate fraction ranged from <0.5 to 54 μmol N m^-2 d⁻¹. Thus, N₂ fixation in the filtrate fraction accounts for on average 50% (ranging from <10% to 84%) of the total N₂ fixation rates. If these results are confirmed generally in the ocean, the new total N₂ fixation flux, which includes fixation in the filtrate fraction, possibly doubles the original estimates; therefore, the revised influx may reduce the imbalance in the global oceanic fixed nitrogen budget.Thu, 12 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2351/2010/<b>Trends and regional distributions of land and ocean carbon sinks</b><br /><br />Biogeosciences, 7, 2351-2367, 2010<br /><br />Author(s): J. L. Sarmiento, M. Gloor, N. Gruber, C. Beaulieu, A. R. Jacobson, S. E. Mikaloff Fletcher, S. Pacala, and K. Rodgers<br /><br />We show here an updated estimate of the net land carbon sink (NLS) as a function of time from 1960 to 2007 calculated from the difference between fossil fuel emissions, the observed atmospheric growth rate, and the ocean uptake obtained by recent ocean model simulations forced with reanalysis wind stress and heat and water fluxes. Except for interannual variability, the net land carbon sink appears to have been relatively constant at a mean value of −0.27 Pg C yr⁻¹ between 1960 and 1988, at which time it increased abruptly by −0.88 (−0.77 to −1.04) Pg C yr⁻¹ to a new relatively constant mean of −1.15 Pg C yr⁻¹ between 1989 and 2003/7 (the sign convention is negative out of the atmosphere). This result is detectable at the 99% level using a t-test. The land use source (LU) is relatively constant over this entire time interval. While the LU estimate is highly uncertain, this does imply that most of the change in the net land carbon sink must be due to an abrupt increase in the land sink, LS = NLS – LU, in response to some as yet unknown combination of biogeochemical and climate forcing. A regional synthesis and assessment of the land carbon sources and sinks over the post 1988/1989 period reveals broad agreement that the Northern Hemisphere land is a major sink of atmospheric CO₂, but there remain major discrepancies with regard to the sign and magnitude of the net flux to and from tropical land.Fri, 06 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2339/2010/<b>Heavy metal incorporation in foraminiferal calcite: results from multi-element enrichment culture experiments with <i>Ammonia tepida</i></b><br /><br />Biogeosciences, 7, 2339-2350, 2010<br /><br />Author(s): D. Munsel, U. Kramar, D. Dissard, G. Nehrke, Z. Berner, J. Bijma, G.-J. Reichart, and T. Neumann<br /><br />The incorporation of heavy metals into carbonate tests of the shallow water benthic foraminifer <i>Ammonia tepida</i> was investigated under controlled laboratory conditions. Temperature, salinity, and pH of the culture solutions were kept constant throughout the duration of this experiment, while trace metal concentrations were varied. Concentrations of Ni, Cu, and Mn were set 5-, 10-, and 20 times higher than levels found in natural North Sea water; for reference, a control experiment with pure filtered natural North Sea water was also analysed. The concentrations of Cu and Ni from newly grown chambers were determined by means of both μ-synchrotron XRF and Laser Ablation Inductively Coupled Plasma Mass Spectroscopy (LA-ICP-MS). The results of both independent analytical techniques agreed within the analytical uncertainty. In general, the concentration of the analysed elements in the tests increased in line with their concentration in the culture solutions. Potential toxic and/or chemical competition effects might have resulted in the decreased incorporation of Ni and Cu into the calcite of the specimens exposed to the highest elemental concentrations. Mn incorporation exhibited large variability in the experiment with the 20-fold increased element concentrations, potentially due to antagonistic effects with Cu. The partition coefficients of Cu and Ni were calculated to be 0.14 ± 0.02 and 1.0 ± 0.5, respectively, whereas the partition coefficient of Mn was estimated to be least 2.4. These partition coefficients now open the way for reconstructing past concentrations for these elements in sea water.Fri, 06 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2327/2010/<b>Heterotrophic denitrification vs. autotrophic anammox – quantifying collateral effects on the oceanic carbon cycle</b><br /><br />Biogeosciences, 7, 2327-2337, 2010<br /><br />Author(s): W. Koeve and P. Kähler<br /><br />The conversion of fixed nitrogen to N₂ in suboxic waters is estimated to contribute roughly a third to total oceanic losses of fixed nitrogen and is hence understood to be of major importance to global oceanic production and, therefore, to the role of the ocean as a sink of atmospheric CO₂. At present heterotrophic denitrification and autotrophic anammox are considered the dominant sinks of fixed nitrogen. Recently, it has been suggested that the trophic nature of pelagic N₂-production may have additional, "collateral" effects on the carbon cycle, where heterotrophic denitrification provides a shallow source of CO₂ and autotrophic anammox a shallow sink. Here, we analyse the stoichiometries of nitrogen and associated carbon conversions in marine oxygen minimum zones (OMZ) focusing on heterotrophic denitrification, autotrophic anammox, and dissimilatory nitrate reduction to nitrite and ammonium in order to test this hypothesis quantitatively. For open ocean OMZs the combined effects of these processes turn out to be clearly heterotrophic, even with high shares of the autotrophic anammox reaction in total N₂-production and including various combinations of dissimilatory processes which provide the substrates to anammox. In such systems, the degree of heterotrophy (ΔCO₂:ΔN₂), varying between 1.7 and 6.5, is a function of the efficiency of nitrogen conversion. On the contrary, in systems like the Black Sea, where suboxic N-conversions are supported by diffusive fluxes of NH₄⁺ originating from neighbouring waters with sulphate reduction, much lower values of ΔCO₂:ΔN₂ can be found. However, accounting for concomitant diffusive fluxes of CO₂, the ratio approaches higher values similar to those computed for open ocean OMZs. Based on this analysis, we question the significance of collateral effects concerning the trophic nature of suboxic N-conversions on the marine carbon cycle.Fri, 06 Aug 2010 00:00:00 +0200http://www.biogeosciences.net/7/2311/2010/<b>An inverse analysis reveals limitations of the soil-CO₂ profile method to calculate CO₂ production and efflux for well-structured soils</b><br /><br />Biogeosciences, 7, 2311-2325, 2010<br /><br />Author(s): B. Koehler, E. Zehe, M. D. Corre, and E. Veldkamp<br /><br />Soil respiration is the second largest flux in the global carbon cycle, yet the underlying below-ground process, carbon dioxide (CO₂) production, is not well understood because it can not be measured in the field. CO₂ production has frequently been calculated from the vertical CO₂ diffusive flux divergence, known as "soil-CO₂ profile method". This relatively simple model requires knowledge of soil CO₂ concentration profiles and soil diffusive properties. Application of the method for a tropical lowland forest soil in Panama gave inconsistent results when using diffusion coefficients (<I>D</I>) calculated based on relationships with soil porosity and moisture ("physically modeled" <I>D</I>). Our objective was to investigate whether these inconsistencies were related to (1) the applied interpolation and solution methods and/or (2) uncertainties in the physically modeled profile of <I>D</I>. First, we show that the calculated CO₂ production strongly depends on the function used to interpolate between measured CO₂ concentrations. Secondly, using an inverse analysis of the soil-CO₂ profile method, we deduce which <I>D</I> would be required to explain the observed CO₂ concentrations, assuming the model perception is valid. In the top soil, this inversely modeled <I>D</I> closely resembled the physically modeled <I>D</I>. In the deep soil, however, the inversely modeled <I>D</I> increased sharply while the physically modeled <I>D</I> did not. When imposing a constraint during the fit parameter optimization, a solution could be found where this deviation between the physically and inversely modeled <I>D</I> disappeared. A radon (Rn) mass balance model, in which diffusion was calculated based on the physically modeled or constrained inversely modeled <I>D</I>, simulated observed Rn profiles reasonably well. However, the CO₂ concentrations which corresponded to the constrained inversely modeled <I>D</I> were too small compared to the measurements. We suggest that, in well-structured soils, a missing description of steady state CO₂ exchange fluxes across water-filled pores causes the soil-CO₂ profile method to fail. These fluxes are driven by the different diffusivities in inter- vs. intra-aggregate pores which create permanent CO₂ gradients if separated by a "diffusive water barrier". These results corroborate other studies which have shown that the theory to treat gas diffusion as homogeneous process, a precondition for use of the soil-CO₂ profile method, is inaccurate for pore networks which exhibit spatial separation between CO₂ production and diffusion out of the soil.Wed, 04 Aug 2010 00:00:00 +0200