ALBERT

Description: Not all calcite ballast is created equal: differing effects of foraminiferan and coccolith calcite on the formation and sinking of aggregates Biogeosciences Discussions, 10, 14861-14885, 2013 Author(s): K. Schmidt, C. L. De La Rocha, M. Gallinari, and G. Cortese Correlation between particulate organic carbon (POC) and calcium carbonate sinking through the deep ocean has led to the idea that ballast provided by calcium carbonate is important for the export of POC from the surface ocean. While this idea is certainly to some extent true, it is worth considering in more nuance, for example, examining the different effects on the aggregation and sinking of POC of small, non-sinking calcite particles like coccoliths and large, rapidly sinking calcite like planktonic foraminiferan tests. We have done that here in a simple experiment carried out in roller tanks that allow particles to sink continuously without being impeded by container walls. Coccoliths were efficiently incorporated into aggregates that formed during the experiment, increasing their sinking speed compared to similarly sized aggregates lacking added calcite ballast. The foraminiferan tests, which sank as fast as 700 m d −1 , became associated with only very minor amounts of POC. In addition, when they collided with other, larger, foraminferan-less aggregates, they fragmented them into two smaller, more slowly sinking aggregates. While these effects were certainly exaggerated within the confines of the roller tanks, they clearly demonstrate that calcium carbonate ballast is not just calcium carbonate ballast- different forms of calcium carbonate ballast have notably different effects on POC aggregation, sinking, and export.

Description: Phenology as a strategy for carbon optimality: a global model Biogeosciences Discussions, 10, 15107-15152, 2013 Author(s): S. Caldararu, D. W. Purves, and P. I. Palmer Phenology is essential to our understanding of biogeochemical cycles and the climate system. We develop a global mechanistic model of leaf phenology based on the hypothesis that phenology is a strategy for optimal carbon gain at the canopy level so that trees adjust leaf gains and losses in response to environmental factors such as light, temperature and soil moisture, to achieve maximum carbon assimilation. We fit this model to five years of satellite observations of leaf area index (LAI) using a Bayesian fitting algorithm. We show that our model is able to reproduce phenological patterns for all vegetation types and use it to explore variations in growing season length and the climate factors that limit leaf growth for different biomes. Phenology in wet tropical areas is limited by leaf age physiological constraints while at higher latitude leaf seasonality is limited by low temperature and light availability. Leaf growth in grassland regions is limited by water availability but often in combination with other factors. This model will advance the current understanding of phenology for ecosystem carbon models and our ability to predict future phenological behaviour.

Description: Timing of sea ice retreat can alter phytoplankton community structure in the western Arctic Ocean Biogeosciences Discussions, 10, 15153-15180, 2013 Author(s): given_name prefix surname suffix, A. Fujiwara, T. Hirawake, K. Suzuki, I. Imai, and S.-I. Saitoh This study assesses the response of phytoplankton assemblages to recent climate change, especially with regard to the shrinking of sea ice in the northern Chukchi Sea of the western Arctic Ocean. Distribution patterns of phytoplankton groups in the late summers of 2008–2010 were analyzed based on HPLC pigment signatures and, the following four major algal groups were inferred via multiple regression and cluster analyses: prasinophytes, diatoms, haptophytes and dinoflagellates. A remarkable interannual difference in the distribution pattern of the groups was found in the northern basin area. Haptophytes dominated and dispersed widely in warm surface waters in 2008, whereas prasinophytes dominated in cold water in 2009 and 2010. A difference in the onset date of sea ice retreat was evident among years – the sea ice retreat in 2008 was 1–2 months earlier than in 2009 and 2010. The spatial distribution of early sea ice retreat matched the areas in which a shift in algal community composition was observed. Steel-Dwass's multiple comparison tests were used to assess the physical, chemical and biological parameters of the four clusters. We found a statistically significant difference in temperature between the haptophyte-dominated cluster and the other clusters, suggesting that the change in the phytoplankton communities was related to the earlier sea ice retreat in 2008 and the corollary increase in sea surface temperatures. Longer periods of open water during the summer, which are expected in the future, may affect food webs and biogeochemical cycles in the western Arctic due to shifts in phytoplankton community structure.

Description: Uptake of phytodetritus by benthic foraminifera under oxygen depletion at the Indian Margin (Arabian Sea) Biogeosciences Discussions, 10, 15305-15335, 2013 Author(s): A. J. Enge, U. Witte, M. Kucera, and P. Heinz Benthic foraminifera in sediments on the Indian margin of the Arabian Sea where the oxygen minimum zone (OMZ) impinges on the continental slope are exposed to particularly severe levels of oxygen depletion. Food supply for the benthic community is high but delivered in distinct pulses during upwelling and water mixing events associated with summer and winter monsoon periods. In order to investigate the response by benthic foraminifera to such pulsed food delivery under oxygen concentrations of less than 0.1 mL L −1 (4.5 μmol L −1 ), an in situ isotope labeling experiment ( 13 C, 15 N) was performed at the western continental slope of India at 540 m water depth (OMZ core region). The assemblage of living foraminifera (〉125 μm) in the uppermost centimeter at this depth is characterized by an unexpectedly high population density of 3982 ind. 10 cm −2 and a strong dominance by few calcareous species. For the experiment, we concentrated on the nine most abundant taxa, which constitute 93% of the entire foraminifera population at 0–1 cm sediment depth. Increased concentrations of 13 C and 15 N in the cytoplasm indicate that all investigated taxa took up the labeled phytodetritus during the 4 day experimental phase. In total, these nine species had assimilated 113.8 mg C m −2 (17.5% of the total added carbon). The uptake of nitrogen by the three most abundant taxa ( Bolivina aff. B. dilatata , Cassidulina sp., Bulimina gibba ) was 2.7 mg N m −2 (2% of the total added nitrogen) and showed the successful application of 15 N as tracer in foraminiferal studies. The short-term response to the offered phytodetritus varied largely among foraminiferal species with Uvigerina schwageri being by far the most important species in short-term processing whereas the most abundant taxa Bolivina aff. B. dilatata and Cassidulina sp. showed comparably low uptake of the offered food. We suggest that the observed species-specific differences are related to individual biomass of species and to specific feeding preferences. The high numbers of living foraminifera and their rapid response to deposited fresh phytodetritus demonstrate the importance of foraminifera in short-term carbon cycling under oxygen-depleted conditions. We propose that foraminifera at the studied site benefit from unique adaptations in their metabolisms to nearly anoxic conditions as well as from the exclusion of macrofauna and the resulting relaxation of competition for food and low predation pressure.

Description: Summertime canopy albedo is sensitive to forest thinning Biogeosciences Discussions, 10, 15373-15414, 2013 Author(s): J. Otto, D. Berveiller, F.-M. Bréon, N. Delpierre, G. Geppert, A. Granier, W. Jans, A. Knohl, A. Kuusk, B. Longdoz, E. Moors, M. Mund, B. Pinty, M.-J. Schelhaas, and S. Luyssaert Despite an emerging body of literature linking canopy albedo to forest management, understanding of the process is still fragmented. We combined a stand-level forest gap model with a canopy radiation transfer model and satellite-derived model parameters to quantify the effects of forest thinning, that is removing trees at a certain time during the forest rotation, on summertime canopy albedo. The effects of different forest species (pine, beech, oak) and four thinning strategies (light to intense thinning regimes) were examined. During stand establishment, summertime canopy albedo is driven by tree species. In the later stages of stand development, the effect of tree species on summertime canopy albedo decreases in favour of an increasing influence of forest thinning on summertime canopy albedo. These trends continue until the end of the rotation where thinning explains up to 50% of the variance in near-infrared canopy albedo and up to 70% of the variance in visible canopy albedo. More intense thinning lowers the summertime shortwave albedo in the canopy by as much as 0.02 compared to unthinned forest. The structural changes associated with forest thinning can be described by the change in LAI in combination with crown volume. However, forests with identical canopy structure can have different summertime albedo values due to their location: the further north a forest is situated, the more the solar zenith angle increases and thus the higher is the summertime canopy albedo, independent of the wavelength. Despite the increase of absolute summertime canopy albedo values with latitude, the difference in canopy albedo between managed and unmanaged forest decreases with increasing latitude. Forest management thus strongly altered summertime forest albedo.

Description: Oxygen minimum zone of the open Arabian Sea: variability of oxygen and nitrite from daily to decadal time scales Biogeosciences Discussions, 10, 15455-15517, 2013 Author(s): K. Banse, S. W. A. Naqvi, P. V. Narvekar, J. R. Postel, and D. A. Jayakumar The oxygen minimum zone (OMZ) of the Arabian Sea is the thickest of the three oceanic OMZs, which is of global biogeochemical significance because of denitrification in the upper part leading to N 2 and N 2 O production. The residence time of the OMZ water is believed to be less than a decade. The upper few hundred meters of this zone are nearly anoxic but non-sulfidic and still support animal (metazoan) pelagic life, possibly as a result of episodic injections of O 2 by physical processes. The very low O 2 values obtained with the new STOX sensor in the eastern tropical South Pacific probably also characterize the Arabian Sea OMZ, but there is no apparent reason as to why the temporal trends of the historic data should not hold. We report on discrete measurements of dissolved O 2 and NO 2 - , besides temperature and salinity, made between 1959 and 2004 well below the tops of the sharp pycno- and oxyclines near 150, 200, 300, 400, and 500 m depth. We assemble nearly all O 2 determinations (originally, 849 values, 695 in the OMZ) by the visual endpoint detection of the iodometric Winkler procedure, which in our data base yields about 0.04 mL L −1 (∼2 μM) O 2 above the endpoint from modern automated titration methods. We find 632 values acceptable (480 from 150 stations in the OMZ). The data are grouped in zonally-paired boxes of 1° lat. and 2° long. centered at 8°, 10°, 12°, 15°, 18°, 20°, and 21° N along 65° E and 67° E. The latitudes of 8–12° N, outside the OMZ, are only treated in passing. The principal results are as follows: (1) an O 2 climatology for the upper OMZ reveals a marked seasonality at 200 to 500 m depth with O 2 levels during the northeast monsoon and spring intermonsoon season elevated over those during the southwest monsoon season (median difference, 0.08 mL L −1 [3.5 μM]). The medians of the slopes of the seasonal regressions of O 2 on year for the NE and SW monsoon seasons are −0.0043 and −0.0019 mL L −1 a −1 , respectively (−0.19 and −0.08 μM a −1 ; n = 10 and 12, differing at p = 0.01); (2) four decades of statistically significant decreases of O 2 between 15° and 20° N but a trend to a similar increase near 21° N are observed. The balance of the mechanisms that more or less annually maintain the O 2 levels are still uncertain. At least between 300 and 500 m the annual reconstitution of the decrease is inferred to be due to lateral, isopycnal re-supply of O 2 , while at 200 (250?) m it is diapycnal, most likely by eddies. Similarly, recent models show large vertical advection of O 2 well below the pycno- cum -oxycline. The spatial (within drift stations) and temporal (daily) variability in hydrography and chemistry is large also below the principal pycnocline. The seasonal change of hydrography is considerable even at 500 m. There is no trend in the redox environment for a quarter of a century at a GEOSECS station near 20° N. In the entire OMZ the slopes on year within seasons for the quite variable NO 2 - (taken as an indicator of active denitrification) do not show a clear pattern. Also, future O 2 or nutrient budgets for the OMZ should not be based on single cruises or sections obtained during one season only. Steady state cannot be assumed any longer for the intermediate layers of the central Arabian Sea.

Description: Stable isotopes dissect food webs from top to the bottom Biogeosciences Discussions, 10, 14923-14952, 2013 Author(s): J. J. Middelburg Stable isotopes have been used extensively to study food web functioning, i.e. the flow of energy and matter among organisms. Traditional food-web studies are based on the natural variability of carbon and nitrogen isotopes and are limited to larger organisms that can be physically separated from their environment. Recent developments allow isotope ratio measurements of microbes and this in turn allows then measurement of entire food webs, i.e. from small producers at the bottom to large consumers at the top. Here, I provide a concise review on the use and potential of stable isotope to reconstruct end-to-end food webs. I will first discuss food web reconstruction based on natural abundances isotope data and will then show that the use of stable isotopes as deliberately added tracers provides complementary information. Finally, challenges and opportunities for end-to-end food web reconstructions in a changing world are discussed.

Description: Responses of carbon dioxide flux and plant biomass to drought in a treed peatland in northern Alberta: a climate change perspective Biogeosciences Discussions, 10, 14999-15031, 2013 Author(s): T. M. Munir, B. Xu, M. Perkins, and M. Strack Northern peatland ecosystems represent large carbon stocks that are susceptible to changes such as accelerated mineralization due to water table lowering expected under a climate change scenario. During the growing seasons of 2011 and 2012 we monitored CO 2 fluxes and plant biomass along a microtopographic gradient (hummocks-hollows) in an undisturbed dry continental boreal treed bog (control) and a nearby site that was drained (drained) in 2001. Ten years of drainage in the bog significantly increased coverage of shrubs at hummocks and lichens at hollows. Considering measured hummock coverage and including tree incremental growth, we estimate that the control site was a larger sink in 2011 of −40 than that of −13 g C m −2 in 2012 while the drained site was a source of 144 and 140 g C m −2 over the same years. We infer that, drainage induced changes in vegetation growth led to increased biomass to counteract a portion of soil carbon losses. These results suggest that spatial variability (microtopography) and changes in vegetation community in boreal peatlands will affect how these ecosystems respond to lowered water table potentially induced by climate change.

Description: The coccolithophores Emiliania huxleyi and Coccolithus pelagicus : extant populations from the Norwegian-Iceland Sea and Fram Strait Biogeosciences Discussions, 10, 15077-15106, 2013 Author(s): C. V. Dylmer, J. Giraudeau, V. Hanquiez, and K. Husum Extant coccolithophores and their relation to the governing oceanographic features in the northern North Atlantic were investigated along two zonal transects of surface water sampling, both conducted during summer 2011 and fall 2007. The northern transects crossed Fram Strait and its two opposing boundary currents (West Spitsbergen Current and East Greenland Current), while the southern transects sampled the Norwegian and Iceland Seas (passing the island Jan Mayen) from the Lofoten Islands to the continental margin off Eastern Greenland. The distribution of the dominant coccolithophore species Emiliania huxleyi and Coccolithus pelagicus is discussed in view of both the surface hydrology at the time of sampling and the structure of the surface mixed layer. Remote-sensing images as well as CTD and ARGO profiles are used to constrain the physico-chemical state of the surface water at the time of sampling. Both transects were characterized by strong seasonal differences in bulk coccolithophore standing stocks with maximum values of 53 × 10 3 cells L −1 for the northern transect and 72 × 10 3 cells L −1 for the southern transect in fall and summer, respectively. The highest recorded bulk cell densities are essentially explained by E. huxleyi . This species shows a zonal shift in peak abundance in the Norwegian-Iceland Seas from a summer maximum in the Lofoten gyre to peak cell densities around the island Jan Mayen in fall. Vertical mixing of Atlantic waters west of Lofoten Island, a phenomenom related to pervasive summer large scale atmospheric changes in the eastern Nordic Seas, on one hand, and strengthened influence of melt-water and related surface water stratification around the island Jan Mayen during fall, on the other hand, explains the observed seasonal migration of the E. huxleyi peak production area, as well as the seasonal change in dominating species within the Iceland Sea. In addition our datasets are indicative of a well-defined maximum boundary temperature of 6 °C for the production of C. pelagicus in the northern North Atlantic. The Fram Strait transects provides, to our knowledge, a first view of the zonal distribution of extant coccolithophores in this remote setting during summer and fall. Our datasets are indicative of a seasonal change in the species community from an E. huxleyi -dominated assemblage during summer to a C. pelagicus -rich population during fall. Here, higher irradiance and increased Atlantic water influence during summer favored the production of the opportunistic species E. huxleyi close to the Arctic Front, whereas the peak production area during fall, with high concentrations of C. pelagicus , lays in true Arctic/Polar waters.

Description: Anthropogenic and natural methane fluxes in Switzerland synthesized within a spatially-explicit inventory Biogeosciences Discussions, 10, 15181-15224, 2013 Author(s): R. V. Hiller, D. Bretscher, T. DelSontro, T. Diem, W. Eugster, R. Henneberger, S. Hobi, E. Hodson, D. Imer, M. Kreuzer, T. Künzle, L. Merbold, P. A. Niklaus, B. Rihm, A. Schellenberger, M. H. Schroth, C. J. Schubert, H. Siegrist, J. Stieger, N. Buchmann, and D. Brunner We present the first high-resolution (500 m × 500 m) gridded methane (CH 4 ) emission inventory for Switzerland, which integrates the national emission totals reported to the United Nations Framework Convention on Climate Change (UNFCCC) and recent CH 4 flux studies conducted by research groups across Switzerland. In addition to anthropogenic emissions, we also include natural and semi-natural CH 4 fluxes, i.e., emissions from lakes and reservoirs, wetlands, wild animals as well as uptake by forest soils. National CH 4 emissions were disaggregated using detailed geostatistical information on source locations and their spatial extent and process- or area-specific emission factors. In Switzerland, the highest CH 4 emissions in 2011 originated from the agricultural sector (150 Gg CH 4 yr −1 ), mainly produced by ruminants and manure management, followed by emissions from waste management (15 Gg CH 4 yr −1 ) mainly from landfills and the energy sector (12 Gg CH 4 yr −1 ), which was dominated by emissions from natural gas distribution. Compared to the anthropogenic sources, emissions from natural and semi-natural sources were relatively small (6 Gg CH 4 yr −1 ), making up only 3 % of the total emissions in Switzerland. CH 4 fluxes from agricultural soils were estimated to be not significantly different from zero (between −1.5 and 0 Gg CH 4 yr −1 ), while forest soils are a CH 4 sink (approx. −2.8 Gg CH 4 yr −1 ), partially offsetting other natural emissions. Estimates of uncertainties are provided for the different sources, including an estimate of spatial disaggregation errors deduced from a comparison with a global (EDGAR v4.2) and a European CH 4 inventory (TNO/MACC). This new spatially-explicit emission inventory for Switzerland will provide valuable input for regional scale atmospheric modeling and inverse source estimation.

Description: Seasonal trends of dry and bulk concentration of nitrogen compounds over a rain forest in Ghana Biogeosciences Discussions, 10, 15225-15255, 2013 Author(s): F. Fattore, T. Bertolini, S. Materia, S. Gualdi, A. Thongo M'Bou, G. Nicolini, R. Valentini, A. De Grandcourt, D. Tedesco, and S. Castaldi African tropical forests of the equatorial belt might receive significant input of extra nitrogen derived from biomass burning occurring in the north savanna belt and transported equator wards by NE winds. In order to test this hypothesis an experiment was set up in a tropical rain forest in the National park of Ankasa (Ghana) aiming at: quantifying magnitude and seasonal variability of concentrations of N compounds, present as gas and aerosol (dry nitrogen) or in the rainfall (bulk nitrogen), over the studied forest; relating their seasonal variability to trends of local and regional winds and rainfall and to variations of fire events in the region. Three Delta systems, implemented for monthly measurements of NO 2 , were mounted over a tower at 45 m height, 20 m above forest canopy to sample gas (NH 3 , NO 2 , HNO 3 , HCl, SO 2 ) and aerosol (NH 4 + , NO 3 − , and several ions), together with three tanks for bulk rainfall collection (to analyze NH 4 + , NO 3 − and ion concentration). The tower was provided with a sonic anemometer to estimate local wind data. The experiment started in October 2011 and data up to October 2012 are presented. To interpret the observed seasonal trends of measured compounds, local and regional meteo data and regional satellite fire data were analyzed. The concentration of N compounds significantly increased from December to April, during the drier period, peaking in December-February when North Eastern winds (Harmattan) were moving dry air masses over the West central African region and the inter tropical convergence zone (ITCZ) was at its minimum latitude over the equator. This period also coincided with peaks of fire in the whole region. On the contrary, N concentration in gas, aerosol and rain decreased from May to October when prevalent winds arrived from the sea (South-East), during the Monsoon period. Both ionic compositions of rain and analysis of local wind direction showed a significant and continuous presence of see-breeze at site. The ionic composition of rain water resulted much closer to see water and poorer in N compounds from May to October.

Description: Inferences from CO 2 and CH 4 concentration profiles at the Zotino Tall Tower Observatory (ZOTTO) on local summer-time ecosystem fluxes Biogeosciences Discussions, 10, 15337-15372, 2013 Author(s): J. Winderlich, C. Gerbig, O. Kolle, and M. Heimann The Siberian region is still sparsely covered by ecosystem observatories, which motivates to exploit existing datasets to gain spatially and temporally better-resolved carbon fluxes. The Zotino Tall Tower Observatory (ZOTTO, 60°48' N, 89°21' E) observations of CO 2 and CH 4 mole fractions as well as meteorological parameters from six different heights up to 301 m allow for an additional estimate of surface-atmosphere fluxes of CO 2 and CH 4 for the Middle-Siberian region since 2009. The total carbon flux is calculated from the storage and the turbulent flux component. The gradients between the different tower levels determine the storage flux component, which dominates the local fluxes, especially during night. As a correction term, the turbulent flux component was estimated by the modified Bowen ratio method based on the sensible heat flux measurements at the top of the tower. The gained average night time fluxes (23:00 to 04:00 local time) are 2.7 ± 1.1 μmol (m 2 s) −1 for CO 2 and 5.6 ± 4.5 nmol (m 2 s) −1 for CH 4 during the summer months June-September in 2009 and 2011. During day, the method is limited due to numeric instabilities from vanishing vertical gradients; however, the derived CO 2 fluxes exhibit reasonable diurnal shape and magnitude compared to the eddy covariance technique, which become available at the site in 2012. Therefore, the tall tower data facilitates the extension of the new eddy covariance flux dataset back in time. The diurnal signal of the CH 4 flux is predominantly characterized by a strong morning transition, which is explained by local topographic effects.

Description: Live foraminiferal faunas (Rose Bengal stained) from the northern Arabian Sea: links with bottom-water oxygenation Biogeosciences Discussions, 10, 15257-15304, 2013 Author(s): C. Caulle, K. A. Koho, M. Mojtahid, G. J. Reichart, and F. J. Jorissen Live (Rose Bengal stained) benthic foraminifera from the Murray Ridge, within and below the northern Arabian Sea Oxygen Minimum Zone (OMZ), were studied in order to determine the relationship between faunal composition, bottom-water oxygenation (BWO), pore-water chemistry and organic matter (organic carbon and phytopigment) distribution. A series of multicores were recovered from a ten-station oxygen (BWO: 2–78 μM) and bathymetric (885–3010 m depth) transect during the winter monsoon in January 2009. Foraminifera were investigated from three different size fractions (63–125 μm, 125–150 μm and 〉 150 μm). The larger foraminifera (〉 125 μm) were strongly dominated by agglutinated species (e.g. Reophax spp.). In contrast, in the 63–125 μm fraction, calcareous taxa were more abundant, especially in the core of the OMZ, suggesting an opportunistic behaviour. On the basis of a Principal Component Analysis, three foraminiferal groups were identified, reflecting the environmental parameters along the study transect. The faunas from the shallowest stations, in the core of the OMZ (BWO: 2 μM), were composed of "low oxygen" species, typical of the Arabian Sea OMZ (e.g., Rotaliatinopsis semiinvoluta , Praeglobobulimina spp. , Bulimina exilis, Uvigerina peregrina type parva ). These taxa are adapted to the very low BWO conditions and to high phytodetritus supplies. The transitional group, typical for the lower part of the OMZ (BWO: 5–16 μM), is composed of more cosmopolitan taxa tolerant to low-oxygen concentrations ( Globocassidulina subglobosa , Ehrenbergina trigona ). Below the OMZ (BWO: 26–78 μM), where food availability is more limited and becomes increasingly restricted to surficial sediments, more cosmopolitan calcareous taxa were present, such as Bulimina aculeata, Melonis barleeanus, Uvigerina peregrina and Epistominella exigua . Miliolids were uniquely observed in this last group, reflecting the higher BWO. At these deeper sites, the faunas exhibit a clear depth succession of superficial, intermediate and deep-infaunal microhabitats, because of the deeper oxygen and nitrate penetration into the sediment.

Description: Landscape-scale changes in forest structure and functional traits along an Andes-to-Amazon elevation gradient Biogeosciences Discussions, 10, 15415-15454, 2013 Author(s): G. P. Asner, C. Anderson, R. E. Martin, D. E. Knapp, R. Tupayachi, T. Kennedy-Bowdoin, F. Sinca, and Y. Malhi Elevation gradients provide opportunities to explore environmental controls on forest structure and functioning, but plot-based studies have proven highly variable due to limited geographic scope. We used airborne imaging spectroscopy and LiDAR (light detection and ranging) to quantify changes in three-dimensional forest structure and canopy functional traits in a series of 25 ha landscapes distributed along a 3300 m elevation gradient from lowland Amazonia to treeline in the Peruvian Andes. Canopy greenness, photosynthetic fractional cover and exposed non-photosynthetic vegetation varied as much across lowland forests (100–200 m) as they did from the lowlands to the Andean treeline (3400 m). Elevation was positively correlated with canopy gap density and understory vegetation cover, and negatively related to canopy height and vertical profile. Increases in gap density were tightly linked to increases in understory plant cover, and larger gaps (20–200 m 2 produced 25–30 times the response in understory cover than did smaller gaps ( 〈 5 m 2 . Scaling of gap size to gap frequency was, however, relatively constant along the elevation gradient, which when combined with other canopy structural information, indicates equilibrium turnover patterns from the lowlands to treeline. Our results provide a first landscape-scale quantification of forest structure and canopy functional traits with changing elevation, thereby improving our understanding of disturbance, demography and ecosystem processes in the Andes-to-Amazon corridor.

Description: Springtime phytoplankton dynamics in the Arctic Krossfjorden and Kongsfjorden (Spitsbergen) as a function of glacier proximity Biogeosciences Discussions, 10, 15519-15557, 2013 Author(s): A. M.-T. Piquet, W. H. van de Poll, R. J. W. Visser, C. Wiencke, H. Bolhuis, and A. G. J. Buma The hydrographic properties of the Kongsfjorden – Krossfjorden system (79° N, Spitsbergen) are affected by Atlantic water incursions as well as glacier meltwater runoff. This results in strong physical gradients (temperature, salinity and irradiance) within the fjords. Here, we tested the hypothesis that glaciers affect phytoplankton dynamics as early as the productive spring bloom period. During two campaigns in 2007 (late spring) and 2008 (early spring) we studied hydrographic characteristics and phytoplankton variability along 2 transects in both fjords, using HPLC-CHEMTAX pigment fingerprinting, molecular fingerprinting (DGGE) and sequencing of 18S rRNA genes. The sheltered inner fjord locations remained colder during spring as opposed to the outer locations. Vertical light attenuation coefficients increased from early spring onwards, at all locations, but in particular at the inner locations. During the end of spring, meltwater input had stratified surface waters throughout the fjords. The inner fjord locations were characterized by overall lower phytoplankton biomass. Furthermore HPLC-CHEMTAX data revealed that diatoms and Phaeocystis sp. were replaced by small nano- and picophytoplankton during late spring, coinciding with low nutrient availability. The innermost stations showed higher relative abundances of nano- and picophytoplankton throughout, notably of cyanophytes and cryptophytes. Molecular fingerprinting revealed a high similarity between inner fjord samples from early spring and late spring samples from all locations, while outer samples from early spring clustered separately. We conclude that glacier influence, mediated by early meltwater input, modifies phytoplankton biomass and composition already during the spring bloom period, in favor of low biomass and small cell size communities. This may affect higher trophic levels especially when regional warming further increases the period and volume of meltwater.

Description: Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion based model MOSAIC Biogeosciences Discussions, 10, 15613-15640, 2013 Author(s): O. Monga, P. Garnier, V. Pot, E. Coucheney, N. Nunan, W. Otten, and C. Chenu This paper deals with the simulation of microbial degradation in soil within pore space at microscopic scale. Pore space was described using sphere network coming from a geometrical modeling algorithm. The biological model was improved regarding previous work in order to include transformation of dissolved organic compounds and diffusion processes. Our model was tested using experimental results of a simple substrate decomposition (Fructose) within a simple media (the sand). Diverse microbial communities were inoculated. Separated incubations in microcosms were carried out using 5 different bacterial communities at 2 different water potentials of −10 cm and −100 cm of water. We calibrated the biological parameters by means of experimental data obtained at high water content and we tested the model without any parameters change at low water content. Same as for experimental data, our simulation results showed the decrease in water content involved the decrease of mineralisation. The model was able to simulate the decrease of connectivity between substrate and microorganism due the decrease of water content.

Description: Influence of temperature and CO 2 on the strontium and magnesium composition of coccolithophore calcite Biogeosciences Discussions, 10, 15559-15586, 2013 Author(s): M. N. Müller, M. Lebrato, U. Riebesell, J. Barcelos e Ramos, K. G. Schulz, S. Blanco-Ameijeiras, S. Sett, A. Eisenhauer, and H. M. Stoll Marine calcareous sediments provide a fundamental basis for paleoceanographic studies aiming to reconstruct past oceanic conditions and understand key biogeochemical element cycles. Calcifying unicellular phytoplankton (coccolithophores) are a major contributor to both carbon and calcium cycling by photosynthesis and the production of calcite (coccoliths) in the euphotic zone and the subsequent long-term deposition and burial into marine sediments. Here we present data from controlled laboratory experiments on four coccolithophore species and elucidate the relation between the divalent cation (Sr, Mg and Ca) partitioning in coccoliths and cellular physiology (growth, calcification and photosynthesis). Coccolithophores were cultured under different seawater temperature and carbonate chemistry conditions. The partition coefficient of strontium ( D Sr ) was positively correlated with both carbon dioxide ( p CO 2 ) and temperature but displayed no coherent relation to particulate organic and inorganic carbon production rates. Furthermore, D Sr correlated positively with cellular growth rates when driven by temperature but no correlation was present when changes in growth rates were p CO 2 -induced. The results demonstrate the complex interaction between environmental forcing and physiological control on the strontium partitioning in coccolithophore calcite. The partition coefficient of magnesium ( D Mg ) displayed species-specific differences and elevated values under nutrient limitation. No conclusive correlation between coccolith D Mg and temperature was observed but p CO 2 induced a rising trend in coccolith D Mg . Interestingly, the best correlation was found between coccolith D Mg and chlorophyll a production suggesting that chlorophyll a and calcite associated Mg originate from the same intracellular pool. These results give an extended insight into the driving factors that lead to variations in the coccolith Mg / Ca ratio and can be used for Sr / Ca and Mg / Ca paleoproxy calibration.

Description: Forest NEP is significantly driven by previous year's weather Biogeosciences Discussions, 10, 15587-15611, 2013 Author(s): S. Zielis, S. Etzold, R. Zweifel, W. Eugster, M. Haeni, and N. Buchmann Understanding the response of forest net ecosystem productivity (NEP) to environmental drivers under climate change is highly relevant for predictions of annual forest carbon (C) flux budgets. Modeling annual forest NEP with soil–vegetation–atmosphere transfer models (SVATs), however, remains challenging due to unknown responses of forests to weather of the previous year. In this study, we addressed the influence of previous year's weather on the inter-annual variability of NEP for a subalpine spruce forest in Switzerland. Analysis of long-term (1997–2011) eddy covariance measurements showed that the Norway spruce forest Davos Seehornwald was a consistent sink for atmospheric CO 2 , sequestering 210 ± 88 g C m −2 per year on average. Previous year's weather strongly affected inter-annual variability of NEP, increasing the explained variance in linear models to 53% compared to 20% without previous year's weather. Thus, our results highlight the need to consider previous year's weather in modeling annual C budgets of forests. Furthermore, soil temperature in the current year's spring played a major role controlling annual NEP, mainly by influencing gross primary productivity early in the year, with spring NEP accounting for 56% of annual NEP. Consequently, we expect an increase in net CO 2 uptake with future climate warming, as long as no other resources become limiting.

Description: Synoptic evaluation of carbon cycling in Beaufort Sea during summer: contrasting river inputs, ecosystem metabolism and air–sea CO 2 fluxes Biogeosciences Discussions, 10, 15641-15710, 2013 Author(s): A. Forest, P. Coupel, B. Else, S. Nahavandian, B. Lansard, P. Raimbault, T. Papakyriakou, Y. Gratton, L. Fortier, J.-É. Tremblay, and M. Babin The accelerated decline in Arctic sea ice combined with an ongoing trend toward a more dynamic atmosphere is modifying carbon cycling in the Arctic Ocean. A critical issue is to understand how net community production (NCP; the balance between gross primary production and community respiration) responds to changes and modulates air–sea CO 2 fluxes. Using data collected as part of the ArcticNet-Malina 2009 expedition in southeastern Beaufort Sea (Arctic Ocean), we synthesize information on sea ice, wind, river, water column properties, metabolism of the planktonic food web, organic carbon fluxes and pools, as well as air–sea CO 2 exchange, with the aim of identifying indices of ecosystem response to environmental changes. Data were analyzed to develop a non-steady-state carbon budget and an assessment of NCP against air–sea CO 2 fluxes. The mean atmospheric forcing was a mild upwelling-favorable wind (~5 km h −1 ) blowing from the N-E and a decaying ice cover ( 600 mg C m −2 d −1 ) over the shelf prior to our survey, (2) freshwater dilution by river runoff and ice melt, and (3) the presence of cold surface waters offshore. Only the Mackenzie River delta and localized shelf areas directly affected by upwelling were identified as substantial sources of CO 2 to the atmosphere (〉10mmol C m −2 d −1 ). Although generally

Description: Foraminiferal survival after long term experimentally induced anoxia Biogeosciences Discussions, 10, 9243-9284, 2013 Author(s): D. Langlet, E. Geslin, C. Baal, E. Metzger, F. Lejzerowicz, B. Riedel, M. Zuschin, J. Pawlowski, M. Stachowitsch, and F. J. Jorissen Anoxia has been successfully induced in four benthic chambers installed on the Northern Adriatic seafloor from 1 week to 10 months. To accurately determine whether benthic foraminifera can survive experimentally induced prolonged anoxia, the CellTrackerGreen method has been applied. Numerous individuals have been found living at all sampling times and at all sampling depths, showing that benthic foraminifera can survive up to 10 months of anoxia with co-occurring hydrogen sulphides. However, foraminiferal standing stocks decrease with sampling time in an irregular way. A large difference in standing stock between two cores samples in initial conditions indicates the presence of a large spatial heterogeneity of the foraminiferal faunas. An unexpected increase in standing stocks after 1 month is tentatively interpreted as a reaction to increased food availability due to the massive mortality of infaunal macrofaunal organisms. After this, standing stocks decrease again in a core sampled after 2 months of anoxia, to attain a minimum in the cores sampled after 10 months. We speculate that the trend of overall decrease of standing stocks is not due to the adverse effects of anoxia and hydrogen sulphides, but rather due to a continuous diminution of labile organic matter.

Description: Environmental controls on the Emiliania huxleyi calcite mass Biogeosciences Discussions, 10, 9285-9313, 2013 Author(s): M. T. Horigome, P. Ziveri, M. Grelaud, K.-H. Baumann, G. Marino, and P. G. Mortyn Although ocean acidification is expected to impact (bio)calcification by decreasing the seawater carbonate ion concentration, [CO 3 2− ], there exists evidence of non-uniform response of marine calcifying plankton to low seawater [CO 3 2− ]. This raises questions on the role of environmental factors other than acidification and on the complex physiological responses behind calcification. Here we investigate the synergistic effect of multiple environmental parameters, including temperature, nutrient (nitrate and phosphate) availability, and seawater carbonate chemistry on the coccolith calcite mass of the cosmopolitan coccolithophore Emiliania huxleyi , the most abundant species in the world ocean. We use a suite of surface (late Holocene) sediment samples from the South Atlantic and southwestern Indian Ocean taken from depths lying well above the modern lysocline. The coccolith calcite mass in our results presents a latitudinal distribution pattern that mimics the main oceanographic features, thereby pointing to the potential importance of phosphorus and temperature in determining coccolith mass by affecting primary calcification and possibly driving the E. huxleyi morphotype distribution. This evidence does not necessarily argue against the potentially important role of the rapidly changing seawater carbonate chemistry in the future, when unabated fossil fuel burning will likely perturb ocean chemistry beyond a critical point. Rather our study highlights the importance of evaluating the combined effect of several environmental stressors on calcifying organisms to project their physiological response(s) in a high CO 2 world and improve interpretation of paleorecords.

Description: UV-induced carbon monoxide emission from living vegetation Biogeosciences Discussions, 10, 9373-9388, 2013 Author(s): D. Bruhn, K. R. Albert, T. N. Mikkelsen, and P. Ambus The global burden of carbon monoxide (CO) is rather uncertain. In this paper we address the potential for UV-induced CO emission by living terrestrial vegetation surfaces. Real-time measurements of CO concentrations were made with a cavity enhanced laser spectrometer connected in closed loop to either an ecosystem chamber or a plant-leaf scale chamber. Leaves of all examined plant species exhibited emission of CO in response to artificial UV-radiation as well as the UV-component of natural solar radiation. The UV-induced rate of CO emission exhibited a rather low dependence on temperature, indicating an abiotic process. The emission of CO in response to the UV-component of natural solar radiation was also evident at the ecosystem scale.

Description: Nutrient dynamics in tropical rivers, estuarine-lagoons, and coastal ecosystems along the eastern Hainan Island Biogeosciences Discussions, 10, 9091-9147, 2013 Author(s): R. H. Li, S. M. Liu, Y. W. Li, G. L. Zhang, J. L. Ren, and J. Zhang Nutrient dynamics were studied along the eastern Hainan Island based on field observations during 2006–2009, to understand nutrient biogeochemical processes and to have an overview of human perturbations on coastal ecosystems in this tropical region. The concentrations of nutrients in the rivers had seasonal variations enriched with dissolved inorganic nitrogen (DIN). High riverine concentrations of nitrate were mainly originated from agricultural fertilizer input. The ratios of DIN : PO 4 3− ranged from 37 to 1063, suggesting preferential PO 4 3− relative to nitrogen in the rivers. The areal yields of dissolved silicate (DSi) varied from 76 to 448 × 10 3 mol km −2 yr −1 due to erosion over the drainage area, inducing high levels of DSi among worldwide tropical systems. Aquaculture ponds contained high concentrations of NH 4 + (up to 157 μM) and DON (up to 130 μM). Particulate phosphorus concentrations (0.5 ∼1.4 μM) were in lower level comparied with estuaries around the world. Particulate silicate levels in rivers and lagoons were lower than global average level. Nutrient biogeochemistry in coastal areas were affected by human activities (e.g. aquaculture, agriculture), as well as natural events such as typhoon. Nutrient concentrations were low because open sea water dispersed land-derived nutrients. Nutrient budgets were built based on a steady-state box model, which showed that riverine fluxes would be magnified by estuarine processes (e.g. regeneration, desorption) in the Wenchanghe/Wenjiaohe Estuary, Wanquan River estuary, and the Laoyehai Lagoon except in the Xiaohai Lagoon. Riverine and groundwater input were the major sources of nutrients to the Xiaohai Lagoon and the Laiyehai Lagoon, respectively. Riverine input and aquaculture effluent were the major sources of nutrients to the eastern coastal of Hainan Island. Nutrient inputs to the coastal ecosystem can be increased by typhoon-induced runoff of rainwater, and phytoplankton bloom in the sea would be caused.

Description: Southern Hemisphere imprint for Indo–Asian summer monsoons during the last glacial period as revealed by Arabian Sea productivity records Biogeosciences Discussions, 10, 9315-9343, 2013 Author(s): T. Caley, S. Zaragosi, J. Bourget, P. Martinez, B. Malaizé, F. Eynaud, L. Rossignol, T. Garlan, and N. Ellouz-Zimmermann The monsoon is one of the most important climatic phenomena: it promotes inter-hemispheric exchange of energy and affects the economical prosperity of several countries exposed to its seasonal seesaw. Previous studies in both the Indian and Asian monsoon systems have suggested a dominant north hemispheric (NH) control on summer monsoon dynamics at the scale of suborbital-millennial climatic changes, while the forcing/response of Indian and Asian monsoons at the orbital scale remains a matter of debate. Here nine marine sediment cores distributed across the whole Arabian Sea are used to build a regional surface marine productivity signal. The productivity signal is driven by the intensity of Indian summer monsoon winds. Results demonstrate the existence of an imprint of suborbital Southern Hemisphere (SH) temperature changes (i.e., Antarctica) on the Indian summer monsoon during the last glacial period, challenging the traditional and exclusive NH forcing hypothesis. Meanwhile, during the last deglaciation, the NH plays a more significant role. The δ 18 O signal recorded in the Asian monsoon speleothem records could be exported by winds from the Indian summer monsoon region, as recently proposed in modelling exercise, explaining the SH signature observed in Asian cave speleothems. Contrary to the view of a passive response of Indian and Asian monsoons to NH anomalies, the present results strongly suggest that the Indo–Asian summer monsoon plays an active role in amplifying millennial inter-hemispheric asymmetric patterns. Additionally, this study helps to decipher the observed differences between Indian and Asian-speleothem monsoonal records at the orbital-precession scale.

Description: Heterogeneity of impacts of high CO 2 on the North Western European Shelf Biogeosciences Discussions, 10, 9389-9413, 2013 Author(s): Y. Artioli, J. C. Blackford, G. Nondal, R. G. J. Bellerby, S. L. Wakelin, J.T. Holt, M. Butenschön, and J. I. Allen The increase in atmospheric CO 2 is a dual threat to the marine environment: from one side it drives climate change leading to changes in water temperature, circulation patterns and stratification intensity; on the other side it causes a decrease in pH (Ocean Acidification or OA) due to the increase in dissolved CO 2 . Assessing the combined impact of climate change and OA on marine ecosystems is a challenging task: the response of the ecosystem to a single driver is highly variable and still uncertain, as well as the interaction between these that could be either synergistic or antagonistic. In this work we use the coupled oceanographic-ecosystem model POLCOMS-ERSEM driven by climate forcing to study the interaction between climate change and OA. We focus in particular on primary production and nitrogen speciation. The model has been run in three different configurations in order to separate the impacts of ocean acidification from those due to climate change. The model shows significant interaction among the drivers and high variability in the spatial response of the ecosystem. Impacts of climate change and of OA on primary production have similar magnitude, compensating in some area and exacerbating in others. On the contrary, the direct impact of OA on nitrification is much lower than the one imposed by climate change.

Description: On the role of mesoscale eddies for the biological productivity and biogeochemistry in the eastern tropical Pacific Ocean off Peru Biogeosciences Discussions, 10, 9179-9211, 2013 Author(s): L. Stramma, H. W. Bange, R. Czeschel, A. Lorenzo, and M. Frank Mesoscale eddies seem to play an important role for both the hydrography and biogeochemistry of the eastern tropical Pacific Ocean (ETSP) off Peru. However, detailed surveys of these eddies are not available, which has so far hampered an in depth understanding of their implications for nutrient distribution and biological productivity. In this study three eddies along a section at 16°45' S have been surveyed intensively during R/V Meteor cruise M90 in November 2012. A coastal mode water eddy, an open ocean mode water eddy and an open ocean cyclonic eddy have been identified and sampled in order to determine both their hydrographic properties and their influence on the biogeochemical setting of the ETSP. In the thermocline the temperature of the coastal anticyclonic eddy was up to 2 °C warmer, 0.2 more saline and the swirl velocity was up to 35 cm s –1 . The observed temperature and salinity anomalies, as well as swirl velocities of both types of eddies were about twice as large as had been described for the mean eddies in the ETSP and the observed heat and salt anomalies (AHA, ASA) show a much larger variability than the mean AHA and ASA. We found that the eddies contributed significantly to productivity by maintaining pronounced subsurface maxima of chlorophyll. Based on a comparison of the coastal (young) mode water eddy and the open ocean (old) mode water eddy we conclude that the aging of eddies when they detach from the coast and move westward to the open ocean considerably influences the eddies' properties: chlorophyll maxima are weaker and nutrients are subducted. The coastal mode water eddy was found to be a hotspot of nitrogen loss in the OMZ, whereas, the open ocean cyclonic eddy was of negligible importance for nitrogen loss. Our results show that the important role the eddies play in the ETSP can only be fully deciphered and understood through dedicated high spatial and temporal resolution oceanographic/biogeochemical surveys.

Description: Soil moisture modifies the response of soil respiration to temperature in a desert shrub ecosystem Biogeosciences Discussions, 10, 9213-9242, 2013 Author(s): B. Wang, T. S. Zha, X. Jia, B. Wu, Y. Q. Zhang, and S. G. Qin The response of soil respiration (Rs) to soil temperature and moisture have been well documented in forests, but data and information from desert shrub ecosystems are limited. Soil CO 2 efflux from a desert shrub ecosystem was measured continuously with automated chambers in Ningxia, northwest China, from June to October 2012. The responses of Rs to Ts was strongly affected diurnally by soil moisture, with the diel variation in Rs being strongly related to 10 cm soil temperature (Ts) at moderate and high soil volumetric water content (VWC), but less related to Ts at low VWC. Ts typically lagged Rs by 3–4 h, however, the lag time varied in relation to VWC, with increased lag times at low VWC. Over the seasonal cycle, daily mean Rs was positively correlated with Ts when VWC exceeded 0.08 m 3 m −3 , but became decoupled from Ts when VWC dropped below this threshold. The annual temperature sensitivity of Rs ( Q 10 ) was 1.5. The short-term sensitivity of Rs to Ts, computed using three-day windows, varied significantly over the seasonal cycle; the short-term Q 10 was negatively correlated with Ts and positively correlated with VWC. These results suggest the potential for a negative feedback to climate warming in desert ecosystems, related to the impact of low soil moisture on Rs. The results highlight the biological causes of diel hysteresis between Rs and Ts and the need for carbon cycle models to account for the interacting effects of Ts and VWC as joint determinants of Rs in desert ecosystem.

Description: Do successive climate extremes weaken the resistance of plant communities? An experimental study using plant assemblages Biogeosciences Discussions, 10, 9149-9177, 2013 Author(s): F. E. Dreesen, H. J. De Boeck, I. A. Janssens, and I. Nijs The probability that plant communities undergo successive climate extremes increases under climate change. Exposure to an extreme event might elicit acclimatory responses and thereby greater resistance to a subsequent event, but might also reduce resistance if the recovery period is too short or resilience too low. Using experimental plant assemblages, we compared the effects of two successive extremes (either two drought extremes, two heat extremes or two drought + heat extremes) to those of assemblages being exposed only to the second extreme. Additionally, the recovery period between the successive extremes was varied (2, 3.5 or 6 weeks). Among the different types of climate extremes, combined drought + heat extremes induced substantial leaf and plant mortality, while the effects of drought and heat extremes were smaller. Preceding drought + heat extremes lowered the resistance in terms of leaf survival to a subsequent drought + heat extreme if the recovery period was 2 weeks, even though the leaves had completely recovered during that interval. No reduced resistance to subsequent extremes was recorded with longer recovery times or with drought or heat extremes. Despite mortality on the short term, the drought + heat and the heat extremes increased the end-of-season aboveground biomass, independent of the number of events or the recovery period. These results show that the effect of a preceding extreme event disappears quite quickly, but that recurrent climate extremes with short time intervals can weaken the resistance of herbaceous plant assemblages. This can however be compensated afterwards through rapid recovery and secondary, positive effects in the longer term.

Description: Climate and land use change impacts on global terrestrial ecosystems, fire, and river flows in the HadGEM2-ES Earth System Model using the Representative Concentration Pathways Biogeosciences Discussions, 10, 6171-6223, 2013 Author(s): R. A. Betts, N. Golding, P. Gonzalez, J. Gornall, R. Kahana, G. Kay, L. Mitchell, and A. Wiltshire A new generation of an Earth System Model now includes a number of land surface processes directly relevant to analyzing potential impacts of climate change. This model, HadGEM2-ES, allows us to assess the impacts of climate change, multiple interactions, and feedbacks as the model is run. This paper discusses the results of century-scale HadGEM2-ES simulations from an impacts perspective–specifically, terrestrial ecosystems and water resources–for four different scenarios following the Representative Concentration Pathways (RCPs), being used for next assessment report of the Intergovernmental Panel on Climate Change (IPCC). Over the 21st Century, simulated changes in global and continential-scale terrestrial ecosystems due to climate change appear to be very similar in all 4 RCPs, even though the level of global warming by the end of the 21st Century ranges from 2 °C in the lowest scenario to 5.5° in the highest. A warming climate generally favours broadleaf trees over needleleaf, needleleaf trees over shrubs, and shrubs over herbaceous vegetation, resulting in a poleward shift of temperate and boreal forests and woody tundra in all scenarios. Although climate related changes are slightly larger in scenarios of greater warming, the largest differences between scenarios arise at regional scales as a consequence of different patterns of anthropogenic land cover change. In the model, the scenario with the lowest global warming results in the most extensive decline in tropical forest cover due to a large expansion of agriculture. Under all four RCPs, fire potential could increase across extensive land areas, particularly tropical and sub-tropical latitudes. River outflows are simulated to increase with higher levels of CO 2 and global warming in all projections, with outflow increasing with mean temperature at the end of the 21st Century at the global scale and in North America, Asia, and Africa. In South America, Europe, and Australia, the relationship with climate warming and CO 2 rise is less clear, probably as a result of land cover change exerting a dominant effect in those regions.

Description: Horizontal distribution of Fukushima-derived radiocesium in zooplankton in the northwestern Pacific Ocean Biogeosciences Discussions, 10, 6143-6170, 2013 Author(s): M. Kitamura, Y. Kumamoto, H. Kawakami, E. C. Cruz, and K. Fujikura The magnitude of the 9.0 Tohoku earthquake and the ensuing tsunami on 11 March 2011, inflicted heavy damage on the Fukushima Dai-ichi nuclear power plant (FNPP1). Fission products were emitted, falling over a broad range in the northern hemisphere, and water contaminated with radionuclides leaked into the ocean. In this study, we described the horizontal distribution of the Fukushima-derived radiocesium in zooplankton and in seawater in the western North Pacific Ocean (500–2100 km from the FNPP1) 10 months after the accident. 134 Cs and 137 Cs were detected in zooplankton and seawater from all the stations. Because of its short half-lives, 134 Cs detected in our samples could only be derived from the FNPP1 accident. The highest 137 Cs activity in zooplankton was same order of magnitude as that one month after the accident, and average activity was one or two orders of magnitude higher than 137 Cs activities observed before the accident around Japan. Horizontally, the radiocesium activity concentrations in zooplankton were high at around 25° N while those in surface seawater were high at around the transition area between the Kuroshio and the Oyashio Currents (36–40° N). We observed subsurface radiocesium maxima in density range of the North Pacific Subtropical Mode Water and occurrence of many diel vertical migratory zooplanktons. These suggested that the high activity concentrations in the subtropical zooplankton at around 25° N were connected to the subsurface radiocesium and active vertical migration of zooplankton. However, the high activity concentrations of radiocesium in subsurface seawater did not necessarily follow the higher radiocesium activity in zooplankton. Biological characteristics of zooplankton community possibly influenced how large was contamination of radiocesium in the community but it is still unknown what kind of biological factors were important.

Description: Estimating carbonate parameters from hydrographic data for the intermediate and deep waters of the Southern Hemisphere Oceans Biogeosciences Discussions, 10, 6225-6257, 2013 Author(s): H. C. Bostock, S. E. Mikaloff Fletcher, and M. J. M. Williams Using GLODAP and CLIVAR ocean carbon data, we have developed several multiple linear regression (MLR) algorithms to estimate alkalinity and dissolved inorganic carbon (DIC) in the intermediate and deep waters of the Southern Hemisphere (south of 25° S) from only hydrographic data (temperature, salinity and dissolved oxygen). A Monte Carlo experiment was used to identify a potential density (σ θ ) of 27.5 as an optimal break point between the two regimes with different MLR algorithms. The algorithms provide a good estimate of DIC ( R 2 =0.98) and alkalinity ( R 2 =0.91), and excellent agreement for aragonite and calcite saturation states ( R 2 =0.99). Combining the algorithms with the CSIRO Atlas of Regional Seas (CARS), we have been able to map the calcite saturation horizon (CSH) and aragonite saturation horizon (ASH) for the Southern Ocean at a spatial resolution of 0.5°. These maps are more detailed and more consistent with oceanography than the gridded GLODAP data. The high resolution ASH map reveals a dramatic circumpolar shoaling at the Polar Front. North of 40° S the CSH is deepest in the Atlantic (~ 4000 m) and shallower in the Pacific Ocean (~ 2750 m), while the CSH sits between 3200 and 3400 m in the Indian Ocean.

Description: Productivity of aboveground coarse wood biomass and stand age related to soil hydrology of Amazonian forests in the Purus-Madeira interfluvial area Biogeosciences Discussions, 10, 6417-6459, 2013 Author(s): B. B. L. Cintra, J. Schietti, T. Emillio, D. Martins, G. Moulatlet, P. Souza, C. Levis, C. A. Quesada, and J. Schöngart The ongoing demand for information on forest productivity has increased the number of permanent monitoring plots across the Amazon. Those plots, however, do not comprise the whole diversity of forest types in the Amazon. The complex effects of soil, climate and hydrology on the productivity of seasonally waterlogged interfluvial wetland forests are still poorly understood. The presented study is the first field-based estimate for tree ages and wood biomass productivity in the vast interfluvial region between the Purus and Madeira rivers. We estimate stand age and wood biomass productivity by a combination of tree-ring data and allometric equations for biomass stocks of eight plots distributed along 600 km in the Purus-Madeira interfluvial area that is crossed by the BR-319 highway. We relate stand age and wood biomass productivity to hydrological and edaphic conditions. Mean productivity and stand age were 5.6 ± 1.1 Mg ha −1 yr −1 and 102 ± 18 yr, respectively. There is a strong relationship between tree age and diameter, as well as between mean diameter increment and mean wood density within a plot. Regarding the soil hydromorphic properties we find a positive correlation with wood biomass productivity and a negative relationship with stand age. Productivity also shows a positive correlation with the superficial phosphorus concentration. In addition, superficial phosphorus concentration increases with enhanced soil hydromorphic condition. We raise three hypotheses to explain these results: (1) the reduction of iron molecules on the saturated soils with plinthite layers close to the surface releases available phosphorous for the plants; (2) the poor structure of the saturated soils creates an environmental filter selecting tree species of faster growth rates and shorter life spans and (3) plant growth on saturated soil is favored during the dry season, since there should be low restrictions for soil water availability.

Description: Sources and fate of terrestrial dissolved organic carbon in lakes of a Boreal Plains region recently affected by wildfire Biogeosciences Discussions, 10, 6093-6141, 2013 Author(s): D. Olefeldt, K. J. Devito, and M. R. Turetsky Downstream mineralization and sedimentation of terrestrial dissolved organic carbon (DOC) render lakes important for landscape carbon cycling in the boreal region, with regulating processes potentially sensitive to perturbations associated with climate change including increased occurrence of wildfire. In this study we assessed chemical composition and reactivity (during both dark and UV incubations) of DOC from lakes and terrestrial sources within a peatland-rich western boreal plains region partially affected by a recent wildfire. While wildfire was found to increase aromaticity of DOC in peat pore-water above the water table, it had no effect on concentrations or composition of DOC from peatland wells and neither affected mineral well or lake DOC characteristics. Lake DOC composition reflected a mixing of peatland and mineral groundwater, with a greater influence of mineral sources to lakes in coarse- than fine-textured settings. Peatland DOC was less biodegradable than mineral DOC, but both mineralization and sedimentation of peatland DOC increased substantially during UV incubations through selective removal of aromatic humic and fulvic acids. DOC composition in lakes with longer residence times had characteristics consistent with increased UV-mediated processing. We estimate that about half of terrestrial DOC inputs had been lost within lakes, mostly due to UV-mediated processes. The importance of within-lake losses of aromatic DOC from peatland sources through UV-mediated processes indicate that terrestrial-aquatic C linkages in the study region are largely disconnected from recent terrestrial primary productivity. Together, our results suggest that characteristics of the study region (climate, surface geology and lake morphometry) render linkages between terrestrial and aquatic C cycling insensitive to the effects of wildfire by determining dominant terrestrial sources and within-lake processes of DOC removal.

Description: Solute specific scaling of inorganic nitrogen and phosphorus uptake in streams Biogeosciences Discussions, 10, 6671-6693, 2013 Author(s): R. O. Hall Jr., M. A. Baker, E. J. Rosi-Marshall, and J. L. Tank Stream ecosystem processes such as nutrient cycling may vary with stream position in the watershed. Using a scaling approach, we examined the relationship between stream size and nutrient uptake length, which represents the mean distance that a dissolved solute travels prior to removal from the water column. Ammonium uptake length increased proportionally with stream size measured as specific discharge (discharge/stream width) with a scaling exponent = 1.01. In contrast, the scaling exponent for nitrate (NO 3 − ) was 1.19 and for soluble reactive phosphorus (SRP) was 1.35, suggesting that uptake lengths for these nutrients increased more rapidly than increases in specific discharge. Additionally, the ratio of nitrogen (N) uptake length to SRP uptake length declined with stream size; there was lower demand for SRP relative to N as stream size increased. Ammonium and NO 3 − uptake velocity positively related with stream metabolism, while SRP did not. Finally, we related the scaling of uptake length and specific discharge to that of stream length using Hack's law and downstream hydraulic geometry. Ammonium uptake length increased less than proportionally with distance from the headwaters, suggesting a strong role for larger streams and rivers in regulating nutrient transport.

Description: Responses of lower trophic-level organisms to typhoon passage on the outer shelf of the East China Sea: an incubation experiment Biogeosciences Discussions, 10, 6605-6635, 2013 Author(s): N. Yasuki, K. Suzuki, and A. Tsuda Typhoons can induce vertical mixing, upwelling, or both in the water column due to strong wind stress. These events can induce phytoplankton blooms in the oligotrophic ocean after typhoon passage. However, little is known about the responses of lower trophic-level organisms or changes in the community structure following the passage of typhoons, particularly in offshore regions. Therefore, we evaluated community succession on the outer shelf of the East China Sea through on-deck bottle incubation experiments simulating hydrographic conditions after the passage of a typhoon. Under all of the experimental conditions we tested, chlorophyll a concentrations increased more than 9-fold within 6 days, and these algal cells were mainly composed of large diatoms (〉10 μm). Ciliates also increased along with the diatom bloom. These results suggest that increases in diatom and ciliate populations may enhance biogenic carbon export in the water column. Typhoons can affect not only phytoplankton productivity, but also the composition of lower trophic-level organisms and biogeochemical processes in oligotrophic offshore regions.

Description: Icehouse-greenhouse variations in marine denitrification Biogeosciences Discussions, 10, 14769-14813, 2013 Author(s): T. J. Algeo, P. A. Meyers, R. S. Robinson, H. Rowe, and G. Q. Jiang Long-term secular variation in the isotopic composition of seawater fixed nitrogen (N) is poorly known. Here, we document variation in the N-isotopic composition of marine sediments (δ 15 N sed ) since 660 Ma (million years ago) in order to understand major changes in the marine N cycle through time and their relationship to first-order climate variation. During the Phanerozoic, greenhouse climate modes were characterized by low δ 15 N sed (∼ −2 to +2‰) and icehouse climate modes by high δ 15 N sed (∼ +4 to +8‰). Shifts toward higher δ 15 N sed occurred rapidly during the early stages of icehouse modes, prior to the development of major continental glaciation, suggesting a potentially important role for the marine N cycle in long-term climate change. Reservoir box modeling of the marine N cycle demonstrates that secular variation in δ 15 N sed was likely due to changes in the dominant locus of denitrification, with a shift in favor of sedimentary denitrification during greenhouse modes owing to higher eustatic (global sea-level) elevations and greater on-shelf burial of organic matter, and a shift in favor of water-column denitrification during icehouse modes owing to lower eustatic elevations, enhanced organic carbon sinking fluxes, and expanded oceanic oxygen-minimum zones. The results of this study provide new insights into operation of the marine N cycle, its relationship to the global carbon cycle, and its potential role in modulating climate change at multimillion-year timescales.

Description: Technical Note: Disturbance of soil structure can lead to release of methane entrapped in glacier forefield soils Biogeosciences Discussions, 10, 14815-14834, 2013 Author(s): P. A. Nauer, E. Chiri, J. Zeyer, and M. H. Schroth Investigations of sources and sinks of atmospheric CH 4 are needed to understand the global CH 4 cycle and climate-change mitigation options. Glaciated environments might play a critical role due to potential feedbacks with global glacial meltdown. In an emerging glacier forefield, an ecological shift occurs from an anoxic, potentially methanogenic subglacial sediment to an oxic proglacial soil, in which soil-microbial consumption of atmospheric CH 4 is initiated. The development of this change in CH 4 turnover can be quantified by soil-gas profile analysis. We found evidence for CH 4 entrapped in glacier forefield soils when comparing two methods for the collection of soil-gas samples: a modified steel rod (SR) designed for one-time sampling and rapid screening (samples collected ~ 1 min after hammering the SR into the soil), and a novel multi-level sampler (MLS) for repetitive sampling through a previously installed access tube (samples collected weeks after access-tube installation). In glacier forefields on siliceous bedrock, sub-atmospheric CH 4 concentrations were observed with both methods. Conversely, elevated soil-CH 4 concentrations were observed in calcareous glacier forefields, but only in samples collected with the SR, while MLS samples all showed sub-atmospheric CH 4 concentrations. Time-series SR soil-gas sampling (additional samples collected 2, 3, 5, and 7 min after hammering) confirmed the transient nature of the elevated soil-CH 4 concentrations, which were decreasing from ~ 100 μL L −1 towards background levels within minutes. This hints towards the existence of entrapped CH 4 in calcareous glacier forefield soil that can be released when sampling soil-gas with the SR. Laboratory experiments with miniature soil cores collected from two glacier forefields confirmed CH 4 entrapment in these soils. Treatment by sonication and acidification resulted in a massive release of CH 4 from calcareous cores (on average 0.3–1.8 μg CH 4 (g d.w.) −1 ); release from siliceous cores was 1–2 orders of magnitude lower (0.02–0.03 μg CH 4 (g d.w.) −1 ). Clearly, some form of CH 4 entrapment exists in calcareous glacier forefield soils, and to a much lesser extent in siliceous glacier forefield soils. Its nature and origin remain unclear and will be subject of future investigations.

Description: Dynamics of particulate organic carbon flux in a global ocean model Biogeosciences Discussions, 10, 14715-14767, 2013 Author(s): I. D. Lima, P. J. Lam, and S. C. Doney The sinking of particulate organic carbon (POC) is a key component of the ocean carbon cycle and plays an important role in the global climate system. However, the processes controlling the fraction of primary production that is exported from the euphotic zone (export ratio) and how much of it survives respiration in the mesopelagic to be sequestered in the deep ocean (transfer efficiency) are not well understood. In this study, we use a three-dimensional, coupled physical-biogeochemical model (CCSM-BEC) to investigate the processes controlling the export of particulate organic matter from the euphotic zone and its flux to depth. We also compare model results with sediment trap data and other parameterizations of POC flux to depth to evaluate model skill and gain further insight into the causes of error and uncertainty in POC flux estimates. In the model, export ratios are mainly a function of diatom relative abundance and temperature while absolute fluxes and transfer efficiency are driven by mineral ballast composition of sinking material. The temperature dependence of the POC remineralization length scale is modulated by denitrification under low O 2 concentrations and lithogenic (dust) fluxes. Lithogenic material is an important control of transfer efficiency in the model, but its effect is restricted to regions of strong atmospheric dust deposition. In the remaining regions, CaCO 3 content of exported material is the main factor affecting transfer efficiency. The fact that mineral ballast composition is inextricably linked to plankton community structure results in correlations between export ratios and ballast minerals fluxes (opal and CaCO 3 ), and transfer efficiency and diatom relative abundance that do not necessarily reflect ballast or direct ecosystem effects, respectively. This suggests that it might be difficult to differentiate between ecosystem and ballast effects in observations. The model's skill at reproducing sediment trap observations is equal to or better than that of other parameterizations. However, the sparseness and relatively large uncertainties of sediment trap data makes it difficult to accurately evaluate the skill of the model and other parameterizations. More POC flux observations, over a wider range of ecological regimes, are necessary to thoroughly evaluate and test model results and better understand the processes controlling POC flux to depth in the ocean.

Description: Thin terrestrial sediment deposits on intertidal sandflats: effects on pore water solutes and juvenile bivalve burial behaviour Biogeosciences Discussions, 10, 14835-14860, 2013 Author(s): A. Hohaia, K. Vopel, and C. A. Pilditch Changes in land use and climate increase the supply of terrestrial sediment (hereafter, TS) to coastal waters worldwide but the effects of these sediments on benthic ecosystem functioning are not well known. Past experiments with defaunated, intertidal sediment suggested a link between the de-oxygenation of sediments underlying a thin (mm) layer of TS and reduced burial rates of juvenile macrofaunal recruits. We examined this link predicting that surficial TS deposits will still negatively affect burial when applied to sediments that are initially well oxygenated due to bioturbation (C) or depleted of organic matter (D). We observed the behaviour of post-settlement juveniles of the tellinid bivalve \textit{Macomona liliana} on the surface of four treatments; C, D, and the same sediments to which we added a thin layer of TS (CTS, DTS). Pore water analyses confirmed that the diffusive impedance of the 1.7–1.9 mm TS deposit decreased the oxygenation of the underlying intertidal sediment (CTS) but not that of the depleted sediment (DTS). Unexpectedly, (1) the application of a TS deposit significantly increased but not decreased the probability of burial, irrespectively of treatment, and (2) juveniles more likely buried into C than into D. We attribute the failure to document a negative effect of TS on the recruits' burial to the activity of the resident macroinfauna (CTS) or the absence of organic matter (DTS). Our results underline the important role of the resident macrofauna in mediating the stress response of benthic ecosystems.

Description: Calcium carbonate corrosivity in an Alaskan inland sea Biogeosciences Discussions, 10, 14887-14922, 2013 Author(s): W. Evans, J. T. Mathis, and J. N. Cross Ocean acidification is the hydrogen ion increase caused by the oceanic uptake of anthropogenic CO 2 , and is a focal point in marine biogeochemistry, in part, because this chemical reaction reduces calcium carbonate (CaCO 3 ) saturation states (Ω) to levels that are corrosive (i.e. Ω ≤ 1) to shell-forming marine organisms. However, other processes can drive CaCO 3 corrosivity; specifically, the addition of tidewater glacial melt. Carbonate system data collected in May and September from 2009 through 2012 in Prince William Sound (PWS), a semi-enclosed inland sea located on the south-central coast of Alaska that is ringed with fjords containing tidewater glaciers, reveal the unique impact of glacial melt on CaCO 3 corrosivity. Initial limited sampling was expanded in September 2011 to span large portions of the western and central sound, and included two fjords proximal to tidewater glaciers: Icy Bay and Columbia Bay. The observed conditions in these fjords affected CaCO 3 corrosivity in the upper water column (

Description: Surface circulation and upwelling patterns around Sri Lanka Biogeosciences Discussions, 10, 14953-14998, 2013 Author(s): A. de Vos, C. B. Pattiaratchi, and E. M. S. Wijeratne Sri Lanka occupies a unique location within the equatorial belt in the northern Indian Ocean with the Arabian Sea on its western side and the Bay of Bengal on its eastern side. The region is characterised by bi-annually reversing monsoon winds resulting from seasonal differential heating and cooling of the continental land mass and the ocean. This study explored elements of the dynamics of the surface circulation and coastal upwelling in the waters around Sri Lanka using satellite imagery and the Regional Ocean Modelling System (ROMS) configured to the study region and forced with ECMWF interim data. The model was run for 2 yr to examine the seasonal and shorter term (∼10 days) variability. The results confirmed the presence of the reversing current system in response to the changing wind field: the eastward flowing Southwest Monsoon Current (SMC) during the Southwest (SW) monsoon transporting 11.5 Sv and the westward flowing Northeast Monsoon Current (NMC) transporting 9.5 Sv during the Northeast (NE) monsoon, respectively. A recirculation feature located to the east of Sri Lanka during the SW monsoon, the Sri Lanka Dome, is shown to result from the interaction between the SMC and the Island of Sri Lanka. Along the eastern and western coasts, during both monsoon periods, flow is southward converging along the south coast. During the SW monsoon the Island deflects the eastward flowing SMC southward whilst along the east coast the southward flow results from the Sri Lanka Dome recirculation. The major upwelling region, during both monsoon periods, is located along the south coast and is shown to be due to flow convergence and divergence associated with offshore transport of water. Higher surface chlorophyll concentrations were observed during the SW monsoon. The location of the flow convergence and hence the upwelling centre was dependent on the relative strengths of wind driven flow along the east and west coasts: during the SW (NE) monsoon the flow along the western (eastern) coast was stronger and hence the upwelling centre was shifted to the east (west). The presence of upwelling along the south coast during both monsoon periods may explain the blue whale ( Balaenoptera musculus ) aggregations in this region.

Description: Strong sensitivity of Southern Ocean carbon uptake and nutrient cycling to wind stirring Biogeosciences Discussions, 10, 15033-15076, 2013 Author(s): K. B. Rodgers, O. Aumont, S. E. Mikaloff Fletcher, Y. Plancherel, L. Bopp, C. de Boyer Montégut, D. Iudicone, R. F. Keeling, G. Madec, and R. Wanninkhof Here we test the hypothesis that winds have an important role in determining the rate of exchange of CO 2 between the atmosphere and ocean through wind stirring over the Southern Ocean. This is tested with a sensitivity study using an ad hoc parameterization of wind stirring in an ocean carbon cycle model. The objective is to identify the way in which perturbations to the vertical density structure of the planetary boundary in the ocean impacts the carbon cycle and ocean biogeochemistry. Wind stirring leads to reduced uptake of CO 2 by the Southern Ocean over the period 2000–2006, with differences of order 0.9 Pg C yr −1 over the region south of 45° S. Wind stirring impacts not only the mean carbon uptake, but also the phasing of the seasonal cycle of carbon and other species associated with ocean biogeochemistry. Enhanced wind stirring delays the seasonal onset of stratification, and this has large impacts on both entrainment and the biological pump. It is also found that there is a strong sensitivity of nutrient concentrations exported in Subantarctic Mode Water (SAMW) to wind stirring. This finds expression not only locally over the Southern Ocean, but also over larger scales through the impact on advected nutrients. In summary, the large sensitivity identified with the ad hoc wind stirring parameterization offers support for the importance of wind stirring for global ocean biogeochemistry, through its impact over the Southern Ocean.

Description: Impact of seawater Ca 2+ on the calcification and calcite Mg/Ca of Amphistegina lessonii Biogeosciences Discussions, 11, 17463-17489, 2014 Author(s): A. Mewes, G. Langer, S. Thoms, G. Nehrke, G.-J. Reichart, L. J. de Nooijer, and J. Bijma Mg/Ca ratios in foraminiferal tests are routinely used as paleo temperature proxy, but on long timescales, also hold the potential to reconstruct past seawater Mg/Ca. Impact of both temperature and seawater Mg/Ca on Mg incorporation in foraminifera have been quantified by a number of studies. The underlying mechanism responsible for Mg incorporation in foraminiferal calcite and its sensitivity to environmental conditions, however, is not fully identified. A recently published biomineralization model (Nehrke et al., 2013) proposes a combination of transmembrane transport and seawater leakage or vacuolization to link calcite Mg/Ca to seawater Mg/Ca and explains inter-species variability in Mg/Ca ratios. To test the assumptions of this model, we conducted a culture study in which seawater Mg/Ca was manipulated by varying [Ca 2+ ] and keeping [Mg 2+ ] constant. Foraminiferal growth rates, test thickness and calcite Mg/Ca of newly formed chambers were analyzed. Results showed optimum growth rates and test thickness at Mg/Ca closest to that of ambient seawater. Calcite Mg/Ca is positively correlated to seawater Mg/Ca, indicating that not absolute seawater [Ca 2+ ] and [Mg 2+ ], but the telative ratio controls Mg/Ca in tests. These results demonstrate that the calcification process cannot be based only on seawater vacuolization, supporting the mixing model proposed by Nehrke et al. (2013). Here we, however, suggest a transmembrane transport fractionation that is not as strong as suggested by Nehrke et al. (2013).

Description: Fluxes of carbon and nutrients to the Iceland Sea surface layer and inferred primary productivity and stoichiometry Biogeosciences Discussions, 11, 15399-15433, 2014 Author(s): E. Jeansson, R. G. J. Bellerby, I. Skjelvan, H. Frigstad, S. R. Ólafsdóttir, and J. Ólafsson Fluxes of carbon and nutrients to the upper 100 m of the Iceland Sea are evaluated. The study utilises hydro-chemical data from the Iceland Sea time-series station (68.00° N, 12.67° W), for the years between 1993 and 2006. By comparing data of dissolved inorganic carbon (DIC) and nutrients in the surface layer (upper 100 m), and a sub-surface layer (100–200 m), we calculate monthly deficits in the surface, and use these to deduce the surface layer fluxes that affect the deficits: vertical mixing, horizontal advection, air–sea exchange, and biological activity. The deficits show a clear seasonality with a minimum in winter, when the mixed layer is at the deepest, and a maximum in early autumn, when biological uptake has removed much of the nutrients. The annual vertical fluxes of DIC and nitrate amounts to 1.7 ± 0.3 and 0.23 ± 0.07 mol m −2 yr −1 , respectively, and the annual air–sea uptake of atmospheric CO 2 is 4.4 ± 1.1 mol m −2 yr −1 . The biologically driven changes in DIC during the year relates to net community production (NCP), and the net annual NCP corresponds to export production, and is here calculated to 6.1 ± 0.9 mol C m −2 yr −1 . The typical, median C : N ratio during the period of net community uptake is 11, and thus clearly higher than Redfield, but is varying during the season.

Description: Technical Note: Artificial coral reef mesocosms for ocean acidification investigations Biogeosciences Discussions, 11, 15463-15505, 2014 Author(s): J. Leblud, L. Moulin, A. Batigny, P. Dubois, and P. Grosjean The design and evaluation of replicated artificial mesocosms are presented in the context of a thirteen month experiment on the effects of ocean acidification on tropical coral reefs. They are defined here as (semi)-closed (i.e. with or without water change from the reef) mesocosms in the laboratory with a more realistic physico-chemical environment than microcosms. Important physico-chemical parameters (i.e. pH, p O 2 , p CO 2 , total alkalinity, temperature, salinity, total alkaline earth metals and nutrients availability) were successfully monitored and controlled. Daily variations of irradiance and pH were applied to approach field conditions. Results highlighted that it was possible to maintain realistic physico-chemical parameters, including daily changes, into artificial mesocosms. On the other hand, the two identical artificial mesocosms evolved differently in terms of global community oxygen budgets although the initial biological communities and physico-chemical parameters were comparable. Artificial reef mesocosms seem to leave enough degrees of freedom to the enclosed community of living organisms to organize and change along possibly diverging pathways.

Description: Phytoplankton community structure in the North Sea: coupling between remote sensing and automated in situ analysis at the single cell level Biogeosciences Discussions, 11, 15621-15662, 2014 Author(s): M. Thyssen, S. Alvain, A. Lefèbvre, D. Dessailly, M. Rijkeboer, N. Guiselin, V. Creach, and L.-F. Artigas Phytoplankton observation in the ocean can be a challenge in oceanography. Accurate estimations of their biomass and dynamics will help to understand ocean ecosystems and refine global climate models. This requires relevant datasets of phytoplankton at a functional level and on a daily and sub meso scale. In order to achieve this, an automated, high frequency, dedicated scanning flow cytometer (SFC, Cytobuoy, NL), has been developed to cover the entire size range of phytoplankton cells whilst simultaneously taking pictures of the largest of them. This cytometer was directly connected to the water inlet of a~pocket Ferry Box during a cruise in the North Sea, 8–12 May 2011 (DYMAPHY project, INTERREG IV A "2 Seas"), in order to identify the phytoplankton community structure of near surface waters (6 m) with a high resolution spacial basis (2.2 ± 1.8 km). Ten groups of cells, distinguished on the basis of their optical pulse shapes, were described (abundance, size estimate, red fluorescence per unit volume). Abundances varied depending on the hydrological status of the traversed waters, reflecting different stages of the North Sea blooming period. Comparisons between several techniques analyzing chlorophyll a and the scanning flow cytometer, using the integrated red fluorescence emitted by each counted cell, showed significant correlations. The community structure observed from the automated flow cytometry was compared with the PHYSAT reflectance anomalies over a daily scale. The number of matchups observed between the SFC automated high frequency in situ sampling and the remote sensing was found to be two to three times better than when using traditional water sampling strategies. Significant differences in the phytoplankton community structure within the two days for which matchups were available, suggest that it is possible to label PHYSAT anomalies not only with dominant groups, but at the level of the community structure.

Description: Long term effects on regional European boreal climate due to structural vegetation changes Biogeosciences Discussions, 11, 15507-15547, 2014 Author(s): J. H. Rydsaa, F. Stordal, and L. M. Tallaksen Amplified warming at high latitudes over the past decades has led to changes in the boreal and arctic climate system, such as structural changes in high latitude ecosystems and soil moisture properties. These changes trigger land-atmosphere feedbacks, through altered energy partitioning in response to changes in albedo and surface water fluxes. Local scale changes in the arctic and boreal zone may propagate to affect large scale climatic features. In this study, MODIS land surface data are used with the Weather Research and Forecasting model (WRF V3.5.1) and Noah LSM, in a series of experiments to simulate the influence of structural vegetation changes over a Northern European boreal ecosystem. Emphasis is placed on surface energy partitioning and near surface atmospheric variables, in order to investigate changes in atmospheric response due to observed and anticipated structural vegetation changes. We find that a northward migration of evergreen needle leaf forest into tundra regions causes an increase in latent rather than sensible heat fluxes, increased near surface temperatures and boundary layer height. Shrub expansion in tundra areas has only small effects on surface fluxes. However, it influences near surface wind speeds and boundary layer height. Northward migration of mixed forest across the present southern border of the boreal forest has largely opposite effects on surface fluxes and the near surface atmosphere, and acts to moderate the overall mean regional effects of boreal forest migration on the near surface atmosphere.

Description: Spatial variability and hotspots of soil N 2 O fluxes from intensively grazed grassland Biogeosciences Discussions, 11, 15327-15360, 2014 Author(s): N. J. Cowan, P. Norman, D. Famulari, P. E. Levy, D. S. Reay, and U. M. Skiba One hundred N 2 O flux measurements were made from an area of intensively managed grazed grassland in central Scotland using a high resolution dynamic chamber method. The field contained a variety of features from which N 2 O fluxes were measured including a manure heap, patches of decaying grass silage, and areas of increased sheep activity. Individual fluxes varied significantly across the field varying from 2 to 79 000 μg N 2 O-N m −2 h −1 . Soil samples were collected at 55 locations to investigate relationships between soil properties and N 2 O flux. Fluxes of N 2 O correlated strongly with soil NO 3 − concentrations. Distribution of NO 3 − and the high spatial variability of N 2 O flux across the field are shown to be linked to the distribution of waste from grazing animals and the resultant reactive nitrogen compounds in the soil which are made available for microbiological processes. Features within the field such as shaded areas and manure heaps contained significantly higher available nitrogen than the rest of the field. Although these features only represented 1.1% of the area of the field, they contributed to over 55% of the total estimated daily N 2 O flux.

Description: Size-fractionated dissolved primary production and carbohydrate composition of the coccolithophore Emiliania huxleyi Biogeosciences Discussions, 11, 15289-15325, 2014 Author(s): C. Borchard and A. Engel Extracellular release (ER) by phytoplankton is the major source of fresh dissolved organic carbon (DOC) in marine ecosystems and accompanies primary production during all growth phases. Little is known, so far, on size and composition of released molecules, and to which extent ER occurs passively, by leakage, or actively, by exudation. Here, we report on ER by the widespread and bloom-forming coccolithophore Emiliania huxleyi grown under steady state conditions in phosphorus controlled chemostats (N : P = 29, growth rate of μ = 0.2 d −1 ). 14 C incubations were accomplished to determine primary production (PP), comprised by particulate (PO 14 C) and dissolved organic carbon (DO 14 C), and the concentration and composition of particulate combined carbohydrates (pCCHO), and of high molecular weight (〉1 kDa, HMW) dissolved combined carbohydrates (dCCHO) as major components of ER. Information on size distribution of ER products was obtained by investigating distinct size classes (

Description: Autonomous profiling float observations of the high biomass plume downstream of the Kerguelen plateau in the Southern Ocean Biogeosciences Discussions, 11, 17413-17462, 2014 Author(s): M. Grenier, A. Della Penna, and T. W. Trull Natural iron fertilisation from Southern Ocean islands results in high primary production and phytoplankton biomass accumulations readily visible in satellite ocean colour observations. These images reveal great spatial complexity with highly varying concentrations of chlorophyll, presumably reflecting both variations in iron supply and conditions favouring phytoplankton accumulation. To examine the second aspect, in particular the influences of variations in temperature and stratification, we deployed four autonomous profiling floats in the Antarctic Circumpolar Current near the Kerguelen plateau in the Indian sector of the Southern Ocean. Each "bio-profiler" measured more than 250 profiles of temperature ( T ), salinity ( S ), dissolved oxygen, chlorophyll fluorescence (Chl a ), and particle backscatter in the top 300 m of the water column, sampling up to 5 profiles per day along meandering trajectories extending up to 1000 km. Comparison of surface Chl a estimates (top 50 m depth; analogous to values from satellite images) with total water column inventories revealed largely linear relationships, suggesting that dilution of chlorophyll by mixed layer depth variations plays only a minor role in the spatial distributions observed by satellite, and correspondingly that these images provide credible information on total and not just surface biomass accumulations. Regions of very high Chl a accumulation (1.5–10 μg L -1 ) were associated predominantly with a narrow T – S class of surface waters, which appears to derive from the northern Kerguelen plateau. In contrast, waters with only moderate Chl a enrichments (0.5–1.5 μg L -1 ) displayed no clear correlation with water properties, including no dependence on mixed layer depth, suggesting a diversity of sources of iron and/or its efficient dispersion across filaments of the plume. The lack of dependence on mixed layer depth also indicates a limited influence on production by light limitation. One float became trapped in a cyclonic eddy, allowing temporal evaluation of the water column in early autumn. During this period, decreasing surface Chl a inventories corresponded with decreases in oxygen inventories on sub-mixed layer density surfaces, consistent with significant export of organic matter and its respiration and storage as dissolved inorganic carbon in the ocean interior. These results are encouraging for the expanded use of autonomous observing platforms to study biogeochemical, carbon cycle, and ecological problems, although the complex blend of Lagrangian and Eulerian sampling achieved by the floats suggests that arrays rather than single floats will often be required.

Description: On the use of the post-closure method uncertainty band to evaluate the performance of land surface models against eddy covariance flux data Biogeosciences Discussions, 11, 16911-16951, 2014 Author(s): J. Ingwersen, K. Imukova, P. Högy, and T. Streck The energy balance of eddy covariance (EC) flux data is normally not closed. Therefore, at least if used for modeling, EC flux data are usually post-closed, i.e. the measured turbulent fluxes are adjusted so as to close the energy balance. At the current state of knowledge, however, it is not clear how to partition the missing energy in the right way. Eddy flux data therefore contain some uncertainty due to the unknown nature of the energy balance gap, which should be considered in model evaluation and the interpretation of simulation results. We propose to construct the post-closure method uncertainty band (PUB), which essentially designates the differences between non-adjusted flux data and flux data adjusted with the three post-closure methods (Bowen ratio, latent heat flux (LE) and sensible heat flux ( H ) method). To demonstrate this approach, simulations with the NOAH-MP land surface model were evaluated based on EC measurements conducted at a winter wheat stand in Southwest Germany in 2011, and the performance of the Jarvis and Ball–Berry stomatal resistance scheme was compared. The width of the PUB of the LE was up to 110 W m –2 (21% of net radiation). Our study shows that it is crucial to account for the uncertainty of EC flux data originating from lacking energy balance closure. Working with only a single post-closing method might result in severe misinterpretations in model-data comparisons.

Description: Carbon, oxygen and biological productivity in the Southern Ocean in and out the Kerguelen plume: CARIOCA drifter results Biogeosciences Discussions, 11, 16877-16909, 2014 Author(s): L. Merlivat, J. Boutin, and F. d'Ovidio The Kerguelen Plateau region in the Indian sector of the Southern Ocean supports annually a large-scale phytoplankton bloom which is naturally fertilized with iron. As part of the second Kerguelen Ocean and Plateau compared Study expedition (KEOPS2) in austral spring (October–November 2011), one Carioca buoy was deployed east of the Kerguelen plateau. It drifted eastward downstream in the Kerguelen plume. Hourly surface measurements of p CO 2 , O 2 and ancillary observations were collected between 1 November 2011 to 12 February 2012 with the aim of characterizing the spatial and temporal variability of the biological Net Community Production (NCP) downstream the Kerguelen plateau, assess the impact of iron-induced productivity on the biological carbon consumption and consequently on the CO 2 flux exchanged at the air–sea interface. The trajectory of the buoy until mid-December was within the longitude range, 72–83° E, close to the polar front and then in the polar frontal zone, PFZ, until 97° E. From 17 November to 16 December, the buoy drifted within the Kerguelen plume following a filament carrying dissolved iron, DFe, for a total distance of 700 km. In the first part of the trajectory, the ocean surface waters are a sink for CO 2 and a source for CO 2 , with fluxes of respective mean values equal to −8 and +38 mmol CO 2 m −2 d −1 . Eastward, as the buoy escapes the iron enriched filament, the fluxes are in opposite direction, with respective mean values of +5 and −48 mmol O 2 m −2 d −1 . These numbers clearly indicate the strong impact of biological processes on the biogeochemistry in the surface waters within the Kerguelen plume in November-mid-December, while it is undetectable eastward in the PFZ from mid-December to mid-February. While the buoy follows the Fe enriched filament, simultaneous observations of dissolved inorganic carbon, DIC, and dissolved oxygen, O 2 , highlight biological events lasting from 2 to 4 days. Stoichiometric ratios, O 2 /C, between 1.1 and 1.4 are observed indicating new and regenerated production regimes. NCP estimates range from 60 to 140 mmol C m −2 d −1 . Based on the relationship between the time a water parcel has left the plateau and its iron content, we have highlighted that the main control on the value of NCP is the availability of iron in the upper water column, with the largest NCP occurring in waters that have recently left the plateau and presented the highest iron concentrations.

Description: Comparison of UV/Vis and FDOM sensors for in situ monitoring of stream DOC concentrations Biogeosciences Discussions, 11, 16855-16876, 2014 Author(s): G.-Y. Yoo, Y. Jeong, E.-J. Lee, J.-H. Park, and N.-H. Oh Optical measurements using ultra-violet/visible (UV/Vis) spectrophotometric sensors and fluorescent dissolved organic matter (FDOM) sensors have recently been used as proxies of dissolved organic carbon (DOC) concentrations of streams and rivers at high temporal resolution. Despite of the merits of the sensors, temperature changes and particulate matter in water can interfere the sensor readings, over- or under-estimating DOC concentrations. However, little efforts have been made to compare responses of the two types of the sensors in natural conditions. We conducted both laboratory experiments and in situ monitoring with a UV/Vis sensor and a FDOM sensor during the three storm events in the fall of 2012 and the spring of 2013 in a forest stream in Korea in order to compare their performance. Laboratory experiments using the Suwannee River natural organic matter, humic acid, and fulvic acid demonstrated strong linear relationships between both the sensor signals and measured DOC concentrations with R 2 ≥ 0.98. Although temperature compensation might not be needed for the UV/Vis sensor, it was sensitive to relativley small changes in turbidity. In contrast, the FDOM sensor was insenstive to relatively low turbidity while the FDOM sensor outputs decreased significantly as temperature increased, requiring temperature compensated FDOM (e.g. FDOM 20 for 20 °C) for in situ monitoring of DOC. The results suggest that both sensors can be employed as a~proxy for stream DOC concentrations after temperature and turbidity compensation in a forest stream where terrestrially derived humic-like materials are dominant components.

Description: Modeling the impact of riverine DON removal by marine bacterioplankton on primary production in the Arctic Ocean Biogeosciences Discussions, 11, 16953-16992, 2014 Author(s): V. Le Fouest, M. Manizza, B. Tremblay, and M. Babin The planktonic and biogeochemical dynamics of the Arctic shelves exhibit a strong variability in response to Arctic warming. In this study, in order to elucidate on the processes regulating the production of phytoplankton (PP) and bacterioplankton (BP) and their interactions, we employ a biogeochemical model coupled to a pan-Arctic ocean-sea ice model (MITgcm) to explicitly simulate and quantify the contribution of usable dissolved organic nitrogen (DON) drained by the major circum-Arctic rivers on PP and BP in a scenario of melting sea ice (1998–2011). Model simulations suggest that on average between 1998 and 2011, the removal of usable RDON by bacterioplankton is responsible of a ~26% increase of the annual BP for the whole Arctic Ocean. With respect to total PP, the model simulates an increase of ~8% on an annual basis and of ~18% in summer. Recycled ammonium is responsible for the PP increase. The recycling of RDON by bacterioplankton promotes higher BP and PP but there is no significant temporal trend in the BP : PP ratio within the ice-free shelves over the 1998–2011 period. This suggests no significant evolution in the balance between autotrophy and heterotrophy in the last decade with a constant annual flux of RDON into the coastal ocean although changes in RDON supply and further reduction in sea ice cover could potentially alter this delicate balance.

Description: The influence of land cover change in the Asian monsoon region on present-day and mid-Holocene climate Biogeosciences, 8, 1499-1519, 2011 Author(s): A. Dallmeyer and M. Claussen Using the general circulation model ECHAM5/JSBACH, we investigate the biogeophysical effect of large-scale afforestation and deforestation in the Asian monsoon domain on present-day and mid-Holocene climate. We demonstrate that the applied land cover change does not only modify the local climate but also change the climate in North Africa and the Middle East via teleconnections. Deforestation in the Asian monsoon domain enhances the rainfall in North Africa. In parts of the Sahara summer precipitation is more than doubled. In contrast, afforestation strongly decreases summer rainfall in the Middle East and even leads to the cessation of the rainfall-activity in some parts of this region. Regarding the local climate, deforestation results in a reduction of precipitation and a cooler climate as grass mostly has a higher albedo than forests. However, in the core region of the Asian monsoon the decrease in evaporative cooling in the monsoon season overcompensates this signal and results in a net warming. Afforestation has mainly the opposite effect, although the pattern of change is less clear. It leads to more precipitation in most parts of the Asian monsoon domain and a warmer climate except for the southern regions where a stronger evaporation decreases near-surface temperatures in the monsoon season. When prescribing mid-Holocene insolation, the pattern of local precipitation change differs. Afforestation particularly increases monsoon rainfall in the region along the Yellow River which was the settlement area of major prehistoric cultures. In this region, the effect of land cover change on precipitation is half as large as the orbitally-induced precipitation change. Thus, our model results reveal that mid- to late-Holocene land cover change could strongly have contributed to the decreasing Asian monsoon precipitation during the Holocene known from reconstructions.

Description: An algorithm for detecting Trichodesmium surface blooms in the South Western Tropical Pacific Biogeosciences Discussions, 8, 5653-5689, 2011 Author(s): C. Dupouy, D. Benielli-Gary, J. Neveux, Y. Dandonneau, and T. K. Westberry Trichodesmium , a major colonial cyanobacterial nitrogen fixer, forms large blooms in NO 3 -depleted tropical oceans and enhances CO 2 sequestration by the ocean due to its ability to fix dissolved dinitrogen. Thus, its importance in C and N cycles requires better estimates of its distribution at basin to global scales. However, existing algorithms to detect them from satellite have not yet been successful in the South Western Tropical Pacific (SWTP). Here, a novel approach based on radiance anomaly spectra (RAS) observed in SeaWiFS imagery is used to detect Trichodesmium during the austral summertime in the SWTP. Selected pixels are characterized by a restricted range of parameters quantifying RAS spectra quantitative parameters (e.g. slope, intercept, curvature). The fraction of valid pixels identified as Trichodesmium surface blooms in the region 5° S–25° S 160° E–190° E is low (between 0.01 and 0.2 %), but is about 100 times higher than suggested by previous algorithms. This represents a total surface area which varies from 1500 to 20 000 km 2 . A monthly distribution of Trichodesmium surface accumulations in the SWTP is presented which demonstrates that the number of selected pixels peaks in November–February each year, consistent with field observations. This approach was validated with in situ observations of Trichodesmium surface accumulations for the period 1998–2010.

Description: Origin and fate of the secondary nitrite maximum in the Arabian Sea Biogeosciences, 8, 1565-1577, 2011 Author(s): P. Lam, M. M. Jensen, A. Kock, K. A. Lettmann, Y. Plancherel, G. Lavik, H. W. Bange, and M. M. M. Kuypers The Arabian Sea harbours one of the three major oxygen minimum zones (OMZs) in the world's oceans, and it alone is estimated to account for ~10–20 % of global oceanic nitrogen (N) loss. While actual rate measurements have been few, the consistently high accumulation of nitrite (NO 2 − ) coinciding with suboxic conditions in the central-northeastern part of the Arabian Sea has led to the general belief that this is the region where active N-loss takes place. Most subsequent field studies on N-loss have thus been drawn almost exclusively to the central-NE. However, a recent study measured only low to undetectable N-loss activities in this region, compared to orders of magnitude higher rates measured towards the Omani Shelf where little NO 2 − accumulated (Jensen et al., 2011). In this paper, we further explore this discrepancy by comparing the NO 2 − -producing and consuming processes, and examining the relationship between the overall NO 2 − balance and active N-loss in the Arabian Sea. Based on a combination of 15 N-incubation experiments, functional gene expression analyses, nutrient profiling and flux modeling, our results showed that NO 2 − accumulated in the central-NE Arabian Sea due to a net production via primarily active nitrate (NO 3 − ) reduction and to a certain extent ammonia oxidation. Meanwhile, NO 2 − consumption via anammox, denitrification and dissimilatory nitrate/nitrite reduction to ammonium (NH 4 + ) were hardly detectable in this region, though some loss to NO 2 − oxidation was predicted from modeled NO 3 − changes. No significant correlation was found between NO 2 − and N-loss rates ( p 〉0.05). This discrepancy between NO 2 − accumulation and lack of active N-loss in the central-NE Arabian Sea is best explained by the deficiency of labile organic matter that is directly needed for further NO 2 − reduction to N 2 O, N 2 and NH 4 + , and indirectly for the remineralized NH 4 + required by anammox. Altogether, our data do not support the long-held view that NO 2 − accumulation is a direct activity indicator of N-loss in the Arabian Sea or other OMZs. Instead, NO 2 − accumulation more likely corresponds to long-term integrated N-loss that has passed the prime of high and/or consistent in situ activities.

Description: Carbon dioxide fluxes over an ancient broadleaved deciduous woodland in southern England Biogeosciences, 8, 1595-1613, 2011 Author(s): M. V. Thomas, Y. Malhi, K. M. Fenn, J. B. Fisher, M. D. Morecroft, C. R. Lloyd, M. E. Taylor, and D. D. McNeil We present results from a study of canopy-atmosphere fluxes of carbon dioxide from 2007 to 2009 above a site in Wytham Woods, an ancient temperate broadleaved deciduous forest in southern England. Gap-filled net ecosystem exchange (NEE) data were partitioned into gross primary productivity (GPP) and ecosystem respiration ( R e ) and analysed on daily, monthly and annual timescales. Over the continuous 24 month study period annual GPP was estimated to be 21.1 Mg C ha −1 yr −1 and R e to be 19.8 Mg C ha −1 yr −1 ; net ecosystem productivity (NEP) was 1.2 Mg C ha −1 yr −1 . These estimates were compared with independent bottom-up estimates derived from net primary productivity (NPP) and flux chamber measurements recorded at a plot within the flux footprint in 2008 (GPP = 26.5 ± 6.8 Mg C ha −1 yr −1 , R e = 24.8 ± 6.8 Mg C ha −1 yr −1 , biomass increment = ~1.7 Mg C ha −1 yr −1 ). Over the two years the difference in seasonal NEP was predominantly caused by changes in ecosystem respiration, whereas GPP remained similar for equivalent months in different years. Although solar radiation was the largest influence on daily values of CO 2 fluxes ( R 2 = 0.53 for the summer months for a linear regression), variation in R e appeared to be driven by temperature. Our findings suggest that this ancient woodland site is currently a substantial sink for carbon, resulting from continued growth that is probably a legacy of past management practices abandoned over 40 years ago. Our GPP and R e values are generally higher than other broadleaved temperate deciduous woodlands and may represent the influence of the UK's maritime climate, or the particular species composition of this site. The carbon sink value of Wytham Woods supports the protection and management of temperate deciduous woodlands (including those managed for conservation rather than silvicultural objectives) as a strategy to mitigate atmospheric carbon dioxide increases.

Description: Rainfall patterns after fire differentially affect the recruitment of three Mediterranean shrubs Biogeosciences Discussions, 8, 5761-5786, 2011 Author(s): J. M. Moreno, E. Zuazua, B. Pérez, B. Luna, A. Velasco, and V. Resco de Dios In fire-prone environments, the "event-dependent hypothesis" states that plant population changes are driven by the unique set of conditions of a fire (e.g., fire season, climate). Climate variability, in particular changes in rainfall patterns, can be most important for seeder species, since they must regenerate after fire from seeds, and for Mediterranean shrublands, given the high yearly variability of rainfall in these ecosystems. Yet, the role of rainfall variability and its interaction with fire characteristics (e.g., fire season) on plant populations has received little attention. Here we investigated the changes in seedling emergence and recruitment of three seeder species ( Cistus ladanifer , Erica umbellata and Rosmarinus officinalis ) after fires lit during three different years and at two times during the fire season (early and late in the fire season) to account for potential changes in the soil seed-bank during the year. Three plots were burned at each season, for a total of 18 plots burned during the three years. After fire, emerged seedlings were tallied, tagged and monitored during three years (two the last burning year). Rainfall during the study period was rather variable, and in some years was well below average. Seedling emergence after fire varied by a factor of 3 to 10, depending on the species and on the burning year. The bulk of seedling emergence occurred in the first year after fire, and seedling recruitment at the end of the study period was tightly correlated with this early emergence. Seedling emergence in E umbellata and R officinalis , but not in C ladanifer , were correlated with precipitation in the fall and winter immediately after the fire, being E umbellata most sensitive to low rainfall. Fire season was generally not an important factor in controlling emergence and recruitment. We discuss how projected changes in rainfall patterns with global warming can alter the balance of species in this shrubland, and can drive some species to near local extinction.

Description: Constraining global methane emissions and uptake by ecosystems Biogeosciences, 8, 1643-1665, 2011 Author(s): R. Spahni, R. Wania, L. Neef, M. van Weele, I. Pison, P. Bousquet, C. Frankenberg, P. N. Foster, F. Joos, I. C. Prentice, and P. van Velthoven Natural methane (CH 4 ) emissions from wet ecosystems are an important part of today's global CH 4 budget. Climate affects the exchange of CH 4 between ecosystems and the atmosphere by influencing CH 4 production, oxidation, and transport in the soil. The net CH 4 exchange depends on ecosystem hydrology, soil and vegetation characteristics. Here, the LPJ-WHyMe global dynamical vegetation model is used to simulate global net CH 4 emissions for different ecosystems: northern peatlands (45°–90° N), naturally inundated wetlands (60° S–45° N), rice agriculture and wet mineral soils. Mineral soils are a potential CH 4 sink, but can also be a source with the direction of the net exchange depending on soil moisture content. The geographical and seasonal distributions are evaluated against multi-dimensional atmospheric inversions for 2003–2005, using two independent four-dimensional variational assimilation systems. The atmospheric inversions are constrained by the atmospheric CH 4 observations of the SCIAMACHY satellite instrument and global surface networks. Compared to LPJ-WHyMe the inversions result in a~significant reduction in the emissions from northern peatlands and suggest that LPJ-WHyMe maximum annual emissions peak about one month late. The inversions do not put strong constraints on the division of sources between inundated wetlands and wet mineral soils in the tropics. Based on the inversion results we diagnose model parameters in LPJ-WHyMe and simulate the surface exchange of CH 4 over the period 1990–2008. Over the whole period we infer an increase of global ecosystem CH 4 emissions of +1.11 Tg CH 4 yr −1 , not considering potential additional changes in wetland extent. The increase in simulated CH 4 emissions is attributed to enhanced soil respiration resulting from the observed rise in land temperature and in atmospheric carbon dioxide that were used as input. The long-term decline of the atmospheric CH 4 growth rate from 1990 to 2006 cannot be fully explained with the simulated ecosystem emissions. However, these emissions show an increasing trend of +3.62 Tg CH 4 yr −1 over 2005–2008 which can partly explain the renewed increase in atmospheric CH 4 concentration during recent years.

Description: Phosphorus transformations as a function of pedogenesis: a synthesis of soil phosphorus data using Hedley fractionation method Biogeosciences Discussions, 8, 5907-5934, 2011 Author(s): X. Yang and W. M. Post In spite of the importance of phosphorus (P) as a limiting nutrient in terrestrial ecosystems, our understanding of terrestrial P dynamics and our ability to model P cycling are hampered by the lack of consistent measurements of soil P. The Hedley fractionation method provides a comprehensive assessment of soil P and has been widely used in recent decades. Here we expand an earlier study that summarized Hedley P data from the literature to create a larger Hedley P database and further investigate the relationships between distributions of different forms of P and the stages of soil development. Our expanded Hedley P database generally supports what the Walker and Syers (1976) conceptual model predicts: the gradual decrease and eventual depletion of primary mineral P (mainly apatite P); the continual increase and eventual dominance of occluded P; and the overall decrease of total P during soil development. However the analysis disagrees with Walker and Syers (1976) in that we found labile inorganic P(Pi) and secondary Pi (non-occluded P in Walker and Syers' model) to be a significant fraction of total P throughout all soil orders with different weathering stages. By analyzing the Hedley-labile P and vegetation P demand, we found that the amount of labile P is much greater than vegetation demand, even in highly weathered soils commonly considered P limited. We conclude that measured Hedley-labile P should not be defined as plant available P since most of this labile P likely ends up as immobilized by microbes. Our analysis of the database also shows that carbon (C) and nitrogen (N) in soil organic matter are closely linked in all soil orders, but P is decoupled from C and N in highly weathered soils with larger variations of nitrogen:organic P (N:Po) ratio and higher mean values of N:Po ratio, compared to slightly and intermediately weathered soils.

Description: Corrigendum to "A culture-based calibration of benthic foraminiferal paleotemperature proxies: δ 18 O and Mg/Ca results" published in Biogeosciences, 7, 1335–1347, 2010 Biogeosciences, 8, 1521-1521, 2011 Author(s): H. L. Filipsson, J. M. Bernhard, S. A. Lincoln, and D. C. McCorkle No abstract available.

Description: Greenhouse gas flux measurements in a forestry-drained peatland indicate a large carbon sink Biogeosciences Discussions, 8, 5787-5825, 2011 Author(s): A. Lohila, K. Minkkinen, M. Aurela, J.-P. Tuovinen, T. Penttilä, and T. Laurila Drainage for forestry purposes changes the conditions in the peat and leads to increased growth of shrubs and trees. Concurrently, the production and uptake of the greenhouse gases carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O) are likely to change: due to the accelerated decomposition of oxic peat, drained peatlands are generally considered to loose peat carbon (C). We measured CO 2 exchange with the eddy covariance (EC) method above a drained nutrient-poor peatland forest in Southern Finland for 16 months in 2004–2005. The site, classified as a dwarf-shrub pine bog, had been ditched about 35 years earlier. CH 4 and N 2 O fluxes were measured at 2–5 week intervals with the chamber technique. Drainage had resulted in a relatively little change in the water table level, being on average 40 cm below the ground in 2005. The annual net ecosystem exchange was −870 g CO 2 m −2 yr −1 in the calendar year 2005, varying from −810 to −900 g CO 2 m −2 yr −1 during the 16 month period under investigation. The site was a small sink of CH 4 (−0.12 g CH 4 m −2 yr −1 ) and a small source of N 2 O (0.10 g N 2 O m −2 yr −1 ). Photosynthesis was detected throughout the year when the air temperature exceeded −3 °C. As the annual accumulation of C in the above and below ground tree biomass (550 g CO 2 m −2 ) was significantly less than the net exchange of CO 2 , about 300 g CO 2 m −2 yr −1 (~80 g C m −2 ) was likely to have accumulated as organic matter into the peat soil. This is a higher average accumulation rate than previously reported for natural northern peatlands, and the first time C accumulation has been shown, by EC measurements, to occur in a drained peatland. Our results suggest that forestry-drainage may significantly increase the CO 2 uptake rate of nutrient-poor peatland ecosystems.

Description: Effect of mosaic representation of vegetation in land surface schemes on simulated energy and carbon balances Biogeosciences Discussions, 8, 5849-5879, 2011 Author(s): R. Li and V. K. Arora Energy and carbon balance implications of representing vegetation using a composite or mosaic approach in a land surface scheme are investigated. In the composite approach the attributes of different plant functional types (PFTs) present in a grid cell are aggregated in some fashion for energy and water balance calculations. The resulting physical environmental conditions (including net radiation, soil moisture and soil temperature) are common to all PFTs and affect their ecosystem processes. In the mosaic approach energy and water balance calculations are performed separately for each PFT tile using its own vegetation attributes, so each PFT "sees" different physical environmental conditions and its carbon balance evolves somewhat differently from that in the composite approach. Simulations are performed at selected boreal, temperate and tropical locations to illustrate the differences caused by using the composite versus the mosaic approaches of representing vegetation. Differences in grid averaged primary energy fluxes are generally less than 5 % between the two approaches. Grid-averaged carbon fluxes and pool sizes can, however, differ by as much as 46 %. Simulation results suggest that differences in carbon balance between the two approaches arise primarily through differences in net radiation which directly affects net primary productivity, and thus leaf area index and vegetation biomass.

Description: Underestimated effects of low temperature during early growing season on carbon sequestration of a subtropical coniferous plantation Biogeosciences, 8, 1667-1678, 2011 Author(s): W.-J. Zhang, H.-M. Wang, F.-T. Yang, Y.-H. Yi, X.-F. Wen, X.-M. Sun, G.-R. Yu, Y.-D. Wang, and J.-C. Ning The impact of air temperature in early growing season on the carbon sequestration of a subtropical coniferous plantation was discussed through analyzing the eddy flux observations at Qianyanzhou (QYZ) site in southern China from 2003 to 2008. This site experienced two cold early growing seasons (with temperature anomalies of 2–5 °C) in 2005 and 2008, and a severe summer drought in 2003. Results indicated that the low air temperature from January to March was the major factor controlling the inter-annual variations in net carbon uptake at this site, rather than the previously thought summer drought. The accumulative air temperature from January to February showed high correlation ( R 2 =0.970, p

Description: Mega fire emissions in Siberia: potential supply of bioavailable iron from forests to the ocean Biogeosciences, 8, 1679-1697, 2011 Author(s): A. Ito Significant amounts of carbon and nutrients are released to the atmosphere due to large fires in forests. Characterization of the spatial distribution and temporal variation of the intense fire emissions is crucial for assessing the atmospheric loadings of trace gases and aerosols. This paper discusses issues of the representation of forest fires in the estimation of emissions and the application to an atmospheric chemistry transport model (CTM). The potential contribution of forest fires to the deposition of bioavailable iron (Fe) into the ocean is highlighted, with a focus on mega fires in eastern Siberia. Satellite products of burned area, active fire, and land cover are used to estimate biomass burning emissions in conjunction with a biogeochemical model. Satellite-derived plume height from MISR is used for the injection height of boreal forest fire emissions. This methodology is applied to quantify fire emission rates in each three-dimensional grid location in the high latitude Northern Hemisphere (〉30° N latitude) over a 5-yr period from 2001 to 2005. There is large interannual variation in forest burned area during 2001–2005 (13–49 × 10 3 km 2 yr −1 ) which results in a corresponding variation in the annual emissions of carbon monoxide (CO) (14–81 Tg CO y −1 ). Satellite observations of CO column from MOPITT are used to evaluate the model performance in simulating the spatial distribution and temporal variation of the fire emissions. The model results for CO enhancements due to eastern Siberian fires are in good agreement with MOPITT observations. These validation results suggest that the model using emission rates estimated in this work is able to describe the interannual changes in CO due to intense forest fires. Bioavailable iron is derived from atmospheric processing of relatively insoluble iron from desert sources by anthropogenic pollutants (mainly sulfuric acid formed from oxidation of SO 2 ) and from direct emissions of soluble iron from combustion sources. Emission scenarios for IPCC AR5 report (Intergovernmental Panel on Climate Change; Fifth Assessment Report) suggest that anthropogenic SO 2 emissions are suppressed in the future to improve air quality. In future warmer and drier climate, severe fire years such as 2003 may become more frequent in boreal regions. The fire emission rates estimated in this study are applied to the aerosol chemistry transport model to examine the relative importance of biomass burning sources of soluble iron compared to those from dust sources. The model reveals that extreme fire events contribute to a significant deposition of soluble iron (20–40 %) to downwind regions over the western North Pacific Ocean, compared to the dust sources with no atmospheric processing by acidic species. These results suggest that the supply of nutrients from large forest fires plays a role as a negative biosphere-climate feedback with regards to the ocean fertilization.

Description: The effect of resource history on the functioning of soil microbial communities is maintained across time Biogeosciences, 8, 1477-1486, 2011 Author(s): A. D. Keiser, M. S. Strickland, N. Fierer, and M. A. Bradford Historical resource conditions appear to influence microbial community function. With time, historical influences might diminish as populations respond to the contemporary environment. Alternatively, they may persist given factors such as contrasting genetic potentials for adaptation to a new environment. Using experimental microcosms, we test competing hypotheses that function of distinct soil microbial communities in common environments (H1 a ) converge or (H1 b ) remain dissimilar over time. Using a 6 × 2 (soil community inoculum × litter environment) full-factorial design, we compare decomposition rates in experimental microcosms containing grass or hardwood litter environments. After 100 days, communities that develop are inoculated into fresh litters and decomposition followed for another 100 days. We repeat this for a third, 100-day period. In each successive, 100-day period, we find higher decomposition rates (i.e. functioning) suggesting communities function better when they have an experimental history of the contemporary environment. Despite these functional gains, differences in decomposition rates among initially distinct communities persist, supporting the hypothesis that dissimilarity is maintained across time. In contrast to function, community composition is more similar following a common, experimental history. We also find that "specialization" on one experimental environment incurs a cost, with loss of function in the alternate environment. For example, experimental history of a grass-litter environment reduced decomposition when communities were inoculated into a hardwood-litter environment. Our work demonstrates experimentally that despite expectations of fast growth rates, physiological flexibility and rapid evolution, initial functional differences between microbial communities are maintained across time. These findings question whether microbial dynamics can be omitted from models of ecosystem processes if we are to predict reliably global change effects on biogeochemical cycles.

Description: Experimental fossilisation of viruses from extremophilic Archaea Biogeosciences, 8, 1465-1475, 2011 Author(s): F. Orange, A. Chabin, A. Gorlas, S. Lucas-Staat, C. Geslin, M. Le Romancer, D. Prangishvili, P. Forterre, and F. Westall The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. Traces of life on the early Earth were preserved by the precipitation of silica on the organic structures. We present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 – Sulfolobus islandicus rod-shaped virus 2, TPV1 – Thermococcus prieurii virus 1, and PAV1 – Pyrococcus abyssi virus 1). Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope) over several months in a manner similar to that of other experimentally and naturally fossilised microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles.

Description: Soil organic matter dynamics in a North America tallgrass prairie after 9 yr of experimental warming Biogeosciences, 8, 1487-1498, 2011 Author(s): X. Cheng, Y. Luo, X. Xu, R. Sherry, and Q. Zhang The influence of global warming on soil organic matter (SOM) dynamics in terrestrial ecosystems remains unclear. In this study, we combined soil fractionation with isotope analyses to examine SOM dynamics after nine years of experimental warming in a North America tallgrass prairie. Soil samples from the control plots and the warmed plots were separated into four aggregate sizes (〉2000 μm, 250–2000 μm, 53–250 μm, and

Description: Contributions of agricultural plants and soils to N 2 O emission in a farmland Biogeosciences Discussions, 8, 5505-5535, 2011 Author(s): J. Li, X. Lee, Q. Yu, X. Tong, Z. Qin, and B. Macdonald The goal of this study was to quantify the roles of plants and soil in the N 2 O budget of a cropland in North China. Plant and soil N 2 O fluxes were measured with transparent and dark plant chambers and soil chambers, respectively, in three adjacent fields of fertilized cotton, fertilized maize and unfertilized soybean. During the observation period, the soil flux was 448 ± 89, 230 ± 74 and 90 ± 14 μg N 2 O m −2 h −1 in cotton, maize and soybean fields, respectively. The plant flux was 54 ± 43 and 16 ± 41 μg N 2 O m −2 h −1 , about 10 % and 26 % to the total ecosystem flux, for the cotton and the soybean field, respectively. Ignoring the contribution of plants would cause an obvious underestimation on the ecosystem N 2 O flux. The influence of sunlight on plant N 2 O flux was insignificant. However, in the cotton field, the responses of the plant N 2 O flux to air temperature and soil ammonium content were significant under sunlight but insignificant under darkness, suggesting that stomatal activity might influence the release process. In the cotton field, temperature sensitivity of plant N 2 O emission was 1.13, much lower than the value of soil flux (5.74). No relationship was found between plant N 2 O flux and soil nitrate content. It was implied that nitrate reduction in plants might not be the main source of plant N 2 O emission under field conditions. The seasonal patterns of the soil and plant N 2 O emissions were similarly affected by fertilization, indicating that plants might serve as a passive conduit transporting N 2 O produced in the soil.

Description: What controls biological productivity in coastal upwelling systems? Insights from a comparative modeling study Biogeosciences Discussions, 8, 5617-5652, 2011 Author(s): Z. Lachkar and N. Gruber The magnitude of the biological productivity in Eastern Boundary Upwelling Systems (EBUS) is traditionally viewed as directly reflecting the upwelling intensity. Yet, different EBUS show different sensitivities of productivity to upwelling-favorable winds (Carr and Kearns, 2003). Here, using a comparative modeling study of the California Current System (California CS) and Canary Current System (Canary CS), we show how physical and environmental factors, such as light, temperature and cross-shore circulation modulate the response of biological productivity to upwelling strength. To this end, we made a series of eddy-resolving simulations of the California CS and Canary CS using the Regional Ocean Modeling System (ROMS), coupled to a nitrogen based Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) ecosystem model. We find the nutrient content of the euphotic zone to be 20 % smaller in the Canary CS relative to the California CS. Yet, the biological productivity is 50 % smaller in the latter. This is due to: (1) a faster nutrient-replete growth in the Canary CS relative to the California CS, related to a more favorable light and temperature conditions in the Canary CS, and (2) the longer nearshore water residence times in the Canary CS which lead to larger buildup of biomass in the upwelling zone, thereby enhancing the productivity. The longer residence times in the Canary CS appear to be associated with the wider continental shelves and the lower eddy activity characterizing this upwelling system. This results in a weaker offshore export of nutrients and organic matter, thereby increasing local nutrient recycling and enhancing the coupling between new and export production in the Northwest African system. Our results suggest that climate change induced perturbations such as upwelling favorable wind intensification might lead to contrasting biological responses in the California CS and the Canary CS, with major implications for the biogeochemical cycles and fisheries in these two ecosystems.

Description: How to link soil C pools with CO 2 fluxes? Biogeosciences, 8, 1523-1537, 2011 Author(s): Y. Kuzyakov Despite the importance of carbon (C) pools and CO 2 fluxes in terrestrial ecosystems and especially in soils, as well as many attempts to assign fluxes to specific pools, this challenge remains unsolved. Interestingly, scientists investigating pools are not closely linked with scientists studying fluxes. This review therefore focused on experimental approaches enabling soil C pools to be linked with CO 2 flux from the soil. The background, advantages and shortcomings of uncoupled approaches (measuring only pools or fluxes) and of coupled approaches (measuring both pools and fluxes) were evaluated and their prerequisites – steady state of pools and isotopic steady state – described. The uncoupled approaches include: (i) monitoring the decrease of C pools in long-term fallow bare soil lacking C input over decades, (ii) analyzing components of CO 2 efflux dynamics by incubating soil without new C input over months or years, and (iii) analyzing turnover rates of C pools based on their 13 C and 14 C isotopic signature. The uncoupled approaches are applicable for non-steady state conditions only and have limited explanatory power. The more advantageous coupled approaches partition simultaneously pools and fluxes based on one of three types of changes in the isotopic signature of input C compared to soil C: (i) abrupt permanent, (ii) gradual permanent, and (iii) abrupt temporary impacts. I show how the maximal sensitivity of the approaches depends on the differences in the isotopic signature of pools with fast and slow turnover rates. The promising coupled approaches include: (a) δ 13 C of C pools and CO 2 efflux from soil after C 3 /C 4 vegetation changes or in FACE experiments (both corresponding to continuous labeling), (b) addition of 13 C or 14 C labeled organics (corresponding to pulse labeling), and (c) bomb- 14 C. I show that physical separation of soil C pools is not a prerequisite to estimate pool size or to link pools with fluxes. Based on simple simulation of C aging in soil after the input, the discordance of MRT of C in pools and of C released in CO 2 was demonstrated. This discordance of MRT between pools and fluxes shows that the use of MRT of pools alone underestimates the fluxes at least for two times. The future challenges include combining two or more promising approaches to elucidate more than two C sources for CO 2 fluxes, and linking scientific communities investigating the pools with those investigating the fluxes.

Description: Sources of short-lived bromocarbons in the Iberian upwelling system Biogeosciences, 8, 1551-1564, 2011 Author(s): S. Raimund, B. Quack, Y. Bozec, M. Vernet, V. Rossi, V. Garçon, Y. Morel, and P. Morin Seawater concentrations of the four brominated trace gases, dibromomethane (CH 2 Br 2 ), bromodichloromethane (CHBrCl 2 ), dibromochloromethane (CHBr 2 Cl) and bromoform (CHBr 3 ) were measured at different depths of the water column in the Iberian upwelling off Portugal during summer 2007. Statistical analysis of the data set revealed three distinct clusters, caused by different sea surface temperature. Bromocarbon concentrations were elevated in recently upwelled and aged upwelled waters (mean values of 30 pmol l −1 for CHBr 3 ), while concentrations in the open ocean were significantly lower (7.4 pmol l −1 for CHBr 3 ). Comparison with other productive marine areas revealed that the Iberian upwelling had higher halocarbon concentrations than the Mauritanian upwelling. However, the concentrations off the Iberian Peninsula were still much lower than those of coastal macroalgal-influenced waters or those of Polar regions dominated by cold water adapted diatoms. Correlations with biological variables and marker pigments indicated that phytoplankton was a source of bromocarbon in the open ocean. By contrast, in upwelled water masses along the coast, halocarbons showed weaker correlations to marker pigments but were significantly influenced by the tidal frequency. Our results indicate a strong intertidal coastal source of bromocarbon and transport by surface currents of these enriched waters towards the upwelling region.

Description: A systematic approach for comparing modeled biospheric carbon fluxes across regional scales Biogeosciences, 8, 1579-1593, 2011 Author(s): D. N. Huntzinger, S. M. Gourdji, K. L. Mueller, and A. M. Michalak Given the large differences between biospheric model estimates of regional carbon exchange, there is a need to understand and reconcile the predicted spatial variability of fluxes across models. This paper presents a set of quantitative tools that can be applied to systematically compare flux estimates despite the inherent differences in model formulation. The presented methods include variogram analysis, variable selection, and geostatistical regression. These methods are evaluated in terms of their ability to assess and identify differences in spatial variability in flux estimates across North America among a small subset of models, as well as differences in the environmental drivers that best explain the spatial variability of predicted fluxes. The examined models are the Simple Biosphere (SiB 3.0), Carnegie Ames Stanford Approach (CASA), and CASA coupled with the Global Fire Emissions Database (CASA GFEDv2), and the analyses are performed on model-predicted net ecosystem exchange, gross primary production, and ecosystem respiration. Variogram analysis reveals consistent seasonal differences in spatial variability among modeled fluxes at a 1° × 1° spatial resolution. However, significant differences are observed in the overall magnitude of the carbon flux spatial variability across models, in both net ecosystem exchange and component fluxes. Results of the variable selection and geostatistical regression analyses suggest fundamental differences between the models in terms of the factors that explain the spatial variability of predicted flux. For example, carbon flux is more strongly correlated with percent land cover in CASA GFEDv2 than in SiB or CASA. Some of the differences in spatial patterns of estimated flux can be linked back to differences in model formulation, and would have been difficult to identify simply by comparing net fluxes between models. Overall, the systematic approach presented here provides a set of tools for comparing predicted grid-scale fluxes across models, a task that has historically been difficult unless standardized forcing data were prescribed, or a detailed sensitivity analysis performed.

Description: Impacts of UV radiation on plankton community metabolism along the Humboldt Current System Biogeosciences Discussions, 8, 5827-5848, 2011 Author(s): N. Godoy, A. Canepa, S. Lasternas, E. Mayol, S. Ruíz-Halpern, S. Agustí, J. C. Castilla, and C. M. Duarte The Humbolt Current System along the Chilean coast is one of the most productive regions in the world, where UV levels are particularly high due to stratospheric ozone depletion. Research has shown that phytoplankton photosynthesis can be severely inhibited by surface radiation and there are concerns that this will reduce not only algal carbon fixation, but also the carbon supply for higher trophic level. Experimental estimates of community metabolism (NCP, GPP and R) and the impacts of UV on community metabolism were assessed at 8 stations along the meridional track by the Humbold-2009 cruise (54.80° S–23.85° S) on board RV Hespérides from 5 to 15 March 2009. The results showed an increase UVB penetration towards the Equator, along the Humboldt Current System, suggesting a more important impact of UVB radiation towards the north. The metabolic rates observed were within average values reported for the Ocean Pacific and did not show the water mass investigated to be exceptionally productive at the time of the study. Experimental evaluation of the effect of UVB radiation on surface waters, those most strongly affected by UVB, showed that UVB radiation suppressed net community production, resulting in a dominance of heterotrophic communities in surface waters, compared to the prevalence of autotrophic communities inferred when materials, excluding UVB radiation, are used for incubation. These results show that UVB radiation, which has increased greatly in the study area, may have suppressed net community production of the plankton communities, possibly driving plankton communities in the Southwest Pacific towards CO 2 sources.

Description: Effect of ocean acidification on otolith development in larvae of a tropical marine fish Biogeosciences, 8, 1631-1641, 2011 Author(s): P. L. Munday, V. Hernaman, D. L. Dixson, and S. R. Thorrold Calcification in many invertebrate species is predicted to decline due to ocean acidification. The potential effects of elevated CO 2 and reduced carbonate saturation state on other species, such as fish, are less well understood. Fish otoliths (earbones) are composed of aragonite, and thus, might be susceptible to either the reduced availability of carbonate ions in seawater at low pH, or to changes in extracellular concentrations of bicarbonate and carbonate ions caused by acid-base regulation in fish exposed to high p CO 2 . We reared larvae of the clownfish Amphiprion percula from hatching to settlement at three pH NBS and p CO 2 levels (control: ~pH 8.15 and 404 μatm CO 2 ; intermediate: pH 7.8 and 1050 μatm CO 2 ; extreme: pH 7.6 and 1721 μatm CO 2 ) to test the possible effects of ocean acidification on otolith development. There was no effect of the intermediate treatment (pH 7.8 and 1050 μatm CO 2 ) on otolith size, shape, symmetry between left and right otoliths, or otolith elemental chemistry, compared with controls. However, in the more extreme treatment (pH 7.6 and 1721 μatm CO 2 ) otolith area and maximum length were larger than controls, although no other traits were significantly affected. Our results support the hypothesis that pH regulation in the otolith endolymph can lead to increased precipitation of CaCO 3 in otoliths of larval fish exposed to elevated CO 2 , as proposed by an earlier study, however, our results also show that sensitivity varies considerably among species. Importantly, our results suggest that otolith development in clownfishes is robust to even the more pessimistic changes in ocean chemistry predicted to occur by 2100.

Description: Biomineralization of dolomite and magnesite discovered in tropical coralline algae: a biological solution to the geological dolomite problem Biogeosciences Discussions, 8, 5881-5906, 2011 Author(s): M. C. Nash, U. Troitzsch, B. N. Opdyke, J. M. Trafford, B. D. Russell, and D. I. Kline Dolomite is a magnesium-rich carbonate mineral abundant in fossil carbonate reef platforms but surprisingly rare in modern sedimentary environments, a conundrum known as the ''Dolomite Problem". Marine sedimentary dolomite has been interpreted to form by an unconfirmed, post-depositional diagenetic process, despite minimal experimental success at replicating this. Here we show that dolomite, accompanied by magnesite, forms within living crustose coralline alga, Hydrolithon onkodes , a prolific global tropical reef species. Chemical micro-analysis of the coralline skeleton reveals that not only are the cell walls calcitised, but that cell spaces are typically filled with magnesite, rimmed by dolomite, or both. Mineralogy was confirmed by X-ray diffraction. Thus there are at least three mineral phases present (magnesium calcite, dolomite and magnesite) rather than one or two (magnesium calcite and brucite) as previously thought. Our results are consistent with dolomite occurrences in coralline algae rich environments in fossil reefs. Instead of a theory of post-depositional dolomitisation, we present evidence revealing biomineralization that can account for the massive formations seen in the geologic record. Additionally, our findings imply that previously unrecognized dolomite and magnesite have formed throughout the Holocene. This discovery together with the scale of coralline algae dominance in past shallow carbonate environments raises the possibility that environmental factors driving this biological dolomitisation process have influenced the global marine magnesium/calcium cycle. Perhaps, most importantly, we reveal that what has been considered a geological process can be a biological process, having many implications for both disciplines.

Description: Transport and fate of hexachlorocyclohexanes in the oceanic air and surface seawater Biogeosciences Discussions, 8, 5537-5562, 2011 Author(s): Z. Xie, B. P. Koch, A. Möller, R. Sturm, and R. Ebinghaus Hexachlorocyclohexanes (HCHs) are ubiquitous organic pollutants derived from pesticide application. They are subject to long-range transport, persistent in the environment, and capable of accumulation in biota. Shipboard measurements of HCH isomers (α-, γ- and β-HCH) in surface seawater and boundary layer atmospheric samples were conducted in the Atlantic and the Southern Ocean in October to December of 2008. ΣHCHs concentrations (the sum of α-, γ- and β-HCH) in the lower atmosphere ranged from 11.8 to 36.9 pg m −3 (mean: 26.6 ± 11.0 pg m −3 ) in the Northern Hemisphere (NH), and from 1.5 to 4.0 pg m −3 (mean: 2.8 ± 1.1 pg m −3 ) in the Southern Hemisphere (SH), respectively. Water concentrations were: α-HCH 0.33–46.8 pg l −1 , γ-HCH 0.02–33.2 pg l −1 and β-HCH 0.11–2 pg l −1 . HCH concentrations decreased from the North Atlantic to the Southern Ocean, indicating historical use of HCHs in the NH. Spatial distribution showed increasing concentrations from the equator towards North and South latitudes illustrating the concept of cold condensation and less interhemispheric mixing process. In comparison to concentrations measured in 1987–1999/2000, gaseous HCHs were slightly lower, while dissolved HCHs decreased by factor of 2–3 orders of magnitude. Air-water exchange gradients suggested net deposition for α-HCH (mean: 3759 pg m −2 day −1 ) and γ-HCH (mean: 1987 pg m −2 day −1 ), whereas β-HCH varied between equilibrium (volatilization:

Description: Confocal Raman microscopy as a tool to describe different mineral and organic phases at high spatial resolution within marine biogenic carbonates: case study on Nerita undata (Gastropoda, Neritopsina) Biogeosciences Discussions, 8, 5563-5585, 2011 Author(s): G. Nehrke and J. Nouet Marine biogenic carbonates formed by invertebrates (e.g. corals and mollusk shells) represent complex composites of one or more mineral phases and organic molecules. This complexity ranges from the macroscopic structures observed with the naked eye down to sub micrometric structures only revealed by micro analytical techniques. Understanding to what extent and how organisms can control the formation of these structures requires that the mineral and organic phases can be identified and their spatial distribution related. Here we demonstrate the capability of confocal Raman microscopy applied to cross sections of a shell of Nerita undata to describe the distribution of calcite and aragonite including their crystallographic orientation with high lateral resolution (∼300 nm). Moreover, spatial distribution of functional groups of organic compounds can be simultaneously acquired, allowing to specifically relate them to the observed microstructures. The data presented in this case study highlights the possible new contributions of this method to the description of modalities of Nerita undata shell formation, and what could be expected of its application to other marine biogenic carbonates. Localization of areas of interest would also allow further investigations using more localized methods, such as TEM that would provide complementary information on the relation between organic molecules and crystallographic lattice.

Description: Exploring B/Ca as a pH proxy in bivalves: relationships between Mytilus californianus B/Ca and environmental data from the northeast Pacific Biogeosciences Discussions, 8, 5587-5616, 2011 Author(s): S. J. McCoy, L. F. Robinson, C. A. Pfister, J. T. Wootton, and N. Shimizu A distinct gap in our ability to understand changes in coastal biology that may be associated with recent ocean acidification is the paucity of directly measured ocean environmental parameters at coastal sites in recent decades. Thus, many researchers have turned to sclerochronological reconstructions of water chemistry to document the historical seawater environment. In this study, we explore the relationships between B/Ca and pH to test the feasibility of B/Ca measured on the ion probe as a pH proxy in the California mussel, Mytilus californianus . We compare the M. californianus B/Ca record to directly measured environmental data during mussel growth 1999–2009 to determine the correlation between B/Ca and seawater chemistry and discuss methods for assigning sample chronology when sampling an organism with variable growth rates.

Description: Monoterpene and sesquiterpene emissions from Quercus coccifera exhibit interacting responses to light and temperature Biogeosciences Discussions, 8, 5691-5728, 2011 Author(s): M. Staudt and L. Lhoutellier Light and temperature are known to be the most important environmental factors controlling biogenic volatile organic compound (BVOC) emissions from plants, but little is known about their interdependencies especially for BVOCs other than isoprene. We studied light responses at different temperatures and temperature responses at different light levels of foliar BVOC emissions, photosynthesis and chlorophyll fluorescence on Quercus coccifera , an evergreen oak widespread in Mediterranean shrublands. More than 50 BVOCs were detected in the emissions from Q. coccifera leaves most of them being isoprenoids plus a few green leaf volatiles (GLVs). Under standard conditions non-oxygenated monoterpenes (MT-hc) accounted for about 90 % of the total BVOC release (mean ± SD: 738 ± 378 ng m −2 projected leaf area s −1 or 13.1 ± 6.9 μg g −1 leaf dry weight h −1 ) and oxygenated monoterpenes (MT-ox) and sesquiterpenes (SQTs) accounted for the rest in about equal proportions. Except GLVs, emissions of all BVOCs responded positively to light and temperature. The light responses of MT and SQT emissions resembled that of CO 2 -assimilation and were little influenced by the assay temperature: at high assay temperature, MT-hc emissions saturated at lower light levels than at standard assay temperature and tended even to decrease in the highest light range. The emission responses to temperature showed mostly Arrhenius-type response curves, whose shapes in the high temperature range were clearly affected by the assay light level and were markedly different between isoprenoid classes: at non-saturating light, all isoprenoids showed a similar temperature optimum (~43 °C), but, at higher temperatures, MT-hc emissions decreased faster than MT-ox and SQT emissions. At saturating light, MT-hc emissions peaked already around 37 °C and rapidly dropped at higher temperatures, whereas MT-ox and SQT emissions strongly increased between 40 and 50 °C accompanied by a burst of GLVs. In all experiments, decreases of MT-hc emissions under high temperatures were correlated with decreases in CO 2 -assimilation and/or photosynthetic electron transport. We conclude that light and temperature can have interactive short-term effects on the quantity and quality of BVOC emissions from Q. coccifera through substrate limitations of MT biosynthesis occurring at temperatures supraoptimal for photosynthetic processes that are exacerbated by oxidative stress and membrane damages. Such interactive effects are likely to occur frequently during hot and dry summers and simulations made in this work showed that they may have important consequences for emission predictions.

Description: Organic sediment formed during inundation of a degraded fen grassland emits large fluxes of CH 4 and CO 2 Biogeosciences, 8, 1539-1550, 2011 Author(s): M. Hahn-Schöfl, D. Zak, M. Minke, J. Gelbrecht, J. Augustin, and A. Freibauer Peatland restoration by inundation of drained areas can alter local greenhouse gas emissions as CO 2 and CH 4 . Factors that can influence these emissions include the quality and amount of substrates available for anaerobic degradation processes and the sources and availability of electron acceptors. In order to learn about possible sources of high CO 2 and CH 4 . emissions from a rewetted degraded fen grassland, we performed incubation experiments that tested the effects of fresh plant litter in the flooded peats on pore water chemistry and CO 2 and CH 4 . production and emission. The position in the soil profile of the pre-existing drained peat substrate affected initial rates of anaerobic CO 2 production subsequent to flooding, with the uppermost peat layer producing the greatest specific rates of CO 2 evolution. CH 4 production rates depended on the availability of electron acceptors and was significant only when sulfate concentrations were reduced in the pore waters. Very high specific rates of both CO 2 (maximum of 412 mg C d −1 kg −1 C) and CH 4 production (788 mg C d −1 kg −1 C) were observed in a new sediment layer that accumulated over the 2.5 years since the site was flooded. This new sediment layer was characterized by overall low C content, but represented a mixture of sand and relatively easily decomposable plant litter from reed canary grass killed by flooding. Samples that excluded this new sediment layer but included intact roots remaining from flooded grasses had specific rates of CO 2 (max. 28 mg C d −1 kg −1 C) and CH 4 (max. 34 mg C d −1 kg −1 C) production that were 10–20 times lower than for the new sediment layer and were comparable to those of a newly flooded upper peat layer. Lowest rates of anaerobic CO 2 and CH 4 production (range of 4–8 mg C d −1 kg −1 C and

Description: Stand age and tree species affect N 2 O and CH 4 exchange from afforested soils Biogeosciences Discussions, 8, 5729-5760, 2011 Author(s): J. R. Christiansen and P. Gundersen Afforestation of former agricultural land is a means to mitigate anthropogenic greenhouse gas emissions. The objectives of this study were to assess the effect of pedunculate oak and Norway Spruce of different stand ages (13–17 and 40 yr after afforestation, respectively) on N 2 O and CH 4 exchange and identify the environmental factors responsible for the differences in gas exchange between tree species of different ages. N 2 O and CH 4 fluxes (mean ± SE) were measured for two years at an afforested site. No species difference was documented for N 2 O emission (oak: 4.2 ± 0.7 μg N 2 O-N m −2 h −1 , spruce: 4.0 ± 1 μg N 2 O-N m −2 h −1 ) but the youngest stands (1.9 ± 0.3 μg N 2 O-N m −2 h −1 ) emitted significantly less N 2 O than older stands (6.3 ± 1.2 μg N 2 O-N m −2 h −1 ). CH 4 exchange did not differ significantly between tree species (oak: −8.9 ± 0.9, spruce: −7.7 ± 1) or stand age (young: −7.3 ± 0.9 μg CH 4 -C m −2 h −1 , old: −9.4 ± 1 μg CH 4 -C m −2 h −1 ) but interacted significantly; CH 4 oxidation increased with age in oak and decreased with age for Norway Spruce. We conclude that the exchange of N 2 O and CH 4 from the forest soil undergoes a quick and significant transition in the first four decades after planting in both oak and Norway Spruce related to physical changes in the top soil and availability of soil N.

Description: Controls over aboveground forest carbon density on Barro Colorado Island, Panama Biogeosciences, 8, 1615-1629, 2011 Author(s): J. Mascaro, G. P. Asner, H. C. Muller-Landau, M. van Breugel, J. Hall, and K. Dahlin Despite the importance of tropical forests to the global carbon cycle, ecological controls over landscape-level variation in live aboveground carbon density (ACD) in tropical forests are poorly understood. Here, we conducted a spatially comprehensive analysis of ACD variation for a continental tropical forest – Barro Colorado Island, Panama (BCI) – and tested site factors that may control such variation. We mapped ACD over 1256 ha of BCI using airborne Light Detection and Ranging (LiDAR), which was well-correlated with ground-based measurements of ACD in Panamanian forests of various ages ( r 2 = 0.84, RMSE = 17 Mg C ha −1 , P 〈 0.0001). We used multiple regression to examine controls over LiDAR-derived ACD, including slope angle, forest age, bedrock, and soil texture. Collectively, these variables explained 14 % of the variation in ACD at 30-m resolution, and explained 33 % at 100-m resolution. At all resolutions, slope (linked to underlying bedrock variation) was the strongest driving factor; standing carbon stocks were generally higher on steeper slopes. This result suggests that physiography may be more important in controlling ACD variation in Neotropical forests than currently thought. Although BCI has been largely undisturbed by humans for a century, past land-use over approximately half of the island still influences ACD variation, with younger forests (80–130 years old) averaging ~15 % less carbon storage than old-growth forests (〉400 years old). If other regions of relatively old tropical secondary forests also store less carbon aboveground than primary forests, the effects on the global carbon cycle could be substantial and difficult to detect with traditional satellite monitoring.

Description: Species-specific trajectories of nitrogen isotopes in Indiana hardwood forests, USA Biogeosciences Discussions, 8, 5935-5954, 2011 Author(s): K. K. McLauchlan and J. M. Craine Humans have drastically altered the global nitrogen (N) cycle, and these alterations have begun to affect a variety of ecosystems. In North America, N deposition rates are highest in the Central US, yet there are few studies that examine whether N availability has been increasing to different tree species in the forests of the region. To determine the species-specific trajectories of N availability in secondary temperate forests experiencing high N deposition, we measured the N concentrations and composition of stable N isotopes in wood of four tree species from six hardwood forest remnants in Northern Indiana, USA. Annual nitrogen deposition rates averaged 5.8 kg ha −1 from 2000 to 2008 in this region. On average, wood δ 15 N values in Quercus alba have been increasing steadily over the past 100 yr. In contrast, wood δ 15 N values have been declining in three other hardwood species – Acer saccharum , Carya ovata , and Fagus grandifolia – over the same time period. The species-specific trends suggest a change in the partitioning of ammonium and nitrate among species, a change in nitrification rates, and/or offsetting changes in the dependence of species on mycorrhizal fungi. With no apparent net change in wood δ 15 N over the past century at the stand level, on average there appears to have been little change in N availability for these forests despite high levels of N deposition in the region.

Description: Beyond the Fe-P-redox connection: preferential regeneration of phosphorus from organic matter as a key control on Baltic Sea nutrient cycles Biogeosciences, 8, 1699-1720, 2011 Author(s): T. Jilbert, C. P. Slomp, B. G. Gustafsson, and W. Boer Patterns of regeneration and burial of phosphorus (P) in the Baltic Sea are strongly dependent on redox conditions. Redox varies spatially along water depth gradients and temporally in response to the seasonal cycle and multidecadal hydrographic variability. Alongside the well-documented link between iron oxyhydroxide dissolution and release of P from Baltic Sea sediments, we show that preferential remineralization of P with respect to carbon (C) and nitrogen (N) during degradation of organic matter plays a key role in determining the surplus of bioavailable P in the water column. Preferential remineralization of P takes place both in the water column and upper sediments and its rate is shown to be redox-dependent, increasing as reducing conditions become more severe at greater water-depth in the deep basins. Existing Redfield-based biogeochemical models of the Baltic may therefore underestimate the imbalance between N and P availability for primary production, and hence the vulnerability of the Baltic to sustained eutrophication via the fixation of atmospheric N. However, burial of organic P is also shown to increase during multidecadal intervals of expanded hypoxia, due to higher net burial rates of organic matter around the margins of the deep basins. Such intervals may be characterized by basin-scale acceleration of all fluxes within the P cycle, including productivity, regeneration and burial, sustained by the relative accessibility of the water column P pool beneath a shallow halocline.

Description: Decreased summer drought affects plant productivity and soil carbon dynamics in Mediterranean woodland Biogeosciences Discussions, 8, 5955-5990, 2011 Author(s): M. F. Cotrufo, G. Alberti, I. Inglima, H. Marjanović, D. LeCain, A. Zaldei, A. Peressotti, and F. Miglietta Precipitation patterns are expected to change in the Mediterranean region within the next decades, with projected decreases in total rainfall and increases in extreme events. We manipulated precipitation patterns in a Mediterranean woodland, dominated by Arbutus unedo L., to study the effects of changing precipitation regimes on above-ground net primary production (ANPP) and soil C dynamics, specifically plant-derived C input to soil and soil respiration (SR). Experimental plots were exposed to either a 20 % reduction of throughfall or to water addition targeted at maintaining soil water content above a minimum of 10 % v/v. Treatments were compared to control plots which received ambient precipitation. The throughfall manipulation experiment started in 2004 and we report data up to the 2009 growing season. Enhanced soil moisture during summer months highly stimulated annual stem primary production, litter fall, SR and net annual plant-derived C input to soil which on average increased by 130 %, 26 %, 50 % and 220 %, respectively, as compared to control. In contrast, the 20 % reduction in throughfall (equivalent to 10 % reduction of precipitation) did not significantly change soil moisture at the site, and therefore did not significantly affect ANPP or SR. We conclude that minor changes (around 10 % reduction) in precipitation amount are not likely to significantly affect ANPP or soil C dynamics in Mediterranean woodland. However, if summer rain increases, C cycling will significantly accelerate but soil C stocks are not likely to be changed in the short-term. More studies involving modelling of long term C dynamics are needed to predict if the estimated increases in soil C input under wet conditions is going to be sustained and if labile C is being substituted to stable C, with a negative effect on long term soil C stocks.

Description: Novel applications of carbon isotopes in atmospheric CO 2 : what can atmospheric measurements teach us about processes in the biosphere? Biogeosciences Discussions, 8, 4603-4631, 2011 Author(s): A. P. Ballantyne, J. B. Miller, I. T. Baker, P. P. Tans, and J. W. C. White Conventionally, measurements of carbon isotopes in atmospheric CO 2 (δ 13 CO 2 ) have been used to partition fluxes between terrestrial and ocean carbon pools. However, novel analytical approaches combined with an increase in the spatial extent and frequency of δ 13 CO 2 measurements allow us to conduct a global analysis of δ 13 CO 2 variability to infer the isotopic composition of source CO 2 to the atmosphere (δ s ). This global analysis yields coherent seasonal patterns of isotopic enrichment. Our results indicate that seasonal values of δ s are more highly correlated with vapor pressure deficit ( r =0.404) than relative humidity ( r =0.149). We then evaluate two widely used stomatal conductance models and determine that Leuning Model, which is primarily driven by vapor pressure deficit is more effective globally at predicting δ s (RMSE = 1.7 ‰) than the Ball-Berry model, which is driven by relative humidity (RMSE = 2.8) ‰. Thus stomatal conductance on a global scale may be more sensitive to changes in vapor pressure deficit than relative humidity. This approach highlights a new application of using δ 13 CO 2 measurements to test global models.

Description: How accurately can soil organic carbon stocks and stock changes be quantified by soil inventories? Biogeosciences, 8, 1193-1212, 2011 Author(s): M. Schrumpf, E. D. Schulze, K. Kaiser, and J. Schumacher Precise determination of changes in organic carbon (OC) stocks is prerequisite to understand the role of soils in the global cycling of carbon and to verify changes in stocks due to management. A large dataset was collected to form base to repeated soil inventories at 12 CarboEurope sites under different climate and land-use, and with different soil types. Concentration of OC, bulk density (BD), and fine earth fraction were determined to 60 cm depth at 100 sampling points per site. We investigated (1) time needed to detect changes in soil OC, assuming future re-sampling of 100 cores; (2) the contribution of different sources of uncertainties to OC stocks; (3) the effect of OC stock calculation on mass rather than volume base for change detection; and (4) the potential use of pedotransfer functions (PTF) for estimating BD in repeated inventories. The period of time needed for soil OC stocks to change strongly enough to be detectable depends on the spatial variability of soil properties, the depth increment considered, and the rate of change. Cropland sites, having small spatial variability, had lower minimum detectable differences (MDD) with 100 sampling points (105 ± 28 gC m −2 for the upper 10 cm of the soil) than grassland and forest sites (206 ± 64 and 246 ± 64 gC m −2 for 0–10 cm, respectively). Expected general trends in soil OC indicate that changes could be detectable after 2–15 yr with 100 samples if changes occurred in the upper 10 cm of stone-poor soils. Error propagation analyses showed that in undisturbed soils with low stone contents, OC concentrations contributed most to OC stock variability while BD and fine earth fraction were more important in upper soil layers of croplands and in stone rich soils. Though the calculation of OC stocks based on equivalent soil masses slightly decreases the chance to detect changes with time at most sites except for the croplands, it is still recommended to account for changing bulk densities with time. Application of PTF for the estimation of bulk densities caused considerable underestimation of total variances of OC stocks if the error associated with the PTF was not accounted for, which rarely is done in soil inventories. Direct measurement of all relevant parameters approximately every 10 yr is recommended for repeated soil OC inventories.

Description: Quantifying methane emissions from rice paddies in Northeast China by integrating remote sensing mapping with a biogeochemical model Biogeosciences, 8, 1225-1235, 2011 Author(s): Y. Zhang, Y. Y. Wang, S. L. Su, and C. S. Li The Sanjiang Plain located in Northeastern China is one of the major rice producing regions in the country. However, differing from the majority rice regions in Southern China, the Sanjinag Plain possesses a much cooler climate. Could the rice paddies in this domain be an important source of global methane? To answer this question, methane (CH 4 ) emissions from the region were calculated by integrating remote sensing mapping with a process-based biogeochemistry model, Denitrification and Decomposition or DNDC. To quantify regional CH 4 emissions from the plain, the model was first tested against a two-year dataset of CH 4 fluxes measured at a typical rice field within the domain. A sensitivity test was conducted to find out the most sensitive factors affecting CH 4 emissions in the region. Based on the understanding gained from the validation and sensitivity tests, a geographic information system (GIS) database was constructed to hold the spatially differentiated input information to drive DNDC for its regional simulations. The GIS database included a rice map derived from the Landsat TM images acquired in 2006, which provided crucial information about the spatial distribution of the rice fields within the domain of 10.93 million ha. The modeled results showed that the total 1.44 million ha of rice paddies in the plain emitted 0.48–0.58 Tg CH 4 -C in 2006 with spatially differentiated annual emission rates ranging between 38.6–943.9 kg CH 4 -C ha −1 , which are comparable with that observed in Southern China. The modeled data indicated that the high SOC contents, long crop season and high rice biomass enhanced CH 4 production in the cool paddies. The modeled results proved that the northern wetland agroecosystems could make important contributions to global greenhouse gas inventory.

Description: Soil carbon stock increases in the organic layer of boreal middle-aged stands Biogeosciences, 8, 1279-1289, 2011 Author(s): M. Häkkinen, J. Heikkinen, and R. Mäkipää Changes in the soil carbon stock can potentially have a large influence on global carbon balance between terrestrial ecosystems and atmosphere. Since carbon sequestration of forest soils is influenced by human activities, reporting of the soil carbon pool is a compulsory part of the national greenhouse gas (GHG) inventories. Various soil carbon models are applied in GHG inventories, however, the verification of model-based estimates is lacking. In general, the soil carbon models predict accumulation of soil carbon in the middle-aged stands, which is in good agreement with chronosequence studies and flux measurements of eddy sites, but they have not been widely tested with repeated measurements of permanent plots. The objective of this study was to evaluate soil carbon changes in the organic layer of boreal middle-aged forest stands. Soil carbon changes on re-measured sites were analyzed by using soil survey data that was based on composite samples as a first measurement and by taking into account spatial variation on the basis of the second measurement. By utilizing earlier soil surveys, a long sampling interval, which helps detection of slow changes, could be readily available. The range of measured change in the soil organic layer varied from −260 to 1260 g m −2 over the study period of 16–19 years and 23 ± 2 g m −2 per year, on average. The increase was significant in 6 out of the 38 plots from which data were available. Although the soil carbon change was difficult to detect at the plot scale, the overall increase measured across the middle-aged stands agrees with predictions of the commonly applied soil models. Further verification of the soil models is needed with larger datasets that cover wider geographical area and represent all age classes, especially young stands with potentially large soil carbon source.

Description: Measuring and modelling the isotopic composition of soil respiration: insights from a grassland tracer experiment Biogeosciences, 8, 1333-1350, 2011 Author(s): U. Gamnitzer, A. B. Moyes, D. R. Bowling, and H. Schnyder The carbon isotopic composition (δ 13 C) of CO 2 efflux (δ 13 C efflux ) from soil is generally interpreted to represent the actual isotopic composition of the respiratory source (δ 13 C Rs ). However, soils contain a large CO 2 pool in air-filled pores. This pool receives CO 2 from belowground respiration and exchanges CO 2 with the atmosphere (via diffusion and advection) and the soil liquid phase (via dissolution). Natural or artificial modification of δ 13 C of atmospheric CO 2 (δ 13 C atm ) or δ 13 C Rs causes isotopic disequilibria in the soil-atmosphere system. Such disequilibria generate divergence of δ 13 C efflux from δ 13 C Rs (termed "disequilibrium effect"). Here, we use a soil CO 2 transport model and data from a 13 CO 2 / 12 CO 2 tracer experiment to quantify the disequilibrium between δ 13 C efflux and δ 13 C Rs in ecosystem respiration. The model accounted for diffusion of CO 2 in soil air, advection of soil air, dissolution of CO 2 in soil water, and belowground and aboveground respiration of both 12 CO 2 and 13 CO 2 isotopologues. The tracer data were obtained in a grassland ecosystem exposed to a δ 13 C atm of −46.9 ‰ during daytime for 2 weeks. Nighttime δ 13 C efflux from the ecosystem was estimated with three independent methods: a laboratory-based cuvette system, in-situ steady-state open chambers, and in-situ closed chambers. Earlier work has shown that the δ 13 C efflux measurements of the laboratory-based and steady-state systems were consistent, and likely reflected δ 13 C Rs . Conversely, the δ 13 C efflux measured using the closed chamber technique differed from these by −11.2 ‰. Most of this disequilibrium effect (9.5 ‰) was predicted by the CO 2 transport model. Isotopic disequilibria in the soil-chamber system were introduced by changing δ 13 C atm in the chamber headspace at the onset of the measurements. When dissolution was excluded, the simulated disequilibrium effect was only 3.6 ‰. Dissolution delayed the isotopic equilibration between soil CO 2 and the atmosphere, as the storage capacity for labelled CO 2 in water-filled soil pores was 18 times that of soil air. These mechanisms are potentially relevant for many studies of δ 13 C Rs in soils and ecosystems, including FACE experiments and chamber studies in natural conditions. Isotopic disequilibria in the soil-atmosphere system may result from temporal variation in δ 13 C Rs or diurnal changes in the mole fraction and δ 13 C of atmospheric CO 2 . Dissolution effects are most important under alkaline conditions.

Description: Spatial and temporal resolution of carbon flux estimates for 1983–2002 Biogeosciences, 8, 1309-1331, 2011 Author(s): L. M. P. Bruhwiler, A. M. Michalak, and P. P. Tans We discuss the spatial and temporal resolution of monthly carbon flux estimates for the period 1983–2002 using a fixed-lag Kalman Smoother technique with a global chemical transport model, and the GLOBALVIEW data product. The observational network has expanded substantially over this period, and the flux estimates are better constrained provided by observations for the 1990's in comparison to the 1980's. The estimated uncertainties also decrease as observational coverage expands. In this study, we use the Globalview data product for a network that changes every 5 yr, rather than using a small number of continually-operating sites (fewer observational constraints) or a large number of sites, some of which may consist almost entirely of extrapolated data. We show that the discontinuities resulting from network changes reflect uncertainty due to a sparse and variable network. This uncertainty effectively limits the resolution of trends in carbon fluxes, and is a potentially significant source of noise in assimilation systems that allow changes in observation distribution between assimilation time steps. The ability of the inversion to distinguish, or resolve, carbon fluxes at various spatial scales is examined using a diagnostic known as the resolution kernel. We find that the global partition between land and ocean fluxes is well-resolved even for the very sparse network of the 1980's, although prior information makes a significant contribution to the resolution. The ability to distinguish zonal average fluxes has improved significantly since the 1980's, especially for the tropics, where the zonal ocean and land biosphere fluxes can be distinguished. Care must be taken when interpreting zonal average fluxes, however, since the lack of air samples for some regions in a zone may result in a large influence from prior flux estimates for these regions. We show that many of the TransCom 3 source regions are distinguishable throughout the period over which estimates are produced. Examples are Boreal and Temperate North America. The resolution of fluxes from Europe and Australia has greatly improved since the 1990's. Other regions, notably Tropical South America and the Equatorial Atlantic remain practically unresolved. Comparisons of the average seasonal cycle of the estimated carbon fluxes with the seasonal cycle of the prior flux estimates reveals a large adjustment of the summertime uptake of carbon for Boreal Eurasia, and an earlier onset of springtime uptake for Temperate North America. In addition, significantly larger seasonal cycles are obtained for some ocean regions, such as the Northern Ocean, North Pacific, North Atlantic and Western Equatorial Pacific, regions that appear to be well-resolved by the inversion.

Description: Biogeochemical indicators of peatland degradation – a case study of a temperate bog in northern Germany Biogeosciences Discussions, 11, 16825-16854, 2014 Author(s): J. P. Krüger, J. Leifeld, S. Glatzel, S. Szidat, and C. Alewell Peatlands store a great proportion of the global soil carbon pool and can loose carbon via the atmosphere due to degradation. In Germany, most of the greenhouse gas emissions from organic soils are attributed to sites managed as grassland. Here we investigated a land-use gradient from near-natural wetland (NW) to an extensively managed (GE) to an intensively managed grassland site (GI), all formed in the same bog complex in northern Germany. Vertical depth profiles of δ 13 C, δ 15 N, ash content, C/N ratio, bulk density, as well as radiocarbon ages were studied to identify peat degradation and to calculate carbon loss. At all sites, including the near-natural site, δ 13 C depth profiles indicate aerobic decomposition in the upper horizons. Depth profiles of δ 15 Ndiffered significantly between sites with increasing δ 15 N values in the top layers with increasing intensity of use, indicating that the peat is more decomposed. At both grassland sites, the ash content peaked within the first centimeter. In the near-natural site, ash contents were highest in 10–60 cm depth. This indicates that not only the managed grasslands, but also the near-natural site, is influenced by anthropogenic activities, most likely due to the drainage of the surrounding area. However, we found very young peat material in the first centimeter of the NW, indicating recent peat growth. The NW site accumulates carbon today even though it is and probably was influenced by anthropogenic activities in the past indicated by δ 13 C and ash content depth profiles. Based on the enrichment of ash content and changes in bulk density, we calculated carbon loss from these sites in retrograde. As expected land use intensification leads to a higher carbon loss which is supported by the higher peat ages at the intensive managed grassland site. All investigated biogeochemical parameters together indicate degradation of peat due to (i) conversion to grassland, (ii) historical drainage as well as recent development and (iii) land use intensification.

Description: Sensitivity of the air–sea CO 2 exchange in the Baltic Sea and Danish inner waters to atmospheric short term variability Biogeosciences Discussions, 11, 16993-17042, 2014 Author(s): A. S. Lansø, J. Bendtsen, J. H. Christensen, L. L. Sørensen, H. Chen, H. A. J. Meijer, and C. Geels Minimising the uncertainties in estimates of air–sea CO 2 exchange is an important step toward increasing the confidence in assessments of the CO 2 cycle. Using an atmospheric transport model makes it possible to investigate the direct impact of atmospheric parameters on the air–sea CO 2 flux along with its sensitivity to e.g. short-term temporal variability in wind speed, atmospheric mixing height and the atmospheric CO 2 concentration. With this study the importance of high spatiotemporal resolution of atmospheric parameters for the air–sea CO 2 flux is assessed for six sub-basins within the Baltic Sea and Danish inner waters. A new climatology of surface water partial pressure of CO 2 ( p CO 2 ) has been developed for this coastal area based on available data from monitoring stations and underway p CO 2 measuring systems. Parameterisations depending on wind speed were applied for the transfer velocity to calculate the air–sea CO 2 flux. Two model simulations were conducted – one including short term variability in atmospheric CO 2 (VAT), and one where it was not included (CAT). A seasonal cycle in the air–sea CO 2 flux was found for both simulations for all sub-basins with uptake of CO 2 in summer and release of CO 2 to the atmosphere in winter. During the simulated period 2005–2010 the average annual net uptake of atmospheric CO 2 for the Baltic Sea, Danish Straits and Kattegat was 287 and 471 Gg C yr -1 for the VAT and CAT simulations, respectively. The obtained difference of 184 Gg C yr -1 was found to be significant, and thus ignoring short term variability in atmospheric CO 2 does have a sizeable effect on the air–sea CO 2 exchange. The combination of the atmospheric model and the new p CO 2 fields has also made it possible to make an estimate of the marine part of the Danish CO 2 budget for the first time. A net annual uptake of 2613 Gg C yr -1 was found for the Danish waters. A large uncertainty is connected to the air–sea CO 2 flux in particular caused by the transfer velocity parameterisation and the applied p CO 2 climatology. However, the present study underlines the importance of including short term variability in the atmospheric CO 2 concentration in future model studies of the air–sea exchange in order to minimise the uncertainty.

Description: Do climate factors govern soil microbial community composition and biomass at a regional scale? Biogeosciences Discussions, 11, 17729-17756, 2014 Author(s): L. Ma, C. Guo, X. Lü, S. Yuan, and R. Wang Soil microbial communities play important role in organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about factors driving soil microbial community composition at large scales. The objective of this study was to determine whether climate dominates among environmental factors governing microbial community composition and biomass at a regional scale. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations in North-East China Transect (850 km x 50 km). The results showed that soil water availability and land use changes exhibited the dominant effects on soil microbial community composition and biomass at the regional scale, while climate factors (expressed as a function of large-scale spatial variation) did not show strong relationships with distribution of microbial community composition. Likewise, factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Wetter soils had higher contributions of gram-positive bacteria, whereas drier soils had higher contributions of gram-negative bacteria and fungi. Heavily disturbed soils had lower contributions of gram-negative bacteria and fungi than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate factors, commonly known to structure distribution of macroorganisms, were not the most important drivers governing regional pattern of microbial communities because of inclusion of irrigated and managed practices. In comparison, soil water regime and land use types appear to be primary determinants of microbial community composition and biomass.

Description: Fossilized bioelectric wire – the trace fossil Trichichnus Biogeosciences Discussions, 11, 17707-17728, 2014 Author(s): M. Kędzierski, A. Uchman, Z. Sawlowicz, and A. Briguglio The trace fossil Trichichnus is proposed as an indicator of fossil bioelectric bacterial activity at the interface oxic – anoxic zone of marine sediments. This fulfils the idea that such processes, commonly found in the modern realm, should be also present in the geological past. Trichichnus is an exceptional trace fossil due to its very thin diameter (mostly less than 1 mm) and common pyritic filling. It is ubiquitous in some fine-grained sediments, where it has been interpreted as a burrow formed deeper than any other trace fossils, below the redox boundary. Trichichnus formerly referred to as deeply burrowed invertebrates, has been found as remnant of a fossilized intrasediment bacterial mat that is pyritized. As visualized in 3-D by means of X-ray computed microtomography scanner, Trichichnus forms dense filamentous fabric, which reflects that produced by modern large, mat-forming, sulphide-oxidizing bacteria, belonging mostly to Trichichnus -related taxa, which are able to house a complex bacterial consortium. Several stages of Trichichnus formation, including filamentous, bacterial mat and its pyritization, are proposed to explain an electron exchange between oxic and suboxic/anoxic layers in the sediment. Therefore, Trichichnus can be considered a fossilized "electric wire".

Description: Nitrate limitation and ocean acidification interact with UV-B to reduce photosynthetic performance in the diatom Phaeodactylum tricornutum Biogeosciences Discussions, 11, 17675-17706, 2014 Author(s): W. Li, K. Gao, and J. Beardall It has been proposed that ocean acidification (OA) will interact with other environmental factors to influence the overall impact of global change on biological systems. Accordingly we investigated the influence of nitrogen limitation and OA on the physiology of diatoms by growing the diatom Phaeodactylum tricornutum Bohlin under elevated (1000 μatm, HC) or ambient (390 μatm, LC) levels of CO 2 with replete (110 μmol L -1 , HN) or reduced (10 μmol L -1 , LN) levels of NO 3 - and subjecting the cells to solar radiation with or without UV irradiance to determine their susceptibility to UV radiation (280–400 nm). Our results indicate that OA and UVB induced significantly higher inhibition of both the photosynthetic rate and quantum yield under LN than under HN conditions. UVA or/and UVB increased the cells' non-photochemical quenching (NPQ) regardless of the CO 2 levels. Under LN and OA conditions, activity of superoxide dismutase and catalase activities were enhanced, along with the highest sensitivity to UVB and the lowest ratio of repair to damage of PSII. HC-grown cells showed a faster recovery rate of yield under HN but not under LN conditions. The finding that nitrate limitation and ocean acidification interact with UV-B to reduce photosynthetic performance of the diatom P. tricornutum implies that ocean primary production and the marine biological C pump will be affected by the OA under multiple stressors.

Description: Vegetation heterogeneity and landscape position exert strong controls on soil CO 2 efflux in a moist, Appalachian watershed Biogeosciences Discussions, 11, 17631-17673, 2014 Author(s): J. W. Atkins, H. E. Epstein, and D. L. Welsch In topographically complex watersheds, landscape position and vegetation heterogeneity can alter the soil water regime through both lateral and vertical redistribution, respectively. These alterations of soil moisture may have significant impacts on the spatial heterogeneity of biogeochemical cycles throughout the watershed. To evaluate how landscape position and vegetation heterogeneity affect soil CO 2 efflux ( F SOIL ) we conducted observations across the Weimer Run watershed (373 ha), located near Davis, West Virginia, for three growing seasons with varying precipitation (2010 – 1042 mm; 2011 – 1739 mm; 2012 – 1244 mm; precipitation data from BDKW2 station, MesoWest, University of Utah). An apparent soil temperature threshold of 11 °C at 12 cm depth on F SOIL was observed in our data – where F SOIL rates greatly increase in variance above this threshold. For analysis, F SOIL values above this threshold were isolated and examined. Differences in F SOIL among years were apparent by elevation ( F 4,633 = 3.17; p = 0.013) and by vegetation cover ( F 4, 633 = 2.96; p = 0.019). For the Weimer Run watershed, vegetation exerts the major control on soil CO 2 efflux ( F SOIL ), with the plots beneath shrubs at all elevations for all years showing the greatest mean rates of F SOIL (6.07 μmol CO 2 m -2 s -1 ) compared to plots beneath closed-forest canopy (4.69 μmol CO 2 m -2 s -1 ) and plots located in open, forest gaps (4.09 μmol CO 2 m -2 s -1 ) plots. During periods of high soil moisture, we find that CO 2 efflux rates are constrained and that maximum efflux rates in this system occur during periods of average to below average soil water availability. These findings offer valuable insight into the processes occurring within these topographically complex, temperate and humid systems, and the interactions of abiotic and biotic factors mediating biogeochemical cycles. With possible changing rainfall patterns as predicted by climate models, it is important to understand the couplings between water and carbon cycling at the watershed and landscape scales, and their potential dynamics under global change scenarios.

Description: Daily burned area and carbon emissions from boreal fires in Alaska Biogeosciences Discussions, 11, 17579-17629, 2014 Author(s): S. Veraverbeke, B. M. Rogers, and J. T. Randerson Boreal fires burn carbon-rich organic soils, thereby releasing large quantities of trace gases and aerosols that influence atmospheric composition and climate. To better understand the factors regulating boreal fire emissions, we developed a statistical model of carbon consumption by fire for Alaska with a spatial resolution of 500 m and a temporal resolution of one day. We used the model to estimate variability in carbon emissions between 2001 and 2012. Daily burned area was mapped using imagery from the Moderate Resolution Imaging Spectroradiometer combined with perimeters from the Alaska Large Fire Database. Carbon consumption was calibrated using available field measurements from black spruce forests in Alaska. We built two nonlinear multiplicative models to separately predict above- and belowground carbon consumption by fire in response to environmental variables including elevation, day of burning within the fire season, pre-fire tree cover and the differenced normalized burn ratio (dNBR). Higher belowground consumption occurred later in the season and for mid-elevation regions. Aboveground and belowground consumption also increased as a function of tree cover and the dNBR, suggesting a causal link between the processes regulating these two components of consumption. Between 2001 and 2012, the median fuel consumption was 2.48 kg C m -2 and the median pixel-based uncertainty (SD of prediction error) was 0.38 kg C m -2 . There were considerable amounts of burning in other cover types than black spruce and consumption in pure black spruce stands was generally higher. Fuel consumption originated primarily from the belowground fraction (median = 2.30 kg C m -2 for all cover types and 2.63 kg C m -2 for pure black spruce stands). Total carbon emissions varied considerably from year to year, with the highest emissions occurring during 2004 (67 Tg C), 2005 (44 Tg C), 2009 (25 Tg C), and 2002 (16 Tg C) and a mean of 14 Tg C per year between 2001 and 2012. Our analysis highlights the importance of accounting for the spatial heterogeneity within fuels and consumption when extrapolating emissions in space and time. This data on daily burned area and emissions may be useful for in understanding controls and limits on fire growth, and predicting potential feedbacks of changing fire regimes.