ALBERT

Description: Flux variations and vertical distributions of microzooplankton (Radiolaria) in the western Arctic Ocean: environmental indices in a warming Arctic Biogeosciences Discussions, 11, 16645-16701, 2014 Author(s): T. Ikenoue, K. R. Bjørklund, S. B. Kruglikova, J. Onodera, K. Kimoto, and N. Harada The vertical distribution of radiolarians was investigated using a vertical multiple plankton sampler (100–0, 250–100, 500–250 and 1000–500 m water depths, 62 μm mesh size) at the Northwind Abyssal Plain and southwestern Canada Basin in September 2013. To investigate seasonal variations in the flux of radiolarians in relation to sea-ice and water masses, time series sediment trap system was moored at Station NAP (75°00' N, 162°00' W, bottom depth 1975 m) in the western Arctic Ocean during October 2010–September 2012. We showed characteristics of fourteen abundant radiolarian taxa related to the vertical hydrographic structure in the western Arctic Ocean. We found the Ceratocyrtis histricosus , a warm Atlantic water species, in net samples, indicating that it has extended its habitat into the Pacific Winter Water. The radiolarian flux was comparable to that in the North Pacific Oceans. Amphimelissa setosa was dominant during the open water and the beginning and the end of ice cover seasons with well-grown ice algae, ice fauna and with alternation of stable water masses and deep vertical mixing. During the sea-ice cover season, however, oligotrophic and cold-water tolerant Actinommidae was dominant and the productivity of radiolaria was lower and its species diversity was greater, which might be associated with the seasonal increase of solar radiation that induce the growth of algae on the ice and the other phytoplankton species under the sea-ice. These indicated that the dynamics of sea-ice was a major factor affecting the productivity, distribution, and composition of radiolarian fauna.

Description: Observation-based modelling of permafrost carbon fluxes with accounting for deep carbon deposits and thermokarst activity Biogeosciences Discussions, 11, 16599-16643, 2014 Author(s): T. Schneider von Deimling, G. Grosse, J. Strauss, L. Schirrmeister, A. Morgenstern, S. Schaphoff, M. Meinshausen, and J. Boike High-latitude soils store vast amounts of perennially frozen and therefore inert organic matter. With rising global temperatures and consequent permafrost degradation, a part of this carbon store will become available for microbial decay and eventual release to the atmosphere. We have developed a simplified, two-dimensional multi-pool model to estimate the strength and timing of future carbon dioxide (CO 2 ) and methane (CH 4 ) fluxes from newly thawed permafrost carbon (i.e. carbon thawed when temperatures rise above pre-industrial levels). We have especially simulated carbon release from deep deposits in Yedoma regions by describing abrupt thaw under thermokarst lakes. The computational efficiency of our model allowed us to run large, multi-centennial ensembles under various scenarios of future warming to express uncertainty inherent to simulations of the permafrost-carbon feedback. Under moderate warming of the representative concentration pathway (RCP) 2.6 scenario, cumulated CO 2 fluxes from newly thawed permafrost carbon amount to 20 to 58 petagrammes of carbon (Pg-C) (68% range) by the year 2100 and reach 40 to 98 Pg-C in 2300. The much larger permafrost degradation under strong warming (RCP8.5) results in cumulated CO 2 release of 42–141 and 157–313 Pg-C (68% ranges) in the years 2100 and 2300, respectively. Our estimates do only consider fluxes from newly thawed permafrost but not from soils already part of the seasonally thawed active layer under preindustrial climate. Our simulated methane fluxes contribute a few percent to total permafrost carbon release yet they can cause up to 40% of total permafrost-affected radiative forcing in the 21st century (upper 68% range). We infer largest methane emission rates of about 50 Tg-CH 4 year –1 around the mid of the 21st century when simulated thermokarst lake extent is at its maximum and when abrupt thaw under thermokarst lakes is accounted for. CH 4 release from newly thawed carbon in wetland-affected deposits is only discernible in the 22nd and 23rd century because of the absence of abrupt thaw processes. We further show that release from organic matter stored in deep deposits of Yedoma regions does crucially affect our simulated circumpolar methane fluxes. The additional warming through the release from newly thawed permafrost carbon proved only slightly dependent on the pathway of anthropogenic emission and amounts about 0.03–0.14 °C (68% ranges) by end of the century. The warming increased further in the 22nd and 23rd century and was most pronounced under the RCP6.0 scenario with adding 0.16–0.39 °C (68% range) to simulated global mean surface air temperatures in the year 2300.

Description: Distribution of black carbon in Ponderosa pine litter and soils following the High Park wildfire Biogeosciences Discussions, 11, 16799-16824, 2014 Author(s): C. M. Boot, M. Haddix, K. Paustian, and M. F. Cotrufo Black carbon (BC), the heterogeneous product of burned biomass, is a critical component in the global carbon cycle, yet timescales and mechanisms for incorporation into the soil profile are not well understood. The High Park Fire, which took place in northwestern Colorado in the summer of 2012, provided an opportunity to study the effects of both fire intenstiy and geomorphology on properties of carbon (C), nitrogen (N), and BC in the Cache La Poudre River drainage. We sampled montane Ponderosa pine litter, 0–5 cm soils, and 5–15 cm soils four months post-fire in order to examine the effects of slope and burn intensity on %C, C stocks, %N and black carbon (g kg −1 C, and g m −2 ). We developed and implemented the benzene polycarboxylic acid (BPCA) method for quantifying BC. With regard to slope, we found that steeper slopes had higher C : N than shallow slopes, but that there was no difference in black carbon content or stocks. BC content was greatest in the litter in burned sites (19 g kg −1 C), while BC stocks were greatest in the 5–15 cm subsurface soils (23 g m −2 ). At the time of sampling, none of the BC deposited on the land surface post-fire had been incorporated into to either the 0–5 cm or 5–15 cm soil layers. The ratio of B5CA : B6CA (less condensed to more condensed BC) indicated there was significantly more older, more processed BC at depth. Total BC soil stocks were relatively low compared to other fire-prone grassland and boreal forest systems, indicating most of the BC produced in this system is likely transported off the surface through erosion events. Future work examining mechanisms for BC transport will be required for understanding the role BC plays in the global carbon cycle.

Description: Effects of cloudiness on carbon dioxide exchange over an irrigated maize cropland in northwestern China Biogeosciences Discussions, 8, 1669-1691, 2011 Author(s): B. C. Zhang, J. J. Cao, Y. F. Bai, S. J. Yang, L. Hu, and Z. G. Ning Clouds can strongly influence solar radiation and affects other microclimatic factors (such as air temperature and vapour pressure deficit), and those changed environmental conditions may exert strong effects on carbon exchange between terrestrial ecosystems and the atmosphere. In this study, we analyzed how canopy photosynthesis and ecosystem respiration respond to changes in cloudy conditions, based on two years of eddy-covariance and meteorological data from an irrigated maize cropland in Yingke oasis of northwestern China. The results showed that net carbon uptake was more negative under cloudy than under clear conditions, it indicates that net carbon uptake increased under cloudy days. The rate of ecosystem respiration (Re) decreased under cloudy conditions due to decreased air temperature. However, photosynthesis was suppressed by the decreasing air temperature and vapour pressure deficit (VPD) under cloudy skies. Thus, the enhancement of net carbon uptake under cloudy skies mainly contributed from increasing photosynthesis with diffuse radiation. Those results improve our understanding of the effects of cloud cover on carbon exchange process in maize (C4) cropland, and improve our understanding of the driver improving net carbon uptake under cloudy conditions.

Description: The effect of resource history on the functioning of soil microbial communities is maintained across time Biogeosciences Discussions, 8, 1643-1667, 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: Impacts of land cover and climate data selection on understanding terrestrial carbon dynamics and the CO 2 airborne fraction Biogeosciences Discussions, 8, 1617-1642, 2011 Author(s): B. Poulter, D. C. Frank, E. L. Hodson, and N. E. Zimmermann Terrestrial and oceanic carbon cycle processes remove ~ 55% of global carbon emissions, with the remaining 45%, known as the "airborne fraction", accumulating in the atmosphere. The long-term dynamics of the component fluxes contributing to the airborne fraction are challenging to interpret, but important for informing fossil-fuel emission targets and for monitoring the trends of biospheric carbon fluxes. Climate and land-cover forcing data for terrestrial ecosystem models are a largely unexplored source of uncertainty in terms of their contribution to understanding airborne fraction dynamics. Here we present results using a single dynamic global vegetation model forced by an ensemble experiment of climate (CRU, ERA-Interim, NCEP-DOE II), and diagnostic land-cover datasets (GLC2000, GlobCover, MODIS). Forcing uncertainties resulted in a large range of simulated global carbon fluxes, up to 13% for net primary production (52.4 to 60.2 Pg C a −1 ) and 19% for soil respiration (44.2 to 54.8 Pg C a −1 ). The sensitivity of contemporary global terrestrial carbon fluxes to climate strongly depends on forcing data (1.2–5.9 Pg C K −1 or 0.5 to 2.7 ppmv CO 2 K −1 ), but weakening carbon sinks in sub-tropical regions and strengthening carbon sinks in northern latitudes are found to be robust. The climate and land-cover combination that best correlate to the inferred carbon sink, and with the lowest residuals, is from observational data (CRU) rather than reanalysis climate data and with land-cover categories that have more stringent criteria for forest cover (MODIS). Since 1998, an increasing positive trend in residual error from bottom-up accounting of global sinks and sources (from 0.03 (1989–2005) to 0.23 Pg C a −1 (1998–2005)) suggests that either modeled drought sensitivity of carbon fluxes is too high, or that the trend toward decreased net land-use fluxes (~ 0.5 Pg C) is overestimated.

Description: Longitudinal variability of the biogeochemical role of Mediterranean aerosols in the Mediterranean Sea Biogeosciences, 8, 1067-1080, 2011 Author(s): E. Ternon, C. Guieu, C. Ridame, S. L'Helguen, and P. Catala The Mediterranean Sea is a semi-enclosed basin characterized by a strong thermal stratification during summer during which the atmosphere is the main source of new nutrients to the nutrient-depleted surface layer. From aerosol sampling and microcosm experiments performed during the TransMed BOUM cruise (June–July 2008) we showed that: (i) the Mediterranean atmosphere composition (Al, Fe, P) was homogeneous over ~28° of longitude and was a mixture with a constant proportion of anthropogenic contribution and a variable but modest contribution of crustal aerosols. This quite stable composition over a one month period and a long transect (~2500 km) allowed to define the Mediterranean atmospheric "background" that characterizes the summer season in the absence of major Saharan event and forest fires, (ii) primary production significantly increased at all tested stations after aerosols addition collected on-board and after Saharan dust analog addition, indicating that both additions relieved on-going (co)-limitations. Although both additions significantly increased the N 2 fixation rates at the western station, diazotrophic activity remained very low (~0.2 nmol N L −1 d −1 ), (iii) due to the presence of anthropogenic particles, the probable higher solubility of nutrients associated with mixed aerosols (crustal + anthropogenic contribution), conferred a higher fertilizing potential to on-board collected aerosol as compared to Saharan dust analog. Finally, those experiments showed that atmospheric inputs from a mixed atmospheric event ("summer rain" type) or from a high-intensity Saharan event would induce comparable response by the biota in the stratified Mediterranean SML, during summer.

Description: Height-diameter allometry of tropical forest trees Biogeosciences, 8, 1081-1106, 2011 Author(s): T. R. Feldpausch, L. Banin, O. L. Phillips, T. R. Baker, S. L. Lewis, C. A. Quesada, K. Affum-Baffoe, E. J. M. M. Arets, N. J. Berry, M. Bird, E. S. Brondizio, P. de Camargo, J. Chave, G. Djagbletey, T. F. Domingues, M. Drescher, P. M. Fearnside, M. B. França, N. M. Fyllas, G. Lopez-Gonzalez, A. Hladik, N. Higuchi, M. O. Hunter, Y. Iida, K. A. Salim, A. R. Kassim, M. Keller, J. Kemp, D. A. King, J. C. Lovett, B. S. Marimon, B. H. Marimon-Junior, E. Lenza, A. R. Marshall, D. J. Metcalfe, E. T. A. Mitchard, E. F. Moran, B. W. Nelson, R. Nilus, E. M. Nogueira, M. Palace, S. Patiño, K. S.-H. Peh, M. T. Raventos, J. M. Reitsma, G. Saiz, F. Schrodt, B. Sonké, H. E. Taedoumg, S. Tan, L. White, H. Wöll, and J. Lloyd Tropical tree height-diameter ( H:D ) relationships may vary by forest type and region making large-scale estimates of above-ground biomass subject to bias if they ignore these differences in stem allometry. We have therefore developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries. Utilising this database, our objectives were: 1. to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap). 2. to ascertain if the H:D relationship is modulated by climate and/or forest structural characteristics (e.g. stand-level basal area, A ). 3. to develop H:D allometric equations and evaluate biases to reduce error in future local-to-global estimates of tropical forest biomass. Annual precipitation coefficient of variation ( P V ), dry season length ( S D ), and mean annual air temperature ( T A ) emerged as key drivers of variation in H:D relationships at the pantropical and region scales. Vegetation structure also played a role with trees in forests of a high A being, on average, taller at any given D . After the effects of environment and forest structure are taken into account, two main regional groups can be identified. Forests in Asia, Africa and the Guyana Shield all have, on average, similar H:D relationships, but with trees in the forests of much of the Amazon Basin and tropical Australia typically being shorter at any given D than their counterparts elsewhere. The region-environment-structure model with the lowest Akaike's information criterion and lowest deviation estimated stand-level H across all plots to within amedian −2.7 to 0.9% of the true value. Some of the plot-to-plot variability in H:D relationships not accounted for by this model could be attributed to variations in soil physical conditions. Other things being equal, trees tend to be more slender in the absence of soil physical constraints, especially at smaller D . Pantropical and continental-level models provided less robust estimates of H , especially when the roles of climate and stand structure in modulating H:D allometry were not simultaneously taken into account.

Description: Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea Biogeosciences Discussions, 8, 4421-4457, 2011 Author(s): C. Jeanthon, D. Boeuf, O. Dahan, F. Le Gall, L. Garczarek, E. M. Bendif, and A.-C. Lehours Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll- a (BChl- a ), the light-harvesting pigment of AAP bacteria. BChl- a -containing colonies represented a low part of the cultivable fraction. In total, 52 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria . The most frequently isolated strains belonged to Citromicrobium bathyomarinum , and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl- a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM , the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94%) was affiliated with the Gammaproteobacteria . The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding of the AAP bacteria ecology, especially in the Mediterranean Sea and likely globally.

Description: Anthropogenic impact on biogenic Si pools in temperate soils Biogeosciences Discussions, 8, 4391-4419, 2011 Author(s): W. Clymans, E. Struyf, G. Govers, F. Vandevenne, and D. J. Conley Human land use changes directly affect silica (Si) mobilisation and Si storage in terrestrial ecosystems and influence Si export from the continents, although the magnitudes of the impact are unknown. Yet biogenic silica (BSi) in soils is an understudied aspect. We have quantified and compared total biogenic (PSi a ) and easily soluble (PSi e ) Si pools at four sites along a gradient of disturbance in southern Sweden. An estimate of the magnitude of change in temperate continental BSi pools due to human disturbance is provided. Land use clearly affects BSi pools and their distribution. Total PSi a and PSi e for a continuous forested site at Siggaboda Nature Reserve (66 900 ± 22 800 kg SiO 2 ha −1 and 952 ± 16 kg SiO 2 ha −1 ) are significantly higher than disturbed land use types from the Råshult Culture Reserve including arable land (28 800 ± 7200 kg SiO 2 ha −1 and 239 ± 91 kg SiO 2 ha −1 ), pasture sites (27 300 ± 5980 kg SiO 2 ha −1 and 370 ± 129 kg SiO 2 ha −1 ) and grazed forest (23 600 ± 6370 kg SiO 2 ha −1 and 346 ± 123 kg SiO 2 ha −1 ). Vertical PSi a and PSi e profiles show significant ( p

Description: Response of δ 13 C in plant and soil respiration to a water pulse Biogeosciences Discussions, 8, 4493-4527, 2011 Author(s): Y. Salmon, N. Buchmann, and R. L. Barnard Stable carbon isotopes have been used to assess the coupling between changes in environmental conditions and the response of soil or ecosystem respiration, usually by studying the time-lagged response of δ 13 C of respired CO 2 (δ 13 C R ) to changes in photosynthetic carbon isotope discrimination (Δ i ). However, the lack of a systematic response of δ 13 C R to environmental changes in field studies stresses the need to better understand the mechanisms to this response. We experimentally created a wide range of carbon allocation and respiration conditions in Fagus sylvatica mesocosms, by growing saplings under different temperatures and girdling combinations. After a period of drought, a water pulse was applied and the short-term responses of δ 13 C in soil CO 2 efflux (δ 13 C R soil ) and δ 13 C in aboveground plant respiration (δ 13 C R above ) were measured, as well as leaf gas exchange rates and soil microbial biomass δ 13 C responses. Both δ 13 C R soil and δ 13 C R above values of all the trees decreased immediately after the water pulse. These responses were not driven by changes in Δ i , but rather by a fast release of C stored in roots and shoots. Changes in δ 13 C R soil associated with the water pulse were significantly positively correlated with changes in stomatal conductance, showing a strong impact of the plant component on δ 13 C R soil . However, three days after the water pulse in girdled trees, changes in δ 13 C R soil were related to changes in microbial biomass δ 13 C, suggesting that changes in the carbon source respired by soil microorganisms also contributed to the response of δ 13 C R soil . Our study shows that improving our mechanistic understanding of the responses of δ 13 C R to changes in environmental conditions requires the understanding of not only the plant's physiological responses, but also the responses of soil microorganisms and of plant-microbial interactions.

Description: Paleofires and the dynamics of carbon cycling in Chinese Loess Plateau over the last two glacial cycles Biogeosciences Discussions, 8, 4459-4492, 2011 Author(s): X. Wang and Z. L. Ding The spatio-temporal changes in trace gas emissions and burnt biomass by paleofires in Chinese Loess Plateau over the last two glacial cycles have been reconstructed using vegetation (C3/C4) specific fire emission factors and black carbon records in three loess-paleosol sections. Results show that the average mass emission rate (AMER) of total trace gases (TTG) and burnt biomass by fires (BBF) in glacial periods are 1~2 times higher than in interglacial periods, and they display a clear southward decrease during both glacial and interglacial periods. This pattern reflects the combined control on paleofire emissions by climate-induced fire regimes and succession of vegetation types. The substantial increases in TTG-AMER and BBF during the late Holocene relative to the middle-to-early Holocene at Lingtai and Weinan support existing conclusion that increased anthropogenic fire activities have occurred in Middle and Southern Plateau during late Holocene. To assess the influence of paleofires on soil carbon stocks, the ratios of BBF to above-ground net primary productivity (ANPP), estimated by magnetic susceptibility-based paleorainfall and paleotemperature reconstruction, were calculated. In the Northern Plateau, the BBF/ANPP ratios during glacial periods are nearly 90%, about 2~3 times higher than during interglacial periods, suggesting paleofires may be the overwhelming force modulating the cycling of terrestrial organic carbon in the region. However, in Middle and Southern Plateau, the large decrease in BBF/ANPP ratios to around 20% and 10% respectively during glacial and interglacial periods suggests that paleofires have had a minor impact on carbon storage in these areas during both glacial and interglacial periods.

Description: Recent global CO 2 flux inferred from atmospheric COsub〉2 observations and its regional analyses Biogeosciences Discussions, 8, 3497-3536, 2011 Author(s): F. Deng and J. M. Chen The net surface exchange of CO 2 for the years 2002–2007 is inferred from 12 181 atmospheric CO 2 concentration data with a time-dependent Bayesian synthesis inversion scheme. Monthly CO 2 fluxes are optimized for 30 regions of the North America and 20 regions for the rest of the globe. Although there have been many previous multiyear inversion studies, the reliability of atmospheric inversion techniques is not yet been systematically evaluated for quantifying regional interannual variability in the carbon cycle. In this study, the global interannual variability of the CO 2 flux is found to be dominated by terrestrial ecosystems and is mostly caused by tropical land, and the variations of regional terrestrial carbon fluxes are closely related to climate variations. These interannual variations are mostly caused by abnormal meteorological conditions in a few months in the year or part of a growing season and cannot be well represented using annual means, suggesting that we should pay attention to monthly or submonthly climate variations in ecosystem modeling. We find that, excluding fossil fuel and biomass burning emissions, terrestrial ecosystems and oceans absorb an average of 3.63±0.49 and 1.94±0.41 Pg C/yr, respectively. The terrestrial uptake is mainly in northern land while the tropical and southern lands contribute 0.62±0.47, and 0.67±0.34 Pg C/yr to the sink, respectively. In North America, terrestrial ecosystems absorb 0.89±0.18 Pg C/yr on average with a strong flux density found in the south-east of the continent.

Description: Modelling post-fire vegetation recovery in Portugal Biogeosciences Discussions, 8, 4559-4601, 2011 Author(s): A. Bastos, C. Gouveia, C. C. DaCamara, and R. M. Trigo Wildfires in Mediterranean Europe have been increasing in number and extension over the last decades and constitute one of the major disturbances of these ecosystems. Portugal is the country with more burnt area in the last decade and the years of 2003 and 2005 were particularly devastating, the total burned areas of 425 000 and 338 000 ha being several times higher than the corresponding average. The year of 2005 further coincided with one of the most severe droughts since early 20th century. Due to different responses of vegetation to diverse fire regimes and to the complexity of landscape structures, fires have complex effects on vegetation recovery. Remote sensing has revealed to be a powerful tool in studying vegetation dynamics and in monitoring post-fire vegetation recovery, which is crucial to land-management and to prevent erosion. The main goals of the present work are (i) to assess the accuracy of a vegetation recovery model previously developed by the authors; (ii) to assess the model's performance, namely its sensitivity to initial conditions, to the temporal length of the input dataset and to missing data; (iii) to study vegetation recovery over two selected areas that were affected by two large wildfire events in the fire seasons of 2003 and 2005, respectively. The study relies on monthly values of NDVI over 11 yr (1998–2009), at 1 × 1 km spatial resolution, as obtained by the VEGETATION instrument. According to results from sensitivity analysis, the model is robust and able to provide good estimations of recovery times of vegetation when the regeneration process is regular, even when missing data is present. In what respect to the two selected burnt scars, results indicate that fire damage is a determinant factor of regeneration, as less damaged vegetation recovers more rapidly, which is mainly justified by the high coverage of Pinus Pinaster over the area, and by the fact that coniferous forests tend to recover slower than transitional woodland-shrub, which tend to dominate the areas following the fire event.

Description: Quantifying in-situ gas hydrates at active seep sites in the eastern Black Sea using pressure coring technique Biogeosciences Discussions, 8, 4529-4558, 2011 Author(s): K. Heeschen, M. Haeckel, I. Klaucke, M. K. Ivanov, and G. Bohrmann In the eastern Black Sea, we determined methane (CH 4 ) concentrations, gas hydrate volumes and their vertical distribution from combined gas and chloride (Cl − ) measurements within pressurized sediment cores. The total gas volume collected from the cores corresponds to concentrations of 1.2–1.4 mol of methane per kg porewater at in-situ pressure, which is equivalent to a gas hydrate saturation of 15–18% of pore volume and amongst the highest values detected in shallow seep sediments. At the central seep site, a high-resolution Cl − profile resolves the upper gas hydrate stability boundary and a continuous layer of hydrates in a sediment column of 120 cm thickness. Including this information, a more precise gas hydrate saturation of 22–24% pore volume can be calculated. This is higher in comparison to a saturation calculated from the Cl − profile alone, resulting in 14.4%. The likely explanation is an active gas hydrate formation from CH 4 gas ebullition. The hydrocarbons at Batumi Seep are of shallow biogenic origin (CH 4 〉 99.6%), at Pechori Mound they originate from deeper thermocatalytic processes as indicated by the lower ratios of C 1 to C 2 –C 3 and the presence of C 5 .

Description: Revisiting land cover observations to address the needs of the climate modelling community Biogeosciences Discussions, 8, 7713-7740, 2011 Author(s): S. Bontemps, M. Herold, L. Kooistra, A. van Groenestijn, A. Hartley, O. Arino, I. Moreau, and P. Defourny One of the relevant processes driven by political discussion under the United Framework Convention on Climate Change is the monitoring of Essential Climate Variables. Land Cover is one of those variables and efforts are therefore to be made to develop land cover observation approaches which meet the climate modelling community expectations. This paper aims at contributing to this necessity. First, consultation mechanisms were established with the climate modelling community to identify its specific requirements in terms of satellite-based global land cover products. This assessment highlighted specific needs in terms of land cover characterization and products accuracy, stability and consistency that are currently not met. Based on this outcome, the paper calls into question the current land cover representation and for revisiting global land cover mapping approaches. Increasing the flexibility of current classification systems and making the mapping techniques less sensitive to the period of observation are proposed as two key aspects to enhance the usability of global land cover dataset.

Description: Integration of remote sensing data and surface observations to estimate the impact of the russian wildfires over Europe and Asia during August 2010 Biogeosciences Discussions, 8, 7741-7790, 2011 Author(s): L. Mei, Y. Xue, G. de Leeuw, J. Guang, Y. Wang, Y. Li, H. Xu, L. Yang, T. Hou, X. He, C. Wu, J. Dong, and Z. Chen A series of wildfires broke out in western Russia starting in late July of 2010. Harmful particulates and gases released into the local Russian atmosphere have been reported, as have possible negative consequences for the global atmosphere. In this study, an extremely hazy area and its transport trajectory on Russian wildfires were analysed using aerosol optical depth (AOD) images retrieved via the synergy method from Moderate Resolution Imaging Spectroradiometer (MODIS) data. In addition, we used trace gases (NO 2 and SO 2 ) and CO 2 products measured using Ozone Monitoring Instrument (OMI) data, vertical distribution of AOD data retrieved from Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) data, the mass trajectory analyses, synoptic maps from a HYSPLIT model simulation and ground-based data, including AERONET (both AOD and Ångström exponent) data and PM 2.5 . First, an Optimal Smoothing (OS) scheme was used to develop more precise and reliable AOD data based on multiple competing predictions made using several AOD retrieval models; then, integrated AOD and PM 2.5 data were related using a chemical transport model (GEOS-Chem), and the integrated AOD and visibility data were related using a 6S model. The results show that the PM 2.5 concentration is 3–5 times the normal amount based on both satellite data and in situ values with peak daily mean concentrations of approximately 500 μg m −3 . Also, the visibility of many parts of Russia, even Moscow, was less than 100 m; in some areas, the visibility was less than 50 m. Additionally, the possible impact on neighbouring countries due to the long-transport effect was also analysed during 31 July and 15 August 2010. A comparison of the satellite aerosol products and ground observations from the neighbouring countries suggests that wildfires in western Russian have had little impact on most European and Asian countries, the exceptions being Finland, Estonia, Ukraine and Kyrgyzstan. However, a possible impact on the Arctic region was also identified; such an effect would have a serious influence on the polar atmospheric environment and on animals such as polar bears.

Description: Biogeochemical controls on the bacterial population in the eastern Atlantic Ocean Biogeosciences Discussions, 8, 7791-7821, 2011 Author(s): S. B. Neogi, B. P. Koch, P. Schmitt-Kopplin, C. Pohl, G. Kattner, S. Yamasaki, and R. J. Lara Little is known about bacterial dynamics in the oligotrophic ocean, particularly about its cultivable population. We examined the abundance of total and cultivable bacteria in relation to changes in biogeochemical conditions in the eastern Atlantic Ocean with special regard to Vibrio spp., a group of bacteria that can cause diseases in human and aquatic organisms. Surface, deep water and plankton samples ( 55 μm) were collected between 50° N and 24° S. Chlorophyll- a was very low (

Description: Characterization of the bio-optical anomaly and diurnal variability of the particulate matter, as seen from the scattering and backscattering coefficients, in ultra-oligotrophic eddies of the Mediterranean Sea Biogeosciences Discussions, 8, 7859-7919, 2011 Author(s): H. Loisel, V. Vantrepotte, K. Norkvist, X. Mériaux, M. Kheireddine, J. Ras, M. Pujo-Pay, Y. Combet, K. Leblanc, R. Mauriac, D. Dessailly, and T. Moutin The variability of the inherent optical properties is investigated in the ultra-oligotrophic waters of the Mediterranean Sea sampled during the BOUM experiment performed during the early summer 2008. Bio-optical relationships found for the ultra-oligotrophic waters of the three anticyclonic gyres sampled significantly depart from the mean standard relationships provided for the global ocean, confirming the particular character of these Mediterranean waters. These optical anomalies are diversely related to the specific biological and environmental conditions occurring in the studied ecosystem. Specifically, the surface specific phytoplankton absorption coefficient exhibits values lower than those expected from the general relationships mainly in relation with a high contribution of relatively large sized phytoplankton. Conversely, the particulate backscattering coefficient, b bp , values are much higher than the mean standard values for a given chlorophyll- a concentration, TChl- a . This feature can presumably be related to the relevant influence of highly refractive submicrometer particles of Saharan origin in the surface layer of the water column. The present measurements also show that the Mediterranean Sea is greener than TChl- a alone indicates, as already stressed in previous studies. This color anomaly is partly explained by the estimated colored dissolved organic matter and submicrometer particles absorption coefficients, and to a greater extent by the high b bp /TChl- a values assuming that these particles backscatter light similarly in the green and blue parts of the visible spectrum. The diel variation of both the particulate matter attenuation and backscattering coefficients were also investigated specifically. Despite some differences in the timing and the magnitude of the daily oscillations found for these optical parameters, potential for the backscattering coefficient daily oscillation to be used, similarly to that for the attenuation coefficient, as a proxy for estimating carbon community production budget has been highlighted for the first time. This result is particularly relevant for present and future geostationary spatial ocean color missions.

Description: Contrasting biogeochemistry of nitrogen in the Atlantic and Pacific oxygen minimum zones Biogeosciences Discussions, 8, 8001-8039, 2011 Author(s): E. Ryabenko, A. Kock, H. W. Bange, M. A. Altabet, and D. W. R. Wallace We present new data for the stable isotope ratio of inorganic nitrogen species from the contrasting oxygen minimum zones (OMZs) of the Eastern Tropical North Atlantic, south of Cape Verde, and the Eastern Tropical South Pacific off Peru. Differences in minimum oxygen concentration and corresponding N-cycle processes for the two OMZs are reflected in strongly contrasting δ 15 N distributions. Pacific surface waters are marked by strongly positive values for δ 15 N-NO 3 − reflecting fractionation associated with subsurface N-loss and partial NO 3 − utilization. This contrasts with negative values in NO 3 − depleted surface waters of the Atlantic which are lower than can be explained by N supply via N 2 fixation. We suggest the negative values reflect inputs of nitrate, possibly transient, associated with deposition of Saharan dust. Strong signals of N-loss processes in the subsurface Pacific OMZ are evident in the isotope and N 2 O data, both of which are compatible with a contribution of canonical denitrification to overall N-loss. However the apparent N isotope fractionation factor observed is relatively low (ε d = 11.4 ‰) suggesting an effect of influence from denitrification in sediments. Identical positive correlation of N 2 O vs. AOU for waters with oxygen concentrations [O 2 ] 〉 50 μmol l −1 in both regions reflect a nitrification source. Sharp decrease in N 2 O concentrations is observed in the Pacific OMZ due to denitrification under oxygen concentrations O 2 〈 5 μmol l −1 .

Description: Carbon dioxide emissions from an Acacia plantation on peatland in Sumatra, Indonesia Biogeosciences Discussions, 8, 8269-8302, 2011 Author(s): J. Jauhiainen, A. Hooijer, and S. E. Page Peat surface CO 2 emission, groundwater table depth and peat temperature were monitored for two years along transects in an Acacia plantation on thick tropical peat (〉4 m) in Sumatra, Indonesia. A total of 2300 emission measurements were taken at 144 locations. The autotrophic root respiration component of the CO 2 emission was separated from heterotrophic emissions caused by peat oxidation in three ways: (i) by comparing CO 2 emissions within and beyond the tree rooting zone, (ii) by comparing CO 2 emissions with and without peat trenching (i.e. cutting any roots remaining in the peat beyond the tree rooting zone), and (iii) by comparing CO 2 emissions before and after Acacia tree harvesting. On average, the contribution of root respiration to daytime CO 2 emission is 21 % along transects in mature tree stands. At locations 0.5 m from trees this is up to 80 % of the total emissions, but it is negligible at locations more than 1.3 m away. This means that CO 2 emission measurements well away from trees are free of any root respiration contribution and thus represent only peat oxidation emission. We find daytime mean annual CO 2 emission from peat oxidation alone of 94 t ha −1 yr −1 at a mean water table depth of 0.8 m, and a minimum emission value of 80 t ha −1 yr −1 after correction for the effect of diurnal temperature fluctuations, which resulted in a 14.5 % reduction of the daytime emission. There is a positive correlation between mean long-term water table depths and peat oxidation CO 2 emission. However, no such relation is found for instantaneous emission/water table depth within transects and it is clear that factors other than water table depth also affect peat oxidation and total CO 2 emissions. The increase in the temperature of the surface peat due to plantation development may explain over 50 % of peat oxidation emissions.

Description: Eutrophication and warming effects on long-term variation of zooplankton in Lake Biwa Biogeosciences, 8, 1383-1399, 2011 Author(s): C. H. Hsieh, Y. Sakai, S. Ban, K. Ishikawa, T. Ishikawa, S. Ichise, N. Yamamura, and M. Kumagai We compiled and analyzed long-term (1961–2005) zooplankton community data in response to environmental variations in Lake Biwa. Environmental data indicate that Lake Biwa had experienced eutrophication (according to the total phosphorus concentration) in the late 1960s and recovered to a normal trophic status around 1985, and then has exhibited warming since 1990. Total zooplankton abundance showed a significant correlation with total phytoplankton biomass. Following a classic pattern, the cladoceran/calanoid and cyclopoid/calanoid abundance ratio was related positively to eutrophication. The zooplankton community exhibited a significant response to the boom and bust of phytoplankton biomass as a consequence of eutrophication-reoligotriphication and warming. Moreover, our analyses suggest that the Lake Biwa ecosystem exhibited a hierarchical response across trophic levels; that is, higher trophic levels may show a more delayed response or no response to eutrophication than lower ones. We tested the hypothesis that the phytoplankton community can better explain the variation of the zooplankton community than bulk environmental variables, considering that the phytoplankton community may directly affect the zooplankton succession through predator-prey interactions. Using a variance partition approach, however, we did not find strong evidence to support this hypothesis. We further aggregated zooplankton according to their feeding types (herbivorous, carnivorous, omnivorous, and parasitic) and taxonomic groups, and analyzed the aggregated data. While the pattern remains similar, the results are less clear comparing the results based on finely resolved data. Our research suggests that zooplankton can be bio-indicators of environmental changes; however, the efficacy depends on data resolution.

Description: A new concept for simulation of vegetated land surface dynamics – Part 1: The event driven phenology model Biogeosciences Discussions, 8, 5281-5333, 2011 Author(s): V. Kovalskyy and G. M. Henebry Phenologies of the vegetated land surface are being used increasingly for diagnosis and prognosis of climate change consequences. Current prospective and retrospective phenological models stand far apart in their approaches to the subject. We report on an exploratory attempt to implement a phenological model based on a new event driven concept which has both diagnostic and prognostic capabilities in the same modeling framework. This Event Driven Phenological Model (EDPM) is shown to simulate land surface phenologies and phenophase transition dates in agricultural landscapes based on assimilation of weather data and land surface observations from spaceborne sensors. The model enables growing season phenologies to develop in response to changing environmental conditions and disturbance events. It also has the ability to ingest remotely sensed data to adjust its output to improve representation of the modeled variable. We describe the model and report results of initial testing of the EDPM using Level 2 flux tower records from the Ameriflux sites at Mead, Nebraska, USA, and at Bondville, Illinois, USA. Simulating the dynamics of normalized difference vegetation index based on flux tower data, the predictions by the EDPM show good agreement (RMSE 〈 0.08; r 2 〉0.8) for maize and soybean during several growing seasons at different locations. This study presents the EDPM used in the companion paper (Kovalskyy and Henebry, 2011) in a coupling scheme to estimate daily actual evapotranspiration over multiple growing seasons.

Description: Chemical composition of modern and fossil Hippopotamid teeth and implications for paleoenvironmental reconstructions and enamel formation: 1. major and minor element variation Biogeosciences Discussions, 8, 5197-5250, 2011 Author(s): G. Brügmann, J. Krause, T. C. Brachert, O. Kullmer, F. Schrenk, I. Ssemmanda, and D. F. Mertz Bioapatite in mammalian teeth is readily preserved in continental sediments and represents a very important archive for reconstructions of environment and climate evolution. This project intends to provide a detailed data base of major, minor and trace element and isotope tracers for tooth apatite using a variety of microanalytical techniques. The aim is to identify specific sedimentary environments and to improve our understanding on the interaction between internal metabolic processes during tooth formation and external nutritional control and secondary alteration effects. Here, we use the electron microprobe, to determine the major and minor element contents of fossil and modern molar enamel, cement and dentin from hippopotamids. Most of the studied specimens are from different ecosystems in Eastern Africa, representing modern and fossil lakustrine (Lake Kikorongo, Lake Albert, and Lake Malawi) and modern fluvial environments of the Nile River system. Secondary alteration effects in particular FeO, MnO, SO 3 and F concentrations, which are 2 to 10 times higher in fossil than in modern enamel; secondary enrichments in fossil dentin and cement are even higher. In modern and fossil enamel, along sections perpendicular to the enamel-dentin junction (EDJ) or along cervix-apex profiles, P 2 O 5 and CaO contents and the CaO/P 2 O 5 ratios are very constant (StdDev ~1 %). Linear regression analysis reveals very tight control of the MgO ( R 2 ∼0.6), Na 2 O and Cl variation (for both R 2 〉0.84) along EDJ-outer enamel rim profiles, despite large concentration variations (40 % to 300 %) across the enamel. These minor elements show well defined distribution patterns in enamel, similar in all specimens regardless of their age and origin, as the concentration of MgO and Na 2 O decrease from the enamel-dentin junction (EDJ) towards the outer rim, whereas Cl displays the opposite variation. Fossil enamel from hippopotamids which lived in the saline Lake Kikorongo have a much higher MgO/Na 2 O ratio (∼1.11) than those from the Neogene fossils of Lake Albert (MgO/Na 2 O∼0.4), which was a large fresh water lake like those in the western Branch of the East African Rift System today. Similarly, the MgO/Na 2 O ratio in modern enamel from the White Nile River (∼0.36), which has a Precambrian catchment of dominantly granite and gneisses and passes through several saline zones, is higher than that from the Blue Nile River, whose catchment is the Neogene volcanic Ethiopian Highland (MgO/Na 2 O∼0.22). Thus, particularly MgO/Na 2 O might be a sensitive fingerprint for environments where river and lake water have suffered strong evaporation. Enamel formation in mammals takes place at successive mineralization fronts within a confined chamber where ion and molecule transport is controlled by the surrounding enamel organ. During the secretion and maturation phases the epithelium generates different fluid composition, which in principle, should determine the final composition of enamel apatite. This is supported by co-linear relationships between MgO, Cl and Na 2 O which can be interpreted as binary mixing lines. However, if maturation starts after secretion is completed the observed element distribution can only be explained by recrystallization of existing and addition of new apatite during maturation. Perhaps the initial enamel crystallites precipitating during secretion and the newly formed bioapatite crystals during maturation equilibrate with a continuously evolving fluid. During crystallization of bioapatite the enamel fluid becomes continuously depleted in MgO and Na 2 O, but enriched in Cl which results in the formation of MgO, and Na 2 O-rich, but Cl-poor bioapatite near the EDJ and MgO- and Na 2 O-poor, but Cl-rich bioapatite at the outer enamel rim. The linkage between lake and river water composition, bioavailability of elements for plants, animal nutrition and tooth formation is complex and multifaceted. The quality and limits of the MgO/Na 2 O and other proxies have to be established with systematic investigations relating chemical distribution patterns to sedimentary environment and to growth structures developing as secretion and maturation proceed during tooth formation.

Description: Carbonate system in the water masses of the Southeast Atlantic sector of the Southern Ocean during February and March 2008 Biogeosciences, 8, 1401-1413, 2011 Author(s): M. González-Dávila, J. M. Santana-Casiano, R. A. Fine, J. Happell, B. Delille, and S. Speich Carbonate system variables were measured in the South Atlantic sector of the Southern Ocean along a transect from South Africa to the southern limit of the Antarctic Circumpolar Current (ACC) from February to March 2008. Eddies detached from the retroflection of the Agulhas Current increased the gradients observed along the fronts. Minima in the fugacity of CO 2 , f CO 2 , and maxima in pH on either side of the frontal zone were observed, noting that within the frontal zone f CO 2 reached maximum values and pH was at a minimum. Vertical distributions of water masses were described by their carbonate system properties and their relationship to CFC concentrations. Upper Circumpolar Deep Water (UCDW) and Lower Circumpolar Deep Water (LCDW) offered pH T,25 values of 7.56 and 7.61, respectively. The UCDW also had higher concentrations of CFC-12 (〉0.2 pmol kg −1 ) as compared to deeper waters, revealing that UCDW was mixed with recently ventilated waters. Calcite and aragonite saturation states (Ω) were also affected by the presence of these two water masses with high carbonate concentrations. The aragonite saturation horizon was observed at 1000 m in the subtropical area and north of the Subantarctic Front. At the position of the Polar Front, and under the influence of UCDW and LCDW, the aragonite saturation horizon deepened from 800 m to 1500 m at 50.37° S, and reached 700 m south of 57.5° S. High latitudes proved to be the most sensitive areas to predicted anthropogenic carbon increase. Buffer coefficients related to changes in [CO 2 ], [H + ] and Ω with changes in dissolved inorganic carbon ( C T ) and total alkalinity ( A T ) offered minima values in the Antarctic Intermediate Water and UCDW layers. These coefficients suggest that a small increase in C T will sharply decrease the status of pH and carbonate saturation. Here we present data that suggest that south of 55° S, surface water will be under-saturated with respect to aragonite within the next few decades.

Description: Distribution of typical denitrifying functional genes and diversity of the nirS -encoding bacterial community related to environmental characteristics of river sediments Biogeosciences Discussions, 8, 5251-5280, 2011 Author(s): S. Huang, C. Chen, Q. Wu, R. Zhang, and X. Yang Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0–25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate ( narG ), nitrite ( nirS , nirK and nrfA ), and nitrous oxide ( nosZ ) reductase genes from the sediment samples. Assemblages of nirS , nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5–15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78–94 %) between the nirS sequences recovered from Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic N (DIN: NH 4 + , NO 2

Description: Alternative methods to predict actual evapotranspiration illustrate the importance of accounting for phenology – Part 2: The event driven phenology model Biogeosciences Discussions, 8, 5335-5378, 2011 Author(s): V. Kovalskyy and G. M. Henebry Evapotranspiration ( ET ) flux constitutes a major component of both the water and energy balances at the land surface. Among the many factors that control evapotranspiration, phenology poses a major source of uncertainty in attempts to predict ET . Contemporary approaches to ET modeling and monitoring frequently summarize the complexity of the seasonal development of vegetation cover into static phenological trajectories (or climatologies) that lack sensitivity to changing environmental conditions. The Event Driven Phenology Model (EDPM) offers an alternative, interactive approach to representing phenology. This study presents the results of an experiment designed to illustrate the differences in ET arising from various techniques used to mimic phenology in models of land surface processes. The experiment compares and contrasts two realizations of static phenologies derived from long-term satellite observations of the Normalized Difference Vegetation Index (NDVI) against canopy trajectories produced by the interactive EDPM trained on flux tower observations. The assessment was carried out through validation of predicted ET against records collected by flux tower instruments. The VegET model (Senay, 2008) was used as a framework to estimate daily actual evapotranspiration and supplied with seasonal canopy trajectories produced by the EDPM and traditional techniques. The interactive approach presented the following advantages over phenology modeled with static climatologies: (a) lower prediction bias in crops; (b) smaller root mean square error in daily ET – 0.5 mm per day on average; (c) stable level of errors throughout the season similar among different land cover types and locations; and (d) better estimation of season duration and total seasonal ET .

Description: Free and protected soil organic carbon dynamics respond differently to abandonment of mountain grassland Biogeosciences Discussions, 8, 9943-9976, 2011 Author(s): S. Meyer, J. Leifeld, M. Bahn, and J. Fuhrer Land-use change (LUC) and management are among the major driving forces of soil carbon (C) storage. Abandonment of mountain grassland promotes accumulation of aboveground biomass and litter, but related responses of soil organic matter (SOM) dynamics are uncertain. To determine SOM-C turnover we sampled 0–10 cm of soils along land-use gradients (hay meadows, grazed pastures and abandoned grasslands) in the European Alps varying in management intensity at Stubai Valley (MAT: 3 °C, P: 1097 mm) in Austria and Matsch Valley (MAT: 6.6 °C, P: 527 mm) in Italy. We determined C input and decomposition rates of labile water-floatable and free particulate organic matter (wPOM, fPOM

Description: Apparent oxygen utilization rates calculated from tritium and helium-3 profiles at the Bermuda Atlantic Time-series Study site Biogeosciences Discussions, 8, 9977-10015, 2011 Author(s): R. H. R. Stanley, S. C. Doney, W. J. Jenkins, and D. E. Lott, III We present three years of Apparent Oxygen Utilization Rates (AOUR) estimated from oxygen and tracer data collected over the ocean thermocline at monthly resolution between 2003 and 2006 at the Bermuda Atlantic Time-series Study (BATS) site. We estimate water ages by calculating a transit time distribution from tritium and helium-3 data. The vertically integrated AOUR over the upper 500 m, which is a regional estimate of export, during the three years is 3.1 ± 0.5 mol O 2 m −2 yr −1 . This is comparable to previous AOUR-based estimates of export production at the BATS site but is several times larger than export estimates derived from sediment traps or 234 Th fluxes. We compare AOUR determined in this study to AOUR measured in the 1980s and show AOUR is significantly greater today than decades earlier because of changes in AOU, rather than changes in ventilation rates. The changes in AOU may be a methodological artefact associated with problems with early oxygen measurements.

Description: Effects of soil rewetting and thawing on soil gas fluxes: a review of current literature and suggestions for future research Biogeosciences Discussions, 8, 9847-9899, 2011 Author(s): D.-G. Kim, R. Vargas, B. Bond-Lamberty, and M. R. Turetsky The rewetting of dry soils and the thawing of frozen soils are short-term, transitional phenomena in terms of hydrology and the thermodynamics of soil systems. The impact of these short-term phenomena on larger scale ecosystem fluxes has only recently been fully appreciated, and a growing number of studies show that these events affect various biogeochemical processes including fluxes of soil gases such as carbon dioxide (CO 2 ), methane (CH 4 ), nitrous oxide (N 2 O), ammonia (NH 3 ) and nitric oxide (NO). Global climate models predict that future climatic change is likely to alter the frequency and intensity of drying-rewetting events and thawing of frozen soils, highlighting the importance of understanding how rewetting and thawing will influence soil gas fluxes. Here we summarize findings in a new database based on 338 studies conducted from 1956 to 2010, and highlight open research questions. The database revealed conflicting results following rewetting and thawing in various terrestrial ecosystems, ranging from large increases in gas fluxes to non-significant changes. An analysis of published field studies ( n = 142) showed that after rewetting or thawing, CO 2 , CH 4 , N 2 O, NO and NH 3 fluxes increase from pre-event fluxes following a power function, with no significant differenced among gases. We discuss possible mechanisms and controls that regulate flux responses, and note that a high temporal resolution of flux measurements is critical to capture rapid changes in gas fluxes after these soil perturbations. Finally, we propose that future studies should investigate the interactions between biological (i.e. microbial community and gas production) and physical (i.e. flux, diffusion, dissolution) changes in soil gas fluxes, and explore synergistic experimental and modelling approaches.

Description: Tracing the transport of colored dissolved organic matter in water masses of the Southern Beaufort Sea: relationship with hydrographic characteristics Biogeosciences Discussions, 8, 11003-11040, 2011 Author(s): A. Matsuoka, A. Bricaud, R. Benner, J. Para, R. Sempéré, L. Prieur, S. Bélanger, and M. Babin Light absorption by colored dissolved organic matter (CDOM) ( a CDOM (λ)) plays an important role in the heat budget of the Arctic Ocean, contributing to the recent decline in sea ice, as well as in biogeochemical processes. We investigated a CDOM (λ) in the Southern Beaufort Sea where a significant amount of CDOM is delivered by the Mackenzie River. In the surface layer, a CDOM (440) showed a strong and negative correlation with salinity, indicating strong river influence and conservative transport in the river plume. Below the mixed layer, a weak but positive correlation between a CDOM (440) and salinity was observed above the upper halocline, resulting from the effect of removal of CDOM due to brine rejection and lateral intrusion of Pacific summer waters into these layers. In contrast, the relationship was negative in the upper and the lower haloclines, suggesting these waters originated from Arctic coastal waters. DOC concentrations in the surface layer were strongly correlated with a CDOM (440) ( r 2 = 0.97), suggesting that this value can be estimated in this area, using a CDOM (440) that is retrieved using satellite ocean color data. Implications for estimation of DOC concentrations in surface waters using ocean color remote sensing are discussed.

Description: Landscape patterns of soil oxygen and atmospheric greenhouse gases in a northern hardwood forest landscape Biogeosciences Discussions, 8, 10859-10893, 2011 Author(s): S. F. Werner, C. T. Driscoll, P. M. Groffman, and J. B. Yavitt The production and consumption of the greenhouse gases, carbon dioxide (CO 2 ), nitrous oxide (N 2 O), and methane (CH 4 ), are controlled by redox reactions in soils. Together with oxygen (O 2 ), seasonal and spatial dynamics of these atmospheric gases can serve as robust indicators of soil redox status, respiration rates, and nitrogen cycling. We examined landscape patterns of soil oxygen and greenhouse gas dynamics in Watershed 3 at the Hubbard Brook Experimental Forest, NH, USA. We analyzed depth profiles of soil O 2 , CO 2 , N 2 O, and CH 4 approximately bimonthly for one year. Soil gas depth profiles were obtained from several different soil types encompassing a range of topographic positions, drainage classes, and organic matter content. Soil O 2 was a good predictor of greenhouse gas concentrations. Unsaturated soils always had O 2 concentrations 〉18 %, while saturated soils had O 2 ranging from 0 to 18 %. For unsaturated soils, changes in CO 2 were nearly stoichiometric with O 2 . High concentrations of CH 4 (〉10 μL L −1 ) were typically associated with saturated soils; CH 4 was typically below atmospheric concentrations ( 5000 nL L −1 ) were found only in well-aerated soils after summer rainfall events and in marginally-anoxic soils; N 2 O was consumed (

Description: Annual emissions of CH 4 and N 2 O, and ecosystem respiration, from eight organic soils in Western Denmark managed by agriculture Biogeosciences Discussions, 8, 10017-10067, 2011 Author(s): S. O. Petersen, C. C. Hoffmann, C.-M. Schäfer, G. Blicher-Mathiesen, L. Elsgaard, K. Kristensen, S. E. Larsen, S. B. Torp, and M. H. Greve The use of organic soils by agriculture involves drainage and tillage, and the resulting increase in C and N turnover can significantly affect their greenhouse gas balance. This study estimated annual fluxes of CH 4 and N 2 O, and ecosystem respiration ( R eco ), from eight organic soils managed by agriculture. The sites were located in three regions representing different landscape types and climatic conditions, and three land use categories (arable crops, AR, grass in rotation, RG, and permanent grass, PG) were covered. The normal management at each site was followed, except that no N inputs occurred during the monitoring period from August 2008 to October 2009. The stratified sampling strategy further included six sampling points in three blocks at each site. Environmental variables (precipitation, PAR, air and soil temperature, soil moisture, groundwater level) were monitored continuously and during sampling campaigns, where also groundwater samples were taken for analysis. Gaseous fluxes were monitored on a three-weekly basis, giving 51, 49 and 38 field campaigns for land use categories AR, PG and RG, respectively. Climatic conditions in each region during monitoring were representative based on 20-yr averages. Peat layers were shallow, typically 0.5 to 1 m, and with a pH of 4–5. At six sites annual emissions of N 2 O were in the range 3 to 24 kg N 2 O-N ha −1 , but at two arable sites (spring barley, potato) net emissions of 38 and 61 kg N 2 O-N ha −1 were recorded. Both were characterized by fluctuating groundwater with elevated SO 4 2− concentrations. Annual fluxes of CH 4 were generally small, as expected, ranging from –2 to 4 kg CH 4 ha −1 . However, two permanent grasslands had tussocks of Juncus effusus (soft rush) in sampling points that were consistent sources of CH 4 throughout the year. Emission factors for organic soils in rotation and permanent grass, respectively, were estimated to be 0.011 and 0.47 g m −2 for CH 4 , and 2.5 and 0.5 g m −2 for N 2 O. This first documentation of CH 4 and N 2 O emissions from managed organic soils in Denmark confirms the levels and wide ranges of emissions previously reported for this region. However, the factorial approach also identified links between gaseous emissions and site-specific conditions with respect to soil, groundwater and vegetation which point to areas of future research that may account for part of the variability and hence lead to improved emission factors or models.

Description: Localising the nitrogen imprint of the Paris food supply: the potential of organic farming and changes in human diet Biogeosciences Discussions, 8, 10979-11002, 2011 Author(s): G. Billen, J. Garnier, V. Thieu, M. Silvestre, S. Barles, and P. Chatzimpiros The Seine watershed has long been the food-supplying hinterland of Paris, providing most of the animal and vegetal protein consumed in the city. Nowadays, because of the land specialisation of agriculture made possible by the shift from manure-based to synthetic nitrogen fertilisation, the Seine watershed, although it exports 80% of its huge cereal production, still provides most of the cereal consumed by the Paris agglomeration. The meat and milk supply originate, however, mainly from regions in the North and West of France, specialised in animal farming and importing about 30% of their feed from South America. As it works today, this system is responsible for a severe nitrate contamination of surface groundwater resources. Herein two scenarios of re-localising Paris's food supply are explored, based on organic farming and local provision of animal feed. We show that for the Seine watershed it is technically possible to design an agricultural system able to provide all the plant- and animal-based food required by the population, to deliver sub-root water meeting the drinking water standards and still to export a significant proportion of its production to areas less suitable for cereal cultivation. Decreasing the share of animal products in the human diet has a strong impact on the nitrogen imprint of urban food supply.

Description: Processes controlling the Si-isotopic composition in the Southern Ocean and application for paleoceanography Biogeosciences Discussions, 8, 10155-10185, 2011 Author(s): F. Fripiat, A.-J. Cavagna, F. Dehairs, A. de Brauwere, L. André, and D. Cardinal Southern Ocean biogeochemical processes have an impact on global marine primary production and global elemental cycling, e.g. by likely controlling glacial-interglacial p CO 2 variation. The natural silicon isotopic composition (δ 30 Si) of sedimentary biogenic silica has been used to reconstruct past Si-consumption:supply ratio in the surface waters. We present a new dataset in the Southern Ocean which includes for the first time summer δ 30 Si signatures of suspended biogenic silica (i) for the whole water column at three stations and (ii) in the mixed layer at seven stations from the sub-tropical zone up to the Weddell Gyre. In general, the biogenic silica isotopic composition at depth reflected a mixed layer origin and seemed not affected by any diagenetic effect in the water column, even if in the northern part of the Weddell Gyre an effect of biogenic silica dissolution cannot be ruled out. We develop a mechanistic understanding of the processes involved in the modern Si-isotopic balance, by implementing a mixed layer model. We observe that the accumulated biogenic silica (sensu Rayleigh) should satisfactorily describe the δ 30 Si composition of biogenic silica exported out of the mixed layer, within the limit of the current analytical precision on the δ 30 Si. The failures of previous models (Rayleigh and steady state) become apparent especially at the end of the productive period in the mixed layer, when biogenic silica production is low. This results from: (1) a higher biogenic silica dissolution:production ratio imposing a lower net fractionation factor and (2) a higher Si-supply:Si-uptake ratio supplying light Si-isotopes into the mixed layer. The latter effect is especially expressed when the summer mixed layer becomes strongly Si-depleted together with a large vertical silicic acid gradient.

Description: A model study on the sensitivity of surface ocean CO 2 pressure with respect to the CO 2 gas exchange rate Biogeosciences Discussions, 8, 10797-10821, 2011 Author(s): P. Landschützer, J. F. Tjiputra, K. Assmann, and C. Heinze Rising CO 2 concentrations in the atmosphere and a changing climate are expected to alter the air-sea CO 2 flux through changes in the respective control factors for gas exchange. In this study we determine the sensitivity of the CO 2 fluxes on the gas transfer velocity using the MICOM-HAMOCC isopycnic carbon cycle model. The monthly generated MICOM-HAMOCC output data are suitable to investigate seasonal variabilities concerning the exchange of CO 2 . In a series of 3 sensitivity runs the wind dependent gas exchange rate is increased by 44%, both in the northern and southern westerly regions, as well as in the equatorial area to investigate the effect of regional variations of the gas transfer rate on the air-sea fluxes and the distribution of the ocean surface p CO 2 . For the period between 1948–2009, the results show that locally increasing gas transfer rates do not play an important role concerning the global uptake of carbon from the atmosphere. While effects on a global and annual scale are low, the regional and intra-annual variability shows remarkable variations in the gas fluxes and the surface p CO 2 . An accurate quantification of the variable gas transfer velocity therefore provides a potential source to enhance model predictions over small spatial and temporal scales and to successfully reconcile model results on surface p CO 2 and air-sea CO 2 fluxes with observations.

Description: Multiple-factor controls on terrestrial N 2 O flux over North America from 1979 through 2010 Biogeosciences Discussions, 8, 10935-10977, 2011 Author(s): X. F. Xu, H. Q. Tian, M. L. Liu, W. Ren, G. S. Chen, C. Q. Lu, and C. Zhang Nitrous oxide (N 2 O) is a potent greenhouse gas which also contributes to the depletion of stratospheric ozone (O 3 ). However, the magnitude and underlying mechanisms for the spatiotemporal variations in the terrestrial sources of N 2 O are still far from certain. Using a process-based ecosystem model (DLEM – the Dynamic Land Ecosystem Model) driven by multiple global change factors, including climate variability, nitrogen (N) deposition, rising atmospheric CO 2 , trophospheric O 3 pollution, N fertilizer application, and land conversion, the spatial and temporal variations in terrestrial N 2 O flux over North America were examined and attributed to various driving factors. From 1979 to 2010, the North America accumulatively emitted 55.1 ± 0.8 Tg N 2 O-N (1 Tg = 10 12 g), of which global change factors contributed 2.8 ± 1.0 Tg N 2 O-N, and baseline emission contributed 52.3 ± 0.6 Tg N 2 O-N. Climate variability, N deposition, O 3 pollution, N fertilizer application, and land conversion increased N 2 O emission by 0.3 ± 0.7 Tg N 2 O-N, 0.5 ± 0.1 Tg N 2 O-N, 0.11 ± 0.02 Tg N 2 O-N, 1.2 ± 0.1 Tg N 2 O-N, and 0.2 ± 0.02 Tg N 2 O-N, respectively. The elevated atmospheric CO 2 led to a decrease in terrestrial N 2 O emission by 0.5 ± 0.07 Tg N 2 O-N. The interactive effect among multiple factors enhanced N 2 O emission by 0.9 ± 0.3 Tg N 2 O-N over the 32 years. At country level, climate variability and elevated atmospheric CO 2 decreased, while all other single factors and multiple-factor interaction enhanced N 2 O emission in the United States of America (USA) over the study period. During the same time period, elevated atmospheric CO 2 and multiple-factor interaction decreased, while other factors enhanced N 2 O emission from Canada. Elevated atmospheric CO 2 and land conversion decreased while other factors enhanced N 2 O emission from Mexico. The interactive effects among climate variables play a predominant role in controlling climate -induced changes in N 2 O emission at both continental and country levels. Central and southeastern parts of the North America – including central Canada, central USA, southeastern USA, and all of Mexico – experienced increases in N 2 O emission from 1979 to 2010. The effects of climate variability and multiple-factor interaction dominating the inter-annual variations in terrestrial N 2 O emission at both continental and country levels indicate that projected changes in the global climate system during this century may substantially alter the regime of N 2 O emission from terrestrial ecosystems. They also imply that the interactive effect among global change factors may significantly affect N 2 O flux, needing more investigations through field experiments.

Description: Simulation of anthropogenic CO 2 uptake in the CCSM3.1 ocean circulation-biogeochemical model: comparison with data-based estimates Biogeosciences Discussions, 8, 10895-10933, 2011 Author(s): S. Wang, J. K. Moore, F. W. Primeau, and S. Khatiwala The global ocean has taken up a large fraction of the CO 2 released by human activities since the industrial revolution. Quantifying the oceanic anthropogenic carbon (C ant ) inventory and its variability is important for predicting the future global carbon cycle. The detailed comparison of data-based and model-based estimates is essential for the validation and continued improvement of our prediction capabilities. So far, three global estimates of oceanic C ant inventory that are "data-based" and independent of global ocean circulation models have been produced: one based on the ΔC * method, and two are based on reconstructions of the Green function for the surface-to-interior transport, the TTD method and the maximum entropy inversion method (KPH). The KPH method, in particular, is capable of reconstructing the history of C ant inventory through the industrial era. In the present study we use forward model simulations of the Community Climate System Model (CCSM3.1) to estimate the C ant inventory and compare the results with the data-based estimates. We also use the simulations to test several assumptions of the KPH method, including the assumption of constant climate and circulation, which is common to all the data-based estimates. Though the integrated estimates of global C ant inventories are consistent with each other, the regional estimates show discrepancies up to 50 %. The CCSM3 model underestimates the total C ant inventory, in part due to weak mixing and ventilation in the North Atlantic and Southern Ocean. Analyses of different simulation results suggest that key assumptions about ocean circulation and air-sea disequilibrium in the KPH method are generally valid on the global scale, but may introduce significant errors in C ant estimates on regional scales. The KPH method should also be used with caution when predicting future oceanic anthropogenic carbon uptake.

Description: Role of land surface processes and diffuse/direct radiation partitioning in simulating the European climate Biogeosciences Discussions, 8, 11601-11630, 2011 Author(s): E. L. Davin and S. I. Seneviratne The influence of land processes and in particular of diffuse/direct radiation partitioning on surface fluxes and associated regional-scale climate feedbacks is investigated. ERA-40 driven simulations over Europe are performed using the COSMO-CLM 2 Regional Climate Model (RCM). Two alternative Land Surface Models (LSMs), a 2nd generation LSM (TERRA_ML) and a more advanced 3rd generation LSM (Community Land Model version 3.5), and two versions of the atmospheric component are tested, as well as a revised coupling procedure allowing for variations in diffuse/direct light partitioning at the surface, and their accounting by the land surface component. Overall, the RCM performance for various variables (e.g., surface fluxes, temperature and precipitation) is improved when using the more advanced 3rd generation LSM. These improvements are of the same order of magnitude as those arising from a new version of the atmospheric component, demonstrating the benefit of using a realistic representation of land surface processes for regional climate simulations. Taking into account variability in diffuse/direct light partitioning at the surface further improves the model performance in terms of summer temperature variability at the monthly and daily time scales. Comparisons with observations show that the RCM realistically captures temporal variations in diffuse/direct light partitioning as well as the evapotranspiration sensitivity to these variations. Our results suggest that a modest but consistent fraction (up to 3 %) of the overall variability in summer temperature can be explained by variations in the diffuse to direct ratio.

Description: Rapid carbon cycling in the oligotrophic ocean Biogeosciences Discussions, 8, 11661-11687, 2011 Author(s): C. M. Duarte and S. Agustí The dynamics of organic carbon production, release and bacterial use was examined across a range of communities spanning from highly oligotrophic ones in the Subtropical Atlantic Ocean, mesotrophic ones in the Mediterranean Sea and productive ones in the Northern African upwelling and the Southern Ocean. A comparative analysis of experiments examining total and particulate organic carbon production across a range of time scales (15 min to 24 h) for 20 communities with contrasting phytoplankton cell status, as assessed by cell lysis rates, and the use of a simple inverse model was used to resolve patterns of carbon flow in the microbial food web. Communities in productive ocean waters accumulated organic carbon over hourly time scales, whereas only a small fraction of net primary production accumulated in communities from oligotrophic waters. These communities supported high phytoplankton cell lysis rates leading to a rapid flux of organic carbon to bacteria, which had high affinity for phytoplankton-derived carbon, much of which was rapidly respired. Conventional assessments of primary production in the oligotrophic ocean severely underestimate net phytoplankton production, as carbon flow in microbial communities from oligotrophic ocean waters occurs within short (minutes) time scales. This explains difficulties to reconcile estimates of primary production with independent estimates of carbon use by bacteria in oligotrophic marine ecosystems.

Description: Spatial variations of nitrogen trace gas emissions from tropical mountain forests in Nyungwe, Rwanda Biogeosciences Discussions, 8, 11631-11660, 2011 Author(s): N. Gharahi Ghehi, C. Werner, L. Cizungu Ntaboba, J. J. Mbonigaba Muhinda, E. Van Ranst, K. Butterbach-Bahl, R. Kiese, and P. Boeckx Globally, tropical forest soils represent the second largest source of N 2 O and NO. However, there is still considerable uncertainty on the spatial variability and soil properties controlling N trace gas emission. To investigate how soil properties affect N 2 O and NO emission, we carried out an incubation experiment with soils from 31 locations in the Nyungwe tropical mountain forest in southwestern Rwanda. All soils were incubated at three different moisture levels (50, 70 and 90% water filled pore space (WFPS)) at 17 °C. Nitrous oxide emission varied between 4.5 and 400 μg N m −2 h −1 , while NO emission varied from 6.6 to 265 μg N m −2 h −1 . Mean N 2 O emission at different moisture levels was 46.5 ± 11.1 (50% WFPS), 71.7 ± 11.5 (70% WFPS) and 98.8 ± 16.4 (90% WFPS) μg N m −2 h −1 , while mean NO emission was 69.3 ± 9.3 (50% WFPS), 47.1 ± 5.8 (70% WFPS) and 36.1 ± 4.2 (90% WFPS) μg N m −2 h −1 . The latter suggests that climate (i.e. dry vs. wet season) controls N 2 O and NO emissions. Positive correlations with soil carbon and nitrogen indicate a biological control over N 2 O and NO production. But interestingly N 2 O and NO emissions also showed a negative correlation (only N 2 O) with soil pH and a positive correlation with free iron. The latter suggest that chemo-denitrification might, at least for N 2 O, be an important production pathway. In conclusion improved understanding and process based modeling of N trace gas emission from tropical forests will not only benefit from better spatial explicit trace gas emission and basic soil property monitoring, but also by differentiating between biological and chemical pathways for N trace gas formation.

Description: Effects of seawater p CO 2 changes on the calcifying fluid of scleractinian corals Biogeosciences Discussions, 9, 2655-2689, 2012 Author(s): S. Hohn and A. Merico Rising atmospheric CO 2 concentrations due to anthropogenic emissions induce changes in the ocean carbonate chemistry and a drop in ocean pH. This acidification process is expected to harm calcifying organisms like coccolithophores, molluscs, echinoderms, and corals. A severe decline in coral abundance is, for example, expected by the end of this century with associated disastrous effects on reef ecosystems. Despite the growing importance of the topic, little progress has been made with respect to modelling the impact of acidification on coral calcification. Here we present a model for a coral polyp that simulates the carbonate system in four different compartments: the seawater, the polyp tissue, the coelenteron, and the calicoblastic layer. Precipitation of calcium carbonate takes place in the metabolically controlled calicoblastic layer beneath the polyp tissue. The model is adjusted to a state of activity as observed by direct microsensor measurements in the calcifying fluid. Simulated CO 2 perturbation experiments reveal decreasing calcification rates under elevated p CO 2 despite strong metabolic control of the calcifying fluid. Diffusion of CO 2 through the tissue into the calicoblastic layer increases with increasing seawater p CO 2 leading to decreased aragonite saturation in the calcifying fluid of the coral polyp. Our modelling study provides important insights into the complexity of the calcification process at the organism level and helps to quantify the effect of ocean acidification on corals.

Description: The role of the seagrass Posidonia oceanica in the cycling of trace elements Biogeosciences Discussions, 9, 2623-2653, 2012 Author(s): C. Sanz-Lázaro, P. Malea, E. T. Apostolaki, I. Kalantzi, A. Marín, and I. Karakassis The aim of this work was to study the role of the seagrass Posidonia oceanica on the cycling of a wide set of trace elements (Ag, As, Ba, Bi, Cd, Co, Cr, Cs, Cu, Fe, Ga, Li, Mn, Ni, Pb, Rb, Sr, Tl, V and Zn). We measured the concentration of these trace elements in the different compartments of P. oceanica (leaves, rhizomes, roots and epibiota) in a non-polluted seagrass meadow representative of the Mediterranean and calculated the annual budget from a mass balance. We provide novel data on accumulation dynamics of many trace elements in P. oceanica compartments and demonstrate that trace element accumulation patterns are mainly determined by plant compartment rather than by temporal variability. Epibiota was the compartment which showed the greatest concentrations for most trace elements. Thus, they constitute a key compartment when estimating trace element transfer to higher trophic levels by P. oceanica . For most trace elements, translocation seemed to be low and acropetal. Zn, Cd, Sr and Rb were the trace elements that showed the highest release rate through decomposition of plant detritus, while Cs, Tl and Bi the lowest. P. oceanica acts as a sink of potentially toxic trace elements (Ni, Cr, As and Ag), which can be sequestered, decreasing their bioavailability. P. oceanica may have a relevant role in the cycling of trace elements in the Mediterranean.

Description: Direct observations of diel biological CO 2 fixation in the oceans Biogeosciences Discussions, 9, 2153-2168, 2012 Author(s): H. Thomas, S. E. Craig, B. J. W. Greenan, W. Burt, G. J. Herndl, S. Higginson, L. Salt, E. H. Shadwick, and J. Urrego-Blanco Much of the variability in the surface ocean's carbon cycle can be attributed to the availability of sunlight, through processes such as heat fluxes and photosynthesis, which regulate over a wide range of time scales. The critical processes occurring on timescales of a day or less, however, have undergone few investigations, and most of these have been limited to a time span of several days to months, or exceptionally, for longer periods. Optical methods have helped to infer short-term biological variability, however corresponding investigations of the oceanic CO 2 system are lacking. We employ high-frequency CO 2 and optical observations covering the full seasonal cycle on the Scotian Shelf, Northwestern Atlantic Ocean, in order to unravel diel periodicity of the surface ocean carbon cycle and its effects on annual budgets. Significant diel periodicity occurs only if the water column is sufficiently stable as observed during seasonal warming. During that time biological CO 2 drawdown, or net community production (NCP), is delayed for several hours relative to the onset of photosynthetically available radiation (PAR), due to diel cycles in chlorophyll- a concentration and to grazing, both of which, we suggest, inhibit NCP in the early morning hours. In summer, NCP decreases by more than 90 %, coinciding with the seasonal minimum of the mixed layer depth and resulting in the disappearance of the diel CO 2 periodicity in the surface waters.

Description: Contribution of flowering trees to urban atmospheric biogenic volatile organic compound emissions Biogeosciences Discussions, 9, 3145-3172, 2012 Author(s): R. Baghi, D. Helmig, A. Guenther, T. Duhl, and R. Daly Emissions of biogenic volatile organic compounds (BVOC) from urban trees during and after blooming were measured during spring and early summer 2009 in Boulder, Colorado. Air samples were collected onto solid adsorbent cartridges from branch enclosures on the tree species crabapple, horse chestnut, honey locust, and hawthorn. These species constitute ~65 % of the insect-pollinated fraction of the flowering tree canopy (excluding catkin-producing trees) from the street area managed by the City of Boulder. Samples were analyzed for C 10 –C 15 BVOC by thermal desorption and gas chromatography coupled to a flame ionization detector and a mass spectrometer (GC/FID/MS). Identified emissions and emission rates from these four tree species during the flowering phase were found to vary over a wide range. Monoterpene emissions were identified for honey locust, horse chestnut and hawthorn. Sesquiterpene emissions were observed in horse chestnut and hawthorn samples. Crabapple flowers were found to emit significant amounts of benzyl alcohol and benzaldehyde. Floral BVOC emissions increased with temperature, generally exhibiting exponential temperature dependence. Changes in BVOC speciation during and after the flowering period were observed for every tree studied. Emission rates were significantly higher during the blooming compared to the vegetative state for crabapple and honey locust. Total normalized (30 °C) monoterpene emissions from honey locust were higher during flowering (5.26 μg Cg −1 h −1 ) than after flowering (1.23 μg Cg −1 h −1 ). The total normalized BVOC emission rate from crabapple (93 μg Cg −1 h −1 ) during the flowering period is of the same order as isoprene emissions from oak trees, which are among the highest BVOC emissions observed from plants to date. These findings illustrate that during the relatively brief springtime flowering period, floral emissions constitute by far the most significant contribution to the BVOC flux from these tree species, some of which are leafless at this time. Experimental results were integrated into the MEGAN biogenic emission model and simulations were performed to estimate the contribution of floral BVOC emissions to the total urban BVOC flux during the spring flowering period. The floral BVOC emitted during this three-month simulation are equivalent to 11 % of the cumulative monoterpene flux for the Boulder urban area.

Description: Contributions of ectomycorrhizal fungal mats to forest soil respiration Biogeosciences Discussions, 9, 1635-1666, 2012 Author(s): C. L. Phillips, L. A. Kluber, J. P. Martin, B. A. Caldwell, and B. J. Bond Distinct aggregations of fungal hyphae and rhizomorphs, or "mats" formed by some genera of ectomycorrhizal (EcM) fungi are common features of soils in coniferous forests of the Pacific Northwest. We measured in situ respiration rates of Piloderma mats and neighboring non-mat soils in an old-growth Douglas-fir forest in Western Oregon to investigate whether there was an incremental increase in respiration from mat soils, and to estimate mat contributions to total soil respiration. We found that areas where Piloderma mats colonized the organic horizon often had higher soil surface flux than non-mats, with the incremental increase in respiration averaging 16 % across two growing seasons. Both soil physical factors and biochemistry were related to the higher surface flux of mat soils. When air-filled pore space was low (high soil moisture), soil CO 2 production was concentrated into near-surface soil horizons where mats tend to colonize, resulting in greater apparent differences in respiration between mat and non-mat soils. Respiration rates were also correlated with the activity of chitin-degrading soil enzymes. This suggests that the elevated activity of fungal mats may be related to consumption or turnover of chitinous fungal cell-wall materials. We found Piloderma mats present across 57 % of the soil surface in the study area, and use this value to estimate a respiratory contribution from mats at the stand-scale of about 9 % of total soil respiration. The activity of EcM mats, which includes both EcM fungi and microbial associates, was estimated to constitute a substantial portion of total soil respiration in this old-growth Douglas-fir forest.

Description: Remote sensing-based estimation of gross primary production in a subalpine grassland Biogeosciences Discussions, 9, 1711-1758, 2012 Author(s): M. Rossini, S. Cogliati, M. Meroni, M. Migliavacca, M. Galvagno, L. Busetto, E. Cremonese, T. Julitta, C. Siniscalco, U. Morra di Cella, and R. Colombo This study investigates the performances in a terrestrial ecosystem of gross primary production (GPP) estimation of a suite of spectral vegetation indexes (VIs) that can be computed from currently orbiting platforms. Vegetation indexes were computed from near-surface field spectroscopy measurements collected using an automatic system designed for high temporal frequency acquisition of spectral measurements in the visible near-infrared region. Spectral observations were collected for two consecutive years in Italy in a subalpine grassland equipped with an Eddy Covariance (EC) flux tower which provides continuous measurements of net ecosystem carbon dioxide (CO 2 ) exchange (NEE) and the derived GPP. Different VIs were calculated based on ESA-MERIS and NASA-MODIS spectral bands and correlated with biophysical (Leaf Area Index, LAI; fraction of photosynthetically active radiation intercepted by green vegetation, f IPAR g ), biochemical (chlorophyll concentration) and ecophysiological (green light-use efficiency, LUE g ) canopy variables. In this study, the normalized difference vegetation index (NDVI) showed better correlations with LAI and f PAR g ( r = 0.90 and 0.95, respectively), the MERIS terrestrial chlorophyll index (MTCI) with leaf chlorophyll content ( r = 0.91) and the Photochemical Reflectance Index (PRI 551 ), computed as ( R 531 − R 551 )/( R 531 + R 551 ) with LUE g ( r = 0.64). Subsequently, these VIs were used to estimate GPP using different modelling solutions based on the light-use efficiency model describing the GPP as driven by the photosynthetically active radiation absorbed by green vegetation (APAR g ) and by the efficiency (ε) with which plants use the absorbed radiation to fix carbon via photosynthesis. Results show that GPP can be successfully modelled with a combination of VIs and meteorological data or VIs only. Vegetation indexes designed to be more sensitive to chlorophyll content explained most of the variability in GPP in the ecosystem investigated, characterized by a strong seasonal dynamic of GPP. Accuracy in GPP estimation slightly improves when taking into account high frequency modulations of GPP driven by incident PAR or modelling LUE g with the PRI in model formulation. Similar results were obtained for both measured daily VIs and VIs obtained as 16-day composite time series and then downscaled from the compositing period to daily scale (resampled data). However, the use of resampled data rather than measured daily input data decreases the accuracy of the total GPP estimation on an annual basis.

Description: Soil organic carbon storage changes in coastal wetlands of the modern Yellow River Delta from 2000 to 2009 Biogeosciences Discussions, 9, 1759-1779, 2012 Author(s): J. Yu, Y. Wang, Y. Li, H. Dong, D. Zhou, G. Han, H. Wu, G. Wang, P. Mao, and Y. Gao Soil carbon sequestration plays an essential role in mitigating CO 2 increases and the subsequently global greenhouse effect. The storages and dynamics of soil organic carbon (SOC) of 0–30 cm soil depth in different landscape types including beaches, reservoir and pond, reed wetland, forest wetland, bush wetland, farmland, building land, bare land (severe saline land) and salt field in the modern Yellow River Delta (YRD), were studied based on the data of the regional survey and laboratory analysis. The landscape types were classified by the interpretation of remote sensing images of 2000 and 2009, which was calibrated by field survey results. The results revealed an increase of 10.59 km 2 in the modem YRD area from 2000 to 2009. The SOC density varied ranging from 0.73 kg m −2 to 21.60 kg m −2 at depth of 30 cm. There were ~3.97 × 10 6 t and 3.98 × 10 6 t SOC stored in the YRD in 2000 and 2009, respectively. The SOC storages changed greatly in beaches, bush wetland, farm land and salt field which were affected dominantly by anthropogenic activities. The area of the YRD increased greatly within 10 yr, however, the small increase of SOC storage in the region was observed due to landscape changes, indicating that the modern YRD was a potential carbon sink and anthropogenic activity was a key factor for SOC change.

Description: Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies Biogeosciences Discussions, 9, 1781-1792, 2012 Author(s): C. J. M. Hoppe, G. Langer, S. D. Rokitta, D. A. Wolf-Gladrow, and B. Rost The growing field of ocean acidification research is concerned with the investigation of organisms' responses to increasing p CO 2 values. One important approach in this context is culture work using seawater with adjusted CO 2 levels. As aqueous p CO 2 is difficult to measure directly in small scale experiments, it is generally calculated from two other measured parameters of the carbonate system (often A T , C T or pH). Unfortunately, the overall uncertainties of measured and subsequently calculated values are often unknown. Especially under high p CO 2 , this can become a severe problem with respect to the interpretation of physiological and ecological data. In the few datasets from ocean acidification research where all three of these parameters were measured, p CO 2 values calculated from A T and C T are typically about 30 % lower (i.e. ~300 μatm at a target p CO 2 of 1000 μatm) than those calculated from A T and pH or C T and pH. This study presents and discusses these discrepancies as well as likely consequences for the ocean acidification community. Until this problem is solved, one has to consider that calculated parameters of the carbonate system (e.g. p CO 2 , calcite saturation state) may not be comparable between studies, and that this may have important implications for the interpretation of CO 2 perturbation experiments.

Description: Riverine influence on the tropical Atlantic Ocean biogeochemistry Biogeosciences Discussions, 9, 1945-1969, 2012 Author(s): L. Cotrim da Cunha and E. T. Buitenhuis We assess the role of riverine inputs of N, Si, Fe, organic and inorganic C in the tropical Atlantic Ocean using a global ocean biogeochemistry model. We use two sensitivity tests to investigate the role of the western (South American Rivers) and eastern (African Rivers) riverine nutrient inputs on the tropical Atlantic Ocean biogeochemistry (between 20° S–20° N and 70° W–20°). Increased nutrient availability from river inputs in this area (compared to an extreme scenario with no river nutrients) leads to an increase in 14 % (0.7 Pg C a −1 ) in open ocean primary production (PP), and 21 % (0.2 Pg C a −1 ) in coastal ocean PP. We estimate very modest increases in open and coastal ocean export production and sea-air CO 2 fluxes. Results suggest that in the tropical Atlantic Ocean, the large riverine nutrient inputs on the western side have a larger impact on primary production and sea-air CO 2 exchanges. On the other hand, African river inputs, although smaller than South American inputs, have larger impact on the coastal and open tropical Atlantic Ocean export production. This is probably due to a combination of nutrient trapping in upwelling areas off the Congo River outflow, and differences in delivered nutrient ratios leading to alleviation in limitation conditions mainly for diatoms.

Description: Hydrologic control of the oxygen isotope ratio of ecosystem respiration in a semi-arid woodland Biogeosciences Discussions, 10, 1-48, 2013 Author(s): J. H. Shim, H. H. Powers, C. W. Meyer, A. Knohl, T. E. Dawson, W. J. Riley, W. T. Pockman, and N. McDowell We conducted high frequency measurements of the δ 18 O value of atmospheric CO 2 from a juniper ( Juniperus monosperma ) woodland in New Mexico, USA, over a four-year period to investigate climatic and physiological regulation of the δ 18 O value of ecosystem respiration ( δ R ). Rain pulses reset δ R with the dominant water source isotope composition, followed by progressive enrichment of δ R . Transpiration ( E T ) was significantly related to post-pulse δ R enrichment because leaf water δ 18 O value showed strong enrichment with increasing vapor pressure deficit that occurs following rain. Post-pulse δ R enrichment was correlated with both E T and the ratio of E T to soil evaporation ( E T / E S ). In contrast, soil water δ 18 O value was relatively stable and δ R enrichment was not correlated with E S . Model simulations captured the large post-pulse δ R enrichments only when the offset between xylem and leaf water δ 18 O value was modeled explicitly and when a gross flux model for CO 2 retro-diffusion was included. Drought impacts δ R through the balance between evaporative demand, which enriches δ R , and low soil moisture availability, which attenuates δ R enrichment through reduced E T . The net result, observed throughout all four years of our study, was a negative correlation of post-precipitation δ R enrichment with increasing drought.

Description: Coral Patch seamount (NE Atlantic) – a sedimentological and macrofaunal reconnaissance based on video and hydroacoustic surveys Biogeosciences Discussions, 9, 18707-18753, 2012 Author(s): C. Wienberg, P. Wintersteller, L. Beuck, and D. Hebbeln The present study provides new knowledge about the so far largely unexplored Coral Patch seamount which is located in the NE Atlantic Ocean half-way between the Iberian Peninsula and Madeira. For the first time a detailed hydroacoustic mapping (MBES) in conjunction with video surveys (ROV, camera sled) were performed to describe the sedimentological and biological characteristics of this sub-elliptical ENE-WSW elongated seamount. Video observations were restricted to the south-western summit area of Coral Patch seamount (area: ~ 8 km 2 , water depth: 560–760 m) and revealed that this part of the summit is dominated by exposed hard substrate, whereas soft sediment is just a minor substrate component. Although exposed hardgrounds are dominant for this summit area, and thus, offer suitable habitat for settlement by benthic organisms, the macrofauna shows rather low abundance and diversity. In particular, scleractinian framework-building cold-water corals are apparently rare with very few isolated and small-sized live occurrences of the species Lophelia pertusa and Madrepora oculata . In contrast, dead coral framework and coral rubble are more frequent pointing to a higher abundance of cold-water corals on Coral Patch during the recent past. This is even supported by the observation of fishing lines that got entangled with rather fresh-looking coral frameworks. Overall, long lines and various species of commercially important fish were frequently observed emphasising the potential of Coral Patch as an important target for fisheries that may have impacted the entire benthic community. Hydroacoustic seabed classification covered the entire summit of Coral Patch and its northern and southern flanks (area: 560 km 2 ; water depth: 560–2660 m) and revealed extended areas dominated by mixed and soft sediments at the northern flank and to a minor degree at its easternmost summit and southern flank. Nevertheless, also these data predict most of the summit area to be dominated by exposed bedrock which would offer suitable habitat for benthic organisms. By comparing the locally restricted video observations and the broad-scale monitoring of a much larger and deeper seafloor area as derived by hydroacoustic seabed classification, it becomes obvious that habitat information obtained by in situ sampling may provide a rather scattered pattern about the entire seamount ecosystem. Solely with a combination of both methods, a satisfactory approach to describe the diverse characteristics of a seamount ecosystem can be derived which is in turn indispensable for future scientific monitoring campaigns as well as management and conservation purposes.

Description: High-resolution measurements of atmospheric molecular hydrogen and its isotopic composition at the West African coast of Mauritania Biogeosciences Discussions, 9, 18799-18829, 2012 Author(s): S. Walter, A. Kock, and T. Röckmann Oceans are a net source of molecular hydrogen (N 2 ) to the atmosphere, where nitrogen (N 2 ) fixation is assumed to be the main biological production pathway besides photochemical production from organic material. The sources can be distinguished using isotope measurements because of clearly differing isotopic signatures of the produced hydrogen. Here we present the first ship-borne measurements of atmospheric molecular H 2 mixing ratio and isotopic composition at the West African coast of Mauritania (16–25° W, 17–24° N). This area is one of the biologically most active regions of the world's oceans with seasonal upwelling events and characterized by strongly differing hydrographical/biological properties and phytoplankton community structures. The aim of this study was to identify areas of H 2 production and distinguish H 2 sources by isotopic signatures of atmospheric H 2 . Besides this a diurnal cycle of atmospheric H 2 was investigated. For this more than 100 air samples were taken during two cruises in February 2007 and 2008, respectively. During both cruises a transect from the Cape Verde Island towards the Mauritanian Coast was sampled. In 2007 additionally four days were sampled with a high resolution of one sample per hour. Our results clearly indicate the influence of local sources and suggest the Banc d'Arguin as a pool for precursors for photochemical H 2 production, whereas N 2 fixation could not be identified as a H 2 source during these two cruises. With our experimental setup we could demonstrate that variability in diurnal cycles is probably influenced and biased by released precursors for photochemical H 2 production and the origin of air masses. This means for further investigations that just measuring the mixing ratio of H 2 is insufficient to explain the variability of a diurnal cycle and support is needed, e.g. by isotopic measurements. However, measurements of H 2 mixing ratios, which are easy to conduct online during ship cruises could be a helpful tool to easily identify production areas of biological precursors such as VOC's for further investigations.

Description: Physical transport properties of marine microplastic pollution Biogeosciences Discussions, 9, 18755-18798, 2012 Author(s): A. Ballent, A. Purser, P. de Jesus Mendes, S. Pando, and L. Thomsen Given the complexity of quantitative collection, knowledge of the distribution of microplastic pollution in many regions of the world ocean is patchy, both spatially and temporally, especially for the subsurface environment. However, with knowledge of typical hydrodynamic behavior of waste plastic material, models predicting the dispersal of pelagic and benthic plastics from land sources into the ocean are possible. Here we investigate three aspects of plastic distribution and transport in European waters. Firstly, we assess patterns in the distribution of plastics found in fluvial strandlines of the North Sea and how distribution may be related to flow velocities and distance from source. Second, we model transport of non-buoyant preproduction pellets in the Nazaré Canyon of Portugal using the MOHID system after assessing the density, settling velocity, critical and depositional shear stress characteristics of such waste plastics. Thirdly, we investigate the effect of surface turbulences and high pressures on a range of marine plastic debris categories (various densities, degradation states and shapes tested) in an experimental water column simulator tank and pressure laboratory. Plastics deposited on North Sea strandlines varied greatly spatially, as a function of material composition and distance from source. Model outputs indicated that such dense production pellets are likely transported up and down canyon as a function of tidal forces, with only very minor net down canyon movement. Behaviour of plastic fragments under turbulence varied greatly, with the dimensions of the material, as well as density, playing major determining roles. Pressure was shown to affect hydrodynamic behaviours of only low density foam plastics at pressures ≥ 60 bar.

Description: Biological soil crusts on initial soils: organic carbon dynamics and chemistry under temperate climatic conditions Biogeosciences Discussions, 10, 851-894, 2013 Author(s): A. Dümig, M. Veste, F. Hagedorn, T. Fischer, P. Lange, R. Spröte, and I. Kögel-Knabner Numerous studies have been carried out on the community structure and diversity of biological soil crusts (BSCs) as well as their important functions on ecosystem processes. However, the amount of BSC-derived organic carbon (OC) input into soils and its chemical composition under natural conditions has rarely been investigated. In this study, different development stages of algae- and moss-dominated BSCs were investigated on a~natural (

Description: Incorporating genomic information and predicting gene expression patterns in a simplified biogeochemical model Biogeosciences Discussions, 10, 815-850, 2013 Author(s): P. Wang, A. B. Burd, M. A. Moran, R. R. Hood, V. J. Coles, and P. L. Yager We present results from a new marine plankton model that combines selective biogeochemical processes with genetic information. The model allows for phytoplankton to adapt to a changing environment by invoking different utilization pathways for acquisition of nutrients (nitrogen and phosphorus) in response to concentration changes. The simulations use simplified environmental conditions represented by a continuously stirred tank reactor, which is populated by 96 different types of phytoplankton that differ in their physiological characteristics and nutrient uptake/metabolism genes. The results show that the simulated phytoplankton community structure is conceptually consistent with observed regional and global phytoplankton biogeography, the genome content from the dominant types of phytoplankton reflects the imposed environmental constraints, and the transcription of the gene clusters is qualitatively simulated according to the environmental changes. The model shows the feasibility of including genomic knowledge into a biogeochemical model and is suited to understanding and predicting changes in marine microbial community structure and function, and to simulating the biological response to rapid environmental changes.

Description: A~model for variable phytoplankton stoichiometry based on cell protein regulation Biogeosciences Discussions, 10, 3241-3279, 2013 Author(s): J. A. Bonachela, S. D. Allison, A. C. Martiny, and S. A. Levin The elemental ratios of marine phytoplankton emerge from complex interactions between the biotic and abiotic components of the ocean, and reflect the plastic response of individuals to changes in their environment. The stoichiometry of phytoplankton is, thus, dynamic and dependent on the physiological state of the cell. We present a theoretical model for the dynamics of the carbon, nitrogen and phosphorus contents of a phytoplankton population. By representing the regulatory processes controlling nutrient uptake, and focusing on the relation between nutrient content and protein synthesis, our model qualitatively replicates existing experimental observations for nutrient content and ratios. The population described by our model takes up nutrients in proportions that match the input ratios for a broad range of growth conditions. In addition, there are two zones of single-nutrient limitation separated by a wide zone of co-limitation. Within the co-limitation zone, a single point can be identified where nutrients are supplied in an optimal ratio. The existence of a wide co-limitation zone affects the standard picture for species competing for nitrogen and phosphorus, which shows here a much richer pattern. However, additional comprehensive laboratory experiments are needed to test our predictions. Our model contributes to the understanding of the global cycles of oceanic nitrogen and phosphorus, as well as the elemental ratios of these nutrients in phytoplankton populations.

Description: Seasonal signatures in SFG vibrational spectra of the sea surface nanolayer at Boknis Eck Time Series Station (SW Baltic Sea) Biogeosciences Discussions, 10, 3177-3201, 2013 Author(s): K. Laß, H. W. Bange, and G. Friedrichs The very thin sea surface nanolayer on top of the sea surface microlayer, sometimes just one monomolecular layer thick, forms the interface between ocean and atmosphere. Due to the small dimension and tiny amount of substance, knowledge about the development of the layer in the course of the year is scarce. In this work, the sea surface nanolayer at Boknis Eck Time Series Station (BE), southwestern Baltic Sea, has been investigated over a period of three and a half years. Surface water samples were taken monthly by screen sampling and were analyzed in terms of organic content and composition by sum frequency generation spectroscopy, which is specifically sensitive to interfacial layers. A yearly periodicity has been observed with a pronounced abundance of sea surface nanolayer material (such as carbohydrate-rich material) during the summer months. On the basis of our results we conclude that the abundance of organic material in the nanolayer at Boknis Eck is not directly related to phytoplankton abundance. We suggest that indeed sloppy feeding of zooplankton together with photochemical and/or microbial processing of organic precursor compounds are responsible for the pronounced seasonality.

Description: Food quality regulates the metabolism and reproduction of Temora longicornis Biogeosciences Discussions, 10, 3203-3239, 2013 Author(s): R. Nobili, C. Robinson, E. Buitenhuis, and C. Castellani A laboratory study was undertaken to determine the effect of food quality on feeding, respiration, reproduction and the resulting carbon budget of Temora longicornis . The stoichiometric ratios N : P, C : N and C : P of Rhodomonas salina were used as indicators of food quality. R. salina was grown in media with different inorganic nutrient concentrations to produce food for T. longicornis with particulate organic N : P ratios ranging from 10 : 1 to 23 : 1. Feeding rate was not affected by food quality. Maximum respiration (R), egg production rate (EPR), assimilation efficiency (AE), gross growth efficiency (GGE) and metabolic increment (MI) occurred when T. longicornis was fed on phytoplankton with a food quality of 16N : 1P. EPR, GGE and AE also decreased with decreasing C : N ratio and the energy required to produce eggs (CoE) decreased with decreasing N : P ratio, indicative of nitrogen-dependent production. These data suggest that an algal composition of 16N : 1P defines the Threshold Elemental Ratio (TER) and is the optimum diet for T. longicornis . The variations in metabolic rates and the resulting carbon budget are proportional to the quality of food ingested. GGE was negatively affected at dietary ratios above and below 16N : 1P, which in the natural environment could lead to a decline in species biomass with detrimental consequences for fisheries and carbon export. Field data show that phytoplankton organic N : P ratios can change on decadal timescales, and that an increase in the food N : P ratio can co-occur with a shift to smaller sized zooplankton and a change in species abundance. Further research is required to assess how much of the change in zooplankton community structure and activity can be attributed to changes in food quality, rather than to changes in temperature and food quantity.

Description: Microhabitat and shrimp abundance within a Norwegian cold-water coral ecosystem Biogeosciences Discussions, 10, 3365-3396, 2013 Author(s): A. Purser, J. Ontrup, T. Schoening, L. Thomsen, R. Tong, V. Unnithan, and T. W. Nattkemper Cold-water coral reefs are highly heterogeneous ecosystems comprising of a range of diverse microhabitats. In a typical European cold-water coral reef various biogenic habitats (live colonies of locally common coral species such as Lophelia pertusa, Paragorgia arborea and Primnoa resedaeformis , dead coral structure, coral rubble) may be surrounded and intermixed with non-biogenic habitats (soft sediment, hardground, gravel/pebbles, steep walls). To date, studies of distribution of sessile fauna across these microhabitats have been more numerous than those investigating mobile fauna distribution. In this study we quantified shrimp densities associated with key CWC habitat categories at the Røst reef, Norway, by analysing image data collected by towed video sled. We also investigated shrimp distribution patterns on the local scale (

Description: Climate change and ocean acidification impacts on lower trophic levels and the export of organic carbon to the deep ocean Biogeosciences Discussions, 10, 3455-3522, 2013 Author(s): A. Yool, E. E. Popova, A. C. Coward, D. Bernie, and T. R. Anderson Most future projections forecast significant and ongoing climate change during the 21st century, but with the severity of impacts dependent on efforts to restrain or reorganise human activity to limit carbon dioxide (CO 2 ) emissions. A major sink for atmospheric CO 2 , and a key source of biological resources, the World Ocean is widely anticipated to undergo profound physical and – via ocean acidification – chemical changes as direct and indirect results of these emissions. Given strong biophysical coupling, the marine biota is also expected to experience strong changes in response to this anthropogenic forcing. Here we examine the large-scale response of ocean biogeochemistry to climate and acidification impacts during the 21st century for Representative Concentration Pathways (RCPs) 2.6 and 8.5 using an intermediate complexity global ecosystem model, Medusa–2.0. The primary impact of future change lies in stratification-led declines in the availability of key nutrients in surface waters, which in turn leads to a global decrease (1990s vs. 2090s) in ocean productivity (−6.3%). This impact has knock-on consequences for the abundances of the low trophic level biogeochemical actors modelled by Medusa–2.0 (−5.8%), and these would be expected to similarly impact higher trophic level elements such as fisheries. Related impacts are found in the flux of organic material to seafloor communities (−40.7% at 1000 m), and in the volume of ocean suboxic zones (+12.5%). A sensitivity analysis removing an acidification feedback on calcification finds that change in this process significantly impacts benthic communities, suggesting that a better understanding of the OA-sensitivity of calcifying organisms, and their role in ballasting sinking organic carbon, may significantly improve forecasting of these ecosystems. For all processes, there is geographical variability in change, and changes are much more pronounced under RCP 8.5 than the RCP 2.6 scenario.

Description: Controlled experimental aquarium system for multi-stressor investigation: carbonate chemistry, oxygen saturation, and temperature Biogeosciences Discussions, 10, 3431-3453, 2013 Author(s): E. E. Bockmon, C. A. Frieder, M. O. Navarro, L. A. White-Kershek, and A. G. Dickson As the field of ocean acidification has grown, researchers have increasingly turned to laboratory experiments to understand the impacts of increased CO 2 on marine organisms. However, other changes such as ocean warming and deoxygenation are occurring concurrently with the increasing CO 2 concentrations, complicating the anthropogenic impact on organisms. This experimental aquarium design allows for independent regulation of CO 2 concentration, O 2 levels, and temperature in a controlled environment to study the impacts of multiple stressors. The system has the flexibility for a wide range of treatment chemistry, seawater volumes, and study organisms. Control of the seawater chemistry is achieved by equilibration of a chosen gas mixture with seawater using a Liqui-Cel ® membrane contactor. Included as examples, two experiments performed using the system have shown control of CO 2 between approximately 500–1400 μatm and O 2 from 80–240 μmol kg −1 . Temperature has been maintained to 0.5 °C or better in the range of 10–17 °C. On a weeklong timescale, control results in variability in pH of less than 0.007 pH units and in oxygen concentration less than 3.5 μmol kg −1 . Longer experiments, over a month, have been completed with reasonable but lessened control, still better than 0.08 pH units and 13 μmol kg −1 O 2 . The ability to study the impacts of multiple stressors in the laboratory simultaneously, as well as independently, will be an important part of understanding the response of marine organisms to a high-CO 2 world.

Description: Mangroves facing climate change: landward migration potential in response to projected scenarios of sea level rise Biogeosciences Discussions, 10, 3523-3558, 2013 Author(s): D. Di Nitto, G. Neukermans, N. Koedam, H. Defever, F. Pattyn, J. G. Kairo, and F. Dahdouh-Guebas Mangrove forests prominently occupy an intertidal boundary position where the effects of sea level rise will be fast and well visible. This study in East Africa (Gazi Bay, Kenya) addresses the question whether mangroves can be resilient to a rise in sea level by focusing on their potential to migrate towards landwards areas. The combinatory analysis between remote sensing, DGPS-based ground truth and digital terrain models (DTM) unveils how real vegetation assemblages can shift under different projected (minimum (+9 cm), relative (+20 cm), average (+48 cm) and maximum (+88 cm)) scenarios of sea level rise (SLR). Under SLR scenarios up to 48 cm by the year 2100, the landward extension remarkably implies an area increase for each of the dominant mangrove assemblages, except for Avicennia marina and Ceriops tagal , both on the landward side. On one hand, the increase of most species in the first 3 scenarios, including the socio-economically most important species in this area, Rhizophora mucronata and C. tagal on the seaward side, strongly depends on the colonisation rate of these species. On the other hand, a SLR scenario of +88 cm by the year 2100 indicates that the area flooded only by equinoctial tides strongly decreases due to the topographical settings at the edge of the inhabited area. Consequently, the landward Avicennia -dominated assemblages will further decrease as a formation if they fail to adapt to a more frequent inundation. The topography is site-specific; however non-invadable areas can be typical for many mangrove settings.

Description: Continuing 137 Cs release to the sea from the Fukushima Dai-ichi Nuclear Power Plant through 2012 Biogeosciences Discussions, 10, 3577-3595, 2013 Author(s): J. Kanda Rate of cesium-137 ( 137 Cs) release to the sea from the Fukushima Dai-ichi Nuclear Power Plant was estimated until September 2012. Based on publicly released data of 137 Cs in seawater near the power plant by Tokyo Electric Power Company, a continuing release of radionuclides to the sea is strongly suggested. The plant has an artificial harbour facility, and the exchange rate of harbour water with surrounding seawater was estimated by decrease of radioactivity immediately after an intense event of radioactive water release. The estimated exchange rate of water in the harbour is 0.44 day −1 during the period from 6 to 19 April 2011. 137 Cs radioactivity of the harbour water is substantially higher than seawater outside and remained relatively stable after June 2011. A quasi-steady state was assumed with continuous water exchange, and an average release rate of 137 Cs was estimated to be 93 GBq day −1 in summer 2011 and 8.1 GBq day −1 in summer 2012.

Description: Upper Arctic Ocean water masses harbor distinct communities of heterotrophic flagellates Biogeosciences Discussions, 10, 3397-3430, 2013 Author(s): A. Monier, R. Terrado, M. Thaler, A. M. Comeau, E. Medrinal, and C. Lovejoy The ubiquity of heterotrophic flagellates (HFL) in marine waters has been recognized for several decades, but the phylogenetic diversity of these small (ca. 0.8–20 μm cell diameter), mostly phagotrophic protists in the pelagic zone of the ocean is underappreciated. Community composition of microbes, including HFL, is the result of past and current environmental selection, and different taxa may be indicative of food webs that cycle carbon and energy very differently. While all oceanic water columns can be density stratified due to the temperature and salinity characteristics of different water masses, the Arctic Ocean is particularly well stratified, with nutrients often limiting in surface waters and most photosynthetic biomass confined to a subsurface chlorophyll maximum (SCM) layer. This physically well-characterized system provided an opportunity to explore the community diversity of HFL across a wide region, and down the water column. We used high-throughput DNA sequencing techniques as a rapid means of surveying the diversity of HFL communities in the southern Beaufort Sea (Canada), targeting the surface, the SCM and just below the SCM. In addition to identifying major clades and their distribution, we explored the micro-diversity within the globally significant but uncultivated clade of marine stramenopiles (MAST-1) to examine the possibility of niche differentiation within the stratified water column. Our results strongly implied that HFL community composition was determined by water mass rather than geographical location across the Beaufort Sea. Future work should focus on the biogeochemical and ecological repercussions of different HFL communities in the face of climate driven changes to the physical structure of the Arctic Ocean.

Description: Effects of precipitation on soil respiration and its temperature/moisture sensitivity in three subtropical forests in Southern China Biogeosciences Discussions, 9, 15667-15698, 2012 Author(s): H. Jiang, Q. Deng, G. Zhou, D. Hui, D. Zhang, S. Liu, G. Chu, and J. Li Both long-term observation data and model simulations suggest an increasing chance of serious drought in the dry season and extreme flood in the wet season in Southern China, yet little is known about how changes in precipitation pattern will affect soil respiration in the region. We conducted a field experiment to study the responses of soil respiration to precipitation manipulations – precipitation exclusion to mimic drought, double precipitation to simulate flood, and ambient precipitation (Abbr. EP, DP and AP, respectively) – in three subtropical forests in Southern China. The three forests include Masson pine forest (PF), coniferous and broadleaved mixed forest (MF) and monsoon evergreen broadleaved forest (BF). Our observations showed that altered precipitation can strongly influence soil respiration, not only through the well-known direct effects of soil moisture, but also by modification on both moisture and temperature sensitivity of soil respiration. In the dry season, soil respiration and its temperature sensitivity in the three forests showed rising trends with precipitation increase, and its moisture sensitivity showed an opposite trend. In the wet season, the EP treatment also decreased soil respiration and its temperature sensitivity, and enhanced moisture sensitivity in all three forests. Soil respiration under the DP treatment increased significantly in the PF only, and no significant change was found for either moisture or temperature sensitivity. However, the DP treatment in the MF and BF reduced temperature sensitivity significantly. Our results indicated that soil respiration would decrease in the three subtropical forests if soil moisture continues to decrease in the future. More rainfall in the wet season could have limited effect on the response of soil respiration to the rising of temperature in the BF and MF.

Description: Revisiting factors controlling methane emissions from high-arctic tundra Biogeosciences Discussions, 9, 15853-15900, 2012 Author(s): M. Mastepanov, C. Sigsgaard, T. Tagesson, L. Ström, M. P. Tamstorf, M. Lund, and T. R. Christensen Among the numerous studies of methane emission from northern wetlands the number of measurements carried on at high latitudes (north of the Arctic Circle) is very limited, and within these there is a bias towards studies of the growing season. Here we present results of five years of automatic chamber measurements at a high-arctic location in Zackenberg, NE Greenland covering both the growing seasons and two months of the following freeze-in period. The measurements show clear seasonal dynamics in methane emission. The start of the growing season increase in CH 4 fluxes were strongly related to the date of snow melt. The greatest variation in fluxes between the study years were observed during the first part of the growing season. Somewhat surprisingly this variability could not be explained by commonly known factors controlling methane emission, i.e. temperature and water table position. Late in the growing season CH 4 emissions were found to be very similar between the study years (except the extremely dry 2010) despite large differences in climatic factors (temperature and water table). Late-season bursts of CH 4 coinciding with soil freezing in the autumn were observed at least during three years between 2006 and 2010. The accumulated emission during the freeze-in CH 4 bursts was comparable in size with the growing season emission for the year 2007, and about one third of the growing season emissions for the years 2009 and 2010. In all three cases the CH 4 burst was accompanied by a~corresponding episodic increase in CO 2 emission, which can compose a significant contribution to the annual CO 2 flux budget. The most probable mechanism of the late season CH 4 and CO 2 bursts is physical release of gases, accumulated in the soil during the growing season. In this study we investigate the drivers and links between growing season and late season fluxes. The reported surprising seasonal dynamics of CH 4 emissions at this site show that there are important occasions where conventional knowledge on factors controlling methane emissions is overruled by other processes, acting in longer than seasonal time scales. Our findings suggest the importance of multiyear studies with continued focus on shoulder seasons.

Description: Distribution of methane in the Lena Delta and Buor Khaya Bay, Russia Biogeosciences Discussions, 9, 16213-16237, 2012 Author(s): I. Bussmann The Lena River is one of the largest Russian rivers draining into the Laptev Sea. The permafrost areas surrounding the Lena are predicted to melt at increasing rates due to global temperature increases. With this melting, large amounts of carbon – either organic or as methane – will reach the waters of the Lena and the adjacent Buor Khaya Bay (Laptev Sea). Methane concentrations and the isotopic signal of methane in the waters of the Lena Delta and estuary were monitored from 2008 to 2010. Meltwater run-off of permafrost soils produced hotspots for methane input into the river system (median concentration 1500 nM) compared with concentrations of around 100 nM observed in the main channels of the Lena. Within the river, especially at sites with meltwater input, microbiological experiments indicated strong in situ methane production but a very low methane oxidation potential. In the estuary of Buor Khaya Bay, methane concentrations decreased towards background levels of 20 nM. Here, the strong stratification of the water column permits the dilution of methane with seawater, and methane is released mainly by diffusion into the atmosphere.

Description: Spectrally resolved efficiencies of carbon monoxide (CO) photoproduction in the Western Canadian Arctic: particles versus solutes Biogeosciences Discussions, 9, 16161-16211, 2012 Author(s): G. Song, H. Xie, S. Bélanger, and M. Babin Spectrally resolved efficiency (i.e. apparent quantum yield, AQY) of carbon monoxide (CO) photoproduction is a useful indicator of substrate photoreactivity and a crucial parameter for modeling CO photoproduction rates in the water column. Recent evidence has suggested that CO photoproduction from particles in marine waters is significant compared to the well-known CO production from chromophoric dissolved organic matter (CDOM) photodegradation. Although CDOM-based CO AQY spectra have been extensively determined, little is known of this information on the particulate phase. Using water samples collected from the Mackenzie estuary, shelf, and Canada Basin in the Southeastern Beaufort Sea, the present study for the first time quantified the AQY spectra of particle-based CO photoproduction and compared them with the concomitantly determined CDOM-based CO AQY spectra. CO AQYs of both particles and CDOM decreased with wavelength but the spectral shape of the particulate AQY was flatter in the visible regime. This feature resulted in a disproportionally higher visible light-driven CO production by particles, thereby increasing the ratio of particle- to CDOM-based CO photoproduction with depth in the euphotic zone. In terms of depth-integrated production in the euphotic zone, CO formation from CDOM was dominated by the ultraviolet (UV, 290–400 nm) radiation whereas UV and visible light played roughly equal roles in CO production from particles. Spatially, CO AQY of bulk particulate matter (i.e. the sum of organics and inorganics) augmented from the estuary to shelf to basin while CO AQY of CDOM trended inversely. Water from the deep chlorophyll maximum layer revealed higher CO AQYs than did surface water for both particles and CDOM. CO AQY of bulk particulate matter exceeded that of CDOM on the shelf and in the basin but the sequence reversed in the estuary. Mineral absorption-corrected CO AQY of particulate organic matter (POM) was, however, greater than its CDOM counterpart in all three sub-regions and displayed magnitudes in the estuary that were no inferior to those in shelf and offshore waters. In terms of CO photoproduction, POM was thus more photoreactive than CDOM, irrespective of the organic matter's origins (i.e. terrigenous or marine). Riverine CDOM exhibited higher photoreactivity than marine CDOM and land-derived POM appeared similarly or more photoreactive than marine POM. AQY-based modeling indicates that CO photoproduction in the study area is underestimated by 13–48 % if the particulate term is ignored.

Description: Radium-based estimates of cesium isotope transport and total direct ocean discharges from the Fukushima Nuclear Power Plant accident Biogeosciences Discussions, 9, 16139-16160, 2012 Author(s): M. A. Charette, C. F. Breier, P. B. Henderson, S. M. Pike, I. I. Rypina, S. R. Jayne, and K. O. Buesseler Radium has four naturally occurring isotopes that have proven useful in constraining water mass source, age, and mixing rates in the coastal and open ocean. In this study, we used radium isotopes to determine the fate and flux of runoff-derived cesium from the Fukushima Nuclear Power Plant (NPP). During a June 2011 cruise, the highest Cs concentrations were found along the eastern shelf of northern Japan, from Fukushima south, to the edge of the Kuroshio current, and in an eddy ∼ 130 km from the NPP site. Locations with the highest cesium also had some of the highest radium activities, suggesting much of the direct ocean discharges of Cs remained in the coastal zone 2–3 months after the accident. We used a short-lived Ra isotope ( 223 Ra, t 1/2 = 11.4 d) to derive an average water mass age ( T r ) in the coastal zone of 32 days. To ground-truth the Ra age model, we conducted a direct, station-by-station comparison of water mass ages with a numerical oceanographic model and found them to be in excellent agreement (model avg. T r = 27 days). From these independent T r values and the inventory of Cs within the water column at the time of our cruise, we were able to calculate an offshore 134 Cs flux of 3.9–4.6 × 10 13 Bq d −1 . Radium-228 ( t 1/2 = 5.75 yr) was used to derive a vertical eddy diffusivity ( K z ) of 0.7 m 2 d −1 (0.1 cm 2 s −1 ); from this K z and 134 Cs inventory, we estimated a 134 Cs flux across the pycnocline of 1.8 × 10 4 Bq d −1 for the same time period. On average, our results show that horizontal mixing loss of Cs from the coastal zone was ∼ 10 9 greater than vertical exchange below the surface mixed layer. Finally, a mixing/dilution model that utilized our Ra-based and oceanographic model water mass ages produced a direct ocean discharge of 134 Cs from the FNPP of 11–16 PBq at the time of the peak release in early April 2011. Our results can be used to calculate discharge of other water-soluble radionuclides that were released to the ocean directly from the Fukushima NPP.

Description: Soil respiration compartments on an aging managed heathland: can model selection procedures contribute to our understanding of ecosystem processes? Biogeosciences Discussions, 9, 16239-16301, 2012 Author(s): G. R. Kopittke, E. E. van Loon, A. Tietema, and D. Asscheman Soil respiration studies are increasingly undertaken with the aim of quantifying C fluxes and predicting changes for the future. The interpretation of field data into annual C loss predictions requires the use of modeling tools which generally include model variables related to the underlying drivers of soil respiration, such as soil temperature, soil moisture and plant activity. Very few studies have reported using model selection procedures in which structurally different models are calibrated, then validated on separate observation datasets and the outcomes critically compared. This study utilized thorough model selection procedures to determine soil heterotrophic (microbial) and autotrophic (root) respiration for a heathland chronosequence. The model validation process identified that none of the six measured plant variables explained any data variation when included in models with soil temperature, which contradicts many current studies. The best predictive model used a generalized linear mixed effect model format with soil temperature as the only variable. There were no heterotrophic respiration differences between the community ages. In contrast, autotrophic respiration was significantly greater on the youngest vegetation (55 % of total soil respiration in summer) and decreased as the plants aged (oldest vegetation: 37 % of total soil respiration in summer). Total annual soil C loss from the youngest and oldest communities was estimated to be 650 and 435 g C m −2 yr −1 respectively. Heathlands are cultural landscapes which are managed through cyclical cutting, burning or grazing practices. Understanding the C fluxes from these ecosystems provides information on the optimal management cycle-time to maximize C uptake and minimize C output. Inclusion of the predicted soil fluxes into a preliminary ecosystem C balance suggested that the youngest vegetation is a C sink while the oldest vegetation is a C source, indicating that shorter management cycles could reduce C emissions.

Description: Biological production in the Bellingshausen Sea from oxygen-to-argon ratios and oxygen triple isotopes Biogeosciences Discussions, 9, 16033-16085, 2012 Author(s): K. Castro-Morales, N. Cassar, and J. Kaiser We present estimates of mixed layer net community oxygen production ( N ) and gross oxygen production ( G ) of the Bellingshausen Sea in March and April 2007. N was derived from oxygen-to-argon (O 2 / Ar) ratios; G was derived using the dual-delta method from triple oxygen isotope measurements. In addition, O 2 profiles were collected at 253 CTD stations. N is often approximated by the biological oxygen air-sea exchange flux ( F bio ) based on the O 2 / Ar supersaturation, assuming that significant horizontal or vertical fluxes are absent. Here, we show that the effect of vertical fluxes alone can account for F bio values 〈 0 in large parts of the Bellingshausen Sea towards the end of the productive season, which could be mistaken to represent net heterotrophy. Thus, improved estimates of mixed-layer N can be derived from the sum of F bio , F e (entrainment from the upper thermocline during mixed-layer deepening) and F v (diapycnal eddy diffusion across the base of the mixed layer). In the Winter Sea Ice Zone (WSIZ), the corresponding correction results in a small change of F bio = (30 ± 17) mmol m −2 d −1 to N = (34 ± 17) mmol m −2 d −1 . However, in the permanent open ocean zone (POOZ), the original F bio value of (−17 ± 10) mmol m −2 d −1 gives a corrected value for N of (−2 ± 18) mmol m −2 d −1 . We hypothesize that in the WSIZ enhanced water column stability due to the release of freshwater and nutrients from sea-ice melt may account for the higher N-value. These results stress the importance of accounting for physical biases when estimating mixed layer-marine productivity from in situ O 2 / Ar ratios.

Description: Constraints from atmospheric CO 2 and satellite-based vegetation activity observations on current land carbon cycle trends Biogeosciences Discussions, 9, 16087-16138, 2012 Author(s): D. Dalmonech and S. Zaehle Terrestrial ecosystem models used for Earth system modelling show a significant divergence in future patterns of ecosystem processes, in particular carbon exchanges, despite a seemingly common behaviour for the contemporary period. An in-depth evaluation of these models is hence of high importance to achieve a better understanding of the reasons for this disagreement. Here, we develop an extension for existing benchmarking systems by making use of the complementary information contained in the observational records of atmospheric CO 2 and remotely-sensed vegetation activity to provide a firm set of diagnostics of ecosystem responses to climate variability in the last 30 yr at different temporal and spatial scales. The selection of observational characteristics (traits) specifically considers the robustness of information given the uncertainties in both data and evaluation analysis. In addition, we provide a baseline benchmark, a minimum test that the model under consideration has to pass, to provide a more objective, quantitative evaluation framework. The benchmarking strategy can be used for any land surface model, either driven by observed meteorology or coupled to a climate model. We apply this framework to evaluate the offline version of the MPI-Earth system model's land surface scheme JSBACH. We demonstrate that the complementary use of atmospheric CO 2 and satellite based vegetation activity data allows to pinpoint specific model failures that would not be possible by the sole use of atmospheric CO 2 observations.

Description: Seasonal and spatial comparisons of phytoplankton growth and mortality rates due to microzooplankton grazing in the northern South China Sea Biogeosciences Discussions, 9, 16005-16032, 2012 Author(s): B. Chen, L. Zheng, B. Huang, S. Song, and H. Liu We conducted a comprehensive investigation on the microzooplankton herbivory effect on phytoplankton in the northern South China Sea (SCS) using the seawater dilution technique at surface and deep chlorophyll maximum (DCM) layers in two cruises (July–August of 2009 and January of 2010). We compared vertical (surface vs. DCM), spatial (onshore vs. offshore), and seasonal (summer vs. winter) differences of phytoplankton growth (μ 0 ) and microzooplankton grazing rates ( m ). During summer, both μ 0 and m were significantly higher at the surface than at the layer of DCM, which was below the mixed layer. During winter, surface μ 0 was significantly higher than at DCM, while m was not significantly different between the two layers, both of which were contained within the mixed layer. Surface μ 0 was, on average, significantly higher in summer than in winter; while average surface m was not different between the two seasons. There were no significant cross-shelf trends of μ 0 in summer or winter surface waters. In surface waters, μ 0 was not correlated with ambient nitrate concentrations and the effect of nutrient enrichment on phytoplankton growth was not pronounced. There was a decreasing trend of m from shelf to basin surface waters in summer, but not in winter. Microzooplankton grazing effect on phytoplankton ( m /μ 0 ) did not increase with distance offshore, suggesting that the importance of microzooplankton as grazers of phytoplankton may not decrease in onshore waters. On average, microzooplankton grazed 73% and 65% of the daily primary production in summer and winter, respectively.

Description: Interconnectivity vs. isolation of prokaryotic communities in European deep-sea mud volcanoes Biogeosciences Discussions, 9, 17377-17400, 2012 Author(s): M. G. Pachiadaki and K. A. Kormas By exploiting the available data on 16S rRNA gene sequences – spanning over a sampling period of more than 10 yr – retrieved from sediments of the Haakon Mosby mud volcano (HMMV), Gulf of Cadiz (GoC) and eastern Mediterranean (Amsterdam and Kazan mud volcanoes; AMSMV, KZNMV) mud volcanoes/pockmarks, we investigated whether these systems are characterized by high (interconnectivity) or low (isolation) connection degree based on shared bacterial and archaeal phylotypes. We found only two archaeal and two bacterial phylotypes to occur in all three sites and a few more that were found in two of the three sites. Although the number of shared species depends a lot on the analysis depth of each sample, the majority of the common phylotypes were related mostly to cold seep deep-sea habitats, while for some of them their relative abundance was high enough to be considered as key-species for the habitat they were found. As new tools, like next generation sequencing platforms, are more appropriate for revealing greater depth of diversity but also allow sample replication and uniform sampling protocols, and gain wider recognition and usage, future attempts are more realistic now for fully elucidating the degree of specificity in deep-sea mud volcanoes and pockmarks microbial communities.

Description: Density and distribution of megafauna at the Håkon Mosby Mud Volcano (the Barents Sea) based on image analysis Biogeosciences Discussions, 9, 17475-17517, 2012 Author(s): E. Rybakova (Goroslavskaya), S. Galkin, M. Bergmann, T. Soltwedel, and A. Gebruk During a survey of the Håkon Mosby Mud Volcano (HMMV), located on the Bear Island Fan in the southwest Barents Sea at ~ 1250 m water depth, different habitats inside the volcano caldera and outside it were photographed using a towed camera platform, an Ocean Floor Observation System (OFOS). Three transects were performed across the caldera and one outside, in the background area, each transect was ~ 2 km in length. We compared the density, taxa richness and diversity of non-symbiotrophic megafauna in areas inside the volcano caldera with different bacterial mat and pogonophoran tubeworm cover. Significant variations in megafaunal composition, density and distribution were found between considered areas. Total megafaunal density was highest in areas of dense pogonophoran populations (mean 52.9 ind. m −2 ) followed by areas of plain light-coloured sediment that were devoid of bacterial mats and tubeworms (mean 37.7 ind. m −2 ). The lowest densities were recorded in areas of dense bacterial mats (mean ≤ 1.4 ind. m −2 ). Five taxa contributed to most of the observed variation: the ophiuroid Ophiocten gracilis , lysianassid amphipods, the pycnogonid Nymphon macronix , the caprellid Metacaprella horrida and the fish Lycodes squamiventer . In agreement with previous studies, three zones within the HMMV caldera were distinguished, based on different habitats and megafaunal composition: "bacterial mats", "pogonophoran fields" and "plain light-coloured sediments". The zones were arranged almost concentrically around the central part of the caldera that was devoid of visible megafauna. The total number of taxa showed little variation inside (24 spp.) and outside the caldera (26 spp.). The density, diversity and composition of megafauna varied substantially between plain light-coloured sediment areas inside the caldera and the HMMV background. Megafaunal density was lower in the background (mean 25.3 ind. m −2 ) compared to areas of plain light-coloured sediments inside the caldera.

Description: Phosphorus sorption and buffering mechanisms in suspended sediments from the Yangtze Estuary and Hangzhou Bay, China Biogeosciences Discussions, 9, 17519-17538, 2012 Author(s): M. Li, M. J. Whelan, G. Wang, and S. M. White The adsorption isotherm and the mechanism of the buffering effect are important controls on phosphorus behaviors in estuaries and are important for estimating phosphate concentrations in aquatic environments. In this paper, we derive phosphate adsorption isotherms in order to investigate sediment adsorption and buffering capacity for phosphorus discharged from sewage outfalls in the Yangtze Estuary and Hangzhou Bay near Shanghai, China. Experiments were also carried out at different temperatures in order to explore the buffering effects for phosphate. The results show that P sorption in sediments with low fine particle fractions was best described using exponential equations. Some P interactions between water and sediment may be caused by the precipitation of CaHPO 4 from Ca 2+ and HPO 4 2− when the phosphate concentration in the liquid phase is high. Results from the buffering experiments suggest that the Zero Equilibrium Phosphate Concentrations (EPC 0 ) vary from 0.014 mg l −1 to 0.061 mg l −1 , which are consistent with measured phosphate concentrations in water samples collected at the same time as sediment sampling. Values of EPC 0 and linear sorption coefficients ( K ) in sediments with high fine particle and organic matter contents are relatively high, which implies that they have high buffering capacity. Both EPC 0 and K increase with increasing temperature, indicating a higher P buffering capacity at high temperatures.

Description: Seasonal, daily and diel N 2 effluxes in permeable carbonate sediments Biogeosciences Discussions, 9, 17437-17473, 2012 Author(s): B. D. Eyre, I. R. Santos, and D. T. Maher Benthic metabolism and inorganic nitrogen and N 2 flux rates (denitrification) were measured in permeable carbonate sands from Heron Island (Great Barrier Reef). Some of the N 2 flux rates were among the highest measured in sediments. All benthic fluxes showed a significant difference between seasons with higher rates in summer and late summer. There was no distinct response of the benthic system to mass coral spawning. Instead, changes in benthic fluxes over 12 days in summer appears to be driven by tidal changes in water depth and associated changes in phytosynthetically active radiation reaching the sediments. Dark N 2 fluxes were strongly correlated to benthic oxygen consumption across all sites and seasons ( r 2 = 0.64; p 〈 0.005; slope = 0.036). However, there were seasonal differences with a steeper slope in summer than winter reflecting either more efficient coupling between respiration and nitrification-denitrification at higher temperatures or different sources of organic matter. Adding data from published studies on carbonate sands revealed two slopes in the dark N 2 flux versus benthic oxygen consumption relationship. The lower slope (0.035) was most likely due to high carbon : nitrogen (C : N) organic matter from coral reefs, but competition by benthic microalgae for nitrogen, N-fixation or inefficient coupling between respiration and nitrification-denitrification can not be excluded. The steeper slope (0.089) was most likely due to respiration being driven by low C : N phyto-detritus. If the different slopes were driven by the sources of organic matter then global estimates of continental shelf denitrification are probably about right. In contrast, global estimates of continental shelf may be over-estimated if the low slope was due to inefficient coupling between respiration and nitrification-denitrification and also due to reduced N 2 effluxes in the light associated with competition by benthic microalgae for nitrogen and N-fixation.

Description: Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic) Biogeosciences Discussions, 9, 17401-17435, 2012 Author(s): E. Ortega-Retuerta, F. Joux, W. H. Jeffrey, and J.-F. Ghiglione We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea, Canadian Arctic Ocean, with a particular focus on free-living vs. particle-attached communities. Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between particle-attached (PA) and free-living (FL) bacterial communities in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (proxy of DOC and CDOM), suspended particles, amino acids and chlorophyll a . 16S rRNA genes pyrosequencing of selected samples confirmed these significant differences from river to sea and also between PA and FL fractions only in open sea samples, and PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria , while the FL sea sample was dominated by Alphaproteobacteria . Finally, the coast and river samples, both PA and FL fractions, were dominated by Betaproteobacteria , Alphaproteobacteria and Actinobacteria . These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a~basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particles load.

Description: Physical and biogeochemical forcing of oxygen changes in the tropical eastern South Pacific along 86° W: 1993 versus 2009 Biogeosciences Discussions, 9, 17583-17618, 2012 Author(s): P. J. Llanillo, J. Karstensen, J. L. Pelegrí, and L. Stramma Temporal changes of the water mass distribution and biogeochemical cycling in the tropical eastern South Pacific are investigated based on the extended Optimum Multi-Parameter (OMP) method. Two ship occupations of a meridional section along 85°50´ W, from 14° S to 1° N, are analysed, one during a relatively warm (El Niño/El Viejo, March 1993) and the other during a cold (La Niña/La Vieja, February 2009) upper-ocean phase. The largest El Niño – Southern Oscillation (ENSO) impact was found in the water properties and water mass distribution in the upper 250 m. The most prominent change is the vertical motion of the Oxygen Minimum Zone (OMZ) associated to the hypoxic Equatorial Subsurface Water (ESSW). During a cold phase the core of the ESSW is found at shallower layers, replacing the shallow (top 250 m) Subtropical Surface Water (STW) and allowing an intrusion of oxygen-rich and nutrient-poor Antarctic Intermediate Water (AAIW) in the depth range of 300 to 600 m. The shift in the vertical location of the intrusion of AAIW in the OMZ induces changes in oxygen advection and respiration, the largest the oxygen supply the greatest the respiration and the lowest the nitrate loss by denitrification. Changes in the intensity of the zonal currents in the Equatorial Current System, that ventilate the OMZ from the west, are used to explain the patchy latitudinal changes of seawater properties observed along the repeated section. Given that changes down to 800 m depth are observed, not only interannual (ENSO) but also decadal variability (Pacific Decadal Oscillation) is a potential driver for the observed changes.

Description: Benthic communities in the deep Mediterranean Sea: exploring microbial and meiofaunal patterns in slope and basin ecosystems Biogeosciences Discussions, 9, 17539-17581, 2012 Author(s): K. Sevastou, N. Lampadariou, P. N. Polymenakou, and A. Tselepides The long held perception of the deep sea consisting of monotonous slopes and uniform oceanic basins has over the decades given way to the idea of a complex system with wide habitat heterogeneity. Under the prism of a highly diverse environment, a large dataset was used to describe and compare spatial patterns of the dominant small-size components of deep-sea benthos, metazoan meiofauna and bacteria, from Mediterranean basins and slopes. A grid of 73 stations sampled at five geographical areas along the central-eastern Mediterranean basin (central Mediterranean, northern Aegean Sea, Cretan Sea, Libyan Sea, eastern Levantine) spanning over 4 km in depth revealed a high diversity in terms of both metazoan meiofauna and microbial communities. The higher meiofaunal abundance and richness observed in the northern Aegean Sea highlights the effect of productivity on benthic patterns. Non parametric analyses detected no differences for meiobenthic standing stocks and major taxa diversity ( α , β , γ and δ components) between the two habitats (basin vs. slope) for the whole investigated area and within each region, but revealed significant bathymetric trends: abundance and richness follow the well-known gradient of decreasing values with increasing depth, whereas differentiation diversity ( β - and δ -diversity) increases with depth. In spite of a similar bathymetric trend observed for nematode genera richness, no clear pattern was detected with regard to habitat type; the observed number of nematode genera suggests higher diversity in slopes, whereas richness estimator Jack1 found no differences between habitats. On the other hand, δ -diversity was higher at the basin habitat, but no differences were found among depth ranges, though turnover values were high in all pairwise comparisons of the different depth categories. Results of multivariate analysis are in line with the above findings, indicating high within habitat variability of meiofaunal communities and a gradual change of meiofaunal structure towards the abyssal stations. In contrast to meiobenthic results, microbial richness is significantly higher at the basin ecosystem and tends to increase with depth, while community structure varies greatly among samples regardless of the type of habitat, depth or area. The results presented here suggest that differences in benthic parameters between the two habitats are neither strong nor consistent; it appears that within habitat variability is high and differences among depth ranges are more important.

Description: Air-sea exchange of CO 2 at a Northern California coastal site along the California Current upwelling system Biogeosciences Discussions, 9, 17707-17741, 2012 Author(s): H. Ikawa, I. Faloona, J. Kochendorfer, K. T. Paw U, and W. C. Oechel Uncertainty in the air-sea CO 2 exchange (CO 2 flux) in coastal upwelling zones is attributed to high temporal variability, which is caused by changes in ocean currents. Upwelling transports heterotrophic, CO 2 enriched water to the surface and releases CO 2 to the atmosphere, whereas the presence of nutrient-rich water at the surface supports high primary production and atmospheric CO 2 uptake. To quantify the effects of upwelling on CO 2 fluxes, we measured CO 2 flux at a coastal upwelling site off of Bodega Bay, California, during the summer of 2007 and the fall of 2008 using the eddy covariance technique and the bulk method with p CO 2 measurements from November 2010 to July 2011. Variations in sea surface temperatures (SST) and alongshore wind speeds suggest that the measurement period in 2007 coincided with a typical early-summer upwelling period and the measurement period in 2008 was during a typical fall relaxation period. A strong source of CO 2 (~1.5 ± 7 SD (standard deviation) g C m −2 day −1 ) from the ocean to the atmosphere during the upwelling period was concurrent with high salinity, low SST, and low chlorophyll density. In contrast, a weak source of CO 2 flux (~0.2 ± 3 SD g C m −2 day −1 ) was observed with low salinity, high SST and high chlorophyll density during the relaxation period. Similarly, the sink and source balance of CO 2 flux was highly related to salinity and SST during the p CO 2 measurement periods; high salinity and low SST corresponded to high p CO 2 , and vice versa. We estimated that the coastal area off Bodega Bay was likely a source of CO 2 to the atmosphere based on the following conclusions: (1) the overall CO 2 flux estimated from both eddy covariance and p CO 2 measurements showed a source of CO 2 ; (2) although the relaxation period during the 2008 measurements were favorable to CO 2 uptake, CO 2 flux during this period was still a slight source, (3) salinity and SST were found to be good predictors of the CO 2 flux for both eddy covariance and p CO 2 measurements, and historical data of daily averaged SST and salinity between 1988 to 2011 show that 99% of the data falls within the range of our observation in May–June 2007, August–September 2008 and November 2010–July 2011 indicating that our data set was representative of the annual variations in the sea state. Based on the developed relationship between p CO 2 and SST and salinity, the average annual CO 2 flux between 1988 and 2011 was estimated to be ~35 mol C m −2 yr −1 . The peak monthly CO 2 flux of ~7 mol C m −2 month −1 accounted for about 30% of the dissolved inorganic carbon in the surface mixed-layer.

Description: Trophic state of sediments from two deep continental margins off Iberia: a biomimetic approach Biogeosciences Discussions, 9, 17619-17650, 2012 Author(s): A. Dell'Anno, A. Pusceddu, C. Corinaldesi, M. Canals, S. Heussner, L. Thomsen, and R. Danovaro The trophic state of benthic deep-sea ecosystems can greatly influence key ecological processes (e.g. biomass production and nutrient cycling). Thus, assessing the trophic state of the sediment at different spatial and temporal scales is crucial for a better understanding of deep-sea ecosystem functioning. Here, using a biomimetic approach based on enzymatic digestion of protein and carbohydrate pools, we assess the bioavailability of organic detritus and its nutritional value in the uppermost layer of deep-sea sediments from open slopes and canyons of the Catalan (NW Mediterranean) and Portuguese (NE Atlantic) continental margins, offshore east and west Iberia, respectively. Patterns of sediment trophic state were analyzed in relation to increasing water depth, including repeated samplings over a 3 yr period in the Catalan margin. Bioavailable organic matter and its nutritional value were significantly higher in the Portuguese margin than in the Catalan margin, thus reflecting differences in primary productivity of surface waters reported for the two regions. Similarly, sediments of the Catalan margin were characterized by significantly higher food quantity and quality in spring, when higher primary production processes occur in surface waters, than in summer and autumn. In both continental margins, bioavailable organic C concentrations did not vary or increase with increasing water depth. Differences in the benthic trophic state of canyons against open slopes were more evident in the Portuguese than in the Catalan margin. Overall our findings indicate that deep-sea sediments are characterized by relatively high amounts of bioavailable organic matter. We suggest that the interactions between biological-related processes in surface waters and particle transport and deposition dynamics can play a crucial role in shaping the quantity and distribution of bioavailable organic detritus and its nutritional value along deep continental margins.

Description: Effects of increased p CO 2 and geographic origin on purple sea urchin ( Strongylocentrotus purpuratus ) calcite elemental composition Biogeosciences Discussions, 9, 17939-17973, 2012 Author(s): M. LaVigne, T. M. Hill, E. Sanford, B. Gaylord, A. D. Russell, E. A. Lenz, J. D. Hosfelt, and M. K. Young Ocean acidification will likely have negative impacts on invertebrates producing skeletons composed of calcium carbonate. Skeletal solubility is partly controlled by the incorporation of "foreign" ions (such as Mg and Sr) into the crystal lattice of these skeletal structures, a process that is sensitive to a variety of biological and environmental factors. Here we explore the effects of life stage, oceanographic region of origin, and changes in the partial pressure of carbon dioxide in seawater ( p CO 2 ) on trace elemental composition in the purple sea urchin ( Strongylocentrotus purpuratus ). We show that, similar to other urchin taxa, adult purple sea urchins have the ability to precipitate skeleton composed of a range of biominerals spanning low to high magnesium calcites. Mg/Ca and Sr/Ca ratios were substantially lower in adult spines compared to adult tests. On the other hand, trace elemental composition was invariant among adults collected from four oceanographically distinct regions along the US west coast (Oregon, Northern California, Central California, and Southern California). Skeletons of newly settled juvenile urchins that originated from adults from the four regions exhibited intermediate Mg/Ca and Sr/Ca between adult spine and test endmembers, indicating that skeleton precipitated during early life stages is more soluble than adult spines and less soluble than adult tests. Mean skeletal Mg/Ca or Sr/Ca of juvenile skeleton did not vary with source region when larvae were reared under present-day, global-average seawater carbonate conditions (400 ppm; pH = 8.02 ± 0.03 1 SD; Ω calcite = 3.3 ± 0.2 1 SD). However, when reared under elevated CO 2 (900 ppm; pH = 7.72 ± 0.03; Ω calcite = 1.8 ± 0.1), skeletal Sr/Ca in juveniles exhibited increased variance across the four regions. Although larvae from the northern populations (Oregon, Northern California, Central California) did not exhibit differences in Mg or Sr incorporation under elevated CO 2 (Sr/Ca = 2.09 ± 0.06 mmol mol −1 ; Mg/Ca = 66.9 ± 4.1 mmol mol −1 ), juveniles of Southern California origin partitioned ∼ 8% more Sr into their skeletons when exposed to higher CO 2 (Sr/Ca = 2.26 ± 0.05 vs. 2.10 ± 0.03 mmol mol −1 1 SD). Together these results suggest that the diversity of carbonate minerologies present across different skeletal structures and life stages in purple sea urchins does not translate into an equivalent plasticity of response associated with geographic variation or temporal shifts in seawater properties. Rather, composition of S. purpuratus skeleton precipitated during both early and adult life history stages appears relatively robust to spatial gradients and predicted changes in seawater carbonate chemistry for 2100. An exception to this trend may arise during early life stages, where certain populations of purple sea urchins may alter skeletal mineral precipitation rates and composition beyond a given CO 2 threshold. The degree to which this latter geochemical plasticity might affect mineral stability and solubility in a future, altered ocean requires additional study.

Description: Bioavailability of sinking organic matter in the Blanes canyon and the adjacent open slope (NW Mediterranean Sea) Biogeosciences Discussions, 9, 18295-18330, 2012 Author(s): P. Lopez-Fernandez, S. Bianchelli, A. Pusceddu, A. Calafat, A. Sanchez-Vidal, and R. Danovaro Submarine canyons are sites of intense energy and material exchange between the shelf and the deep adjacent basins. To test the hypothesis that active submarine canyons represent preferential conduits of available food for the deep-sea benthos, two mooring lines were deployed at 1200 m depth from November 2008 to November 2009 inside the Blanes canyon and on the adjacent open slope (Catalan Margin, NW Mediterranean Sea). We investigated the fluxes, biochemical composition and food quality of sinking organic carbon (OC). OC fluxes in the canyon and the open slope varied among sampling periods, though not consistently in the two sites. In particular, while in the open slope the highest OC fluxes were observed in August 2009, in the canyon the highest OC fluxes occurred in April–May 2009. For almost the entire study period, the OC fluxes in the canyon were significantly higher than those in the open slope, whereas OC contents of sinking particles collected in the open slope were consistently higher than those in the canyon. This result confirms that submarine canyons are effective conveyors of OC to the deep sea, particles transferred are predominantly of inorganic origin, significantly higher than that reaching the open slope at a similar water depth. Using multivariate statistical tests, two major clusters of sampling periods were identified: one in the canyon that grouped trap samples collected in December 2008, concurrently with the occurrence of a major storm at the sea surface, and associated with increased fluxes of nutritionally available particles from the upper shelf. Another cluster grouped samples from both the canyon and the open slope collected in March 2009, concurrently with the occurrence of the seasonal phytoplankton bloom at the sea surface, and associated with increased fluxes of total phytopigments. Our results confirm the key ecological role of submarine canyons for the functioning of deep-sea ecosystems, and highlight the importance of canyons in linking episodic storms and primary production occurring at the sea surface to the deep sea floor.

Description: Influence of increasing dissolved inorganic carbon concentrations and decreasing pH on chemolithoautrophic bacteria from oxic-sulfidic interfaces Biogeosciences Discussions, 9, 18371-18395, 2012 Author(s): K. Mammitzsch, G. Jost, and K. Jürgens Increases in the dissolved inorganic carbon (DIC) concentration are expected to cause a decrease in the pH of ocean waters, a process known as ocean acidification. In oxygen-deficient zones this will add to already increased DIC and decreased pH values. It is not known how this might affect microbial communities and microbially mediated processes. In this study, the potential effects of ocean acidification on chemolithoautotrophic prokaryotes of marine oxic-anoxic transition zones were investigated, using the chemoautotrophic denitrifying ε -proteobacterium " Sulfurimonas gotlandica " strain GD1 as a model organism. This and related taxa use reduced sulfur compounds, e.g. sulfide and thiosulfate, as electron donors and were previously shown to be responsible for nitrate removal and sulfide detoxification in redox zones of the Baltic Sea water column but occur also in other oxygen-deficient marine systems. Bacterial cell growth within a broad range of DIC concentrations and pH values was monitored and substrate utilization was determined. The results showed that the DIC saturation concentration for growth was already reached at 800 μM, which is well below in situ DIC levels. The pH optimum was between 6.6 and 8.0. Within a pH range of 6.6–7.1 there was no significant difference in substrate utilization; however, at lower pH values cell growth decreased sharply and cell-specific substrate consumption increased. These findings suggest that a direct effect of ocean acidification, with the predicted changes in pH and DIC, on chemolithoautotrophic bacteria such as " S. gotlandica " str. GD1 is generally not very probable.

Description: Apparent optical properties of the Canadian Beaufort Sea – Part 1: Observational overview and water column relationships Biogeosciences Discussions, 10, 4025-4065, 2013 Author(s): D. Antoine, S. B. Hooker, S. Belanger, A. Matsuoka, and M. Babin A data set of radiometric measurements collected in the Beaufort Sea (Canadian Arctic) in August 2009 (MALINA project) is analysed in order to describe apparent optical properties (AOPs) in this sea, which is subject to dramatic environmental changes for several decades. The two properties derived from the measurements are the spectral diffuse attenuation coefficient for downward irradiance, K d , and the spectral remote sensing reflectance, R rs . The former controls light propagation in the upper water column. The latter determines how light is backscattered out of the water and becomes eventually observable from a satellite ocean colour sensor. The data set includes offshore clear waters of the Beaufort basin as well as highly turbid waters of the Mackenzie River plumes. In the clear waters, we show K d values that are much larger in the ultraviolet and blue parts of the spectrum than what could be anticipated considering the chlorophyll concentration. A larger contribution of absorption by coloured dissolved organic matter (CDOM) is responsible for this high K d values, as compared to other oligotrophic areas. In turbid waters, attenuation reaches extremely high values, driven by high loads of particulate materials and also by a large CDOM content. In these two extreme types of waters, current satellite chlorophyll algorithms fail. This is questioning the role of ocean colour remote sensing in the Arctic when R rs from only the blue and green bands are used. Therefore, other parts of the spectrum (e.g. the red) should be explored if one aims at quantifying interannual changes in chlorophyll in the Arctic from space. The very peculiar AOPs in the Beaufort Sea also advocate for developing specific light propagation models when attempting to predict light availability for photosynthesis at depth.

Description: Development of a regional-scale pollen emission and transport modeling framework for investigating the impact of climate change on allergic airway disease Biogeosciences Discussions, 10, 3977-4023, 2013 Author(s): R. Zhang, T. Duhl, M. T. Salam, J. M. House, R. C. Flagan, E. L. Avol, F. D. Gilliland, A. Guenther, S. H. Chung, B. K. Lamb, and T. M. VanReken Exposure to bioaerosol allergens such as pollen can cause exacerbations of allergenic airway disease (AAD) in sensitive populations, and thus cause serious public health problems. Assessing these health impacts by linking the airborne pollen levels, concentrations of respirable allergenic material, and human allergenic response under current and future climate conditions is a key step toward developing preventive and adaptive actions. To that end, a regional-scale pollen emission and transport modeling framework was developed that treats allergenic pollens as non-reactive tracers within the WRF/CMAQ air-quality modeling system. The Simulator of the Timing and Magnitude of Pollen Season (STaMPS) model was used to generate a daily pollen pool that can then be emitted into the atmosphere by wind. The STaMPS is driven by species-specific meteorological (temperature and/or precipitation) threshold conditions and is designed to be flexible with respect to its representation vegetation species and plant functional types (PFTs). The hourly pollen emission flux was parameterized by considering the pollen pool, friction velocity, and wind threshold values. The dry deposition velocity of each species of pollen was estimated based on pollen grain size and density. An evaluation of the pollen modeling framework was conducted for southern California for the period from March to June 2010. This period coincided with observations by the University of Southern California's Children's Health Study (CHS), which included O 3 , PM 2.5 , and pollen count, as well as measurements of exhaled nitric oxide in study participants. Two nesting domains with horizontal resolutions of 12 km and 4 km were constructed, and six representative allergenic pollen genera were included: birch tree, walnut tree, mulberry tree, olive tree, oak tree, and brome grasses. Under the current parameterization scheme, the modeling framework tends to underestimate walnut and peak oak pollen concentrations, and tends to overestimate grass pollen concentrations. The model shows reasonable agreement with observed birch, olive, and mulberry tree pollen concentrations. Sensitivity studies suggest that the estimation of the pollen pool is a major source of uncertainty for simulated pollen concentrations. Achieving agreement between emission modeling and observed pattern of pollen releases is the key for successful pollen concentration simulations.

Description: Carbon dioxide fluxes at an intensively cultivated temperate lowland peatland in the East Anglian Fens, UK Biogeosciences Discussions, 10, 4193-4223, 2013 Author(s): R. Morrison, A. M. J. Cumming, H. E. Taft, J. Kaduk, S. E. Page, D. L. Jones, R. J. Harding, and H. Balzter This study reports the first recorded CO 2 flux measurements of a drained and intensively cultivated lowland peatland in the East Anglian Fens (UK) using the eddy covariance technique. Measurements were made over a complete lettuce crop rotation and a subsequent fallow period. Maximum average daytime CO 2 uptake and nocturnal loss rates were −10.39 and 7.63 μmol CO 2 m −2 s −1 , respectively. Daily CO 2 budgets ranged from a net loss of 4.7 to a small net uptake of −1.23 g CO 2 -C m −2 d −1 . Total vertical land/atmosphere CO 2 losses were estimated at 227.11 ± 46.5 g CO 2 -C m −2 for a~120 day measurement period. Losses over a sixty day interval between field preparation and disking of the field at the end of the crop cycle were 74.22 ± 18.8 g CO 2 -C m −2 . The site lost 152.89 ± 30.6 g CO 2 -C m −2 d −1 during a sixty day fallow period. Net ecosystem production was estimated at 117.72 ± 18.8 g CO 2 -C m −2 during the crop cycle and 270.61 ± 46.49 g CO 2 -C m −2 for the entire measurement period when harvested crop exports were accounted for. These results represent the first micrometeorological measurements obtained over degraded lowland peatland in Britain, and illustrate the scale of CO 2 losses associated with agricultural production on temperate organic soils.

Description: Microbial bioavailability regulates organic matter preservation in marine sediments Biogeosciences Discussions, 9, 13187-13210, 2012 Author(s): K. A. Koho, K. G. J. Nierop, L. Moodley, J. J. Middelburg, L. Pozzato, K. Soetaert, J. van der Plicht, and G.-J. Reichart Burial of organic matter (OM) plays an important role in marine sediments, linking the short-term, biological carbon cycle with the long-term, geological subsurface cycle. It is well established that low-oxygen conditions promote organic carbon burial in marine sediments. However, the mechanism remains enigmatic. Here we report biochemical quality, microbial degradability, OM preservation and accumulation along an oxygen gradient in the Indian Ocean. Our results show that more OM, and of biochemically higher quality, accumulates under low oxygen conditions. Nevertheless, microbial degradability does not correlate with the biochemical quality of OM. This decoupling of OM biochemical quality and microbial degradability, or bioavailability, violates the ruling paradigm that higher quality implies higher microbial processing. The inhibition of bacterial OM remineralisation may play an important role in the burial of organic matter in marine sediments and formation of oil source rocks.

Description: Impact of an 8.2-kyr-like event on methane emissions in northern peatlands Biogeosciences Discussions, 9, 13243-13286, 2012 Author(s): S. Zürcher, R. Spahni, F. Joos, M. Steinacher, and H. Fischer Rapid changes in atmospheric methane (CH 4 ), temperature and precipitation are documented by Greenland ice core data both for glacial times (the so called Dangaard-Oeschger (DO) events) as well as for a cooling event in the early Holocene (the 8.2 kyr event). The onsets of DO warm events are paralleled by abrupt increases in CH 4 by up to 250 ppbv in a few decades. Vice versa, the 8.2 kyr event is accompanied by an intermittent decrease in CH 4 of about 80 ppbv over 150 yr. The abrupt CH 4 changes are thought to mainly originate from source emission variations in tropical and boreal wet ecosystems, but complex process oriented bottom-up model estimates of the changes in these ecosystems during rapid climate changes are still missing. Here we present simulations of CH 4 emissions from northern peatlands with the LPJ-Bern dynamic global vegetation model. The model represents CH 4 production and oxidation in soils and transport by ebullition, through plant aerenchyma, and by diffusion. Parameters are tuned to represent site emission data as well as inversion-based estimates of northern wetland emissions. The model is forced with climate input data from freshwater hosing experiments using the NCAR CSM1.4 climate model to simulate an abrupt cooling similar to the widespread 8.2 kyr event. As a main result we get a concentration reduction of ~10 ppbv per degree K change of mean northern hemispheric surface temperature in peatlands. This sensitivity comprises effects on peatland emissions of similar size by the temperature itself as well as by the accompanying change in precipitation rate, hence water table. Comparison with the ice core record reveals that a change in boreal peatland emissions alone could not completely account for the 80 ppbv methane decline during the 8.2 kyr event, pointing to a significant contribution from tropical wetlands to this event.

Description: Temporal variation of nitrate and phosphate transport in headwater catchments: the hydrological controls and landuse alteration Biogeosciences Discussions, 9, 13211-13241, 2012 Author(s): T.-Y. Lee, J.-C. Huang, S.-J. Kao, and C.-P. Tung Oceania Rivers are hotspots of high DIN (dissolved inorganic nitrogen) and DIP (dissolved inorganic phosphorus) transport. However, the effects of hydrologic controls and land use alternation on the temporal variations of DIN and DIP are rarely documented. In this study, we monitored the nitrate and phosphate concentrations from three headwater catchments with different cultivation gradients at a 3-day interval. This sampling scheme was supplemented with a 3-h interval monitoring during typhoon periods. The results showed that the DIN and DIP yields in the pristine, moderately cultivated, and intensively cultivated watersheds were 7.52/0.31, 31.17/0.30, and 40.96/0.52 kg ha −1 yr −1 , respectively. The high DIN yields are comparable to the intensively and extensively disturbed large rivers around the world. These N yields may be due to a high level of nitrogen deposition, rainfall-runoff, and fertilizer application. The importance of event sampling was indicated by the contribution of the three typhoons to the annual DIN and DIP fluxes, which were 30% and 60%, respectively. Both DIN and DIP fluxes significantly increased as the cultivation gradient increased. The DIN and DIP ratio varied from 54 to 230 depending on the decrease of the cultivation gradient. This value is higher than the global mean of ~18. Thus, we speculate that nitrogen saturation occurs in the headwater catchments of Oceania Rivers. The results obtained provide fundamental clues of DIN and DIP yield of Oceania Rivers, which are helpful in understanding the impact of human disturbance on headwater watersheds.

Description: Ammonia emissions from cattle urine and dung excreted on pasture Biogeosciences Discussions, 9, 13287-13318, 2012 Author(s): J. Laubach, A. Taghizadeh-Toosi, S. J. Gibbs, R. R. Sherlock, F. M. Kelliher, and S. P. P. Grover Twelve cattle were kept for three days in a circular area of 16 m radius on short pasture and fed with freshly-cut pasture. Ammonia (NH 3 ) emissions from the urine and dung excreted by the cattle were measured with a micrometeorological mass-balance method, during the cattle presence and for 10 subsequent days. Daily-integrated emission rates peaked on day 3 of the experiment (last day of cattle presence) and declined steadily for five days thereafter. Urine patches were the dominant sources for these emissions. On day 9, a secondary emissions peak occurred, with dung pats likely to be the main sources. This interpretation is based on simultaneous observations of the pH evolution in urine patches and dung pats created next to the circular plot. Feed and dung samples were analysed to estimate the amounts of nitrogen (N) ingested and excreted. Total N volatilised as NH 3 was 19.8 (±0.9) % of N intake and 22.4 (±1.3) % of N excreted. The bimodal shape of the emissions time series allowed to infer separate estimates for volatilisation from urine and dung, respectively, with the result that urine accounted for 88.6 (±2.6) % of the total NH 3 emissions. The emissions from urine represented 25.5 (±2.0) % of the excreted urine-N, while the emissions from dung amounted to 11.6 (±2.7) % of the deposited dung-N. Emissions from dung may have continued after day 13 but were not resolved by the measurement technique. A simple resistance model shows that the magnitude of the emissions from dung is controlled by the resistance of the dung crust.

Description: Isoprene emissions from a tundra ecosystem Biogeosciences Discussions, 9, 13351-13396, 2012 Author(s): M. J. Potosnak, B. M. Baker, L. LeStourgeon, S. M. Disher, K. L. Griffin, and M. S. Bret-Harte Whole-system fluxes of isoprene from a~moist acidic tundra ecosystem and leaf-level emission rates of isoprene from a common species ( Salix pulchra ) in that same ecosystem were measured during three separate field campaigns. The field campaigns were conducted during the summers of 2005, 2010 and 2011 and took place at the Toolik Field Station (68.6° N, 149.6° W) on the north slope of the Brooks Range in Alaska, USA. The maximum rate of whole-system isoprene flux measured was over 1.2 mg C m −2 h −1 with an air temperature of 22 ° C and a PAR level over 1500 μmol m −2 s −1 . Leaf-level isoprene emission rates for S. pulchra averaged 12.4 nmol m −2 s −1 (27.4 μg C gdw −1 h −1 ) extrapolated to standard conditions (PAR = 1000 μmol m −2 s −1 and leaf temperature = 30° C). Leaf-level isoprene emission rates were well characterized by the Guenther algorithm for temperature, but less so for light. Chamber measurements from a nearby moist acidic tundra ecosystem with less S. pulchra emitted significant amounts of isoprene, but at lower rates (0.45 mg C m −2 h −1 ). Comparison of our results to predictions from a global model found broad agreement, but a detailed analysis revealed some significant discrepancies. An atmospheric chemistry box model predicts that the observed isoprene emissions have a significant impact on Arctic atmospheric chemistry, including the hydroxyl radical (OH). Our results support the prediction that isoprene emissions from Arctic ecosystems will increase with global climate change.

Description: Seasonal measurements of total OH reactivity fluxes, total ozone loss rates and missing emissions from Norway spruce in 2011 Biogeosciences Discussions, 9, 13497-13536, 2012 Author(s): A.C. Nölscher, E. Bourtsoukidis, B. Bonn, J. Kesselmeier, J. Lelieveld, and J. Williams Numerous reactive volatile organic compounds (VOCs) are emitted into the atmosphere by vegetation. Most biogenic VOCs are highly reactive towards the atmosphere's most important oxidant, the hydroxyl (OH) radical. One way to investigate the chemical interplay between biosphere and atmosphere is through the measurement of total OH reactivity, the total loss rate of OH radicals. This study presents the first determination of total OH reactivity emission rates (measurements via the Comparative Reactivity Method) based on a branch cuvette enclosure system mounted on a Norway spruce (Picea abies) throughout spring, summer and autumn 2011. In parallel separate VOC emission rates were monitored by a Proton Transfer Reaction-Mass Spectrometer (PTR-MS), and total ozone (O 3 ) loss rates were obtained inside the cuvette. Total OH reactivity emission rates were in general temperature and light dependent, showing strong diel cycles with highest values during daytime. Monoterpene emissions contributed most, accounting for 56–69% of the measured total OH reactivity flux in spring and early summer. However, during late summer and autumn the monoterpene contribution decreased to 11–16%. At this time, a large missing fraction of the total OH reactivity emission rate (70–84%) was found when compared to the VOC budget measured by PTR-MS. Total OH reactivity and missing total OH reactivity emission rates reached maximum values in late summer corresponding to the period of highest temperature. Total O 3 loss rates within the closed cuvette showed similar diel profiles and comparable seasonality to the total OH reactivity fluxes. Total OH reactivity fluxes were also compared to emissions from needle storage pools predicted by a temperature-only dependent algorithm. Deviations of total OH reactivity fluxes from the temperature-only dependent emission algorithm were observed for occasions of mechanical and heat stress. While for mechanical stress, induced by strong wind, measured VOCs could explain total OH reactivity emissions, during heat stress they could not. The temperature driven algorithm matched the diel course much better in spring than in summer, indicating a different production and emission scheme for summer and early autumn. During these times, unmeasured and possibly unknown primary biogenic emissions contributed significantly to the observed total OH reactivity flux.

Description: Increasing cloudiness in Arctic damps the increase in phytoplankton primary production due to sea ice receding Biogeosciences Discussions, 9, 13987-14012, 2012 Author(s): S. Bélanger, M. Babin, and J.-E. Tremblay The Arctic Ocean and its marginal seas are among the marine regions most affected by climate change. Here we present the results of a diagnostic model used to elucidate the main drivers of primary production (PP) trends over the 1998–2010 period at pan-Arctic and local (i.e. 9.28 km resolution) scales. Photosynthetically active radiation (PAR) above and below the sea surface was estimated using precomputed look-up tables of spectral irradiance and satellite-derived cloud optical thickness and cloud fraction parameters from the International Satellite Cloud Climatology Project (ISCCP) and sea ice concentration from passive microwaves data. A spectrally resolved PP model, designed for optically complex waters, was then used to produce maps of PP trends. Results show that incident PAR above the sea surface (PAR(0+)) has significantly decreased over the whole Arctic and sub-Arctic Seas, except over the perrennially sea ice covered waters of the Central Arctic Ocean. This fading of PAR(0+) (+8% decade –1 ) was caused by increasing cloudiness May and June. Meanwhile PAR penetrating the ocean (PAR(0–)) increased only along the sea ice margin over the large Arctic continental shelf where sea ice concentration declined sharply since 1998. Overall, PAR(0–) slightly increased in the Circum Arctic (+3.4% decade –1 ), while it decreased when considering both Arctic and sub-Arctic Seas (–3% decade –1 ). We showed that rising phytoplankton biomass (i.e. chlorophyll a ) normalized by the diffuse attenuation of photosynthetically usable radiation (PUR) by phytoplankton accounted for a larger proportion of the rise in PP than did the increase in light availability due to sea-ice loss in several sectors and particularly in perrennially and seasonally open waters. Against a general backdrop of rising productivity over Arctic shelves, significant negative trends were observed in regions known for their great biological importance such as the coastal polynyas of Northern Greenland.

Description: Storage and stability of organic carbon in soils as related to depth, occlusion within aggregates, and attachment to minerals Biogeosciences Discussions, 9, 13085-13133, 2012 Author(s): M. Schrumpf, K. Kaiser, G. Guggenberger, T. Persson, I. Kögel-Knabner, and E.-D. Schulze Conceptual models suggest that stability and age of organic carbon (OC) in soil depends on the source of plant litter, occlusion within aggregates, incorporation in organo-mineral complexes, and location within the soil profile. Various tools like density fractionation, mineralization experiments, and radiocarbon analyses have been used to study the importance of these mechanisms. We systematically apply them to a range of European soils to test whether general controls emerge even for soils that vary in vegetation, soil types, parent material, and land use. At each of the 12 study sites, 10 soil cores were sampled in 10 cm depth intervals to 60 cm depth and subjected to density separation. Bulk soil samples and density fractions (free light fractions – fLF, occluded light fractions – oLF, heavy fractions – HF) were analysed for OC, total nitrogen (TN), δ 13 C, and Δ 14 C. Bulk samples were also incubated to determine mineralizable OC. Declining OC-normalized CO 2 release and increasing age with soil depth confirm greater stability of OC in subsoils across sites. Depth profiles of LF-OC matched those of roots, which in turn reflect plant functional types in soil profiles not subject to ploughing. Modern Δ 14 C signatures and positive correlation between mineralizable C and fLF-OC indicate the fLF is an easily available energy and nutrient source for subsurface microbes. Fossil C derived from the geogenic parent material affected the age of OC especially in the LF at three study sites. The overall importance of OC stabilization by binding to minerals was demonstrated by declining OC-normalized CO 2 release rates with increasing contributions of HF-OC to bulk soil OC and the low Δ 14 C values of HF-OC. The stability of HF-OC was greater in subsoils than in topsoils; nevertheless, a portion of HF-OC was active throughout the profile. The decrease in Δ 14 C (increase in age) of HF-OC with soil depth was related to soil pH as well as to dissolved OC fluxes. This indicates that dissolved OC translocation contributes to the formation of subsoil HF-OC and shapes the Δ 14 C profiles. While quantitatively less important than OC in the HF, consistent older ages of oLF-OC than fLF-OC indicate that occlusion of LF-OC in aggregates also contributes to OC stability in subsoils. Overall, our results showed that association with minerals is the most important factor in stabilization of OC in soils.

Description: The non-steady-state oceanic CO 2 signal: its importance, magnitude and a novel way to detect it Biogeosciences Discussions, 9, 13161-13186, 2012 Author(s): B. I. McNeil and R. J. Matear The ocean's role has been pivotal in modulating rising atmospheric CO 2 levels since the industrial revolution, sequestering over a quarter of all fossil-fuel derived CO 2 emissions. Net oceanic uptake of CO 2 has roughly doubled between the 1960's (~1 Pg C yr −1 ) and 2000's (~2 Pg C yr −1 ), with expectations it will continue to absorb even more CO 2 with rising future atmospheric CO 2 levels. However, recent CO 2 observational analyses along with numerous model predictions suggest the rate of oceanic CO 2 uptake is already slowing, largely as a result of a natural decadal-scale outgassing signal. This recent and unexpected CO 2 outgassing signal represents a paradigm-shift in our understanding of the oceans role in modulating atmospheric CO 2 . Current tracer-based estimates for the ocean storage of anthropogenic CO 2 assume the ocean circulation and biology is in steady state, thereby missing the new and potentially important "non-steady-state" CO 2 outgassing signal. By combining data-based techniques that assume the ocean is in steady-state, with techniques that constrain the net oceanic CO 2 uptake signal, we show how to extract the non-steady-state CO 2 signal from observations. Over the entire industrial era, the non-steady-state CO 2 outgassing signal (~13 ± 10 Pg C) is estimated to represent about 9% of the total net CO 2 inventory change (~142 Pg C). However between 1989 and 2007, the non-steady-state CO 2 outgassing signal (~6.3 Pg C) has likely increased to be ~18% of net oceanic CO 2 storage over that period (~36 Pg C), a level which cannot be ignored. The present uncertainty of our data-based techniques for oceanic CO 2 uptake limit our capacity to quantify the non-steady-state CO 2 signal, however with more data and better certainty estimates across a~range of diverse methods, this important and growing CO 2 signal could be better constrained in the future.

Description: Diversity pattern of nitrogen fixing microbes in nodules of Trifolium arvense (L.) at different initial stages of ecosystem development Biogeosciences Discussions, 9, 13135-13160, 2012 Author(s): S. Schulz, M. Engel, D. Fischer, F. Buegger, M. Elmer, G. Welzl, and M. Schloter Legumes can be considered as pioneer plants during ecosystem development, as they form a symbiosis with different nitrogen fixing rhizobia species, which enable the plants to grow on soils with low available nitrogen content. In this study we compared the abundance and diversity of nitrogen fixing microbes based on the functional marker gene nifH , which codes for a subunit of the Fe-protein of the dinitrogenase reductase, in nodules of different size classes of Trifolium arvense (L.). Additionally, carbon and nitrogen contents of the bulk soil and plant material were measured. Plants were harvested from different sites, reflecting 2 (2a) and 5 (5a) yr of ecosystem development, of an opencast lignite mining area in the south of Cottbus, Lower Lusatia (Germany) where the artificial catchment "Chicken Creek" was constructed to study the development of terrestrial ecosystems. Plants from the 5a site revealed higher amounts of carbon and nitrogen, although nifH gene abundances in the nodules and carbon and nitrogen contents between the two soils did not differ significantly. Analysis of the nifH clone libraries showed a significant effect of the nodule size on the community composition of nitrogen fixing microbes. Medium sized nodules (2–5 mm) contained a uniform community composed of Rhizobium leguminosarum bv. trifolii , whereas the small nodules ( 〈 2 mm) consisted of a diverse community including clones with non- Rhizobium nifH gene sequences. Regarding the impact of the soil age on the community composition a clear distinction between the small and the medium nodules can be made. While clone libraries from the medium nodules were pretty similar at both soil ages, soil age had a significant effect on the community compositions of the small nodules, where the proportion of R. leguminosarum bv. trifolii increased with soil age.

Description: The climate dependence of the terrestrial carbon cycle; including parameter and structural uncertainties Biogeosciences Discussions, 9, 13439-13496, 2012 Author(s): M. J. Smith, M. C. Vanderwel, V. Lyutsarev, S. Emmott, and D. W. Purves The feedback between climate and the terrestrial carbon cycle will be a key determinant of the dynamics of the Earth System over the coming decades and centuries. However Earth System Model projections of the terrestrial carbon-balance vary widely over these timescales. This is largely due to differences in their carbon cycle models. A major goal in biogeosciences is therefore to improve understanding of the terrestrial carbon cycle to enable better constrained projections. Essential to achieving this goal will be assessing the empirical support for alternative models of component processes, identifying key uncertainties and inconsistencies, and ultimately identifying the models that are most consistent with empirical evidence. To begin meeting these requirements we data-constrained all parameters of all component processes within a global terrestrial carbon model. Our goals were to assess the climate dependencies obtained for different component processes when all parameters have been inferred from empirical data, assess whether these were consistent with current knowledge and understanding, assess the importance of different data sets and the model structure for inferring those dependencies, assess the predictive accuracy of the model, and to identify a methodology by which alternative component models could be compared within the same framework in future. Although formulated as differential equations describing carbon fluxes through plant and soil pools, the model was fitted assuming the carbon pools were in states of dynamic equilibrium (input rates equal output rates). Thus, the parameterised model is of the equilibrium terrestrial carbon cycle. All but 2 of the 12 component processes to the model were inferred to have strong climate dependencies although it was not possible to data-constrain all parameters indicating some potentially redundant details. Similar climate dependencies were obtained for most processes whether inferred individually from their corresponding data sets or using the full terrestrial carbon model and all available data sets, indicating a strong overall consistency in the information provided by different data sets under the assumed model formulation. A notable exception was plant mortality, in which qualitatively different climate dependencies were inferred depending on the model formulation and data sets used, highlighting this component as the major structural uncertainty in the model. All but two component processes predicted empirical data better than a null model in which no climate dependency was assumed. Equilibrium plant carbon was predicted especially well (explaining around 70% of the variation in the withheld evaluation data). We discuss the advantages of our approach in relation to advancing our understanding of the carbon cycle and enabling Earth System Models make better constrained projections.