ALBERT

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Description: 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: Greenstreet, S. P. R., Fraser, H. M., Rogers, S. I., Trenkel, V. M., Simpson, S. D., and Pinnegar, J. K. 2012. Redundancy in metrics describing the composition, structure, and functioning of the North Sea demersal fish community. – ICES Journal of Marine Science, 69: 8–22. Broader ecosystem management objectives for North Sea demersal fish currently focus on restoring community size structure. However, most policy drivers explicitly concentrate on restoring and conserving biodiversity, and it has not yet been established that simply restoring demersal fish size composition will be sufficient to reverse declines in biodiversity and ensure a generally healthy community. If different aspects of community composition, structure, and function vary independently, then to monitor all aspects of community general health will require application of a suite of metrics. This assumes low redundancy among the metrics used in any such suite and implies that addressing biodiversity issues specifically will require explicit management objectives for particular biodiversity metrics. This issue of metric redundancy is addressed, and 15 metrics covering five main attributes of community composition, structure, and function are applied to groundfish survey data. Factor analysis suggested a new interpretation of the metric information and indicated that a minimum suite of seven metrics was necessary to ensure that all changes in the general health of the North Sea demersal fish community were monitored properly. Covariance among size-based and species-diversity metrics was low, implying that restoration of community size structure would not necessarily reverse declines in species diversity.

Description: Dankel, D. J., Aps, R., Padda, G., Röckmann, C., van der Sluijs, J. P., Wilson, D. C., and Degnbol, P. 2012. Advice under uncertainty in the marine system. – ICES Journal of Marine Science, 69: 3–7. There is some uncertainty in the fisheries science–policy interface. Although progress has been made towards more transparency and participation in fisheries science in ICES Areas, routine use of state-of-the-art quantitative and qualitative tools to address uncertainty systematically is still lacking. Fisheries science that gives advice to policy-making is plagued by uncertainties; the stakes of the policies are high and value-laden and need therefore to be treated as an example of "post-normal science" (PNS). To achieve robust governance, understanding of the characteristics and implications of the scientific uncertainties for management strategies need to come to the centre of the table. This can be achieved using state-of-the-art tools such as pedigree matrices and uncertainty matrices, as developed by PNS scholars and used in similar science–policy arenas on other complex issues. An explicit extension of the peer community within maritime systems will be required to put these new tools in place. These new competences become even more important as many countries within the ICES Area are now embarking on new policies.

Description: Browman, H.I. 2012. Quo Vadimus. – ICES Journal of Marine Science, 69: 1–2.

Description: Hüssy, K., Coad, J. O., Farrell, E. D., Clausen, L. A. W., and Clarke, M. W. 2012. Age verification of boarfish ( Capros aper ) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 34–40. The boarfish ( Capros aper ) is a pelagic species of recent interest to the fishing industry, with landings increasing by 〉500% over the past 3 years. The objective of the study was to provide a method for age determination based on whole sagittal otoliths, with the results to be used in stock assessment. Translucent zones laid down at regular intervals are identified by marginal increment analysis as seasonally recurring. Translucent zones are formed between September/October and March/April, regardless of fish age. The occurrence of the first annulus is validated by analysis of presumed daily growth increments. Subsequent annulus deposition is homogenous between individuals and allows general guidelines to be derived for interpreting the age of boarfish using their otoliths.

Description: Kim, D., Yang, E. J., Kim, K. H., Shin, C-W., Park, J., Yoo, S., and Hyun, J-H. 2012. Impact of an anticyclonic eddy on the summer nutrient and chlorophyll a distributions in the Ulleung Basin, East Sea (Japan Sea). – ICES Journal of Marine Science, 69: 23–29. The impact of the anticyclonic Ulleung Warm Eddy (UWE) on the vertical distributions of nutrient and chlorophyll a (Chl a ) concentrations in the Ulleung Basin (UB) was investigated during the contrasting summers of 2005 and 2007. The physical structure of the water column was characterized by an intrathermocline eddy (ITE) in 2005, whereas the UWE remained distant from the sampling transect in 2007. Water column structures appeared to be highly stratified, and nutrients in the surface waters were totally depleted at all stations. In 2005, an exceptionally high concentration of Chl a (5.5 mg m –3 ) was measured below the surface mixed layer in the eddy core (station D3), and values of ~2.5 mg m –3 were observed at the eddy edge (stations D2 and D4). Formation of an ITE efficiently mixed surface and deep-ocean waters, the latter supplying sufficient nutrients to generate an extremely high concentration of Chl a at the base of the subsurface layer. Overall, the results indicated that the anticyclonic UWE plays a key ecological role in supporting substantial phytoplankton biomass in the nutrient-depleted surface waters in summer and maintaining high benthic mineralization in the deep-sea sediments of the UB.

Description: Franchini, P., Sola, L., Crosetti, D., Milana, V., and Rossi, A. R. 2012. Low levels of population genetic structure in the gilthead sea bream, Sparus aurata , along the coast of Italy. – ICES Journal of Marine Science, 69: 41–50. The gilthead sea bream, Sparus aurata , is a coastal, commercially important fish. Contrasting results concerning the genetic structure of the species at different geographic scales have been reported. Here, an investigation is made into the population genetic structure of S. aurata along the coast of Italy, using samples analysed previously and material from new sampling sites (12) and using different microsatellite loci (10). One sample from the eastern Atlantic and three temporal replicates from one site were also included. The presence of a weak (overall F ST = 0.0072), but significant, genetic population subdivision was detected by F -statistics. Temporal replicates indicate genetic data consistency over time. Isolation by distance between the Atlantic and the coast of Italy is suggested by a Mantel test. The distributional pattern of genetic variance obtained by analysis of molecular variation reflects the geographic sampling areas, but is only partially congruent with the results obtained with fewer sites and loci. The dispersal of passive eggs/larvae by the main currents appears to contribute to shaping the gene flow. Given the intensity of sea bream aquaculture activities in Italy, the possibility that aquaculture may have partially contributed to the population genetic pattern detected cannot be excluded.

Description: Charrier, F., Mazel, V., Caraguel, J-M., Abdallah, Y., Le Gurun, L. L., Legault, A., and Laffaille, P. 2012. Escapement of silver-phase European eels, Anguilla anguilla , determined from fishing activities in a Mediterranean lagoon (Or, France). – ICES Journal of Marine Science, 69: 30–33. Escapement of silver eels from a Mediterranean lagoon was estimated by a capture–tagging–recapture and automated tag-reading study. The population of silver-phase eels in the lagoon was estimated to be 13.2 kg ha –1 , with an escapement rate from the commercial fishery of 76.8%.

Description: Jennings, S., and Lee, J. 2012. Defining fishing grounds with vessel monitoring system data. – ICES Journal of Marine Science, 69: 51–63. Methods for defining fishing grounds to support marine spatial planning and management are developed, applied, and compared. The methods are broadly applicable and repeatable because they use vessel monitoring system (VMS) data that are archived and increasingly accessible. For several fleets at regional and national scales, an attempt is made to assess how the choice of criteria for defining grounds influences (i) size, shape, and location, (ii) overlap among grounds, and (iii) the extent to which annual and multi-annual patterns of fishing activity describe grounds used seasonally or by individual vessels. The results show that grounds defined by excluding infrequently fished margins (areas with 〈10% of total fishing activity) are typically 50% smaller than total fished area. However, landings weight or value (LWV) per unit activity can be higher at the margins, with 10% of activity usually accounting for 10–20% of LWV. The removal of fishing activity in the margins, as a consequence of regulation or fleet behaviour, would lead to disproportionately greater reductions in interactions with other fisheries, sectors, and the environment. Accessible high-resolution information on the "anatomy" of all fishing grounds would better inform debates on the allocation and the use of marine space and the integration of fisheries and environmental management.

Description: Bentley, N., Kendrick, T. H., Starr, P. J., and Breen, P. A. 2012. Influence plots and metrics: tools for better understanding fisheries catch-per-unit-effort standardizations. – ICES Journal of Marine Science, 69: 84–88. Standardization of catch per unit effort using generalized linear models (GLMs) is a common procedure that attempts to remove the confounding effects of variables other than abundance. Simple plots and metrics are described to assist understanding the standardization effects of explanatory variables included in GLMs, illustrated with an example based on New Zealand trevally ( Caranx lutescens ) data.

Description: Aldrin, M., Mortensen, B., Storvik, G., Nedreaas, K., Aglen, A., and Aanes, S. 2012. Improving management decisions by predicting fish bycatch in the Barents Sea shrimp fishery. – ICES Journal of Marine Science, 69: 64–74. When the bycatch of juvenile fish within the Barents Sea shrimp fishery is too large, the area is closed to fishing for a certain period. Bycatch is estimated from sampled trawl hauls, for which the shrimp yield is recorded, along with the total number of various bycatch fish species. At present, bycatch estimation is based on a simple estimator, the sum of the number of fish caught within the area of interest within a small time window, divided by the corresponding shrimp yield (in weight). No historical data are used. A model-based estimation is proposed in which spatio-temporal models are constructed for the variation in both the yield of shrimp and the amount of bycatch in space and time. The main effects are described through generalized additive models, and local dependence structures are specified through correlated random effects. Model estimation includes historical and recent data. Experiments with both simulated and real data show that the model-based estimator outperforms the present simple estimator when a low or moderate number of samples (e.g. 〈20) is available, whereas the two estimators are equally good when the number of samples is high.

Description: Jiao, Y., Smith, E. P., O'Reilly, R., and Orth, D. J. 2012. Modelling non-stationary natural mortality in catch-at-age models. – ICES Journal of Marine Science, 69: 105–118. Non-stationarity in the natural mortality of many species has been discussed among research scientists, but no generally applicable models/methods have been developed where a statistical catch-at-age (SCA) model framework is used. Using the Atlantic weakfish ( Cynoscion regalis ) fishery as an example, several SCA models are developed to assess the population dynamics, then compared. Models used included (i) an SCA with constant natural mortality, (ii) an SCA with unknown natural mortality, but with a hierarchical prior distribution from a mixture of distributions based on life-history information, (iii) an SCA with age-specific unknown natural mortality, (iv) an SCA with time-varying natural mortality, following a random-walk process, and (v) an SCA with age-specific time-varying natural mortality. The last two models imply that the population dynamics are not stationary. A Bayesian approach was used to estimate parameters, and performance of the models was compared through goodness-of-fit and the retrospective patterns of the models. A simulation study was then conducted to test the uncertainty resulting from model selection, the efficiency of using the best model selected based on deviance information criterion, and whether changes in natural mortality could be detected. An SCA with time-varying natural mortality, following a random-walk process, is proposed for the example fishery here. The estimated non-stationary temporal patterns in natural mortality were linked further to climate–ocean oscillation indices, to diagnose possible mechanisms/linkages to these temporal variations in natural mortality.

Description: Juntunen, T., Vanhatalo, J., Peltonen, H., and Mäntyniemi, S. 2012. Bayesian spatial multispecies modelling to assess pelagic fish stocks from acoustic- and trawl-survey data. – ICES Journal of Marine Science, 69: 95–104. A Bayesian spatial model was constructed to estimate the abundance of multiple fish species in a pelagic environment. Acoustic- and trawl-survey data were combined with environmental data to predict the spatial distribution of (i) the acoustic backscattering of fish, (ii) the relative proportion of each species, and (iii) their mean length in the Gulf of Finland in the northeastern Baltic Sea. By combining the three spatial model layers, the spatial distribution of the biomass of each species was estimated. The model consists of a linear predictor on environmental variables and a spatial random effect given by a Gaussian process. A Bayesian approach is a natural choice for the task because it provides a theoretically justified means of summarizing the uncertainties from various model layers. In the study area, three species dominate pelagic waters: sprat ( Sprattus sprattus ), herring ( Clupea harengus ), and three-spined stickleback ( Gasterosteus aculeatus ). Results are presented for each model layer and for estimated total biomass for each species in 2 x 2 km lattices. The posterior mean and central 95% credible intervals of total biomass were sprat 45.7 kt (27.7–71.6), herring 24.6 kt (9.7–41.3), and three-spined stickleback 1.9 kt (0.9–3.2).

Description: Smith, W. K., and Solow, A. R. 2012. Missing and presumed lost: extinction in the ocean and its inference. – ICES Journal of Marine Science, 69: 89–94. The number of modern extinctions in the ocean is unknown. The actual demise of the last individual of a species is essentially unobservable, so extinction can only be inferred. Statistical methods are described for inferring extinction from sighting records, species–area considerations, and taxonomic samples collected at two different times. The methods are illustrated using a variety of real datasets, including a sighting record of the Caribbean monk seal and results from three surveys of benthic invertebrates.

Description: Delavenne, J., Metcalfe, K., Smith, R. J., Vaz, S., Martin, C. S., Dupuis, L., Coppin, F., and Carpentier, A. 2012. Systematic conservation planning in the eastern English Channel: comparing the Marxan and Zonation decision-support tools. – ICES Journal of Marine Science, 69: 75–83. The systematic conservation approach is now commonly used for the design of efficient marine protected area (MPA) networks, and identifying these priority areas often involves using specific conservation-planning software. Several such software programmes have been developed in recent years, each differing in the underlying algorithms used. Here, an investigation is made into whether the choice of software influences the location of priority areas by comparing outputs from Marxan and Zonation, two widely used conservation-planning, decision-support tools. Using biological and socio-economic data from the eastern English Channel, outputs are compared and it is shown that the two software packages identified similar sets of priority areas, although the relatively wide distribution of habitat types and species considered offered much flexibility. Moreover, the similarity increased with increasing spatial constraint, especially when using real-world cost data, suggesting that the choice of cost metric has a greater influence on conservation-planning analyses than the choice of software. However, Marxan generally produced more efficient results and Zonation produced results with greater connectivity, so the most appropriate software package will depend on the overall goals of the MPA planning process.

Description: Andersen, B. S., Ulrich, C., Eigaard, O. R., and Christensen, A-S. 2012. Short-term choice behaviour in a mixed fishery: investigating métier selection in the Danish gillnet fishery. – ICES Journal of Marine Science, 69: 131–143. The study presents a short-term effort allocation modelling approach based on a discrete choice random utility model combined with a survey questionnaire to examine the selection of métiers (a combination of fishing area and target species) in the Danish North Sea gillnet fishery. Key decision variables were identified from the survey questionnaire, and relevant proxies for the decision function were identified based on available landings and effort information. Additional variables from the survey questionnaire were further used to validate and verify the outcome of the choice model. Commercial fishers in a mixed fishery make use of a number of decision variables used previously in the literature, but also a number of decision parameters rarely explicitly accounted for, such as price, weather, and management regulation. The seasonal availability of individual target species and within-year changes in monthly catch ration were the main explanatory drivers, but gillnetters were also responsive to information on the whole fishery, fish prices, and distance travelled to fishing grounds. Heterogeneous responses were evident from geographic differences in home harbour, which underpins the need to understand alternative fishing strategies among individual gillnetters better.

Description: Calise, L., and Knutsen, T. 2012. Multifrequency target strength of northern krill ( Meganyctiphanes norvegica ) swimming horizontally. – ICES Journal of Marine Science, 69: 119–130. Multifrequency acoustic measurements on ex situ horizontally swimming krill were made in a novel experimental setting. An ensemble of northern krill ( Meganyctiphanes norvegica ) was introduced to a large enclosure (a mesocosm), and acoustic backscatter was sampled using a multifrequency (70, 120, and 200 kHz) echosounder (Simrad EK60). Two submerged lamps were placed at opposite sides of the mesocosm and switched on and off to induce the krill, by light attraction, to swim horizontally through the acoustic beams. By tracking echoes, animal displacement, swimming speed, and target strength ( TS ) by frequency were estimated. The dominant and secondary modes of the total-length distribution were 21.8 ± 3.0 and 27.8 ± 2.7 mm, respectively. Although krill orientation was assumed stable and the ping rate was high, the range and inter-ping variability of the average TS values were large, decreasing and increasing with frequency, respectively. The overall TS frequency response observed and concurrent measurements at 120 and 200 kHz confirm the theoretical expectation that the acoustic backscatter from the investigated organisms were confined to the Rayleigh and Geometric scattering regions, a finding that might both aid acoustic identification and size-group separation of in situ northern krill.

Description: Factors influencing the stable carbon isotopic composition of suspended and sinking organic matter in the coastal Antarctic sea ice environment Biogeosciences Discussions, 8, 11041-11088, 2011 Author(s): S. F. Henley, A. L. Annett, R. S. Ganeshram, D. S. Carson, K. Weston, X. Crosta, A. Tait, J. Dougans, A. E. Fallick, and A. Clarke A high resolution time-series analysis of stable carbon isotopic signatures in particulate organic carbon (δ 13 C POC ) and associated biogeochemical parameters in sea ice and surface waters provides an insight into the factors affecting δ 13 C POC in the coastal western Antarctic Peninsula (WAP) sea ice environment. The study covers two austral summer seasons in Ryder Bay, northern Marguerite Bay between 2004 and 2006. A shift in diatom species composition during the 2005/2006 summer bloom to near-complete biomass dominance of Proboscia inermis is strongly correlated with a large ~10‰ negative isotopic shift in δ 13 C POC that cannot be explained by a concurrent change in concentration or isotopic signature of CO 2 . We hypothesise that the δ 13 C POC shift may be driven by the contrasting biochemical mechanisms and utilisation of carbon-concentrating mechanisms in different diatom species. These short-lived yet pronounced negative δ 13 C POC excursions drive a 4‰ decrease in the seasonal average δ 13 C POC signal, which is transferred to sediment traps and core-top sediments and consequently has the potential for preservation in the sedimentary record. This 4‰ difference between seasons of contrasting sea ice conditions and upper water column stratification matches the full amplitude of glacial-interglacial Southern Ocean δ 13 C POC variability and, as such, we invoke phytoplankton species changes as a potentially important factor influencing sedimentary δ 13 C POC . We also find significantly higher δ 13 C POC in sea ice than surface waters, consistent with autotrophic carbon fixation in a semi-closed environment and possible contributions from post-production degradation, biological utilisation of HCO 3 - and production of exopolymeric substances (EPS). This study demonstrates the importance of surface water diatom speciation effects and isotopically heavy sea ice-derived material for δ 13 C POC in Antarctic coastal environments and underlying sediments, with consequences for the utility of diatom-based δ 13 C POC in the sedimentary record.

Description: Critical loads of nitrogen deposition and critical levels of atmospheric ammonia for mediterranean evergreen woodlands Biogeosciences Discussions, 8, 11139-11163, 2011 Author(s): P. Pinho, M. R. Theobald, T. Dias, Y. S. Tang, C. Cruz, M. A. Martins-Loução, C. Máguas, M. Sutton, and C. Branquinho Nitrogen (N) has emerged in recent years as a key factor associated with global changes, with impacts on biodiversity, ecosystems functioning and human health. In order to ameliorate the effects of excessive N, safety thresholds have been established, such as critical loads (deposition fluxes) and levels (concentrations). For Mediterranean ecosystems, few studies have been carried out to assess these parameters. Our objective was therefore to determine the critical loads of N deposition and long-term critical levels of atmospheric ammonia for Mediterranean evergreen woodlands. For that we have considered changes in epiphytic lichen communities, which have been shown to be one of the most sensitive to excessive N. Based on a classification of lichen species according to their tolerance to N we grouped species into response functional groups, which we used as a tool to determine the critical loads and levels. This was done under Mediterranean climate, in evergreen cork-oak woodlands, by sampling lichen functional diversity and annual atmospheric ammonia concentrations and modelling N deposition downwind from a reduced N source (a cattle barn). By modelling the highly significant relationship between lichen functional groups and N deposition, the critical load was estimated to be below 26 kg (N) ha −1 yr −1 , which is within the upper range established for other semi-natural ecosystems. By modelling the highly significant relationship of lichen functional groups with annual atmospheric ammonia concentration, the critical level was estimated to be below 1.9 μg m −3 , in agreement with recent studies for other ecosystems. Taking into account the high sensitivity of lichen communities to excessive N, these values should be taken into account in policies that aim at protecting Mediterranean woodlands from the initial effects of excessive N.

Description: Glover, K. A., Skaala, Ø., Limborg, M., Kvamme, C., and Torstensen, E. Microsatellite DNA reveals population genetic differentiation among sprat ( Sprattus sprattus ) sampled throughout the Northeast Atlantic, including Norwegian fjords. – ICES Journal of Marine Science, 68: 2145–2151. Sprat ( Sprattus sprattus ), small pelagic shoaling fish, were sampled from the Celtic, North, and Baltic seas, and 10 Norwegian fjords. Significant overall genetic differentiation was observed among samples when analysed with eight microsatellite DNA loci (Global F ST = 0.0065, p 〈 0.0001). The greatest genetic differences were observed between the Baltic and all other samples (largest pairwise F ST = 0.043, p 〈 0.0001). No significant genetic differentiation was observed between a sample from the Celtic Sea (CEL) and the North Sea (NSEA; F ST = 0.001, p = 0.16), but variable levels of genetic differentiation were observed among samples collected from Norwegian fjords (pairwise F ST ranging from 0 to 0.0096, most non-significant). All fjord samples were significantly differentiated to NSEA and CEL samples. Further, all fjord samples displayed reduced allelic richness compared with NSEA and CEL samples. Clearly, sprat display population genetic differentiation throughout the Northeast Atlantic, and there may be limited connectivity between Norwegian fjord and sea-going populations.

Description: Mahévas, S., Vermard, Y., Hutton, T., Iriondo, A., Jadaud, A., Maravelias, C. D., Punzón, A., Sacchi, J., Tidd, A., Tsitsika, E., Marchal, P., Goascoz, N., Mortreux, S., and Roos, D. 2011. An investigation of human vs. technology-induced variation in catchability for a selection of European fishing fleets. – ICES Journal of Marine Science, 68: 2252–2263. The impact of the fishing effort exerted by a vessel on a population depends on catchability, which depends on population accessibility and fishing power. The work investigated whether the variation in fishing power could be the result of the technical characteristics of a vessel and/or its gear or whether it is a reflection of inter-vessel differences not accounted for by the technical attributes. These inter-vessel differences could be indicative of a skipper/crew experience effect. To improve understanding of the relationships, landings per unit effort (lpue) from logbooks and technical information on vessels and gears (collected during interviews) were used to identify variables that explained variations in fishing power. The analysis was undertaken by applying a combination of generalized additive models and generalized linear models to data from several European fleets. The study highlights the fact that taking into account information that is not routinely collected, e.g. length of headline, weight of otter boards, or type of groundrope, will significantly improve the modelled relationships between lpue and the variables that measure relative fishing power. The magnitude of the skipper/crew experience effect was weaker than the technical effect of the vessel and/or its gear.

Description: Attwood, C. G., Petersen, S. L., and Kerwath, S. E. 2011. Bycatch in South Africa's inshore trawl fishery as determined from observer records. – ICES Journal of Marine Science, 68: 2163–2174. Ship-based observer data were analysed to describe the volume, composition, utilization, and size structure of catches made by South Africa's inshore trawlers. The sampling rate was 3.5% of all trawls, including unsorted and discard samples. In all, 137 nominal species were recorded. Analysis of species composition separated the trawling grounds into seven areas, providing a framework for stratifying the ground for catch estimation and for selection of representative areas for conservation. The target species, Merluccius capensis and Austroglossus pectoralis , made up 58% of the pre-discard catch. Trachurus trachurus , Pterogymnus laniarius , Raja spp., and Chelidonichthys spp. constituted another 23%. Pre-discard catch volumes of the entire fleet were estimated. The average annual pre-discard catch of M. capensis and A. pectoralis was 9653 and 504 t, respectively, closely matching landing statistics. Argyrosomus inodorus , Rhabdosargus globiceps , Argyrozona argyrozona , and Atractoscion aequidens averaged 294, 230, 107, and 83 t annually, respectively, indicating significant overlap with the handline fishery for A. inodorus and A. argyrozona . A comparison of species composition in unsorted and discard samples revealed the species being preferentially retained. Argyrosomus inodorus and A. aequidens were trawled mainly below their size at maturity. Management needs to consider other species when determining catch or effort limits and area restrictions.

Description: Aanes, S., Nedreaas, K., and Ulvatn, S. 2011. Estimation of total retained catch based on frequency of fishing trips, inspections at sea, transhipment, and VMS data. – ICES Journal of Marine Science, 68: 1598–1605. The satellite-based vessel monitoring system in the Norwegian Economic Zone provides detailed information about individual trips by vessels. Vessel sizes are available through official registries, and the storage capacity for fish is estimated using the established conversion factors as a function of the vessel's gross registered tonnage. Scientists have had access to the database of both transport and fishing vessels, with records for individual trips, in addition to information about the total round weight (whole fish) of cod and haddock for trips inspected by the coastguard. The analysis assumes that trips with complete documentation of the fish on board are a random sample, so allowing estimation of the mean amount of both cod and haddock per trip, and annual totals give the number of trips per vessel annually. ICES has accepted this methodology for estimating illegal, unregulated, and unreported (IUU) catches, which has resulted in 15 000–166 000 t (3–35%) being added to the officially reported landings of Northeast Arctic cod during the years 2002–2008. IUU landings have decreased in recent years, but are so important for assessment and management that estimates continue to be made annually.