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This paper presents the application of the Linear Quadratic Optimal Control (LQOC) method for a parameter optimization problem in a marine ecosystem model. The ecosystem model simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column with temperature and turbulent diffusivity profiles taken from a three-dimensional ocean circulation model.We present the linearization method which is based on the available observations. The linearization is necessary to apply the LQOC method on the nonlinear system of state equations. We show the form of the linearized time-variant problems and the resulting two algebraic Riccati Equations. By using the LQOC method, we are able to introduce temporally varying periodic model parameters and to significantly improve -- compared to the use of constant parameters -- the fit of the model output to given observational data. [ABSTRACT FROM AUTHOR]

A new generation of an Earth System Model now includes a number of land surface processes directly relevant to analyzing potential impacts of climate change. This model, HadGEM2-ES, allows us to assess the impacts of climate change, multiple interactions, and feedbacks as the model is run. This paper discusses the results of century-scale HadGEM2-ES simulations from an impacts perspective--specifically, terrestrial ecosystems and water resources--for four different scenarios following the Representative Concentration Pathways (RCPs), being used for next assessment report of the Intergovernmental Panel on Climate Change (IPCC). Over the 21st Century, simulated changes in global and continential-scale terrestrial ecosystems due to climate change appear to be very similar in all 4 RCPs, even though the level of global warming by the end of the 21st Century ranges from 2°C in the lowest scenario to 5.5°in the highest. A warming climate generally favours broadleaf trees over needleleaf, needleleaf trees over shrubs, and shrubs over herbaceous vegetation, resulting in a poleward shift of temperate and boreal forests and woody tundra in all scenarios. Although climate related changes are slightly larger in scenarios of greater warming, the largest differences between scenarios arise at regional scales as a consequence of different patterns of anthropogenic land cover change. In the model, the scenario with the lowest global warming results in the most extensive decline in tropical forest cover due to a large expansion of agriculture. Under all four RCPs, fire potential could increase across extensive land areas, particularly tropical and sub-tropical latitudes. River outflows are simulated to increase with higher levels of CO2 and global warming in all projections, with outflow increasing with mean temperature at the end of the 21st Century at the global scale and in North America, Asia, and Africa. In South America, Europe, and Australia, the relationship with climate warming and CO2 rise is less clear, probably as a result of land cover change exerting a dominant effect in those regions. [ABSTRACT FROM AUTHOR]

Coastal hypoxia and anoxia have become a global key stressor to marine ecosystems, with almost 500 dead zones recorded wordwide. By triggering cascading effects from the individual organism to the community and ecosystem-level, oxygen depletions threat marine biodiversity and can alter ecosystem structure and function. By integrating both physiological function and ecological processes, animal behaviour is ideal for assessing the stress state of benthic macrofauna to low dissolved oxygen. The initial response of organisms can serve as an early-warning signal, while the successive behavioural reactions of key species indicate hypoxia levels and help assess community degradation. Here we document the behavioural responses of a representative spectrum of benthic macrofauna in the natural setting in the Northern Adriatic Sea, Mediterranean. We experimentally induced small-scale anoxia with a benthic chamber in 24 m depth to overcome the difficulties in predicting the onset of hypoxia, which often hinders full documentation in the field. The behavioural reactions were documented with a time-lapse camera. Oxygen depletion elicited significant and re-peatable changes in general (visibility, locomotion, body movement and posture, location) and species-specific reactions in virtually all organisms (302 individuals from 32 species and 2 species groups). Most atypical (stress) behaviours were associated with specific oxygen thresholds: arm-tipping in the ophiuroid Ophiothrix quinquemac-ulata, for example, with the onset of mild hypoxia (<2mLO2L-1), the emergence of polychates on the sediment surface with moderate hypoxia (< 1 mLO2 L-1), the emergence of the infaunal sea urchin Schizaster canaliferus on the sediment with severe hypoxia (< 0.5mLO2L-1) and heavy body rotations in sea anemones with anoxia. Other species changed their activity patterns, i.e. circadian rhythm in the hermit crab Paguristes eremita or the bioherm-associated crab Pisidia longimana. Intra- and interspecific reactions were weakened or changed: decapods ceased defensive and territorial behaviour, and predator-prey interactions and relationships shifted. This nuanced scale of resolution is a useful tool to interpret present benthic community status (behaviour) and past mortalities (community composition, e.g. survival of tolerant species). This information on the sensitivity (onset of stress response), tolerance (mortality, survival), and characteristics (i.e. life habit, functional role) of key species also helps predict potential future changes in benthic structure and ecosystem functioning. This integrated approach can transport complex ecological processes to the public and decision-makers and help de?ne speci?c monitoring, assessment and conservation plans. [ABSTRACT FROM AUTHOR]

Soils are a crucial component of the Earth System; they comprise a large portion of terrestrial carbon stocks, mediate the supply and demand of nutrients, and influence the overall response of terrestrial ecosystems to perturbations. In this paper, we develop a new soil biogeochemistry model for the Community Land Model, version 4 (CLM4). The new model includes a vertical dimension to carbon (C) and nitrogen (N) pools and transformations, a more realistic treatment of mineral N pools, flexible treatment of the dynamics of decomposing carbon, and a radiocarbon (14C) tracer. We describe the model structure, comparison against site-level and global observations, and overall effect of the revised soil model on CLM carbon dynamics. Site-level comparisons to radiocarbon and bulk soil C observations support the idea that soil C turnover is reduced at depth beyond what is expected from environmental controls by temperature, moisture, and oxygen that are considered in the model. The revised soil model predicts substantially more and older soil C, particularly at high latitudes, where it resolves a permafrost soil C pool, in better agreement with observations. In addition the 20th century C dynamics of the model are more realistic than the baseline model, with more terrestrial C uptake over the 20th century due to reduced N downregulation and longer turnover times of decomposing C. [ABSTRACT FROM AUTHOR]

Based on a wide range of empirical data we investigated surface and vegetation dynamics in the artificial initial ecosystem "Chicken Creek" (Lusatia, Germany) in the years 2008-2011. We scrutinized three different hypotheses concerning (1) the relations between initial geomorphological and substrate characteristics with surface structure and terrain properties, (2) the effects of the latter on the occurrence of grouped plant species, and (3) vegetation density effects on terrain surface change. Our data comprise annual vegetation monitoring results, terrestrial laser scans twice a year, annual groundwater levels, and initially measured soil characteristics. Using Generalized Linear Models (GLMM) and Generalized Additive Mixed Models (GAMM) we can mostly confirm our hypotheses, revealing statistically significant relations that partly reflect object or period specific effects but also more general processes which mark the transition from a geo-hydro towards a bio-geo-hydro system, where pure geomorphology or substrate feedbacks are changing into vegetation-substrate feedback processes. [ABSTRACT FROM AUTHOR]

In this paper, we investigate similarities of effects of soil environmental drivers on year-round daily soil fluxes of nitrous oxide and methane for three distinct semi-natural or natural ecosystems: temperate spruce forest, Germany; tropical rain forest, Queensland, Australia; and ungrazed semi-arid steppe, Inner Mongolia, China. Annual cumulative fluxes of nitrous oxide and methane varied markedly among ecosystems, with nitrous oxide fluxes being highest for the tropical forest site (tropical forest: 0.96 kg N ha-1 yr-1; temperate forest: 0.67 kg N ha-1 yr-1; steppe: 0.22 kg N ha-1 yr-1), while rates of soil methane uptake were approximately equal for the temperate forest (3.45 kg C ha-1 yr-1) and the steppe (3.39 kg C ha-1 yr-1), but lower for the tropical forest site (2.38 kg C ha-1 yr-1). In order to allow for cross-site comparison of effects of changes in soil moisture and soil temperature on fluxes of methane and nitrous oxide, we used a normalization approach. Data analysis with normalized data revealed that across sites, optimum rates of methane uptake are found at environmental conditions representing approximately average site environmental conditions. This might have rather important implications for understanding effects of climate change on soil methane uptake potential, since any shift in environmental conditions is likely to result in a reduction of soil methane uptake ability. For nitrous oxide, our analysis revealed expected patterns: highest nitrous oxide emissions under moist and warm conditions and large nitrous oxide fluxes if soils are exposed to freeze-thawing effects at sufficient high soil moisture contents. However, the explanatory power of relationships of soil moisture or soil temperature to nitrous oxide fluxes remained rather poor (≤ 0.36). When combined effects of changes in soil moisture and soil temperature were considered, the explanatory power of our empirical relationships with regard to temporal variations in nitrous oxide fluxes were at maximum about 50%. This indicates that other controlling factors such as N and C availability or microbial community dynamics might exert a significant control on the temporal dynamic of nitrous oxide fluxes. Though underlying microbial processes such as nitrification and denitrification are sensitive to changes in the environmental regulating factors, important regulating factors like moisture and temperature seem to have both synergistic and antagonistic effects on the status of other regulating factors. Thus we cannot expect a simple relationship between them and the pattern in the rate of emissions, associated with denitrification or nitrification in the soils. In conclusion, we hypothesize that our approach of data generalization may prove beneficial for the development of environmental response models which can be used across sites, and which are needed to help better understanding climate change feed-backs on biospheric sinks or sources of nitrous oxide and methane. [ABSTRACT FROM AUTHOR]

In this study, we investigate the phytoplankton community response, with emphasis on ecophysiology and succession, after two experimental additions of Saharan dust in the surface layer of a low-nutrient low-chlorophyll ecosystem in the Mediterranean Sea. Three mesocosms were amended with evapocondensed dust to simulate realistic Saharan dust events while three additional mesocosms were kept unamended and served as controls. Experiments consisted in two consecutive dust additions and samples were daily collected at different depths (-0.1, -5 and -10m) during one week, starting before each addition occurred. Data concerning HPLC pigment analysis on two size classes (<3 and >3 µm), electron transport rate (ETR) versus irradiance curves, non-photochemical fluorescence quenching (NPQ) and phytoplankton cell abundance (measured by flow cytometry), are presented and discussed in this paper. Results show that picophytoplankton mainly respond to the first dust addition, while the second addition leads to an increase of both pico- and nano-/microphytoplankton. Ecophysiological changes in the phytoplankton community are revealed, and an increase in NPQ development, as well as in pigment concentration per cell, follows the dust additions. ETR does not show large variations between dust-amended and control conditions, while biomass increases in response to the dust additions. Furthermore, the biomass increase observed during this mesocosm experiment allows us to attempt a quantitative assessment and parameterization of the onset of a phytoplankton bloom in a nutrient-limited ecosystem. These results are discussed focusing on the adaptation of picophytoplankton to such a nutrient-limited mixed layer system, as well as on size-dependent competition ability in phytoplankton. [ABSTRACT FROM AUTHOR]

To assess the responses of nitrogen and greenhouse gas emissions to pan-European changes in land cover, land management and climate, an integrated dynamic model, INTEGRATOR, has been developed. This model includes both simple process-based descriptions and empirical relationships, and uses detailed GIS-based environmental and farming data in combination with various downscaling methods. This paper analyses the propagation of uncertainties in model inputs and model parameters to outputs of INTEGRATOR, using a Monte Carlo analysis. Uncertain model inputs and parameters were represented by probability distributions, while spatial correlation in these uncertainties was taken into account by assigning correlation coefficients at various spatial scales. The uncertainty propagation was analysed for the emissions of NH3, N2O and NOx and N leaching to groundwater and N surface runoff to surface water for the entire EU27 and for individual countries. Results show large uncertainties for N leaching and N runoff (relative errors of ~19% for Europe as a whole), and smaller uncertainties for emission of N2O, NH3 and NOx (relative errors of ~12%). Uncertainties for Europe as a whole were much smaller compared to uncertainties at Country level, because errors partly cancelled out due to spatial aggregation. [ABSTRACT FROM AUTHOR]

Land models, which have been developed by the modeling community in the past two decades to predict future states of ecosystems and climate, have to be critically evaluated for their performance skills of simulating ecosystem responses and feedback to climate change. Benchmarking is an emerging procedure to measure and evaluate performance of models against a set of defined standards. This paper proposes a benchmarking framework for evaluation of land models. The framework includes (1) targeted aspects of model performance to be evaluated; (2) a set of benchmarks as defined references to test model performance; (3) metrics to measure and compare performance skills among models so as to identify model strengths and deficiencies; and (4) model improvement. Component 4 may or may not be involved in a benchmark analysis but is an ultimate goal of general modeling research. Land models are required to simulate exchange of water, energy, carbon and sometimes other trace gases between the atmosphere and the land-surface, and should be evaluated for their simulations of biophysical processes, biogeochemical cycles, and vegetation dynamics across timescales in response to both weather and climate change. Benchmarks that are used to evaluate models generally consist of direct observations, data-model products, and data-derived patterns and relationships. Metrics of measuring mismatches between models and benchmarks may include (1) a priori thresholds of acceptable model performance and (2) a scoring system to combine data-model mismatches for various processes at different temporal and spatial scales. The benchmark analyses should identify clues of weak model performance for future improvement. Iterations between model evaluation and improvement via benchmarking shall demonstrate progress of land modeling and help establish confidence in land models for their predictions of future states of ecosystems and climate. [ABSTRACT FROM AUTHOR]

Degradation of coastal ecosystems by eutrophication is largely defined by nitrogen loading from land via surface and groundwater flows. However, indicators of water quality are highly variable due to a myriad of other drivers, including temperature and precipitation. To evaluate these drivers, we examined spatial and temporal trends in a 22 year record of summer water quality data from 122 stations in 17 embayments within Buzzards Bay, MA (USA), collected through a citizen science monitoring program managed by Buzzards Bay Coalition. To identify spatial patterns across Buzzards Bay's embayments, we used a principle component and factor analysis and found that rotated factor loadings indicated little correlation between inorganic nutrients and organic matter and chlorophyll a (Chl a) concentration. Factor scores showed that embayment geomorphology in addition to nutrient loading was a strong driver of water quality, where embayments with surface water inputs showed larger biological impacts than embayments dominated by groundwater influx. A linear regression analysis of annual summertime water quality indicators over time revealed that from 1992 to 2013, most embayments (15 of 17) exhibited an increase in temperature (mean rate of 0.082 ± 0.025 (SD) °C yr-1) and Chl a (mean rate of 0.0171 ± 0.0088 log10 (Chl a; mgm-3)yr-1, equivalent to a 4.0% increase per year). However, only 7 embayments exhibited an increase in total nitrogen (TN) concentration (mean rate 0.32 ± 0.47 (SD)μM yr-1). Average summertime log10 (TN) and log10 (Chl a) were correlated with an indication that yield of Chl a per unit total nitrogen increased with time suggesting the estuarine response to TN may have changed because of other stressors such as warming, altered precipitation patterns, or changing light levels. These findings affirm that nitrogen loading and physical aspects of embayments are essential in explaining observed ecosystem response. However, climate-related stressors may also need to be considered by managers because increased temperature and precipitation may worsen water quality and partially offset benefits achieved by reducing nitrogen loading. [ABSTRACT FROM AUTHOR]

Oceanic upwelling velocities are too small to be measured directly. The surface disequilibrium of the ³He/4He ratio provides an indirect method to infer vertical velocities at the base of the mixed layer. Samples of helium isotopes were taken from two coastal upwelling regions, off Peru on cruise M91, and off Mauritania on 3 cruises. The helium- 3 flux into the mixed layer also depends on the diapycnal mixing. Direct observations of the vertical diffusivity have been performed on all 4 cruises and are also used in this study. The resulting upwelling velocities in the coastal regions vary between 1.1x10-5 and 2.8x10-5ms-1 for all cruises. Vertical velocities off the equator can also be inferred from the divergence of the wind driven Ekman transport. In the coastal regimes, the agreement between wind and helium derived upwelling is fairly good at least for the mean values. Further offshore, the helium derived upwelling still reaches 1x10-5ms-1, whereas the wind driven upwelling from Ekman suction is smaller by at least one order of magnitude. One reason for this difference might be eddy induced upwelling. Both advective and diffusive nutrient fluxes into the mixed layer are calculated based on the helium derived vertical velocities and the measured vertical diffusivities. The advective part of these fluxes makes up at least 50% of the total. The nutrient flux into the mixed layer in the coastal upwelling regimes is equivalent to a net community production (NCP) of 1.3gCm² d-1 off Peru and 1.6-1.9 gCm² d-1 off Mauritania. [ABSTRACT FROM AUTHOR]

Drought has been a concern of global and regional water, carbon and energy cycles. From 1999 to 2011, North China experienced a multiyear precipitation reduction, which decreased significantly water availability as indicated by decreased soil moisture and Palmer Drought Severity Index. In this study, three light use efficiency models (CASA, MODIS-GPP and EC-LUE) and one dynamic vegetation model (IBIS) were used to characterize the impacts of long-term drought on terrestrial carbon fluxes over the North China. All of four models showed the reduction in averaged GPP of 0.026-0.047 Pg C yr-1 from 1999 to 2011 compared to 1982-2011. Based on IBIS model, simulated ecosystem respiration fell from 1999 to 2011 by 0.016 Pg C yr-1. Multiple precipitation reduction changed the regional carbon uptake of 0.0014 Pg C yr-1 from 1982 to 1998 to a net source of 0.018 Pg C yr-1. Moreover, a pronounced decrease of maize yield was found ranging from 1999 to 2011 versus the average of 1978-2011 at almost all provinces over the study region. The largest reduction of maize yield occurred in the Beijing (2499 kg ha-1 yr-1), Jilin (2180 kg ha-1 yr-1), Tianjing (1923 kg ha-1 yr-1) and Heilongjiang (1791 kg ha-1 yr-1), and maize yield anomaly was significantly correlated with the precipitation through May and September over the entire study area. Our results revealed that recent climate change, and especially drought-induced water stress, is the dominant cause of the reduction in the terrestrial carbon sink. [ABSTRACT FROM AUTHOR]

In order to investigate the mechanism of spatial dynamics of picoplankton community (bacteria and Synechococcus spp.) and estimate the carbon flux of the microbial food web in the oligotrophic Taiwan Warm Current Water of subtropical marine pelagic ecosystem, we conducted size-fractionation experiments in five cruises by the R/V Ocean Research II during the summers of 2010 and 2011 in the southern East China Sea. We carried out culture experiments using surface water which, according to a temperature-salinity (T-S) diagram, is characterized as oligotrophic Taiwan Current Warm Water. We found a negative correlation between bacteria growth rate and temperature, indicating that the active growth of heterotrophic bacteria might be induced by nutrients lifted from deep layer by cold upwelling water. This finding suggests that the area we studied was a bottom-up control pelagic ecosystem. We suggest that the microbial food web of an oligotrophic ecosystem may be changed from top-down control to resource supply (bottom-up control) when a physical force brings nutrient into the oligotrophic ecosystem. Upwelling brings nutrient-rich water to euphotic zone and promotes bacteria growth, increasing the picoplankton biomass which increased the consumption rate of nanoflagellate. The net growth rate (growth rate--grazing rate) becomes negative when the densities of bacteria and Synechococcus spp. are lower than the threshold values. The interaction between growth and grazing will limit the abundances of bacteria (105 -106 cells mL -1) and Synechococcus spp. (104 -105 cells mL-1) within a narrow range, forming a predator-prey eddy. Meanwhile, 62% of bacteria production and 55% of Synechococcus spp. production are transported to higher trophic level (nanoflagellate), though the cascade effect might cause an underestimation of both percentages of transported carbon. Based on the increasing number of sizes we found in the size-fractionation experiments, we estimated that the predation values were underestimated by 28.3% for bacteria and 34.6% for Synechococcus spp. Taking these corrections into consideration, we conclude that picoplankton production is balanced by nonoflagellate grazing and the diet of nanoflagellate is composed of 64% bacteria and 36% Synechococcus spp. [ABSTRACT FROM AUTHOR]

To model phytoplankton primary production from remotely sensed data a method to estimate photosynthetic parameters describing the photosynthetic rates per unit biomass is required. Variability in these parameters must be related to environmental variables that are measurable remotely. In the Arctic, a limited number of measurements of photosynthetic parameter have been carried out with the concurrent environmental variables needed. Therefore, to improve the accuracy of remote estimates of phytoplankton primary production as well as our ability to predict changes in the future such measurements and relationship to environmental variables are required. During the MALINA cruise, a large dataset of these parameters were obtained. Together with previously published datasets, we use environmental and trophic variables to provide functional relationships for these parameters. In particular, we describe several specific aspects: the maximum rate of photosynthesis (Pmaxchl) normalized to chlorophyll decreases with depth and is higher for communities composed of large cells; the saturation parameter (Ek) decreases with depth but is independent of the community structure; and the initial slope of the photosynthesis versus irradiance curve (αchl) normalized to chlorophyll is independent of depth but is higher for communities composed of larger cells. The photosynthetic parameters were not influenced by temperature over the range encountered during the cruise (-2 to 8 °C). [ABSTRACT FROM AUTHOR]

We conducted high frequency measurements of the δ18 O value of atmospheric CO2 from a juniper (Juniperus monosperma) woodland in New Mexico, USA, over a four- year period to investigate climatic and physiological regulation of the δ18O value of ecosystem respiration (δR). Rain pulses reset δR with the dominant water source isotope composition, followed by progressive enrichment of δR. Transpiration (ET) was significantly related to post-pulse δR enrichment because leaf water δ18O value showed strong enrichment with increasing vapor pressure deficit that occurs following rain. Post-pulse δR enrichment was correlated with both ET and the ratio of ET to soil evaporation (ET/ES). In contrast, soil water δ18O value was relatively stable and δR enrichment was not correlated with ES. Model simulations captured the large post-pulse δR enrichments only when the offset between xylem and leaf water δ18O value was modeled explicitly and when a gross flux model for CO2 retro-diffusion was included. Drought impacts δR through the balance between evaporative demand, which enriches δR, and low soil moisture availability, which attenuates δR enrichment through reduced ET. The net result, observed throughout all four years of our study, was a negative correlation of post-precipitation δR enrichment with increasing drought. [ABSTRACT FROM AUTHOR]

We compared the functional response of a biogeochemical data assimilation model versus an empirical satellite-derived algorithm in describing the variation of four phytoplankton (diatoms, cyanobacteria, coccolithophores and chlorophytes) groups globally and in 12 major oceanographic basins. Global mean differences of all groups were within ~15% of an independent observation data base for both approaches except for satellite-derived chlorophytes. Diatoms and cyanobacteria concentrations were significantly (p < 0.05) correlated with the independent observation data base for both methods. Coccolithophore concentrations were only correlated with the in situ data for the model approach and the chlorophyte concentration was only significantly correlated to the in situ data for the satellite-derived approach. Using monthly means from 1998–2007, the seasonal variation from the satellite-derived approach and model were significantly correlated in 11 regions for diatoms and in 9 for coccolithophores but only in 3 and 2 regions for cyanobacteria and chlorophytes. Most disagreement on the seasonal variation of phytoplankton composition occurred in the North Pacific and Antarctic where, except for diatoms, no significant correlation could be found between the monthly mean concentrations derived from both approaches. In these two regions there was also an overestimate of diatom concentration by the model of ~60% whereas the satellite-derived approach was closer to in situ data (8-26% underestimate). Chlorophytes were the group for which both approaches differed most and that was furthest from the in situ data. These results highlight the strengths and weaknesses of both approaches and allow us to make some suggestions to improve our approaches to understanding phytoplankton dynamics and distribution. [ABSTRACT FROM AUTHOR]

We investigated the production of ammonium via photodegradation of dissolved organic matter (DOM) in the coastal upwelling system off central Chile (36° S). Photoam-monification experiments were carried out using exudates obtained from representative diatom species (Chaetoceros muelleri and Thalassiosira minuscule) and natural marine DOM under simulated solar radiation conditions. Additionally, we evaluated the use of photoproduced ammonium by natural microbial communities and separated ammonium oxidizing archaea and bacteria by using GC-7 as an inhibitor of the archaeal community. We found photoammonification operating at two levels: via the transformation of DOM by UV radiation (abiotic ammonification) and via the simultaneous occurrence of abiotic phototransformation and biological remineralization of DOM into NH4+ (referred as gross photoproduction of NH4+). The maximum rates of abiotic ammonification reached 0.057 µmol L-1 h-1, whereas maximum rates of gross photopro- duction reached 0.746 µmol L-1 h-1. Our results also suggest that ammonium oxidizing archaea could dominate the biotic remineralization induced by photodegradation of organic matter and consequently play an important role in the local N cycle. Abiotic ammonium photoproduction in coastal upwelling systems could support between 7 and 50%of the spring-summer phytoplankton NH4+ demand. Surprisingly, gross ammonium photoproduction (remineralization induced by abiotic ammonification) might support 50 to 180% of spring-summer phytoplankton NH4+ assimilation. [ABSTRACT FROM AUTHOR]

We present a Simple Diagnostic Photosynthesis and Respiration Model (SDPRM) that has been developed based on pre-existing formulations. The photosynthesis model is based on the light use efficiency logic, suggested by Monteith (1977), for calculating the Gross Primary Production (GPP) while the ecosystem respiration (Reco) model is based on the formulations introduced by Lloyd and Taylor (1994) and modified by Reichstein et al. (2003). SDPRM is driven by satellite-derived fAPAR (fraction of Absorbed Photosynthetically Active Radiation) and climate data from NCEP/NCAR. The model estimates 3-hourly values of GPP for seven major biomes and daily Reco. The motivation is to provide a-priori fields of surface CO2 fluxes with fine temporal and spatial scales, and their derivatives with respect to adjustable model parameters, for atmospheric CO2 inversions. The estimated fluxes from SDPRM showed that the model is capable of producing flux estimates consistent with the ones inferred from atmospheric CO2 inversion or simulated from process-based models. In this Technical Note, different analyses were carried out to test the sensitivity of the estimated fluxes of GPP and Reco to their driving forces. The spatial patterns of the climatic controls (temperature, precipitation, water) on the interannual variability of GPP are consistent with previous studies even though SDPRM has a very simple structure and few adjustable parameters, and hence it is much easier to modify than more sophisticated process-based models used in these previous studies. According to SDPRM, the results show that temperature is a limiting factor for the interannual variability of Reco over the cold boreal forest, while precipitation is the main limiting factor of Reco over the tropics and the southern hemisphere, consistent with previous regional studies. [ABSTRACT FROM AUTHOR]

The Arctic Ocean (AO) undergoes profound changes of its physical and biotic environments due to climate change. The greater light exposure and stratification alter its plankton ecosystem structure, functioning and productivity promoting oligotrophy in some areas as the Beaufort Sea. A one-dimension (1-D) physical-biological coupled model based on the large multiparametric database of the Malina project in the Beaufort Sea was used (i) to infer the functioning and nitrogen fluxes within the summer plankton ecosystem and (ii) to assess the model sensitivity to key light-associated processes involved in nutrient recycling and phytoplankton growth. The coupled model suggested that ammonium photochemically produced from photosensitive dissolved organic nitrogen (i.e. photoammonification process) was a necessary nitrogen source to achieve the observed levels of microbial biomass and production. It contributed to ca. two-thirds and one-third of the simulated surface (0-10 m) and depth-integrated primary and bacterial production, respectively. The model also suggested that carbon to chlorophyll ratios for small (<5 µm) phytoplankton (ca. 15-45 gg-1) lower than those commonly used in biogeochemical models applied to the AO were required to simulate the observed herbivorous versus microbial food web competition and realistic nitrogen fluxes in the Beaufort Sea oligotrophic waters. In face of accelerating Arctic warming, more attention should be paid in the future to the mechanistic processes involved in food webs and functional groups competition, nutrient recycling and primary production in poorly productive waters of the AO as they are expected to expand rapidly. [ABSTRACT FROM AUTHOR]

Microbial respiration depends on microclimatic variables and carbon (C) substrate availability, all of which are altered when ecosystems experience major disturbance. Widespread tree mortality, currently affecting piñon-juniper ecosystems in Southwestern North America, may affect C substrate availability in several ways; for example, via litterfall pulses and loss of root exudation. To determine piñnon mortality effects on C and water limitation of microbial respiration, we applied field amendments (sucrose and water) to two piñnon-juniper sites in central New Mexico, USA: one with a recent (<1 yr), experimentally-induced mortality event and a nearby site with live canopy. We monitored the respiration response to water and sucrose applications to the litter surface and to the underlying mineral soil surface, testing the following hypotheses: (1) soil respiration in a piñnon-juniper woodland is water- and labile C-limited in both the litter layer and mineral soil; (2) water and sucrose applications increase temperature sensitivity of respiration; (3) the mortality-affected site will show a reduction in C limitation in the litter; (4) the mortality-affected site will show an enhancement of C limitation in the mineral soil. Litter respiration at both sites responded to increased water availability, yet surprisingly, mineral soil respiration was not limited by water. Temperature sensitivity was enhanced by some of the sucrose and water treatments. Consistent with hypothesis 3, C limitation of litter respiration was lower at the recent mortality site compared to the intact canopy site. Results following applications to the mineral soil 20 suggest the presence of abiotic effects of increasing water availability, precluding our ability to measure labile C limitation in soil. Widespread piñon mortality may decrease labile C limitation of litter respiration, at least during the first growing season following mortality. [ABSTRACT FROM AUTHOR]

Present and future levels of primary production (PP) in the Arctic Ocean (AO) depend on nutrient inputs to the photic zone via vertical mixing, upwelling and external sources. In this regard, the importance of horizontal river supply relative to oceanic processes is poorly constrained at the panarctic scale. We compiled extensive historical (1954-2012) data on discharge and nutrient concentrations to estimate fluxes of nitrate, soluble reactive phosphate (SRP), silicate, DOC, DON, PON and POC from 9 large Arctic rivers and assess their potential impact on the biogeochemistry of shelf waters. Several key points can be emphasized from this analysis. The contribution of riverine nitrate to new PP (PPnew) is very small at the regional scale (<1% to ca. 6.2 %) and negligible at the panarctic scale (ca. 0.73%), in agreement with recent studies. By consuming all this nitrate, oceanic phytoplankton would be able to use only ca. 13.5%and 6.6-17.5% of the river supply of silicate at the panarctic and regional scales, respectively. Corresponding figures for SRP are ca. 27.8% and 18.4-44.4 %. On the Beaufort and Bering shelves, riverine SRP cannot fulfil phytoplankton requirements. On a seasonal basis, the removal of riverine nitrate, silicate and SRP would be the highest in spring and not in summer when AO shelf waters are nitrogen-limited. Riverine DON is potentially an important nitrogen source for the planktonic ecosystem in summer, when ammonium supplied through the photoammonification of refractory DON (ca. 3.9x109 mol N) may exceed the combined riverine supply of nitrate and ammonium (ca. 2.9x109 mol N). Nevertheless, overall nitrogen limitation of AO phytoplankton is expected to persist even when projected increases of riverine DON and nitrate supply are taken into account. This analysis underscores the need to better contrast oceanic nutrient supply processes with the composition and fate of changing riverine nutrient deliveries in future scenarios of plankton community structure, function and production in the coastal AO. [ABSTRACT FROM AUTHOR]

Here we report a time series of experiments performed in a microcosm to test the response of hypersaline microbial mats to diverse atmospheric CO2 conditions. Different from most part of the literature, our study used a sample chamber were carbon dioxide concentration was controlled. Our aim was to test the effect of different atmospheric CO2 conditions in benthic gross and net primary production, and respiration. This study showed for the first time to our knowledge absolute carbon limitation in a microbial mat. Oxygen concentration profile varied from a flattened shape to almost linear when atmospheric CO2 at the chamber reached 0 ppm, with NPP reaching 0 nmol cm-3 s-1 throughout most part of the profile. In this conditions sediment community respiration represented 100% of GPP. Extreme close coupling between primary production and respiration in microbial mats can be even self-sustainable in environments with temporally no atmospheric CO2 available. When submitted to even high CO2 concentrations (550 ppm), our sample showed a characteristic shape that indicate limitation composed by a more rectilinear oxygen profile, and NPP peaks mainly restricted to deeper layers. Therefore, we suggest that phototrophic communities in aquatic shallow ecosystems can be carbon limited. This limitation could be common especially in ecosystems submitted to variable water depth conditions, like coastal lagoons and intertidal sediments. [ABSTRACT FROM AUTHOR]

Net community production (NCP) and ratios of carbon to nutrient consumption were studied during a large-scale mesocosm experiment on ocean acidification in Kongsfjorden, West Spitsbergen, during June-July 2010. Nutrient-deplete fjord water with natural phyto- and bacteriaplankton assemblages, enclosed in nine mesocosms of ∼50m³ volume, was exposed to pCO2 levels ranging from 185 to 1420 µatm on initial state. Mean values of pCO2 levels during experiment ranged from 175 to 1085 µatm in different mesocosms. Phytoplankton growth was stimulated by nutrient addition. In this study NCP is estimated as a cumulative change in dissolved inorganic carbon concentrations. Stoichiometric couping between inorganic carbon and nutrient is shown as a ratio of a cumulative NCP to a cumulative change in inorganic nutrients. Three peaks of chlorophyll a concentration occurred during the experiment. Accordingly the experiment was divided in three phases. Overall cumulative NCP was similar in all mesocosms by the final day of experiment. However, NCP varied among phases, showing variable response to CO2 perturbation. Carbon to nitrogen (C:N) and carbon to phosphorus (C: P) uptake ratios were estimated only for the period after nutrient addition (post-nutrient period). For the total post-nutrient period ratios were close to Redfield proportions, however varied from it in different phases. The response of C:N and C: P uptake ratios to CO2 perturbation was different for three phases of the experiment, reflecting variable NCP and dependence on changing microbial community. Through the variable NCP, C:N and C: P uptake ratios for 31 days of the experiment we show a flexibility of biogeochemical response establishing a strong microbial loop in Kongsfjorden under different CO2 scenarios. [ABSTRACT FROM AUTHOR]

The article presents a study that demonstrates the applications of the Biogeochemical Transport and Reactions (CLM4-BeTR) in regional and global biogeochemistry modeling and climate predictability. It outlines the functions of the model in which its transport code are evaluated through several analytical test cases. The study shows that the method provides detailed comparison between ecosystem observation and predictions.

Rising atmospheric CO2 concentrations due to anthropogenic emissions induce changes in the ocean carbonate chemistry and a drop in ocean pH. This acidification process is expected to harm calcifying organisms like coccolithophores, molluscs, echinoderms, and corals. A severe decline in coral abundance is, for example, expected by the end of this century with associated disastrous effects on reef ecosystems. Despite the growing importance of the topic, little progress has been made with respect to modelling the impact of acidification on coral calcification. Here we present a model for a coral polyp that simulates the carbonate system in four different compartments: the seawater, the polyp tissue, the coelenteron, and the calicoblastic layer. Precipitation of calcium carbonate takes place in the metabolically controlled calicoblastic layer beneath the polyp tissue. The model is adjusted to a state of activity as observed by direct microsensor measurements in the calcifying fluid. Simulated CO2 perturbation experiments reveal decreasing calcification rates under elevated pCO2 despite strong metabolic control of the calcifying fluid. Diffusion of CO2 through the tissue into the calicoblastic layer increases with increasing seawater pCO2 leading to decreased aragonite saturation in the calcifying fluid of the coral polyp. Our modelling study provides important insights into the complexity of the calcification process at the organism level and helps to quantify the effect of ocean acidification on corals. [ABSTRACT FROM AUTHOR]

Geomorphic characteristics have been used as scaling parameters to predict water and other fluxes in many systems. In this study, we combined geomorphic analysis with in-situ mass balance studies of nitrate retention (NR) to evaluate which geomorphic scaling parameters best predicted NR in a tidal freshwater wetland ecosystem. Geomorphic characteristics were measured for 267 individual marshes that constitute the freshwater tidal wetland ecosystem of the Patuxent River, Maryland. Nitrate retention was determined from mass balance measurements conducted at the inlets of marshes of varying size (671, 5705, and 536 873m²) over a period of several years. Mass balance measurements indicate that NR is proportional to total water flux over the tidal cycle. Relationships between estimated tidal prism (total water volume) for spring tides and various geomorphic parameters (marsh area, total channel length, and inlet width) were defined and compared to field data. From these data, NR equations were determined for each geomorphic parameter, and used to estimate NR for all marshes in the ecosystem for a reference spring (high) tide. The resulting ecosystem NR estimates were evaluated for: (a) accuracy and completeness of geomorphic data, b) relationship between the geomorphic parameters and hydrologic flux, and (c) the ability to adapt the geomorphic parameter to varying tidal conditions. This analysis indicated that inlet width data were the most complete and provided the best estimate of ecosystem nitrate retention. Predictions based on marsh area were significantly lower than the inlet width-based predictions. Cumulative probability distributions of nitrate retention indicate that the largest 3-4% of the marshes retained half of the total nitrate for the ecosystem. [ABSTRACT FROM AUTHOR]

The terrestrial biosphere is currently a strong sink for anthropogenic CO2 emissions. Through the radiative properties of CO2 the strength of this sink has a direct influence on the radiative budget of the global climate system. The accurate assessment of this sink and its evolution under a changing climate is, hence, paramount for any efficient management strategies of the terrestrial carbon sink to avoid dangerous climate change. Unfortunately, simulations of carbon and water fluxes with terrestrial biosphere models exhibit large uncertainties. A considerable fraction of this uncertainty is reflecting uncertainty in the parameter values of the process formulations within the models. This paper describes the systematic calibration of the process parameters of a terrestrial biosphere model against two observational data streams: remotely sensed FAPAR provided by the MERIS sensor and in situ measurements of atmospheric CO2 provided by the GLOBALVIEW flask sampling network. We use the Carbon Cycle Data Assimilation System (CCDAS) to systematically calibrate some 70 parameters of the terrestrial biosphere model BETHY. The simultaneous assimilation of all observations provides parameter estimates and uncertainty ranges that are consistent with the observational information. In a subsequent step these parameter uncertainties are propagated through the model to uncertainty ranges for predicted carbon fluxes. We demonstrate the consistent assimilation for two different set-ups: first at site scale, where MERIS FAPAR observations at a range of sites are used as simultaneous constraints, and second at global scale, where the global MERIS FAPAR product and atmospheric CO2 are used simultaneously. On both scales the assimilation improves the match to independent observations. We quantify how MERIS data improve the accuracy of the current and future (net and gross) carbon flux estimates (within and beyond the assimilation period). We further demonstrate the use of an interactive mission benefit analysis tool built around CCDAS to support the design of future space missions. We find that, for long-term averages, the benefit of FAPAR data is most pronounced for hydrological quantities, and moderate for quantities related to carbon fluxes from ecosystems. The benefit for hydrological quantities is highest for semi-arid tropical or sub-tropical regions. Length of mission or sensor resolution is of minor importance. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Coupled nitrification-denitrification plays a critical role in the removal of excess nitrogen, which is chiefly caused by humans, to mitigate estuary and coastal eutrophication. Despite its obvious importance, limited information about the relationships between nitrifying and denitrifying microbial communities in estuaries, and their controlling factors have been documented. By analyzing the ammonia monooxygenase gene amoA, including archaeal and bacterial amoA, and the dissimilatory nitrite reductase gene nirS using clone libraries and quantitative PCR (qPCR), we investigated the nitrifying and denitrifying microbial communities in the estuary of turbid subtropical Yangtze River (YRE), the largest river in Asia. The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria, suggesting that the archaea might play a dominant role in nitrification in the YRE. Compared with the amoA gene, a distinctly higher level of diversity but lower gene copy numbers were found for the nirS gene suggesting lower denitrification than nitrification potential. 15N incubation experiments indicated that nitrification rates were strongly correlated with amoA gene abundances while denitrification rates were below detection limit. In general, the abundances of the amoA and nirS genes were significantly higher in the bottom samples than the surface ones, and in the high-turbidity river mouth, were distinctly higher in the particle-associated (> 3 μm) than the free-living (0.2 ~ 3 μm) communities. Notably, analysis of correlations between the gene abundances suggested potential gene-based coupling between nitrification and denitrification, especially for the particle-associated assemblages. Statistical analysis of correlations between the community structure, gene abundances and environmental variables further revealed that dissolved oxygen and total suspended material might be the key factors controlling community spatial structure and regulating nitrification and denitrification potentials in the YRE ecosystem. [ABSTRACT FROM AUTHOR]

Dissolved organic carbon (DOC) concentrations -- mainly of terrestrial origin -- are increasing worldwide in inland waters. The biodegradability of the DOC varies depending on quantity and chemical quality. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. It is therefore crucial to understand the processes controlling the bacterial turnover of additional allochthonous and autochthonous DOC in aquatic systems. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (13C-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (algae lysate). We then determined bacterial carbon consumption, activities, and community composition together with the carbon flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and fractions of low and high molecular weight substances (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. In parallel to these differences in chemical composition, we observed a higher availability of allochthonous C as evidenced by increased DOC consumption and bacterial growth efficiencies (BGE) when solely allochthonous C was provided. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption from 52 to 68% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substances (HS) fraction and an increase in bacterial biomass. Stable C isotope analyses of phospholipid fatty acids (PLFA) and respired dissolved inorganic carbon (DIC) supported a preferential assimilation of autochthonous C and respiration of the allochthonous C. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover. [ABSTRACT FROM AUTHOR]

The analysis of the shape of excitation-emission matrices (EEMs) is a relevant tool for exploring the origin, transport and fate of dissolved organic matter (DOM) in aquatic ecosystems. Within this context, the decomposition of EEMs is acquiring a notable relevance. A simple mathematical algorithm that automatically deconvolves single EEM is described, creating new possibilities for the comparison of DOM fluorescence properties and EEMs that are very different from each other. A mixture model approach is adopted to decompose complex surfaces into sub-peaks. The laplacian operator and the Nelder--Mead optimization algorithm are implemented to individuate and automatically locate potential peaks in the EEM landscape. A small heterogeneous data set of 21 EEMs from a human-impacted Mediterranean river is used to describe the model application and to illustrate a strategy that optimises the search for the optimal output. [ABSTRACT FROM AUTHOR]

A process-oriented niche specification (PONS) model was constructed to quantify climatic controls on the distribution of ecosystems, based on the vegetation map of China. PONS uses general hypotheses about bioclimatic controls to provide a "bridge" between statistical niche models and more complex process-based models. Canonical correspondence analysis provided an overview of relationships between the abundances of 55 plant communities in 0.1° grid cells and associated mean values of 20 predictor variables. Of these, GDD (accumulated degree days above 0 ° C) Cramer--Prentice α (an estimate of the ratio of actual to equilibrium evapotranspiration) and mGDD5 (mean temperature during the period above 5 ° C) showed the greatest predictive power. These three variables were used to develop generalized linear models for the probability of occurrence of 16 vegetation classes, aggregated from the original 55 types by k-means clustering according to bioclimatic similarity. Each class was hypothesized to possess a unimodal relationship to each bioclimate variable, independently of the other variables. A simple calibration was used to generate vegetation maps from the predicted probabilities of the classes. Modelled and observed vegetation maps showed good to excellent agreement (κ = 0.745). A sensitivity study examined modelled responses of vegetation distribution to spatially uniform changes in temperature, precipitation and [CO2], the latter included via an offset to α (based on an independent, data-based light use efficiency model for forest net primary production). Warming shifted the boundaries of most vegetation classes northward and westward while temperate steppe and desert replaced alpine tundra and steppe in the southeast of the Tibetan Plateau. Increased precipitation expanded mesic vegetation at the expense of xeric vegetation. The effect of [CO2] doubling was roughly equivalent to increasing precipitation by ~ 30%, favouring woody vegetation types, particularly in northern China. Agricultural zones in northern China responded most strongly to warming, but also benefited from increases in precipitation and [CO2]. These results broadly conform to previously published findings made with the process-based model BIOME4, but they add regional detail and realism and extend the earlier results to include cropping systems. They provide a potential basis for a broad-scale assessment of global change impacts on natural and managed ecosystems. [ABSTRACT FROM AUTHOR]

Arctic field studies have indicated that the air temperature, soil moisture and vegetation at a site influence the quantity of snow accumulated, and that snow accumulation can alter growing season soil moisture and vegetation. Climate change is predicted to bring about warmer air temperatures, greater snow accumulation and northward movements of the shrub and tree lines. Understanding the response of northern environments to changes in snow and growing season land surface characteristics requires: (1) insights into the present-day linkages between snow and growing season land surface characteristics; and (2) the ability to continue to monitor these associations over time across the vast pan-Arctic. The objective of this study was therefore to examine the pan-Arctic (north of 60° N) linkages between two temporally distinct data products created from AMSR-E satellite passive microwave observations: GlobSnow snow water equivalent, and NTSG (growing season air temperature, soil moisture and vegetation transmissivity). Due to the complex and interconnected nature of processes determining snow and growing season land surface characteristics, these associations were analyzed using the modern non-parametric technique of Alternating Conditional Expectations (ACE), as this approach does not impose a predefined analytic form. Findings indicate that regions with lower vegetation transmissivity (more biomass) at the start and end of the growing season tend to accumulate less snow at the start and end of the snow season, possibly due to interception and shading. Warmer air temperatures at the start and end of the growing season were associated with diminished snow accumulation at the start and end of the snow season. High latitude sites with warmer mean annual growing season temperatures tended to accumulate more snow, probably due to the greater availability of water vapor for snow season precipitation at warmer locations. Regions with drier soils preceding snow onset tended to accumulate greater quantities of snow, likely because drier soils freeze faster and more thoroughly than wetter soils. Understanding and continuing to monitor these linkages at the regional scale using the ACE approach can allow insights to be gained into the complex response of Arctic ecosystems to climate-driven shifts in air temperature, vegetation, soil moisture and snow accumulation. [ABSTRACT FROM AUTHOR]

The dynamics of dissolved organic carbon (DOC) have been intensively studied in mature ecosystems, but little is known about DOC dynamics and the significance of DOC as a substrate for microbial activity in early-successional catchments. We determined the concentration, chemical composition, source, radiocarbon age, and bioavailability of DOC along the hydrological flow path from soil solution to a downstream pond in a recently constructed catchment (Chicken Creek Catchment, Germany). Soil solution, upwelling ground water, subsurface water in an alluvial fan, and pond water all had high DOC concentrations (averages of 6.0-11.6mgDOCL-1), despite small carbon stocks in either vegetation or soil of the early-successional catchment. The mean 14C age of DOC in upwelling ground water was 2600 to 2800 yr. Solid-state CPMAS 13C NMR revealed a higher proportion of aromatic compounds (32%) and a lower proportion of carbohydrates (33%) in upwelling ground water than in pond water (18% and 45%, respectively). The 14C age and 13C NMR spectra suggest that DOC was partly mobilized from charred organic matter of the Quaternary substrate. In an experimental 70-days incubation experiment, 20% of the total DOC was found to be bioavailable, irrespective of the water type. Origin of microbial communities (enriched from soil, stream sediment or pond water) had only marginal effects on overall DOC utilization. Overall, these data suggest that the old DOC can support microbial activity during early ecosystem succession to some extent, although the largest fraction is recalcitrant DOC that is exported from the catchment once it has been mobilized. [ABSTRACT FROM AUTHOR]

Interest in seamount research has gathered momentum over the past five years in an effort to understand the physical, geochemical and biological characteristics as well as the interconnectedness of seamount ecosystems. The majority of biological seamount research has concentrated upon the rich and diverse suspension feeding organisms that dominate the megafauna, such as gorgonians and antipatharian corals; by comparison there have been few studies that have investigated the no less enigmatic, but possibly just as important infauna. To help fill this knowledge gap, the macrofaunal community was sampled from a total of five stations along a northerly transect (capturing water depths from ~130m to ~3300m), on Senghor Seamount (NE Atlantic). The focus of this study is on the polychaete communities. Polychaete abundance peaked at the summit and a mid-slope station (~1500m), a pattern mirrored by the biomass values. The polychaete community along the transect appeared to be particularly diverse, with 135 species nominally identified to putative species from a total of 954 individuals. A diversity maximum was identified on the upper slope at ~800m depth, with species diversity, richness and evenness also all peaking at this station. Depth is likely to be a significant factor in determining levels of similarity between stations. [ABSTRACT FROM AUTHOR]

Mud volcanoes are a special type of cold seeps where life is based on chemoautotrophic processes. They are considered as extreme environments and are characterised by unique megafaunal and macrofaunal communities. However, very few studies on mud volcanoes taking into account the smaller meiobenthic communities have been carried out. Two mud volcanoes were explored during the MEDECO cruise (2007) with the Remotely Operated Vehicle (ROV) Victor-6000; Amsterdam, located south of Turkey between 1700 and 2000m depth (Anaximander mud field) and Napoli, south of Crete, located along the Mediterranean Ridge at about 2000m depth (Olimpi mud field). The major aim of this study was to describe distributional patterns of meiofaunal communities and nematode assemblages from different seep microhabitats. Meiofaunal taxa and nematode assemblages at both mud volcanoes differed significantly from other Mediterranean sites in terms of standing stocks, dominance and species diversity. Density and biomass values were significantly higher at the seep sites, particularly at Amsterdam. Nematodes, the dominant meiofaunal taxon, displayed deeper penetration vertically into the sediment at the seep areas, indicating that biological rather than physicochemical factors are responsible for their vertical distribution. Patterns of nematode diversity varied, displaying both very high or very low species richness and dominance, depending on the habitat studied. The Lamellibrachia periphery and mussel bed of Napoli exhibited the highest species richness while the reduced sediments of Amsterdam yielded a species-poor nematode community, dominated by two successful species; one belonging to the genus Aponema and the other to the genus Sabatieria. Analysis of β-diversity showed that habitat heterogeneity of mud volcanoes contributed substantially to the total nematode species richness in the eastern Mediterranean Sea. These observations indicate a strong influence of mud volcanoes and cold-seep ecosystems on the meiofaunal communities and nematode assemblages. [ABSTRACT FROM AUTHOR]

We investigated the mechanisms of phytoplankton competition during the spring bloom, one of the most dramatic seasonal events in lower-trophic level ecosystems, in four state-of-the-art Plankton Functional Type (PFTs) models: PISCES, NEMURO, Plank- TOM5 and CCSM-BEC. In particular, we investigated the relative importance of different ecophysiological processes on the determination of the community structure, focusing both on the bottom-up and the top-down controls. The models reasonably reproduced the observed global distribution and seasonal variation of phytoplankton biomass. The fraction of diatoms with respect to the total phytoplankton biomass increases with the magnitude of the spring bloom in all models. However, the governing mechanisms differ between models, despite the fact that current PFT models represent ecophysiological processes using the same types of parameterizations. The increasing trend in the percentage of diatoms with increasing bloom magnitude is mainly caused by a stronger nutrient dependence of photosynthesis for diatoms compared to nanophytoplankton (bottom-up control). The difference in the maximum photosynthesis rate plays an important role in NEMURO and PlankTOM5 and determines the absolute values of the percentage of diatoms during the bloom. In CCSM-BEC, the light dependency of photosynthesis plays an important role in the North Atlantic and the Southern Ocean. The grazing pressure by zooplankton (top-down control), however, strongly contributes to the dominance of diatoms in PISCES and CCSM-BEC. The regional differences in the percentage of diatoms in PlankTOM5 are mainly determined by top-down control. These differences in the mechanisms suggest that the response of marine ecosystems to climate change could significantly differ among models, even if the present-day ecosystem is reproduced to a similar degree of confidence. For further understanding of plankton competition and for the prediction of future change in marine ecosystems, it is important to understand the relative differences in each physiological rate and life history rate in the bottom-up and the top-down controls between PFTs. [ABSTRACT FROM AUTHOR]

We investigated how the interactive effects of hydrography, topography and intrinsic community dynamics influence the assembly of species and functional traits across multiple spatial scales of a cold-water coral reef seascape. In a novel approach for these ecosystems, we use a spatially resolved complex three-dimensional flow model of hydrography to help explain assembly patterns. Forward selection of distance-based Moran's eigenvector mapping (dbMEM) variables identified two submodels of spatial scales at which communities are structured: broad-scale (across reef) and fine-scale (within reef). Canonical variance partitioning revealed broad-scale structures created mainly by variability in bathymetry and hydrography across reefs, which manifest as relatively narrow environmental niches for predators and scavenging detritivores. Fine-scale assembly was related more to processes that create spatially autocorrelated patches of fauna within a reef due to restricted dispersal in sessile fauna but social mating interactions and food supply in more mobile organisms. Our study implies that perturbations such as habitat fragmentation and altered hydrodynamic regimes have the potential to induce significant changes in the structure and function of cold-water coral reef ecosystems at spatial scales that span the entire seascape. [ABSTRACT FROM AUTHOR]

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

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

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

Undisturbed peatlands represent long term net sinks of carbon; however, peat extraction converts these systems into large and persistent sources of greenhouse gases. Although rewetting and restoration following peat extraction have taken place over the last several decades, very few studies have investigated the longer term impact of this restoration on peatland carbon balance. We determined the annual carbon balance of a former horticulturally-extracted peatland restored 10 yr prior to the study and compared these values to the carbon balance measured at neighboring unrestored and natural sites. Carbon dioxide (CO2) and methane (CH4) fluxes were measured using the chamber technique biweekly during the growing season from May to October 2010 and three times over the winter period. Dissolved organic carbon (DOC) export was measured from remnant ditches in the unrestored and restored sites. During the growing season the restored site had greater uptake of CO2 than the natural site when photon flux density was greater than 1000 µmolm-2 s-1, while the unrestored site remained a source of CO2. Ecosystem respiration was similar between natural and restored sites, which were both significantly lower than the unrestored site. Methane flux remained low at the restored site except from open water pools, created as part of restoration, and remnant ditches. Export of DOC during the growing season was 5.0 and 28.8 g m-2 from the restored and unrestored sites, respectively. Due to dry conditions during the study year all sites acted as net carbon sources with annual balance of the natural, restored and unrestored sites of 250.7, 148.0 and 546.6 g C m-2, respectively. Although hydrological conditions and vegetation community at the restored site remained intermediate between natural and unrestored conditions, the site acted as a smaller source of carbon than the natural peatland suggesting that near natural carbon balance can be returned ~ 10 yr post-restoration. [ABSTRACT FROM AUTHOR]

Changes in land use across the semiarid grasslands of Northern Mexico have driven a decline of plant cover and alteration of plant species composition. A number of different plant communities have resulted from these changes, however, their implications on the carbon cycle and regional carbon balance are still poorly understood. Here, we examined the effects of plant cover loss and changes in species composition on net ecosystem CO2 exchange (NEE) and their biotic and abiotic controls. Five typical plant community types were examined in the semiarid grassland by encasing the entire above-ground ecosystem using the geodesic dome method. Sites included an oat crop (crop), a moderately grazed grassland (moderate grazing), a 28 yr-old grazing exclosure (exclosure), an overgrazed site with low perennial grass cover (overgrazed), and an overgrazed site presenting shrub encroachment (shrub encroachment). For natural vegetation, rates of daytime NEE for sites with a high plant cover (exclosure and moderate grazing) were similar (P > 0.05) as compared to sites with low plant cover (overgrazed and shrub encroachment). However, night time NEE (carbon loss) was more than double (P < 0.05) for sites with high plant cover compared to sites with low cover, resulting into slight C sinks for the low plant cover sites and neutral or sources for the high plant cover sites on an annual basis. Differences in plant cover and its associated biomass defined the sensitivity to environmental controls. Thus, daytime NEE in low plant cover sites reached light compensation points at lower PPFD values than those from high plant cover sites. Differences in species composition did not influence NEE rates even though there were transient or permanent changes in C3 vs. C4 functional groups. [ABSTRACT FROM AUTHOR]

Chemosynthetic communities in the deep-sea can be found at hydrothermal vents, cold seeps, whale falls and wood falls. While these communities have been suggested to exist in isolation from solar energy, much of the life associated with them relies either directly or indirectly on photosynthesis in the surface waters of the oceans. The sun indirectly provides oxygen, a byproduct of photosynthesis, which aerobic chemosynthetic microorganisms require to synthesize organic carbon from CO2. Planktonic life stages of many vent and cold seep invertebrates also directly feed on photosynthetically produced organic matter as they disperse to new vent and seep systems. While a large portion of the life at deep-sea chemosynthetic habitats can be linked to the sun and so could not survive without it, a small portion of anaerobically chemosynthetic microorganisms can persist in its absence. These small and exotic organisms have developed a way of life in the deep-sea which involves the use of resources originating in their entirety from terrestrial sources. [ABSTRACT FROM AUTHOR]

Zooplankton play an essential role in marine food webs and understanding how community-level growth rates of zooplankton vary in the field is critical for predicting how marine ecosystem function may vary in the face of environmental changes. Here, we used the artificial cohort method to examine the effects of temperature, body size, and chlorophyll concentration (a proxy for food) on weight-specific growth rates for copepod communities in the East China Sea. Specifically, we tested the hypothesis that copepod community growth rates can be described by the metabolic theory of ecology (MTE), linking spatio-temporal variation of copepod growth rate with temperature and their body size. Our results generally agree with predictions made by the MTE and demonstrate that weight-specific growth rates of copepod communities in our study area are positively related with temperature and negatively related to body size. However, the regression coefficients of body size do not approach the theoretical predictions. Furthermore, we find that the deviation from the MTE predictions may be partly attributed to the effect of food availability (which is not explicitly accounted for by the MTE). In addition, significant difference in the coefficients of temperature and body size exists among taxonomic groups. Our results suggest that considering the effects of food limitation and taxonomy is necessary to better understand copepod growth rates under in situ conditions, and such effects on the MTE-based prediction needs further investigation. [ABSTRACT FROM AUTHOR]

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

The understanding of biochemical feed-back mechanisms in the climate system is lacking knowledge in relation to bi-directional ammonia (NH3) exchange between natural ecosystems and the atmosphere. We therefore study the atmospheric NH3 fluxes during a 25 days period during autumn 2010 (21 October-15 November) for the Danish beech forest, Lille Bøgeskov, to address the hypothesis that NH3 emissions occur from deciduous forests in relation to leaf fall. This is accomplished by using observations of vegetation status, NH3 fluxes and model calculations. Vegetation status was observed using plant area index (PAI) and leaf area index (LAI). NH3 fluxes were measured using the relaxed eddy accumulation (REA) method. The REA based NH3 concentrations were compared to NH3 denuder measurements. Model calculations were obtained with the Danish Ammonia MOdelling System (DAMOS). 57.7% of the fluxes measured showed emission and 19.5% showed deposition. The mean NH3 flux was 0.087±0.19 µgNH3-Nm-2 s-1 . A clear tendency of the flux going from negative (deposition) to positive (emission) fluxes of up to 0.96±0.40 µgNH3-Nm-2 s -1 throughout the measurement period was found. In the leaf fall period (23 October-8 November), an increase in the atmospheric NH3 concentrations was related to the increasing forest NH3 flux. The modelled concentration from DAMOS fits well the measured concentrations before leaf fall. During and after leaf fall, the modelled concentrations are too low. The results indicate that the missing contribution to atmospheric NH3 concentration from vegetative surfaces related to leaf fall are of a relatively large magnitude. We therefore conclude that emissions from deciduous forests are important to include in model calculations of atmospheric NH3 for forest ecosystems. Finally, diurnal variations in the measured NH3 concentrations were related to meteorological conditions, forest phenology and the spatial distribution of local anthropogenic NH3 sources. This suggests that an accurate description of ammonia fluxes over forest ecosystems requires a dynamic description of atmospheric and vegetation processes. [ABSTRACT FROM AUTHOR]

In initial ecosystems concentrations of all macro- and micronutrients can be considered as extremely low. Plant litter therefore strongly influences the development of a degraders' food web and is an important source for C and N input into soil in such ecosystems. In the present study, a 13C litter decomposition field experiment was performed for 30 weeks in initial soils from a post-mining area near the city of Cottbus (Germany). Two of this regions' dominant but contrasting pioneering plant species (Lotus corniculatus L. and Calamagrostis epigejos L.) were chosen to investigate the effects of litter quality on the litter decomposing microbial food web in initially nutrient-poor substrates. The results clearly indicate the importance of litter quality, mainly the amount of N stored in the litter material and its bioavailability for the degradation process and the development of microbial communities in the detritusphere and bulk soil. Whereas the degradation process of the L. corniculatus litter which had a low C/N ratio was fast and most pronounced changes in the microbial community structure were observed 1-4 weeks after litter addition, the degradation of the C. epigejos litter material was slow and microbial community changes mainly occurred at between 4 and 30 weeks after litter addition to the soil. However for both litter materials a clear indication for the importance of fungi for the degradation process was observed both on the abundance level as well as on the level of 13C incorporation (activity). [ABSTRACT FROM AUTHOR]

Coastal hypoxia, the depletion of oxygen concentration in coastal waters, is becoming more prominent on a global scale. Changes in climate and nutrient loadings are two aspects of global change that are expected to profoundly impact coastal hypoxia. We investigated the role of these drivers on the evolution of hypoxia in a stratified, temperate coastal system using a one-dimensional model. The model couples three submodels, describing the physical characteristics, the pelagic ecosystem and benthic diagenesis. The model is calibrated for the Central North Sea but the model approach is generic, and can be applied in stratified coastal ecosystems. Our results indicate that the projected changes in climatological conditions for the North Sea over the next 100 yr will increase the risk of hypoxia. On average the oxygen concentration is predicted to decrease by 17 µM, mostly due to a reduced solubility at higher water temperature (responsible for 65% of the decrease). Increased stratification (22 %) and enhanced biological rates due to higher water temperature (13 %) also affect the future oxygen concentration. Nutrient loadings also have a strong effect on the occurrence of hypoxia. Decreasing nutrient concentrations strongly decreases the probability of hypoxic events, stressing the importance of continued extensive eutrophication management to mitigate the effect of increased temperature. [ABSTRACT FROM AUTHOR]

To study the effects of the physical environment on carbon and nutrients cycles dynamics in the north eastern shelf of the Gulf of Cáadiz, changes in currents, tides, salinity, temperature, carbon system parameters (fugacity of CO2 (fCO2), dissolved organic carbon, dissolved inorganic carbon and pH) and others related (dissolved oxygen, total dissolved nitrogen, nutrients and suspended particulate matter) were measured in transects across the Guadalquivir Estuary and Bay of Cáadiz mouths. Thus, the main objective of this study is to investigate the influence of these inner ecosystems on the carbon and nutrient distributions in the adjacent continental shelf. Three cruises have been undertaken in June 2006, November 2006 and February 2007, each one covering one complete tidal cycle during June, both systems were exporting components to the adjacent continental shelf of the Gulf of Cáadiz. In an annual scale, Guadalquivir Estuary exported components while Bay of Cáadiz imported them. Diurnal variability of fCO2 could have a potentially important implication on the estimate of air-sea CO2 fluxes. Monthly studies should be undertaken to completely understand this dynamic system. [ABSTRACT FROM AUTHOR]