Biogeosciences

Abstract. The Global Fire Assimilation System (GFASv1.0) calculates biomass burning emissions by assimilating Fire Radiative Power (FRP) observations from the MODIS instruments onboard the Terra and Aqua satellites. It corrects for gaps in the observations, which are mostly due to cloud cover, and filters spurious FRP observations of volcanoes, gas flares and other industrial activity. The combustion rate is subsequently calculated with land cover-specific conversion factors. Emission factors for 40 gas-phase and aerosol trace species have been compiled from a literature survey. The corresponding daily emissions have been calculated on a global 0.5° × 0.5° grid from 2003 to the present. General consistency with the Global Fire Emission Database version 3.1 (GFED3.1) within its accuracy is achieved while maintaining the advantages of an FRP-based approach: GFASv1.0 makes use of the quantitative information on the combustion rate that is contained in the FRP observations, and it detects fires in real time at high spatial and temporal resolution. GFASv1.0 indicates omission errors in GFED3.1 due to undetected small fires. It also exhibits slightly longer fire seasons in South America and North Africa and a slightly shorter fire season in Southeast Asia. GFASv1.0 has already been used for atmospheric reactive gas simulations in an independent study, which found good agreement with atmospheric observations. We have performed simulations of the atmospheric aerosol distribution with and without the assimilation of MODIS aerosol optical depth (AOD). They indicate that the emissions of particulate matter need to be boosted by a factor of 2–4 to reproduce the global distribution of organic matter and black carbon. This discrepancy is also evident in the comparison of previously published top-down and bottom-up estimates. For the time being, a global enhancement of the particulate matter emissions by 3.4 is recommended. Validation with independent AOD and PM10 observations recorded during the Russian fires in summer 2010 show that the global Monitoring Atmospheric Composition and Change (MACC) aerosol model with GFASv1.0 aerosol emissions captures the smoke plume evolution well when organic matter and black carbon are enhanced by the recommended factor. In conjunction with the assimilation of MODIS AOD, the use of GFASv1.0 with enhanced emission factors quantitatively improves the forecast of the aerosol load near the surface sufficiently to allow air quality warnings with a lead time of up to four days.

Abstract. The net flux of carbon from land use and land-cover change (LULCC) accounted for 12.5% of anthropogenic carbon emissions from 1990 to 2010. This net flux is the most uncertain term in the global carbon budget, not only because of uncertainties in rates of deforestation and forestation, but also because of uncertainties in the carbon density of the lands actually undergoing change. Furthermore, there are differences in approaches used to determine the flux that introduce variability into estimates in ways that are difficult to evaluate, and not all analyses consider the same types of management activities. Thirteen recent estimates of net carbon emissions from LULCC are summarized here. In addition to deforestation, all analyses considered changes in the area of agricultural lands (croplands and pastures). Some considered, also, forest management (wood harvest, shifting cultivation). None included emissions from the degradation of tropical peatlands. Means and standard deviations across the thirteen model estimates of annual emissions for the 1980s and 1990s, respectively, are 1.14 ± 0.23 and 1.12 ± 0.25 Pg C yr−1 (1 Pg = 1015 g carbon). Four studies also considered the period 2000–2009, and the mean and standard deviations across these four for the three decades are 1.14 ± 0.39, 1.17 ± 0.32, and 1.10 ± 0.11 Pg C yr−1. For the period 1990–2009 the mean global emissions from LULCC are 1.14 ± 0.18 Pg C yr−1. The standard deviations across model means shown here are smaller than previous estimates of uncertainty as they do not account for the errors that result from data uncertainty and from an incomplete understanding of all the processes affecting the net flux of carbon from LULCC. Although these errors have not been systematically evaluated, based on partial analyses available in the literature and expert opinion, they are estimated to be on the order of ± 0.5 Pg C yr−1.

Abstract. The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 28 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st century. However, for most of these habitats the global area covered is unknown or has been only very roughly estimated; an even smaller – indeed, minimal – proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation thus shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps. Here, chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased productivity through specific physical processes, such as topographic modification of currents and enhanced transport of particles and detrital matter. Because of its unique abiotic attributes, the deep sea hosts a specialized fauna. Although there are no phyla unique to deep waters, at lower taxonomic levels the composition of the fauna is distinct from that found in the upper ocean. Amongst other characteristic patterns, deep-sea species may exhibit either gigantism or dwarfism, related to the decrease in food availability with depth. Food limitation on the seafloor and water column is also reflected in the trophic structure of heterotrophic deep-sea communities, which are adapted to low energy availability. In most of these heterotrophic habitats, the dominant megafauna is composed of detritivores, while filter feeders are abundant in habitats with hard substrata (e.g. mid-ocean ridges, seamounts, canyon walls and coral reefs). Chemoautotrophy through symbiotic relationships is dominant in reducing habitats. Deep-sea biodiversity is among of the highest on the planet, mainly composed of macro and meiofauna, with high evenness. This is true for most of the continental margins and abyssal plains with hot spots of diversity such as seamounts or cold-water corals. However, in some ecosystems with particularly "extreme" physicochemical processes (e.g. hydrothermal vents), biodiversity is low but abundance and biomass are high and the communities are dominated by a few species. Two large-scale diversity patterns have been discussed for deep-sea benthic communities. First, a unimodal relationship between diversity and depth is observed, with a peak at intermediate depths (2000–3000 m), although this is not universal and particular abiotic processes can modify the trend. Secondly, a poleward trend of decreasing diversity has been discussed, but this remains controversial and studies with larger and more robust data sets are needed. Because of the paucity in our knowledge of habitat coverage and species composition, biogeographic studies are mostly based on regional data or on specific taxonomic groups. Recently, global biogeographic provinces for the pelagic and benthic deep ocean have been described, using environmental and, where data were available, taxonomic information. This classification described 30 pelagic provinces and 38 benthic provinces divided into 4 depth ranges, as well as 10 hydrothermal vent provinces. One of the major issues faced by deep-sea biodiversity and biogeographical studies is related to the high number of species new to science that are collected regularly, together with the slow description rates for these new species. Taxonomic coordination at the global scale is particularly difficult, but is essential if we are to analyse large diversity and biogeographic trends.

Abstract. Forested tropical peatlands in Southeast Asia store at least 42 000 Million metric tonnes (Mt) of soil carbon. Human activity and climate change threatens the stability of this large pool, which has been decreasing rapidly over the last few decades owing to deforestation, drainage and fire. In this paper we estimate the carbon dioxide (CO2) emissions resulting from drainage of lowland tropical peatland for agricultural and forestry development which dominates the perturbation of the carbon balance in the region. Present and future emissions from drained peatlands are quantified using data on peatland extent and peat thickness, present and projected land use, water management practices and decomposition rates. Of the 27.1 Million hectares (Mha) of peatland in Southeast Asia, 12.9 Mha had been deforested and mostly drained by 2006. This latter area is increasing rapidly because of increasing land development pressures. Carbon dioxide (CO2) emission caused by decomposition of drained peatlands was between 355 Mt y−1 and 855 Mt y−1 in 2006 of which 82% came from Indonesia, largely Sumatra and Kalimantan. At a global scale, CO2 emission from peatland drainage in Southeast Asia is contributing the equivalent of 1.3% to 3.1% of current global CO2 emissions from the combustion of fossil fuel. If current peatland development and management practices continue, these emissions are predicted to continue for decades. This warrants inclusion of tropical peatland CO2 emissions in global greenhouse gas emission calculations and climate mitigation policies. Uncertainties in emission calculations are discussed and research needs for improved estimates are identified.

Abstract. Future ocean acidification has the potential to adversely affect many marine organisms. A growing body of evidence suggests that many species could suffer from reduced fertilization success, decreases in larval- and adult growth rates, reduced calcification rates, and even mortality when being exposed to near-future levels (year 2100 scenarios) of ocean acidification. Little research focus is currently placed on those organisms/taxa that might be less vulnerable to the anticipated changes in ocean chemistry; this is unfortunate, as the comparison of more vulnerable to more tolerant physiotypes could provide us with those physiological traits that are crucial for ecological success in a future ocean. Here, we attempt to summarize some ontogenetic and lifestyle traits that lead to an increased tolerance towards high environmental pCO2. In general, marine ectothermic metazoans with an extensive extracellular fluid volume may be less vulnerable to future acidification as their cells are already exposed to much higher pCO2 values (0.1 to 0.4 kPa, ca. 1000 to 3900 μatm) than those of unicellular organisms and gametes, for which the ocean (0.04 kPa, ca. 400 μatm) is the extracellular space. A doubling in environmental pCO2 therefore only represents a 10% change in extracellular pCO2 in some marine teleosts. High extracellular pCO2 values are to some degree related to high metabolic rates, as diffusion gradients need to be high in order to excrete an amount of CO2 that is directly proportional to the amount of O2 consumed. In active metazoans, such as teleost fish, cephalopods and many brachyuran crustaceans, exercise induced increases in metabolic rate require an efficient ion-regulatory machinery for CO2 excretion and acid-base regulation, especially when anaerobic metabolism is involved and metabolic protons leak into the extracellular space. These ion-transport systems, which are located in highly developed gill epithelia, form the basis for efficient compensation of pH disturbances during exposure to elevated environmental pCO2. Compensation of extracellular acid-base status in turn may be important in avoiding metabolic depression. So far, maintained "performance" at higher seawater pCO2 (>0.3 to 0.6 kPa) has only been observed in adults/juveniles of active, high metabolic species with a powerful ion regulatory apparatus. However, while some of these taxa are adapted to cope with elevated pCO2 during their regular embryonic development, gametes, zygotes and early embryonic stages, which lack specialized ion-regulatory epithelia, may be the true bottleneck for ecological success – even of the more tolerant taxa. Our current understanding of which marine animal taxa will be affected adversely in their physiological and ecological fitness by projected scenarios of anthropogenic ocean acidification is quite incomplete. While a growing amount of empirical evidence from CO2 perturbation experiments suggests that several taxa might react quite sensitively to ocean acidification, others seem to be surprisingly tolerant. However, there is little mechanistic understanding on what physiological traits are responsible for the observed differential sensitivities (see reviews of Seibel and Walsh, 2003; Pörtner et al., 2004; Fabry et al., 2008; Pörtner, 2008). This leads us to the first very basic question of how to define general CO2 tolerance on the species level.

Abstract. Biochar is widely recognized as an efficient tool for carbon sequestration and soil fertility. The understanding of its chemical and physical properties, which are strongly related to the type of the initial material used and pyrolysis conditions, is crucial to identify the most suitable application of biochar in soil. A selection of organic wastes with different characteristics (e.g., rice husk (RH), rice straw (RS), wood chips of apple tree (Malus pumila) (AB), and oak tree (Quercus serrata) (OB)) were pyrolyzed at different temperatures (400, 500, 600, 700, and 800 °C) in order to optimize the physicochemical properties of biochar as a soil amendment. Low-temperature pyrolysis produced high biochar yields; in contrast, high-temperature pyrolysis led to biochars with a high C content, large surface area, and high adsorption characteristics. Biochar obtained at 600 °C leads to a high recalcitrant character, whereas that obtained at 400 °C retains volatile and easily labile compounds. The biochar obtained from rice materials (RH and RS) showed a high yield and unique chemical properties because of the incorporation of silica elements into its chemical structure. The biochar obtained from wood materials (AB and OB) showed high carbon content and a high absorption character.

Abstract. Estuaries are biogeochemical hot spots because they receive large inputs of nutrients and organic carbon from land and oceans to support high rates of metabolism and primary production. We synthesize published rates of annual phytoplankton primary production (APPP) in marine ecosystems influenced by connectivity to land – estuaries, bays, lagoons, fjords and inland seas. Review of the scientific literature produced a compilation of 1148 values of APPP derived from monthly incubation assays to measure carbon assimilation or oxygen production. The median value of median APPP measurements in 131 ecosystems is 185 and the mean is 252 g C m−2 yr−1, but the range is large: from −105 (net pelagic production in the Scheldt Estuary) to 1890 g C m−2 yr−1 (net phytoplankton production in Tamagawa Estuary). APPP varies up to 10-fold within ecosystems and 5-fold from year to year (but we only found eight APPP series longer than a decade so our knowledge of decadal-scale variability is limited). We use studies of individual places to build a conceptual model that integrates the mechanisms generating this large variability: nutrient supply, light limitation by turbidity, grazing by consumers, and physical processes (river inflow, ocean exchange, and inputs of heat, light and wind energy). We consider method as another source of variability because the compilation includes values derived from widely differing protocols. A simulation model shows that different methods reported in the literature can yield up to 3-fold variability depending on incubation protocols and methods for integrating measured rates over time and depth. Although attempts have been made to upscale measures of estuarine-coastal APPP, the empirical record is inadequate for yielding reliable global estimates. The record is deficient in three ways. First, it is highly biased by the large number of measurements made in northern Europe (particularly the Baltic region) and North America. Of the 1148 reported values of APPP, 958 come from sites between 30 and 60° N; we found only 36 for sites south of 20° N. Second, of the 131 ecosystems where APPP has been reported, 37% are based on measurements at only one location during 1 year. The accuracy of these values is unknown but probably low, given the large interannual and spatial variability within ecosystems. Finally, global assessments are confounded by measurements that are not intercomparable because they were made with different methods. Phytoplankton primary production along the continental margins is tightly linked to variability of water quality, biogeochemical processes including ocean–atmosphere CO2 exchange, and production at higher trophic levels including species we harvest as food. The empirical record has deficiencies that preclude reliable global assessment of this key Earth system process. We face two grand challenges to resolve these deficiencies: (1) organize and fund an international effort to use a common method and measure APPP regularly across a network of coastal sites that are globally representative and sustained over time, and (2) integrate data into a unifying model to explain the wide range of variability across ecosystems and to project responses of APPP to regional manifestations of global change as it continues to unfold.

Abstract. This paper presents the model SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes), which is a vertical (1-D) integrated radiative transfer and energy balance model. The model links visible to thermal infrared radiance spectra (0.4 to 50 μm) as observed above the canopy to the fluxes of water, heat and carbon dioxide, as a function of vegetation structure, and the vertical profiles of temperature. Output of the model is the spectrum of outgoing radiation in the viewing direction and the turbulent heat fluxes, photosynthesis and chlorophyll fluorescence. A special routine is dedicated to the calculation of photosynthesis rate and chlorophyll fluorescence at the leaf level as a function of net radiation and leaf temperature. The fluorescence contributions from individual leaves are integrated over the canopy layer to calculate top-of-canopy fluorescence. The calculation of radiative transfer and the energy balance is fully integrated, allowing for feedback between leaf temperatures, leaf chlorophyll fluorescence and radiative fluxes. Leaf temperatures are calculated on the basis of energy balance closure. Model simulations were evaluated against observations reported in the literature and against data collected during field campaigns. These evaluations showed that SCOPE is able to reproduce realistic radiance spectra, directional radiance and energy balance fluxes. The model may be applied for the design of algorithms for the retrieval of evapotranspiration from optical and thermal earth observation data, for validation of existing methods to monitor vegetation functioning, to help interpret canopy fluorescence measurements, and to study the relationships between synoptic observations with diurnally integrated quantities. The model has been implemented in Matlab and has a modular design, thus allowing for great flexibility and scalability.

Abstract. Conversion of tropical peatlands to agriculture leads to a release of carbon from previously stable, long-term storage, resulting in land subsidence that can be a surrogate measure of CO2 emissions to the atmosphere. We present an analysis of recent large-scale subsidence monitoring studies in Acacia and oil palm plantations on peatland in SE Asia, and compare the findings with previous studies. Subsidence in the first 5 yr after drainage was found to be 142 cm, of which 75 cm occurred in the first year. After 5 yr, the subsidence rate in both plantation types, at average water table depths of 0.7 m, remained constant at around 5 cm yr−1. The results confirm that primary consolidation contributed substantially to total subsidence only in the first year after drainage, that secondary consolidation was negligible, and that the amount of compaction was also much reduced within 5 yr. Over 5 yr after drainage, 75 % of cumulative subsidence was caused by peat oxidation, and after 18 yr this was 92 %. The average rate of carbon loss over the first 5 yr was 178 t CO2eq ha−1 yr−1, which reduced to 73 t CO2eq ha−1 yr−1 over subsequent years, potentially resulting in an average loss of 100 t CO2eq ha−1 yr−1 over 25 yr. Part of the observed range in subsidence and carbon loss values is explained by differences in water table depth, but vegetation cover and other factors such as addition of fertilizers also influence peat oxidation. A relationship with groundwater table depth shows that subsidence and carbon loss are still considerable even at the highest water levels theoretically possible in plantations. This implies that improved plantation water management will reduce these impacts by 20 % at most, relative to current conditions, and that high rates of carbon loss and land subsidence are inevitable consequences of conversion of forested tropical peatlands to other land uses.

Abstract. Relative to inorganic nitrogen, concentrations of dissolved organic nitrogen (DON) are often high, even in regions believed to be nitrogen-limited. The persistence of these high concentrations led to the view that the DON pool was largely refractory and therefore unimportant to plankton nutrition. Any DON that was utilized was believed to fuel bacterial production. More recent work, however, indicates that fluxes into and out of the DON pool can be large, and that the constancy in concentration is a function of tightly coupled production and consumption processes. Evidence is also accumulating which indicates that phytoplankton, including a number of harmful species, may obtain a substantial part of their nitrogen nutrition from organic compounds. Ongoing research includes ways to discriminate between autotrophic and heterotrophic utilization, as well as a number of mechanisms, such as cell surface enzymes and photochemical decomposition, that could facilitate phytoplankton use of DON components.