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The global warming potential of nitrous oxide (N2O) and its long atmospheric lifetime mean its presence in the atmosphere is of major concern, and that methods are required to measure and reduce emissions. Large spatial and temporal variations means, however, that simple extrapolation of measured data is inappropriate, and that other methods of quantification are required. Although process-based models have been developed to simulate these emissions, they often require a large amount of input data that is not available at a regional scale, making regional and global emission estimates difficult to achieve. The spatial extent of organic soils means that quantification of emissions from these soil types is also required, but will not be achievable using a process-based model that has not been developed to simulate soil water contents above field capacity or organic soils. The ECOSSE model was developed to overcome these limitations, and with a requirement for only input data that is readily available at a regional scale, it can be used to quantify regional emissions and directly inform land-use change decisions. ECOSSE includes the major processes of nitrogen (N) turnover, with material being exchanged between pools of SOM at rates modified by temperature, soil moisture, soil pH and crop cover. Evaluation of its performance at site-scale is presented to demonstrate its ability to adequately simulate soil N contents and N2O emissions from cropland soils in Europe. Mitigation scenarios and sensitivity analyses are also presented to demonstrate how ECOSSE can be used to estimate the impact of future climate and land-use change on N2O emissions.
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42 degrees C for 24 h and back to 25 degrees C for >= 8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.
Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of delta C-13 and delta N-15 isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the delta C-13 and delta N-15 isotopic signatures from two organic matter (OM) fractions along with soil mineral proxies to identify the likely binding mechanisms involved. We analyzed OM fractions hypothesized to contain carbon stabilized through organo-mineral complexes: (1) OM separated chemically with sodium pyrophosphate (OM(PY)) and (2) OM occluded in micro-structures found in the chemical extraction residue (OM(ER)). Because the OM fractions were separated from five different soils with paired forest and arable land use histories, we could address the impact of land use change on carbon binding and processing mechanisms. We used partial least squares regression to analyze patterns in the isotopic signature of OM with established mineral and chemical proxies indicative for certain binding mechanisms. We found different mechanisms predominate in each land use type. For arable soils, the formation of OM(PY)-Ca-mineral associations was identified as an important OM binding mechanism. Therefore, we hypothesize an increased stabilization of microbial processed OM(PY) through Ca2+ interactions. In general, we found the forest soils to contain on average 10% more stabilized carbon relative to total carbon stocks, than the agricultural counter part. In forest soils, we found a positive relationship between isotopic signatures of OM(PY) and the ratio of soil organic carbon content to soil surface area (SOC/SSA). This indicates that the OM(PY) fractions of forest soils represent layers of slower exchange not directly attached to mineral surfaces. From the isotopic composition of the OM(ER) fraction, we conclude that the OM in this fraction from both land use types have undergone a different pathway to stabilization that does not involve microbial processing, which may include OM which is highly protected within soil micro-structures.
Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.
Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.
Provisioning a sufficient stable source of food requires sound knowledge about current and upcoming threats to agricultural production. To that end machine learning approaches were used to identify the prevailing climatic and soil hydrological drivers of spatial and temporal yield variability of four crops, comprising 40 years yield data each from 351 counties in Germany. Effects of progress in agricultural management and breeding were subtracted from the data prior the machine learning modelling by fitting smooth non-linear trends to the 95th percentiles of observed yield data. An extensive feature selection approach was followed then to identify the most relevant predictors out of a large set of candidate predictors, comprising various soil and meteorological data. Particular emphasis was placed on studying the uniqueness of identified key predictors. Random Forest and Support Vector Machine models yielded similar although not identical results, capturing between 50% and 70% of the spatial and temporal variance of silage maize, winter barley, winter rapeseed and winter wheat yield. Equally good performance could be achieved with different sets of predictors. Thus identification of the most reliable models could not be based on the outcome of the model study only but required expert's judgement. Relationships between drivers and response often exhibited optimum curves, especially for summer air temperature and precipitation. In contrast, soil moisture clearly proved less relevant compared to meteorological drivers. In view of the expected climate change both excess precipitation and the excess heat effect deserve more attention in breeding as well as in crop modelling.
We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
The vesicle-inducing protein in plastids (VIPP1) was suggested to play a role in thylakoid membrane formation via membrane vesicles. As this functional assignment is under debate, we investigated the function of VIPP1 in Chlamydomonas reinhardtii. Using immunofluorescence, we localized VIPP1 to distinct spots within the chloroplast. In VIPP1-RNA interference/artificial microRNA cells, we consistently observed aberrant, prolamellar body-like structures at the origin of multiple thylakoid membrane layers, which appear to coincide with the immunofluorescent VIPP1 spots and suggest a defect in thylakoid membrane biogenesis. Accordingly, using quantitative shotgun proteomics, we found that unstressed vipp1 mutant cells accumulate 14 to 20% less photosystems, cytochrome b(6)f complex, and ATP synthase but 30% more light-harvesting complex II than control cells, while complex assembly, thylakoid membrane ultrastructure, and bulk lipid composition appeared unaltered. Photosystems in vipp1 mutants are sensitive to high light, which coincides with a lowered midpoint potential of the Q(A)/Q(A)(-) redox couple and increased thermosensitivity of photosystem II (PSII), suggesting structural defects in PSII. Moreover, swollen thylakoids, despite reduced membrane energization, in vipp1 mutants grown on ammonium suggest defects in the supermolecular organization of thylakoid membrane complexes. Overall, our data suggest a role of VIPP1 in the biogenesis/assembly of thylakoid membrane core complexes, most likely by supplying structural lipids.
Landscapes can be viewed as spatially heterogeneous areas encompassing terrestrial and aquatic domains. To date, most landscape carbon (C) fluxes have been estimated by accounting for terrestrial ecosystems, while aquatic ecosystems have been largely neglected. However, a robust assessment of C fluxes on the landscape scale requires the estimation of fluxes within and between both landscape components. Here, we compiled data from the literature on C fluxes across the air–water interface from various landscape components. We simulated C emissions and uptake for five different scenarios which represent a gradient of increasing spatial heterogeneity within a temperate young moraine landscape: (I) a homogeneous landscape with only cropland and large lakes; (II) separation of the terrestrial domain into cropland and forest; (III) further separation into cropland, forest, and grassland; (IV) additional division of the aquatic area into large lakes and peatlands; and (V) further separation of the aquatic area into large lakes, peatlands, running waters, and small water bodies These simulations suggest that C fluxes at the landscape scale might depend on spatial heterogeneity and landscape diversity, among other factors. When we consider spatial heterogeneity and diversity alone, small inland waters appear to play a pivotal and previously underestimated role in landscape greenhouse gas emissions that may be regarded as C hot spots. Approaches focusing on the landscape scale will also enable improved projections of ecosystems’ responses to perturbations, e.g., due to global change and anthropogenic activities, and evaluations of the specific role individual landscape components play in regional C fluxes. WIREs Water 2016, 3:601–617. doi: 10.1002/wat2.1147