Global transcriptome analysis and identification of differentially expressed genes after infection of Fragaria vesca with powdery mildew (Podosphaera aphanis)

Background: Podosphaera aphanis, the causal agent of strawberry powdery mildew causes significant economic loss worldwide. Methods: We used the diploid strawberry species Fragaria vesca as a model to study plant pathogen interactions. RNA-seq was employed to generate a transcriptome dataset from two accessions, F. vesca ssp. vesca Hawaii 4 (HW) and F. vesca f. semperflorens Yellow Wonder 5AF7 (YW) at 1 d (1 DAI) and 8 d (8 DAI) after infection. Results: Of the total reads identified about 999 million (92%) mapped to the F. vesca genome. These transcripts were derived from a total of 23,470 and 23,464 genes in HW and YW, respectively from the three time points (control, 1 and 8 DAI). Analysis identified 1,567, 1,846 and 1,145 up-regulated genes between control and 1 DAI, control and 8 DAI, and 1 and 8 DAI, respectively in HW. Similarly, 1,336, 1,619 and 968 genes were up-regulated in YW. Also 646, 1,098 and 624 down-regulated genes were identified in HW, while 571, 754 and 627 genes were down-regulated in YW between all three time points, respectively. Conclusion: Investigation of differentially expressed genes (log2 fold changes �5) between control and 1 DAI in both HW and YW identified a large number of genes related to secondary metabolism, signal transduction; transcriptional regulation and disease resistance were highly expressed. These included flavonoid 3´-monooxygenase, peroxidase 15, glucan endo-1,3-β-glucosidase 2, receptor-like kinases, transcription factors, germin-like proteins, F-box proteins, NB-ARC and NBS-LRR proteins. This is the first application of RNA-seq to any pathogen interaction in strawberry

Robustness despite uncertainty: regional climate data reveal the dominant role of humans in explaining global extinctions of Late Quaternary megafauna

Debate over the late Quaternary megafaunal extinctions has focussed on whether human colonisation or climatic changes were more important drivers of extinction, with few extinctions being unambiguously attributable to either. Most analyses have been geographically or taxonomically restricted and the few quantitative global analyses have been limited by coarse temporal resolution or overly simplified climate reconstructions or proxies. We present a global analysis of the causes of these extinctions which uses high-resolution climate reconstructions and explicitly investigates the sensitivity of our results to uncertainty in the palaeological record. Our results show that human colonisation was the dominant driver of megafaunal extinction across the world but that climatic factors were also important. We identify the geographic regions where future research is likely to have the most impact, with our models reliably predicting extinctions across most of the world, with the notable exception of mainland Asia where we fail to explain the apparently low rate of extinction found in in the fossil record. Our results are highly robust to uncertainties in the palaeological record, and our main conclusions are unlikely to change qualitatively following minor improvements or changes in the dates of extinctions and human colonisation.

A method for merging nadir-sounding climate records, with an application to the global-mean stratospheric temperature data sets from SSU and AMSU

A method is proposed for merging different nadir-sounding climate data records using measurements from high-resolution limb sounders to provide a transfer function between the different nadir measurements. The two nadir-sounding records need not be overlapping so long as the limb-sounding record bridges between them. The method is applied to global-mean stratospheric temperatures from the NOAA Climate Data Records based on the Stratospheric Sounding Unit (SSU) and the Advanced Microwave Sounding Unit-A (AMSU), extending the SSU record forward in time to yield a continuous data set from 1979 to present, and providing a simple framework for extending the SSU record into the future using AMSU. SSU and AMSU are bridged using temperature measurements from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), which is of high enough vertical resolution to accurately represent the weighting functions of both SSU and AMSU. For this application, a purely statistical approach is not viable since the different nadir channels are not sufficiently linearly independent, statistically speaking. The near-global-mean linear temperature trends for extended SSU for 1980–2012 are −0.63 ± 0.13, −0.71 ± 0.15 and −0.80 ± 0.17 K decade−1 (95 % confidence) for channels 1, 2 and 3, respectively. The extended SSU temperature changes are in good agreement with those from the Microwave Limb Sounder (MLS) on the Aura satellite, with both exhibiting a cooling trend of ~ 0.6 ± 0.3 K decade−1 in the upper stratosphere from 2004 to 2012. The extended SSU record is found to be in agreement with high-top coupled atmosphere–ocean models over the 1980–2012 period, including the continued cooling over the first decade of the 21st century.

Global patterns of plant root colonization intensity by mycorrhizal fungi explained by climate and soil chemistry

Aim Most vascular plants on Earth form mycorrhizae, a symbiotic relationship between plants and fungi. Despite the broad recognition of the importance of mycorrhizae for global carbon and nutrient cycling, we do not know how soil and climate variables relate to the intensity of colonization of plant roots by mycorrhizal fungi. Here we quantify the global patterns of these relationships. Location Global. Methods Data on plant root colonization intensities by the two dominant types of mycorrhizal fungi world-wide, arbuscular (4887 plant species in 233 sites) and ectomycorrhizal fungi (125 plant species in 92 sites), were compiled from published studies. Data for climatic and soil factors were extracted from global datasets. For a given mycorrhizal type, we calculated at each site the mean root colonization intensity by mycorrhizal fungi across all potentially mycorrhizal plant species found at the site, and subjected these data to generalized additive model regression analysis with environmental factors as predictor variables. Results We show for the first time that at the global scale the intensity of plant root colonization by arbuscular mycorrhizal fungi strongly relates to warm-season temperature, frost periods and soil carbon-to-nitrogen ratio, and is highest at sites featuring continental climates with mild summers and a high availability of soil nitrogen. In contrast, the intensity of ectomycorrhizal infection in plant roots is related to soil acidity, soil carbon-to-nitrogen ratio and seasonality of precipitation, and is highest at sites with acidic soils and relatively constant precipitation levels. Main conclusions We provide the first quantitative global maps of intensity of mycorrhizal colonization based on environmental drivers, and suggest that environmental changes will affect distinct types of mycorrhizae differently. Future analyses of the potential effects of environmental change on global carbon and nutrient cycling via mycorrhizal pathways will need to take into account the relationships discovered in this study.

What does global mean temperature tell us about local climate?

The subject of climate feedbacks focuses attention on global mean surface air temperature (GMST) as the key metric of climate change. But what does knowledge of past and future GMST tell us about the climate of specific regions? In the context of the ongoing UNFCCC process, this is an important question for policy-makers as well as for scientists. The answer depends on many factors, including the mechanisms causing changes, the timescale of the changes, and the variables and regions of interest. This paper provides a review and analysis of the relationship between changes in GMST and changes in local climate, first in observational records and then in a range of climate model simulations, which are used to interpret the observations. The focus is on decadal timescales, which are of particular interest in relation to recent and near-future anthropogenic climate change. It is shown that GMST primarily provides information about forced responses, but that understanding and quantifying internal variability is essential to projecting climate and climate impacts on regional-to-local scales. The relationship between local forced responses and GMST is often linear but may be nonlinear, and can be greatly complicated by competition between different forcing factors. Climate projections are limited not only by uncertainties in the signal of climate change but also by uncertainties in the characteristics of real-world internal variability. Finally, it is shown that the relationship between GMST and local climate provides a simple approach to climate change detection, and a useful guide to attribution studies.

Recent progress in understanding and projecting regional and global mean sea-level change

Considerable progress has been made in understanding the present and future regional and global sea level in the 2 years since the publication of the Fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change. Here, we evaluate how the new results affect the AR5’s assessment of (i) historical sea level rise, including attribution of that rise and implications for the sea level budget, (ii) projections of the components and of total global mean sea level (GMSL), and (iii) projections of regional variability and emergence of the anthropogenic signal. In each of these cases, new work largely provides additional evidence in support of the AR5 assessment, providing greater confidence in those findings. Recent analyses confirm the twentieth century sea level rise, with some analyses showing a slightly smaller rate before 1990 and some a slightly larger value than reported in the AR5. There is now more evidence of an acceleration in the rate of rise. Ongoing ocean heat uptake and associated thermal expansion have continued since 2000, and are consistent with ocean thermal expansion reported in the AR5. A significant amount of heat is being stored deeper in the water column, with a larger rate of heat uptake since 2000 compared to the previous decades and with the largest storage in the Southern Ocean. The first formal detection studies for ocean thermal expansion and glacier mass loss since the AR5 have confirmed the AR5 finding of a significant anthropogenic contribution to sea level rise over the last 50 years. New projections of glacier loss from two regions suggest smaller contributions to GMSL rise from these regions than in studies assessed by the AR5; additional regional studies are required to further assess whether there are broader implications of these results. Mass loss from the Greenland Ice Sheet, primarily as a result of increased surface melting, and from the Antarctic Ice Sheet, primarily as a result of increased ice discharge, has accelerated. The largest estimates of acceleration in mass loss from the two ice sheets for 2003–2013 equal or exceed the acceleration of GMSL rise calculated from the satellite altimeter sea level record over the longer period of 1993–2014. However, when increased mass gain in land water storage and parts of East Antarctica, and decreased mass loss from glaciers in Alaska and some other regions are taken into account, the net acceleration in the ocean mass gain is consistent with the satellite altimeter record. New studies suggest that a marine ice sheet instability (MISI) may have been initiated in parts of the West Antarctic Ice Sheet (WAIS), but that it will affect only a limited number of ice streams in the twenty-first century. New projections of mass loss from the Greenland and Antarctic Ice Sheets by 2100, including a contribution from parts of WAIS undergoing unstable retreat, suggest a contribution that falls largely within the likely range (i.e., two thirds probability) of the AR5. These new results increase confidence in the AR5 likely range, indicating that there is a greater probability that sea level rise by 2100 will lie in this range with a corresponding decrease in the likelihood of an additional contribution of several tens of centimeters above the likely range. In view of the comparatively limited state of knowledge and understanding of rapid ice sheet dynamics, we continue to think that it is not yet possible to make reliable quantitative estimates of future GMSL rise outside the likely range. Projections of twenty-first century GMSL rise published since the AR5 depend on results from expert elicitation, but we have low confidence in conclusions based on these approaches. New work on regional projections and emergence of the anthropogenic signal suggests that the two commonly predicted features of future regional sea level change (the increasing tilt across the Antarctic Circumpolar Current and the dipole in the North Atlantic) are related to regional changes in wind stress and surface heat flux. Moreover, it is expected that sea level change in response to anthropogenic forcing, particularly in regions of relatively low unforced variability such as the low-latitude Atlantic, will be detectable over most of the ocean by 2040. The east-west contrast of sea level trends in the Pacific observed since the early 1990s cannot be satisfactorily accounted for by climate models, nor yet definitively attributed either to unforced variability or forced climate change.

Future changes of wind energy potentials over Europe in a large CMIP5 multi-model ensemble

A statistical-dynamical downscaling method is used to estimate future changes of wind energy output (Eout) of a benchmark wind turbine across Europe at the regional scale. With this aim, 22 global climate models (GCMs) of the Coupled Model Intercomparison Project Phase 5 (CMIP5) ensemble are considered. The downscaling method uses circulation weather types and regional climate modelling with the COSMO-CLM model. Future projections are computed for two time periods (2021–2060 and 2061–2100) following two scenarios (RCP4.5 and RCP8.5). The CMIP5 ensemble mean response reveals a more likely than not increase of mean annual Eout over Northern and Central Europe and a likely decrease over Southern Europe. There is some uncertainty with respect to the magnitude and the sign of the changes. Higher robustness in future changes is observed for specific seasons. Except from the Mediterranean area, an ensemble mean increase of Eout is simulated for winter and a decreasing for the summer season, resulting in a strong increase of the intra-annual variability for most of Europe. The latter is, in particular, probable during the second half of the 21st century under the RCP8.5 scenario. In general, signals are stronger for 2061–2100 compared to 2021–2060 and for RCP8.5 compared to RCP4.5. Regarding changes of the inter-annual variability of Eout for Central Europe, the future projections strongly vary between individual models and also between future periods and scenarios within single models. This study showed for an ensemble of 22 CMIP5 models that changes in the wind energy potentials over Europe may take place in future decades. However, due to the uncertainties detected in this research, further investigations with multi-model ensembles are needed to provide a better quantification and understanding of the future changes.

Modelled and observed changes in aerosols and surface solar radiation over Europe between 1960 and 2009

Substantial changes in anthropogenic aerosols and precursor gas emissions have occurred over recent decades due to the implementation of air pollution control legislation and economic growth. The response of atmospheric aerosols to these changes and the impact on climate are poorly constrained, particularly in studies using detailed aerosol chemistry–climate models. Here we compare the HadGEM3-UKCA (Hadley Centre Global Environment Model-United Kingdom Chemistry and Aerosols) coupled chemistry–climate model for the period 1960–2009 against extensive ground-based observations of sulfate aerosol mass (1978–2009), total suspended particle matter (SPM, 1978–1998), PM10 (1997–2009), aerosol optical depth (AOD, 2000–2009), aerosol size distributions (2008–2009) and surface solar radiation (SSR, 1960–2009) over Europe. The model underestimates observed sulfate aerosol mass (normalised mean bias factor (NMBF) = −0.4), SPM (NMBF = −0.9), PM10 (NMBF = −0.2), aerosol number concentrations (N30 NMBF = −0.85; N50 NMBF = −0.65; and N100 NMBF = −0.96) and AOD (NMBF = −0.01) but slightly overpredicts SSR (NMBF = 0.02). Trends in aerosol over the observational period are well simulated by the model, with observed (simulated) changes in sulfate of −68 % (−78 %), SPM of −42 % (−20 %), PM10 of −9 % (−8 %) and AOD of −11 % (−14 %). Discrepancies in the magnitude of simulated aerosol mass do not affect the ability of the model to reproduce the observed SSR trends. The positive change in observed European SSR (5 %) during 1990–2009 ("brightening") is better reproduced by the model when aerosol radiative effects (ARE) are included (3 %), compared to simulations where ARE are excluded (0.2 %). The simulated top-of-the-atmosphere aerosol radiative forcing over Europe under all-sky conditions increased by > 3.0 W m−2 during the period 1970–2009 in response to changes in anthropogenic emissions and aerosol concentrations.

Projected changes in tropical cyclones over Vietnam and the South China Sea using a 25 km regional climate model perturbed physics ensemble

The regional climate modelling system PRECIS, was run at 25 km horizontal resolution for 150 years (1949-2099) using global driving data from a five member perturbed physics ensemble (based on the coupled global climate model HadCM3). Output from these simulations was used to investigate projected changes in tropical cyclones (TCs) over Vietnam and the South China Sea due to global warming (under SRES scenario A1B). Thirty year climatological mean periods were used to look at projected changes in future (2069-2098) TCs compared to a 1961-1990 baseline. Present day results were compared qualitatively with IBTrACS observations and found to be reasonably realistic. Future projections show a 20-44 % decrease in TC frequency, although the spatial patterns of change differ between the ensemble members, and an increase of 27-53 % in the amount of TC associated precipitation. No statistically significant changes in TC intensity were found, however, the occurrence of more intense TCs (defined as those with a maximum 10 m wind speed > 35 m/s) was found to increase by 3-9 %. Projected increases in TC associated precipitation are likely caused by increased evaporation and availability of atmospheric water vapour, due to increased sea surface and atmospheric temperature. The mechanisms behind the projected changes in TC frequency are difficult to link explicitly; changes are most likely due to the combination of increased static stability, increased vertical wind shear and decreased upward motion, which suggest a decrease in the tropical overturning circulation.

Connecting climate model projections of global temperature change with the real world

Current state-of-the-art global climate models produce different values for Earth’s mean temperature. When comparing simulations with each other and with observations it is standard practice to compare temperature anomalies with respect to a reference period. It is not always appreciated that the choice of reference period can affect conclusions, both about the skill of simulations of past climate, and about the magnitude of expected future changes in climate. For example, observed global temperatures over the past decade are towards the lower end of the range of CMIP5 simulations irrespective of what reference period is used, but exactly where they lie in the model distribution varies with the choice of reference period. Additionally, we demonstrate that projections of when particular temperature levels are reached, for example 2K above ‘pre-industrial’, change by up to a decade depending on the choice of reference period. In this article we discuss some of the key issues that arise when using anomalies relative to a reference period to generate climate projections. We highlight that there is no perfect choice of reference period. When evaluating models against observations, a long reference period should generally be used, but how long depends on the quality of the observations available. The IPCC AR5 choice to use a 1986-2005 reference period for future global temperature projections was reasonable, but a case-by-case approach is needed for different purposes and when assessing projections of different climate variables. Finally, we recommend that any studies that involve the use of a reference period should explicitly examine the robustness of the conclusions to alternative choices.

Understanding inter-satellite biases of microwave humidity sounders using global simultaneous nadir overpasses

Simultaneous nadir overpasses (SNOs) of polar-orbiting satellites are most frequent in polar areas but can occur at any latitude when the equatorial crossing times of the satellites become close owing to orbital drift. We use global SNOs of polar orbiting satellites to evaluate the intercalibration of microwave humidity sounders from the more frequent high-latitude SNOs. We have found based on sensitivity analyses that optimal distance and time thresholds for defining collocations are pixel centers less than 5 km apart and time differences less than 300 s. These stringent collocation criteria reduce the impact of highly variable surface or atmospheric conditions on the estimated biases. Uncertainties in the estimated biases are dominated by the combined radiometric noise of the instrument pair. The effects of frequency changes between different versions of the humidity sounders depend on the amount of water vapor in the atmosphere. There are significant scene radiance and thus latitude dependencies in the estimated biases and this has to taken into account while intercalibrating microwave humidity sounders. Therefore the results obtained using polar SNOs will not be representative for moist regions, necessitating the use of global collocations for reliable intercalibration.

Non-bee insects are important contributors to global crop pollination

Wild and managed bees are well documented as effective pollinators of global crops of economic importance. However, the contributions by pollinators other than bees have been little explored despite their potential to contribute to crop production and stability in the face of environmental change. Non-bee pollinators include flies, beetles, moths, butterflies, wasps, ants, birds, and bats, among others. Here we focus on non-bee insects and synthesize 39 field studies from five continents that directly measured the crop pollination services provided by non-bees, honey bees, and other bees to compare the relative contributions of these taxa. Non-bees performed 25–50% of the total number of flower visits. Although non-bees were less effective pollinators than bees per flower visit, they made more visits; thus these two factors compensated for each other, resulting in pollination services rendered by non-bees that were similar to those provided by bees. In the subset of studies that measured fruit set, fruit set increased with non-bee insect visits independently of bee visitation rates, indicating that non-bee insects provide a unique benefit that is not provided by bees. We also show that non-bee insects are not as reliant as bees on the presence of remnant natural or seminatural habitat in the surrounding landscape. These results strongly suggest that non-bee insect pollinators play a significant role in global crop production and respond differently than bees to landscape structure, probably making their crop pollination services more robust to changes in land use. Non-bee insects provide a valuable service and provide potential insurance against bee population declines.

An ensemble of eddy-permitting global ocean reanalyses from the MyOcean project

A set of four eddy-permitting global ocean reanalyses produced in the framework of the MyOcean project have been compared over the altimetry period 1993–2011. The main differences among the reanalyses used here come from the data assimilation scheme implemented to control the ocean state by inserting reprocessed observations of sea surface temperature (SST), in situ temperature and salinity profiles, sea level anomaly and sea-ice concentration. A first objective of this work includes assessing the interannual variability and trends for a series of parameters, usually considered in the community as essential ocean variables: SST, sea surface salinity, temperature and salinity averaged over meaningful layers of the water column, sea level, transports across pre-defined sections, and sea ice parameters. The eddy-permitting nature of the global reanalyses allows also to estimate eddy kinetic energy. The results show that in general there is a good consistency between the different reanalyses. An intercomparison against experiments without data assimilation was done during the MyOcean project and we conclude that data assimilation is crucial for correctly simulating some quantities such as regional trends of sea level as well as the eddy kinetic energy. A second objective is to show that the ensemble mean of reanalyses can be evaluated as one single system regarding its reliability in reproducing the climate signals, where both variability and uncertainties are assessed through the ensemble spread and signal-to-noise ratio. The main advantage of having access to several reanalyses differing in the way data assimilation is performed is that it becomes possible to assess part of the total uncertainty. Given the fact that we use very similar ocean models and atmospheric forcing, we can conclude that the spread of the ensemble of reanalyses is mainly representative of our ability to gauge uncertainty in the assimilation methods. This uncertainty changes a lot from one ocean parameter to another, especially in global indices. However, despite several caveats in the design of the multi-system ensemble, the main conclusion from this study is that an eddy-permitting multi-system ensemble approach has become mature and our results provide a first step towards a systematic comparison of eddy-permitting global ocean reanalyses aimed at providing robust conclusions on the recent evolution of the oceanic state.

The impact of variable sea ice roughness on changes in Arctic Ocean surface stress: a model study

The Arctic sea ice cover is thinning and retreating, causing changes in surface roughness that in turn modify the momentum flux from the atmosphere through the ice into the ocean. New model simulations comprising variable sea ice drag coefficients for both the air and water interface demonstrate that the heterogeneity in sea ice surface roughness significantly impacts the spatial distribution and trends of ocean surface stress during the last decades. Simulations with constant sea ice drag coefficients as used in most climate models show an increase in annual mean ocean surface stress (0.003 N/m2 per decade, 4.6%) due to the reduction of ice thickness leading to a weakening of the ice and accelerated ice drift. In contrast, with variable drag coefficients our simulations show annual mean ocean surface stress is declining at a rate of -0.002 N/m2 per decade (3.1%) over the period 1980-2013 because of a significant reduction in surface roughness associated with an increasingly thinner and younger sea ice cover. The effectiveness of sea ice in transferring momentum does not only depend on its resistive strength against the wind forcing but is also set by its top and bottom surface roughness varying with ice types and ice conditions. This reveals the need to account for sea ice surface roughness variations in climate simulations in order to correctly represent the implications of sea ice loss under global warming.

Terrestrial biosphere changes over the last 120 kyr

A new global synthesis and biomization of long (> 40 kyr) pollen-data records is presented and used with sim- ulations from the HadCM3 and FAMOUS climate models and the BIOME4 vegetation model to analyse the dynamics of the global terrestrial biosphere and carbon storage over the last glacial–interglacial cycle. Simulated biome distribu- tions using BIOME4 driven by HadCM3 and FAMOUS at the global scale over time generally agree well with those in- ferred from pollen data. Global average areas of grassland and dry shrubland, desert, and tundra biomes show large- scale increases during the Last Glacial Maximum, between ca. 64 and 74 ka BP and cool substages of Marine Isotope Stage 5, at the expense of the tropical forest, warm-temperate forest, and temperate forest biomes. These changes are re- flected in BIOME4 simulations of global net primary pro- ductivity, showing good agreement between the two models. Such changes are likely to affect terrestrial carbon storage, which in turn influences the stable carbon isotopic composi- tion of seawater as terrestrial carbon is depleted in 13C.