Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere

Background and aims: To form nitrogen-fixing nodules on pea roots, Rhizobium leguminosarum biovar viciae must be competitive in the rhizosphere. Our aim was to identify genes important for rhizosphere fitness. Methods: Signature-tagged mutants were screened using microarrays to identify mutants reduced for growth in pea rhizospheres. Candidate mutants were assessed relative to controls for growth in minimal medium, growth in pea rhizospheres and for infection of peas in mixed inoculants. Mutated genes were identified by DNA sequencing and confirmed by transduction. Results: Of 5508 signature-tagged mutants, microarrays implicated 50 as having decreased rhizosphere fitness. Growth tests identified six mutants with rhizosphere-specific phenotypes. The mutation in one of the genes (araE) was in an arabinose catabolism operon and blocked growth on arabinose. The mutation in another gene (pcaM), encoding a predicted solute binding protein for protocatechuate and hydroxybenzoate uptake, decreased growth on protocatechuate. Both mutants were decreased for nodule infection competitiveness with mixed inoculants, but nodulated peas normally when inoculated alone. Other mutants with similar phenotypes had mutations predicted to affect secondary metabolism. Conclusions: Catabolism of arabinose and protocatechuate in the pea rhizosphere is important for competitiveness of R.l. viciae. Other genes predicted to be involved in secondary metabolism are also important.

Combining satellite observations and reanalysis energy transports to estimate global net surface energy fluxes 1985-2012

Two methods are developed to estimate net surface energy fluxes based upon satellite-based reconstructions of radiative fluxes at the top of atmosphere and the atmospheric energy tendencies and transports from the ERA-Interim reanalysis. Method 1 applies the mass adjusted energy divergence from ERA-Interim while method 2 estimates energy divergence based upon the net energy difference at the top of atmosphere and the surface from ERA-Interim. To optimise the surface flux and its variability over ocean, the divergences over land are constrained to match the monthly area mean surface net energy flux variability derived from a simple relationship between the surface net energy flux and the surface temperature change. The energy divergences over the oceans are then adjusted to remove an unphysical residual global mean atmospheric energy divergence. The estimated net surface energy fluxes are compared with other data sets from reanalysis and atmospheric model simulations. The spatial correlation coefficients of multi-annual means between the estimations made here and other data sets are all around 0.9. There are good agreements in area mean anomaly variability over the global ocean, but discrepancies in the trend over the eastern Pacific are apparent.

Metrics for linking emissions of gases and aerosols to global precipitation changes

Recent advances in understanding have made it possible to relate global precipitation changes directly to emissions of particular gases and aerosols that influence climate. Using these advances, new indices are developed here called the Global Precipitation-change Potential for pulse (GPP_P) and sustained (GPP_S) emissions, which measure the precipitation change per unit mass of emissions. The GPP can be used as a metric to compare the effects of different emissions. This is akin to the global warming potential (GWP) and the global temperature-change potential (GTP) which are used to place emissions on a common scale. Hence the GPP provides an additional perspective of the relative or absolute effects of emissions. It is however recognised that precipitation changes are predicted to be highly variable in size and sign between different regions and this limits the usefulness of a purely global metric. The GPP_P and GPP_S formulation consists of two terms, one dependent on the surface temperature change and the other dependent on the atmospheric component of the radiative forcing. For some forcing agents, and notably for CO2, these two terms oppose each other – as the forcing and temperature perturbations have different timescales, even the sign of the absolute GPP_P and GPP_S varies with time, and the opposing terms can make values sensitive to uncertainties in input parameters. This makes the choice of CO2 as a reference gas problematic, especially for the GPP_S at time horizons less than about 60 years. In addition, few studies have presented results for the surface/atmosphere partitioning of different forcings, leading to more uncertainty in quantifying the GPP than the GWP or GTP. Values of the GPP_P and GPP_S for five long- and short-lived forcing agents (CO2, CH4, N2O, sulphate and black carbon – BC) are presented, using illustrative values of required parameters. The resulting precipitation changes are given as the change at a specific time horizon (and hence they are end-point metrics) but it is noted that the GPPS can also be interpreted as the time-integrated effect of a pulse emission. Using CO2 as a references gas, the GPP_P and GPP_S for the non-CO2 species are larger than the corresponding GTP values. For BC emissions, the atmospheric forcing is sufficiently strong that the GPP_S is opposite in sign to the GTP_S. The sensitivity of these values to a number of input parameters is explored. The GPP can also be used to evaluate the contribution of different emissions to precipitation change during or after a period of emissions. As an illustration, the precipitation changes resulting from emissions in 2008 (using the GPP_P) and emissions sustained at 2008 levels (using the GPP_S) are presented. These indicate that for periods of 20 years (after the 2008 emissions) and 50 years (for sustained emissions at 2008 levels) methane is the dominant driver of positive precipitation changes due to those emissions. For sustained emissions, the sum of the effect of the five species included here does not become positive until after 50 years, by which time the global surface temperature increase exceeds 1 K.

Observational constraints on atmospheric and oceanic cross-equatorial heat transports: revisiting the precipitation asymmetry problem in climate models

Satellite based top-of-atmosphere (TOA) and surface radiation budget observations are combined with mass corrected vertically integrated atmospheric energy divergence and tendency from reanalysis to infer the regional distribution of the TOA, atmospheric and surface energy budget terms over the globe. Hemispheric contrasts in the energy budget terms are used to determine the radiative and combined sensible and latent heat contributions to the cross-equatorial heat transports in the atmosphere (AHT_EQ) and ocean (OHT_EQ). The contrast in net atmospheric radiation implies an AHT_EQ from the northern hemisphere (NH) to the southern hemisphere (SH) (0.75 PW), while the hemispheric difference in sensible and latent heat implies an AHT_EQ in the opposite direction (0.51 PW), resulting in a net NH to SH AHT_EQ (0.24 PW). At the surface, the hemispheric contrast in the radiative component (0.95 PW) dominates, implying a 0.44 PW SH to NH OHT_EQ. Coupled model intercomparison project phase 5 (CMIP5) models with excessive net downward surface radiation and surface-to-atmosphere sensible and latent heat transport in the SH relative to the NH exhibit anomalous northward AHT_EQ and overestimate SH tropical precipitation. The hemispheric bias in net surface radiative flux is due to too much longwave surface radiative cooling in the NH tropics in both clear and all-sky conditions and excessive shortwave surface radiation in the SH subtropics and extratropics due to an underestimation in reflection by clouds.

Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics

Background The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere. Results Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere. Conclusions Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.

Advanced source apportionment of size-resolved trace elements at multiple sites in London during winter

Trace element measurements in PM10–2.5, PM2.5–1.0 and PM1.0–0.3 aerosol were performed with 2 h time resolution at kerbside, urban background and rural sites during the ClearfLo winter 2012 campaign in London. The environment-dependent variability of emissions was characterized using the Multilinear Engine implementation of the positive matrix factorization model, conducted on data sets comprising all three sites but segregated by size. Combining the sites enabled separation of sources with high temporal covariance but significant spatial variability. Separation of sizes improved source resolution by preventing sources occurring in only a single size fraction from having too small a contribution for the model to resolve. Anchor profiles were retrieved internally by analysing data subsets, and these profiles were used in the analyses of the complete data sets of all sites for enhanced source apportionment. A total of nine different factors were resolved (notable elements in brackets): in PM10–2.5, brake wear (Cu, Zr, Sb, Ba), other traffic-related (Fe), resuspended dust (Si, Ca), sea/road salt (Cl), aged sea salt (Na, Mg) and industrial (Cr, Ni); in PM2.5–1.0, brake wear, other traffic-related, resuspended dust, sea/road salt, aged sea salt and S-rich (S); and in PM1.0–0.3, traffic-related (Fe, Cu, Zr, Sb, Ba), resuspended dust, sea/road salt, aged sea salt, reacted Cl (Cl), S-rich and solid fuel (K, Pb). Human activities enhance the kerb-to-rural concentration gradients of coarse aged sea salt, typically considered to have a natural source, by 1.7–2.2. These site-dependent concentration differences reflect the effect of local resuspension processes in London. The anthropogenically influenced factors traffic (brake wear and other traffic-related processes), dust and sea/road salt provide further kerb-to-rural concentration enhancements by direct source emissions by a factor of 3.5–12.7. The traffic and dust factors are mainly emitted in PM10–2.5 and show strong diurnal variations with concentrations up to 4 times higher during rush hour than during night-time. Regionally influenced S-rich and solid fuel factors, occurring primarily in PM1.0–0.3, have negligible resuspension influences, and concentrations are similar throughout the day and across the regions.

Diagnosing links between atmospheric moisture and extreme daily precipitation over the UK

Atmospheric moisture characteristics associated with the heaviest 1% of daily rainfall events affecting regions of the British Isles are analysed over the period 1997–2008. A blended satellite/rain-gauge data set (GPCP-1DD) and regionally averaged daily rain-gauge observations (HadUKP) are combined with the ERA Interim reanalysis. These are compared with simulations from the HadGEM2-A climate model which applied observed sea surface temperature and realistic radiative forcings. Median extreme daily rainfall across the identified events and locations is larger for GPCP (32 mm day−1) than HadUKP and the simulations (∼25 mm day−1). The heaviest observed and simulated daily rainfall events are associated with increased specific humidity and horizontal transport of moisture (median 850 hPa specific humidity of ∼6 g kg−1 and vapour transport of ∼150 g kg−1 m s−1 for both observed and simulated events). Extreme daily rainfall events are less common during spring and summer across much of the British Isles, but in the south east region, they contribute up to 60% of the total number of distinct extreme daily rainfall events during these months. Compared to winter events, the summer events over south east Britain are associated with a greater magnitude and more southerly location of moisture maxima and less spatially extensive regions of enhanced moisture transport. This contrasting dependence of extreme daily rainfall on moisture characteristics implies a range of driving mechanisms that depend upon location and season. Higher spatial and temporal resolution data are required to explore these processes further, which is vital in assessing future projected changes in rainfall and associated flooding.

Recent observed and simulated changes in precipitation over Africa

Multiple observational data sets and atmosphere-only simulations from the Coupled Model Intercomparison Project Phase 5 are analyzed to characterize recent rainfall variability and trends over Africa focusing on 1983–2010. Data sets exhibiting spurious variability, linked in part to a reduction in rain gauge density, were identified. The remaining observations display coherent increases in annual Sahel rainfall (29 to 43 mm yr−1 per decade), decreases in March–May East African rainfall (−14 to −65 mm yr−1 per decade), and increases in annual Southern Africa rainfall (32 to 41 mm yr−1 per decade). However, Central Africa annual rainfall trends vary in sign (−10 to +39 mm yr−1 per decade). For Southern Africa, observed and sea surface temperature (SST)-forced model simulated rainfall variability are significantly correlated (r~0.5) and linked to SST patterns associated with recent strengthening of the Pacific Walker circulation.

Female-specific intergenerational transmission patterns of the human corticolimbic circuitry

Parents have large genetic and environmental influences on offspring’s cognition, behavior, and brain. These intergenerational effects are observed in mood disorders, with particularly robust association in depression between mothers and daughters. No studies have thus far examined the neural bases of these intergenerational effects in humans. Corticolimbic circuitry is known to be highly relevant in a wide range of processes including mood regulation and depression. These findings suggest that corticolimbic circuitry may also show matrilineal transmission patterns. We therefore examined human parent-offspring association in this neurocircuitry, and investigated the degree of association in gray matter volume between parent and offspring. We used voxel-wise correlation analysis in a total of 35 healthy families, consisting of parents and their biological offspring. We found positive associations of regional grey matter volume in the corticolimbic circuit including the amygdala, hippocampus, anterior cingulate cortex, and ventromedial prefrontal cortex between biological mothers and daughters. This association was significantly greater than mother-son, father-daughter, and father-son associations. The current study suggests that the corticolimbic circuitry, which has been implicated in mood regulation, shows a matrilineal specific transmission patterns. Our preliminary findings are consistent with what has been found behaviorally in depression, and may have clinical implications for disorders known to have dysfunction in mood regulation such as depression. Studies such as ours will likely bridge animal work examining gene expression in the brains and clinical symptom-based observations, and provide promising ways to investigate intergenerational transmission patterns in the human brain.

Revisiting trends in wetness and dryness in the presence of internal climate variability and water limitations over land

A theoretically expected consequence of the intensification of the hydrological cycle under global warming is that on average, wet regions get wetter and dry regions get drier (WWDD). Recent studies, however, have found significant discrepancies between the expected pattern of change and observed changes over land. We assess the WWDD theory in four climate models. We find that the reported discrepancy can be traced to two main issues: (1) unforced internal climate variability strongly affects local wetness and dryness trends and can obscure underlying agreement with WWDD, and (2) dry land regions are not constrained to become drier by enhanced moisture divergence since evaporation cannot exceed precipitation over multiannual time scales. Over land, where the available water does not limit evaporation, a “wet gets wetter” signal predominates. On seasonal time scales, where evaporation can exceed precipitation, trends in wet season becoming wetter and dry season becoming drier are also found.

Contrasting fast precipitation responses to tropospheric and stratospheric ozone forcing

The precipitation response to radiative forcing (RF) can be decomposed into a fast precipitation response (FPR), which depends on the atmospheric component of RF, and a slow response, which depends on surface temperature change. We present the first detailed climate model study of the FPR due to tropospheric and stratospheric ozone changes. The FPR depends strongly on the altitude of ozone change. Increases below about 3 km cause a positive FPR; increases above cause a negative FPR. The FPR due to stratospheric ozone change is, per unit RF, about 3 times larger than that due to tropospheric ozone. As historical ozone trends in the troposphere and stratosphere are opposite in sign, so too are the FPRs. Simple climate model calculations of the time-dependent total (fast and slow) precipitation change, indicate that ozone's contribution to precipitation change in 2011, compared to 1765, could exceed 50% of that due to CO2 change.

The status and challenge of global fire modelling

Biomass burning impacts vegetation dynamics, biogeochemical cycling, atmospheric chemistry, and climate, with sometimes deleterious socio-economic impacts. Under future climate projections it is often expected that the risk of wildfires will increase. Our ability to predict the magnitude and geographic pattern of future fire impacts rests on our ability to model fire regimes, either using well-founded empirical relationships or process-based models with good predictive skill. A large variety of models exist today and it is still unclear which type of model or degree of complexity is required to model fire adequately at regional to global scales. This is the central question underpinning the creation of the Fire Model Intercomparison Project - FireMIP, an international project to compare and evaluate existing global fire models against benchmark data sets for present-day and historical conditions. In this paper we summarise the current state-of-the-art in fire regime modelling and model evaluation, and outline what essons may be learned from FireMIP.

Kerb and urban increment of highly time-resolved trace elements in PM10, PM2.5 and PM1.0 winter aerosol in London during ClearfLo 2012

Ambient concentrations of trace elements with 2 h time resolution were measured in PM10–2.5, PM2.5–1.0 and PM1.0–0.3 size ranges at kerbside, urban background and rural sites in London during winter 2012. Samples were collected using rotating drum impactors (RDIs) and subsequently analysed with synchrotron radiation-induced X-ray fluorescence spectrometry (SR-XRF). Quantification of kerb and urban increments (defined as kerb-to-urban and urban-to-rural concentration ratios, respectively), and assessment of diurnal and weekly variability provided insight into sources governing urban air quality and the effects of urban micro-environments on human exposure. Traffic-related elements yielded the highest kerb increments, with values in the range of 10.4 to 16.6 for SW winds (3.3–6.9 for NE) observed for elements influenced by brake wear (e.g. Cu, Sb, Ba) and 5.7 to 8.2 for SW (2.6–3.0 for NE) for other traffic-related processes (e.g. Cr, Fe, Zn). Kerb increments for these elements were highest in the PM10–2.5 mass fraction, roughly twice that of the PM1.0–0.3 fraction. These elements also showed the highest urban increments (~ 3.0), although no difference was observed between brake wear and other traffic-related elements. All elements influenced by traffic exhibited higher concentrations during morning and evening rush hours, and on weekdays compared to weekends, with the strongest trends observed at the kerbside site, and additionally enhanced by winds coming directly from the road, consistent with street canyon effects. Elements related to mineral dust (e.g. Al, Si, Ca, Sr) showed significant influences from traffic-induced resuspension, as evidenced by moderate kerb (3.4–5.4 for SW, 1.7–2.3 for NE) and urban (~ 2) increments and increased concentrations during peak traffic flow. Elements related to regional transport showed no significant enhancement at kerb or urban sites, with the exception of PM10–2.5 sea salt (factor of up to 2), which may be influenced by traffic-induced resuspension of sea and/or road salt. Heavy-duty vehicles appeared to have a larger effect than passenger vehicles on the concentrations of all elements influenced by resuspension (including sea salt) and wearing processes. Trace element concentrations in London were influenced by both local and regional sources, with coarse and intermediate fractions dominated by traffic-induced resuspension and wearing processes and fine particles influenced by regional transport.

O chair o flesh

Group exhibition curated by Matt Packer. Artists: Fabienne Audeoud, Fleur van Dodewaard, Christian Jankowski, Bea McMahon, Kaspar Oppen Samuelsen, Ria Pacquée, Xavier Ribas, Florian Roithmayr, John Russell, Allan Sekula, Morten Torgersrud, Francis Upritchard, Anne de Vries.