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  • Journal article
    Sethi SS, Ewers RM, Jones NS, L Orme CD, Picinali Let al.,

    Robust, real-time and autonomous monitoring of ecosystems with an open, low-cost, networked device

    <jats:title>Abstract</jats:title><jats:p><jats:list list-type="order"><jats:list-item><jats:p>Automated methods of monitoring ecosystems provide a cost-effective way to track changes in natural system’s dynamics across temporal and spatial scales. However, methods of recording and storing data captured from the field still require significant manual effort.</jats:p></jats:list-item><jats:list-item><jats:p>Here we introduce an open source, inexpensive, fully autonomous ecosystem monitoring unit for capturing and remotely transmitting continuous data streams from field sites over long time-periods. We provide a modular software framework for deploying various sensors, together with implementations to demonstrate proof of concept for continuous audio monitoring and time-lapse photography.</jats:p></jats:list-item><jats:list-item><jats:p>We show how our system can outperform comparable technologies for fractions of the cost, provided a local mobile network link is available. The system is robust to unreliable network signals and has been shown to function in extreme environmental conditions, such as in the tropical rainforests of Sabah, Borneo.</jats:p></jats:list-item><jats:list-item><jats:p>We provide full details on how to assemble the hardware, and the open-source software. Paired with appropriate automated analysis techniques, this system could provide spatially dense, near real-time, continuous insights into ecosystem and biodiversity dynamics at a low cost.</jats:p></jats:list-item></jats:list></jats:p>

  • Journal article
    Joos F, Spahni R, Stocker BD, Lienert S, Müller J, Fischer H, Schmitt J, Prentice IC, Otto-Bliesner B, Liu Zet al.,

    N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O changes from the Last Glacial Maximum to the preindustrial – Part II: Terrestrial N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O emissions constrain carbon-nitrogen interactions

    <jats:p>Abstract. Land ecosystems currently take up a quarter of the human-caused carbon dioxide emissions. Future projections of this carbon sink are strikingly divergent, leading to major uncertainties in projected global warming. This situation partly reflects our insufficient understanding of carbon-nitrogen (C-N) interactions and particularly of the controls on biological N fixation (BNF). It is difficult to infer ecosystem responses for century time scales, relevant for global warming, from the comparatively short instrumental records and laboratory or field experiments. Here we analyse terrestrial emissions of nitrous oxide (N2O) over the past 21,000 years as reconstructed from ice-core isotopic data and presented in part I of this study. Changing N2O emissions are interpreted to reflect changes in ecosystem N loss, plant available N, and BNF. The ice-core data reveal a 40 % increase in N2O emissions over the deglaciation, suggestive of a highly dynamic global N cycle whereby sources of plant-available N adjust to meet plant N demand and loss fluxes. Remarkably, the increase occurred in two steps, each realized within maximum two centuries, at the onsets of the northern hemisphere warming events around 14,600 and 11,700 years ago. We applied the LPX-Bern dynamic global vegetation model in deglacial simulations forced with Earth System Model climate data to investigate N2O emission patterns, mechanisms, and C-N coupling. The reconstructed increase in terrestrial emissions is broadly reproduced by the model, given the assumption that BNF positively responds to increasing N demand by plants. In contrast, assuming time- and demand-independent levels of BNF in the model to mimic progressive N limitation of plant growth results in N2O emissions that are incompatible with the reconstruction. Our results suggest the existence of (a) strong biological controls on ecosystem N acquisition, and (b) flexibility in the coupling of the C and N cycles during per

  • Journal article
    Ralph A, Burke T, Nakagawa S, Sánchez-Tójar A, Schroeder Jet al.,

    The causes and consequences of ornament variation in a natural population

    <p>The role of sexual selection in natural populations has long been the subject of debate in evolutionary biology. Ornaments are sexually selected traits, which means they should vary within a population, have a genetic basis, and be associated with fitness. Despite evidence of ornaments meeting these criteria, evolutionary responses to sexual selection are rare in nature. This study focuses on two ornaments in a population of house sparrows; the plumage badge has been well-studied but remains poorly understood and the mask has been largely neglected in the literature. Using quantitative genetic techniques, we estimate the heritability of both traits and test for age-dependency of the heritability estimates. We also estimate the strength and direction of any selection acting upon the traits. We found that both ornaments have low, significant heritability, which does not vary with age. Selection only occurs in a small number of years, although when it does it is positive in both ornaments. We also found that early social environment plays a role in badge size variation. The results of this study suggest that an evolutionary response in the ornaments of this population is unlikely, but we highlight the importance of long-term research to improve our understanding of evolution in natural populations. Studies like these will add to our understanding of sexual selection, the causes of trait variation and the evolutionary potential of traits, which could help us to predict how populations will evolve.</p>

  • Journal article
    Chik HYJ, Estrada C, Wang Y, Vijendra P, Lord A, Schroeder Jet al.,

    Selection on reproductive plasticity in a wild population of blue tits, Cyanistes caeruleus

    <p>In the plant-insect-insectivorous-bird system, changing climates can result in mis-timing in bird reproduction, potentially impacting chick survival. To adapt to earlier prey emergence, birds can make use of phenotypic plasticity, which can be characterized by reaction norms. Despite gaining focus in research, studies on avian reproductive reaction norms as traits are scarce, particularly on laying-date-budburst-date and clutch-size-laying-date reaction norms. Here we examined the possibility of evolution of these two reaction norms from a quantitative genetics viewpoint, and tested whether 1) there is among-individual variance in reaction norms properties (intercept and slope); 2) there is selection on these reaction norm properties; and 3) variances and selection pressures differ between the two reaction norms. Data of oak (genus Quercus) budburst and blue tit (Cyanistes caeruleus) reproduction were collected from a wild population for 18 years. We used bivariate random regression models with a Bayesian approach to test for among-individual variance in reaction norm properties and their covariance with fitness. Individuals significantly differed in intercepts and slopes of both laying-date-budburst-date and clutch-size-laying-date reaction norms, and directional selection was present for an earlier laying date and a larger clutch size, but not on either plasticity. Results suggested that variation in reaction norm properties can be attributed to genetic and environmental effects, and that stabilizing selection on plasticity could be tested as a next step. This study compliments previous research on the evolution of reaction norms and helps shed light on their genetic structure, the context of their selection, and their mediation in birds.</p>

  • Journal article
    van Lieshout SHJ, Froy H, Schroeder J, Burke T, Simons MJP, Dugdale HLet al.,

    Slicing: a sustainable approach to the analysis of long-term biobanks

    <p>The longitudinal study of populations is a core tool for understanding ecological and evolutionary processes. These studies typically collect samples over individual lifetimes and across multiple generations, building up a continuously growing biobank from which samples are then analysed in clusters over time in the laboratory. To ensure data are comparable among clusters we need to account for among-cluster variation and confounding variables, yet this is often ignored. The commonly used approaches in structuring samples for analysis, sequential and randomisation, generate bias due to non-independence between their time of collection and cluster. We propose a new sample selection strategy, slicing, specifically designed to statistically account for this bias. Slicing would, however, be suboptimal if aggregating longitudinal samples of the same individual within a single batch reduces measurement error and thereby increases statistical power to detect within-individual effects, a notion we challenge using simulations. Our slicing approach, whereby recently and previously collected samples are analysed in a cluster together, enables statistical separation of collection time and cluster effects through appropriate mixed models. Additionally, we recommend the use of internal controls (reference samples) to further assess among-cluster variation. Our simulations show similar precision and higher statistical power to detect cohort, within- and between-individual effects when samples are sliced across batches, compared with strategies that aggregate longitudinal samples or use randomised allocation. While the best approach to analysing long-term datasets depends on the structure of the data and questions of interest, it is vital to account for among-cluster and batch variation. This can be achieved through mixed models and appropriate sample selection strategies. Our slicing approach is simple to apply and creates the necessary statistical independence of batch a

  • Journal article
    Pennington HG, Jones R, Kwon S, Bonciani G, Thieron H, Chandler T, Luong P, Morgan S, Przydacz M, Bozkurt T, Bowden S, Craze M, Wallington E, Garnett J, Kwaaitaal M, Panstruga R, Cota E, Spanu PDet al.,

    A fungal ribonuclease-like effector protein inhibits plant host ribosomal RNA degradation

    <jats:title>ABSTRACT</jats:title><jats:p>The biotrophic fungal pathogen <jats:italic>Blumeria graminis</jats:italic> causes the powdery mildew disease of cereals and grasses. Proteins with a predicted ribonuclease (RNase)-like fold (termed RALPHs) comprise the largest set of secreted effector candidates within the <jats:italic>B. graminis</jats:italic> f. sp. <jats:italic>hordei</jats:italic> genome. Their exceptional abundance suggests they play crucial functions during pathogenesis. We show that transgenic expression of RALPH CSEP0064/BEC1054 increases susceptibility to infection in monocotyledenous and dicotyledonous plants. CSEP0064/BEC1054 interacts <jats:italic>in planta</jats:italic> with five host proteins: two translation elongation factors (eEF1α and eEF1γ), two pathogenesis-related proteins (PR5 and PR10) and a glutathione-S-transferase. We present the first crystal structure of a RALPH, CSEP0064/BEC1054, demonstrating it has an RNase-like fold. The protein interacts with total RNA and weakly with DNA. Methyl jasmonate levels modulate susceptibility to aniline-induced host RNA fragmentation. <jats:italic>In planta</jats:italic> expression of CSEP0064/BEC1054 reduces the formation of this RNA fragment. We propose that CSEP0064/BEC1054 is a pseudoenzyme that binds to host ribosomes, thereby inhibiting the action of plant ribosome-inactivating proteins that would otherwise lead to host cell death, an unviable interaction and demise of the fungus.</jats:p>

  • Journal article
    Verhoef A, Moura MSB, Nóbrega R,

    The effect of cloud cover on the radiation-, energy- and carbon balance of a seasonally dry tropical forest in Brazil (Caatinga)

    <jats:p> &amp;lt;p&amp;gt;The Caatinga is a seasonally dry tropical forest, which is the dominant vegetation type in the northeastern region of Brazil. Its many plant species have adapted to the semiarid climate through different biophysical and physiological traits and drought survival strategies. In recent years, this region has endured a number of prolonged droughts that have adversely affected this already severely water-limited region. Despite the relatively small amounts of rainfall (with annual rainfall ranging approximately between 100&amp;amp;#8211;800 mm/year), there is an almost perpetual occurrence of clouds due to the regional atmospheric circulation; broadly speaking cumulus or cumulonimbus in the rainy season, and mostly stratocumulus during the transition from wet to dry, and dry seasons. &amp;amp;#160;We studied the effect of cloud cover on the radiation balance, as well on the surface energy- and carbon balance of a pristine Caatinga area from 2011 to 2018.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;This study used radiation and weather data obtained from a SONDA BSRN radiation station, as well from a flux tower installed in the study area; both were near the urban areaofPetrolina, Brazil. Furthermore, radio-sounding data collected nearby were employed to obtain column integrated atmospheric water vapour, to estimate atmospheric emissivity.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;We derived cloudiness from a number of indirect methods (using shortwave- and longwave incoming radiation) at diurnal, seasonal and multi-year timescales. We also employed observed cloud cover data, including those from sky-cameras, for verification.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Estimates of clear-sky atmospheric emissivity were required to determine cloud cover.&amp;amp;#160; These were obtained from well-known equations (e.g., Brunt, Brutsaert and Prata) using tower air temperature and/or vapour press

  • Journal article
    Nóbrega R, Sandoval D, Prentice C,

    Changes in root zone storage capacity and their effects on river discharge and gross primary production

    <jats:p> &amp;lt;p&amp;gt;Root zone storage capacity (R&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt;) is a parameter widely used in terrestrial ecosystem models that estimate the amount of soil moisture available for transpiration. However, R&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; is subject to large uncertainty, due to the lack of data on the distribution of soil properties and the depth of plant roots that actively take up water. Our study makes use of a mass-balance approach to investigate R&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; in different ecosystems, and changes in water fluxes caused by land-cover change. The method needs no land-cover or soil information, and uses precipitation (P) and evapotranspiration (ET) time series to estimate the seasonal water deficit. To account for some of the uncertainty in ET, we use different methods for ET estimation, including methods based on satellite estimates, and modelling approaches that back-calculate ET from other ecosystem fluxes. We show that reduced ET due to land-cover change reduces R&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt;, which in turn increases baseflow in regions with a strong rainfall seasonality. This finding allows us to analyse the trade-off between gross primary production and hydrological fluxes at river basin scales. We also consider some ideas on how to use mass-balance R&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; in water-stress functions as incorporated in existing terrestrial ecosystem models.&amp;lt;/p&amp;gt; </jats:p>

  • Working paper
    Sethi SS, Ewers RM, Jones NS, Signorelli A, Picinali L, Orme CDLet al.,

    SAFE Acoustics: an open-source, real-time eco-acoustic monitoring network in the tropical rainforests of Borneo

    , Publisher: Cold Spring Harbor Laboratory

    <jats:title>Abstract</jats:title><jats:p><jats:list list-type="order"><jats:list-item><jats:p>Automated monitoring approaches offer an avenue to deep, large-scale insight into how ecosystems respond to human pressures. Since sensor technology and data analyses are often treated independantly, there are no open-source examples of end-to-end, real-time ecological monitoring networks.</jats:p></jats:list-item><jats:list-item><jats:p>Here, we present the complete implementation of an autonomous acoustic monitoring network deployed in the tropical rainforests of Borneo. Real-time audio is uploaded remotely from the field, indexed by a central database, and delivered via an API to a public-facing website.</jats:p></jats:list-item><jats:list-item><jats:p>We provide the open-source code and design of our monitoring devices, the central web2py database and the ReactJS website. Furthermore, we demonstrate an extension of this infrastructure to deliver real-time analyses of the eco-acoustic data.</jats:p></jats:list-item><jats:list-item><jats:p>By detailing a fully functional, open-source, and extensively tested design, our work will accelerate the rate at which fully autonomous monitoring networks mature from technological curiosities, and towards genuinely impactful tools in ecology.</jats:p></jats:list-item></jats:list></jats:p>

  • Journal article
    Lavergne A, Graven H, Prentice IC,

    Disentangling the relative contributions of atmospheric demand for water and soil water availability on the stomatal limitation of photosynthesis

    <jats:p> &amp;lt;p&amp;gt;Plants open and close their stomata in response to changes in the environment, so they can absorb the CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; they need to grow, while also avoid drying out. Since the activities of leaf stomata determine the exchanges of carbon and water between the vegetation and the atmosphere, it is crucial to incorporate their responses to environmental pressure into the vegetation models predicting carbon and water fluxes on broad spatial and temporal scales. The least-cost optimality theory proposes a simple way to predict leaf behaviour, in particular changes in the ratio of leaf internal (&amp;lt;em&amp;gt;c&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt;) to ambient (&amp;lt;em&amp;gt;c&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;a&amp;lt;/sub&amp;gt;) partial pressure of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, from four environmental variables, i.e. &amp;lt;em&amp;gt;c&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;a&amp;lt;/sub&amp;gt;, growing-season temperature (&amp;lt;em&amp;gt;T&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;g&amp;lt;/sub&amp;gt;), atmospheric vapour pressure deficit (&amp;lt;em&amp;gt;D&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;g&amp;lt;/sub&amp;gt;), and atmospheric pressure (as indexed by elevation, &amp;lt;em&amp;gt;z&amp;lt;/em&amp;gt;). However, even though the theory considers the effect of atmospheric demand for water on &amp;lt;em&amp;gt;c&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;i&amp;lt;/sub&amp;gt;/&amp;lt;em&amp;gt;c&amp;lt;/em&amp;gt;&amp;lt;sub&amp;gt;a&amp;lt;/sub&amp;gt;, it does not predict how dry soils with reduced soil water availability further influence &amp;lt;em&amp;gt;c&amp;lt;/em&

  • Journal article
    Rothman JA, Russell KA, Leger L, McFrederick QS, Graystock Pet al.,

    The direct and indirect effects of environmental toxicants on the health of bumble bees and their microbiomes

    <jats:title>Abstract</jats:title><jats:p>Bumble bees (<jats:italic>Bombus</jats:italic> spp.) are important and widespread insect pollinators, but the act of foraging on flowers can expose them to harmful pesticides and environmental chemicals such as oxidizers and heavy metals. How these compounds directly influence bee survival and indirectly affect bee health via the gut microbiome is largely unknown. As the toxins and toxicants in floral nectar and pollen take many forms, we explored the genomes of core bumblebee microbes (Using RAST) for their potential to detoxify cadmium, copper, selenium, the neonicotinoid pesticide imidacloprid, and hydrogen peroxide - which have all been identified in floral nectar and pollen. We then exposed <jats:italic>Bombus impatiens</jats:italic> workers to varying concentrations of these chemicals spiked into their diet and identified the direct effects on bee survival. Using field realistic doses, we further explored indirect effects on bee microbiomes. We found multiple genes in core gut microbes that have the potential to aid in detoxifying harmful chemicals. We also found that while the chemicals are largely toxic at levels within and above field-realistic concentrations, the field-realistic concentrations - except for imidacloprid - altered the composition of the bee microbiome, potentially causing gut dysbiosis. Overall, our study shows that environmental chemicals found in floral nectar and pollen can directly cause bee mortality, and at field-realistic levels, likely have indirect, deleterious effects on bee health via their influence on the bee microbiome.</jats:p>

  • Journal article
    Nobrega RLB, Guzha AC, Torres GN, Kovacs K, Lamparter G, Amorim RSS, Couto E, Gerold Get al.,

    Identifying hydrological responses of micro-catchments under contrasting land use in the Brazilian Cerrado

    <jats:p>Abstract. In recent decades, the Brazilian Cerrado biome has been affected by intense land-use change, particularly the conversion of natural forest to agricultural land. Understanding the environmental impacts of this land-use change on landscape hydrological dynamics is one of the main challenges in the Amazon agricultural frontier, where part of the Brazilian Cerrado biome is located and where most of the deforestation has occurred. This study uses empirical data from field measurements to characterize controls on hydrological processes from three first-order micro-catchments &lt; 1 km2 in the Cerrado biome. These micro-catchments were selected on the basis of predominant land use including native cerrado vegetation, pasture grass with cattle ranching, and cash crop land. We continuously monitored precipitation, streamflow, soil moisture, and meteorological variables from October 2012 to September 2014. Additionally, we determined the physical and hydraulic properties of the soils, and conducted topographic surveys. We used these data to quantify the water balance components of the study catchments and to relate these water fluxes to land use, catchment physiographic parameters, and soil hydrophysical properties. The results of this study show that runoff coefficients were 0.27, 0.40, and 0.16 for the cerrado, pasture, and cropland catchments, respectively. Baseflow is shown to play a significant role in streamflow generation in the three study catchments, with baseflow index values of more than 0.95. The results also show that evapotranspiration was highest in the cerrado (986 mm yr−1) compared to the cropland (828 mm yr−1) and the pasture (532 mm yr−1). However, discharges in the cropland catchment were unexpectedly lower than that of the cerrado catchment. The normalized discharge was 55 % higher and 57 % lower in the pasture and cropland catchments, respectively, compared with the cerrado catchment. We attribute this findin

  • Journal article
    Nóbrega R, Guzha A, Lamparter G, Amorim R, Couto E, Hughes H, Jungkunst H, Gerold Get al.,

    Impacts of land-use and land-cover change on stream hydrochemistry in the Cerrado and Amazon biomes

  • Journal article
    Maitner BS, Pearse W, Roehrdanz P, Enquist BJ, Sanderson MJet al.,

    APPENDIX C. Re-scaling phylogenetic branches to reflect trait evolution

  • Journal article
    Joshi J, Stocker BD, Hofhansl F, Zhou S, Dieckmann U, Prentice ICet al.,

    Towards a unified theory of plant photosynthesis and hydraulics

    <jats:title>Abstract</jats:title><jats:p>The global carbon and water cycles are governed by the coupling of CO<jats:sub>2</jats:sub> and water vapour exchanges through the leaves of terrestrial plants, controlled by plant adaptations to balance carbon gains and hydraulic risks. We introduce a trait-based optimality theory that unifies the treatment of stomatal responses and biochemical acclimation of plants to environments changing on multiple timescales. Tested with experimental data from 18 species, our model successfully predicts the simultaneous decline in carbon assimilation rate, stomatal conductance, and photosynthetic capacity during progressive soil drought. It also correctly predicts the dependencies of gas exchange on atmospheric vapour pressure deficit, temperature, and CO<jats:sub>2</jats:sub>. Model predictions are also consistent with widely observed empirical patterns, such as the distribution of hydraulic strategies. Our unified theory opens new avenues for reliably modelling the interactive effects of drying soil and rising atmospheric CO<jats:sub>2</jats:sub> on global photosynthesis and transpiration.</jats:p>

  • Journal article
    Nobrega RLB, Guzha AC, Torres GN, Kovacs K, Lamparter G, Amorim RSS, Couto E, Gerold Get al.,

    Supplementary material to &amp;quot;Identifying hydrological responses of micro-catchments under contrasting land use in the Brazilian Cerrado&amp;quot;

  • Journal article
    Christensen A, Piggott M, Sebille EV, Reeuwijk MV, Pawar Set al.,

    Small-scale convective turbulence constrains microbial patchiness

    <jats:title>Abstract</jats:title> <jats:p>Microbes play a primary role in aquatic ecosystems and biogeochemical cycles. Patchiness is a critical component of these activities, influencing biological productivity, nutrient cycling and dynamics across trophic levels. Incorporating spatial dynamics into microbial models is a long-standing challenge, particularly where small-scale turbulence is involved. Here, we combine a realistic simulation of turbulence with an individual-based microbial model to test the key hypothesis that the coupling of motility and turbulence drives intense microscale patchiness. We find that such patchiness is depth-structured and requires high motility: Near the fluid surface, strong convective turbulence overpowers motility, homogenising motile and non-motile microbes equally. In deeper, thermocline-like conditions, highly motile microbes are up to 1.6-fold more patch-concentrated than non-motile microbes. Our results demonstrate that the delicate balance of turbulence and motility that triggers micro-scale patchiness is not a ubiquitous consequence of motility, and that the intensity of such patchiness in real-world conditions is modest.</jats:p>

  • Journal article
    Nóbrega R, Prentice IC,

    Developing a climate-driven root zone water stress function for different climates and ecosystems

    <jats:p>&amp;lt;p&amp;gt;Plant roots have less water available when soils have low moisture content and, consequently, limit their root-to-leaf water potential gradient to protect their xylem, which reduces H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O and CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; exchanges with the atmosphere. In vegetation, hydrological and land-surface models, plant responses to reduced available water in the soil have been implemented in various ways depending on data availability, type of ecosystem, and modelling assumptions. Most models use soil water stress functions &amp;amp;#8211; commonly known as beta functions &amp;amp;#8211; to reduce transpiration and carbon assimilation, by applying a factor that reflects the soil water availability for plants. These functions usually produce reasonably satisfactory results, but rely on the information on soil properties (e.g. wilting point and field capacity) that are not widely available. On a global level, soil information is mediocre, and data uncertainty is compensated by tuning parameters that rarely represent a physiological process. We propose instead the use of a beta function derived from a mass-balance approach focused on the root zone water capacity. This method quantifies the root zone water storage by calculating the accumulated water deficit based on the balance between water influxes and effluxes, and it does not require land-cover or soil information. We assessed how our approach performs compared to those other soil water stress functions. We used global datasets, including WDFE5 and PMLv2, to extract precipitation and evapotranspiration and compute water deficit. For most vegetation types and climates our approach yielded promising results. Worst results were found for some (semi-)arid sites due to the overestimation of the water deficit. We aim to deliver an approach that can be easily applied on global scales.&amp;lt;/p&a

  • Journal article
    Thomson M, Nunta K, Cheyne A, liu Y, Garza-Garcia A, Larrouy-Maumus Get al.,

    Modulation of the cAMP levels with a conserved actinobacteria phosphodiesterase enzyme reduces antimicrobial tolerance in mycobacteria

    <jats:title>Abstract</jats:title><jats:p>Antimicrobial tolerance (AMT) is the gateway to the development of antimicrobial resistance (AMR) and is therefore a major issue that needs to be addressed.</jats:p><jats:p>The second messenger cyclic-AMP (cAMP), which is conserved across all taxa, is involved in propagating signals from environmental stimuli and converting these into a response. In bacteria, such as<jats:italic>M. tuberculosis</jats:italic>,<jats:italic>P. aeruginosa</jats:italic>,<jats:italic>V. cholerae</jats:italic>and<jats:italic>B. pertussis</jats:italic>, cAMP has been implicated in virulence, metabolic regulation and gene expression. However, cAMP signalling in mycobacteria is particularly complex due to the redundancy of adenylate cyclases, which are enzymes that catalyse the formation of cAMP from ATP, and the poor activity of the only known phosphodiesterase (PDE) enzyme, which degrades cAMP into 5’- AMP.</jats:p><jats:p>Based on these two features, the modulation of this system with the aim of investigating cAMP signalling and its involvement in AMT in mycobacteria id difficult.</jats:p><jats:p>To address this pressing need, we identified a new cAMP-degrading phosphodiesterase enzyme (Rv1339) and used it to significantly decrease the intrabacterial levels of cAMP in mycobacteria. This analysis revealed that this enzyme increased the antimicrobial susceptibility of<jats:italic>M. smegmatis</jats:italic>mc<jats:sup>2</jats:sup>155. Using a combination of metabolomics, RNA-sequencing, antimicrobial susceptibility assays and bioenergetics analysis, we were able to characterize the molecular mechanism underlying this increased susceptibility.</jats:p><jats:p>This work represents an important milestone showing that the targeting of cAMP signalling is a promising new avenue for antimicrobial development and expan

  • Journal article
    Joshi J, Stocker B, Hofhansl F, Zhou S, Brännström Å, Prentice IC, Dieckmann Uet al.,

    Eco-evolutionary responses of plant communities to drought and rainfall variability

    <jats:p>&amp;lt;p&amp;gt;The future Earth is projected to experience elevated rainfall variability, with more frequent and intense droughts, as well as high-rainfall events. Increasing CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; concentrations are expected to raise terrestrial gross primary productivity (GPP), whereas water stress is expected to lower GPP. Plant responses to water stress vary strongly with timescale, and plants adapted to different environmental conditions differ in their functional responses. Here, we embed a unified optimality-based theory of stomatal conductance and biochemical acclimation of leaves we have recently developed [Joshi, J. et al. (2020) Towards a unified theory of plant photosynthesis and hydraulics. bioRxiv 2020.12.17.423132] in an eco-evolutionary vegetation-modelling framework, with the goal to investigate emergent functional diversity and associated GPP impacts under different rainfall regimes.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;The model of photosynthesis used here simultaneously predicts the stomatal responses and biochemical acclimation of leaves to atmospheric and soil-moisture conditions. Using three hydraulic traits and two cost parameters, it successfully predicts the simultaneous declines in CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; assimilation rate, stomatal conductance, and leaf photosynthetic capacity caused by drying soil. It also correctly predicts the responses of CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; assimilation rate, stomatal conductance, leaf water potential, and leaf photosynthetic capacity to vapour pressure deficit, temperature, ambient CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;, light intensity, and elevation. Our model therefore captures the synergistic effects of atmospheric and soil drought, as well as of atmospheric CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; changes, on plant photosynthesis

  • Journal article
    Bennett S, Girndt A, Sánchez-Tójar A, Burke T, Simons MJP, Schroeder Jet al.,

    Evidence of paternal effects on telomere length increases in early-life

    <p>Offspring of older parents in many species display decreased longevity, a faster ageing rate and lower fecundity than offspring born to younger parents. Biomarkers, such as telomeres, that tend to shorten as individual age, may provide insight into the mechanisms of parental age effects. Parental age could determine telomere length either through inheritance of shortened telomeres or through indirect effects, such as variation in parental care with parent ages, which in turn might lead to variation in offspring telomere length. There is no current consensus as to the heritability of telomere length, and the direction and extent of parental age effects however. To address this, here we experimentally investigate how parental age is associated with telomere length at two time points in early life in a captive population of house sparrows (Passer domesticus). We experimentally separated parental age from sex effects by allowing the parent birds to only mate with young, or old partners. We found that telomere length of the offspring increased between the age of 0.5 and 3 months at the group and individual level, which has been reported previously predominantly in non-avian taxa. We further show that older fathers produced daughters with a greater early-life increase in telomere length, supporting sex-specific inheritance, and or sex-specific non-genetic effects. Overall, our results highlight the need for more studies testing early-life telomere dynamics and sex-specific heritability of telomere length.</p>

  • Journal article
    Duggan C, Moratto E, Savage Z, Hamilton E, Adachi H, Wu C-H, Leary AY, Tumtas Y, Rothery SM, Maqbool A, Nohut S, Kamoun S, Bozkurt TOet al.,

    Dynamic accumulation of a helper NLR at the plant-pathogen interface underpins pathogen recognition

    <jats:title>Abstract</jats:title><jats:p>Plants employ sensor-helper pairs of NLR immune receptors to recognize pathogen effectors and activate immune responses. Yet the subcellular localization of NLRs pre- and post-activation during pathogen infection remains poorly known. Here we show that NRC4, from the ‘NRC’ solanaceous helper NLR family, undergoes dynamic changes in subcellular localization by shuttling to and from the plant-pathogen haustorium interface established during infection by the Irish potato famine pathogen <jats:italic>Phytophthora infestans.</jats:italic> Specifically, prior to activation, NRC4 accumulates at the extra-haustorial membrane (EHM), presumably to mediate response to perihaustorial effectors, that are recognized by NRC4-dependent sensor NLRs. However not all NLRs accumulate at the EHM, as the closely related helper NRC2, and the distantly related ZAR1, did not accumulate at the EHM. NRC4 required an intact N-terminal coiled coil domain to accumulate at the EHM, whereas the functionally conserved MADA motif implicated in cell death activation and membrane insertion was dispensable for this process. Strikingly, a constitutively autoactive NRC4 mutant did not accumulate at the EHM and showed punctate distribution that mainly associated with the plasma membrane, suggesting that post-activation, NRC4 probably undergoes a conformation switch to form clusters that do not preferentially associate with the EHM. When NRC4 is activated by a sensor NLR during infection however, NRC4 formed puncta mainly at the EHM and to a lesser extent at the plasma membrane. We conclude that following activation at the EHM, NRC4 may spread to other cellular membranes from its primary site of activation to trigger immune responses.</jats:p><jats:sec><jats:title>Significance statement</jats:title><jats:p>Plant NLR immune receptors function as intracellular sensors of pathogen virulence factors

  • Journal article
    Miranda R, Nobrega R, Silva E, Freire J, Filho J, Moura M, Barros A, Saraiva A, Verhoef A, Srinivasan R, Montenegro S, Araújo M, Galvíncio Jet al.,

    Digital soil mapping using machine learning techniques in a varied tropical environment

    <jats:p>&amp;lt;p&amp;gt;Environmental models often require soil maps to represent the spatial variability of soil attributes. However, mapping soils using conventional in-situ survey protocols is time-consuming and costly. As an alternative, digital soil mapping offers a fast-mapping approach that might be used to monitor soil attributes and their interrelationships over large areas. In Brazil, conventional survey methods are still widely used, and thus maps still in development are considered as the state-of-the-art products for decades. In this study, we address this lack of updated spatial information on many soil attributes by producing regional statistical soil models using an innovative framework. This new framework attempts to reduce prediction redundancies due to high multicollinearity, by implementing a Feature Selector algorithm. This is expected to improve a model&amp;amp;#8217;s strength by decreasing its unexplained variance. The framework&amp;amp;#8217;s core is composed of the Soil-Landscape Estimation and Evaluation Program (SLEEP) and a calibrated Gradient Boosting Model capable of modelling the spatial distribution of soil attributes at multiple soil depths. These models allowed us to explain the spatial distribution of some basic soil attributes (physical and chemical), and its environmental drivers. The model training and testing approach used 30 environmental attributes, and data from 223 soil profiles for the state of Pernambuco, Brazil. Our models demonstrated a consistent potential to perform spatial extrapolations with r&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; ranging from 0.8 to 0.97, and PBIAS from -0.51 to 2.03. The properties related to topographic and climatic conditions were dominating when estimating the number of horizons, percentage of silt and the sum of bases (a measure of soil fertility). We believe that our framework features high flexibility, while reducing capital investments when compare

  • Journal article
    Melo DDCD, Anache JAA, Wendland E, Borges VP, Miralles DG, Martens B, Fisher J, Nobrega RLB, Moreno A, Cabral OMR, Rodrigues TR, Bezerra B, Santos e Silva CM, Meira Neto AA, Moura MSB, Marques TV, Campos S, Nogueira JDS, Rosolem R, Souza R, Antonino ACD, Holl D, Galleguillos M, Perez-Quezada JF, Verhoef A, Kutzbach L, Lima JRDS, de Souza ES, Gassman MI, Pérez CF, Tonti N, Posse G, Rains D, Oliveira PTSet al.,

    Are remote sensing evapotranspiration models reliable across South American climates and ecosystems?

  • Working paper
    Carbajo CG, Cornell LJ, Madbouly Y, Lai Z, Yates PA, Tinti M, Tiengwe Cet al.,

    Novel aspects of iron homeostasis in pathogenic bloodstream form <i>Trypanosoma brucei</i>

    , Publisher: Cold Spring Harbor Laboratory

    <jats:title>Abstract</jats:title><jats:p>Iron is an essential regulatory signal for virulence factors in many pathogens. Mammals and bloodstream form (BSF) <jats:italic>Trypanosoma brucei</jats:italic> obtain iron by receptor-mediated endocytosis of transferrin bound to receptors (TfR) but the mechanisms by which <jats:italic>T. brucei</jats:italic> subsequently handles iron remains enigmatic. Here, we analyse the transcriptome of <jats:italic>T. brucei</jats:italic> cultured in iron-rich and iron-poor conditions. We show that adaptation to iron-deprivation induces upregulation of TfR, a cohort of parasite-specific genes (ESAG3, PAGS), genes involved in glucose uptake and glycolysis (THT1 and hexokinase), endocytosis (Phosphatidic Acid Phosphatase, PAP2), and most notably a divergent RNA binding protein RBP5, indicative of a non-canonical mechanism for regulating intracellular iron levels. We show that cells depleted of TfR by RNA silencing import free iron as a compensatory survival strategy. The TfR and RBP5 iron response are reversible by genetic complementation, the response kinetics are similar, but the regulatory mechanisms are distinct. Increased TfR protein is due to increased mRNA. Increased RBP5 expression, however, occurs by a post-transcriptional feedback mechanism whereby RBP5 interacts with its own, and with <jats:italic>PAP2</jats:italic> mRNAs. Further observations suggest that increased RBP5 expression in iron-deprived cells has a maximum threshold as ectopic overexpression above this threshold disrupts normal cell cycle progression resulting in an accumulation of anucleate cells and cells in G2/M phase. This phenotype is not observed with overexpression of RPB5 containing a point mutation (F61A) in its single RNA Recognition Motif. Our experiments shed new light on how <jats:italic>T. brucei</jats:italic> BSFs reorganise their transcriptome to deal with iron stress reveal

  • Working paper
    Demmer JK, Phillips BP, Uhrig OL, Filloux A, Allsopp LP, Bublitz M, Meier Tet al.,

    Structure of ATP synthase from ESKAPE pathogen <i>Acinetobacter baumannii</i>

    , Publisher: Cold Spring Harbor Laboratory

    <jats:title>Abstract</jats:title><jats:p><jats:italic>Acinetobacter baumannii</jats:italic> is a clinically relevant pathogen which causes multi-drug resistant, hospital-acquired infections and is a top priority target for antibiotic development. <jats:italic>Cryo</jats:italic>-EM structures of the <jats:italic>A. baumannii</jats:italic> F<jats:sub>1</jats:sub>F<jats:sub>o</jats:sub>-ATP synthase in three conformational states reveal unique features, which represent attractive sites for the development of novel therapeutics.</jats:p><jats:sec><jats:title>One sentence summary</jats:title><jats:p>Structure of Acinetobacter baumannii ATP synthase</jats:p></jats:sec>

  • Journal article
    Yunus IS, Anfelt J, Hudson EP, Jones PRet al.,

    Synthetic metabolic pathways for conversion of CO<sub>2</sub> into secreted short-to medium-chain hydrocarbons using cyanobacteria

    <jats:title>Abstract</jats:title><jats:p>The objective of this study was to implement direct sunlight-driven conversion of CO<jats:sub>2</jats:sub> into a naturally excreted ready-to-use fuel. We engineered four different synthetic metabolic modules for biosynthesis of short-to medium-chain length hydrocarbons in the model cyanobacterium <jats:italic>Synechocystis</jats:italic> sp. PCC 6803. In module 1, the combination of a truncated clostridial n-butanol pathway with over-expression of the native cyanobacterial aldehyde deformylating oxygenase resulted in small quantities of propane when cultured under closed conditions. Direct conversion of CO<jats:sub>2</jats:sub> into propane was only observed in strains with CRISPRi-mediated repression of three native putative aldehyde reductases. In module 2, three different pathways towards pentane were evaluated based on the polyunsaturated fatty acid linoleic acid as an intermediate. Through combinatorial evaluation of bioreaction ingredients it was concluded that linoleic acid undergoes a spontaneous non-enzymatic reaction to yield pentane and hexanal. When <jats:italic>Synechocystis</jats:italic> was added to the bioreaction, hexanal was converted into 1-hexanol, but there was no further stimulation of pentane biosynthesis. For modules 3 and 4, several different acyl-ACP thioesterases were evaluated in combination with two different decarboxylases. Small quantities of 1-heptene and 1-nonene were observed in strains expressing the desaturase-like enzyme UndB from <jats:italic>Pseudomonas mendocina</jats:italic> in combination with C8-C10 preferring thioestersaes. When UndB instead was combined with a C12-specific ‘<jats:italic>Uc</jats:italic>FatB1 thioesterase, this resulted in ten-fold increase of alkene biosynthesis. When UndB was replaced with the light-dependent FAP decarboxylase, both undecane and tridecane accumulated, a

  • Journal article
    Mengoli G, Agustí-Panareda A, Boussetta S, Harrison SP, Trotta C, Prentice ICet al.,

    Application of an optimality-based model to operate at half-hourly timestep to implement plant acclimation within a land-surface modelling framework

    <jats:p>&amp;lt;p&amp;gt;Vegetation and atmosphere are linked through the perpetual exchange of water, carbon and energy. An accurate representation of the processes involved in these exchanges is crucial in forecasting Earth system states. Although vegetation has become an undisputed key component in land-surface modelling (LSMs), the current generation of models differ in terms of how key processes are formulated. Plant processes react to environmental changes on multiple time scales. Here we differentiate a fast (minutes) and a slower (acclimated &amp;amp;#8211; weeks to months) response. Some current LSMs include plant acclimation, even though they require additional parameters to represent this response, but the majority of them represent only the fast response and assume that this also applies at longer time scales. Ignoring acclimation in this way could be the cause of inconsistent future projections. Our proposition is to include plant acclimation in a LSM schema, without having to include new plant-functional-type-dependent parameters. This is possible by using an alternative model development strategy based on eco-evolutionary theory, which explicitly predicts the acclimation of photosynthetic capacities and stomatal behaviour to environmental variations. So far, this theory has been tested only at weekly to monthly timescales. Here we develop and test an approach to apply an existing optimality-based model of gross primary production (GPP), the P model, at the sub-daily timestep necessary for use in an LSM, making an explicit differentiation between the fast and slow responses of photosynthesis and stomatal conductance. We test model performance in reproducing the diurnal cycle of GPP as recorded by flux tower measurements across different biomes, including boreal and tropical forests. The extended model requires only a few meteorological inputs, and a satellite-derived product for leaf area index or green vegetation cover. It is able to

  • Journal article
    Mengoli G, Prentice IC, Harrison SP,

    Adapting an optimality-based model to predict half-hourly carbon uptake by ecosystems

    <jats:p> &amp;lt;p&amp;gt;Carbon dioxide (CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;) uptake by leaves and its conversion into sugar by photosynthesis &amp;amp;#8211; gross primary production (GPP) &amp;amp;#8211; is the basis for vegetation growth. GPP is important for the carbon cycle, and its interactions with climate are a subject of study in Earth System modelling. One assumption of many current ecosystem models is that key photosynthetic traits, such as the capacities for carboxylation (V&amp;lt;sub&amp;gt;cmax&amp;lt;/sub&amp;gt;) and electron transport (J&amp;lt;sub&amp;gt;max&amp;lt;/sub&amp;gt;&amp;amp;#173;) for ribulose-1,5-bisphosphate (RuBP) regeneration, are constant in time for any given plant functional type. Optimality theory predicts they should vary systematically with growth conditions, both in space and in time, and are not necessarily depend on the plant functional type. Moreover, theory makes specific, quantitative predictions about their (acclimated) community-mean values, predictions well supported by evidence. Neglecting such acclimation could lead to incorrect model estimates of the responses of primary production to climate change.&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;We focus on a proof-of-concept based on a primary production model, the P-model &amp;amp;#8211; which combines the Farquhar-von Caemmerer-Berry model for C&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt; photosynthesis with eco-evolutionary optimality principles for the co-optimization of carboxylation and water transport costs &amp;amp;#8211; to allow the model to reproduce short-term variations in photosynthesis and transpiration as well as longer-term, acclimated variations. Key to this effort is explicitly separating the instantaneous responses of photosynthetic rates, and the slower acclimation of photosynthetic traits. The model also includes a dynamic optimiz

  • Working paper
    Fuchs S, Garrood WT, Beber A, Hammond A, Galizi R, Gribble M, Morselli G, Hui T-YJ, Willis K, Kranjc N, Burt A, Nolan T, Crisanti Aet al.,

    Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation

    , Publisher: Cold Spring Harbor Laboratory

    <jats:title>Abstract</jats:title><jats:p>CRISPR-based homing gene drives can be designed to disrupt essential genes whilst biasing their own inheritance, leading to suppression of mosquito populations in the laboratory. This class of gene drives relies on CRISPR-Cas9 cleavage of a target sequence and copying (‘homing’) therein of the gene drive element from the homologous chromosome. However, target site mutations that are resistant to cleavage yet maintain the function of the essential gene are expected to be strongly selected for. Targeting functionally constrained regions where mutations are not easily tolerated should lower the probability of resistance. Evolutionary conservation at the sequence level is often a reliable indicator of functional constraint, though the actual level of underlying constraint between one conserved sequence and another can vary widely. Here we generated a novel gene drive in the malaria vector <jats:italic>Anopheles gambiae</jats:italic>, targeting an ultra-conserved target site in a haplosufficient essential gene (AGAP029113) required during mosquito development, which fulfils many of the criteria for the target of a population suppression gene drive. We then designed a selection regime to experimentally assess the likelihood of generation and subsequent selection of gene drive resistant mutations at its target site. We simulated, in a caged population, a scenario where the gene drive was approaching fixation, where selection for resistance is expected to be strongest. Continuous sampling of the target locus revealed that a single, restorative, in-frame nucleotide substitution was selected. Our findings show that ultra-conservation alone need not be predictive of a site that is refractory to target site resistance. Our strategy to evaluate resistance <jats:italic>in vivo</jats:italic> could help to validate candidate gene drive targets for their resilience to resistance and help t

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