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The resilience of biodiverse forests to climate change depends on an interplay of adaptive processes operating at multiple temporal and organizational scales. These include short-term acclimation of physiological processes like photosynthesis and respiration, mid-term changes in forest structure due to competition, and long-term changes in community composition arising from competitive exclusion and genetic trait evolution. To investigate the roles of diversity and adaptation for forest resilience, we present Plant-FATE, a parsimonious eco-evolutionary vegetation model. Tested with data from a hyperdiverse Amazonian terra-firme forest, our model accurately predicts multiple emergent ecosystem properties characterizing forest structure and function. Under elevated CO2 conditions, we predict an increase in productivity, leaf area, and aboveground biomass, with the magnitude of this increase declining in nutrient-deprived soils if trees allocate more carbon to the rhizosphere to overcome nutrient limitation. Furthermore, increased aboveground productivity leads to greater competition for light and drives a shift in community composition towards fast-growing but short-lived species characterized by lower wood densities. Such a transition reduces the carbon residence time of woody biomass, dampening carbon-sink strength and potentially rendering the Amazon Forest more vulnerable to future climatic extreme events.

The global terrestrial carbon sink is increasing1,2,3, offsetting roughly a third of anthropogenic CO2 released into the atmosphere each decade1, and thus serving to slow4 the growth of atmospheric CO2. It has been suggested that a CO2-induced long-term increase in global photosynthesis, a process known as CO2 fertilization, is responsible for a large proportion of the current terrestrial carbon sink4,5,6,7. The estimated magnitude of the historic increase in photosynthesis as result of increasing atmospheric CO2 concentrations, however, differs by an order of magnitude between long-term proxies and terrestrial biosphere models7,8,9,10,11,12,13. Here we quantify the historic effect of CO2 on global photosynthesis by identifying an emergent constraint14,15,16 that combines terrestrial biosphere models with global carbon budget estimates. Our analysis suggests that CO2 fertilization increased global annual photosynthesis by 11.85 ± 1.4%, or 13.98 ± 1.63 petagrams carbon (mean ± 95% confidence interval) between 1981 and 2020. Our results help resolve conflicting estimates of the historic sensitivity of global photosynthesis to CO2, and highlight the large impact anthropogenic emissions have had on ecosystems worldwide.

Northern peatlands store large amounts of carbon: 500 ± 100 GtC, according to a consolidated estimate from a diversity of methods1,2,3,4,5,6. However, Nichols and Peteet7 presented an estimate of 1,055 GtC, exceeding previous estimates of carbon stock in global peatlands2 and in northern peatlands by a factor of two. Here we argue that this is an overestimate, caused by systematic bias introduced by their inclusion of 14C dates from mineral deposits and other unsuitable sites, the use of records that lack direct measurements of carbon density, and the methodology issues. Furthermore, their estimate is difficult to reconcile within the top-down constraints imposed by ice-core and marine records, and estimated contributions from other processes that affected the terrestrial carbon storage during the Holocene epoch.

The future Earth is projected to experience elevated rainfall variability, with more frequent and intense droughts, as well as high-rainfall events. Increasing CO2 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. 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 CO2 assimilation rate, stomatal conductance, and leaf photosynthetic capacity caused by drying soil. It also correctly predicts the responses of CO2 assimilation rate, stomatal conductance, leaf water potential, and leaf photosynthetic capacity to vapour pressure deficit, temperature, ambient CO2, light intensity, and elevation. Our model therefore captures the synergistic effects of atmospheric and soil drought, as well as of atmospheric CO2 changes, on plant photosynthesis and transpiration. We embed this model of photosynthesis and transpiration in a trait-height-patch structured eco-evolutionary vegetation model. This model accounts for allometric carbon allocation, height-structured competition for light, patch-structured successional dynamics, and coevolution of plant functional traits. It predicts functional species mixtures and emergent ecosystem properties under different environmental conditions. Using this model, we investigate the evolution of plant hydraulic strategies under different regimes of drought and rainfall variability. Our approach provides an eco-evolutionarily consistent framework to scale up the responses of plant communities from individual plants to ecosystems to provide ecosystem-level predictions of functional diversity, primary production, and plant water use, and could thus be used for reliable projections of the global carbon and water cycles under future climate scenarios.

The global carbon and water cycles are strongly governed by the simultaneous diffusion of CO2 and water vapour through the leaves of terrestrial plants. These diffusive fluxes are controlled by plants’ 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 changing environments. Tested with experimental data from eighteen 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 CO2. Consistent with widely observed patterns, inferred trait values for the analysed species display a spectrum of stomatal strategies, a safety-efficiency trade-off, and a convergence towards low hydraulic safety margins. Our unifying theory opens new avenues for reliably modelling the interactive effects of drying soil and air and rising atmospheric CO2 on global photosynthesis and transpiration.

International audience; We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi- platform and language-agnostic package manager Conda. Currently, Bioconda o ers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bio- conda improves analysis reproducibility by allowing users to de ne isolated environments with de ned software versions, all of which are easily installed and managed without administrative privileges.

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the climate policy process, and project future climate change. Present-day analysis requires the combination of a range of data, algorithms, statistics and model estimates and their interpretation by a broad scientific community. Here we describe datasets and a methodology developed by the global carbon cycle science community to quantify all major components of the global carbon budget, including their uncertainties. We discuss changes compared to previous estimates, consistency within and among components, and methodology and data limitations. Based on energy statistics, we estimate that the global emissions of CO2 from fossil fuel combustion and cement production were 9.5 ± 0.5 PgC yr−1 in 2011, 3.0 percent above 2010 levels. We project these emissions will increase by 2.6% (1.9–3.5%) in 2012 based on projections of Gross World Product and recent changes in the carbon intensity of the economy. Global net CO2 emissions from Land-Use Change, including deforestation, are more difficult to update annually because of data availability, but combined evidence from land cover change data, fire activity in regions undergoing deforestation and models suggests those net emissions were 0.9 ± 0.5 PgC yr−1 in 2011. The global atmospheric CO2 concentration is measured directly and reached 391.38 ± 0.13 ppm at the end of year 2011, increasing 1.70 ± 0.09 ppm yr−1 or 3.6 ± 0.2 PgC yr−1 in 2011. Estimates from four ocean models suggest that the ocean CO2 sink was 2.6 ± 0.5 PgC yr−1 in 2011, implying a global residual terrestrial CO2 sink of 4.1 ± 0.9 PgC yr−1. All uncertainties are reported as ±1 sigma (68% confidence assuming Gaussian error distributions that the real value lies within the given interval), reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. This paper is intended to provide a baseline to keep track of annual carbon budgets in the future. All carbon data presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP_V2012).

The surface of a cell is one of its most important components through which it can communicate with the outside environment, and with other cells. The aim of this volume is to illustrate the contributions made by genetics to the understanding of some important cell surface phenomena. The first series of four contributions deals with a variety of examples of cell-surface genetics from bacteria through to man. The genetics of the bacterial surface provides an interesting model for higher organisms, including problems of transport and cellular interaction. The red cell blood groups, which provided the first example of a clearly defined genetic difference on any cell surface, were also the first such variations whose biochemical basis was clearly established. The remarkable cell surface variants of the trypanosomes must have a genetic basis, whose nature remains a challenge to the molecular geneticist. The last of these four contributions deals with plant incompatibility systems, whose physiology has long suggested mechanisms involving some form of surface recognition. The second set of four contributions concentrates on the functions, genetics, and biochemistry of the major histocompatibility systems of mouse (H-2) and man (HLA). These systems, which have their counterparts in many other species, are now known to encompass a large number of genes controlling cell surface determinants, immune response differences and components of the complement system.

Accurate assessment of anthropogenic carbon dioxide (CO2)emissions and their redistribution among the atmosphere, ocean, andterrestrial biosphere is important to better understand the globalcarbon cycle, support the development of climate policies, and projectfuture climate change. Here we describe datasets and a methodology toquantify all major components of the global carbon budget, includingtheir uncertainties, based on the combination of a range of data,algorithms, statistics and model estimates and their interpretation by abroad scientific community. We discuss changes compared to previousestimates, consistency within and among components, alongsidemethodology and data limitations. CO2 emissions from fossilfuel combustion and cement production (EFF) are based onenergy statistics and cement production data, respectively, whileemissions from Land-Use Change (ELUC), mainly deforestation,are based on combined evidence from land-cover change data, fireactivity associated with deforestation, and models. The globalatmospheric CO2 concentration is measured directly and itsrate of growth (GATM) is computed from the annual changes inconcentration. The mean ocean CO2 sink (SOCEAN) isbased on observations from the 1990s, while the annual anomalies andtrends are estimated with ocean models. The variability inSOCEAN is evaluated with data products based on surveys ofocean CO2 measurements. The global residual terrestrialCO2 sink (SLAND) is estimated by the difference ofthe other terms of the global carbon budget and compared to results ofindependent Dynamic Global Vegetation Models forced by observed climate,CO2 and land cover change (some including nitrogen-carboninteractions). We compare the variability and mean land and ocean fluxesto estimates from three atmospheric inverse methods for three broadlatitude bands. All uncertainties are reported as ±1σ,reflecting the current capacity to characterise the annual estimates ofeach component of the global carbon budget. For the last decadeavailable (2004-2013), EFF was 8.9 ± 0.4 GtCyr-1, ELUC 0.9 ± 0.5 GtC yr-1,GATM 4.3 ± 0.1 GtC yr-1, SOCEAN2.6 ± 0.5 GtC yr-1, and SLAND 2.9 ±0.8 GtC yr-1. For year 2013 alone, EFF grew to 9.9± 0.5 GtC yr-1, 2.3% above 2012, contining the growthtrend in these emissions. ELUC was 0.9 ± 0.5 GtCyr-1, GATM was 5.4 ± 0.2 GtCyr-1, SOCEAN was 2.9 ± 0.5 GtCyr-1 and SLAND was 2.5 ± 0.9 GtCyr-1. GATM was high in 2013 reflecting a steadyincrease in EFF and smaller and opposite changes betweenSOCEAN and SLAND compared to the past decade(2004-2013). The global atmospheric CO2 concentration reached395.31 ± 0.10 ppm averaged over 2013. We estimate thatEFF will increase by 2.5% (1.3-3.5%) to 10.1 ± 0.6 GtCin 2014 (37.0 ± 2.2 GtCO2 yr-1), 65% aboveemissions in 1990, based on projections of World Gross Domestic Productand recent changes in the carbon intensity of the economy. From thisprojection of EFF and assumed constant ELUC for2014, cumulative emissions of CO2 will reach about 545± 55 GtC (2000 ± 200 GtCO2) for 1870-2014,about 75% from EFF and 25% from ELUC. This paperdocuments changes in the methods and datasets used in this new carbonbudget compared with previous publications of this living dataset (LeQuéré et al., 2013, 2014). All observations presented herecan be downloaded from the Carbon Dioxide Information Analysis Center(doi:10.3334/CDIAC/GCP_2014). Italic font highlights significant methodological changesand results compared to the Le Quéré et al. (2015)manuscript that accompanies the previous version of this living data.

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates, consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil-fuel combustion and cement production (EFF) are based on energy statistics, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (G ATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated for the first time in this budget with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO2 and land cover change (some including nitrogen-carbon interactions). All uncertainties are reported as ±1σ , reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2003-2012), EFF was 8.6±0.4 GtC yr-1, ELUC 0.9±0.5 GtC yr-1, GATM 4.3±0.1 GtC yr-1, SOCEAN 2.5±0.5 GtC yr -1, and SLAND 2.8±0.8 GtC yr-1. For year 2012 alone, EFF grew to 9.7±0.5 GtC yr-1, 2.2% above 2011, reflecting a continued growing trend in these emissions, G ATM was 5.1±0.2 GtC yr-1, SOCEAN was 2.9±0.5 GtC yr-1, and assuming an ELUC of 1.0±0.5 GtC yr-1 (based on the 2001-2010 average), S LAND was 2.7±0.9 GtC yr-1. GATM was high in 2012 compared to the 2003-2012 average, almost entirely reflecting the high EFF. The global atmospheric CO2 concentration reached 392.52±0.10 ppm averaged over 2012. We estimate that EFF will increase by 2.1% (1.1- 3.1 %) to 9.9±0.5 GtC in 2013, 61% above emissions in 1990, based on projections of world gross domestic product and recent changes in the carbon intensity of the economy.With this projection, cumulative emissions ofCO2 will reach about 535±55 GtC for 1870-2013, about 70% from EFF (390±20 GtC) and 30% from ELUC (145±50 GtC). This paper also documents any changes in the methods and data sets used in this new carbon budget from previous budgets (Le Quéré et al., 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP-2013-V2.3).

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