Centre for Research on Ecology and Forestry Applications

Significance Agricultural production is vulnerable to climate change. Understanding climate change, especially the temperature impacts, is critical if policymakers, agriculturalists, and crop breeders are to ensure global food security. Our study, by compiling extensive published results from four analytical methods, shows that independent methods consistently estimated negative temperature impacts on yields of four major crops at the global scale, generally underpinned by similar impacts at country and site scales. Multimethod analyses improved the confidence in assessments of future climate impacts on global major crops, with important implications for developing crop- and region-specific adaptation strategies to ensure future food supply of an increasing world population.

Abstract Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy‐in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log‐normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait‐based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on-ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision-making contexts when used within a structured and transparent decision-making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of 'translators' between modellers and decision makers. We encourage species distribution modellers to get involved in real decision-making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.

Although the impacts of exotic plant invasions on community structure and ecosystem processes are well appreciated, the pathways or mechanisms that underlie these impacts are poorly understood. Better exploration of these processes is essential to understanding why exotic plants impact only certain systems, and why only some invaders have large impacts. Here, we review over 150 studies to evaluate the mechanisms underlying the impacts of exotic plant invasions on plant and animal community structure, nutrient cycling, hydrology and fire regimes. We find that, while numerous studies have examined the impacts of invasions on plant diversity and composition, less than 5% test whether these effects arise through competition, allelopathy, alteration of ecosystem variables or other processes. Nonetheless, competition was often hypothesized, and nearly all studies competing native and alien plants against each other found strong competitive effects of exotic species. In contrast to studies of the impacts on plant community structure and higher trophic levels, research examining impacts on nitrogen cycling, hydrology and fire regimes is generally highly mechanistic, often motivated by specific invader traits. We encourage future studies that link impacts on community structure to ecosystem processes, and relate the controls over invasibility to the controls over impact.

Climate is a potent selective force in natural populations, yet the importance of adaptation in the response of plant species to past climate change has been questioned. As many species are unlikely to migrate fast enough to track the rapidly changing climate of the future, adaptation must play an increasingly important role in their response. In this paper we review recent work that has documented climate-related genetic diversity within populations or on the microgeographical scale. We then describe studies that have looked at the potential evolutionary responses of plant populations to future climate change. We argue that in fragmented landscapes, rapid climate change has the potential to overwhelm the capacity for adaptation in many plant populations and dramatically alter their genetic composition. The consequences are likely to include unpredictable changes in the presence and abundance of species within communities and a reduction in their ability to resist and recover from further environmental perturbations, such as pest and disease outbreaks and extreme climatic events. Overall, a range-wide increase in extinction risk is likely to result. We call for further research into understanding the causes and consequences of the maintenance and loss of climate-related genetic diversity within populations.

Beta diversity can be measured in different ways. Among these, the total variance of the community data table Y can be used as an estimate of beta diversity. We show how the total variance of Y can be calculated either directly or through a dissimilarity matrix obtained using any dissimilarity index deemed appropriate for pairwise comparisons of community composition data. We addressed the question of which index to use by coding 16 indices using 14 properties that are necessary for beta assessment, comparability among data sets, sampling issues and ordination. Our comparison analysis classified the coefficients under study into five types, three of which are appropriate for beta diversity assessment. Our approach links the concept of beta diversity with the analysis of community data by commonly used methods like ordination and anova. Total beta can be partitioned into Species Contributions (SCBD: degree of variation of individual species across the study area) and Local Contributions (LCBD: comparative indicators of the ecological uniqueness of the sites) to Beta Diversity. Moreover, total beta can be broken up into within- and among-group components by manova, into orthogonal axes by ordination, into spatial scales by eigenfunction analysis or among explanatory data sets by variation partitioning.

The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries and most terrestrial biomes, we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivity worldwide. The value of biodiversity in maintaining commercial forest productivity alone-US$166 billion to 490 billion per year according to our estimation-is more than twice what it would cost to implement effective global conservation. This highlights the need for a worldwide reassessment of biodiversity values, forest management strategies, and conservation priorities.

Abstract. Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere – the global carbon budget – 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 methodology to quantify the five major components of the global carbon budget and their uncertainties. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on land-cover change data and bookkeeping models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2007–2016), EFF was 9.4 ± 0.5 GtC yr−1, ELUC 1.3 ± 0.7 GtC yr−1, GATM 4.7 ± 0.1 GtC yr−1, SOCEAN 2.4 ± 0.5 GtC yr−1, and SLAND 3.0 ± 0.8 GtC yr−1, with a budget imbalance BIM of 0.6 GtC yr−1 indicating overestimated emissions and/or underestimated sinks. For year 2016 alone, the growth in EFF was approximately zero and emissions remained at 9.9 ± 0.5 GtC yr−1. Also for 2016, ELUC was 1.3 ± 0.7 GtC yr−1, GATM was 6.1 ± 0.2 GtC yr−1, SOCEAN was 2.6 ± 0.5 GtC yr−1, and SLAND was 2.7 ± 1.0 GtC yr−1, with a small BIM of −0.3 GtC. GATM continued to be higher in 2016 compared to the past decade (2007–2016), reflecting in part the high fossil emissions and the small SLAND consistent with El Niño conditions. The global atmospheric CO2 concentration reached 402.8 ± 0.1 ppm averaged over 2016. For 2017, preliminary data for the first 6–9 months indicate a renewed growth in EFF of +2.0 % (range of 0.8 to 3.0 %) based on national emissions projections for China, USA, and India, and projections of gross domestic product (GDP) corrected for recent changes in the carbon intensity of the economy for the rest of the world. This living data update documents changes in the methods and data sets used in this new global carbon budget compared with previous publications of this data set (Le Quéré et al., 2016, 2015b, a, 2014, 2013). All results presented here can be downloaded from https://doi.org/10.18160/GCP-2017 (GCP, 2017).

Elemental stoichiometry constitutes an inherent link between biogeochemistry and the structure and processes within food webs, and thus is at the core of ecosystem functioning. Stoichiometry allows for spanning different levels of biological organization, from cellular metabolism to ecosystem structure and nutrient cycling, and is therefore particularly useful for establishing links between different ecosystem compartments. We review elemental carbon : nitrogen : phosphorus (C:N:P) ratios in terrestrial ecosystems (from vegetation, leaf litter, woody debris, and dead roots, to soil microbes and organic matter). While the stoichiometry of the plant, litter, and soil compartments of ecosystems is well understood, heterotrophic microbial communities, which dominate the soil food web and drive nutrient cycling, have received increasing interest in recent years. This review highlights the effects of resource stoichiometry on soil microorganisms and decomposition, specifically on the structure and function of heterotrophic microbial communities and suggests several general patterns. First, latitudinal gradients of soil and litter stoichiometry are reflected in microbial community structure and function. Second, resource stoichiometry may cause changes in microbial interactions and community dynamics that lead to feedbacks in nutrient availability. Third, global change alters the C:N, C:P, and N:P ratios of primary producers, with repercussions for microbial decomposer communities and critical ecosystem services such as soil fertility. We argue that ecological stoichiometry provides a framework to analyze and predict such global change effects at various scales.

Recent comprehensive data provided through the DAISIE project ( www.europe‐aliens.org ) have facilitated the development of the first pan‐European assessment of the impacts of alien plants, vertebrates, and invertebrates – in terrestrial, freshwater, and marine environments – on ecosystem services. There are 1094 species with documented ecological impacts and 1347 with economic impacts. The two taxonomic groups with the most species causing impacts are terrestrial invertebrates and terrestrial plants. The North Sea is the maritime region that suffers the most impacts. Across taxa and regions, ecological and economic impacts are highly correlated. Terrestrial invertebrates create greater economic impacts than ecological impacts, while the reverse is true for terrestrial plants. Alien species from all taxonomic groups affect “supporting”, “provisioning”, “regulating”, and “cultural” services and interfere with human well‐being. Terrestrial vertebrates are responsible for the greatest range of impacts, and these are widely distributed across Europe. Here, we present a review of the financial costs, as the first step toward calculating an estimate of the economic consequences of alien species in Europe.

Summary Pathways describe the processes that result in the introduction of alien species from one location to another. A framework is proposed to facilitate the comparative analysis of invasion pathways by a wide range of taxa in both terrestrial and aquatic ecosystems. Comparisons with a range of data helped identify existing gaps in current knowledge of pathways and highlight the limitations of existing legislation to manage introductions of alien species. The scheme aims for universality but uses the European Union as a case study for the regulatory perspectives. Alien species may arrive and enter a new region through three broad mechanisms: importation of a commodity, arrival of a transport vector, and/or natural spread from a neighbouring region where the species is itself alien. These three mechanisms result in six principal pathways: release, escape, contaminant, stowaway, corridor and unaided. Alien species transported as commodities may be introduced as a deliberate release or as an escape from captivity. Many species are not intentionally transported but arrive as a contaminant of a commodity, for example pathogens and pests. Stowaways are directly associated with human transport but arrive independently of a specific commodity, for example organisms transported in ballast water, cargo and airfreight. The corridor pathway highlights the role transport infrastructures play in the introduction of alien species. The unaided pathway describes situations where natural spread results in alien species arriving into a new region from a donor region where it is also alien. Vertebrate pathways tend to be characterized as deliberate releases, invertebrates as contaminants and plants as escapes. Pathogenic micro‐organisms and fungi are generally introduced as contaminants of their hosts. The corridor and unaided pathways are often ignored in pathway assessments but warrant further detailed consideration. Synthesis and applications. Intentional releases and escapes should be straightforward to monitor and regulate but, in practice, developing legislation has proved difficult. New introductions continue to occur through contaminant, stowaway, corridor and unaided pathways. These pathways represent special challenges for management and legislation. The present framework should enable these trends to be monitored more clearly and hopefully lead to the development of appropriate regulations or codes of practice to stem the number of future introductions.

Recent world‐wide episodes of tree dieback have been attributed to increasing temperatures and associated drought. Because these events are likely to become more common, improved knowledge of their cumulative effects on resilience and the ability to recover pre‐disturbance conditions is important for forest management. Here we propose several indices to examine components of individual tree resilience based on tree ring growth: resistance (inverse of growth reduction during the episode), recovery (growth increase relative to the minimum growth during the episode), resilience (capacity to reach pre‐episode growth levels) and relative resilience (resilience weighted by the damage incurred during the episode). Based on tree ring analyses, we analyzed historical patterns of tree resilience to successive drought‐induced low growth periods in ponderosa pine trees growing in unmanaged, remote forests of the Rocky Mountains. Low‐growth periods registered in tree rings were related to anomalies in the Palmer drought severity index (PDSI) and were attributed to drought. Independently of the impact of a specific event, subsequent growth after a single low‐growth episode was related to the growth prior to the event. Growth performance differed with tree age: young trees were overall more resistant to low‐growth periods, but older trees recovered better from more recent events. Regardless of tree age, recently burned sites exhibited lower post‐episode growth and lower resistance and resilience than unburned ones. We found mixed evidence for the cumulative effect of past low‐growth episodes: overall, greater impacts of a prior event and greater cumulative effects of past low‐growth periods caused a decrease in resistance. However, we did not find a progressive decrease in resilience over time in old trees. Our results highlight the value of using a combination of estimators to evaluate the different components of resilience. Specifically, while tree responses to disturbance depend on past disturbance episodes, the response is context‐specific and depends on the impact the capacity to recover after disturbance. This suggests that recent increases in forest mortality under current climate trends could relate to thresholds on specific components of resilience (resistance, recovery, resilience itself) rather than to an overall loss of resilience over time. Identifying such thresholds and their underlying mechanisms is a promising area of research with important implications for forest management.

Ratios of nitrogen (N) isotopes in leaves could elucidate underlying patterns of N cycling across ecological gradients. To better understand global-scale patterns of N cycling, we compiled data on foliar N isotope ratios (delta(15)N), foliar N concentrations, mycorrhizal type and climate for over 11,000 plants worldwide. Arbuscular mycorrhizal, ectomycorrhizal, and ericoid mycorrhizal plants were depleted in foliar delta(15)N by 2 per thousand, 3.2 per thousand, 5.9 per thousand, respectively, relative to nonmycorrhizal plants. Foliar delta(15)N increased with decreasing mean annual precipitation and with increasing mean annual temperature (MAT) across sites with MAT >or= -0.5 degrees C, but was invariant with MAT across sites with MAT < -0.5 degrees C. In independent landscape-level to regional-level studies, foliar delta(15)N increased with increasing N availability; at the global scale, foliar delta(15)N increased with increasing foliar N concentrations and decreasing foliar phosphorus (P) concentrations. Together, these results suggest that warm, dry ecosystems have the highest N availability, while plants with high N concentrations, on average, occupy sites with higher N availability than plants with low N concentrations. Global-scale comparisons of other components of the N cycle are still required for better mechanistic understanding of the determinants of variation in foliar delta(15)N and ultimately global patterns in N cycling.

A longer growing season as a result of climate change will in turn affect climate through biogeochemical and biophysical effects.

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health.

Animal and plant life cycles are increasingly shown to depend on temperature trends and patterns. In their Perspective, PeA±uelas and Filella review the evidence that global warming during the 20th century has affected the growth period of plants and the development and behavior of animals from insects to birds. The authors warn that changes in the interdependence between species could have unpredictable consequences for ecosystems, that the lengthening of the plant growing season contributes to the global increased carbon fixation, and that changes in phenology may affect not only ecosystems but also agriculture and sanitation.

Evolutionary and paleoecological studies suggest that fires are natural in the Mediterranean basin. However, the important increase in the number of fires and area burned during the 20th century has created the perception that fires are disasters. In the present paper, we review to what extent fires are generating ecological disasters in the Mediterranean basin, in view of current fire regimes and the long-term human pressure on the landscapes. Specifically, we review studies on post-fire plant regeneration and soil losses. The review suggests that although many Mediterranean ecosystems are highly resilient to fire (shrublands and oak forest), some are fire-sensitive (e.g. pine woodlands). Observed erosion rates are, in some cases, relatively high, especially in high fire severity conditions. The sensitive ecosystems (in the sense of showing strong post-fire vegetation changes and soil losses) are mostly of human origin (e.g. extensive pine plantations in old fields). Thus, although many Mediterranean basin plants have traits to cope with fire, a large number of the ecosystems currently found in this region are strongly altered, and may suffer disasters. Post-fire disasters are not the rule, but they may be important under conditions of previous human disturbances.

To meet collective obligations towards biodiversity conservation and monitoring, it is essential that the world's governments and non-governmental organisations as well as the research community tap all possible sources of data and information, including new, fast-growing sources such as citizen science (CS), in which volunteers participate in some or all aspects of environmental assessments. Through compilation of a database on CS and community-based monitoring (CBM, a subset of CS) programs, we assess where contributions from CS and CBM are significant and where opportunities for growth exist. We use the Essential Biodiversity Variable framework to describe the range of biodiversity data needed to track progress towards global biodiversity targets, and we assess strengths and gaps in geographical and taxonomic coverage. Our results show that existing CS and CBM data particularly provide large-scale data on species distribution and population abundance, species traits such as phenology, and ecosystem function variables such as primary and secondary productivity. Only birds, Lepidoptera and plants are monitored at scale. Most CS schemes are found in Europe, North America, South Africa, India, and Australia. We then explore what can be learned from successful CS/CBM programs that would facilitate the scaling up of current efforts, how existing strengths in data coverage can be better exploited, and the strategies that could maximise the synergies between CS/CBM and other approaches for monitoring biodiversity, in particular from remote sensing. More and better targeted funding will be needed, if CS/CBM programs are to contribute further to international biodiversity monitoring.

Intensification or abandonment of agricultural land use has led to a severe decline of semi-natural habitats across Europe. This can cause immediate loss of species but also time-delayed extinctions, known as the extinction debt. In a pan-European study of 147 fragmented grassland remnants, we found differences in the extinction debt of species from different trophic levels. Present-day species richness of long-lived vascular plant specialists was better explained by past than current landscape patterns, indicating an extinction debt. In contrast, short-lived butterfly specialists showed no evidence for an extinction debt at a time scale of c. 40 years. Our results indicate that management strategies maintaining the status quo of fragmented habitats are insufficient, as time-delayed extinctions and associated co-extinctions will lead to further biodiversity loss in the future.