Institute of Applied Ecology

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

Soil carbon transformation and sequestration have received significant interest in recent years due to a growing need for quantitating its role in mitigating climate change. Even though our understanding of the nature of soil organic matter has recently been substantially revised, fundamental uncertainty remains about the quantitative importance of microbial necromass as part of persistent organic matter. Addressing this uncertainty has been hampered by the absence of quantitative assessments whether microbial matter makes up the majority of the persistent carbon in soil. Direct quantitation of microbial necromass in soil is very challenging because of an overlapping molecular signature with nonmicrobial organic carbon. Here, we use a comprehensive analysis of existing biomarker amino sugar data published between 1996 and 2018, combined with novel appropriation using an ecological systems approach, elemental carbon-nitrogen stoichiometry, and biomarker scaling, to demonstrate a suit of strategies for quantitating the contribution of microbe-derived carbon to the topsoil organic carbon reservoir in global temperate agricultural, grassland, and forest ecosystems. We show that microbial necromass can make up more than half of soil organic carbon. Hence, we suggest that next-generation field management requires promoting microbial biomass formation and necromass preservation to maintain healthy soils, ecosystems, and climate. Our analyses have important implications for improving current climate and carbon models, and helping develop management practices and policies.

Global development has been heavily reliant on the overexploitation of natural resources since the Industrial Revolution. With the extensive use of fossil fuels, deforestation, and other forms of land-use change, anthropogenic activities have contributed to the ever-increasing concentrations of greenhouse gases (GHGs) in the atmosphere, causing global climate change. In response to the worsening global climate change, achieving carbon neutrality by 2050 is the most pressing task on the planet. To this end, it is of utmost importance and a significant challenge to reform the current production systems to reduce GHG emissions and promote the capture of CO2 from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.

China's terrestrial ecosystems have functioned as important carbon sinks. However, previous estimates of carbon budgets have included large uncertainties owing to the limitations of sample size, multiple data sources, and inconsistent methodologies. In this study, we conducted an intensive field campaign involving 14,371 field plots to investigate all sectors of carbon stocks in China's forests, shrublands, grasslands, and croplands to better estimate the regional and national carbon pools and to explore the biogeographical patterns and potential drivers of these pools. The total carbon pool in these four ecosystems was 79.24 ± 2.42 Pg C, of which 82.9% was stored in soil (to a depth of 1 m), 16.5% in biomass, and 0.60% in litter. Forests, shrublands, grasslands, and croplands contained 30.83 ± 1.57 Pg C, 6.69 ± 0.32 Pg C, 25.40 ± 1.49 Pg C, and 16.32 ± 0.41 Pg C, respectively. When all terrestrial ecosystems are taken into account, the country's total carbon pool is 89.27 ± 1.05 Pg C. The carbon density of the forests, shrublands, and grasslands exhibited a strong correlation with climate: it decreased with increasing temperature but increased with increasing precipitation. Our analysis also suggests a significant sequestration potential of 1.9-3.4 Pg C in forest biomass in the next 10-20 years assuming no removals, mainly because of forest growth. Our results update the estimates of carbon pools in China's terrestrial ecosystems based on direct field measurements, and these estimates are essential to the validation and parameterization of carbon models in China and globally.

Significance China has launched six key ecological restoration projects since the late 1970s, but the contribution of these projects to terrestrial C sequestration remains unknown. In this study we examined the ecosystem C sink in the project area (∼16% of the country’s land area) and evaluated the project-induced C sequestration. The total annual C sink in the project area between 2001 and 2010 was estimated to be 132 Tg C per y, over half of which (74 Tg C per y, 56%) was caused by the implementation of the six projects. This finding indicates that the implementation of the ecological restoration projects in China has significantly increased ecosystem C sequestration across the country.

Abstract The COVID-19 pandemic is impacting human activities, and in turn energy use and carbon dioxide (CO 2 ) emissions. Here we present daily estimates of country-level CO 2 emissions for different sectors based on near-real-time activity data. The key result is an abrupt 8.8% decrease in global CO 2 emissions (−1551 Mt CO 2 ) in the first half of 2020 compared to the same period in 2019. The magnitude of this decrease is larger than during previous economic downturns or World War II. The timing of emissions decreases corresponds to lockdown measures in each country. By July 1st, the pandemic’s effects on global emissions diminished as lockdown restrictions relaxed and some economic activities restarted, especially in China and several European countries, but substantial differences persist between countries, with continuing emission declines in the U.S. where coronavirus cases are still increasing substantially.

The effects of plants on the biosphere, atmosphere and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on the literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we reviewed 24 aspects of plant and ecosystem functioning and their relationships with a number of root system traits, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluated the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that belowground traits with the broadest importance in plant and ecosystem functioning are not those most commonly measured. Also, the estimation of trait relative importance for functioning requires us to consider a more comprehensive range of functionally relevant traits from a diverse range of species, across environments and over time series. We also advocate that establishing causal hierarchical links among root traits will provide a hypothesis-based framework to identify the most parsimonious sets of traits with the strongest links on functions, and to link genotypes to plant and ecosystem functioning.

Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon found in average monocultures and similar amounts as those of two commercial monocultures. Species richness effects were strongly associated with functional and phylogenetic diversity. A shrub addition treatment reduced tree productivity, but this reduction was smaller at high shrub species richness. Our results encourage multispecies afforestation strategies to restore biodiversity and mitigate climate change.

International audience

Habitat management involving manipulation of farmland vegetation can exert direct suppressive effects on pests and promote natural enemies. Advances in theory and practical techniques have allowed habitat management to become an important subdiscipline of pest management. Improved understanding of biodiversity-ecosystem function relationships means that researchers now have a firmer theoretical foundation on which to design habitat management strategies for pest suppression in agricultural systems, including landscape-scale effects. Supporting natural enemies with shelter, nectar, alternative prey/hosts, and pollen (SNAP) has emerged as a major research topic and applied tactic with field tests and adoption often preceded by rigorous laboratory experimentation. As a result, the promise of habitat management is increasingly being realized in the form of practical worldwide implementation. Uptake is facilitated by farmer participation in research and is made more likely by the simultaneous delivery of ecosystem services other than pest suppression.

However, the SOC change differed among the major agricultural regions: SOC increased in all major agronomic regions except in Northeast China. The SOC sequestration was largely attributed to increased organic inputs driven by economics and policy: while higher root biomass resulting from enhanced crop productivity by chemical fertilizers predominated before 2000, higher residue inputs following the large-scale implementation of crop straw/stover return policy took over thereafter. The SOC change was negatively related to N inputs in East China, suggesting that the excessive N inputs, plus the shallowness of plow layers, may constrain the future C sequestration in Chinese croplands. Our results indicate that cropland SOC sequestration can be achieved through effectively manipulating economic and policy incentives to farmers.

Global warming may have profound effects on terrestrial ecosystems. However, a comprehensive evaluation of the effects of warming on ecosystem nitrogen (N) pools and dynamics is not available. Here, we compiled data of 528 observations from 51 papers and carried out a meta-analysis of experimental warming effects on 13 variables related to terrestrial N pools and dynamics. We found that, on average, net N mineralization and net nitrification rate were increased by 52.2 and 32.2%, respectively, under experimental warming treatment. N pools were also increased by warming, although the magnitude of this increase was less than that of N fluxes. Soil microbial N and N immobilization were not changed by warming, probably because microbes are limited by carbon sources. Grassland and shrubland/heathland were less responsive to warming than forest, probably because the reduction of soil moisture by warming offset the temperature effect in these areas. Soil heating cable and all-day treatment appeared to be the most effective method on N cycling among all treatment methods. Results of this meta-analysis are useful for better understanding the response of N cycling to global warming and the underlying mechanism of warming effects on plants and ecosystem functions.

Recent studies have shown that the high standard of living enjoyed by people in the richest countries often comes at the expense of CO2 emissions produced with technologies of low efficiency in less affluent, developing countries. Less apparent is that this relationship between developed and developing can exist within a single country's borders, with rich regions consuming and exporting high-value goods and services that depend upon production of low-cost and emission-intensive goods and services from poorer regions in the same country. As the world's largest emitter of CO2, China is a prominent and important example, struggling to balance rapid economic growth and environmental sustainability across provinces that are in very different stages of development. In this study, we track CO2 emissions embodied in products traded among Chinese provinces and internationally. We find that 57% of China's emissions are related to goods that are consumed outside of the province where they are produced. For instance, up to 80% of the emissions related to goods consumed in the highly developed coastal provinces are imported from less developed provinces in central and western China where many low-value-added but high-carbon-intensive goods are produced. Without policy attention to this sort of interprovincial carbon leakage, the less developed provinces will struggle to meet their emissions intensity targets, whereas the more developed provinces might achieve their own targets by further outsourcing. Consumption-based accounting of emissions can thus inform effective and equitable climate policy within China.

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

Summary The rhizosphere priming effect ( RPE ) is a mechanism by which plants interact with soil functions. The large impact of the RPE on soil organic matter decomposition rates (from 50% reduction to 380% increase) warrants similar attention to that being paid to climatic controls on ecosystem functions. Furthermore, global increases in atmospheric CO 2 concentration and surface temperature can significantly alter the RPE . Our analysis using a game theoretic model suggests that the RPE may have resulted from an evolutionarily stable mutualistic association between plants and rhizosphere microbes. Through model simulations based on microbial physiology, we demonstrate that a shift in microbial metabolic response to different substrate inputs from plants is a plausible mechanism leading to positive or negative RPE s. In a case study of the Duke Free‐Air CO 2 Enrichment experiment, performance of the PhotoCent model was significantly improved by including an RPE ‐induced 40% increase in soil organic matter decomposition rate for the elevated CO 2 treatment – demonstrating the value of incorporating the RPE into future ecosystem models. Overall, the RPE is emerging as a crucial mechanism in terrestrial ecosystems, which awaits substantial research and model development. Contents Summary 31 I. Introduction 31 II. Magnitude and driving variables of the rhizosphere priming effect 32 III. Will global environmental change alter the RPE? 34 IV. A game theoretic model: is priming the result of evolutionarily stable strategies? 35 V. A microbial physiology‐based model: simulating positive and negative RPEs 37 VI. A case study: matching simulation results with observations at the Duke FACE 38 VII. Research needs and future perspectives 39 Acknowledgements 41 References 41

Soil warming has the potential to alter both soil and plant processes that affect carbon storage in forest ecosystems. We have quantified these effects in a large, long-term (7-y) soil-warming study in a deciduous forest in New England. Soil warming has resulted in carbon losses from the soil and stimulated carbon gains in the woody tissue of trees. The warming-enhanced decay of soil organic matter also released enough additional inorganic nitrogen into the soil solution to support the observed increases in plant carbon storage. Although soil warming has resulted in a cumulative net loss of carbon from a New England forest relative to a control area over the 7-y study, the annual net losses generally decreased over time as plant carbon storage increased. In the seventh year, warming-induced soil carbon losses were almost totally compensated for by plant carbon gains in response to warming. We attribute the plant gains primarily to warming-induced increases in nitrogen availability. This study underscores the importance of incorporating carbon-nitrogen interactions in atmosphere-ocean-land earth system models to accurately simulate land feedbacks to the climate system.

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25 ha), all stems ≥ 1 cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 °S-61 °N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 °C), changes in precipitation (up to ± 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8 g N m(-2) yr(-1) and 3.1 g S m(-2) yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5 km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.

Minsheng You and colleagues report the whole-genome sequence of the diamondback moth, Plutella xylostella. Their transcriptome analysis from different life stages, together with comparative genomic and phylogenetic analysis, provides insights into herbivore evolution and insect adaptation to plant feeding and detoxification. How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants1, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood2. We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.

Abstract Aim To examine the contribution of large‐diameter trees to biomass, stand structure, and species richness across forest biomes. Location Global. Time period Early 21st century. Major taxa studied Woody plants. Methods We examined the contribution of large trees to forest density, richness and biomass using a global network of 48 large (from 2 to 60 ha) forest plots representing 5,601,473 stems across 9,298 species and 210 plant families. This contribution was assessed using three metrics: the largest 1% of trees ≥ 1 cm diameter at breast height (DBH), all trees ≥ 60 cm DBH, and those rank‐ordered largest trees that cumulatively comprise 50% of forest biomass. Results Averaged across these 48 forest plots, the largest 1% of trees ≥ 1 cm DBH comprised 50% of aboveground live biomass, with hectare‐scale standard deviation of 26%. Trees ≥ 60 cm DBH comprised 41% of aboveground live tree biomass. The size of the largest trees correlated with total forest biomass ( r 2 = .62, p < .001). Large‐diameter trees in high biomass forests represented far fewer species relative to overall forest richness ( r 2 = .45, p < .001). Forests with more diverse large‐diameter tree communities were comprised of smaller trees ( r 2 = .33, p < .001). Lower large‐diameter richness was associated with large‐diameter trees being individuals of more common species ( r 2 = .17, p = .002). The concentration of biomass in the largest 1% of trees declined with increasing absolute latitude ( r 2 = .46, p < .001), as did forest density ( r 2 = .31, p < .001). Forest structural complexity increased with increasing absolute latitude ( r 2 = .26, p < .001). Main conclusions Because large‐diameter trees constitute roughly half of the mature forest biomass worldwide, their dynamics and sensitivities to environmental change represent potentially large controls on global forest carbon cycling. We recommend managing forests for conservation of existing large‐diameter trees or those that can soon reach large diameters as a simple way to conserve and potentially enhance ecosystem services.