Showing papers by "Helmholtz Centre for Environmental Research - UFZ published in 2018"

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Abstract: Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

Nanoparticles in the environment: where do we come from, where do we go to?

Abstract: Nanoparticles serve various industrial and domestic purposes which is reflected in their steadily increasing production volume. This economic success comes along with their presence in the environment and the risk of potentially adverse effects in natural systems. Over the last decade, substantial progress regarding the understanding of sources, fate, and effects of nanoparticles has been made. Predictions of environmental concentrations based on modelling approaches could recently be confirmed by measured concentrations in the field. Nonetheless, analytical techniques are, as covered elsewhere, still under development to more efficiently and reliably characterize and quantify nanoparticles, as well as to detect them in complex environmental matrixes. Simultaneously, the effects of nanoparticles on aquatic and terrestrial systems have received increasing attention. While the debate on the relevance of nanoparticle-released metal ions for their toxicity is still ongoing, it is a re-occurring phenomenon that inert nanoparticles are able to interact with biota through physical pathways such as biological surface coating. This among others interferes with the growth and behaviour of exposed organisms. Moreover, co-occurring contaminants interact with nanoparticles. There is multiple evidence suggesting nanoparticles as a sink for organic and inorganic co-contaminants. On the other hand, in the presence of nanoparticles, repeatedly an elevated effect on the test species induced by the co-contaminants has been reported. In this paper, we highlight recent achievements in the field of nano-ecotoxicology in both aquatic and terrestrial systems but also refer to substantial gaps that require further attention in the future.

Accelerated increase in plant species richness on mountain summits is linked to warming

Abstract: Globally accelerating trends in societal development and human environmental impacts since the mid-twentieth century 1–7 are known as the Great Acceleration and have been discussed as a key indicator of the onset of the Anthropocene epoch 6 . While reports on ecological responses (for example, changes in species range or local extinctions) to the Great Acceleration are multiplying 8, 9 , it is unknown whether such biotic responses are undergoing a similar acceleration over time. This knowledge gap stems from the limited availability of time series data on biodiversity changes across large temporal and geographical extents. Here we use a dataset of repeated plant surveys from 302 mountain summits across Europe, spanning 145 years of observation, to assess the temporal trajectory of mountain biodiversity changes as a globally coherent imprint of the Anthropocene. We find a continent-wide acceleration in the rate of increase in plant species richness, with five times as much species enrichment between 2007 and 2016 as fifty years ago, between 1957 and 1966. This acceleration is strikingly synchronized with accelerated global warming and is not linked to alternative global change drivers. The accelerating increases in species richness on mountain summits across this broad spatial extent demonstrate that acceleration in climate-induced biotic change is occurring even in remote places on Earth, with potentially far-ranging consequences not only for biodiversity, but also for ecosystem functioning and services.

Plant functional trait change across a warming tundra biome

Abstract: The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways.

Abstract: In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.

Global rise in emerging alien species results from increased accessibility of new source pools.

Abstract: Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history Emerging alien species—those never encountered as aliens before—therefore pose a significant challenge to biosecurity interventions worldwide Understanding their temporal trends, origins, and the drivers of their spread is pivotal to improving prevention and risk assessment tools Here, we use a database of 45,984 first records of 16,019 established alien species to investigate the temporal dynamics of occurrences of emerging alien species worldwide Even after many centuries of invasions the rate of emergence of new alien species is still high: One-quarter of first records during 2000–2005 were of species that had not been previously recorded anywhere as alien, though with large variation across taxa Model results show that the high proportion of emerging alien species cannot be solely explained by increases in well-known drivers such as the amount of imported commodities from historically important source regions Instead, these dynamics reflect the incorporation of new regions into the pool of potential alien species, likely as a consequence of expanding trade networks and environmental change This process compensates for the depletion of the historically important source species pool through successive invasions We estimate that 1–16% of all species on Earth, depending on the taxonomic group, qualify as potential alien species These results suggest that there remains a high proportion of emerging alien species we have yet to encounter, with future impacts that are difficult to predict

Bacterial-fungal interactions: ecology, mechanisms and challenges.

Abstract: Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.

Anthropogenic warming exacerbates European soil moisture droughts

Abstract: Anthropogenic warming is anticipated to increase soil moisture drought in the future. However, projections are accompanied by large uncertainty due to varying estimates of future warming. Here, using an ensemble of hydrological and land-surface models, forced with bias-corrected downscaled general circulation model output, we estimate the impacts of 1–3 K global mean temperature increases on soil moisture droughts in Europe. Compared to the 1.5 K Paris target, an increase of 3 K—which represents current projected temperature change—is found to increase drought area by 40% (±24%), affecting up to 42% (±22%) more of the population. Furthermore, an event similar to the 2003 drought is shown to become twice as frequent; thus, due to their increased occurrence, events of this magnitude will no longer be classified as extreme. In the absence of effective mitigation, Europe will therefore face unprecedented increases in soil moisture drought, presenting new challenges for adaptation across the continent. Severe drought plagued Europe in 2003, amplifying heatwave conditions that killed more than 30,000 people. Assuming business as usual, such soil moisture deficits will become twice as frequent in the future and affect up to two-thirds of the European population.

Impacts of species richness on productivity in a large-scale subtropical forest experiment.

Abstract: 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.

Global patterns of tropical forest fragmentation

Abstract: Remote sensing enables the quantification of tropical deforestation with high spatial resolution. This in-depth mapping has led to substantial advances in the analysis of continent-wide fragmentation of tropical forests. Here we identified approximately 130 million forest fragments in three continents that show surprisingly similar power-law size and perimeter distributions as well as fractal dimensions. Power-law distributions have been observed in many natural phenomena such as wildfires, landslides and earthquakes. The principles of percolation theory provide one explanation for the observed patterns, and suggest that forest fragmentation is close to the critical point of percolation; simulation modelling also supports this hypothesis. The observed patterns emerge not only from random deforestation, which can be described by percolation theory, but also from a wide range of deforestation and forest-recovery regimes. Our models predict that additional forest loss will result in a large increase in the total number of forest fragments-at maximum by a factor of 33 over 50 years-as well as a decrease in their size, and that these consequences could be partly mitigated by reforestation and forest protection.

Recent Asian origin of chytrid fungi causing global amphibian declines

Abstract: Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.

Land use driven change in soil pH affects microbial carbon cycling processes

Abstract: Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts We discovered distinct pH controls on microbial mechanisms of carbon accumulation Land use intensification in low-pH soils that increased the pH above a threshold (~62) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates

Biological responses to the press and pulse of climate trends and extreme events

Abstract: The interaction of gradual climate trends and extreme weather events since the turn of the century has triggered complex and, in some cases, catastrophic ecological responses around the world. We illustrate this using Australian examples within a press–pulse framework. Despite the Australian biota being adapted to high natural climate variability, recent combinations of climatic presses and pulses have led to population collapses, loss of relictual communities and shifts into novel ecosystems. These changes have been sudden and unpredictable, and may represent permanent transitions to new ecosystem states without adaptive management interventions. The press–pulse framework helps illuminate biological responses to climate change, grounds debate about suitable management interventions and highlights possible consequences of (non-) intervention.

The Baltic Sea as a time machine for the future coastal ocean

Abstract: Coastal global oceans are expected to undergo drastic changes driven by climate change and increasing anthropogenic pressures in coming decades. Predicting specific future conditions and assessing the best management strategies to maintain ecosystem integrity and sustainable resource use are difficult, because of multiple interacting pressures, uncertain projections, and a lack of test cases for management. We argue that the Baltic Sea can serve as a time machine to study consequences and mitigation of future coastal perturbations, due to its unique combination of an early history of multistressor disturbance and ecosystem deterioration and early implementation of cross-border environmental management to address these problems. The Baltic Sea also stands out in providing a strong scientific foundation and accessibility to long-term data series that provide a unique opportunity to assess the efficacy of management actions to address the breakdown of ecosystem functions. Trend reversals such as the return of top predators, recovering fish stocks, and reduced input of nutrient and harmful substances could be achieved only by implementing an international, cooperative governance structure transcending its complex multistate policy setting, with integrated management of watershed and sea. The Baltic Sea also demonstrates how rapidly progressing global pressures, particularly warming of Baltic waters and the surrounding catchment area, can offset the efficacy of current management approaches. This situation calls for management that is (i) conservative to provide a buffer against regionally unmanageable global perturbations, (ii) adaptive to react to new management challenges, and, ultimately, (iii) multisectorial and integrative to address conflicts associated with economic trade-offs.

Oak genome reveals facets of long lifespan.

Abstract: Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Multiple facets of biodiversity drive the diversity–stability relationship

Abstract: A substantial body of evidence has demonstrated that biodiversity stabilizes ecosystem functioning over time in grassland ecosystems. However, the relative importance of different facets of biodiversity underlying the diversity-stability relationship remains unclear. Here we use data from 39 grassland biodiversity experiments and structural equation modelling to investigate the roles of species richness, phylogenetic diversity and both the diversity and community-weighted mean of functional traits representing the 'fast-slow' leaf economics spectrum in driving the diversity-stability relationship. We found that high species richness and phylogenetic diversity stabilize biomass production via enhanced asynchrony in the performance of co-occurring species. Contrary to expectations, low phylogenetic diversity enhances ecosystem stability directly, albeit weakly. While the diversity of fast-slow functional traits has a weak effect on ecosystem stability, communities dominated by slow species enhance ecosystem stability by increasing mean biomass production relative to the standard deviation of biomass over time. Our in-depth, integrative assessment of factors influencing the diversity-stability relationship demonstrates a more multicausal relationship than has been previously acknowledged.

The changing role of ornamental horticulture in alien plant invasions

Abstract: The number of alien plants escaping from cultivation into native ecosystems is increasing steadily. We provide an overview of the historical, contemporary and potential future roles of ornamental horticulture in plant invasions. We show that currently at least 75% and 93% of the global naturalised alien flora is grown in domestic and botanical gardens, respectively. Species grown in gardens also have a larger naturalised range than those that are not. After the Middle Ages, particularly in the 18th and 19th centuries, a global trade network in plants emerged. Since then, cultivated alien species also started to appear in the wild more frequently than non-cultivated aliens globally, particularly during the 19th century. Horticulture still plays a prominent role in current plant introduction, and the monetary value of live-plant imports in different parts of the world is steadily increasing. Historically, botanical gardens – an important component of horticulture – played a major role in displaying, cultivating and distributing new plant discoveries. While the role of botanical gardens in the horticultural supply chain has declined, they are still a significant link, with one-third of institutions involved in retail-plant sales and horticultural research. However, botanical gardens have also become more dependent on commercial nurseries as plant sources, particularly in North America. Plants selected for ornamental purposes are not a random selection of the global flora, and some of the plant characteristics promoted through horticulture, such as fast growth, also promote invasion. Efforts to breed non-invasive plant cultivars are still rare. Socio-economical, technological, and environmental changes will lead to novel patterns of plant introductions and invasion opportunities for the species that are already cultivated. We describe the role that horticulture could play in mediating these changes. We identify current research challenges, and call for more research efforts on the past and current role of horticulture in plant invasions. This is required to develop science-based regulatory frameworks to prevent further plant invasions.

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.

Abstract: Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.

When we cannot have it all: Ecosystem services trade-offs in the context of spatial planning

Abstract: Spatial planning has to deal with trade-offs between various stakeholders’ wishes and needs as part of planning and management of landscapes, natural resources and/or biodiversity. To make ecosystem services (ES) trade-off research more relevant for spatial planning, we propose an analytical framework, which puts stakeholders, their land-use/management choices, their impact on ES and responses at the centre. Based on 24 cases from around the world, we used this framing to analyse the appearance and diversity of real-world ES trade-offs. They cover a wide range of trade-offs related to ecosystem use, including: land-use change, management regimes, technical versus nature-based solutions, natural resource use, and management of species. The ES trade-offs studied featured a complexity that was far greater than what is often described in the ES literature. Influential users and context setters are at the core of the trade-off decision-making, but most of the impact is felt by non-influential users. Provisioning and cultural ES were the most targeted in the studied trade-offs, but regulating ES were the most impacted. Stakeholders’ characteristics, such as influence, impact faced, and concerns can partially explain their position and response in relation to trade-offs. Based on the research findings, we formulate recommendations for spatial planning.

The impact of even‐aged and uneven‐aged forest management on regional biodiversity of multiple taxa in European beech forests

Abstract: For managed temperate forests, conservationists and policymakers favour fine-grained uneven-aged (UEA) management over more traditional coarse-grained even-aged (EA) management, based on the assumption that within-stand habitat heterogeneity enhances biodiversity. There is, however, little empirical evidence to support this assumption. We investigated for the first time how differently grained forest management systems affect the biodiversity of multiple above- and below-ground taxa across spatial scales. We sampled 15 taxa of animals, plants, fungi and bacteria within the largest contiguous beech forest landscape of Germany and classified them into functional groups. Selected forest stands have been managed for more than a century at different spatial grains. The EA (coarse-grained management) and UEA (fine-grained) forests are comparable in spatial arrangement, climate and soil conditions. These were compared to forests of a nearby national park that have been unmanaged for at least 20 years. We used diversity accumulation curves to compare γ-diversity for Hill numbers 0D (species richness), 1D (Shannon diversity) and 2D (Simpson diversity) between the management systems. Beta diversity was quantified as multiple-site dissimilarity. Gamma diversity was higher in EA than in UEA forests for at least one of the three Hill numbers for six taxa (up to 77%), while eight showed no difference. Only bacteria showed the opposite pattern. Higher γ-diversity in EA forests was also found for forest specialists and saproxylic beetles. Between-stand β-diversity was higher in EA than in UEA forests for one-third (all species) and half (forest specialists) of all taxa, driven by environmental heterogeneity between age-classes, while α-diversity showed no directional response across taxa or for forest specialists. Synthesis and applications. Comparing EA and uneven-aged forest management in Central European beech forests, our results show that a mosaic of different age-classes is more important for regional biodiversity than high within-stand heterogeneity. We suggest reconsidering the current trend of replacing even-aged management in temperate forests. Instead, the variability of stages and stand structures should be increased to promote landscape-scale biodiversity.

Model averaging in ecology: a review of Bayesian, information-theoretic, and tactical approaches for predictive inference

Abstract: In ecology, the true causal structure for a given problem is often not known, and several plausible models and thus model predictions exist. It has been claimed that using weighted averages of these models can reduce prediction error, as well as better reflect model selection uncertainty. These claims, however, are often demonstrated by isolated examples. Analysts must better understand under which conditions model averaging can improve predictions and their uncertainty estimates. Moreover, a large range of different model averaging methods exists, raising the question of how they differ in their behaviour and performance. Here, we review the mathematical foundations of model averaging along with the diversity of approaches available. We explain that the error in model‐averaged predictions depends on each model's predictive bias and variance, as well as the covariance in predictions between models, and uncertainty about model weights. We show that model averaging is particularly useful if the predictive error of contributing model predictions is dominated by variance, and if the covariance between models is low. For noisy data, which predominate in ecology, these conditions will often be met. Many different methods to derive averaging weights exist, from Bayesian over information‐theoretical to cross‐validation optimized and resampling approaches. A general recommendation is difficult, because the performance of methods is often context dependent. Importantly, estimating weights creates some additional uncertainty. As a result, estimated model weights may not always outperform arbitrary fixed weights, such as equal weights for all models. When averaging a set of models with many inadequate models, however, estimating model weights will typically be superior to equal weights. We also investigate the quality of the confidence intervals calculated for model‐averaged predictions, showing that they differ greatly in behaviour and seldom manage to achieve nominal coverage. Our overall recommendations stress the importance of non‐parametric methods such as cross‐validation for a reliable uncertainty quantification of model‐averaged predictions.

Revisiting the recent European droughts from a long-term perspective.

Abstract: Early 21st-century droughts in Europe have been broadly regarded as exceptionally severe, substantially affecting a wide range of socio-economic sectors. These extreme events were linked mainly to increases in temperature and record-breaking heatwaves that have been influencing Europe since 2000, in combination with a lack of precipitation during the summer months. Drought propagated through all respective compartments of the hydrological cycle, involving low runoff and prolonged soil moisture deficits. What if these recent droughts are not as extreme as previously thought? Using reconstructed droughts over the last 250 years, we show that although the 2003 and 2015 droughts may be regarded as the most extreme droughts driven by precipitation deficits during the vegetation period, their spatial extent and severity at a long-term European scale are less uncommon. This conclusion is evident in our concurrent investigation of three major drought types - meteorological (precipitation), agricultural (soil moisture) and hydrological (grid-scale runoff) droughts. Additionally, unprecedented drying trends for soil moisture and corresponding increases in the frequency of agricultural droughts are also observed, reflecting the recurring periods of high temperatures. Since intense and extended meteorological droughts may reemerge in the future, our study highlights concerns regarding the impacts of such extreme events when combined with persistent decrease in European soil moisture.

Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities

Abstract: Because biodiversity is multidimensional and scale-dependent, it is challenging to estimate its change. However, it is unclear (1) how much scale-dependence matters for empirical studies, and (2) if it does matter, how exactly we should quantify biodiversity change. To address the first question, we analysed studies with comparisons among multiple assemblages, and found that rarefaction curves frequently crossed, implying reversals in the ranking of species richness across spatial scales. Moreover, the most frequently measured aspect of diversity - species richness - was poorly correlated with other measures of diversity. Second, we collated studies that included spatial scale in their estimates of biodiversity change in response to ecological drivers and found frequent and strong scale-dependence, including nearly 10% of studies which showed that biodiversity changes switched directions across scales. Having established the complexity of empirical biodiversity comparisons, we describe a synthesis of methods based on rarefaction curves that allow more explicit analyses of spatial and sampling effects on biodiversity comparisons. We use a case study of nutrient additions in experimental ponds to illustrate how this multi-dimensional and multi-scale perspective informs the responses of biodiversity to ecological drivers.

Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential

Abstract: The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming. The effects of caesarean section delivery on mother-to-neonate transmission of microbiota are unclear. Here the authors show that caesarean section delivery can affect the transmission of specific microbial strains and the immunomodulatory potential of the microbiota.

Body-size shifts in aquatic and terrestrial urban communities.

Abstract: Body size is intrinsically linked to metabolic rate and life-history traits, and is a crucial determinant of food webs and community dynamics1,2. The increased temperatures associated with the urban-heat-island effect result in increased metabolic costs and are expected to drive shifts to smaller body sizes 3 . Urban environments are, however, also characterized by substantial habitat fragmentation 4 , which favours mobile species. Here, using a replicated, spatially nested sampling design across ten animal taxonomic groups, we show that urban communities generally consist of smaller species. In addition, although we show urban warming for three habitat types and associated reduced community-weighted mean body sizes for four taxa, three taxa display a shift to larger species along the urbanization gradients. Our results show that the general trend towards smaller-sized species is overruled by filtering for larger species when there is positive covariation between size and dispersal, a process that can mitigate the low connectivity of ecological resources in urban settings 5 . We thus demonstrate that the urban-heat-island effect and urban habitat fragmentation are associated with contrasting community-level shifts in body size that critically depend on the association between body size and dispersal. Because body size determines the structure and dynamics of ecological networks 1 , such shifts may affect urban ecosystem function. The urban-heat-island effect drives community-level shifts towards smaller body sizes; however, habitat fragmentation caused by urbanization favours larger body sizes in species with positive size–dispersal links.

Urban growth and decline: Europe’s shrinking cities in a comparative perspective 1990–2010:

Abstract: At the beginning of the 21st century, the phenomenon of shrinking cities was widely discussed across Europe. Most European countries saw an increasingly ageing population and an internal migration ...