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The increasing severity and frequency of natural disturbances requires a better understanding of their effects on all compartments of biodiversity. In Northern Fennoscandia, recent large-scale moth outbreaks have led to an abrupt change in plant communities from birch forests dominated by dwarf shrubs to grass-dominated systems. However, the indirect effects on the belowground compartment remained unclear. Here, we combined eDNA surveys of multiple trophic groups with network analyses to demonstrate that moth defoliation has far-reaching consequences on soil food webs. Following this disturbance, diversity and relative abundance of certain trophic groups declined (e.g., ectomycorrhizal fungi), while many others expanded (e.g., bacterivores and omnivores) making soil food webs more diverse and structurally different. Overall, the direct and indirect consequences of moth outbreaks increased belowground diversity at different trophic levels. Our results highlight that a holistic view of ecosystems improves our understanding of cascading effects of major disturbances on soil food webs.

Background and aims Soil stability is a key ecosystem function provided by agricultural landscapes. A multitude of influential factors such as soil texture and plant community structure have been suggested, but few studies compare the relative importance of these factors for soil stability in the field. In addition, studies on effects of plant traits on soil stability have ignored intraspecific trait variability despite growing evidence of its importance for ecosystem functioning. Methods Using path model analysis, we quantified the effect of plant functional traits (PFTs), abiotic soil characteristics and vegetation characteristics on three soil stability measures in 30 field margins of an agriculture landscape of Korea. We compare models with and without intraspecific trait variability. Results Variance in soil stability was relatively well explained by our conceptual path model (81 % explained variance for soil aggregate stability, 50 % for penetration resistance and 35 % for soil shear vane strength). The overall most influential variable was root density while vegetation cover and species richness was much less important. Accounting for intraspecific trait variability improved the goodness-of-fit of all path models but not the overall explained variance. However, intraspecific trait variability allowed identifying important direct and indirect effects of PFTs on soil stability that would have remained hidden otherwise. Conclusion We have demonstrated that the consideration of intraspecific trait variability – even though measuring it could strongly limit achievable sample sizes – is essential for uncovering the substantial effect of plant functional community composition on a key ecosystem function, soil stability.

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.

Ecologists carry a well-stocked toolbox with a great variety of sampling methods, statistical analyses and modelling tools, and new methods are constantly appearing. Evaluation and optimisation of these methods is crucial to guide methodological choices. Simulating error-free data or taking high-quality data to qualify methods is common practice. Here, we emphasise the methodology of the 'virtual ecologist' (VE) approach where simulated data and observer models are used to mimic real species and how they are 'virtually' observed. This virtual data is then subjected to statistical analyses and modelling, and the results are evaluated against the 'true' simulated data. The VE approach is an intuitive and powerful evaluation framework that allows a quality assessment of sampling protocols, analyses and modelling tools. It works under controlled conditions as well as under consideration of confounding factors such as animal movement and biased observer behaviour. In this review, we promote the approach as a rigorous research tool, and demonstrate its capabilities and practical relevance. We explore past uses of VE in different ecological research fields, where it mainly has been used to test and improve sampling regimes as well as for testing and comparing models, for example species distribution models. We discuss its benefits as well as potential limitations, and provide some practical considerations for designing VE studies. Finally, research fields are identified for which the approach could be useful in the future. We conclude that VE could foster the integration of theoretical and empirical work and stimulate work that goes far beyond sampling methods, leading to new questions, theories, and better mechanistic understanding of ecological systems.

Climate warming is releasing carbon from soils around the world, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown. Here, we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% ± 31% (mean ± 95% confidence intervals) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration, and CO 2 release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics. In a terrestrial ecosystem, the carbon cycle primarily represents the balance between plants consuming carbon dioxide from the atmosphere and soil microbes releasing carbon stored in the soil into the atmosphere (mostly as carbon dioxide). Given that carbon dioxide traps heat in the atmosphere, the balance of carbon inputs and outputs from an ecosystem can have important consequences for climate change. Rising temperatures caused by climate warming have led plants from lowland ecosystems to migrate uphill and start growing in alpine ecosystems, where temperatures are lower and most carbon is stored in the soil. Soil microbes use carbon stored in the soil and exuded from plants to grow, and they release this carbon – in the form of carbon dioxide – into the atmosphere through respiration. Walker et al. wanted to know how the arrival of lowland plants in alpine ecosystems under climate warming would affect carbon stores in the soil. To answer this question, Walker et al. simulated warmer temperatures by moving turfs (plants and soil) from alpine ecosystems to a warmer downhill site and planting lowland plants into the turfs. They compared the concentration of soil carbon in these turfs to that of soil in alpine turfs that had not been moved downhill and had no lowland plants. Their results showed that the warmed turfs containing lowland plants had a lower concentration of soil carbon. This suggests that climate warming will lead to more soil carbon being released into the atmosphere if lowland plants also migrate into alpine ecosystems. Walker et al. also wanted to know the mechanism through which lowland plants were decreasing soil carbon concentration under warming. They find that lowland plants probably release more small molecules into the soil than alpine plants. Soil microbes use the carbon and nutrients in these molecules to break down more complex molecules in the soil, thereby releasing nutrients and carbon that can then be used in respiration. This finding suggests that soil microbes breakdown and respire native soil carbon faster in the presence of lowland plants, releasing more carbon dioxide into the atmosphere and reducing carbon stores in the soil. Walker et al.’s results reveal a new mechanism through which uphill migration of lowland plants could increase the effects of climate change, in a feedback loop. Further research as to whether this mechanism occurs in different regions and ecosystems could help to quantify the magnitude of this feedback and allow scientists to make more accurate predictions about climate change.

Darwin proposed two seemingly contradictory hypotheses for a better understanding of biological invasions. Strong relatedness of invaders to native communities as an indication of niche overlap could promote naturalization because of appropriate niche adaptation, but could also hamper naturalization because of negative interactions with native species (‘Darwin's naturalization hypothesis’). Although these hypotheses provide clear and opposing predictions for expected patterns of species relatedness in invaded communities, so far no study has been able to clearly disentangle the underlying mechanisms. We hypothesize that conflicting past results are mainly due to the neglected role of spatial resolution of the community sampling. In this study, we corroborate both of Darwin's expectations by using phylogenetic relatedness as a measure of niche overlap and by testing the effects of sampling resolution in highly invaded coastal plant communities. At spatial resolutions fine enough to detect signatures of biotic interactions, we find that most invaders are less related to their nearest relative in invaded plant communities than expected by chance (phylogenetic overdispersion). Yet at coarser spatial resolutions, native assemblages become more invasible for closely-related species as a consequence of habitat filtering (phylogenetic clustering). Recognition of the importance of the spatial resolution at which communities are studied allows apparently contrasting theoretical and empirical results to be reconciled. Our study opens new perspectives on how to better detect, differentiate and understand the impact of negative biotic interactions and habitat filtering on the ability of invaders to establish in native communities.

During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro-ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith’s phylogenetic diversity (PDFaith), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PDFaith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PDFaith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PDFaith) we can obtain a better understanding of assemblage structure.

Understanding the processes that drive the dramatic changes in biodiversity along the productivity gradient remains a major challenge. Insight from simple, bivariate relationships so far has been limited. We combined >11,000 community plots in the French Alps with a molecular phylogeny and trait information for >1200 plant species to simultaneously investigate the relationships between all major biodiversity dimensions and satellite-sensed productivity. Using an approach that tests for differential effects of species dominance, species similarity and the interplay between phylogeny and traits, we demonstrate that unimodal productivity–biodiversity relationships only dominate for taxonomic diversity. In forests, trait and phylogenetic diversity typically increase with productivity, while in grasslands, relationships shift from unimodal to declining with greater land-use intensity. High productivity may increase trait/phylogenetic diversity in ecosystems with few external constraints (forests) by promoting complementary strategies, but under external constraints (managed grasslands) successful strategies are similar and thus the best competitors may be selected. The relationships between ecosystem productivity and plant diversity are complex. Here, the authors show that sites with high productivity typically have reduced species diversity but high functional and phylogenetic diversity, potentially owing to the creation of additional niche space.

Climate warming is supposed to enlarge the area climatically suitable to the naturalization of alien garden plants in temperate regions. However, the effects of a changing climate on the spread of naturalized ornamentals have not been evaluated by spatially and temporarily explicit range modelling at larger scales so far. Here, we assess how climate change and the frequency of cultivation interactively determine the spread of 15 ornamental plants over the 21st century in Europe. We coupled species distribution modelling with simulations of demography and dispersal to predict range dynamics of these species in annual steps across a 250 × 250 m raster of the study area. Models were run under four scenarios of climate warming and six levels of cultivation intensity. Cultivation frequency was implemented as size of the area used for planting a species. Although the area climatically suitable to the 15 species increases, on average, the area predicted to be occupied by them in 2090 shrinks under two of the three climate change scenarios. This contradiction obviously arises from dispersal limitations that were pronounced although we assumed that cultivation is spatially adapting to the changing climate. Cultivation frequency had a much stronger effect on species spread than climate change, and this effect was non‐linear. The area occupied increased sharply from low to moderate levels of cultivation intensity, but levelled off afterwards. Our simulations suggest that climate warming will not necessarily foster the spread of alien garden plants in Europe over the next decades. However, climatically suitable areas do increase and hence an invasion debt is likely accumulating. Restricting cultivation of species can be effective in preventing species spread, irrespective of how the climate develops. However, for being successful, they depend on high levels of compliance to keep propagule pressure at a low level.

Plant communities in forest-grassland ecotones of the European Alps are already suffering from gradual climate change and will likely be exposed to more frequent and intense drought periods in the future. Yet, how gradual climate change and extreme drought will affect the stability of these plant communities is largely unknown. Here, we investigated how drought modulates the effects of gradual climate change on the long-term structural stability of these ecotone communities using a multidimensional approach. Using a spatially explicit landscape vegetation model, we simulated three drought scenarios, on top of gradual changes of climate variables, and their impacts on the dynamics of 24 plant functional groups, distinguishing between forests and grasslands, as well as different land uses. We then used n-dimensional hypervolumes to define community states under the different drought scenarios, and compared them to initial conditions to assess changes in community structural stability. In general, added drought effects did not counteract the long-term consequences of gradual climate changes, although they resulted in quantitatively different effects. Importantly, drought and climate change had non-negligible consequences for taxonomic and functional structure that differed between communities and land-use regimes. For instance, forest taxonomic structure was more overall more stable than grassland's, despite the observed functional shifts towards more warm-adapted species compositions. Conversely, unmanaged grasslands were the least stable, suffering the loss of characteristic alpine species. Also, while frequent and severe drought regimes caused forests to become more variable in time, they had the opposite effect on grasslands. Our results agree with observations of drought- and climate-driven changes in mountain communities of the Alps, and we discuss their relevance for ecosystem management. Importantly, we demonstrate the utility of this multidimensional approach to study community stability for analysing cross-community and cross-disturbance responses to global change.