Aim Environmental DNA (eDNA) is increasingly used for analysing and modelling all‐inclusive biodiversity patterns. However, the reliability of eDNA‐based diversity estimates is commonly compromised by arbitrary decisions for curating the data from molecular artefacts. Here, we test the sensitivity of common ecological analyses to these curation steps, and identify the crucial ones to draw sound ecological conclusions. Location Valloire, French Alps. Taxon Vascular plants and fungi. Methods Using soil eDNA metabarcoding data for plants and fungi from 20 plots sampled along a 1000‐m elevational gradient, we tested how the conclusions from three types of ecological analyses: (a) the spatial partitioning of diversity, (b) the diversity–environment relationship, and (c) the distance–decay relationship, are robust to data curation steps. Since eDNA metabarcoding data also comprise erroneous sequences with low frequencies, diversity estimates were further calculated using abundance‐based Hill numbers, which penalize rare sequences through a scaling parameter, namely the order of diversity q (Richness with q = 0, Shannon diversity with q ~ 1, Simpson diversity with q = 2). Results We showed that results from different ecological analyses had varying degrees of sensitivity to data curation strategies and that the use of Shannon and Simpson diversities led to more reliable results. We demonstrated that molecular operational taxonomic unit clustering, removal of polymerase chain reaction errors and of cross‐sample contaminations had major impacts on ecological analyses. Main conclusions In the Era of Big Data, eDNA metabarcoding is going to be one of the major tools to describe, model and predict biodiversity in space and time. However, ignoring crucial data curation steps will impede the robustness of several ecological conclusions. Here, we propose a roadmap of crucial curation steps for different types of ecological analyses.

Aim It is widely recognized that the prediction of invasion success at large biogeographical scales requires jointly accounting for alien species traits and local community filters, such as abiotic conditions, biotic interactions and propagule pressure. Despite this recognition, interactions between traits and community filters are generally neglected. Here, we aim to address this limitation by developing a hierarchical framework that builds on trait‐based theory to model occurrences of alien species as a function of spatially explicit variables, filtering invasions and their interactions with species traits. Location Herbaceous communities throughout France. Time period c. 1960–2012 (mostly after 1990). Major taxa studied Herbaceous plants. Methods Based on a large dataset of >50,000 community plots, we built a multispecies hierarchical model of the distribution of the 10 most widespread alien plants in French grasslands. In this model, we explicitly account for how plant height, specific leaf area (SLA) and seed mass affect the occurrence of alien species along gradients of human pressure, environmental conditions and native community composition. Finally, we contrast the results to native species responses along the same gradients. Results We show that two out of three traits significantly modulate the responses of species along these broad gradients. Alien plants with exploitative traits (i.e., tall and with high SLA) were less dependent on human pressure, more efficient in resource‐rich environments and better at avoiding competition from native species. These trait–gradient interactions were often unique to alien plants (e.g., human pressure was important only for supporting alien species with low SLA), even though trait ranges of alien and native species were comparable. Ultimately, the modelling of trait–gradient interactions allows spatially explicit estimations of invasion risks by novel species with particular sets of traits. Main conclusions By taking the best from multispecies distribution modelling and trait‐based theory, our framework paves the way for a generalized mechanistic understanding of how traits influence the success of alien plants and their spatial distributions.

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.