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Abstract Facing rapid environmental changes and anthropogenic habitat destruction, animal behavioural plasticity becomes an adaptive potential that needs to be considered in conservation strategies along with, for example, genetic diversity. Here, we evaluate to what extent non‐invasive environmental DNA (eDNA) methods may contribute to the assessment of intraspecies behavioural plasticity in terms of foraging behaviour. We analysed DNA metabarcoding data for plant components in the diet of four neighbouring groups of wild vervet monkeys Chlorocebus pygerythrus to identify intergroup variation (IGV). The faecal samples considered for the analyses were limited to the summer season to minimise the impact of seasonality. Each sample was attributed by observation to individuals with known life history data. A plant survey was conducted in each group home range during the study period to account for environmental variation. We observed mixed results when testing whether IGV in plant consumption was greater than intragroup variation, indicating that the influence of social dynamics must be considered. Intragroup variation was positively correlated with group size. We observed IGV in diet composition among all groups as well as in some pairwise comparisons. We found significant dietary differences between two group pairs when considering only adult females. Lastly, we observed IGV in foraging of specific plants that were not explained by their distribution, suggesting behavioural differences in selectivity between groups. Our study system and organism, being a highly social and non‐threatened primate species, with constant gene flow and overlapping territories between groups, provides an ideal model to evaluate the usage of eDNA‐based methods to better understand the impact of social factors on IGV. Our results highlight the need to consider social and demographic factors, the impact of which remains complicated to disentangle from environmental factors. However, we emphasise the great potential for studying social groups using eDNA and that such studies are needed to better understand intraspecific behavioural plasticity in wild populations.

Glacier tables are structures frequently encountered on temperate glaciers. They consist of a rock supported by a narrow ice foot which forms through differential melting of the ice. In this article, we investigate their formation by following their dynamics on the Mer de Glace (the Alps, France). We report field measurements of four specific glacier tables over the course of several days, as well as snapshot measurements of a field of 80 tables performed on a given day. We develop a simple model accounting for the various mechanisms of the heat transfer on the glacier using local meteorological data, which displays a quantitative agreement with the field measurements. We show that the formation of glacier tables is controlled by the global heat flux received by the rocks, which causes the ice underneath to melt at a rate proportional to the one of the surrounding ice. Under large rocks the ice ablation rate is reduced compared to bare ice, leading to the formation of glacier tables. This thermal insulation effect is due to the warmer surface temperature of rocks compared to the ice, which affects the net long-wave and turbulent fluxes. While the short-wave radiation, which is the main source of heat, is slightly more absorbed by the rocks than the ice, it plays an indirect role in the insulation by inducing a thermal gradient across the rocks which warms them. Under a critical size, however, rocks can enhance ice melting and consequently sink into the ice surface. This happens when the insulation effect is too weak to compensate for a geometrical amplification effect: the external heat fluxes are received on a larger surface than the contact area with the ice. We identified the main parameters controlling the ability of a rock to form a glacier table: the rock thickness, its aspect ratio, and the ratio between the averaged turbulent and short-wave heat fluxes.

Abstract Biodiversity assessments are indispensable tools for planning and monitoring conservation strategies. Camera traps (CT) are widely used to monitor wildlife and have proven their usefulness. Environmental DNA (eDNA)‐based approaches are increasingly implemented for biomonitoring, combining sensitivity, high taxonomic coverage and resolution, non‐invasiveness and easiness of sampling, but remain challenging for terrestrial fauna. However, in remote desert areas where scattered water bodies attract terrestrial species, which release their DNA into the water, this method presents a unique opportunity for their detection. In order to identify the most efficient method for a given study system, comparative studies are needed. Here, we compare CT and DNA metabarcoding of water samples collected from two desert ecosystems, the Trans‐Altai Gobi in Mongolia and the Kalahari in Botswana. We recorded with CT the visiting patterns of wildlife and studied the correlation with the biodiversity captured with the eDNA approach. The aim of the present study was threefold: (a) to investigate how well waterborne eDNA captures signals of terrestrial fauna in remote desert environments, which have been so far neglected in terms of biomonitoring efforts; (b) to compare two distinct approaches for biomonitoring in such environments; and (c) to draw recommendations for future eDNA‐based biomonitoring. We found significant correlations between the two methodologies and describe a detectability score based on variables extracted from CT data and the visiting patterns of wildlife. This supports the use of eDNA‐based biomonitoring in these ecosystems and encourages further research to integrate the methodology in the planning and monitoring of conservation strategies.

Abstract Assessing the diet of wild animals reveals valuable information about their ecology and trophic relationships that may help elucidate dynamic interactions in ecosystems and forecast responses to environmental changes. Advances in molecular biology provide valuable research tools in this field. However, comparative empirical research is still required to highlight strengths and potential biases of different approaches. Therefore, this study compares environmental DNA and observational methods for the same study population and sampling duration. We employed DNA metabarcoding assays targeting plant and arthropod diet items in 823 fecal samples collected over 12 months in a wild population of an omnivorous primate, the vervet monkey (Chlorocebus pygerythrus). DNA metabarcoding data were subsequently compared to direct observations. We observed the same seasonal patterns of plant consumption with both methods; however, DNA metabarcoding showed considerably greater taxonomic coverage and resolution compared to observations, mostly due to the construction of a local plant DNA database. We found a strong effect of season on variation in plant consumption largely shaped by the dry and wet seasons. The seasonal effect on arthropod consumption was weaker, but feeding on arthropods was more frequent in spring and summer, showing overall that vervets adapt their diet according to available resources. The DNA metabarcoding assay outperformed also direct observations of arthropod consumption in both taxonomic coverage and resolution. Combining traditional techniques and DNA metabarcoding data can therefore not only provide enhanced assessments of complex diets and trophic interactions to the benefit of wildlife conservationists and managers but also opens new perspectives for behavioral ecologists studying whether diet variation in social species is induced by environmental differences or might reflect selective foraging behaviors.

Abstract Increasing evidence suggests that agricultural intensification is a threat to many groups of soil biota, but how the impacts of land-use intensity on soil organisms translate into changes in comprehensive soil interaction networks remains unclear. Here for the first time, we use environmental DNA to examine total soil multi-trophic diversity and food web structure for temperate agroecosystems along a gradient of land-use intensity. We tested for response patterns in key properties of the soil food webs in sixteen fields ranging from arable crops to grazed permanent grasslands as part of a long-term management experiment. We found that agricultural intensification drives reductions in trophic group diversity, although taxa richness remained unchanged. Intensification generally reduced the complexity and connectance of soil interaction networks and induced consistent changes in energy pathways, but the magnitude of management-induced changes depended on the variable considered. Average path length (an indicator of food web redundancy and resilience) did not respond to our management intensity gradient. Moreover, turnover of network structure showed little response to increasing management intensity. Our data demonstrates the importance of considering different facets of trophic networks for a clearer understanding of agriculture-biodiversity relationships, with implications for nature-based solutions and sustainable agriculture.

The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified. We investigated fecal microbiomes of Przewalski's horse (PH; Equus ferus przewalskii), the only horses alive today not successfully domesticated by humans, and herded, domestic horse (E. f. caballus) living in adjacent natural grasslands. We discovered PH fecal microbiomes hosted a distinct and more diverse community of bacteria compared to domestic horses, which is likely partly explained by different plant diets as revealed by trnL maker data. Within the PH population, four individuals were born in captivity in European zoos and hosted a strikingly low diversity of fecal microbiota compared to individuals born in natural reserves in France and Mongolia. These results suggest that anthropogenic forces can dramatically reshape equid gastrointestinal microbiomes, which has broader implications for the conservation management of endangered mammals.

Abstract Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large‐scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigate if it can be attributed to interspecific coprophagia. We tested whether experimental artifacts or other sources of DNA could account for dog DNA, regressed dog occurrence in the diet of fox against that of the fox’s main prey, short‐tailed field voles, and consider whether predation or scavenging could explain the presence of dog DNA. Additionally, we determined the calorific value of dog faeces through calorimetric explosion. The high occurrence of dog DNA in the diet of fox, the timing of its increase, and the negative relationship between dog and the fox's main prey, point to dog faeces as the source of DNA in fox scats. Dog faeces being highly calorific, we found that foxes, but not pine martens, regularly exploit them, seemingly as an alternative resource to fluctuating prey. Scattered accounts from the literature may suggest that interspecific coprophagia is a potentially frequent and widespread form of interaction among vertebrates. However, further work should address its prevalence in other systems and the implications for ecological communities. Tools such as metabarcoding offer a way forward.

Abstract Leaf litter habitats shelter a great variety of organisms, which play an important role in ecosystem dynamics. However, monitoring species in leaf litter is challenging, especially in highly diverse environments such as tropical forests, because individuals may easily camouflage themselves or hide in the litter layer. Identifying species based on environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat, without the need for direct observation of individuals. We applied eDNA metabarcoding to analyze large amounts of leaf litter (1 kg per sample) collected in the Brazilian Atlantic forest. We compared two DNA extraction methods, one total and one extracellular, and amplified a fragment of the mitochondrial 18S rRNA gene common to all eukaryotes, to assess the performance of eDNA from leaf litter samples in identifying different eukaryotic taxonomic groups. We also amplified two fragments of the mitochondrial 12S rRNA gene to specifically test the power of this approach for monitoring vertebrate species, with a focus on anurans. Most of the eukaryote sequence reads obtained were classified as Fungi, followed by Metazoa, and Viridiplantae. Most vertebrate sequences were assigned to Homo sapiens; only two sequences assigned to the genus Phyllomedusa and the species Euparkerella brasiliensis can be considered true detections of anurans in our eDNA samples. The detection of taxa varied depending on the DNA extraction method applied. Our results demonstrate that the analysis of eDNA from leaf litter samples has low power for monitoring vertebrate species and should be preferentially applied to describe active and abundant taxa in terrestrial communities, such as Fungi and invertebrates.

Abstract Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. While the identification of food components of plant and animal origin has traditionally been conducted by macro- and microscopical approaches in case of incomplete digestion, molecular methods provide the potential to increase sensitivity and taxonomic resolution. In particular, DNA metabarcoding (PCR-amplification and next generation sequencing of complex DNA mixtures) has seen a rapid growth in the field of wildlife ecology to assess species’ diets from faecal and gastric samples. Despite clear advantages, molecular approaches have not yet been established in routine human forensics to investigate the last meal components of deceased persons. In this pilot study we applied for the first time a DNA metabarcoding approach to assess both plant and vertebrate components of 48 human stomach content samples taken during medicolegal autopsies. We obtained a final dataset with 34 vertebrate and 124 vegetal unique sequences, that were clustered to 9 and 33 operational taxonomic units (OTUs), respectively. Our results suggest that this approach can provide crucial information about circumstances preceding death, and open promising perspectives for biomedical dietary surveys based on digested food items found in the gastrointestinal tract.

Abstract With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as “biodiversity capsules” and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.

Abstract Assessing biodiversity loss and species extinction is necessary to warn society and raise awareness of the impacts of ongoing climate change. Prioritizing protected areas is the pragmatic and applicable management measure under the pressure of ongoing climate change and limited resources to conserve species at risk of extinction. We developed a novel conservation index (CI) to prioritize areas and populations of an endangered mountain tree species that need protection in the face of ongoing climate change, as conservation of all populations may not be realistic. This CI integrates (1) mountain topography to identify potential refugial areas with suitable microclimates, (2) genetic diversity to assess the adaptive capacity of local populations, and (3) hypothetical climate change in the species' range. We applied this CI to Atlas cedar, an endemic and threatened species whose populations are scattered throughout the Moroccan mountains. This index provided a scale for 33 populations studied and suggests that genetically diverse populations located in rugged areas where future local climate may overlap with their current climatic niche should receive a higher conservation priority. This index may also be applicable to other mountain species with scattered populations and is likely to be more accurate if more precise climate data are used at the microrefugia scale.

The past 100 years of ecological research has seen substantial progress in understanding the natural world and likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin such advances, but would additionally benefit from recent developments in the sequence-based quantification of biodiversity from the fields of molecular ecology and genomics. By building on a long and rich history of molecular taxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previously impossible insights into alpha and beta diversity from all domains of life, irrespective of body size. While a number of complementary reviews are available in specialist journals, our aim here is to succinctly describe the different technologies available within the omics toolbox and showcase the opportunities available to contemporary ecologists to advance our understanding of biodiversity and its potential roles in ecosystems. Starting in the field, we walk the reader through sampling and preservation of genomic material, including typical taxonomy marker genes used for species identification. Moving on to the laboratory, we cover nucleic acid extraction approaches and highlight the principal features of using marker gene assessment, metagenomics, metatranscriptomics, single-cell genomics and targeted genome sequencing as complementary approaches to assess the taxonomic and functional characteristics of biodiversity. We additionally provide clear guidance on the forms of DNA found in the environmental samples (e.g. environmental vs. ancient DNA) and highlight a selection of case studies, including the investigation of trophic relationships/food webs. Given the maturity of sequence-based identification of prokaryotes and microbial eukaryotes, more exposure is given to macrobial communities. We additionally illustrate current approaches to genomic data analysis and highlight the exciting prospects of the publicly available data underpinning published sequence-based studies. Given that ecology ‘has to count’, we identify the impact that molecular genetic analyses have had on stakeholders and end-users and predict future developments for the fields of biomonitoring. Furthermore, we conclude by highlighting future opportunities in the field of systems ecology afforded by effective engagement between the fields of traditional and molecular ecology.

Primary biogenic organic aerosols (PBOAs) represent a major fraction of coarse organic matter (OM) in air. Despite their implication in many atmospheric processes and human health problems, we surprisingly know little about PBOA characteristics (i.e., composition, dominant sources, and contribution to airborne particles). In addition, specific primary sugar compounds (SCs) are generally used as markers of PBOAs associated with bacteria and fungi, but our knowledge of microbial communities associated with atmospheric particulate matter (PM) remains incomplete. This work aimed at providing a comprehensive understanding of the microbial fingerprints associated with SCs in PM10 (particles smaller than 10 µm) and their main sources in the surrounding environment (soils and vegetation). An intensive study was conducted on PM10 collected at a rural background site located in an agricultural area in France. We combined high-throughput sequencing of bacteria and fungi with detailed physicochemical characterizations of PM10, soil, and plant samples and monitored meteorological and agricultural activities throughout the sampling period. Results show that in summer SCs in PM10 are a major contributor of OM in air, representing 0.8 % to 13.5 % of OM mass. SC concentrations are clearly determined by the abundance of only a few specific airborne fungal and bacterial taxa. The temporal fluctuations in the abundance of only four predominant fungal genera, namely Cladosporium, Alternaria, Sporobolomyces, and Dioszegia, reflect the temporal dynamics in SC concentrations. Among bacterial taxa, the abundance of only Massilia, Pseudomonas, Frigoribacterium, and Sphingomonas is positively correlated with SC species. These microbes are significantly enhanced in leaf over soil samples. Interestingly, the overall community structure of bacteria and fungi are similar within PM10 and leaf samples and significantly distinct between PM10 and soil samples, indicating that surrounding vegetation is the major source of SC-associated microbial taxa in PM10 in this rural area of France.

Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population‐level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population‐level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present‐day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sedaDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co‐occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present‐day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population‐level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA. [ABSTRACT FROM AUTHOR]

Primary Biogenic Organic Aerosols (PBOA) were recently shown to be produced by only a few types of microorganisms, emitted by the surrounding vegetation in the case of a regionally homogeneous field site. This study presents the first comprehensive description of the structure and main sources of airborne microbial communities associated with temporal trends in Sugar Compounds (SC) concentrations of PM10 in 3 sites under a climatic gradient in France. By combining sugar chemistry and DNA Metabarcoding approaches, we intended to identify PM10-associated microbial communities and their main sources at three sampling-sites in France, under different climates, during the summer of 2018. This study accounted also for the interannual variability in summer airborne microbial community structure (bacteria and fungi only) associated with PM10-SC concentrations during a 2 consecutive years’ survey at one site. Our results showed that temporal changes in PM10-SC in the three sites are associated with the abundance of only a few specific taxa of airborne fungi and bacterial. These taxa differ significantly between the 3 climatic regions studied. The microbial communities structure associated with SC concentrations of PM10 during a consecutive 2-year study remained stable in the rural area. Atmospheric concentration levels of PM10-SC species varied significantly between the 3 study sites, but with no clear difference according to site typology (rural vs. urban), suggesting that SC emissions are related to regional rather than local climatic characteristics. The overall microbial beta diversity in PM10 samples is significantly different from that of the main vegetation around the urban sites studied. This indicates that the airborne microorganisms at these urban sites are not solely from the immediate surrounding vegetation, which contrasts with observations at the scale of a regionally homogeneous rural site in 2017. These results improve our understanding of the spatial behavior of tracers of PBOA emission sources, which need to be better characterized to further implement this important mass fraction of Organic Matter (OM) in Chemical Transport models (CTM).