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Insects and other terrestrial invertebrates are declining in species richness and abundance. This includes the invertebrates associated with herbivore dung, which have been negatively affected by grazing abandonment and the progressive loss of large herbivores since the Late Pleistocene. Importantly, traditional monitoring of these invertebrates is time‐consuming and requires considerable taxonomic expertise, which is becoming increasingly scarce. In this study, we investigated the potential of environmental DNA (eDNA) metabarcoding of cow dung samples for biomonitoring of dung‐associated invertebrates. From eight cowpats we recovered eDNA from 12 orders, 29 families, and at least 54 species of invertebrates (mostly insects), representing several functional groups. Furthermore, species compositions differed between the three sampled habitats of dry grassland, meadow, and forest. These differences were in accordance with the species’ ecology; for instance, several species known to be associated with humid conditions or lower temperatures were found only in the forest habitat. We discuss potential caveats of the method, as well as directions for future study and perspectives for implementation in research and monitoring.

In light of the biodiversity crisis and our limited ability to explain variation in biodiversity, tools to quantify spatial and temporal variation in biodiversity and its underlying drivers are critically needed. Inspired by the recently published ecospace framework, we developed and tested a sampling design for environmental and biotic mapping. We selected 130 study sites (40 × 40 m) across Denmark using stratified random sampling along the major environmental gradients underlying biotic variation. Using standardized methods, we collected site species data on vascular plants, bryophytes, macrofungi, lichens, gastropods and arthropods. To evaluate sampling efficiency, we calculated regional coverage (relative to the known species number per taxonomic group), and site scale coverage (i.e., sample completeness per taxonomic group at each site). To extend taxonomic coverage to organisms that are difficult to sample by classical inventories (e.g., nematodes and non-fruiting fungi), we collected soil for metabarcoding. Finally, to assess site conditions, we mapped abiotic conditions, biotic resources and habitat continuity. BACKGROUND: In light of the biodiversity crisis and our limited ability to explain variation in biodiversity, tools to quantify spatial and temporal variation in biodiversity and its underlying drivers are critically needed. Inspired by the recently published ecospace framework, we developed and tested a sampling design for environmental and biotic mapping. We selected 130 study sites (40 × 40 m) across Denmark using stratified random sampling along the major environmental gradients underlying biotic variation. Using standardized methods, we collected site species data on vascular plants, bryophytes, macrofungi, lichens, gastropods and arthropods. To evaluate sampling efficiency, we calculated regional coverage (relative to the known species number per taxonomic group), and site scale coverage (i.e., sample completeness per taxonomic group at each site). To extend taxonomic coverage to organisms that are difficult to sample by classical inventories (e.g., nematodes and non-fruiting fungi), we collected soil for metabarcoding. Finally, to assess site conditions, we mapped abiotic conditions, biotic resources and habitat continuity.RESULTS: Despite the 130 study sites only covering a minute fraction (0.0005%) of the total Danish terrestrial area, we found 1774 species of macrofungi (54% of the Danish fungal species pool), 663 vascular plant species (42%), 254 bryophyte species (41%) and 200 lichen species (19%). For arthropods, we observed 330 spider species (58%), 123 carabid beetle species (37%) and 99 hoverfly species (33%). Overall, sample coverage was remarkably high across taxonomic groups and sufficient to capture substantial spatial variation in biodiversity across Denmark. This inventory is nationally unprecedented in detail and resulted in the discovery of 143 species with no previous record for Denmark. Comparison between plant OTUs detected in soil DNA and observed plant species confirmed the usefulness of carefully curated environmental DNA-data. Correlations among species richness for taxonomic groups were predominantly positive, but did not correlate well among all taxa suggesting differential and complex biotic responses to environmental variation.CONCLUSIONS: We successfully and adequately sampled a wide range of diverse taxa along key environmental gradients across Denmark using an approach that includes multi-taxon biodiversity assessment and ecospace mapping. Our approach is applicable to assessments of biodiversity in other regions and biomes where species are structured along environmental gradient.

Increasing species richness of light demanding species in forests may not be a conservation concern if we accept a macroecological and evolutionary baseline for biodiversity. Most of the current biodiversity in Europe has evolved in the Pleistocene or earlier, and in ecosystems markedly influenced by dynamic natural processes, including grazing. Many threatened species are associated with high-light forest environments such as forest glades and edges, as these have strongly declined at least partially due to the decline of large herbivores in European forests. Hence, moderate grazing in forests should be an ecological baseline and conservation target rather than a concern.

1. Plants regulate soils and microclimate, provide substrate for heterotrophic taxa, are easy to observe and identify and have a stable taxonomy, which strongly justifies their use as indicators in monitoring and conservation. However, there is no consensus as to whether plants are strong predictors of total multi-taxon species richness. In this study we investigate if general terrestrial species richness can be predicted by vascular plant richness and bioindication. 2. To answer this question, we collected an extensive data set on species richness of vascular plants, bryophytes, macrofungi, lichens, plant-galling arthropods, gastropods, spiders, carabid beetles, hoverflies and genetic richness (Operational Taxonomic Units = OTUs) from environmental DNA metabarcoding. We also constructed a Conservation Index based on threatened red list species. Besides using richness of vascular plants for prediction of other taxonomic groups, we also used plant-derived calibration of the abiotic environment (moisture, soil fertility and light conditions) as well as the degree of anthropogenic impact. 3. Bivariate relationships between plant species richness and other species groups showed no consistent pattern. After taking environmental calibration by bioindication into account, we found a consistent, and for most groups significant, positive effect of plant richness. Plant species richness was also important for richness of fungal OTUs, Malaise OTUs and for the Conservation Index. Our multiple regression analyses revealed 1) a consistently positive effect of plant richness on other taxa, 2) prediction of 12-55% of variation in other taxa and 48% of variation in the total species richness when bioindication and plant richness were used as predictors. 4. Our results justify that vascular plants are strong indicators of total biodiversity across environmental gradients and broad taxonomic realms and therefore a natural first choice for biodiversity monitoring and conservation planning. Plants regulate soils and microclimate, provide substrate for heterotrophic taxa, are easy to observe and identify and have a stable taxonomy, which strongly justifies their use as indicators in monitoring and conservation. However, there is no consensus as to whether plants are strong predictors of total multi-taxon species richness. In this study, we investigate if general terrestrial species richness can be predicted by vascular plant richness and bioindication. To answer this question, we collected an extensive dataset on species richness of vascular plants, bryophytes, macrofungi, lichens, plant-galling arthropods, gastropods, spiders, carabid beetles, hoverflies, and genetic richness (operational taxonomic units = OTUs) from environmental DNA metabarcoding. We also constructed a Conservation Index based on threatened red list species. Besides using richness of vascular plants for prediction of other taxonomic groups, we also used plant-derived calibration of the abiotic environment (moisture, soil fertility and light conditions) as well as the degree of anthropogenic impact. Bivariate relationships between plant species richness and other species groups showed no consistent pattern. After taking environmental calibration by bioindication into account, we found a consistent, and for most groups significant, positive effect of plant richness. Plant species richness was also important for richness of fungal OTUs, Malaise OTUs and for the Conservation Index. Our multiple regression analyses revealed (a) a consistently positive effect of plant richness on other taxa, (b) prediction of 12%–55% of variation in other taxa and 48% of variation in the total species richness when bioindication and plant richness were used as predictors. Our results justify that vascular plants are strong indicators of total biodiversity across environmental gradients and broad taxonomic realms and therefore a natural first choice for biodiversity monitoring and conservation planning.

The impact of large herbivores on ecosystems before modern human activities is an open question in ecology and conservation. For Europe, the controversial wood-pasture hypothesis posits that grazing by wild large herbivores supported a dynamic mosaic of vegetation structures at the landscape scale under temperate conditions before agriculture. The contrasting position suggests that European temperate vegetation was primarily closed forest with relatively small open areas, at most impacted locally by large herbivores. Given the role of modern humans in the world-wide decimations of megafauna during the late Quaternary, to resolve this debate it is necessary to understand herbivore-vegetation interactions before these losses. Here, a synthetic analysis of beetle fossils from Great Britain shows that beetles associated with herbivore dung were better represented during the Last Interglacial (132,000-110,000 y B.P., before modern human arrival) than in the early Holocene (10,000-5,000 y B.P.). Furthermore, beetle assemblages indicate closed and partially closed forest in the early Holocene but a greater mixture of semiopen vegetation and forest in the Last Interglacial. Hence, abundant and diverse large herbivores appear to have been associated with high structural diversity of vegetation before the megafauna extinctions at the end of the Pleistocene. After these losses and in the presence of modern humans, large herbivores generally were less abundant, and closed woodland was more prevalent in the early Holocene. Our findings point to the importance of the formerly rich fauna of large herbivores in sustaining structurally diverse vegetation in the temperate forest biome and provide support for recent moves toward rewilding-based conservation management.