Biology subjects

Ejrnaes, R.

Publications and source records attributed to Ejrnaes, R..

15 recordsLinked to original sources

bioRxiv2024

Environmental drivers of the decline of the fen orchid, Liparis loeselii

BackgroundLiparis loeselii is a rare and declining orchid species restricted to rich fens in the Northern Hemisphere. Habitat destruction, eutrophication, drainage and scrub encroachment have been suggested as reasons for the decline. However, which factors are most important is not well understood. AimsBased on vegetation and environmental properties from extant, potential and historical L. loeselii sites, we i) developed habitat suitability models from either Ellenberg Indicator Values or field-measured environmental properties, and ii) identified the primary reasons for the observed decline of L. loeselii. ResultsNutrient status was the most important predictor for L. loeselii occurrence, followed by hydrology proxies (Ellenberg reaction and Ellenberg moisture). Vegetation height and Ellenberg light were of minor importance. ConclusionEffect partitioning based on sites, from which L. loeselii has gone locally extinct, pinpointed eutrophication and drainage to be the most likely primary drivers of the species demise. Phosphorus limitation induced by discharge of Calcium-rich groundwater seems to be crucial for L. loeselii to sustain populations in landscapes dominated by intensive agricultural.

ecology↗

bioRxiv2022

High nutrient loads hinder successful restoration of natural habitats in freshwater wetlands

Restoration of natural processes in ecosystems is key to halt the biodiversity crisis. Here, we evaluate 20 different stream-valley wetland restoration projects - mainly rewetting - in a large region in Denmark in terms of successful restoration of natural wetland habitats. We used quadratic discriminant analysis and generalized linear models to compare the projects 80 vegetation plots with >50.000 natural wetland-habitat reference plots and modelled the influence of time, grazing, rewetting and nutrient availability on the study plots probabilities of belonging to such natural habitats and their richness of high-quality habitat indicator species. In our study, the probability of a restored wetland being a natural wetland habitat - almost always an alkaline fen - was generally below 10 %. Also, we only found half as many indicator species in restored wetlands than in reference wetlands and we demonstrated that the number of characteristic alkaline fen species did not deviate from what could be expected under the prevailing nutrient conditions. We found a negative effect of nutrient availability on the number of high-quality habitat indicator species and the lowest probability of plots being natural wetlands in the most nutrient rich plots. The effect of grazing was only positive in the first years after restoration and only in the most nutrient rich plots, while the effect of rewetting sites to their historical hydrological conditions was generally negative. Our findings reveal that unnaturally high nutrient availability is probably the core limiting factor for successful restoration of natural wetlands and their associated plant diversity. Implications for practice- To successfully restore natural and characteristic freshwater wetland habitats focus on recreating natural processes and conditions is needed - Restoring natural hydrology and grazing is not enough, the soil and water must be naturally nutrient poor for successful restoration of these habitats - Restoration of stream-valley wetlands such as alkaline springs and fens is more likely to be successful in spring-dominated landscapes where clean groundwater diffusely exfiltrates the soil

ecology↗

bioRxiv2022

Scrub encroachment promotes biodiversity in wetland restoration under eutrophic conditions

Wetlands are important habitats, often threatened by drainage, eutrophication and suppression of ungulate grazing. In many countries, considerable resources are spent combatting scrub encroachment. Here, we hypothesize that encroachment may benefit biodiversity - especially under eutrophic conditions where asymmetric competition among plants compromises conservation targets. We studied the effects of scrub cover, nutrient levels and soil moisture on richness of vascular plants, bryophytes, soil fungi and microbes in open and overgrown wetlands. We also tested the effect of encroachment, eutrophication and soil moisture on indicators of conservation value (red-listed species, indicator species and uniqueness). Plant and bryophyte species richness peaked at low soil fertility, whereas soil fertility promoted soil microbes. Soil fungi responded negatively to increasing soil moisture. Lidar-derived variables reflecting degree of scrub cover had predominantly positive effects on species richness measures. Conservation value indicators had a negative relationship to soil fertility and a positive to encroachment. For plant indicator species, the negative effect of high nutrient levels was offset by encroachment, supporting our hypothesis of competitive release under shade. The positive effect of soil moisture on indicator species was strong in open habitats only. Nutrient poor mires and meadows host many rare species and require conservation management by grazing and natural hydrology. On former arable lands, where restoration of infertile conditions is unfeasible, we recommend rewilding with opportunities for encroachment towards semi-open willow scrub and swamp forest, with the prospect of high species richness in bryophytes, fungi and soil microbes and competitive release in the herb layer.

ecology↗

bioRxiv2021

Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage

Biodiversity of soil microbiota is routinely assessed with environmental DNA-based methods, among which amplification and massive parallel sequencing of marker genes (eDNA metabarcoding) is the most common. Soil microbiota may for example be investigated in relation to biodiversity research or as a tool in forensic investigations. After sampling, the taxonomic composition of soil biotic communities may change. In order to minimize community changes after sampling, it is desirable to reduce biological activity, e.g. by freezing immediately after sampling. However, this may be impossible due to remoteness of study sites or, in forensic cases, where soil has been attached to a questioned item for protracted periods of time. Here we investigated the effect of storage duration and conditions on the assessment of the soil biota with eDNA metabarcoding. We extracted eDNA from freshly collected soil samples and again from the same samples after storage under contrasting temperature conditions. We used five different primer sets targeting bacteria, fungi, protists (cercozoans), general eukaryotes, and plants. For these groups, we quantified differences in richness, evenness and community composition. Subsequently, we tested whether we could correctly infer habitat type and original sample identity after storage using a large reference dataset. We found increased community composition differences with extended storage time and with higher storage temperature. However, for samples stored less than 28 days at a maximum of 20{degrees}C, changes were generally insignificant. Classification models could successfully assign most stored samples to their exact location of origin and correct habitat type even after weeks of storage. Even samples showing larger compositional changes generally retained the original sample as the best match (relative similarity). Our results show that for most biodiversity and forensic applications, storage of samples for days and even several weeks may not be a problem, if storage temperature does not exceed 20{degrees}C. Even after suboptimal storage conditions, significant patterns can be reproduced.

ecology↗

bioRxiv2020

Contrasting impacts of urban and farmland cover on flying insect biomass

Recent studies report declines in biomass, abundance and diversity of terrestrial insect groups. While anthropogenic land use is one likely contributor to this decline, studies assessing land cover as a driver of insect dynamics are rare and mostly restricted in spatial scale and types of land cover. In this study, we used rooftop-mounted car nets in a citizen science project ( InsectMobile) to allow for large-scale geographic sampling of flying insects across Denmark and parts of Germany. Citizen scientists sampled insects along 278 10 km routes in urban, farmland and semi-natural (grassland, wetland and forest) landscapes in the summer of 2018. We assessed the importance of local to landscape-scale effects and land use intensity by relating insect biomass to land cover in buffers of 50, 250, 500 and 1000 m along the routes. We found a negative association of urban cover and a positive association of farmland on insect biomass at a landscape-scale (1000 m buffer) in both countries. In Denmark, we also found positive effects of all semi-natural land covers, i.e. grassland (largest at the landscape-scale, 1000 m), forests (largest at intermediate scales, 250 m), and wetlands (largest at the local-scale, 50 m). The negative association of insect biomass with urban land cover and positive association with farmland were not clearly modified by any variable associated with land use intensity. Our results show that land cover has an impact on flying insect biomass with the magnitude of this effect varying across spatial scales. Since we consistently found negative effects of urban land cover, our findings highlight the need for the conservation of semi-natural areas, such as wetlands, grasslands and forests, in Europe.

ecology↗

bioRxiv2020

Investigating the drivers of macro-fungal dark diversity using LiDAR

Despite the important role of fungi for ecosystems, relatively little is known about the factors underlying the dynamics of their diversity. Moreover, studies do not typically consider their dark diversity: the species absent from an otherwise suitable site. Here, we examined potential drivers of local fungal dark diversity in temperate woodland and open habitats using LiDAR and in-situ field measurements, combined with a systematically collected and geographically comprehensive macro-fungi and plant data set. For the first time, we also estimated species pools of fungi by considering both plant and fungi co-occurrences. The most important LiDAR variables for modelling fungal dark diversity were amplitude and echo ratio, which are both thought to represent vegetation structure. These results suggest that the local fungal dark diversity is highest in production forests like plantations and lowest in more open forests and in open habitats with little woody vegetation. Plant species richness was the strongest explanatory factor overall and negatively correlated with local fungal dark diversity. Soil fertility showed a positive relationship with dark diversity in open habitats. These findings may indicate that the local dark diversity of macro-fungi is highest in areas with a relatively high human impact (typically areas with low plant species richness and high soil fertility). Overall, this study brings novel insights into local macro-fungi dark diversity patterns, suggesting that a multitude of drivers related to both soil and vegetation act in concert to determine fungal dark diversity.

ecology↗

bioRxiv2020

Simple attributes predict the importance of plants as hosts to the richness of fungi and arthropods

Consumers constitute the vast majority of global terrestrial biodiversity. Yet, local consumer richness is poorly understood. Plant species richness offers a simple hypothesis to how the diversification of carbon substrates may promote the diversity of arthropods and fungi. We took this one step further and used databases on plant-consumer interaction links to derive the richness of associated biota per plant species (link score). Using a species inventory of 130 sites we investigated 1) how well the link score could be predicted by plant attributes and 2) if the sum of plant species observed or predicted link scores could predict site richness of arthropods and macrofungi better than plant species richness alone. We found plant link scores to be positively related to plant size, abundance, nativeness and ectomycorrhizal status. Link based indices generally improved prediction of richness, stressing the importance of plants as niche space for the megadiverse groups of insects and fungi.

ecology↗

bioRxiv2020

Exploring a natural baseline for large herbivore biomass

The massive global losses of large mammals in the Pleistocene have triggered severe ecosystem changes including changed nutrient cycles, fire regimes and climate, shifts in biomes and loss of biodiversity. Large herbivores create and diversify resources and living space for other organisms and thereby play an important role in ecosystem functioning and biodiversity conservation. However, even today large herbivores are regulated, hunted and driven to extinction to a degree where intact large-herbivore communities are largely non-existent. Consequently, natural density and biomass of large-herbivores for restoration of ecosystems are poorly known. To address this knowledge gap, we apply the scaling pattern for consumer-producer relationships and show that the biomass of large herbivores in ecosystems across the world is considerably lower than expected from primary productivity. African ecosystems have the strongest consumer-producer relationship and assuming that African ecosystems approach a natural baseline, we use this relationship to predict large herbivore biomass in Europe as an example. Our findings indicate that restoring large herbivore biomass would entail increasing large herbivore biomass by orders of magnitude in most ecosystems, which potentially changes the perspective on large herbivores in conservation and restoration projects.

ecology↗

bioRxiv2019

Multi-taxon inventory reveals highly consistent biodiversity responses to ecospace variation

Amidst the global biodiversity crisis, identifying drivers of biodiversity variation remains a key challenge. Scientific consensus is limited to a few macroecological rules, such as species richness increasing with area, which provide limited guidance for conservation. In fact, few agreed ecological principles apply at the scale of sites or reserve management, partly because most community-level studies are restricted to single habitat types and species groups. We used the recently proposed ecospace framework and a comprehensive data set for aggregating environmental variation to predict multi-taxon diversity. We studied richness of plants, fungi, and arthropods in 130 sites representing the major terrestrial habitat types in Denmark. We found the abiotic environment (ecospace position) to be pivotal for the richness of primary producers (vascular plants, mosses, and lichens) and, more surprisingly, little support for ecospace continuity as a driver. A peak in richness at intermediate productivity adds new empirical evidence to a long-standing debate over biodiversity responses to productivity. Finally, we discovered a dominant and positive response of fungi and insect richness to organic matter accumulation and diversification (ecospace expansion). Two simple models of producer and consumer richness accounted for 77 % of the variation in multi-taxon species richness suggesting a significant potential for generalization beyond individual species responses. Our study widens the traditional conservation focus on vegetation and vertebrate populations unravelling the importance of diversification of carbon resources for diverse heterotrophs, such as fungi and insects.

ecology↗

bioRxiv2019

Dark diversity reveals importance of biotic resources and competition for plant diversity across broad environmental gradients

Species richness is the most commonly used metric to quantify biodiversity. However, examining dark diversity, the group of missing species which can potentially inhabit a site, can provide a more thorough understanding of the processes influencing observed biodiversity and help evaluate the restoration potential of local habitats. So far, dark diversity has mainly been studied for specific habitats or largescale landscapes while less attention has been given to variation across broad environmental gradients or as a result of local conditions and biotic interactions. In this study, we investigate the importance of local environmental conditions in determining dark diversity and observed richness in plant communities across broad environmental gradients. We use the ecospace concept to investigate how abiotic gradients (defined as position), availability of biotic resources (defined as expansion), spatiotemporal extent of habitats (defined as continuity), as well as species interactions through competition, relate to these biodiversity measures. Position variables were important for both plant richness and dark diversity, some with quadratic relationships, e.g., plant richness showing a unimodal response to soil fertility corresponding to the intermediate productivity hypothesis. Competition represented by community mean Grime C showed a negative correlation with plant richness. Besides position, organic carbon was the most important variable for dark diversity, indicating that in late succession habitats such as forests and shrubs, dark diversity is generally low. The importance of Grime C indicate that intermediate disturbance, such as grazing, may facilitate higher species richness and lower dark diversity. Comparing various biodiversity metrics and their influencing factors might reveal important drivers of biodiversity changes and result in better conservation decision-making.

ecology↗

bioRxiv2019

LIDAR explains diversity of plants, fungi, lichens and bryophytes across multiple habitats and large geographic extent

Effective planning and nature management require spatially accurate and comprehensive measures of the factors important for biodiversity. Light detection and ranging (LIDAR also known as light radar) can provide exactly this, and is hereby a promising technology to support future nature management and related applications. However, until now studies evaluating the potential of LIDAR for this field have been highly limited in scope. Here, we assess the potential of LIDAR to estimate the local diversity of four species groups in multiple habitat types, from open grasslands and meadows over shrubland to forests and across a large area (approximately 43.000 km2), providing a crucial step towards enabling the application of LIDAR in practice, planning and policy-making. We assessed the relationships between the species richness of macrofungi, lichens, bryophytes and plants, respectively, and 25 LIDAR-based measures related to potential abiotic and biotic diversity drivers. We used negative binomial Generalized Linear Modelling to construct 19 different relevant models for each species group, and leave-one-region-out cross validation to select the best models. These best models explained 49, 31, 32 and 28 % of the variation in species richness (R2) for macrofungi, lichens, bryophytes and plants respectively. Three LIDAR measures were important and positively related to the richness in three of the four species groups: variation in local heat load, terrain slope and shrub layer height. Four other LIDAR measures were ranked among the three most important for at least one of the species groups: point amplitude entropy, shrub layer density (1.5 - 5 m), medium-tree layer density (10 - 15 m) and variation in biomass. Generally, LIDAR measures exhibited strong associations to the biotic environment, and to some abiotic factors, but was not suitable for representing spatiotemporal continuity. In conclusion, we showed how well LIDAR alone can predict the local biodiversity across habitats. We also showed that several LIDAR measures are highly correlated to important biodiversity drivers, which are notoriously hard to measure in the field. This opens up hitherto unseen possibilities for using LIDAR for cost-effective monitoring and management of local biodiversity across species groups and habitat types even over large areas.

ecology↗

bioRxiv2018

Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?

The majority of Earths biodiversity is unknown. This is particularly true for the vast part of soil biodiversity, which rarely can be observed directly. Metabarcoding of DNA extracted from the environment (eDNA) has become state-of-the-art in assessing soil biodiversity. Also for fungal community profiling eDNA is seen as an attractive alternative to classical surveying based on fruitbodies. However, it is unknown whether eDNA-metabarcoding provides a representative sample of fungal diversity and census of threatened species. Therefore conservation planning and assessment are still based on fruitbody inventories. Based on a dataset of unprecedented width and depth, representing both soil eDNA-metabarcoding and expert inventorying of fungal fruitbodies, we document for the first time the validity of eDNA as practical inventory method and measure of conservation value for fungi. Fruitbody data identified fewer species in total and per site, and had larger variance in site richness. Focusing on macrofungi - the class Agaricomycetes, and in turn the order Agaricales - metrics of total richness and compositional similarity converged between the methods. eDNA was suboptimal for recording the non-soil dwelling fungi. {beta}-diversity was similar between methods, but more variation in community composition could be explained by environmental predictors in eDNA data. The fruitbody survey was slightly better in finding red-listed species. We find a better correspondence between biodiversity indices derived from fungal fruitbodies and DNA-based approaches than indicated in earlier studies. We argue that (historical) fungal community data based on fruitbody forays - with careful selection of taxonomic groups - may be interpreted together with modern DNA-based approaches.

ecology↗

bioRxiv2018

Predicting provenance of forensic soil samples: soil DNA predicts habitat and environmental properties

Environmental DNA is increasingly applied in ecological studies, including forensic ecology where eDNA from soil can be used to pair samples or reveal sample provenance. We collected soil eDNA samples as part of a large national biodiversity research project across 130 sites in Denmark. We investigated the potential for soil eDNA in predicting provenance in terms of environmental conditions, habitat characteristics and geographic regions. We used linear regression for predicting environmental gradients of light, moisture, soil pH and nutrients (represented by Ellenberg Indicator Values, EIVs) and quadratic discriminant analysis (QDA) to predict habitat class and geographic region. We found high predictive power for environmental gradients (R2 > 0.73). The discriminatory power of QDA in predicting habitat characteristics varied from high accuracy in predicting certain forest types, less accurate prediction of heathland and poor accuracy for geographic region. We demonstrate the application of provenance prediction in forensic science by evaluating and discussing two mock crime scenes. Here, we supplement with plant species lists from annotated sequences. Where predictions of environmental gradients and habitat classes give an overall accurate description of a crime scene, care should be taken when interpreting annotated sequences, e.g. due to erroneous assignments in GenBank. The outlined approach clearly demonstrates that basic ecological information that can be extracted from soil eDNA, contributing to the range of potential applications of eDNA in forensic ecology.

ecology↗

bioRxiv2018

Vascular plants are strong predictors of multi-taxon species richness

Plants regulate soils and microclimate, provide substrate for heterotrophic taxa, are easy to observe and identify and have a stable taxonomy, which strongly justifies the use of plants as bioindicators in monitoring and conservation. However, insects and fungi make up the vast majority of species. Surprisingly, it remains untested whether plants are strong predictors of total multi-taxon species richness. 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 OTU richness from environmental DNA metabarcoding. Plant species richness per se was a moderate predictor of richness of other taxa. Taking an ecospace approach to modelling, the addition of plant-derived bioindicators 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.

ecology↗

bioRxiv2017

A systematic survey of regional multitaxon biodiversity: evaluating strategies and coverage

BackgroundIn 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 x 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.\n\nResultsDespite 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 %). Correlations among species richness for taxonomic groups were predominantly positive. 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. Species richness did not correlate well among taxa suggesting differential and complex biotic responses to environmental variation.\n\nConclusionsWe 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.

ecology↗