Biology subjects

Traugott, M.

Publications and source records attributed to Traugott, M..

9 recordsLinked to original sources

bioRxiv2025

Urbanisation and Habitat Shape Resource-Driven Dietary Shifts in Wild Birds

Urbanisation affects bird ecology and evolution, with changes in nutritional intake considered a key driver. However, most studies provide only snapshots of urban bird feeding ecology due to methodological limitations in analysing diets across space and time. Here, we address this gap by examining the diets of two common species with differing feeding ecologies: the great tit (Parus major) and blue tit (Cyanistes caeruleus). Diet samples from 370 birds, captured over a year at 147 locations across an urbanised landscape in Innsbruck, Austria, were molecularly analysed. Results revealed species-and season-specific diet patterns influenced by urbanisation: urban great tits exhibited higher diet diversity but reduced arthropod consumption during the breeding season, while urban blue tits compensated for lower moth intake by increasing their consumption of crab spiders and aphids. Prey consumption mirrored prey availability, highlighting resource-driven dietary shifts. Habitat type also played a significant role, with urban green spaces enhancing plant-based food diversity and residential areas increasing anthropogenic food consumption. These findings support the hypothesis that diet drives fitness and phenotypic differences between urban and rural bird populations. They highlight the need to consider both urbanisation levels and habitat characteristics to fully understand its ecological and evolutionary impacts.

ecology↗

bioRxiv2021

Evaluating 87Sr/86Sr isotope ratios and Sr mass fractions in otoliths of different European freshwater fish species as fishery management tool in an Alpine foreland with limited geological variability

The focus of this study was to assess the potential of otolith microchemistry as a fishery management tool for different European freshwater fish species in an Alpine foreland with a diverse range of different water bodies but low geological variation. 87Sr/86Sr isotope and Sr/Ca ratios in water samples from 26 habitat sites in a pre-alpine catchment region around lake Chiemsee, Germany, an important region for recreational and economic fisheries, were analysed. 87Sr/86Sr isotope ratios and the Sr mass fractions in otoliths of 246 fish out of 16 species were determined using (laser ablation) inductively coupled plasma mass spectrometry ((LA)-ICP-MS). Habitats could be discriminated into three distinct strontium isotope regions (SIGs) and seven clusters with characteristic 87Sr/86Sr isotope and Sr/Ca ratios. The direct comparison of 87Sr/86Sr isotope ratios in water and otolith samples allowed to identify fish that might have been a) migrating b) transferred from other water bodies or c) stocked from fish farms. Sr/Ca ratios in water and the Sr mass fraction in otoliths were highly correlated, although significant differences between species from the same environment could be documented. Sr mass fractions in sagittae of Perca fluviatilis were about 60 % of those in sagittae of Coregonus spp and of lapilli of roach Rutilus rutilus from the same habitats. Different partition factors for water to otolith Sr/Ca mass fractions were determined for different species. Discrimination of fish otoliths by 87Sr/86Sr isotope ratios and Sr mass fractions according to habitat clusters was possible with success rates ranging from 92 % to 100 % for cyprinids, European perch Perca fluviatilis, whitefish Coregonus spp. and European grayling Thymallus thymallus, and was 74 % for salmonids. Otolith microchemistry proved to have great potential to serve as a fishery management tool at smaller spatial scales such as in the studied Alpine foreland when considering the limited variation of 87Sr/86Sr isotope and Sr/Ca ratios, the type and spatial distribution of habitats, and the species and question under investigation. HighlightsO_LIOtolith microchemistry applied in in area with limited geological variability C_LIO_LIFish transferred, stocked or migrated were identified C_LIO_LIRegressions between Sr/Ca ratios in water predict Sr mass fractions in otoliths C_LIO_LISpecies specific Sr discrimination from water into otoliths C_LIO_LIEuropean freshwater fish species assigned to habitat clusters of origin C_LI

ecology↗

bioRxiv2020

Activity, energy use and species identity affect eDNA shedding in freshwater fish

The quantitative measurement of environmental DNA (eDNA) from field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids, and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity, and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which exhibited lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

ecology↗

bioRxiv2020

Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions

The use of sensitive methods is key for the detection of target taxa, from trace amounts of environmental DNA (eDNA) in a sample. In this context, digital PCR (dPCR) enables direct quantification and is commonly perceived as more sensitive than endpoint PCR. However, endpoint PCR coupled with capillary electrophoresis (celPCR) potentially embodies a viable alternative as it quantitatively measures signal strength in Relative Fluorescence Units (RFU). Provided comparable levels of sensitivity are reached, celPCR permits the development of cost-efficient multiplex PCRs, enabling the simultaneous detection of several target taxa. Here, we compared the sensitivity of singleplex and multiplex celPCR to dPCR for species-specific primer pairs amplifying mitochondrial DNA (COI) of fish species occurring in European freshwaters by analysing dilution series of DNA extracts and field-collected water samples. Both singleplex and multiplex celPCR and dPCR displayed comparable sensitivity with reliable positive amplifications starting at two to 10 target DNA copies per {micro}l DNA extract. celPCR was suitable for quantifying target DNA and direct inference of DNA concentrations from RFU was possible after accounting for primer effects. Furthermore, multiplex celPCRs and dPCRs were successfully used for the detection and quantification of fish-eDNA in field-collected water samples, confirming the results of the dilution series experiment and exemplifying the high sensitivity of the two approaches. The possibility of detection and quantification via multiplex celPCR is appealing for the cost-efficient screening of high sample numbers. The present results confirm the sensitivity of this approach thus enabling its application for future eDNA-based monitoring efforts.

molecular biology↗

bioRxiv2020

Scalable, rapid and highly sensitive isothermal detection of SARS-CoV-2 for laboratory and home testing

Global efforts to combat the Covid-19 pandemic caused by SARS-CoV-2 still heavily rely on RT-qPCR-based diagnostic tests. However, their high cost, moderate throughput and reliance on sophisticated equipment limit widespread implementation. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative detection method that has the potential to overcome these limitations. We present a rapid, robust, sensitive and versatile RT-LAMP based SARS-CoV-2 detection assay. Our forty-minute procedure bypasses a dedicated RNA isolation step, is insensitive to carry-over contamination, and uses a hydroxynaphthol blue (HNB)-based colorimetric readout, which allows robust SARS-CoV-2 detection from various sample types. Based on this assay, we have substantially increased sensitivity and scalability by a simple nucleic acid enrichment step (bead-LAMP), established a pipette-free version for home testing (HomeDip-LAMP), and developed open source enzymes that can be produced in any molecular biology setting. Our advanced, universally applicable RT-LAMP assay is a major step towards population-scale SARS-CoV-2 testing.

molecular biology↗

bioRxiv2020

Lateral and longitudinal fish eDNA distribution in dynamic riverine habitats

Assessing the status and distribution of fish populations in rivers is essential for management and conservation efforts in these dynamic habitats. Currently, methods detecting environmental DNA (eDNA) are being established as an alternative and/or complementary approach to the traditional monitoring of fish species. In lotic systems, a sound understanding of hydrological conditions and their influence on the local target detection probability and DNA quantity is key for the interpretation of eDNA-based results. However, the effect of seasonal and diurnal changes in discharge and the comparability of semi-quantitative results between species remain hardly addressed. We conducted a cage experiment with four fish species (three salmonid and one cyprinid species) in a glacier-fed, fish-free river in Tyrol (Austria) during summer, fall, and winter discharge situations (i.e. 25-fold increase from winter to summer). Each season, water samples were obtained on three consecutive days at 13 locations downstream of the cages including lateral sampling every 1-2 m across the wetted width. Fish eDNA was quantified by species-specific endpoint PCR followed by capillary electrophoresis. Close to the cages, lateral eDNA distribution was heterogenous and mirrored cage placement within the stream. In addition to the diluting effect of increased discharge, longitudinal signal changes within the first 20 m were weakest at high discharge. For downstream locations with laterally homogenous eDNA distribution, the signals decreased significantly with increasing distance and discharge. Generally, the eDNA of the larger-bodied salmonid species was less frequently detected, and signal strengths were lower compared to the cyprinid species. This study exemplifies the importance of hydrological conditions for the interpretation of eDNA-based data across seasons. To control for heterogenous eDNA distribution and enable comparisons over time, sampling schemes in lotic habitats need to incorporate hydrological conditions and species traits.

ecology↗

bioRxiv2020

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to the analysis of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, (e.g. "in silico analysis"), and arranged on a 5-level validation scale from "incomplete" to "operational" with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.

molecular biology↗

bioRxiv2017

Combining molecular gut content analysis and functional response models shows how body size affects prey choice in soil predators

O_LIPredator-prey interactions are a core concept of animal ecology and functional response models provide a powerful tool to predict the strength of trophic links and assess motives for prey choice. However, due to their reductionist set-up, these models may not display field conditions, possibly leading to skewed results.\nC_LIO_LIWe tested the validity of functional response models for multiple prey by comparing them with empirical data from DNA-based molecular gut content analysis of two abundant and widespread macrofauna soil predators, lithobiid and geophilomorph centipedes.\nC_LIO_LIWe collected soil and litter dwelling centipedes, screened their gut contents for DNA of nine abundant decomposer and intraguild prey using specific primers and tested for different prey and predator traits explaining prey choice. In order to calculate the functional response of same predators, we used natural prey abundances and functional response parameters from published experiments and compared both approaches.\nC_LIO_LIMolecular gut content results showed that prey choice of centipedes is driven by predator body size and prey identity. Results of functional response models significantly correlated with results from molecular gut content analysis for the majority of prey species.\nC_LIO_LIOverall, the results suggest that functional response models are a powerful tool to predict trophic interactions in soil, however, species-specific traits have to be taken into account to improve predictions.\nC_LI

ecology↗

bioRxiv2017

Comparing three types of dietary samples for prey DNA decay in an insect generalist predator

The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors, however the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, feces and whole consumers (including their gut contents) at different time points post-feeding. All dietary samples were analyzed using multiplex PCR targeting three different length DNA fragments (128 bp, 332 bp and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers prey DNA was detectable significantly longer for all fragment sizes than for feces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from feces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and feces constitute an interesting, non-lethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.

ecology↗