Biology subjects

Beermann, A. J.

Publications and source records attributed to Beermann, A. J..

7 recordsLinked to original sources

bioRxiv2025

Environmental DNA metabarcoding of invertebrate-incubated water supports WFD-compliant and animal-friendly bioassessment with added trait insights

Environmental (eDNA) metabarcoding is recently being considered for bioassessment under the Water Framework Directive (WFD). While tissue-based ("bulk") metabarcoding of macroinvertebrates produces comparable ecological status class values to morphology-based methods, eDNA-based metabarcoding often includes DNA signals from upstream sites, limiting its site-specificity. A promising alternative involves the incubation of locally collected invertebrates in water, followed by eDNA metabarcoding of the incubated water. In this study, we tested the suitability of two different approaches of the incubation strategy for ecological status assessment under the WFD. The first approach uses conventional multi-habitat sampling (MH) for the collection of the local macroinvertebrates and the second natural substrate exposures (NSEs) that are actively colonised. Using metabarcoding of the incubated water from both approaches (MH/NSE eDNA), we compared community composition, trait diversity and the derived ecological status classes (ESCs) to the local signal reference (MH/NSE bulk DNA) and the regional signal reference (stream water eDNA). For both approaches, community and trait composition were highly congruent between the incubated water and bulk samples. Trait composition did not differ between MH and NSE samples or among NSE types (wood-leaf vs. gravel). However, we detected small-scale spatial differences in the trait composition between NSEs placed at different flow regimes (pool vs. riffle). ESCs derived from all approaches (MH/NSE incubated water eDNA, MH/NSE bulk DNA and stream water eDNA) were highly similar and consistent with those from morpho-taxonomic assessments. Our findings support the incubation strategy using the conventional MH sampling as the most suitable approach for a minimally invasive, site-specific stream bioassessment within the context of the WFD.

ecology↗

bioRxiv2024

Fish predation induces drifting and emergence in an experimental stream mesocosm system

Predator-prey interactions are important drivers of adaptation in aquatic communities, shaping the behaviour of invertebrates with cascading effects on community dynamics. Behavioural responses, such as moving with the downstream current (drift) or altering the timing of emergence, can be initiated and reduces the risk of encountering predators. This study aimed to examine the effects of indirect and direct predation pressure on drift behaviour and emergence patterns of aquatic invertebrates. Using an experimental mesocosm setup (ExStream), we analysed how the number of drifting and emerging invertebrates changed with elevated levels of chemical cues from fish (indirect predation, Gasterosteus aculeatus and Cottus rhenanus) and subsequent additional direct predation by Cottus rhenanus over a 9-day period. Our findings show that most of the analysed invertebrate groups displayed noticeable responses to either indirect, direct, or both forms of predation. Furthermore, our study revealed a significant impact of predation on emergence patterns, reducing the number and the size of emergent invertebrates. Given the importance of drift and emergence in dispersion and in facilitating resource flows into terrestrial systems, our findings indicate a strong effect of predation on the communities.

ecology↗

bioRxiv2024

Salinisation and warming disrupt predator-induced drift behaviour in aquatic predator-prey interactions

Predators act as a major selective force impacting biological communities in riverine ecosystems. Often predation risk is mediated by chemical cues upon which prey species display distinct morphological or behavioural defences. For stream invertebrates, predator-induced behaviours can be drifting and hiding. However, anthropogenic stressors increasingly impact freshwater ecosystems, with predicted consequences on the chemical information transfer, potentially affecting anti-predator behaviour. Despite this, knowledge and research on the extent to which these stressors may affect evolved predator-induced behaviour and subsequent ecosystems is scarce. Therefore, we conducted an outdoor mesocosm experiment (ExStream system) at a lowland stream in Germany, in which we investigated the effects of direct and indirect fish predation on invertebrate communities under different stressor conditions. As stressors, we tested elevated salinity (ambient vs + 136 mg/L NaCl), elevated temperature (ambient vs. + 3.4{degrees}C), and the combination of both. Our findings reveal distinct predator-induced drift behaviour, characterised by a greater number of drifting invertebrates and a concurrent reduction in overall invertebrate numbers in the communities. Increased salinity and temperature hampered the predator-induced drift behaviour. Our results support the possibility that stressors negatively impact the preys ability to perceive predators presence and respond appropriately. This disruption may alter predator-prey relationships, thereby affecting communities and potentially ecosystem functions. Highlights[vrecto] We hypothesised that anthropogenic stressors disrupt predator-induced behaviours in invertebrate prey species. [vrecto]Predator-induced drift behaviour was experimentally studied under ambient and elevated salinity and temperature conditions. [vrecto]Fish exposure elicited predator-induced drift behaviour, which decreased the number of invertebrate individuals of the communities. [vrecto]Elevated salt and elevated temperatures alone and in combination did not induce drift behaviour. [vrecto]We found that both stressors disrupted predator-induced drift behaviour, altering the anti-predator response of invertebrate prey. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/601583v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1eef03borg.highwire.dtl.DTLVardef@1ddda7corg.highwire.dtl.DTLVardef@332bdaorg.highwire.dtl.DTLVardef@1842dbb_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

German-wide Malaise trap metabarcoding estimates over 33,000 insect species

Mitigating ongoing losses of insects and their key functions (e.g., pollination) requires accurately tracking large-scale and long-term community changes. However, doing so has been notoriously hindered by uniquely high insect species diversity that requires prohibitively high investments of time, funding, and taxonomic expertise. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1,815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 {euro} per sample, including supplies, labor and maintenance. With on average 1.4M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single OTU. We estimated another 21,403 plausible species, which likely either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany ([~]35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow ([~]80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.

ecology↗

bioRxiv2021

Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can often collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24%, and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 69% and 84%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called bycatch. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

molecular biology↗

bioRxiv2020

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

DNA metabarcoding is increasingly used in research and application to assess biodiversity. Powerful analysis software exists to process raw data. However, when it comes to the translation of sequence read data into biological information many end users with limited bioinformatic expertise struggle with the downstream analysis and explore data only to a minor extent. Thus, there is a growing need for easy-to-use, graphical user interface (GUI) analysis software to analyse and visualise DNA metabarcoding data. We here present TaxonTableTools (TTT), a new platform independent GUI software that aims to fill this gap by providing simple and reproducible analysis and visualisation workflows. TTT uses a so-called "TaXon table" as input. This format can easily be generated within TTT from two input files: a read table and a taxonomy table that can be obtained by various published metabarcoding pipelines. TTT analysis and visualisation modules include e.g. Venn diagrams to compare taxon overlap among replicates, samples or among different analysis methods. It analyses and visualises basic statistics such as read proportion per taxon as well as more sophisticated visualisation such as interactive Krona charts for taxonomic data exploration. Various ecological analyses such as alpha or beta diversity estimates, and rarefaction analysis ordination plots can be produced directly. Data can be explored also in formats required by traditional taxonomy-based analyses of regulatory bioassessment programs. TTT comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) and the Python package index (https://pypi.org/project/taxontabletools/).

bioinformatics↗

bioRxiv2019

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilization of metabarcoding in aquatic biomonitoring.

ecology↗