Biology subjects

Macher, T.-H.

Publications and source records attributed to Macher, T.-H..

8 recordsLinked to original sources

bioRxiv2026

eDNA metabarcoding provides scalable and continuous biodiversity monitoring across the tree of life

Environmental DNA (eDNA) metabarcoding has the potential to substantially expand our knowledge of global biodiversity beyond that provided by conventional approaches. However, the degree to which eDNA data provides real ecological insight, rather than primarily reflecting environmental factors that affect eDNA shedding and degradation, remains unclear. Additional uncertainties arise in terms of cost-effectiveness and whether the price is worth any extra biodiversity information that is gleaned. Here, we established a high-resolution, bi-weekly eDNA time-series in Germany across aquatic and riparian habitats to quantify seasonal biodiversity dynamics, to relate eDNA to different potential environmental drivers, and to parametrize cost estimates. Over one year, eDNA metabarcoding detected more than 1,000 species across multiple trophic levels and primarily revealed real, taxon-specific seasonal patterns, in addition to some relationships to water temperature, discharge, and conductivity. Compared to historical records dating back to 1891, year-round eDNA monitoring increased reported species numbers by 2.4-fold for invertebrates, 2.2-fold for mammals, 1.7-fold for diatoms, 1.2-fold for fish and lamprey, and 1.03-fold for birds. Cumulative biodiversity estimates increased strongly with sampling frequency, demonstrating the value of eDNA for high-frequency time-series monitoring. Moreover, eDNA monitoring was highly cost-effective, providing more than twice the biodiversity information of many conventional surveys for one-sixth the cost, enabling scalable, high-resolution freshwater biodiversity assessments.

ecology↗

bioRxiv2025

Unraveling long-term trends and drivers of fish biodiversity change using environmental DNA metabarcoding of archived samples

AbstractLong-term biodiversity data are critical for assessing, understanding, and predicting ecosystem change globally, but are often limited by their availability. We present the longest eDNA metabarcoding time series for freshwater fishes based on archived suspended particulate matter (SPM) from Germanys Environmental Specimen Bank, covering 17 years (2005-2021) across six major European river systems (Rhine, Danube, Elbe, and their tributaries). From 211 annual samples collected according to highly standardized procedures at 13 sites, we detected 63 fish and lamprey species and traced their spatio-temporal trajectories. eDNA metabarcoding captured significantly declining trends at multiple sites with no recoveries. Common and sensitive species declined at nearly half of sites while invasive species spread. Site occupancy and relative read abundance trends were correlated, providing semi-quantitative indicators. Alpha and beta diversity shifted over time and Bayesian hierarchical models revealed that 19% of species showed significant declines in relative read abundance. The eDNA-derived trends showed strong concordance with long-term regulatory fish monitoring data, validating the patterns across methodological approaches. Random forest models and multivariate analyses identified multiple anthropogenic pollutants, measured from the same SPM samples, as drivers of biodiversity patterns. Pesticides, heavy metals, temperature, and fine sediment negatively affected species richness, with site-specific stressor combinations explaining 29% of community variation. Our results demonstrate that archived SPM, originally collected for chemical monitoring, provides a reliable, dual-purpose monitoring matrix integrating pollution and biodiversity trend assessments simultaneously. This approach enables holistic monitoring of global freshwater ecosystem change and can provide an early warning framework supporting evidence-based environmental management.

ecology↗

bioRxiv2025

Globally unified analysis of riverine eDNA reveals common associations of fish biodiversity with drainage characteristics

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here, we present one of the first global assessments and unified analyses of riverine fish biodiversity using environmental DNA (eDNA) collected from 1818 sites across 113 river systems. We quantified species richness, functional redundancy, phylogenetic diversity, and genetic sequence diversity, and related them to drainage characteristics. Our results showed that eDNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and human activities in shaping biodiversity-area relationships. Catchments in warmer climates consistently enhanced biodiversity accumulation with area, while higher human activity intensity weakened this scaling. Species richness, functional, and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity showed the strongest negative effects in smaller catchments with these impacts diminishing as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients. Our findings demonstrate the power of eDNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

ecology↗

bioRxiv2025

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

The analysis of environmental DNA (eDNA) has revolutionized biodiversity assessments in aquatic ecosystems, enabling non-invasive monitoring of fish communities across diverse regions. However, the global comparability of these eDNA datasets remains ambiguous due heterogeneous sampling protocols and bioinformatic workflows across studies, particularly regarding the robustness of their conclusions on biodiversity assessments. Here, we conducted a meta-analysis of 58 riverine fish eDNA metabarcoding datasets, covering 1,818 sampling sites worldwide, to evaluate the robustness of eDNA-derived biodiversity patterns. We found that species richness estimates and metrics of community structure derived under a common bioinformatic workflow were overall consistent with those of original analyses, despite the relatively high variability in bioinformatic analyses in the respective original studies. Contrastingly, congruence of species identity varied more extensively across datasets, mostly reflecting different completeness and regional relevance of reference databases. Restricting taxonomic assignment to basin-specific species pools improved species identification accuracy, while datasets lacking publicly accessible or well-curated reference data were more prone to mismatches. Year of sampling had a positive effect on taxonomic congruence, such that more recent studies showed increased robustness, also reflecting improved reference database coverage and enhanced species-level identification over time and overall method congruence in more recent years. Overall, the suitability and potential of eDNA for global biodiversity monitoring is corroborating overall robust biodiversity estimates, irrespective of the bioinformatic approaches. Our study underlines the effectiveness and need of further harmonization of bioinformatic workflows and strengthened region-specific reference databases for improved taxonomic resolution and comparability across studies.

ecology↗

bioRxiv2022

It`s raining species: Rainwash eDNA metabarcoding as a minimally invasive method to assess tree canopy invertebrate diversity

O_LIForest canopies are a highly diverse ecosystem, but despite several decades of intense research, there remain substantial gaps in our knowledge of their biodiversity and ecological interactions. One fundamental challenge in canopy research is the limited accessibility of the ecosystem. Consequently, previous studies have relied on the application of either highly invasive methods such as chemical knockdown, or on time-consuming and expensive setups such as canopy walkways or cranes. Therefore, time- and cost-efficient, ideally minimally invasive yet comprehensive applications are required to help close this knowledge gap. High-throughput metabarcoding of environmental DNA (eDNA) collected from water, soil, or air provides a minimally invasive method for biodiversity assessment, yet its potential for canopy biodiversity monitoring has not been explored. C_LIO_LIHerein, we conducted metabarcoding of eDNA washed off the canopy via rainwater to explore its monitoring potential. We placed four 1 m2 rain samplers beneath the canopies of four different tree taxa prior to a major rain event, filtered eDNA from the collected rainwater, and performed cytochrome c oxidase subunit I (COI) metabarcoding to profile the invertebrate community. Additionally, we collected and identified all specimens present in the rainwater for verification. C_LIO_LIWe detected 50 invertebrate species by eDNA metabarcoding, of which 43 were not physically present in the water sample, thus likely representing true canopy biodiversity signals. Furthermore, we observed distinct species occurrence patterns corresponding to the four tree taxa, suggesting that ecological patterns such as host specificity can be assessed using the method. C_LIO_LIIn conclusion, our study provides a proof of principle that rainwash eDNA metabarcoding offers a minimally invasive and comprehensive method for tree canopy diversity monitoring. C_LI

molecular biology↗

bioRxiv2021

Fresh insights into Mediterranean biodiversity: Environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

The Mediterranean region with its islands is among top biodiversity hotspots. It houses numerous freshwater taxa with a high rate of endemism, but is heavily impacted by anthropogenic pressures and global climate change. To conserve biodiversity, reliable data on species and genetic diversity are needed especially for the scarcely known insular freshwater ecosystems. Environmental DNA metabarcoding provide a straight-forward opportunity to assess aquatic biodiversity. Therefore, we conducted the first eDNA metabarcoding study in one stream catchment on Sicily. Specifically, we aimed to i) investigate spatial diversity patterns of macroinvertebrate communities, ii) assess seasonal changes, and iii) check if dispersal barriers can be identified. Water samples were taken at 27 different sites in two seasons and eDNA metabarcoding performed using the COI gene. In total, we detected 98 macroinvertebrate species, including 28 taxa potentially new to Sicily. Exact sequence variant (ESV) and species composition data showed that diversity differed between seasons with less taxa detected in winter. We also detected a dispersal barrier, which had a stronger effect in autumn. Our findings show that eDNA metabarcoding provides valuable information on Sicilian freshwater biodiversity. We therefore encourage its application for understudied regions to better understand the state and dynamics of freshwater biodiversity.

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↗