A5006011875- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Genomics and Phylogenetic Studies
- Identification and Quantification in Food
- Freshwater macroinvertebrate diversity and ecology
- Mycobacterium research and diagnosis
- Species Distribution and Climate Change
- Molecular Biology Techniques and Applications
- Fish Ecology and Management Studies
- Myxozoan Parasites in Aquatic Species
- Aquatic Invertebrate Ecology and Behavior
- Insect and Arachnid Ecology and Behavior
- Advanced biosensing and bioanalysis techniques
- Marine Ecology and Invasive Species
- Genetic diversity and population structure
- Coral and Marine Ecosystems Studies
- Hydrology and Sediment Transport Processes
- Single-cell and spatial transcriptomics
- Lepidoptera: Biology and Taxonomy
- Invertebrate Taxonomy and Ecology
- GABA and Rice Research
- Bacteriophages and microbial interactions
University of Duisburg-Essen
2016-2023
Zoological Research Museum Alexander Koenig
2019-2022
University of Guelph
2017-2021
ETH Zurich
2021
Centre for Biodiversity Genomics
2019
Genomics (United Kingdom)
2019
Ruhr University Bochum
2013-2018
Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from environmental sample and comparison reference database. However, no consensus has emerged regarding laboratory pipelines screen species diversity infer abundances samples. In particular, the effect primer bias detection limit for specimens with low biomass not been systematically examined, when processing samples bulk. We developed tested DNA...
Summary DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large‐scale studies have compared performance with that routine morphological identification. We performed using four primer sets on macroinvertebrate samples from 18 sites across Finland. The were collected 2013 and identified based morphology as part a Finnish monitoring program. Specimens morphologically classified, following standardised protocols, to lowest taxonomic...
A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses environmental conditions. However, generating accurate macroinvertebrate inventories based larval morphology difficult error-prone. Here, DNA metabarcoding provides new opportunities. Its potential accurately identify invertebrates bulk samples species level, has been...
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa maximize recovery. Despite this fact, performance employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests 36 on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs 21 most promising...
Abstract Environmental bulk samples often contain many different taxa that vary several orders of magnitude in biomass. This can be problematic DNA metabarcoding and metagenomic high‐throughput sequencing approaches, as large specimens contribute disproportionately high amounts template. Thus, a few biomass will dominate the dataset, potentially leading to smaller remaining undetected. Sorting by specimen size (as proxy for biomass) balancing tissue used per fraction should improve detection...
Abstract Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it often difficult to detect all the species present in a bulk sample. In particular, sequence recovery given depends on its biomass and mitome copy number as well primer set employed PCR. To examine these variables, we constructed mock community of terrestrial arthropods comprised 374 species. We used this how was impacted when amplicon pools were four ways. The first two protocols involved...
Abstract Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through require sophisticated processing of high‐throughput sequencing data from taxonomically informative barcodes. Various sets universal and taxon‐specific primers have been developed, extending the usability across archaea, bacteria eukaryotes. Accordingly, multitude analysis tools pipelines also developed. Often,...
Species diversity of metazoan bulk samples can be rapidly assessed using cytochrome c oxidase I (COI) metabarcoding. However, in some applications often only degraded DNA is available, e.g. from poorly conserved museum specimens, environmental (eDNA) filtered water or gut content analyses. Here universal primer sets targeting a short COI fragment are advantageous, as they still amplify fragments. Using PrimerMiner, we optimised two freshwater macroinvertebrates based on NCBI and BOLD...
DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput instruments are fairly common, usually requiring reads be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity the process. While Cytochrome c oxidase subunit I (COI) haplotype limited resolving it nevertheless often useful e.g. a phylogeographic context, helping formulate hypotheses taxon distribution and...
Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and large reference database. However, when used metabarcoding, estimation taxa abundances species detection are limited due to primer bias caused by highly variable binding sites across the COI gene. Therefore, we explored ability 16S ribosomal gene as an alternative metabarcoding level assessments. Ten bulk samples, each containing equal amounts tissue from 52 freshwater...
Abstract The viability of DNA metabarcoding for assessment freshwater macrozoobenthos has been demonstrated over the recent years. method matured to a stage where it can be applied monitoring at large scale, keeping pace with increased high‐throughput sequencing capacity. However, workflows and sample tagging need optimised accommodate hundreds samples within single run. Here, we conceptualise streamlined workflow, in which are processed 96‐well plates. Each is replicated starting tissue...
Summary Land‐use changes have degraded ecosystems worldwide. A particular concern for freshwater biodiversity and ecosystem function are stressors introduced by intensified agriculture. Typically several affect simultaneously. However, the combined effects of these multiple on streams rivers still poorly understood, yet critical importance to improve management. We investigated responses benthic macroinvertebrates three globally important agricultural affecting (nutrient enrichment, fine...
Summary DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing standardized gene marker region. Its success often limited due variable binding sites that introduce amplification biases. Thus, the development of optimized primers for communities or taxa under study in certain geographic region and/or ecosystems critical importance. However, no obtaining processing reference sequence data bulk can serve as backbone primer design currently available. We...
A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses environmental conditions. However, generating accurate macroinvertebrate inventories based larval morphology difficult error-prone. Here, DNA metabarcoding provides new opportunities. Its potential accurately identify invertebrates bulk samples species level, has been...
Abstract DNA metabarcoding of freshwater communities typically relies on PCR amplification a fragment the mitochondrial cytochrome c oxidase I (COI) gene with degenerate primers. The advantage COI is its taxonomic resolution and availability an extensive reference database. However, when universal primers are used environmental (eDNA) isolated from water, benthic invertebrate read OTU numbers “watered down,” that is, under represented, compared to whole specimen “bulk samples” due greater...
Abstract Riparian forests are commonly advocated as a key management option to mitigate the effects of agriculture on headwater stream biodiversity and ecosystem functions. However, benefits riparian might be reduced by uninterrupted catchment‐scale pollution. We studied land use multiple ecological endpoints in streams an agricultural landscape. habitat characteristics, water temperature algal accrual, macrophyte, benthic macroinvertebrate fish communities 11 paired forested open reaches...
Chironomids, or non-biting midges, often dominate stream invertebrate communities in terms of biomass, abundance, and species richness play an important role riverine food webs. Despite these clear facts, the insect family Chironomidae is treated as a single ecological studies bioassessments given difficulty to determine specimens further. We investigated stressor responses chironomid operational taxonomic units (OTUs) three globally stressors (increased salinity, fine sediment reduced water...
A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses environmental conditions. However, generating accurate macroinvertebrate inventories based larval morphology difficult error-prone. Here, DNA metabarcoding provides new opportunities. Its potential accurately identify invertebrates bulk samples species level, has been...
Over the last decade, steady advancements have been made in use of DNA-based methods for detection species a wide range ecosystems. This progress has culminated molecular monitoring being employed several enforceable management purposes endangered, invasive, and illegally harvested worldwide. However, routine application to monitor whole communities (typically metabarcoding approach) order assess status ecosystems continues be limited. In aquatic ecosystems, limited is particularly true...
Metabarcoding is increasingly used to assess species diversity by high-throughput sequencing where millions of sequences can be generated in parallel and multiple samples analysed one run. Generating amplified fragments with a unique sequence identifier ('tag') for each sample crucial, as it allows assigning the original samples. The tagging through so-called fusion primers fast cheap alternative commercially produced ligation-based kits. However, little known about potential bias...
Freshwater biomonitoring programmes routinely sample aquatic macroinvertebrates. These samples are time-consuming to collect, as well challenging and costly identify reliably genus or species. Environmental DNA (eDNA) metabarcoding has emerged a surrogate traditional collection techniques been used in whole-community approaches across several taxa ecosystems. However, the usefulness of eDNA-based detection freshwater macroinvertebrates not extensively explored. Few studies have directly...