Florian Leese

University of Duisburg-Essen | uni-due · Aquatic Ecosystem Research

The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water...

Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environm...

Background: The actual connectivity between populations of freshwater organisms is largely determined by species biology, but is also influenced by many area- and site-specific factors, such as water pollution and habitat fragmentation. Therefore, the prediction of effective gene flow, even for well-studied organisms, is difficult. The amphipod cr...

Restriction-site associated DNA sequencing (RAD) has emerged as a powerful marker system for study-ing genome-wide DNA polymorphisms using next-genera-tion sequencing. A recent technical facilitation of RAD is double-digest RAD (ddRAD), which utilizes two restriction enzymes for library preparation. The more flexible and balanced ddRAD allows analy...

Environmental DNA (eDNA) metabarcoding has become a powerful tool for examining fish communities. Prior to the introduction of eDNA-based assessments into regulatory monitoring contexts (e.g., EU Water Framework Directive), there is a demand for meth-odological standardization. To ensure methodical accuracy and to meet regulatory standards , variou...

Background Fungicides are frequently used in agriculture and can enter freshwater ecosystems through multiple pathways. The negative impacts of fungicides on microorganisms, fungi in particular, and their functions such as leaf decomposition have been repeatedly shown. In our previous microcosm experiment with three consecutive cycles of fungicide...

Pesticides are major agricultural stressors for freshwater species. Exposure to pesticides can disrupt the biotic integrity of freshwater ecosystems and impair associated ecosystem functions. Unfortunately, physiological mechanisms through which pesticides affect aquatic organisms are largely unknown. For example, the widely-used insecticide chlora...

Deutsch: Die Kombination aus räumlich und zeitlich hoch aufgelösten Verfahren auf der Basis von Umwelt-DNA (engl. eDNA) und klassischen fischereilichen Methoden ermöglicht ein effizienteres Fischzönosen-Monitoring. So könnte beispielsweise eine jährliche Überprüfung der Gewässer mittels eDNA- Beprobungen die in 2- bis 3-jährlichen Zyklen durchgefüh...

Insects are unique in terms of their high species diversity and deliver key ecological functions. Despite this importance, we know little about true species numbers and biodiversity trends for most insect orders. A key limitation is a lack of time, funding and taxonomic expertise needed to identify the huge number of often small species, of which m...

Most empirical metacommunity studies rely solely on morphological identification of taxa, precluding the species-level identification of several biotic groups, which can influence the characterization of metacommunities. DNA metabarcoding enables inference of species and even intraspecific diversity from community samples but has rarely been used t...

Environmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort and cost. However, eDNA-based species detection in streams and rivers may be influenced by sampling season, location, and other key factors such as water temperature and d...

Environmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort and cost. However, eDNA-based species detection in streams and rivers may be influenced by sampling season, location, and other key factors such as water temperature and d...

Reliable biodiversity data are crucial for environmental research and management. Unfortunately, data paucity prevails for many regions and organismal groups such as aquatic invertebrates. High-throughput DNA-based identification, in particular DNA metabarcoding, has accelerated biodiversity data generation. However, in the process of metabarcoding...

Environmental DNA (eDNA) metabarcoding has become a powerful tool for examining fish communities. The demand for methodological standardization and the implementation of eDNA-based assessments into the regulatory monitoring (e.g., Water Framework Directive) are imminent. To ensure methodical accuracy and to meet regulatory standards, various sampli...

Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a...

Background Freshwaters are exposed to multiple anthropogenic stressors, leading to habitat degradation and biodiversity decline. In particular, agricultural stressors are known to result in decreased abundances and community shifts towards more tolerant taxa. However, the combined effects of stressors are difficult to predict as they can interact i...

Metropolitan research requires multidisciplinary perspectives in order to do justice to the complexities of metropolitan regions. This volume provides a scholarly and accessible overview of key methods and approaches in metropolitan research from a uniquely broad range of disciplines including architectural history, art history, heritage conservati...

DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA‐based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates...

Forest canopies are highly diverse ecosystems, 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...

Background: Microbes are increasingly (re)considered for environmental assessments because they are powerful indicators for the health of ecosystems. The complexity of microbial communities necessitates powerful novel tools to derive conclusions for environmental decision-makers, and machine learning is a promising option in that context. While amp...

In recent years, metropolitan areas are expanding faster than ever, largely affecting neighboring biodiversity and even forming an ecosystem of its own inhabited by often peculiar fauna and flora. Ongoing urbanization is known to affect the metropolitan biodiversity by altering the available habitats, causing biotic homogenization, and introducing...

The increasing production, use and emission of synthetic chemicals into the environment represents a major driver of global change. The large number of synthetic chemicals, limited knowledge on exposure patterns and effects in organisms and their interaction with other global change drivers hamper the prediction of effects in ecosystems. However, r...

DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets increases exponentially. To date no published DNA metabarcoding data processing pipeline exists that is i) platform independent, ii) easy to use (incl. GUI), iii) fast (does scale well with dataset size), and iv)...

Gelatinous zooplankton (GZP; including salps and cnidarians) are reputed to be climate change winners. This so-called “jellification” is affecting several marine ecosystems worldwide, including the Southern Ocean (SO) in particular which has undergone a significant shift from a krill-based to a salp-based ecosystem over the last decades. A better k...

Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration o...

Water flow in river networks is frequently regulated by man‐made in‐stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in‐stream barriers exist worldwide, their impact on dispersal of macroinvertebrates remains unclear. Therefore, we...

Background The emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing numb...

Background The emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing numb...

1. Forest 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 applicatio...

The cover image is based on the Viewpoint A global agenda for advancing freshwater biodiversity research by Alain Maasri et al., https://doi.org/10.1111/ele.13931. Image Credit: Solvin Zankl. image

Many studies in different ecosystems have shown that stressors co-occur and interact with each other to influence organisms. In river networks, local stressors change the quantity and quality of the material that subsidizes downstream sections. However, most of the multiple stressor research has focused on the effects of stressors at the place of t...

This publication is an output from EU COST Action DNAqua-Net (CA 15219 - Developing new genetic tools for bioassessment of aquatic ecosystems in Europe) and would not have been possible without the opportunities for international collaboration provided by the network, supported by COST (European Cooperation in Science and Technology). Therefore, ou...

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global...

The Mediterranean region with its islands is among the 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...

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples....

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this PCR amplification is carried out with primers designed to target a taxonom...

Intermittent rivers and ephemeral streams (IRES) – waterways in which flow ceases periodically or that dry completely – are found worldwide, and their frequency and extent are expected to increase in the future in response to global climate change and growing anthropogenic demand for fresh water. Repeated wet–dry cycles generate highly dynamic sett...

Reliable and comprehensive monitoring data are required to trace and counteract biodiversity loss. High-throughput metabarcoding of DNA extracted from community samples (bulk) or from water or sediment (environmental DNA) has revolutionized biomonitoring, given the capability to assess biodiversity across the tree of life rapidly with feasible effo...

Most metabarcoding protocols for invertebrate bulk samples start with sample homogenisation, followed by DNA extraction, amplification of a specific marker region, and sequencing. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist, yet, no clear recommendation for the basis of almost all me...

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 landsc...

Ziel der biologischen Systematik ist es, die Vielfalt der Organismen zu ordnen und zu benennen. Die Systematik beschäftigt sich mit der Einteilung (Taxonomie), Benennung (Nomenklatur) und Bestimmung von Lebewesen. Die Rekonstruktion der Stammesgeschichte (Phylogenie) und die Aufklärung der Prozesse und Mechanismen, die zur heutigen Vielfalt der Leb...

Die Gesamtheit des Erbmaterials eines Organismus wird als Genom bezeichnet, die Gesamtheit der transkribierten, also abgelesenen und in RNA übersetzten Sequenzen als Transkriptom. Werden Organismengesellschaften mit vielen Individuen und verschiedenen Arten betrachtet spricht man von Metagenomen und Metatranskriptomen. Die genetische Information in...

Zu den wichtigsten Voraussetzungen in der Populationsgenetik zählen sogenannte Nullmodelle, die Erwartungswerte unter neutralen Bedingungen, also ohne den Einfluss von Evolutionsfaktoren, formulieren. Mit diesen Erwartungswerten kann man beobachtete Werte vergleichen und die Abweichungen statistisch quantifizieren. Die Hardy-Weinberg-Regel, auch al...

DNA metabarcoding is a powerful tool to assess arthropod diversity in environmental bulk samples such as Malaise trap, pitfall trap, or hand net samples. While comparative performance tests for different extraction protocols, primers, and Taq polymerases have been made, the effect of different PCR volumes on bulk sample metabarcoding performance is...

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 fre...

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to detect plant and animal taxa in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to...

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 landsc...

Freshwater biodiversity is declining dramatically, and the current biodiversity crisis requires defining bold goals and mobilizing substantial resources to meet the challenges. While the reasons are varied, both research and conservation of freshwater biodiversity lag far behind efforts in the terrestrial and marine realms. We identify fifteen pres...

Abstract 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 freshwater ecosystems act as sinks in the landscap...

Dear participants of DNAQUA2021 International Conference, Undoubtedly, DNAQUA2021 is a major highlight of the EU COST Action DNAqua-Net (CA15219). Even though we cannot claim that the organisation of DNAQUA2021 was a piece of cake, it is simply wonderful to see the great interest in this event. With 1,498 registered participants from 79 nations, 20...

DNA metabarcoding is an efficient tool to characterize invertebrate species composition in environmental samples. Most metabarcoding protocols for invertebrate bulk samples start with sample homogenization, followed by DNA extraction, amplification of a specific marker region and sequencing on a high-throughput sequencer. Many of the above-mentione...

Streams and rivers represent hotspots of biodiversity in their natural state. This biodiversity is declining worldwide due to pollution, exploitation and hydromorphological degradation of these systems. One of the last big, natural rivers in Europe is the Vjosa in the Balkan region. The catchment is characterized by natural flow dynamics, resulting...

The Balkan endemic caddisfly species Drusus osogovicus Kumanski, 1980 that was previously known only from Bulgaria was recently reported from the Republic of North Macedonia as well. However, all data on the presence of the species included only adult specimens as the larval stage remained unknown. In the following study we present the first descri...

Environmental DNA (eDNA) metabarcoding is a new, promising, and non-invasive method to detect biodiversity in aquatic environments. So far, it has mainly been used to screen for fish and amphibian diversity and rarely to detect macroinvertebrates. Typically, DNA metabarcoding relies on PCR amplification of a fragment of the mitochondrial cytochrome...

DNA-based identification methods, such as DNA metabarcoding, are increasingly used as biodiversity assessment tools in research and environmental management. Although powerful analysis software exists to process raw data, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with li...

The Joint Danube Survey (JDS) is a multinational effort in monitoring Danube’s water quality, including its major tributaries. The Danube river stretches over a distance of 2,800 km and flows through or borders 10 different countries to which it is of utter importance as a source of potable water and hydrodynamic power. The JDS is conducted every 6...

Recent studies on diversity of stream amphipods proposed that the Western Carpathians have served as an important glacial refugium of freshwater fauna. If this scenario is true, a considerably high molecular diversity can be expected in this biogeographic region also for other taxa. In our project, we aimed to uncover and characterize molecular div...

Multiple stressors diversely and often adversely affect stream ecosystems around the globe. Therefore, understanding multiple stressor effects on different organisms is essential for a better ecosystem understanding, an accurate water quality assessment and improved ecosystem management. However, while multiple stressor effects should be assessed a...

Bulk macroinvertebrate DNA metabarcoding is proven a useful tool for routine assessment of freshwater ecosystems. Following a small scale study in 2017, using 18 samples from Finland Elbrecht et al. 2017, sampling and metabarcoding efforts were extended to a total of 297 official monitoring samples from Denmark, Sweden, Norway, Iceland, and Finland...

The aim of this pilot study was to investigate the potential of eDNA techniques to detect the presence of the two dragonfly species Cordulegaster heros and Cordulegaster bidentata. Both species are classified as “near threatened” according to the IUCN Red List and are strictly protected in several countries. Monitoring these species with traditiona...

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have...

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated wit...

Freshwater biodiversity is declining dramatically, and the current biodiversity crisis requires defining bold goals and mobilizing substantial resources to meet the challenges. While the reasons are varied, both research and conservation of freshwater biodiversity lag far behind efforts in the terrestrial and marine realms. We identify fifteen pres...

Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms it is challenging to follow intraspecific dynamics over space and time. We propose a new method, Microsatellite PoolSeq Barcoding (MPB), for tracing allele frequency changes in protist populatio...

A recent global meta‐analysis reported a decrease in terrestrial but increase in freshwater insect abundance and biomass (van Klink et al., Science 368, p. 417). The authors suggested that water quality has been improving, thereby challenging recent reports documenting drastic global declines in freshwater biodiversity. We raise two major concerns...

DNA metabarcoding is increasingly used as a tool to assess biodiversity in research and environmental management. Powerful analysis software exists to process raw data. However, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the...