Kathrin Theissinger

Environmental DNA (eDNA) metabarcoding is a widely used approach for biodiversity assessments across ecosystems. In aquatic environments, eDNA is typically collected via active water filtration, which requires specialized equipment and is challenging in turbid waters. This study evaluates the efficiency of an alternative method for lentic (standing) freshwaters based on passive eDNA sampling by submersing low‐cost DNA traps equipped with three collection materials (cellulose nitrate, glass fiber, and coffee filters) in a freshwater pond. We directly compared the results with active filtration performed at the same time and locations. Freshwater communities were identified with a multiplex PCR approach targeting macrophytes, macroinvertebrates, and vertebrates. Results showed that passive sampling was overall comparable to active filtration for detecting macrophyte species, with no significant differences in ASV counts, species richness, or Shannon diversity. For vertebrates, passive sampling recovered similar species richness and ASV counts, although active filtration yielded higher Shannon diversity. For macroinvertebrates, active filtration recovered significantly higher species richness and Shannon diversity than passive sampling in this study system, while overall macroinvertebrate recovery in both methods was likely constrained by marker choice and sampling effort. Furthermore, no significant differences in eDNA capture efficiency were found among the tested collection materials, including the low‐cost paper from coffee filters. We conclude that, due to the ease of field deployment coupled with merging of multiple low‐cost field replicates in the lab, passive sampling with DNA traps offers scalability and flexibility, thereby providing a cost‐ and time‐efficient alternative to active filtration for extensive freshwater biodiversity monitoring.

Background: Repetitive elements, particularly satellite DNA (satDNA), play a significant role in genome evolution and organisation. However, their diversity and evolutionary dynamics remain poorly understood in non-model organisms. Freshwater crayfish (Decapoda, Astacidea) have large genomes with a high chromosome number and are rich in satDNAs. This makes them attractive for studying the impact of satDNA on genome evolution. Results: In this study, we investigated the repetitive genomic landscape of 19 species representing four freshwater crayfish families. Our analysis revealed a high proportion of repetitive DNA in all studied species, with the total repeat content ranging from 30% to 66%. The number of satDNA families was remarkably high (54–622 families per species), with minisatellites (< 100 bp) forming the largest component of the satellitome. Family-specific patterns emerged: Astacidae and Cambaroididae showed the highest satDNA proportions, while Cambaridae and Parastacidae were dominated by Class I transposable elements. Species of the family Parastacidae showed the largest number of unique satDNA clusters and were clearly separated from other families, reflecting their phylogenetic divergence and distinct biogeographic history. We identified specific satDNAs conserved across all species, among them the PlSAT3-411, pointing to their important functional roles as pericentromeric satDNA. Conclusion: This study provides the first comprehensive comparative analysis of satDNA in freshwater crayfish. Our results highlight the dynamic nature of repetitive DNA and underscore its importance in genome organisation and evolutionary history.

In recent years, European countries have intensified efforts to control or limit the spread of invasive freshwater crayfish and the crayfish plague pathogen Aphanomyces astaci , while working to conserve native species such as the noble crayfish ( Astacus astacus ). Although crayfish shed relatively low amounts of DNA into their environment, environmental DNA (eDNA) approaches have proven effective for detecting their presence. A range of protocols and equipment is currently used in eDNA‐based monitoring of freshwater crayfish. To evaluate how methodological variation influences detection accuracy, we conducted the first European interlaboratory ring test using eDNA to detect A. astacus , the invasive signal crayfish Pacifastacus leniusculus , a chronic carrier of A. astaci , and the pathogen itself. The aim is to harmonize monitoring methods for crayfish and disease surveillance across laboratories. Eleven teams from thirteen European countries participated, each using its own equipment and protocols to collect and filter water from indoor tanks and outdoor ponds where the presence of A. astacus and P. leniusculus had been experimentally manipulated, as well as from a natural lake containing a P. leniusculus population. The resulting samples were analyzed in each team's laboratory. Despite methodological differences, all teams successfully detected DNA from both crayfish species in indoor tanks (3–10 crayfish/m ³ ). However, detection accuracy declined in outdoor ponds where crayfish density was an order of magnitude lower (0.32 crayfish/m ³ ). Detection was most variable for A. astaci , likely due to its very low prevalence in the host stock. Our study demonstrates the challenges of achieving consistent eDNA results across laboratories and highlights the importance of interlaboratory comparisons. It also underscores the need to identify sources of variability and error, an essential step toward developing robust and standardized protocols. This multinational intercalibration and exchange of knowledge improved methodology and enhanced reliability in crayfish detection.

Biological invasions contrast with reintroduction projects, where native species are deliberately returned to their natural habitat to restore local biodiversity. Such a reintroduction project is being carried out in the Upper Rhine Valley with the European pond turtle (Emys orbicularis) in the transbordering region between Lauterbourg (France) and Neuburg am Rhein (Germany), hereafter referred as Neu-Woerr. Several ponds have been created to benefit the dispersal of reintroduced turtles. However, this pondscape has been recently widely invaded by the calico crayfish (Faxonius immunis) and partly by the zebra mussel (Dreissena polymorpha). These two invasive non-native species decrease the overall habitat quality due to the massive exploitation of phytoplankton by the zebra mussel as well as macrophytes and macroinvertebrates by the calico crayfish. However, these invasive non-native species are also potential novel prey for the reintroduced turtles. Here, we investigated the trophic interactions under captive conditions between the turtle and the two invasive non-native species. We conducted prey choice tests of turtles with calico crayfish of different sex, size, and shell hardness, as well as with zebra mussels of different size. Additionally, faecal samples of wild caught turtles on Neu-Woerr were sampled and analysed for calico crayfish DNA. Our results demonstrated that the turtles were capable of preying on the calico crayfish in the wild and in captivity, preferring small crayfish individuals, with no sexual preference for the less aggressive female crayfish. For the zebra mussels, turtles preyed preferably on small alive individuals, while they also preyed on larger, yet dead mussels. This study provides new insights into the feeding ecology of the European pond turtle and highlights added benefits and values of reintroduction projects when the reintroduced species additionally acts as a novel predator of invasive species.

Soil ecosystems host some of the most taxonomically and functionally diverse biological communities on Earth, yet long-term trends in their biodiversity remain poorly understood. Here, we analysed soil biodiversity dynamics over 20 years with samples archived in the German Environmental Specimen Bank. We assessed temporal and spatial patterns in α-diversity and β-diversity with shotgun metagenomics across bacteria, fungi, and metazoa. We found no statistically significant temporal trends in α-diversity for any group. Total β-diversity also appeared temporally stable. However, decomposing β-diversity into its balanced variation and abundance gradients revealed taxon-specific compositional restructuring. Bacterial and fungal communities showed signs of compositional homogenisation, while metazoan communities remained more stable. Spatial structuring was pronounced across all groups. Land use emerged as a key spatial predictor of community composition for bacteria and fungi, and geographic locality for metazoans. Our findings show that apparent stability in standard biodiversity indices may mask significant underlying community change. This highlights the need for integrative, taxonomically inclusive approaches to biodiversity monitoring. The combination of environmental specimen banking with metagenomic sequencing offers a powerful framework for uncovering hidden biodiversity trends in soil ecosystems and identifying the drivers of ecological reorganisation under global change.

Background: Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely. Results: Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins. Conclusion: Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.

Crayfish plague is a devastating disease of European freshwater crayfish and is caused by the oomycete Aphanomyces astaci (Ap. astaci), believed to have been introduced to Europe around 1860. All European species of freshwater crayfish are susceptible to the disease, including the white-clawed crayfish Austropotamobius pallipes. Ap. astaci is primarily spread by North American crayfish species and can also disperse rapidly through contaminated wet gear moved between water bodies. This spread, coupled with competition from non-indigenous crayfish, has drastically reduced and fragmented native crayfish populations across Europe. Remarkably, the island of Ireland remained free from the crayfish plague pathogen for over 100 years, providing a refuge for A. pallipes. However, this changed in 1987 when a mass mortality event was linked to the pathogen, marking its introduction to the region. Fortunately, crayfish plague was not detected again in Ireland until 2015 when a molecular analysis linked a mass mortality event in the Erne catchment to Ap. astaci. Since then, the pathogen has appeared across the island. Between 2015 and 2023, Ap. astaci was detected in 18 water catchments, revealing multiple genotypes. Intriguingly, the pathogen in Ireland is present without its natural host species. The uneven distribution of various genetic lineages strongly suggests the human-mediated transport of zoospores via contaminated water equipment as a primary cause of spread. This review details the timeline of these events, Ap. astaci’s introduction into Ireland, and its rapid spread. As well, this review references the genotypes that have been determined, and discusses the issue of non-indigenous crayfish species in Ireland and management efforts.

The crayfish plague is a devastating disease of European freshwater crayfish and is caused by the oomycete Aphanomyces astaci (Ap. astaci), which was introduced to Europe around 1860. All European species of freshwater crayfish are susceptible to the disease, including the white-clawed crayfish Austropotamobius pallipes. The aquatic mould is primarily spread by North American crayfish species and can also disperse rapidly through contaminated wet gear moved between water bodies. This spread, coupled with competition from non-indigenous crayfish, has drastically reduced and fragmented native crayfish populations across Europe. Remarkably, the island of Ireland remained free from the crayfish plague pathogen for over 100 years, providing a refuge for A. pallipes. However, this changed in 1987 when a mass mortality event was linked to the pathogen marking the pathogen's introduction to the region. Fortunately, the plague did not establish and was not detected again in Ireland until 2015 when a molecular analysis linked a mass mortality event in the Erne catchment to Ap. astaci. Since then, the pathogen has appeared across the island. Between 2015 and 2023, Ap. astaci was detected in 18 Irish water catchments, revealing multiple genotypes. Intriguingly, the pathogen in Ireland exists without its natural host species. The uneven distribution of various genetic lineages strongly suggests human-mediated transport of zoospores via contaminated water equipment as a primary cause of spread. This review details the timeline of these events, Ap. astaci’s introductions into Ireland, its rapid spread, the genotypes documented, the issue of non-indigenous crayfish species in Ireland and management efforts.