Freshwater diatom biomonitoring through benthic kick-net metabarcoding.

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status.

An optimised eDNA protocol for detecting fish in lentic and lotic freshwaters using a small water volume.

Environmental DNA is increasingly being used for assessing the presence and relative abundance of fish in freshwater, but existing protocols typically rely on filtering large volumes of water which is not always practical. We compared the effects of water volume, filtration type and eDNA extraction procedures in the detection of fish in three freshwater bodies (pond, lake and river) using a short fragment of the 12s rRNA mtDNA gene. Quantification of eDNA capture efficiency after DNA extraction, as well as amplification efficiency, were evaluated by conventional PCR and quantitative PCR.

Effect of artificial barriers on the distribution of the invasive signal crayfish and Chinese mitten crab.

The role of river obstacles in preventing or facilitating the dispersal and establishment of aquatic invasive species is controversial. Novel detection tools like environmental DNA (eDNA) can be used for monitoring aquatic invasive species (AIS) such as the American signal crayfish (Pacifastacus leniusculus) and the Chinese mitten crab (Eriocheir sinensis), providing information on the effect of barriers on their distribution. We analysed eDNA from both water and surface sediment in three river catchments (Medway, Dee and Stour; Great Britain), with differing levels of connectivity, to determine spatial distribution of the two species, and assessed the effect of barriers on their eDNA detection.

Genetic diversity and parasite facilitated establishment of the invasive signal crayfish () in Great Britain.

Successful establishment of non-native species is strongly influenced, among other factors, by the genetic variation of founding populations, which can be enhanced by multiple introductions through admixture. Coexisting pathogens can also facilitate the establishment of non-native species by detrimentally impacting on the native fauna acting as novel weapons. The signal crayfish () is a highly invasive species, which has caused mass declines of native crayfish in Europe through displacement and transmission of the oomycete (crayfish plague), which is typically lethal to native European crayfish.

Data on optimisation of a multiplex HRM-qPCR assay for native and invasive crayfish as well as the crayfish plague in four river catchments.

The data presented here corresponds to the research paper "Simultaneous detection of invasive signal crayfish, endangered white-clawed crayfish and the crayfish plague using environmental DNA". A crayfish-specific assay was designed and optimised using three real-time PCR supermixes (SYBR™ Green, SsoFast™ EvaGreen® and HOT FIREPol® EvaGreen®). Diagnostic high resolution melt (HRM) data from direct application of assay on both eDNA water samples and field samples from four catchments (two in Wales, two in England) is presented in this article, displaying positive HRM profiles for invasive signal crayfish ( native white-clawed crayfish () and crayfish plague causal agent ().