National reference laboratory research activities

This four-year (CULLEN) PhD scholarship is an applied research collaboration between the Atlantic Technological University (ATU) and the Marine Institute (Galway), in Ireland. The research will focus on using molecular genetics and biochemistry techniques to generate high-impact scientific evidence for the conservation and management of Irish white clawed crayfish. The key tasks of this research will be to (i) characterise the genetic diversity and population structure of Irish white clawed crayfish, (ii) implement established protocols for environmental DNA (eDNA) monitoring of both crayfish and associated water-borne pathogens, (iii) apply ecological modelling to understand population connectivity and colonisation patterns, (iv) address epidemiology aspects and spread of ongoing outbreaks of crayfish plague in Ireland and (v) collaborate with government agencies and conservation stakeholders. The project will involve field sampling in riverine ecosystems across Ireland (e.g. National Crayfish Plague Surveillance Programme and crayfish monitoring campaigns) and laboratory work (e.g. population genetics, ecological modelling and eDNA analysis). Prior experience with basic molecular biology and/or biochemistry is desirable, but training will be provided to the PhD candidate.

Background and project details

Research topic:

The White-Clawed Crayfish, Austropotamobius pallipes (WCC hereafter), is an endangered freshwater crayfish species found in Europe, from the Iberian peninsula to Croatia and up north to the UK. WCC are classified as Endangered in the IUCN Red List and the Irish population is considered to be of substantial conservation importance within Europe. Under Irish and European legislation; WCC is listed on Annex II and Annex V of the EU Habitats Directive, hence 15 Special Areas of Conservation (SACs) have been designated in Ireland.

Populations of WCC have suffered significant declines across its distribution range in Europe. The most significant threats to WCC are pathogens, competition with non-indigenous crayfish species and habitat degradation. One of the most important causes of WCC declines are outbreaks and mass mortality caused by a water mould (Aphanomyces astacii) also known as crayfish plague, which is a notifiable disease whose occurrence and spread is currently monitored the Fish Health Unit of the Marine Institute, as the competent authority and national reference laboratory in Ireland.

Population genetic structure of Irish WCC remains poorly understood, however preliminary analysis of mitochondrial DNA data showed levels of diversity comparable to mainland European populations as well as significant population differentiation within Ireland, which should be further elucidated for management and conservation of Irish WCC populations. This is particularly important in view of potential restocking and/or translocation programmes, which should be mindful of any underlying genetic structure.

The main objectives of the project will be to:

• conduct a comprehensive review of relevant WCC literature and associated genetic resources, including latest protocols for genetic data acquisition and analysis, as well as establishing a reference database with all existing genetic data
• develop and implement a mitogenome sequencing protocol for WCC to better capture genetic variation in Irish WCC and to generate a permanent genetic resource
• conduct a population genetic and phylogeography study of WCC in Ireland using nuclear and mitochondrial markers to provide recommendations on conservation and management
• implement environmental DNA (eDNA) tools to monitor distribution of WCC, pathogens and potential vectors to aid the understanding of pathogen spread dynamics and the identification of potential ark sites
• investigate the immune resistance mechanisms that contribute to the survival of Irish WCC populations exposed to previous crayfish plague outbreaks by characterizing their immune proteins

Foreseen key responsibilities:

• Conduct field work for sample collection, including participation to the National Crayfish Plague Surveillance Programme
• Conduct molecular laboratory procedures, including protein/DNA/eDNA extraction, DNA quantification, PCR, qPCR, gel electrophoresis, microsatellite genotyping, mitogenome sequencing using High Throughput Sequencing technologies, Sanger sequencing and proteomic analysis
• Execute analytical pipelines using dedicated software packages (e.g. R)
• Establish and maintain a reference database for biological and genetic data
• Maintain laboratory notebooks, research records and generate technical reports and data as required by the management team
• Disseminate findings by means of conference/symposia contributions and publication in peer-reviewed scientific journals

The NRL is working closely with Atlantic Technical University, Galway, to support delivery of a master Fellowship focused on the development of novel molecular diagnostic methods for absolute quantification of viral pathogens in farmed Atlantic Salmon and assessment of potential non-invasive sampling techniques.