Beyond 2020 >> Work packages >> Metagenomics


Three lake sediment cores will be collected, one each from Bunaveela lake, Lough Feeagh and Lough Furnace, representing contrasting lake histories and habitat types as per method proposed in the Microbiome work package. A specific time period of interest is the “Little Ice Age” that occurred between the sixteenth and nineteenth century when temperatures dropped globally with particularly cold periods beginning in the mid sixteen hundreds after which temperature rapidly increased. This makes the core layers during the “Little Ice Age” and subsequent warming period ideal samples to assess changes in specie presence, abundance and composition in a warming.
The stomach and faecal samples will be collected from juvenile salmon, brown trout, eel, char and stickleback seasonally and periods corresponding with key life history transitions i.e. smoltification in salmon and trout and silver eel migration in and between contrasting environments. The aerobic scope of eel, stickleback, trout and salmon will be measured by acquiring measurements of standard metabolic rate (SMR) and maximum
metabolic rate (MMR) of fish at different times of the year and from different ecosystems in order to get estimate of capacity of fish species to utilise food items at different times of the year and inform on bio-energetic potential of fish to use utilise food items in the Microbiome work package.

WT 1 Recovery of salmon and trout information from paleo cores (UCD): The UCD research group have established methods to isolate total DNA from sediment cores and developed species specific qPCR assays for salmon and brown trout based on MGB Taqman probes targeting mitochondrial (mt)DNA regions. The assays will be used to simultaneously detect and quantify both salmon and brown trout eDNA concentrations. The task aims at detecting and quantifying eDNA from both salmon and brown trout in different time periods to assess fluctuations in species presence and abundance over time. Using more contemporary core section (e.g. less than 100 YBP) data generated in this WT can be compared to fish count data available in the Newport Facility to calibrate abundance data.
WT 2 Recovery of broader taxonomic info from paleo cores (UCD): Total DNA isolated in WT 1 will be used as template for multi-species PCR amplification using universal primers for mtDNA regions. While the COI and/or COI minibarcodes targeting eukaryotes, while Cytb is particularly well suited to identify teleosts. Similarly, the 16S rRNA is routinely employed to assess for metabarcoding of microbial OTU diversity. Results from metabarcoding will inform on changes in presence, diversity and abundance over time with particular interest in the dynamics following the rapid temperature increase following the “Little Ice Age”.
WT 3 Recovery of eDNA for identifying for broad taxonomic groups from water samples (UCD): While the methods and bioinformatics pipelines used for WT 2 are identical for WT 3, the source of DNA differs. For this task, water samples will be collected from the different environments and filtered to recover biological material. DNA will subsequently be isolated from these filters. Resulting total DNA will be interrogated using the methods and approaches outlined in WT 3. The data generated in the WT will show the contemporary dynamics and function as a baseline for future comparisons.
WT 4 Recovery of DNA from fish stomachs (QUB): Multiple-universal markers (e.g. 16s rRNA, COI) will be deployed to amplify and resolve (i.e.
identify) species across a broad range of taxa from ingested food material. These universal markers are designed to target small fragments sizes, thus making amplification of degraded DNA more reliable. International databases will be exploited to reference biota from sampled material.