Environmental DNA (eDNA) detection
If you are considering applying to the facility to support a project involving eDNA analysis we are able to advise and assist with experimental design.
The University of Sheffield's Molecular Ecology Laboratory also provides DNA detection services: Detection of Great Crested Newt (Triturus cristatus) DNA in water samples.
Please contact Dr Deborah Dawson to discuss any application for project support at our facility.
Our equipment includes a QuantStudio 12K Flex Real-time PCR System (the all-in-one qPCR instrument). This is used for environmental DNA (eDNA) typing, such as screening water samples for the presence of a specific species, eg Great Crested Newt Triturus cristatus.
We use an Illumina MiSeq Sequencer for detecting multiple species from environmental samples, such as the detection of:
- fish species present in lakes identified from water samples
- earthworm biodiversity as a measure of soil health
- parasites or bacteria present in faecal samples, for studies of disease transmission or microbiota
- pollination - plant species represented in pollen taken from the bodies pollinator species
- prey species in faecal material (see diet analysis)
Bespoke one-to-one training and support is provided as required to design the study, complete the lab work, process the sequence data and perform the data analyses.
eDNA projects that we are currently supporting include:
Lesley Lancaster, University of Aberdeen
Native biodiversity in human-impacted habitats: Applying NGS technology to arthropod assemblages in semi-natural and plantation oak woodlands.
Sarah Perkins, Cardiff University
The influence of contaminants and parasitic infection on the gut microbiota of the polar bear (Ursus maritimus)
Richard Davies, University of East Anglia
Effects of florally enhanced field margins on diversity and pollen resource use of hoverfly assemblages
Mark Chapman, University of Southampton
Pollination networks of nectarivorous bats in Mexico and dietary dependence upon the cultivated cactus Stenocereus queretaroensis
Jenny Dunn, University of Lincoln
Ecological predictors of co-infection and phylogenetic relationships between co-infecting haemosporidian parasites.
Penelope Watt, University of Sheffield
The effects of ley cropping on earthworm diversity and abundance
Jonathan Millett, Loughborough University
The function of carnivorous pitcher plants in their native and non-native range: extrinsic vs intrinsic drivers of inquiline community composition
PI: Isabel Douterelo Soler, University of Sheffield, Visitor: Carolina Calero Preciado
Impact of climate change on the microbial ecology of drinking water distribution systems.
NBAF-S R & D
Sara Peixoto & Deborah Dawson, University of Sheffield
Peixoto et al. (submitted) Developing eDNA approaches to monitor Atlantic salmon.
PI: Julia Day, University College London, Visitor: Chris Doble
Testing eDNA metabarcoding approaches for surveying Lake Tanganyika’s hyper-diverse littoral fish communities.
Doble et al. (2019) Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika. Environmental DNA, In press.
PI: Paul Ashton, Edge Hill University, Visitor: Andy Devaynes
Bacterial communities of Blue Tit nest boxes.
PI: Andrew Tanentzap, University of Cambridge. Visitor: Chloé Orland
Temporal colonization of lake sediment by microbial communities along environmental gradients.
PI: Jim Groombridge, University of Kent, Visitor: Andy Buxton
Environmental DNA as an assessment tool for population size estimates of the Great Crested Newt (Triturus cristatus).
The NERC Environmental Omics Facility (NEOF)
Making state-of-the-art molecular genetics facilities and training available to the UK science community.