funding...and cytochrome b) sequenced at ceh on an illumina miseq edna detects lake fish presence...
TRANSCRIPT
![Page 1: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/1.jpg)
Funding
eDNA - a tool for efficient biodiversity monitoring
from rare species to communities and back
Bernd Hänfling
![Page 2: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/2.jpg)
eDNA barcoding and metabarcoding eDNA barcoding:
• Targeted detection • Species-specific primers • Standard or qPCR • Traditional Sequencing
=
Free-floating DNA (from sloughed skin cells faeces/urine, gametes, decaying matter) and
microscopic taxa
Water sampled & filtered (>3 x 15 ml -2L samples)
eDNA metabarcoding: • Screen whole community • (Several) conserved primers • PCR • Next generation sequencing
= Extract DNA
![Page 3: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/3.jpg)
eDNA metabarcoding of lake fish
Aim: • To develop and test eDNA metabarcoding
methods to describe lake fish communities. Motivation: • Water Framework Directive (WFD) lake fish
monitoring. • Currently not carried out to the degree
required by the WFD due to methodological considerations.
• Cost and time • Ethics (gill nets are destructive) • Practicalities on large lakes
Phase I: • Sampling: January 2015
Phase II: • Sampling: September 2015/January2016
![Page 4: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/4.jpg)
eDNA metabarcoding of lake fish
Phase I – sampling: • Three Cumbrian lakes
• Windermere • Derwent Water • Bassenthwaite Lake
• 2L water samples along boat transect at
2m, 5m & 20m depths, as well as shore
sampling.
• Filtered on 0.45 μm membrane filters.
• Two mitochondrial gene fragments (12S
and Cytochrome b) sequenced at CEH on
an Illumina MiSeq
![Page 5: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/5.jpg)
eDNA detects lake fish presence
Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%)
Gill netting survey 2014: 4 (25%)
Gill netting survey 2015: 5 (31%)
0
0.2
0.4
0.6
0.8
1
12S freq
cytb freq
Prop
ortio
n of
site
s pre
sent
Lake Windermere, January 2015 (65 samples)
Hänfling et al. 2016, Molecular Ecology
![Page 6: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/6.jpg)
Prop
ortio
n of
site
s pre
sent
0
0.2
0.4
0.6
0.8
1
12S freq
cytb freq
Lake Windermere, January 2015 (65 samples)
Species not previously recorded 12S: 6 species Cytb: 3 species
eDNA detects lake fish presence
![Page 7: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/7.jpg)
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0 2 4 6 8 10 12 14 16 18
January 2015
Long term rank (based on 30 years of established method surveys)
eDN
A ab
unda
nce
(site
occ
upan
cy)
eDNA reflects species abundance
Windermere both basins
r = - 0.77; P < 0.001
![Page 8: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/8.jpg)
• Perch detected throughout lake
• Arctic charr predominantly North Basin
• Bream more common in South Basin
Spatial distribution of eDNA
Occupancy data demonstrate that species are not equally distributed across the lake e.g.
![Page 9: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/9.jpg)
eDNA distribution reflects fish ecology
Oligotrophic association
Eutrophic association
No association
0
5
10
15
20
25
30
1945 1955 1965 1975 1985 1995 2005Year
Mea
n SR
P in
firs
t 4 w
eeks
(mg
m-3
)North basin
South basin
Hänfling et al. 2016, Molecular Ecology
Mesotrophic
Eutrophic-mesotrophic
![Page 10: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/10.jpg)
eDNA distribution reflects fish ecology
• Large and common species found consistently across transects
• Small littoral species predominantly in shallower habitats
• Arctic charr was only found in midwater and bottom samples
Shore-west 5m
20m Midline
Shore-East
0
0.2
0.4
0.6
0.8
1
eDN
A ab
unda
nce
(12S
)
Windermere North Basin
Sampling in Phase 2
![Page 11: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/11.jpg)
eDNA detection of rare species Vendace (Coregonus albula) in Cumbrian lakes
• Five offshore and one shore line sample in each lake
• Positive detection in two Derwent Water sites, but none in Bassenthwaite Lake (only three individuals caught since 2000)
• Is qPCR more sensitive compared to metabarcoding? Ongoing work with Glenn Rhodes (CEH)
PhD studentship available (UoH collaboration with CEH and SNH): “eDNA monitoring of conservation priority fish in UK freshwaters” Deadline for applications 3rd June 2016
Derwent Water
Bassenthwaite Lake
![Page 12: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/12.jpg)
Summary
• eDNA metabarcoding is highly sensitive for fish species detection and outperforms established methods even in oligotrophic lakes
• Relative abundance estimates from eDNA and long term data correlate strongly.
• eDNA can tell us about species distribution on a small geographical scale and provide important ecological information
• Some differences between shore and offshore sampling… important for monitoring strategies
• Metabarcoding may just be as powerful as single species approaches for detecting rare species
• eDNA based metabarcoding has a huge potential for large scale biodiversity monitoring and to provide data to answer fundamental ecological questions
![Page 13: Funding...and Cytochrome b) sequenced at CEH on an Illumina MiSeq eDNA detects lake fish presence Previously (ever) recorded species: 16 eDNA metabarcoding (Jan-15): 14 (88%) Gill](https://reader031.vdocuments.us/reader031/viewer/2022011823/5edab5f0272674784f04f034/html5/thumbnails/13.jpg)
So long and thanks for all the fish help … UoH team: Dr. Lori Lawson-Handley PostDocs: Dr. Christoph Hahn Dr. Helen Kimbell Dr. Paul Nichols Dr. Harriet Johnson Dr. Hayley Watson Dr. Rose Wilcox Dr. Rob Donnelly PhD students: Joe Li Rosie Blackman Marco Benucci Lynsey Harper
CEH team: Dr. Ian Winfield Dr. Dan Read Dr. Anna Oliver Ben James Janice Fletcher
FBA and MEFGL Bangor for use of facilities!
EA, SEPA and NRW team: Dr. Kerry Walsh Dr. Graeme Peirson Dr. Willie Duncan Dr. Alistair Duguid Dr. Tristan Hatton Ellis