hajibabaei - biomonitoring 2.0 from microbes to mammals – ogi life sciences and mining workshop...

Mehrdad Hajibabaei Biodiversity Institute of Ontario

University of Guelph, Canada

Create a biodiversity map using DNA information Use such a map to monitor species/ecosystems over time and space

Biodiversity is…

Science of unknowns

Known biodiversity: 1.9 million species of plants and animals

Estimated biodiversity: 10 million to

100 million species

Microbiome

Macrobiome

25 parataxonomists 200+ years accumulated experience.

ACG, Costa Rica: large-scale biodiversity inventory

Taxonomic identification

Smithsonian Institution, Washington DC

John Burns

Lawton et al. 1998: Single site in Cameroon Birds: 50 scientist-hours Nematodes: 6000 scientist-hours Barlow et al. 2007 & Gardner et al. 2008: 5 tropical sites 15 taxonomic groups: 18200 person-hours

Challenges inherent in studies including a greater variety of species

Science 14 December 2012

Duhamel, Quebe

Wetlands of Louisiana

After Alberta oil sands open pit mine. Photo: DJ Baird

Before Athabasca River tributary, N Alberta. Photo: DJ Baird

Nunavut

British Columbia Alberta

Northwest Territory

Environmental impact of rapid development in remote regions

Canadian Aquatic Biomonitoring Network

Monitoring >1000 Species Across Canada Differential sensitivity of these species to environmental change

Early Warning System

The reference condition approach

Reference sites

The reference condition approach

Test sites Reference model

Identification Bottleneck

Low capacity (<1000 samples/yr) Low throughput (~12 months) Low resolution (often only to Family-level) Low frequency (~ every 3 years) Labour intensive

A DNA Based ID System for Species

DNA Barcoding

Typical cell has many

Mitochondria (green dots)

mtDNA

CO1

DNA Barcode

Mitochondrial Genome

Miotchondria contain DNA suitable for species identification

Hajibabaei et al. 2006

650 bases of DNA Barcode gene

DNA barcodes distinguish species of tropical Lepidoptera

98% resolution ~5000 individuals in over 500 species

Barcode coverage 10 March 2014

Extract DNA PCR Amplify Sequence

DNA barcoding single specimen workflow

Barcoding “mixed samples” using Next Generation Sequencing

Target DNA barcode libraries

Specimen: mixed environmental sample

Sequence data for selected markers/DNA

barcodes

Spe

cies

iden

titie

s an

d se

quen

ce c

ount

s

NGS (e.g. 454, MiSeq)

Extract e-DNA and amplify DNA barcode genes

Bioinformatics

Environmental barcoding using Next Generation Sequencing

DNA Metasystematics

Soil A Soil B

DNA Metasystematics

Biomonitoring 2.0

Bennett Dam Alberta Oil Sands

ooping Cranes, Wood Buffalo National Park, Canada. Photo: S Rosolen

Objectives 1. Resolving Biomonitoring 1.0 bottlenecks: sampling, sorting, identifying bioindicator species 2. Increasing information content of biomonitoring a. Species level vs. family/genus level for

bioindicators a. Biomonitoring beyond bioindicators: multi-

habitat; comprehensive taxonomic coverage 3. Large-scale pilot in an area of national

importance (e.g. Oil Sands)

BIO 1.0

BIO 2.0

Rocher wetland, Peace-Athabasca Delta

SOIL BENTHOS

AIR WATER

Logistic Challenges

Comparative analysis of environmental DNA barcodes

Biomonitoring

41

Biomonitoring 1.0 vs. Biomonitoring 2.0

Ian King Wendy Monk

Bio

mon

itorin

g 2.

0: N

GS

Dat

a

Bio

mon

itorin

g 1.

0: M

orph

olog

y

nMDS clustering of benthic NGS data

King et al. in prep

Wetlands bio-variability analysis

Phylogenetic profile/diversity Plants and Algae

Hajibabaei et al. in prep

Socio-economic Uptake

26 May

BIO-SAG 49

Ring of Fire Baseline Environmental Data Collection

From taxonomic diversity to functional diversity

Taxonomic barcodes Functional barcodes

Functional Barcodes Measuring Responses to Environmental Stressors

1. NGS comparative transcriptome analysis covering a wide range of organisms commonly used in ecotoxicology exposed to a certain chemical/mixture

2. Target fundamentally conserved cell machinery (e.g., transcription, translation) as taxonomically wide-ranging markers for environmental change (early warning system)

Gina Capretta

Acknowledgments

Team

Funding Genome Canada Ontario Genomics Institute Environment Canada Parks Canada MRI (Ontario) NSERC Canada Foundation for Innovation

Shadi Shokralla (Research Associate) Joel Gibson (Postdoc & PM) Ian King (Postdoc) Terri Porter (Postdoc, McMaster) Jennifer Spall (Graduate student) Lisa Ledger (Graduate student) Nicole Fahner (Graduate student) Michael Wright (Graduate student) Gina Capretta (Graduate student) Katie McGee (Graduate student) Stephanie Boilard (Lab tech) Rafal Dobosz (Bioinformatician)