Mykytczuk - Mining Microbes: Harnessing the Power of the Small – OGI Life Sciences and Mining Workshop 2014

Dr. Nadia C.S. Mykytczuk

Mining Microbes:

Harnessing the Power of the Small

Research Scientist, Vale Living with Lakes Centre

May 6th , 2014

The Sudbury Restoration Story

Terrestrial and aquatic restoration: re-greening, and pH recovery

Turning the Bad & the Ugly… into the Good

Recover metals

from

tailings using

microbes

Grow fuel crops

On tailings

Water treatment

wetlands

- Microbial communities in tailings and AMD

- Well adapted to the specific conditions/extremes

- Potential to harness key species and consortia

- Discover new metabolic functions/networks

Meta-omics in the bioleaching/remediation framework

meta-omics/

microbial isolation

bioleaching/

remediation

environment /

geochemistry abiotic

vs.

biotic

specific

metabolism

selected

traits

Meta-Omics: exploding the “black box”

MICROBIAL DIVERSITY

High-throughput sequencing

High resolution

community diversity

and functional profile

DNA

RNA

protein

healthy contaminated

ENVIRONMENTAL MICROBIOME

Unraveling biodiversity and

ecosystem function

Adapted from Del Chierico et al., 2012

Tapping the AMD microbial community

Have we underestimated diversity? Do we fully understand the microbial

mechanisms ?

general oxidation reaction

FeS2 Fe3+ + H2SO4

Iron & metal sulphides

waste rock/tailings

AMD Cu, Ni, Zn, U, Mo

Everything we thought we knew about AMD: Acidithiobacillus ferrooxidans

SEM of A. ferrooxidans © IMPMC/Hydrosciences

AMD

waste rock

• Most widely studied AMD species • Considerable strain variation • Unique adaptation of interest for tailored biomining

(Mykytczuk et al., 2010 a,b,c; 2011)

100751023270

50501019859

1504010R1

20015010F1

155.02D7

501502D6

MIC* Nickel (mM)MIC* Copper

(mM)

Lower growth

Temp.

Limit (°C)

Strain

100751023270

50501019859

1504010R1

20015010F1

155.02D7

501502D6

MIC* Nickel (mM)MIC* Copper

(mM)

Lower growth

Temp.

Limit (°C)

Strain

Culturing: The importance of strain libraries

type strains

Falconbridge(GlencoreINO) Denison &

Rio Algom mines

D6, D7, R1 F1

Strain selection

Uranium? > 5mM Arsenic?

Northern AMD microbial communities opening the black box

collaboration with L.Leduc

Acidithiobacillus ferrooxidans

and ferrivorans

Genomics of

Cold- and highly

Metal- adapted strains

Metagenomic diversity

of microbial community in AMD (water)

AMD (sediment) tailings

collaborations with T. Merritt, A. Poulain

Diversity and Temporal Variation in AMD microbial community:

Vale Copper Cliff

(Auld et al., 2013, 2014 manuscript)

AMD pond sediments

(Valiquette , 2014 BSc thesis) (> 1% of community

Microbial ecology of Arsenic tailings at Long Lake in Sudbury

(NSERC CREATE: Mine of Knowledge)

Long Lake gold mine tailings: 75-100 years old

Finding high

community

diversity even in 35000 ppm Arsenic tailings

And these microbes are viable

Ecology and molecular biology of the effects of cold temperatures on AMD microbial communities.

NSERC Discovery Goals:

Characterize the AMD “microbiome” to better understand and exploit cold-adapted microbes for biomining in the North

Use meta-omics technology to define AMD

biogeochemistry at cold temperatures

NSERC Discovery Grant 2013-2018

Environmental remediation through bioleaching

• Characterize microbial diversity in seed mixtures

• Build strain library (novel isolates)

• Metagenomic study of bioleaching microbial consortia

Information will help with

tailoring and biomonitoring

active bioleaching tanks

(NSERC ENGAGE: BacTech Environmental)

Snow Lake Manitoba, Arsenic stockpiles

Passive biomining with microbes: the Northern version

Ore pile is leached with community of mining microbes

In situ leaching of mining wastes Using locally adapted strains/consortia

Dilute acid and microbes

Ore pile

Leach liquor with dissolved metals

Electroplating waste rock

AMD metal recovery

Acid/AMD Sprinkler

Leachate

Rubber Lining

Collection ditch

SX/EW

Recirculation

slope

Extraction

Stripping

Electrowinning

Heap

Bioleaching potential in Sudbury

Pilot-scale bioleaching heap as proof of principle of passive bioleaching potential

(NSERC ARD: Cambrian College, Vale)

Existing tailings

Use local AMD as leach liquor

Encourage native microbial community (monitor activity)

Conduct year long test (seasonal variation)

Metagenomic analyses

Determine M+ yields

Determine optimization and scale-up strategies

Cambrian/Vale: Passive leach heap

Harnessing the microbial community

Exploit AMD processes and active microbial

communities

Mining microbes

Metal recovery Waste reduction Remediation Management Molecular technology Understand processes

that promote sustainability

Key microbes In environmental recovery

Completing the mining cycle with: re-mining, remediation, and reclamation

Acknowledgements

Dr. Josef Hamr

Stephen Gravelle

Laurentian University Dr. John Gunn

Dr. Leo Leduc

Dr. Graeme Spiers

Dr. Peter Beckett

Dr. Thomas Merritt

Ryan Auld

Nicole Valiquette

Dr. Leslie Warren

Dr. Alex Poulain

Varun Gupta

Maxime Rivest

Ontario Genomics Institute

Oscar Alvarado

Ross Orr

NSERC CREATE: Mine of Knowledge program

Scientific Mentoring, Applied Research and Training for sustainable MINEs ($1.65 million)

9 PIs, 26 collaborators, >10 affiliated industry/company partners

Train students in a multi-disciplinary research program that will provide highly qualified personnel who will allow the mining industry to maintain its world leadership in environmental management, increasing the global competitiveness

and sustainability of this critical Canadian sector *total of 96 HQP over 6 years

Geomicrobiology Molecular geochemistry and microbiology

biogeochemistry ecotoxicology

Aquatic ecology

Analytical chemistry

M. Amyot

A. Poulain

L. Warren

C. Baron D. Fortin

J. Gunn C. Fortin K. Wilkinson

P. Campbell