General overview of Bioremediation
Damase Khasa
Centre for Forest Research and Institute for
Integrative and Systems Biology, Université
Laval, Québec Canada G1V OA6
Presented during the
Soil Remediation Workshop (With special presentation on
Nextgen sequencing), Pretoria, SA, 27 - 28 May 2014
By
Part I: Bioremediation
Biostimulation
Bioaugmentation
Phytoremediation
Part II: Canadian case study in the
oil sands industry
Outline of presentation
Biostimulation
Bioaugmentation
Phytoremediation
Part I: Bioremediation, An
overview
Pictures depicting worldwide problems
of pollution
Environmental contaminants
•Pollutants
• naturally-occurring compounds in
the environment that are present
in unnaturally high concentrations
• Examples:
• crude oil
• refined oil
• phosphates
• heavy metals
•Xenobiotics
• chemically synthesized
compounds that have never
occurred in nature.
• Examples:
• pesticides
• herbicides
• plastics
S: Pearson education
Sources of contamination
• Industrial spills and
leaks
•Surface
impoundments
•Storage tanks and
pipes
•Landfills and dumps
• Injection wellsModified from Capiro 2003
Sources of contamination
• The major contributors to volatile organic compounds (air
pollution) are from
• Paint industry
• Pharmaceutical industry
• bakeries
• printers
• dry cleaners
• auto body shops
Types of treatment technologies in use to
remove contaminants from the environment•Soil vapor extraction
•Air and hydrogen sparging
•soil washing, in situ soil flushing
•chemical oxidation/reduction
•soil excavation
•pyrometallurgical processes (thermal
desorption, electrokinetical treatment)
•bioremediation
What is bioremediation?
The use of microbes (bacteria and fungi) and plants to break down or degrade toxic chemical compounds that have accumulated in the environment into less toxic or non toxic substances
History of Bioremediation
• ~1900 Advent of biological processes to treat organics derived from human or animal wastes
• ~1950 Approaches to extend wastewater treatment to industrial wastes
• ~1960 Investigations into the bioremediation of synthetic chemicals in wastewaters
• ~1970 Application in hydrocarbon contamination such as oil spills and petroleum in groundwater (more pollution than the natural microbial processes could degrade the pollutants)
• ~1980 Investigations of bioremediation applications for substituted organics
• ~1990 Natural Attenuation of ’70 and ’90
• ~2000 Development of in situ bioremediation; source zone reduction; bioaugmentation
• ~2003 Genomics era of Bioremediation (Cleaning up with genomics by Derek R.Lovley 2003. Nature Reviews 1: 35-44)
S: modified from Capiro 2003
Types or techniques of bioremediation
1) Ex situ bioremediation: contaminants are treated off site
2) In situ bioremediation: contaminants are treated on site
• Natural Attenuation (slow process, not complete enough, not frequently occurring enough to be broadly used for some compounds, especially very difficult or recalcitrant substances)
• Enhanced Bioremediation or Biostimulation is to stimulate/enhance a site’s indigenous subsurface microorganisms by the addition of nutrients (amendments) and electron acceptors such as P, N, O2, C (e.g., in the form of molasses, biochar)
• Bioaugmentation is necessary when metabolic capabilities of microorganisms are not naturally present. Commercially prepared bacterial strains with specific catabolic activities are added (Novozymes Biologicals is a leader in the isolation and selection of novel microbial consortia, +25,000 characterized strains)
• Phytoremediation: extraction of soil pollutants by roots and accumulation or transformation by plants, e.g., hyperaccumulators
The advantages of bioremediation
over other technologies
• permanence
• contaminant is degraded
• potentially low cost
•60-90% less than other technologies (No additional
disposal costs)
• Low maintenance
•Does not create an eyesore
•Capable of impacting source zones and thus, decreasing
site clean-up time
S: Pearson education
Economics of in-situ vs. ex-situ
remediation of contaminated soils
•Cost of treating contaminated soil in
place $80-$100 per ton
•Cost of excavating and trucking
contaminated soil off for incineration
is $400 per ton.
•Over 90% of the chemical substances
classified as hazardous today can be
biodegraded.
S: Pearson education
Contaminants Potentially Amenable to Bioremediation
____________________________________________Readilydegradable_____________
Somewhatdegradable_____________
Difficult todegrade_____________
Generallyrecalcitrant_____________
fuel oils, gasoline creosote, coaltars
chlorinatedsolvents (TCE)
dioxins
ketones andalcohols
pentachloro-phenol (PCP)
some pesticidesand herbicides
polychlorinatedbiphenyls (PCB)
monocyclicaromatics
bicyclic aromatics(naphthalene)
Some challenges for bioremediation of pollutants
and xenobiotics
•Pollutants
•may exist at high, toxic
concentrations
•degradation may
depend on another
nutrient that is in limiting
supply
•Xenobiotics
•microbes may not yet
have evolved
biochemical pathways to
degrade compounds
•may require a
consortium of microbial
populations
Fundamentals of biodegradation reactions
• Aerobic bioremediation
• Microbes use O2 in their metabolism to degrade
contaminants
• Anaerobic bioremediation
• Microbes substitute another chemical for O2 to
degrade contaminants
• Nitrate, iron, sulfate, carbon dioxide, uranium,
technicium, perchlorate
• Cometabolic bioremediation microbes do not gain
energy or carbon from degrading a contaminant.
Instead, the contaminant is degraded via a side
reaction
Bioremediation involves the production of energy in a
redox reaction within microbial cells: an energy source
(electron donor), an electron acceptor, and nutrients.
Electron Donors
• Alcohols and acids
• Almost any common fermentable compound
• Hydrogen apparently universal electron donor,
but no universal substrate
• Hydrocarbon contaminants
• Surfactants
• Etc.
ATP
ACETATE
CO2
Fe(III)
Fe(II)
Metabolism of a Pollutant-degrading Bacterium
*Benzoate
*Toluene
*Phenol
*p-Cresol
*Benzene
*U(VI)
*Co(III)
*Cr(VI)
*Se(VI)
*Pb(II)
*Tc(VII)
*CCl4
*Cl-ethenes
*Cl-aromatics
*Nitro-aromatics
How Microbes Use the Contaminant
• Contaminants may serve as:
• Primary substrate
• enough available to be the sole energy source
• Secondary substrate
• provides energy, not available in high enough concentration
• Cometabolic substrate
• fortuitous transformation of a compound by a microbe relying on some other primary substrate (Cometabolism is generally a slow process). Bacterium uses some other carbon and energy source to partially degrade contaminant (organic aromatic ring compound)
Genetic engineering of bacteria to remove
toxic metals from the environment
Hg2+-metallothein
Hg2+→HgoHg2+
New gene/enzyme
New gene/transport proteinsE. coli bacterium
Hgo (less toxic form of
metal)
Phytoremediation
• ≈350 plant species naturally take up toxic materials
• Sunflowers used to remove radioactive cesium
and strontium from Chernobyl site
• Water hyacinths used to remove arsenic from
water supplies in Bangladesh, India
S: Pearson education
Phytoremediation
• Drawbacks
• Only surface soil (root zone) can be treated
• Cleanup takes several years
Technology Advantages Disadvantages
Soil excavation
1. Quick restoration
(immediate)
2. Effective on limited areas
1. Expensive
2. Inefficient on large areas
3. Less aesthetic
4. Very destructive
Phytoremediation
1. Returns site to its
aesthetical value
2. Less expensive
3. Less destructive
4. Ecological and sustainable
method
5. Supports biodiversity
6. Allows carbon sequestration
7. Give products with
economical value (woods,
NTFP)
1. Slow restoration
2. Additional cost needed for
biomass storing for sites
contaminated by dangerous
products
Comparison between phytoremediation and soil
excavation to restore mine site
Conclusions
• Many factors control biodegradability of a contaminant in the environment
• Before attempting to employ bioremediation technology, one needs to
conduct a thorough characterization of the environment where the
contaminant exists, including the microbiology, geochemistry, mineralogy,
geophysics, and hydrology of the system
• Most organics are biodegradable, but biodegradation requires specific conditions: important to understand the physical and chemical characteristics of the contaminants of interest
• There is no Superbug: understand the possible catabolic pathways of
metabolism and the organisms that possess that capability (functional
genomics and specifically metabolomics)
Conclusions
•Contaminants must be bioavailable and in optimal
concentrations
•Biodegradation rate and extent is controlled by “limiting
factors”: pH, temperature, water content, nutrient
availability, Redox Potential and oxygen content
•Understand the environmental conditions required to:
•Promote growth of desirable organisms
•Provide for the expression of needed organisms
•Engineer the environmental conditions needed to establish favorable conditions and contact organisms and contaminants
Part II: Canadian case study of phytobial
remediation in the oil sands industry
Map of Canada
Syncrude
Albian Sands
Suncor Energy
Canadian Natural
Syncrude
Overburden
Oil sands
Profile of oil sands deposit
Oil extraction
Extraction Process
Bitumen Tailings
Tar Sands
Bitumen
Tailings Discharge to Storage Pond
Materials Requiring Reclamation
Overburden storage Tailings sand
Soft tailings Coke storage
• High ion content (eg. Na+)
• Alkaline pH
• Nutrient depleted
• Residual hydrocarbons, NAs
Tailings sands and tailings water
Athabasca River at
Fort McMurray
• erosion and run-off of
bitumen
• continuous supply of
hydrocarbons to river
• good source of natural
hydrocarbon degraders
• potential source of
obligate hydrocarbon
degraders
Frankia sp.:
N-fixing actinomycete
Alders:
Pioneer species
Definitions
• Actinorhizal plants (200 species, 25 genera)
– alder shrub and tree species (Alnus) are pioneer
species colonizing very poor substrates
Parc Forillon, 2002
Aulne rugueux (A. rugosa)
Host Plants
Alnus crispaAlnus crispa,
AVCi1
• The symbiosis
− root nodulation similar to leguminous plants
− fixation rate (40-300 kg / ha*year)
Growth and Inoculation
of Alders in Greenhouse
Frankia inoculated (right) and non-inoculated control (left) green
alder seedlings planted in oil sands areas in Spring 2005. The
photos were taken in Fall 2007 after three growing season.
Frankia-inoculated alder (A. crispa)
Effects of Frankia inoculation on plant height
(Height), root collar diameter (RCD), and stem
volume of green alder outplanted on Syncrude
W2 site (relatively better reclaimed site) after
three growing seasons. Each value is the
average of 24 seedlings (6 seedlings/replication).
Effects of Frankia inoculation on plant height
(Height), root collar diameter (RCD), and seedling
volume rate of green alder outplanted on
Syncrude saline-alkaline harsh (Cell 46) after
three growing seasons. Each value is the
average of 24 seedlings (6 seedlings/replication).
Effects of Frankia inoculation on stem volume of
green alder outplanted on Syncrude saline-alkaline
harsh site (cell 46) and W2 site after three growing
seasons. The data shows percent (%) increase in
mean stem volume over control treatment on both
sites
Hexadecane
Naphthalene Phenanthrene
Hydrocarbon mineralization in
bulk field soil planted with alders
Hexadecane
Naphthalene Phenanthrene
Hydrocarbon mineralization in the
rhizosphere of alder planted soil
alkB PCR in
field plants
Detection of Frankia
in endophytic community
DGGE Analysis of
Rhizospheric and
Endophytic Microbial
Communities From
Frankia-inoculated (F)
and Non-Inoculated (C)
Alders
Arrow: Frankia
Conclusions and future prospects1. The study of root symbioses in phytoremediation
will help understand their sensitivity, tolerance
and coadaptation capacity under stress
2. The biotechnology of root symbioses on
contaminated soils will help understand and
measure their impact on:
a) the microbial density and diversity in the
rhizosphere,
b) the microbial degradation of contaminants,
c) the global soil quality (phytotoxicity,
nutrients).
Conclusions and future prospects3. Appropriate experimental approaches are
needed to assess the potential of these
microorganisms in the management of
disturbed soils following industrial activity.
4. Methagenomics, functional genomics
(proteomics, transcriptomics and
metabololomics) approaches will
revolutionize the traditional studies of soil
microbial ecology and de novo
bioremediation
Members of the
Biomonitoring and
Remediation Groups, EME,
NRC-Montreal
Acknowledgements
61
THANK YOU
VERY MUCH FOR
YOUR ATTENTION
Top Related