Bioremediati

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Bioremediation Defined
Any process that uses microorganisms, fungi, green plants or
their enzymes to break down harmful chemicals and
pollutants in order to return the environment to its original
natural condition.

Bioremediation is not only about genetics and enzymology

but also about physiology and ultimately ecology.de
Lorenzo V: Systems biology approaches to
bioremediation. Curr Opin Biotechnol 2008, 19:579-589.

Alleviating Pollution
Ex situ or in situ intervention
Natural attenuation
Example: phytoremediation (hyperaccumulators)
store heavy metals in vacuoles
Sebertia acuminata 20% dry weight is nickel.
Plants on side of freeways are taking up lead from gas
exhaust

Bio-stimulation
Add nutrients (nitrate/sulfate) that cause blooms
of naturally occurring microbial bioremediators.
Example: bacteria that metabolize polycyclic aromatic
hydrocarbons or polychlorinated biphenyls

Bio-augmentation
Genetically Modified Bioremediators
Alter organisms to manufacture proteins for desired
metabolism
Yellow poplar tree given enzyme mercuric
reductase thrives in mercury soil, cadmium, TCE
Bacteria gene breaks down TNT is linked to
jellyfish gene that glows. Bacteria spread on soil
glows green near explosives
Chakrabarty first patented oil eater bacterium.
Combined 4 plasmids in one bacterial cell gave it
the ability to degrade four components of crude
oil.

Why do we even need i

We cant seem to stop polluting

Inorganics

Uranium, technicium, sulfur, slfuric acid

Explosives

RDX, TNT

Polyaromatic hydrocarbons

creosote

Chlorinated hydrocarbons

Trichlorethylene, PCBs,
pentachlorophenol

Petroleum hydrocarbons

Gas, gas additives (MTBE), deisel

From mid-1980s up to 90s

numerous attempts were made to
design GMO for environmental
release for pollutants and heavy
metals (USGS).
Failures to program: bacteria doesnt
behave in a predictable fashion from
the lab.

Case Study 1

Case Study 1 cont

Most failures at bioremediation are due to failure of introduced

organisms to thrive in the natural environment or a failure to access
the contaminant. This could be due to:

Lack of nutrients
Predation or parasitism
Competition (GEMs tend to compete poorly with indigenous populations).
Immobility of introduced bacteria
Contaminant concentrations below threshold for organism survival
Organisms may feed on alternative substrates (E. coli and Pseudomonas
diverge genetically from initial inoculum in field trials).

A few examples of failed bioremediation attempts:

Inoculation of soil with aliphatic hydrocarbon degrading bacteria did not
enhance degradation of fuel oil

Venosa AD, Wrenn BA (1996) Selective enumeration of aromatic and aliphatic

hydrocarbon degrading bacteria by a mostprobable number procedure. Can. J.
Microbiol.42: 252258

A Pseudomonas sp. shown in lab cultures to degrade 1,4-dichlorophenol failed

to degrade the compound when added to surface soils

Sayler GS, Ripp S (2000) Field applications of genetically engineered microorganisms

for bioremediation processes. Curr Opin Biotechnol 11:286-289

Case study 2:
degradation of crude oil by halophilic Archaea

Defining bioremediation by natural attenuation

what is the environment? what is the pollutant?
are bacterial, Archaeal, and/or plant species present that degrade the
pollutant of interest?
what conditions (nutrient, temperature, pH, salt etc) are necessary for
that activity?

Defining bioremediation by natural attenuation:

hydrocarbon degradation in the Arabian Gulf hypersaline coast
what is the environment? what is the pollutant?
the hypersaline coast of the Arabian coast
crude oil (hydrocarbons)

West, Ian. 2008. Qatar - sabkhas, evaporites and

some other desert features: an introduction.
http://www.soton.ac.uk/~imw/Qatar-

Defining bioremediation by natural attenuation:

hydrocarbon degradation in the Arabian Gulf hypersaline coast
what is the environment? what is the pollutant?
the hypersaline coast of the Arabian coast
crude oil (hydrocarbons)

are bacterial, Archaeal, and/or plant species present that degrade the
pollutant of interest?

2 Haloferax strains
1 Halobacterium strain
1 Halococcus strain
environmental samples

grow on minimal mineral plates

with crude oil vapor as sole
carbon/energy source

(Al-Mailem et al., 2010 Extremophiles)

Defining bioremediation by natural attenuation:

hydrocarbon degradation in the Arabian Gulf hypersaline coast
are bacterial, Archaeal, and/or plant species present that degrade the
pollutant of interest?
C18 hydrocarbon

autoclaved control
Haloferax isolate
Halobacterium isolate
Halococcus isolate
gas-liquid chromatography to measure
hydrocarbon degradation
(Al-Mailem et al., 2010 Extremophiles)

Defining bioremediation by natural attenuation:

hydrocarbon degradation in the Arabian Gulf hypersaline coast
what conditions (nutrient, temperature, pH, salt etc) are necessary for
that activity?
increased salt increased hydrocarbon degradation

Haloferax isolate
Haloferax
Haloferax isolate
isolate
Halococcus isolate
Halobacterium isolate

(Al-Mailem et al., 2010 Extremophiles)

How could this hydrocarbon degradation activity by

Haloarchaea be improved?

General strategies for improving microbial bioremediation: stimulation or augmentation

Some existing bio-engineering tools

University of Minnesota Biocatalysis/Biodegradation
Database (UMBBD): enzymes, pathways, reactions,
compounds from hundreds of bacterial species of interest
(Gao et al., 2010)
MetaRouter: tracks possible breakdowns from a starting point
using all possible reactions (Pazos et al., 2005)
in silico modeling of altered strains: ex. Optstrain (Pharkya et
al. 2004), DESHARKY (Rodrigo et al. 2008)

How could this hydrocarbon degradation activity by

Haloarchaea be improved?

How could systems level knowledge help design stimulation or augmentation strategies?

need to know network topology of the pathway being added or altered as well as the
influence of the environment on that pathway
understand coupling of pathways to better integrate the engineered or altered pathway into
the rest of the host system
understand demands created by the new flux on resources needed for growth/survival:
energy, carbon, redox balance, transcriptional and translation capacity
is it possible to compensate by altering regulation by TFs etc, or by adding or deleting other
pathways?
understand effect of environment on pathway flux
understand role of noise in pathway regulation
if cooperation between multiple microbial species is used, then systems analysis can
evaluate impact of biodegradative flux on the multispecies consortia