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Exploiting microbes to degrade wastes and xenobiotics


Wastewater, Pesticides, herbicides, petrochemicals and products (eg. ... used by oil industry to destroy oily wastes, also used for sludges from sewage ... – PowerPoint PPT presentation

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Title: Exploiting microbes to degrade wastes and xenobiotics

  • Bioremediation
  • Exploiting microbes to degrade wastes and
  • Dr. William Stafford
  • wstafford_at_uwc.ac.za

  • Bioremediation is defined as the process whereby
    organic wastes are biologically degraded under
    controlled conditions to an innocuous state, or
    to levels below concentration limits established
    by regulatory authorities.
  • Wastewater, Pesticides, herbicides,
    petrochemicals and products (eg. Oil, Plastics,,
    trichloroethene, polychlorobiphenyls (PCBs),
    dioxins dibenzofurans, and heavy metals can all
    persist in the environment.

Agent orange 2,4 Dichlorophenoxyacetic acid and
2,4,5-Trichlorophenoxyacetic acid
The need for Bioremediation
  • The quality of life on Earth is linked
    inextricably to the overall quality of the
  • The problems associated with contaminated sites
    now assume increasing prominence in many
  • Contaminated lands generally result from past
    industrial activities when awareness of the
    health and environmental effects connected with
    the production, use, and disposal of hazardous
    substances were less well recognized than today.
  • Bioremediation clean up contaminated site

  • In many cases the clean-up of contaminated sites
    has been carried out using physical and chemical
    methods such as immobilization, removal (dig and
    dump), thermal, and solvent treatments.
  • Bioremediation is cheaper than the chemical and
    physical options, and can deal with lower
    concentrations of contaminants more effectively,
    although the process may take longer.
  • Bioremediation typically uses naturally occurring
    bacteria and fungi or plants to degrade or
    detoxify substances hazardous to human health
    and/or the environment.

Bioremediation methods
  • Use the indigenous microbial population.
  • Encourage the indigenous population.
  • Bioaugmentation the addition of adapted or
    designed inoculants.
  • Use of genetically modified micro-organisms.
  • Phytoremediation.

Bioremediation strategies
In situ technologies Bioremediation Technologies
  • Criteria for in situ bioremediation
  • 1) microbes must exist that can biotransform
  • 2) organisms must be able to convert chemicals at
    reasonable rates and meet regulatory standards,
  • 3) toxic breakdown products must not be formed
  • 4) site must not contain specific microbial
  • 5) favorable conditions must be present
    (achievable), 6) cost must be less or equivalent
    to other technologies.

Landfarming (land treatment).
  • Frequently used by oil industry to destroy oily
    wastes, also used for sludges from sewage plants,
    power plants, industrial facilities. Add wastes,
    contaminated water or contaminated soils to
    fertile soils, containing microbial populations.
    Important considerations 1) fertilization to
    achieve optimum CNP, 2) supplementation to
    provide available oxygen (tilling) 3) moisture
    control, 4) inoculation (optional) 5) pH control
  • For these treatments, soil typically rests on
    liner system with engineered drainage systems in

  • In natural ecosystems, plants act as filters and
    metabolize substances generated by nature.
  • Phytoremediation uses higher plants to remove
  • Processes includes uptake into the plant and
    biodegradation by microorganisms colonizing root
    surfaces and rooting zone (rhizosphere).
  • Numerous plant types have been assessed and been
    found to be successful including various wetland
    plants (cattails, rushes, etc.), metal
    accumulating plants (astragalis), hybrid poplars
    (for TCE).
  • Limited to surface sediments 1-2 m deep.
    Furthermore, contaminants that are strongly
    sorbed onto the physical soil matrix may be
    resistant to phytoremediation.

  • Bioventing is the most common in situ treatment
    and involves supplying air and nutrients through
    wells to contaminated soil to stimulate the
    indigenous bacteria. Bioventing employs low air
    flow rates and provides only the amount of oxygen
    necessary for the biodegradation while minimizing
    volatilization and release of contaminants to the
  • Biosparging involves the injection of air under
    pressure below the water table to increase
    groundwater oxygen concentrations and enhance the
    rate of biological degradation of contaminants by
    naturally occurring bacteria. Biosparging
    increases the mixing in the saturated zone and
    thereby increases the contact between soil and

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  • Bioaugmentation
  • Bioaugmentation (seeding) has been used some in
    situ in soil and groundwater decontamination. A
    problem is that the nonindigenous microorganisms
    may not well enough with an indigenous population
    to develop and sustain long-term useful
    population levels
  • Composting technology
  • Contaminated material is mixed with readily
    degradable organic material (straw, bark, wood
    chips, etc.). Mixture is fertilized as
    appropriate, and adequate moisture and oxygen are
    maintained. In composting, microbial activity
    produces heat, which builds up in the compost
    (50-60C and higher). Composting has been
    successfully used for chlorophenols such as
    trinitrotoluene (TNT).

30 VSS destructionAerobic, mostlyPasteurization
(50 to 70 C)Static pile 28 days then 30 day
cureWindrow 30 days, 55 CIn vesselFeed
sludge solids 40
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Ex situ technologies Bioremediation Technologies
  • Bioreactors
  • A bioreactor is a contained system where
    contaminated materials are mixed in a matrix and
    environmental variables can be controlled.
    Systems can be either static or stirred.
    Influent and effluent measurements determine
    relative success and provide for monitoring of
    final material.
  • There are two main Bioreactor designs batch and
    chemostat (continuous flow). Batch reactors have
    the advantage of simplicity, ease of disposal,
    control over effluent release. Chemostats offer
    more flexibility of controlling growth rates and
    degradation rates and avoid toxicity problems,
    associated with contaminants such as TCE.

  • Another type of contained reactor system is the
    fixed film or immobilized cell bioreactor.
    Microbial cells become attached to an appropriate
    matrix (glass beads, fibers, polyurethane foam,
    alginate beads, activated carbon or
    polyacrylamide beads, etc.). The cells form a
    thin film, a biofilm, that becomes tolerant to
    greater concentrations of chemicals than free
    living cells are. The chemical solution is then
    passed over the biofilm, which results in rapid
    biodegradation due to high cell density and
    activity. The biofilter is a bioreactor designed
    to destroy volatile contaminants. Microorganisms
    are grown on solid matrices, and a contaminant
    gas stream is passed through the matrix.
    Microbial action destroys the contaminants.

  • Bioremediation- transformations in detail
  • Oxic Degradation of Hydrocarbons
  • Microbes that utilize hydrocarbons
  • Pseudomonas spp. ,Mycobacterium, Nocardia
  • Some yeasts and molds
  • Long chain aliphatic hydrocarbons are converted
    into fatty acids by oxidation of a terminal
    carbon (to an alcohol, then an aldehyde, then a
    carboxylic acid). The fatty acids thus generated
    are activated with CoA and simply fed into the
    normal pathway for fatty acid degradation - beta
  • Which of the following (a, b, c, d, e) would be
    recalcitrant to oxic degradation?
  • Generally, hydrocarbons that have additional
    groups (e.g. -CH3 , -Cl atoms) at the position
    destined to become the beta-carbon in the beta
    oxidation pathway will be recalcitrant to oxic
    degradation. However, a hydroxyl group is
    favorable at this position since the pathway
    normally generates a beta alcohol anyway. A
    double bond between the alpha and the beta
    carbons is also favorable.

  • Oxic degradation of aromatic hydrocarbons
  • Complex aromatic compounds are first converted to
    a "starting substrate" such as catechol. Probably
    using a monooxygenase
  • A dioxygenase breaks open the aromatic ring of
    catechol, producing cis,cis-muconate, an
    unsaturated dicarboxylic acid
  • This product is then oxidized to acetyl-CoAs by
    the aforementioned beta oxidation path.
    Substitution of aromatic rings (e.g. with -CH3 or
    -Cl) interferes with the oxic degradation of the
    aromatic ring.
  • For instance, the herbicides 2,4-D and 2,4,5- are
    aromatic rings, respectively containing two and
    three chlorine substitutions. The additional
    chlorine atom makes 2,4,5-T five-fold less
    degradable compared to 2,4 D.

Anoxic Degradation of Xenobiotics
  • In anoxic environments, since oxygen is not
    available as an electron acceptor, microorganisms
    utilize alternates such as nitrate, sulfate and
    ferric iron. or xenobiotics as another electron
  • Two broad strategies for anoxic degradation
  • Reductive dechlorination e.g. the substrate
    3-chlorobenzoate can be dechlorinated by
    reduction of the chlorine atom, producing
    benzoate and chloride anion
  • e.g. denitrifiers and sulfate reducing bacteria

Reductive ring cleavage
  • E.g. benzoate can be converted to a saturated
    dicarboxylic acid. There are three principal
    steps in the conversion
  • (i) Activation - ATP energy is usred to attach
    CoA to the carboxylic acid group of benzoate,
    producing a reactive mixed anhydride.
  • (ii) Reduction - NADPH is used to reduce the
    carbons within the aromatic ring to produce
  • (iii) Ring cleavage - carbon 2 of the hexanyl
    ring is oxidized (to an alcohol, then a
    ketone, then a carboxylic acid), leading to
    the cleavage of the ring system.
  • (iv) The saturated dicarboxylic acid product
    is oxidized to acetyl-CoAs by the
    beta- oxidation pathway.

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  • New possibilities
  • Bioremediation Rocks JAMAIS CASCIO DEC12 2003
  • Geobacter sulfurreducens -- get used to seeing
    that name. It may well be the key to cleaning up
    some of the most dangerous radioactive wastes
    sites around. Best of all, it's completely
  • G. sulfurreducens is a microbe that is able to
    turn the soluble form of uranium contaminating
    groundwater around nuclear weapons production
    sites (such as Rifle Mill in Colorado) into an
    easily-collected precipitate. Researchers with
    the Department of Energy have managed to use the
    bacteria to reduce uranium in the groundwater
    around Rifle Mill by 90. The microbe occurs
    naturally in the ground its growth is stimulated
    by adding vinegar to the soil.
  • But now, biologists at The Institute for Genomic
    Research (TIGR) in Rockville, Maryland, have
    sequenced the microbe's DNA, figuring out how it
    manages to detect and "eat" uranium, producing
    minute amounts of electricity. Their report is in
    today's edition of Science the illustration at
    right is from their online supporting material.
    TIGR and University of Massachusetts in Amherst
    researchers believe that they will be able to
    manipulate the microbe's genome to make its
    uranium-electricity conversion faster and more

Genomics and bioremediators!
See Lovely, D.R. Cleaning up with Genomics
applying molecular biology to bioremediation.
Nature Reviews Microbiology October 2003.
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