Cleaning Up With Genomics: Applying Molecular Biology To Bioremediation

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Cleaning Up With Genomics Applying Molecular
Biology To Bioremediation

• By Derek R. Lovley
• Presented by Manal Ismail

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Background

• Microorganisms can aid in environmental
  restoration by oxidizing, binding, immobilizing,
  volatilizing or otherwise transforming
  contaminants.
• Bioremediation is simpler, cheaper and more
  environmentally friendly than other waste
  treatment methods like excavation and disposal.
• Bioremediation strategies are based on knowledge
  of the microorganisms that live in the
  contaminated environments.
• Unfortunately much of the required information
  about the use of microorganisms in bioremediation
  is not readily available.
• We need to construct models that predict the
  activity of microorganisms during bioremediation.

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Overview of bioremediaton

• Microorganisms use a diversity of enzymatic
  processes to remove contaminants.
• One example is the oxidation of toxic, organic
  contaminants to nontoxic products like carbon
  dioxide.
• Fe (III) is often the most abundant potential
  electron acceptor in subsurface environments.
• Geobacter species can oxidize organic compounds
  with the reduction of Fe (III) to Fe (II).
• Shewanella oneidensis was found to reduce U (VI)
  to U (IV) in culture, thus it is used for
  bioremediating uranium contaminated ground water,
  but have not been shown to be important in metal
  reduction.
• One of the most important types of bioremediation
  is reductive dechlorination, in which microbes
  remove chlorines from contaminants, by using
  these compounds as electron acceptors.

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Materials and MethodsA. Pre-genomic approaches
to bioremediation

• Samples from contaminated environment are
  incubated in the laboratory and the rates of
  contaminant degradation are documented.
• Attempts are made to isolate organisms
  responsible for bioremediation.
• This provides estimate of the potential metabolic
  activity of the microbial community, but doesnt
  tell much about the organisms responsible for
  bioremediation or why certain amendments
  stimulate their activity.
• Before the application of molecular techniques,
  we still dont know whether the organisms are
  responsible for bioremediation or not.

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Materials and Methods B. The 16S rRNA
approach

• 16S rRNA genes are highly conserved genes that
  are found in all microorganisms and provide
  phylogenic characterization of microorganisms.
• Scientists found that microorganisms that
  predominate during bioremediation are closely
  related to organisms that can be cultured from
  subsurface environments.
• The problem is that many of the organisms
  involved in bioremediation cannot be cultured or
  grown in the lab hence it is still not possible
  to study them.

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Materials and MethodsC. Analysis of Genes
involved in Bioremediation

• This can yield more information about microbial
  processes than the rRNA analysis.
• There is positive correlation between abundance
  of genes involved in bioremediation and the
  potential for degradation of contaminant.
• However, the genes for bioremediation can be
  present but not expressed.
• Often, increased mRNA concentrations for genes
  involved in bioremediation can be associated with
  higher rates of contaminant degradation.
• Highly sensitive methods that can detect mRNA for
  key bioremediation genes in single cells are now
  available. This technique coupled with 16SrRNA
  probing of the same environmental samples could
  provide data on which phylogenic groups of
  organisms are expressing the genes of interest.

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Materials and MethodsD. Genome enabled studies
of pure cultures

• Whole-genome sequencing is very helpful in
  promoting the understanding of bioremediation-rele
  vant microorganismsm, whose physiology has not
  previously been studied.
• By using whole-genome DNA microarrays, it is now
  possible to analyze the expression of all the
  genes in each genome under various environmental
  conditions.
• Also proteomic techniques enable researchers to
  identify which proteins are expressed.
• As genetic systems for organismsms involved in
  bioremediation are available, it is possible to
  elucidate the functions of many genes that were
  not known.

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Materials and MethodsE. In Silico Biology

• This is a technique to develop models of cell
  metabolism.
• Using this, we can predict the functioning of an
  organism in a complex environment not only in a
  laboratory culture.
• Substrates that can be metabolized and the
  nutrients that are required from the environment
  to support growth can be successfully predicted,
  as can the growth rates under various conditions.
• Such modeling can also greatly enhance the
  elucidation of the physiology of a particular
  microorganism.
• So far, such models have been limited to
  primarily to E.coli and pathogens.

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F. Environmental genomics BAC to the Future

• It could soon be possible to apply many of the
  same genome-enabled techniques that are being
  used in the study of mixed communities in
  contaminated environments.
• For example, genomic DNA extracted from
  environmental samples can be cloned into large
  cloning vectors, like Bacterial artificial
  chromosomes (BACs), to make a library of
  environmental genomic DNA.
• This allows evaluation of the genotype of
  microorganisms for which, as yet, there are not
  any pure-culture isolates.

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Results
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Conclusion

• The application of genome-enabled techniques to
  the study of bioremediation is clearly in its
  infancy.
• There are many technical issues that will need to
  be addressed before some of the more novel
  approaches like environmental genome sequencing,
  arrays or in silico modeling can be routinely
  used.