Environmental Engineering Reference
In-Depth Information
microorganisms; and amendments to microor-
ganisms with desired bioremediation capabilities.
for key bioremediation genes in single cells are
now available. This technique, coupled with 16S
rRNA probing of the same environmental sam-
ples, could provide data on which phylogenetic
groups of organisms are expressing the genes of
interest.
The 16S rRNA Approach
A significant advance
in the field of microbial ecology was the find-
ing that the sequences of highly conserved genes
that are found in all microorganisms, most nota-
bly the 16S rRNA genes could provide a phylo-
genetic characterization of the microorganisms
that comprise microbial communities. This was
a boon to the field of bioremediation because it
meant that by analyzing 16S rRNA sequences in
contaminated environments, it was possible to
determine definitively the phylogenetic place-
ment of the microorganisms that are associated
with bioremediation processes.
Application of Genomics
Although the molec-
ular techniques have outlined to improve our
understanding of bioremediation, investigations
in this field are on the cusp of a new era which
promises for the first time to provide a global
insight into the metabolic potential and activity
of microorganisms living in contaminated envi-
ronments. This is the “genomics era” of bio-
remediation. With the application of genome-
enabled techniques to the study of not only
pure cultures, but also environmental samples,
it will be possible to develop the models that
are needed to model microbial activity predica-
tively under various bioremediation strategies
(Fig.
1.6
).
The application of genomics to bioremedia-
tion initially revolutionized the study of pure
cultures, which serve as models for important
bioremediation processes (Nierman and Nel-
son
2002
). Complete, or nearly complete, ge-
nome sequences are now available for several
organisms that are important in bioremediation
(Table
1.1
). Whole genome sequencing is espe-
cially helpful in promoting the understanding of
bioremediation-relevant microorganisms, whose
physiology has not previously been studied in
detail. For example, as noted earlier, molecular
analyses have indicated that
Geobacter
species
are important in the bioremediation of organic
and metal contaminants in subsurface environ-
ments. The sequencing of several genomes of
microorganisms of the genus
Geobacter
, as well
as closely related organisms, has significantly
altered the concept of how
Geobacter
species
function in contaminated subsurface environ-
ments. For instance, before the sequencing of
the
Geobacter
genomes,
Geobacter
species were
thought to be nonmotile, but genes encoding fla-
gella were subsequently discovered in the
Geo-
bacter
genomes. Further investigations revealed
Analysis of Genes Involved in Bioremedia-
tion
Examining the presence and expression of
the key genes involved in bioremediation can
yield more information on microbial processes
than analysis of 16S rRNA sequences. In general,
there is a positive correlation between the relative
abundance of the genes involved in bioremedia-
tion and the potential for contaminant degrada-
tion. However, the genes for bioremediation can
be present but not expressed. Therefore, there has
been an increased, emphasis on quantifying the
levels of mRNA for key bioremediation genes.
Often, increased mRNA concentrations can be, at
least qualitatively, associated with higher rates of
contaminant degradation. For example, the con-
centrations of mRNA for
nahA
, a gene involved
in aerobic degradation of naphthalene were posi-
tively correlated with rates of naphthalene deg-
radation in hydrocarbon-contaminated soil. The
reduction of soluble ionic mercury, Hg(II), to
volatile Hg(0), is one mechanism for removing
mercury from water; the concentration of mRNA
for
merA
, a gene involved in Hg(II) reduction
was highest in mercury contaminated waters with
the highest rates of Hg(II) reduction. However,
the concentration of
merA
was not always pro-
portional to the rate of Hg(II) reduction illustrat-
ing that factors other than gene transcription can
control the rates of bioremediation processes.
Highly sensitive methods that can detect mRNA
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