Enzymes that are particularly involved in bioremediation of hydrocarbon
compounds are dehydrogenase, oxygenase and enzymes that can degrade lignin,
which includes: fungal laccases and peroxidase including both lignin peroxidase and
manganese peroxidase. These extracellular enzymes catalyze free radical formation
by carrying out oxidation and rendering destabilization of bonds in a molecule
(Haritash and Kaushik2009). A broad range of bacteria and fungi produces several
extracellular enzymes including proteases, cellulases, amylases, xylanases,
phosphatases, phytases and esterases. These biocatalysts not only are physiologically important for living organisms but also help to catalyze the hydrolysis of large
molecules (Gianfreda and Rao 2004).
15.6 Molecular and Omnics Approaches Used
for the Modification of Microbes to Increase
Bioremediation
Applications of genetically engineered microbes (GEMs) in biodegradation have
been in limelight to improvise the biodegradation of toxic wastes under in vitro
conditions over past decades. The GEMs have the high biodegradative capacity;
therefore, they are used in bioremediation process monitoring, strain monitoring,
stress response, end-point analysis and toxicity assessment (Das and Chandran 2011;
Singh et al. 2011; Joutey et al. 2013). A GEM is a microbe whose genetic material
has been transformed by the use of genetic engineering techniques, which are
collectively known as rDNA technology (Joutey et al. 2013). Recombinant DNA
technology targets the utilization of various techniques including PCR, in situ
hybridization, antisense RNA technique, enzyme-specific antibodies and sitedirected mutagenesis, which allows betterment of the metabolic structure of
microorganisms and helps in higher accumulation of heavy metals or decreases
their harmful effect, by the cleaning of water bodies. The most commonly used
method among these includes engineering techniques with single genes or operon
system, construction of pathway and modification of the sequences of genes that
already exist. Tests of DNA can show the presence of specific microbial potential
and by using enzyme-specific immunoglobulins can predict the action of metabolic
enzymes in the process of biodegradation of pollutants. DNA probes those targets
only particular genetic sequences, i.e. the particular genes which are responsible for
the bioremediating capability of a microbe, which can be used to identify and
characterize a polluted site throughout the process of bioremediation. The genetically first two modified bacterial strains were P. aeruginosa (NRRL B-5472) and
P. putida (NRRL B-5473); both of these contained genes for the biodegradation of
naphthalene, salicylate and camphor. Pseudomonas fluorescens HK44, which is
capable of degrading naphthalene, presents the first example of a GEM for purpose
of bioremediation (Coelho et al. 2015). Enzymatic bioremediation improvised by
molecular tools can be particularly suitable to meet the demands of a place where
rapid remediation is necessary to eliminate pollutants. Molecular tools help us to
increase expression levels by manipulations of not only physiochemical conditions
15 The Role of Microorganisms in Remediation of Environmental Contaminants
441
compounds are dehydrogenase, oxygenase and enzymes that can degrade lignin,
which includes: fungal laccases and peroxidase including both lignin peroxidase and
manganese peroxidase. These extracellular enzymes catalyze free radical formation
by carrying out oxidation and rendering destabilization of bonds in a molecule
(Haritash and Kaushik2009). A broad range of bacteria and fungi produces several
extracellular enzymes including proteases, cellulases, amylases, xylanases,
phosphatases, phytases and esterases. These biocatalysts not only are physiologically important for living organisms but also help to catalyze the hydrolysis of large
molecules (Gianfreda and Rao 2004).
15.6 Molecular and Omnics Approaches Used
for the Modification of Microbes to Increase
Bioremediation
Applications of genetically engineered microbes (GEMs) in biodegradation have
been in limelight to improvise the biodegradation of toxic wastes under in vitro
conditions over past decades. The GEMs have the high biodegradative capacity;
therefore, they are used in bioremediation process monitoring, strain monitoring,
stress response, end-point analysis and toxicity assessment (Das and Chandran 2011;
Singh et al. 2011; Joutey et al. 2013). A GEM is a microbe whose genetic material
has been transformed by the use of genetic engineering techniques, which are
collectively known as rDNA technology (Joutey et al. 2013). Recombinant DNA
technology targets the utilization of various techniques including PCR, in situ
hybridization, antisense RNA technique, enzyme-specific antibodies and sitedirected mutagenesis, which allows betterment of the metabolic structure of
microorganisms and helps in higher accumulation of heavy metals or decreases
their harmful effect, by the cleaning of water bodies. The most commonly used
method among these includes engineering techniques with single genes or operon
system, construction of pathway and modification of the sequences of genes that
already exist. Tests of DNA can show the presence of specific microbial potential
and by using enzyme-specific immunoglobulins can predict the action of metabolic
enzymes in the process of biodegradation of pollutants. DNA probes those targets
only particular genetic sequences, i.e. the particular genes which are responsible for
the bioremediating capability of a microbe, which can be used to identify and
characterize a polluted site throughout the process of bioremediation. The genetically first two modified bacterial strains were P. aeruginosa (NRRL B-5472) and
P. putida (NRRL B-5473); both of these contained genes for the biodegradation of
naphthalene, salicylate and camphor. Pseudomonas fluorescens HK44, which is
capable of degrading naphthalene, presents the first example of a GEM for purpose
of bioremediation (Coelho et al. 2015). Enzymatic bioremediation improvised by
molecular tools can be particularly suitable to meet the demands of a place where
rapid remediation is necessary to eliminate pollutants. Molecular tools help us to
increase expression levels by manipulations of not only physiochemical conditions
15 The Role of Microorganisms in Remediation of Environmental Contaminants
441