analysis of microbial diversity, their evolution as well as adaption. First,
metagenomics has greatly enhanced the knowledge that how microbes form
“bucket-brigades” for degrading xenobiotic compounds. It will help in the future
to find out basic processes of microbes and mention how the composition of a
community could be best complemented to enable degradation of a contaminant
when quorum sensing between various species is compulsory, to occur through
group process rather than by individual species. Metagenomics will provide an
appropriate database that will, in turn, provide construction of huge stock of genes
for the production of novel strains of microbes to be utilized for bioremediation
purposes.
The term “proteomics” was introduced in 1995. Proteomic studies are particularly
significant because it helps to observe the phenotype which is directly obtained by
the action of proteins than genome sequence (Kumavath and Deverapalli 2013).
Proteomics provides improved results when this technique is combined with
metabolomics and transcriptomics. Profiling of protein for the treatment of polluted
sites uses SDS–PAGE to characterize the microbes along with the ecology which is
responsible for the process of bioremediation. While studies of ecology focused on
the natural adaptations of the microorganisms in the surroundings they live, application of proteomics, the studies have given understanding into the systems used for
adaptation, precisely under thermophilic conditions. Proteomics is also important in
studying the physiological adaptations that microorganisms encounter during the
process of biodegradation (Malla et al. 2018). The advancements in 2-D electrophoresis (2-DE) used in compartmental proteomics had been made by a technique based
on multidimensional protein identification technology (MudPIT). Matrix-associated
laser desorption/ionization time-of-flight MS (MALDI-TOF-MS) is then repeatedly
used advancement of mass spectroscopy which has revolutionized environmental
proteome technique to identify the protein of interest in few minutes, removed from
2-DE gels, by the generation of peptide mass fingerprinting for identification of
protein of interest. Surface-enhanced laser-desorption-ionization MS (SELDI-TOFMS) is the amalgamation of direct portions of sample loaded on a chip impregnated
with MALDI-TOF-MS analysis. Several proteins that express differentially were
analysed by the use of SELDI-TOF-MS in Mytilus edulis which was introduced to
polyaromatic hydrocarbons and heavy metals (Kumavath and Deverapalli 2013).
Though proteomics would continue to focus on functional transcriptomics, as the
protein molecules are the leading players in an on-site enzymatic reaction by
microbes, along with this every molecule of protein represents itself as the last
product of gene expression. Complete profiling of protein provides not only knowledge about every single living organism, but also enlightens about the fate as well as
the destination of a molecule of protein present in and out of the cell can be identified
only with the help of transcriptomics and proteomics approaches both together
(Coelho et al. 2015).
The subgroup of the genes that are transcribed in any of the given living
organisms is called the transcriptome that presents a dynamic link among genome,
proteome and cellular phenotype. DNA microarray is an efficient tool in
transcriptomics that enables one to determine the expression level of every gene of
15 The Role of Microorganisms in Remediation of Environmental Contaminants
445
metagenomics has greatly enhanced the knowledge that how microbes form
“bucket-brigades” for degrading xenobiotic compounds. It will help in the future
to find out basic processes of microbes and mention how the composition of a
community could be best complemented to enable degradation of a contaminant
when quorum sensing between various species is compulsory, to occur through
group process rather than by individual species. Metagenomics will provide an
appropriate database that will, in turn, provide construction of huge stock of genes
for the production of novel strains of microbes to be utilized for bioremediation
purposes.
The term “proteomics” was introduced in 1995. Proteomic studies are particularly
significant because it helps to observe the phenotype which is directly obtained by
the action of proteins than genome sequence (Kumavath and Deverapalli 2013).
Proteomics provides improved results when this technique is combined with
metabolomics and transcriptomics. Profiling of protein for the treatment of polluted
sites uses SDS–PAGE to characterize the microbes along with the ecology which is
responsible for the process of bioremediation. While studies of ecology focused on
the natural adaptations of the microorganisms in the surroundings they live, application of proteomics, the studies have given understanding into the systems used for
adaptation, precisely under thermophilic conditions. Proteomics is also important in
studying the physiological adaptations that microorganisms encounter during the
process of biodegradation (Malla et al. 2018). The advancements in 2-D electrophoresis (2-DE) used in compartmental proteomics had been made by a technique based
on multidimensional protein identification technology (MudPIT). Matrix-associated
laser desorption/ionization time-of-flight MS (MALDI-TOF-MS) is then repeatedly
used advancement of mass spectroscopy which has revolutionized environmental
proteome technique to identify the protein of interest in few minutes, removed from
2-DE gels, by the generation of peptide mass fingerprinting for identification of
protein of interest. Surface-enhanced laser-desorption-ionization MS (SELDI-TOFMS) is the amalgamation of direct portions of sample loaded on a chip impregnated
with MALDI-TOF-MS analysis. Several proteins that express differentially were
analysed by the use of SELDI-TOF-MS in Mytilus edulis which was introduced to
polyaromatic hydrocarbons and heavy metals (Kumavath and Deverapalli 2013).
Though proteomics would continue to focus on functional transcriptomics, as the
protein molecules are the leading players in an on-site enzymatic reaction by
microbes, along with this every molecule of protein represents itself as the last
product of gene expression. Complete profiling of protein provides not only knowledge about every single living organism, but also enlightens about the fate as well as
the destination of a molecule of protein present in and out of the cell can be identified
only with the help of transcriptomics and proteomics approaches both together
(Coelho et al. 2015).
The subgroup of the genes that are transcribed in any of the given living
organisms is called the transcriptome that presents a dynamic link among genome,
proteome and cellular phenotype. DNA microarray is an efficient tool in
transcriptomics that enables one to determine the expression level of every gene of
15 The Role of Microorganisms in Remediation of Environmental Contaminants
445