strategies. These techniques not only prove the existence of microbes in polluted
sites but also reveal the undetectable complex relationships among them.
This book chapter presents an overview of the different applications of molecular
methods in bioremediation of hydrocarbons and other pollutants in environmental
matrices and an outline of recent advances in the applications of such techniques.
Keywords Bioremediation · Metagenomics · Metaproteomics · Metabolomics ·
Pyrosequencing · Biodegradation · PCR · DGGE · DNA hybridization
1 Introduction
The tremendous increases in industrialization and in the extraction of natural
resources have created extreme environmental contamination and pollution. Many
toxic compounds have been dispersed in numerous contaminated sites. Varied
evidence shows higher risks to human health: cocktails of pollutants in nature are
causing a global epidemic of cancer and other degenerative diseases. These types of
pollutants are mainly classified as inorganic or organic. To make environments safe
for human habitation and food consumption, developing innovative and economically low-cost solutions for decontaminating polluted environments is a challenging
task. In developed countries such as the UK, USA, Canada, Australia, Japan, and
European countries, much progress has been made as compared to India. In India,
evaluation of the developments in laboratories is urgently needed.
New molecular techniques provide a novel opportunity to proceed with the
required microbial culturing and have greatly increased the available methods for
delineating bacterial diversity and functionality during the bioremediation of hazardous industrial waste. Currently, only a fraction of the potent microorganisms
involved in biodegradation can be cultured by using standard laboratory agars and
different pollutants from various ecosystems (Chikere 2000; Malik et al. 2008).
Comparative study between molecular/metagenomic and culture-dependent
methods states that only about 1% of all microorganisms are amenable to culture
(Mallik et al. 2008). In many cases, the concept of phylogenetic diversity has been
key for the development of more effective microbial culture methods by the
improvement of media, extended incubation period, and various growth factors
such as temperature, pH, and atmospheric conditions (Rajendhran and Gunasekaran
2011). However, it is the subject of great efforts to evaluate the total microbial
diversity/dynamics in various environments, a persisting challenge especially during
bioremediation of industrial hazardous waste (Chikere and Ughala 2011; Chikere
et al. 2011a, b). For evaluation of microbial communities, research experiments rely
on new rapid methods for characterization of cellular constituents such as proteins
(enzymes), nucleic acids, and specific compounds (Maila 2005; Maila et al. 2005,
2006; Montiel et al. 2009). These molecules can be extracted directly from the
polluted soil and used to elucidate microbial community composition during bioremediation (Simon and Daniel 2011). This book chapter presents recent techniques
438
S. K. Shekhar et al.
sites but also reveal the undetectable complex relationships among them.
This book chapter presents an overview of the different applications of molecular
methods in bioremediation of hydrocarbons and other pollutants in environmental
matrices and an outline of recent advances in the applications of such techniques.
Keywords Bioremediation · Metagenomics · Metaproteomics · Metabolomics ·
Pyrosequencing · Biodegradation · PCR · DGGE · DNA hybridization
1 Introduction
The tremendous increases in industrialization and in the extraction of natural
resources have created extreme environmental contamination and pollution. Many
toxic compounds have been dispersed in numerous contaminated sites. Varied
evidence shows higher risks to human health: cocktails of pollutants in nature are
causing a global epidemic of cancer and other degenerative diseases. These types of
pollutants are mainly classified as inorganic or organic. To make environments safe
for human habitation and food consumption, developing innovative and economically low-cost solutions for decontaminating polluted environments is a challenging
task. In developed countries such as the UK, USA, Canada, Australia, Japan, and
European countries, much progress has been made as compared to India. In India,
evaluation of the developments in laboratories is urgently needed.
New molecular techniques provide a novel opportunity to proceed with the
required microbial culturing and have greatly increased the available methods for
delineating bacterial diversity and functionality during the bioremediation of hazardous industrial waste. Currently, only a fraction of the potent microorganisms
involved in biodegradation can be cultured by using standard laboratory agars and
different pollutants from various ecosystems (Chikere 2000; Malik et al. 2008).
Comparative study between molecular/metagenomic and culture-dependent
methods states that only about 1% of all microorganisms are amenable to culture
(Mallik et al. 2008). In many cases, the concept of phylogenetic diversity has been
key for the development of more effective microbial culture methods by the
improvement of media, extended incubation period, and various growth factors
such as temperature, pH, and atmospheric conditions (Rajendhran and Gunasekaran
2011). However, it is the subject of great efforts to evaluate the total microbial
diversity/dynamics in various environments, a persisting challenge especially during
bioremediation of industrial hazardous waste (Chikere and Ughala 2011; Chikere
et al. 2011a, b). For evaluation of microbial communities, research experiments rely
on new rapid methods for characterization of cellular constituents such as proteins
(enzymes), nucleic acids, and specific compounds (Maila 2005; Maila et al. 2005,
2006; Montiel et al. 2009). These molecules can be extracted directly from the
polluted soil and used to elucidate microbial community composition during bioremediation (Simon and Daniel 2011). This book chapter presents recent techniques
438
S. K. Shekhar et al.