Chapter 18
Molecular Technologies for Assessment
of Bioremediation and Characterization
of Microbial Communities at PollutantContaminated Sites
Sudhir Kumar Shekhar, Jai Godheja, and Dinesh Raj Modi
Abstract Among the various microbial biodegradation techniques, molecular
microbiology methods have revolutionized microbial biotechnology, thus leading
to rapid and high-throughput methods for culture-independent assessment and
exploitation of microbes present in polluted environments. Whether organic or
inorganic, pollutants present in contaminated sites can cause an imbalance in the
ecosystem by affecting the flora and fauna. The efficiency of naturally occurring
microorganisms for field bioremediation could be significantly improved by the
microbial molecular biology approach for its comparatively high efficiency and
safety. Many techniques, including polymerase chain reaction (PCR), fluorescent
in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), amplified ribosomal DNA restriction
analysis (ARDRA), terminal-restriction fragment length polymorphism (TRFLP),
single-strand conformation polymorphism (SSCP), and ribosomal intergenic spacer
analysis (RISA) can be selectively employed in microbial flora and ecology research.
Recent methods such as genotypic profiling, metagenomics, ultrafast genome
pyrosequencing, metatranscriptomics, metaproteomics, and metabolomics have provided exemplary knowledge about microbial communities and their role in the
bioremediation of environmental pollutants.
Only 1% of the microbial diversity can be cultured by traditional techniques.
Thus, the application of molecular techniques in studying microbial populations in
polluted sites without the need for culturing has led to the discovery of novel and
previously unrecognized microorganisms. Such complex microbial diversity and
dynamics in contaminated soil offer a clear opportunity for bioremediation
S. K. Shekhar · D. R. Modi (*)
Department of Biotechnology (DBT), School for Bioscience and Biotechnology (SBBT),
Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh,
India
J. Godheja
School of Life and Allied Sciences, ITM University, Naya Raipur, Chhattisgarh, India
© Springer Nature Singapore Pte Ltd. 2020
R. N. Bharagava, G. Saxena (eds.), Bioremediation of Industrial Waste for
Environmental Safety, https://doi.org/10.1007/978-981-13-3426-9_18
437
Molecular Technologies for Assessment
of Bioremediation and Characterization
of Microbial Communities at PollutantContaminated Sites
Sudhir Kumar Shekhar, Jai Godheja, and Dinesh Raj Modi
Abstract Among the various microbial biodegradation techniques, molecular
microbiology methods have revolutionized microbial biotechnology, thus leading
to rapid and high-throughput methods for culture-independent assessment and
exploitation of microbes present in polluted environments. Whether organic or
inorganic, pollutants present in contaminated sites can cause an imbalance in the
ecosystem by affecting the flora and fauna. The efficiency of naturally occurring
microorganisms for field bioremediation could be significantly improved by the
microbial molecular biology approach for its comparatively high efficiency and
safety. Many techniques, including polymerase chain reaction (PCR), fluorescent
in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), amplified ribosomal DNA restriction
analysis (ARDRA), terminal-restriction fragment length polymorphism (TRFLP),
single-strand conformation polymorphism (SSCP), and ribosomal intergenic spacer
analysis (RISA) can be selectively employed in microbial flora and ecology research.
Recent methods such as genotypic profiling, metagenomics, ultrafast genome
pyrosequencing, metatranscriptomics, metaproteomics, and metabolomics have provided exemplary knowledge about microbial communities and their role in the
bioremediation of environmental pollutants.
Only 1% of the microbial diversity can be cultured by traditional techniques.
Thus, the application of molecular techniques in studying microbial populations in
polluted sites without the need for culturing has led to the discovery of novel and
previously unrecognized microorganisms. Such complex microbial diversity and
dynamics in contaminated soil offer a clear opportunity for bioremediation
S. K. Shekhar · D. R. Modi (*)
Department of Biotechnology (DBT), School for Bioscience and Biotechnology (SBBT),
Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, Uttar Pradesh,
India
J. Godheja
School of Life and Allied Sciences, ITM University, Naya Raipur, Chhattisgarh, India
© Springer Nature Singapore Pte Ltd. 2020
R. N. Bharagava, G. Saxena (eds.), Bioremediation of Industrial Waste for
Environmental Safety, https://doi.org/10.1007/978-981-13-3426-9_18
437