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© The Author(s), under exclusive license to Springer Nature Switzerland AG 2020
R. K. Dubey et al., Unravelling the Soil Microbiome, SpringerBriefs in
Environmental Science, https://doi.org/10.1007/978-3-030-15516-2_3
Chapter 3
Methods for Exploring Soil Microbial
Diversity
Abstract Belowground microbial processes are at the helm of terrestrial ecosystem functions, and the enormous diversity of soil microorganisms acts as a key
player. Thus, understanding the community dynamics of microorganisms in the soil
is essential to know their distribution, abundance, and structure. Further, it is also
important to know how these communities are shaped in structure and function in
response to changes in space and time. Various microbial diversity analysis methods—fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphisms, and the automated
version of ribosomal intergenic spacer analysis, RISA (ARISA)—have been developed to analyse the diversity of soil microorganisms based on their genetic structure. However, methods such as phospholipid and fatty acid analysis utilise the
differences in lipid components of the microbial cell membrane to analyse their
diversity. In the present chapter, we explore the conventional methods of soil microbial diversity analysis.
Keywords Automated RISA (ribosomal intergenic spacer analysis (ARISA) ·
Community dynamics · Denaturing gradient gel electrophoresis (DGGE) ·
Fluorescence in situ hybridization (FISH) · Terminal restriction fragment length
polymorphism (T-RFLP)
Since the inception of soil microbiology, various techniques have been employed
for identification and characterization of soil microbial communities (Fig. 3.1). The
microbial identification techniques commonly utilised for improving scientific
understanding are explained in the further sections.
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2020
R. K. Dubey et al., Unravelling the Soil Microbiome, SpringerBriefs in
Environmental Science, https://doi.org/10.1007/978-3-030-15516-2_3
Chapter 3
Methods for Exploring Soil Microbial
Diversity
Abstract Belowground microbial processes are at the helm of terrestrial ecosystem functions, and the enormous diversity of soil microorganisms acts as a key
player. Thus, understanding the community dynamics of microorganisms in the soil
is essential to know their distribution, abundance, and structure. Further, it is also
important to know how these communities are shaped in structure and function in
response to changes in space and time. Various microbial diversity analysis methods—fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphisms, and the automated
version of ribosomal intergenic spacer analysis, RISA (ARISA)—have been developed to analyse the diversity of soil microorganisms based on their genetic structure. However, methods such as phospholipid and fatty acid analysis utilise the
differences in lipid components of the microbial cell membrane to analyse their
diversity. In the present chapter, we explore the conventional methods of soil microbial diversity analysis.
Keywords Automated RISA (ribosomal intergenic spacer analysis (ARISA) ·
Community dynamics · Denaturing gradient gel electrophoresis (DGGE) ·
Fluorescence in situ hybridization (FISH) · Terminal restriction fragment length
polymorphism (T-RFLP)
Since the inception of soil microbiology, various techniques have been employed
for identification and characterization of soil microbial communities (Fig. 3.1). The
microbial identification techniques commonly utilised for improving scientific
understanding are explained in the further sections.