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Metagenomics: New Challenges Ahead in Molecular Soil Ecology

BY: Dr. Suresh Kaushik | Category: Environmental-Biotechnology | Submitted: 2013-06-26 16:09:37
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Article Summary: "Metagenomics is the culture-independent analysis of a mixture of microbial genomes using an approach based either on expression or on sequencing. This involves isolating DNA from an environmental sample, cloning the DNA into a suitable vector, transforming the clones into a host bacterium and screening the resulting transformant.."

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Metagenomics is the culture-independent analysis of a mixture of microbial genomes using an approach based either on expression or on sequencing. The term is derived and coined from the statistical concept of meta-analysis and genomics to capture the notion of analysis of a collection of similar but not identical items. The meta-analysis is a process of statistically combining separate analyses, that is, analysis of analysis. Metagenomics is the application of the methods of genomics to microbial assemblages. It involves studying the genetic makeup of many microbes in an environment simultaneously, and makes accessible the many types of microbes that cannot be grown in the lab and therefore cannot be studies using the central tool of classical microbiology. Metagenomics also enables the study of entire microbial communities, offering a window to intact microbial system. The emerging field of metagenomics presents the greatest opportunity to revolutionize understanding of the living world.


Metagenomics is the analysis of all of the microbial genomes from our environment. It requires neither prior cultivation of the organism present, nor prior knowledge of the community inhabitants or target sequences. This involves isolating DNA from an environmental sample, cloning the DNA into a suitable vector, transforming the clones into a host bacterium and screening the resulting transformants. The multi-step process consists of four steps namely,

• Isolation of genetic material
• Manipulation of the genetic material
• Library construction
• Analysis of genetic material in the metagenomics library

Soil is considered as a complex environment, which appears to be a major reservoir of microbial genetic diversity. Methods described for metagenomics DNA isolation from soil samples can be broadly classified into direct and indirect extraction procedures.
The next advance was the construction of a metagenomics library with DNA derived from a mixture of organisms. Metagenomics libraries are created by shotgun cloning DNA fragment from an environment samples.
Two types of screening have been used to identify clones carrying desired traits from metagenomics libraries:


This can involve complete sequencing of clones containing phylogenetic anchors that indicate the taxonomic group. Random sequencing can also be conducted. Once a gene of interest is identified, phylogenetic anchors can be sought in the flanking DNA to provide a link of phylogeny with a functional gene. This approach produced the first genomic sequence linked to a 16S rRNA gene of an uncultured Archaeon. Similarly, the sequence of flanking DNA revealed a bacteriorhodopsin-like gene, which was shown to produce a photoreceptor, in the seawater bacteria that affiliated with the gamma-proteobacteria. This led to the insight that bacteriorhodopsin genes are not limited to Archaea but is abundant among the Protobacteria of the ocean.

This has been initiated with clones from diverse soils carrying 16S rRNA genes that affiliate with the Acidobacterium phylum, abundant in soil and highly diverse and about which little is known. Complete sequence of the estimate about 500 kb of Acidobacterium DNA in metagenomics libraries may provide insight into the subgroup of bacteria in this phylum that have never been cultured.


The frequency of metagenomic clones that express any given activity is very low. The scarcity of active clones, therefore, necessitates development of efficient screen and selections for discovery of new activities or molecules. Soil microbial diversity is immense and the vast majority of that diversity remains uncultured. The soil metagenome may be too large to sequence completely in the near future. This microbial diversity of soil contains vast untapped resources of microbial processes that may have significant scientific, practical or profitable potential. Soil metagenome could be a source for novel microbial products without cultivating or identifying the organism responsible. For this we have to look for specific functions with selective media and to screen many clones. Deciding what activities to look for and how many clones to screen are significant decisions that may depend on several factors including the size of the fragment inserts and the activities of interest. Advances in the availability of vectors and host strains are increasing the potential for finding novel bioproducts and catalytic enzymes from soil metagenome. Other promising applications that may come from soil metagenome libraries are antitumor agents and novel biodegradive pathways for xenobiotics. Many companies such as Diversa Corporation (San Diego) involved in mining microbial genomes from unique environments for economically viable enzyme, biochemical pathways, agricultural products, new pharmaceuticals and other products.


Much has been learned from early metagenomics studies and new researches are in process to know which steps in the process commonly present, difficulties and obstacles. It is the daunting task of understanding the genomics of uncultivated microorganisms or whole environmental genomes with respect to identifying the functions of genes as compared with a well-studied and easily cultivated microorganism.
Metagemomics produces a snapshot of the microbial community genome at a specific point in time and space. The most abundant DNA will come from the most abundant or most readily lysed cells, not necessarily the most environmentally important or interesting soil organisms.


Little is known about soil microbial biodiversity as compared to other environments, but now it is possible to unlock some of the secrets of the soil which is not possible earlier. Soil microbial biodiversity and community analysis lives now in the era of "Meta" where massive sequencing, metagenomics, metaproteomics and metatranscriptomics will allow us to survey a comprehensive range of data about soil microbial diversity, ecology and function.

About Author / Additional Info:
Dr. Suresh Kaushik
A Biotechnological Professional from India

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Comments on this article: (3 comments so far)

Comment By Comment
Sonali Bhawsar - Author
2013-07-01 22:21:23 650
Sir, this is extremely useful article and very precisely written! I would like to know if metagenomics is suitable for analysing river microflora, considering dynamic nature of aquatic ecosystem? Thank you.
Suresh Kaushik - Author
2013-07-05 09:55:45 656
Thank you very much for your comments. You are right that river is a dynamic freshwater aquatic ecosystem. But river microfauna community analysis can be performed. There are many methods to study such a dynamic ecosystem. Few studies have been carried out in dynamic environment like river or streams. Many have specifically targeted biofilm communities or suspended bacterioplankton in large flowing river. As you know freshwater habitats harbor microbial taxa distinct from those routinely detected in marine and terrestrial ecosystem. For metagenomics study in the river, DNA can be isolated from soil samples collected from river bed at specific time or season and location or site for temporal and spatial community analysis. Thank you.
simon peter
2013-08-24 06:24:52 680
Prof. this is such a wonderful article. Can we apply metagenomics in studying viruses?

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