**3. Soil metagenomics: a concept**

Even though soil microbes dominate the biosphere, most microbes in nature have not been studied because the standard culturing techniques could help in the study of those organisms which can be cultured on artificial media and rest of the organisms are still unknown since lack of the universal artificial media and growth conditions. Instead of cultivating different organisms in pure form and studying the morphology and characteristics, metagenomics, studies all the organisms present in the environmental sample at once by the combining traditional microbiology and molecular biology. Microbial diversity is the major driving force of fundamental metabolic processes in dynamic environment like soil and a number of microbial species are associated with the plant rhizosphere. Therefore, a basic understanding of diversity of soil biota is required in order to preserve the integrity, function and long term sustainability of natural and managed terrestrial ecosystems. The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation [10].

Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world and their functions in different ecosystem. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members in order to identify the microbes in the community. The new approach and its attendant technologies will bring to light the myriad capabilities of microbial communities that drive the planet's energy and nutrient cycles, maintain the health of its inhabitants, and shape the evolution of life. Metagenomics is expected to generate knowledge of microbial interactions so that they can be harnessed to improve human health, food security, and energy production.

Metagenomics combines the power of genomics, bioinformatics, and systems biology. Operationally, it is novel in that it involves study of the genomes of many organisms simultaneously. It provides new access to the microbial world. Although community ecology is not new to microbiology, the power of genomics in the study of communities brings in an unparalled opportunity.

Meta in the first sense means that this new science seeks to understand biology at the aggregate level, transcending the individual organism to focus on the genes in the community and how genes might influence each other's activities in serving collective functions. In the second sense, meta also recognizes the need to develop computational methods that maximize understanding of the genetic composition and activities of communities so complex that they can only be sampled, never completely characterized.

Metagenomics, still a very new science, has already produced a wealth of knowledge about the uncultured microbial world because of its radically new ways of understanding microbial world. All metagenomics studies take the same first step: DNA is extracted directly from all the microbes living in a particular environment. The mixed sample of DNA can then be analyzed directly, or cloned into a form maintainable in laboratory bacteria, creating a library that contains the genomes of all the microbes found in that environment.

Since the invention of the simple microscope by Anton Von Leeuwenhoek we are able to identify and study only 1% of the total microbial diversity available on Earth. The rest of the 99% of the microbes are not easily accessible to us as they are busy with their life cycle and maintenance of the microbial balance of our planet. Our current knowledge about the culturable microbial techniques is unable to achieve the complete picture of the diversity and functions of the micro-organisms residing

#### *Soil Metagenomics: Concepts and Applications DOI: http://dx.doi.org/10.5772/intechopen.88958*

even in a single environment. Thus the development of new techniques holds huge potential to overcome the difficulties to capture complete microbial profile.

The study of microbial diversity is very much important in a particular habitat as the microbes helps in maintenance or modification of the environment and it is also responsible for survival of surrounding organisms and also helps in the process of evolution of the other living organisms. It is therefore, time to investigate the intricate relationship between the soil microbiota and plants and how this relationship benefits both of the organisms in spite of the environmental changes.

In 1904, Lorenz Hiltner coined the term, "rhizosphere"—a word partly originated from the Greek word "rhiza", meaning root which describes the plant-root interface [11]. Hiltner described the rhizosphere as the area around a plant root that is inhabited by a unique population of microorganisms. But in recent years based on the relative proximity and influence to root the rhizosphere is refined to include three zones. The endorhizosphere includes cortex and endodermis in which microbes occur in very close association with the roots of the plant; they are present inside the roots and referred to as endophyte at times. They are resultant of plant root exudates which attract them to colonize the roots. The rhizoplane is the medial zone directly adjacent to the root including the root epidermis and mucilage. The outermost zone is the ectorhizosphere which extends from the rhizoplane out into the bulk soil and it is the house to the organisms which are either free living or non-symbionts which are highly influenced by management or cultural practices. The rhizosphere is not a region of definable size or shape, but consists of a gradient in chemical, biological and physical properties which change both radially and longitudinally along the roots.

**Figure 1.** *Methods for studying microbial diversity harboring in the soil.*

Discovering the microbiota of the soil environment requires selection of the suitable method(s) for capturing the maximum diversity at a particular time and space. It is obvious that based on a particular interest of the researcher, the approach to understand microbial diversity may be different from others or same. To determine spatial heterogeneity, considerable amount of work is still needed, for example, how representative a 0.1 mg sample of soil is with respect to the larger environment from which it was taken. Selection of proper method for extracting the meaningful information is very much important to escape the biasness of the results or to reduce the error rate in estimating the diversity by using statistical significance as well. To understand the overall microbial diversity, the researchers use one or combination of the methods given below for collecting the maximum information using their own standard sample size (**Figure 1**).
