**3. The need for microbial identification and characterization**

It is well recognized that the microorganisms have an abundant quantity and diversity than other organisms on the planet [4]. Nevertheless, the division of the microbial diversity at global scales is still partially understood. The microbial diversity and composition structure are significantly affected by environmental elements [62]. As a result, indexing, cataloging and proof of the microorganisms are prerequisites for the exploration [62]. Microbial diversity in any habitat is more related to the substantial amount of species existed at a specific time [63, 64]. As the earth microbial community plays essential roles in soil health management, agro-ecosystem, accessibility of growing nutrition as well as turnover tasks of organic material in soil, they are hugely influenced by both anthropogenic and natural activities [65, 66]. For instance, many microbes that are helpful to the ecosystem services are currently threatened because of inferior agricultural practices, local weather transforming patterns, ground as well as land degradation, etc. [67, 68]. In recent years, the use of artificial fertilizers, herbicides, fungicides, and other pesticides has resulted in the deterioration of the soil microflora and diversity [7, 31, 69]. Therefore, the microorganisms with the changing atmosphere will offer a broader picture of the way the microbes are shifting the functional characteristics of soils and their flourishing in the endangered ecosystems [69, 70].

## **4. Metagenomics for sustainable agricultural practices**

Nowadays, most of the environmental focus in agriculture is on achieving agricultural sustainability. Many metagenomic initiatives have been completed in the area of agriculture but do not hold some promise to assist the marginal farmers [71–73]. Therefore, productive scientific studies are required, which might be used the growers' income and help agriculture [74]. The latest advances in the soil metagenomics emerge as an extraordinary area of research because of the assignment of understanding the associated microorganisms in development and plant growth [75, 76]. Likewise, restoration of the microbial population was determined to improve grain yield as well as soil health [77]. Metagenomics can predict the soil microbes' structure and the impact on microbial groups of connected niches [9, 35].

Sustainable agricultural methods consist of different microhabitats with excellent environmental fluctuations and genetic biodiversity [78]. Reports from agrarian soils confirmed that there are high microbial stock and plant development promotion pursuits [79]. Many studies are showing the latest metagenomic improvements in agriculture [76–78]. Soil microbes play a crucial part for triggering the plant development, stress reactions, as well as defense in vegetation [80, 81]. Understanding the connection between the soil microbiota and plants using soil metagenomics is hugely advantageous in developing the crop systems [1, 82]. Metagenomics research of the soils supplemented with organic manures from several farm animals will be a lot valuable in formulating the fertilization tactics [12, 65]. For renewable agricultural production, helpful microbes of agricultural value can function as an essential alternative [39, 73]. Metagenomics compensation can address basic restorative questions associated with agriculturally significant microorganisms [83].

Direct DNA extraction and characterization through PCR and metagenomic survey have developed the study of soil ecosystem [81]. Applying metagenomics of plant-microbial association can be used to study interaction with beneficial microbes among pathogenic strains, infect recently, profitable endosymbionts inside these beneficial microbes (AMF) like nitrifying bacteria, (phosphate solubilizing bacteria) PSB and plant growth-promoting abilities are found [84]. The specificity of plant-microbial symbiosis development can be easily understood at the molecular level both for agronomic and horticulture crops, using forward and reverse genetic approaches [85]. As reported earlier, microbial inoculation has the potential of increasing plant production and sustainability in agricultural fields, so the metagenomics study can reveal the distinct microbial strains interacting with which chemical compound in the mycorrhizospheric soil and to acknowledge community structure, horizontal gene transfer analysis and phylogeny of microbes interacting with other environmental factors [86, 87]. Also, the exact niche information of microbial communities infecting soil adhering to the roots, surface between roots and soil, the surface of roots, or colonizing with the roots, can be drawn [87]. As we know this interaction is bi-directional, plant gets the essential nutrients from the soil, and in return, these rhizospheric and/or root microbiotas get the photosynthesis-derived organic compounds, and this process is known as rhizodeposition [88]. Thus, this crucial symbiosis that underlying plant-microbe community associations can be easily implicit by metagenomics for agricultural purposes because the NGS which can determine the relative abundance of microbe whether it is culturable in laboratory conditions or not [89]. In addition, the results of hundreds of samples simultaneously can be obtained on the same day as the samples are loaded [89].

**5**

**Figure 1.**

modes [108–111].

*Soil Metagenomics: Prospects and Challenges DOI: http://dx.doi.org/10.5772/intechopen.93306*

**5. Amplicon sequencing and bioprospecting of metagenomes**

amplicon sequencing working with marker genes [92].

**6. Soil metagenomics: pipelines and outputs**

steps in soil metagenomics are enlisted below and shown in **Figure 2**.

*Metagenomic analysis of environmental microbial sampling based on nucleic acids***.**

In the amplicon sequencing study, first, soil DNA is extracted, and next, 16S/18S rDNA sequences are amplified using a specific set of particular primers targeting variable areas of 16S/18S rDNA, accompanied by filtration of fragments using magnetic beads [54, 90–92]. Consequently, adapters are ligated, and the library of fragments (clones) is amplified along with the samples are sequenced utilizing NGS platform (**Figure 1**). The dataset obtained after sequencing is used for the identification of microbial diversity [54, 55]. Using NGS and the related software, it is doable to solve extremely complicated microbiota compositions with greater precision and to relate the microbial ecosystem of the soil [16, 55, 92], although, it must be considered for accurate data and analysis interpretation while choosing

From the start of metagenomics, the study of novel metabolite/biomolecule (DNA polymerases, cellulases, lipases/esterases, chitinases and antibiotics) from the microbial assembly was its first application, and this has advanced with the development of NGS techniques for calculating comparison between community metagenome, meta-proteomics, and meta-transcriptomics [93, 94]. Techniques for recovering novel metabolite that comprise cloning of the microbial DNA from the environment then constructing a small/large-insert libraries, which can be done either by function-based or sequence-based screening of metagenomic libraries are shown in **Table 1**. The resulting metagenomic libraries subsequently transformed in several hosts like Escherichia coli (mostly), *Sulfolobus solfataricus*, *Thermus thermophilus*, *Streptomyces*, and *Proteobacteria* show significant differences in expression

Metagenomics was initiated with the aim of DNA cloning and screening, and now it has made significant advances in microbiology, evolution, and ecology [91, 92]. These first projects not merely proved the concept of the metagenomics but additionally unraveled enormous gene diversity within the microbial world. The various

*Mycorrhizal Fungi - Utilization in Agriculture and Forestry*

connected niches [9, 35].

microorganisms [83].

**4. Metagenomics for sustainable agricultural practices**

Nowadays, most of the environmental focus in agriculture is on achieving agricultural sustainability. Many metagenomic initiatives have been completed in the area of agriculture but do not hold some promise to assist the marginal farmers [71–73]. Therefore, productive scientific studies are required, which might be used the growers' income and help agriculture [74]. The latest advances in the soil metagenomics emerge as an extraordinary area of research because of the assignment of understanding the associated microorganisms in development and plant growth [75, 76]. Likewise, restoration of the microbial population was determined to improve grain yield as well as soil health [77]. Metagenomics can predict the soil microbes' structure and the impact on microbial groups of

Sustainable agricultural methods consist of different microhabitats with excellent environmental fluctuations and genetic biodiversity [78]. Reports from agrarian soils confirmed that there are high microbial stock and plant development promotion pursuits [79]. Many studies are showing the latest metagenomic improvements in agriculture [76–78]. Soil microbes play a crucial part for triggering the plant development, stress reactions, as well as defense in vegetation [80, 81]. Understanding the connection between the soil microbiota and plants using soil metagenomics is hugely advantageous in developing the crop systems [1, 82]. Metagenomics research of the soils supplemented with organic manures from several farm animals will be a lot valuable in formulating the fertilization tactics [12, 65]. For renewable agricultural production, helpful microbes of agricultural value can function as an essential alternative [39, 73]. Metagenomics compensation can address basic restorative questions associated with agriculturally significant

Direct DNA extraction and characterization through PCR and metagenomic survey have developed the study of soil ecosystem [81]. Applying metagenomics of plant-microbial association can be used to study interaction with beneficial microbes among pathogenic strains, infect recently, profitable endosymbionts inside these beneficial microbes (AMF) like nitrifying bacteria, (phosphate solubilizing bacteria) PSB and plant growth-promoting abilities are found [84]. The specificity of plant-microbial symbiosis development can be easily understood at the molecular level both for agronomic and horticulture crops, using forward and reverse genetic approaches [85]. As reported earlier, microbial inoculation has the potential of increasing plant production and sustainability in agricultural fields, so the metagenomics study can reveal the distinct microbial strains interacting with which chemical compound in the mycorrhizospheric soil and to acknowledge community structure, horizontal gene transfer analysis and phylogeny of microbes interacting with other environmental factors [86, 87]. Also, the exact niche information of microbial communities infecting soil adhering to the roots, surface between roots and soil, the surface of roots, or colonizing with the roots, can be drawn [87]. As we know this interaction is bi-directional, plant gets the essential nutrients from the soil, and in return, these rhizospheric and/or root microbiotas get the photosynthesis-derived organic compounds, and this process is known as rhizodeposition [88]. Thus, this crucial symbiosis that underlying plant-microbe community associations can be easily implicit by metagenomics for agricultural purposes because the NGS which can determine the relative abundance of microbe whether it is culturable in laboratory conditions or not [89]. In addition, the results of hundreds of samples simultaneously can be obtained on the same day as the

**4**

samples are loaded [89].
