Soil Metagenomics: Prospects and Challenges

*Prashant Kaushik, Opinder Singh Sandhu, Navjot Singh Brar, Vivek Kumar, Gurdeep Singh Malhi, Hari Kesh and Ishan Saini*

## **Abstract**

The better strategies to examine RNA or DNA from soil allow us to understand the microbial diversity and features in the soil, which are challenging to identify by typical culture techniques. In this direction, the literature on soil metagenomics and its usefulness is ever-increasing and so as its implementation experiences. Omics techniques are going to assist the metagenomics in achieving agricultural sustainability. In doing so, essential understanding on the reference soil would serve to help upcoming soil survey initiatives, lessening bias and raising objectivity. Although the interpretation of limited details has influenced microbial ecologists, the scope of methodological bias remains unfamiliar. A detailed catalog of functional genes and soil microorganisms does not yet exist for any soil. Overall, this chapter provides thoughts related to the soil metagenomics, its importance, and conventional methods of analysis, along with prospects and challenges of soil metagenomics.

**Keywords:** genomics, soil, microbes, metagenomics

#### **1. Introduction**

Soil is a robust and brilliantly vast ecosystem (2000–8.3 million bacterial species per gram). Therefore, it serves as a vast reservoir for microorganisms inhabiting in a niche that is different within the specific soil ecosystem, which can be pathogenic or beneficial [1–4]. Each proportion of soil whether in grasslands, forests, or deserts (i.e., sand, silt, clay, and organic matter) offers habitats for nematodes and a large number of microbes that vary from bacteria and are also useful in nutrient cycling [5–8]. Moreover, the distinct microhabitat dwelled by microorganisms with the capability to adjust and established their colony to the specific niche [9]. The crucial factors which influence the microbial load in the soil ecosystem include soil pH, organic compound, and temperature [10–12]. The chemical or physical activity does not merely determine the development of soil but the constant unfolding of different microbial species, which include or may improve the attributes of soils, regarding the development of function and structure [13, 14]. Soil supplies protection to different soil harboring animals, reptiles, and insects, along with a tremendous number of microbes inside the soil aggregates [15].

In this direction, the field of metagenomics continues to be a ground-breaking technology, which has made it possible to explore microbial diversity with its full

potential [16]. Besides the soil ecosystem, microbes could quickly react to anthropogenic pressures, making it feasible to be an indication of soil quality as well as wellness [17, 18]. Lately, efforts have been attempted to determine genes from environmental samples via culture-independent techniques [19, 20]. However, they had been amplified or perhaps recognized due to their similarity to the earlier identified genes, that invalidates for exploiting novel elements of metal resistance [21, 22]. As the development of culture-independent metagenomic methods, it has been employed to evaluate the soil microbial community as well as enhances our awareness of the soil ecosystem [17, 20]. Furthermore, the soil microbial communities are primarily made up of some dominant species and numerous other rare taxa [23].

The ones with a low abundance might be from some novel microbial lineages and might play a vital function in biogeochemical interactions of the soil–plant system [24]. Therefore, the information obtained from the full metagenomic sequencing is crucial to expose the genomic data of low abundance populations as well as to disclose their activity in the soil [6]. It has been effectively released into investigating numerous varied microbial niches in the human gut, grassland soil, and aquatic ecosystem [25–27]. Furthermore, attempts have been established to evaluate the abundance of soil microbes as well as the genes involved in heavy metals' opposition from agricultural soils [28, 29]. Additionally, soil metagenomics beyond estimating the soil microorganisms can also help in getting a concept about the soil and its habitat based on the different soil types [30]. This chapter provides the importance of soil metagenomics and standard methods of analysis, along with challenges and prospects of soil metagenomics.

### **2. Soil health and metagenomics**

Soil is an interconnected system because of its microorganisms despite getting incredible and unique capability to adjust to life changes; soil microbes are hypersensitive to land management and also weather changes [1, 11, 14]. Based on this information, our ancestors learned the ability to grow plants and created different cultivation methods like inoculating mycorrhizal fungi with food and floral crops to decrease the impact of soil-borne diseases [31–34]. With a most varied ecosystem with a composition of known and unknown microbial species, the soil provides an ecological niche [34, 35]. The biochemistry of soil reflects many anonymous functions that are a lot essential for sustenance of life [35–37]. Nevertheless, the latest technologies utilizing heavy machinery and management methods intensified agriculture and have resulted in the degeneration of the cultivable farmlands through damage of fertility, soil structure as well as the soil microbial life [38–40]. In a nutshell, lots of arable areas have switched to uncultivable or saline soil [38]. Agricultural land is simultaneously getting forfeited to nonagricultural uses [39]. The generation of soil, which primarily contains carbon twice as much as the atmosphere, is a complex phenomenon and requires lots of years for the formation of 1 cm topsoil [41]. Metagenomics data can be used to investigate the gene sequencing helpful in microbial symbiosis, as this is the most ancient symbiosis of nature of around 400 million years [42]. With the increased population pressure, the concern around worldwide sustainability also increases. Therefore, improving and sustaining the qualities of soil is an utmost concern for many years. Thus, soil health gets among the most crucial aspects of agriculture [8, 24].

Metagenomics offers an entirely new method of looking at the microbial community that has transformed contemporary microbiology and also has the potential to revolutionize comprehension approaches of the various ecosystems [43, 44]. In metagenomics, the strength of genomic examination is put on to whole

**3**

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

environmental samples [30].

easily be caught within biofilms [60, 61].

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

of soils and their flourishing in the endangered ecosystems [69, 70].

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

populations of microorganisms [45]. Metagenomics approaches are throwing light on the myriad abilities of microbial communities that operate the planet's energy and nutrient cycles and form the evolution of life [46, 47]. Metagenomics is anticipated to produce awareness of microbial interactions; therefore, it is used to enhance human well-being, energy production, and food security [48]. Metagenomics combines the strength of genomics, systems biology and bioinformatics and power of genomics within the research of communities generates an unparalleled ability [43, 45]. Metagenomics, still a very new science, but has produced insightful information about the microbial community due to its radically unique means of realizing the microbial world [49, 50]. The diverse test of DNA may subsequently be analyzed directly, or even cloned into a type maintainable in lab bacteria, developing a library which has the genomes of all of the microbes present in that environment [51–53]. Nevertheless, the launch of the cultureindependent approaches eliminates the obstacles and barriers in understanding the

Metagenomics initially targeted the shotgun sequencing; these days it's just as helpful for the scientific studies regarding marker genes *viz*. 16S rRNA by employing NGS (next-generation sequencing) systems, by extracting the specific region of DNA encoding 16S rRNA which is then amplified, sequenced, and identified based on similarities in gene sequence available in public databases [54, 55]. NGS, along with polymerase chain reaction (PCR), and DNA fingerprinting techniques have become increasingly rapid, effective, sensitive, and cost-efficient [55]. Cultureindependent tactics are needed on the immediate extraction of soil DNA and later check out the genes encoding rRNA [56]. The exploration of following generation sequencing as well as analysis has accomplished in revealing the undiscovered microbial framework in a variety of earth ecosystems [57–59]. A comprehensive research of the soil metagenome provided the useful characterization of soil microorganisms linked to the genes in nutrient cycling [58]. Nevertheless, efforts are now being directed in exploring the predictions of gene operates in conditions of the actual role of theirs in situ, particularly in the soil, where metagenomes can

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

*Mycorrhizal Fungi - Utilization in Agriculture and Forestry*

up of some dominant species and numerous other rare taxa [23].

challenges and prospects of soil metagenomics.

**2. Soil health and metagenomics**

crucial aspects of agriculture [8, 24].

potential [16]. Besides the soil ecosystem, microbes could quickly react to anthropogenic pressures, making it feasible to be an indication of soil quality as well as wellness [17, 18]. Lately, efforts have been attempted to determine genes from environmental samples via culture-independent techniques [19, 20]. However, they had been amplified or perhaps recognized due to their similarity to the earlier identified genes, that invalidates for exploiting novel elements of metal resistance [21, 22]. As the development of culture-independent metagenomic methods, it has been employed to evaluate the soil microbial community as well as enhances our awareness of the soil ecosystem [17, 20]. Furthermore, the soil microbial communities are primarily made

The ones with a low abundance might be from some novel microbial lineages and might play a vital function in biogeochemical interactions of the soil–plant system [24]. Therefore, the information obtained from the full metagenomic sequencing is crucial to expose the genomic data of low abundance populations as well as to disclose their activity in the soil [6]. It has been effectively released into investigating numerous varied microbial niches in the human gut, grassland soil, and aquatic ecosystem [25–27]. Furthermore, attempts have been established to evaluate the abundance of soil microbes as well as the genes involved in heavy metals' opposition from agricultural soils [28, 29]. Additionally, soil metagenomics beyond estimating the soil microorganisms can also help in getting a concept about the soil and its habitat based on the different soil types [30]. This chapter provides the importance of soil metagenomics and standard methods of analysis, along with

Soil is an interconnected system because of its microorganisms despite getting incredible and unique capability to adjust to life changes; soil microbes are hypersensitive to land management and also weather changes [1, 11, 14]. Based on this information, our ancestors learned the ability to grow plants and created different cultivation methods like inoculating mycorrhizal fungi with food and floral crops to decrease the impact of soil-borne diseases [31–34]. With a most varied ecosystem with a composition of known and unknown microbial species, the soil provides an ecological niche [34, 35]. The biochemistry of soil reflects many anonymous functions that are a lot essential for sustenance of life [35–37]. Nevertheless, the latest technologies utilizing heavy machinery and management methods intensified agriculture and have resulted in the degeneration of the cultivable farmlands through damage of fertility, soil structure as well as the soil microbial life [38–40]. In a nutshell, lots of arable areas have switched to uncultivable or saline soil [38]. Agricultural land is simultaneously getting forfeited to nonagricultural uses [39]. The generation of soil, which primarily contains carbon twice as much as the atmosphere, is a complex phenomenon and requires lots of years for the formation of 1 cm topsoil [41]. Metagenomics data can be used to investigate the gene sequencing helpful in microbial symbiosis, as this is the most ancient symbiosis of nature of around 400 million years [42]. With the increased population pressure, the concern around worldwide sustainability also increases. Therefore, improving and sustaining the qualities of soil is an utmost concern for many years. Thus, soil health gets among the most

Metagenomics offers an entirely new method of looking at the microbial community that has transformed contemporary microbiology and also has the potential to revolutionize comprehension approaches of the various ecosystems [43, 44]. In metagenomics, the strength of genomic examination is put on to whole

**2**

populations of microorganisms [45]. Metagenomics approaches are throwing light on the myriad abilities of microbial communities that operate the planet's energy and nutrient cycles and form the evolution of life [46, 47]. Metagenomics is anticipated to produce awareness of microbial interactions; therefore, it is used to enhance human well-being, energy production, and food security [48]. Metagenomics combines the strength of genomics, systems biology and bioinformatics and power of genomics within the research of communities generates an unparalleled ability [43, 45]. Metagenomics, still a very new science, but has produced insightful information about the microbial community due to its radically unique means of realizing the microbial world [49, 50]. The diverse test of DNA may subsequently be analyzed directly, or even cloned into a type maintainable in lab bacteria, developing a library which has the genomes of all of the microbes present in that environment [51–53]. Nevertheless, the launch of the cultureindependent approaches eliminates the obstacles and barriers in understanding the environmental samples [30].

Metagenomics initially targeted the shotgun sequencing; these days it's just as helpful for the scientific studies regarding marker genes *viz*. 16S rRNA by employing NGS (next-generation sequencing) systems, by extracting the specific region of DNA encoding 16S rRNA which is then amplified, sequenced, and identified based on similarities in gene sequence available in public databases [54, 55]. NGS, along with polymerase chain reaction (PCR), and DNA fingerprinting techniques have become increasingly rapid, effective, sensitive, and cost-efficient [55]. Cultureindependent tactics are needed on the immediate extraction of soil DNA and later check out the genes encoding rRNA [56]. The exploration of following generation sequencing as well as analysis has accomplished in revealing the undiscovered microbial framework in a variety of earth ecosystems [57–59]. A comprehensive research of the soil metagenome provided the useful characterization of soil microorganisms linked to the genes in nutrient cycling [58]. Nevertheless, efforts are now being directed in exploring the predictions of gene operates in conditions of the actual role of theirs in situ, particularly in the soil, where metagenomes can easily be caught within biofilms [60, 61].
