Soil Metagenomics: Prospects and Challenges

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.

Metagenomics approaches to understanding soil health in environmental research - a review

“…Since the origin of metagenomics, many advances have been made in the study and knowledge of structural and functional microorganisms diversity, species identification, the characterization of new genes (Nacke et al, 2011), and discovering enzymatic activities and active compounds (Craig et al, 2010). However, metagenomic studies have not been used to study soil health until recently (Kaushik et al, 2021). The discovery through metagenomics of the enormous diversity of non-culturable microorganisms, linked to the present-day knowledge of new genomes, has allowed the association of specific members to these microbial communities with transformations that soils may be experiencing (Long et al, 2016).…”

Integration of Omics Approaches Enhances the Impact of Scientific Research in Environmental Applications

“…Omics applications in environmental research may effectively support chemical risk assessment by providing the key input in current analytical frameworks such as Adverse Outcome Pathways (AOPs) or Source-To-Outcome (STO) pathways [ 43 , 44 ]. Omics approaches offer a new perspective on microbial communities and could revolutionise the understanding of complex and diverse ecosystems [ 45 ], as well as processes such as bioremediation [ 46 ]. Analysing biological phenomena through a single omics approach can provide an understanding of biological mechanisms in response to environmental exposure and alterations in ecosystems [ 47 ].…”

Use of Arbuscular Mycorrhizal Fungi for Vegetable Crops

“…Many plants can host the AMF fungi, but few plants are susceptible to the microbial growth and tends to show negative impact on their growth. Several plants like onions, garlic, carrots, tomatoes and herbs show high positivity with the use of AMF inoculants even though they are grown in pots or trays [39]. Also, certain annual flower beds like ornamental grasses, aloe etc are highly responsive to the fungal growth [40].…”