Unravelling the Soil Microbiome

Soil microorganisms play a vital role in soil functions influencing the biogeochemical cycle, soil fertility, plant health, and aboveground ecosystems. The soil harbours more diverse communities of microorganisms than any other environmental component. We have a narrow understanding of how microbial diversity regulates soil functioning and in turn affects ecosystem sustainability. Studies of soil microorganism-mediated processes responsible for soil functions have largely been neglected. With increasing pressure on soils to meet the demands of the rapidly increasing human population for food, fodder, fibre, biofuel, timber, clean water, etc., it is imperative that research in soil microbiology focuses on the structure and functions of the soil microorganisms to delineate microbe-mediated soil processes and optimise them for enhanced production and better soil function. Moreover, soil also acts as a reservoir of carbon because its soil carbon sequestration potential helps in reducing atmospheric CO₂ levels. However, it is believed that warming climate conditions in the changing climate can negatively affect the carbon sequestration potential and other functions of the soil. To negate the climate impacts arising from increased CO₂ emissions from the soil, it is essential that we have a deep understanding of the processes of soil carbon storage. As the microbial activities in the soil largely regulate its functions, including soil carbon sequestration, it is important to gain deeper insights into the soil microbial world to address the issues of climate change and food security.

One of the key functions of soil microorganisms is to promote plant health and increase soil productivity. Some indigenous microorganisms of contaminated soil systems also have the capability to degrade the soil contaminants, and thus are frequently used in bioremediation purposes. Most of these microbes belong to the category of plant growth-promoting microorganisms, which perform various functions including providing nutrients to the plants, conferring disease resistance, and combating temperature, salinity, and other abiotic stresses. These microbes also support the growth of plants in degraded and contaminated soil systems, aiding phyto-remediation. In coming decades, food security and climate change are expected to be the most serious problems for the planet Earth. Plant growth-promoting microorganisms can provide a sustainable solution to these problems by increasing the production of crop plants, and reducing the use of chemical fertilizers and pesticides, thus decreasing agricultural pollution. The enormous diversity of soil microorganisms gives an excellent opportunity for exploring new plant growth-promoting rhizobacteria; however, only 1% of the total soil microorganisms are culturable in nature, so the majority of the promising strains remain unexplored. The advent of the novel ‘omic’ technologies provides an excellent opportunity to harness this potential of the belowground microbial world.

Belowground microbial processes are at the helm of terrestrial ecosystem functions, and the enormous diversity of soil microorganisms acts as a key player. Thus, understanding the community dynamics of microorganisms in the soil is essential to know their distribution, abundance, and structure. Further, it is also important to know how these communities are shaped in structure and function in response to changes in space and time. Various microbial diversity analysis methods—fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphisms, and the automated version of ribosomal intergenic spacer analysis, RISA (ARISA)—have been developed to analyse the diversity of soil microorganisms based on their genetic structure. However, methods such as phospholipid and fatty acid analysis utilise the differences in lipid components of the microbial cell membrane to analyse their diversity. In the present chapter, we explore the conventional methods of soil microbial diversity analysis.

Soil metagenomic analysis was previously limited by technological restrictions and the few reference genomes. The advent of next-generation ‘omics’ technologies has provided high-throughput methods for analysing community structure and reconstructing soil metagenomes. High-throughput sequencing technology and single-cell genomics have revolutionized metagenomic analysis by enabling large-scale sequencing at reduced sequencing costs with less time required. In the present chapter we discuss various technological advances in metagenomics, their processes and the methods of data analysis, and metagenomic success stories under various environments that can be applied for studying the functional and structural diversity of soil microorganisms.

Metatranscriptomics and metaproteomics are major breakthroughs of the next-generation sequencing technologies. Metatranscriptomics and metaproteomics not only provide information about the taxonomic structure of the microorganisms in soil but also provide information about their functional attributes and diversity. Gene expression under varying environmental conditions can be analysed by polymerase chain reactions and microarray. Similarly, techniques such as metatranscriptomics can be used for genome-wide gene expression analysis, providing novel insights about the ecology of the microorganism-mediated processes. In the present chapter we have highlighted the importance, benefits, challenges, process, and procedures of metatranscriptomics and metaproteomics for analysing microbial communities from diverse environments. Metatranscriptomics and metaproteomics have carried out significant revolutions in the field of microbial ecology via exploring the plant–microbe and microbe–microbe interactions.

Metagenomic approaches aid in exploring the structural and functional diversity of soil microorganisms. Sequence analysis of the large amount of data generated from soil microbial communities sequencing is a challenging issue. It is made feasible through bioinformatics tools, which provide sequence pipelines for the high-throughput screening of the soil metagenomic libraries. Such sequence analysis of metagenomic datasets reveals the genetic structure, gene prediction, proposed functions, and metabolic pathways of the analyzed microbial communities. Bioinformatic tools provide statistical procedures not only for comparison of metagenomic libraries but also to report the sampling and library creation artifacts. Here we discuss the bioinformatics tools for accessing the metagenomic information and platforms for data storage within databases (GenBank env), access, synthesis, and analysis.

Harnessing the potential of the microbiome can provide cleaner and greener solutions to various environmental challenges. Globally, microbiome research is a continuously evolving field, with researchers aiming to explore the structural and functional characteristics of the microbiomes in various environmental compartments. Still, there are various system-level knowledge gaps in microbiome research. Therefore, unravelling the complex and dynamic microbial crosstalk in the soil system and the multitrophic interactions will certainly provide new impetus for harnessing the real potential of the soil microbiome for multipurpose environmental benefits.