Cutting edge tools in the field of soil microbiology

• Published in: Current research in microbial sciences Vol. 6; p. 100226
• Main Authors: Garg, Diksha, Patel, Niketan, Rawat, Anamika, Rosado, Alexandre Soares
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2024; Elsevier
• Subjects: Metagenomics; Microarray; Microbiology; NanoSIMS; Next generation sequencing; Review; Soil microbiology; NanoSIMS; Metagenomics; Microbiology; Microarray; Next generation sequencing; Soil microbiology
• ISSN: 2666-5174; 2666-5174
• DOI: 10.1016/j.crmicr.2024.100226

•The use of metagenomics in soil microbiology is the subject of this review, which also discusses the potential and current limitations of the field.•The several methods of metagenomic sequencing and how they are used in soil microbiology are discussed in this article.•The advancements in metagenomics are anticipated to continue shaping the future of soil microbiology research, despite the limitations, such as the difficulty of finding the right sequencing method for specific genes. The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes. [Display omitted]