REVIEW article
Front. Soil Sci.
Sec. Soil Biology, Ecosystems and Biodiversity
Next-Generation Sequencing Approaches for Soil Microbiome Research
Provisionally accepted
- 1Moscow Center for Advanced Studies, 20, Kulakova Str., Moscow, Russia
- 2Federal State Autonomous Educational Institution of Higher Education I.M.Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenovskiy University), Moscow, Russia
- 3Institute of Ecology, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
DNA sequencing technologies play a key role in modern soil microbiome research, providing a deep understanding of its structure and functional role in ecosystems. 16S rRNA gene, region of 18S-ITS-28S sequencing and shotgun sequencing using modern sequencing technologies (Illumina, Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT)) allow us to identify the diversity and dynamics of microbial communities with high accuracy and resolution, which significantly expands our knowledge of biological processes and interactions between microorganisms in the soil. Soil microbiome analysis using sequencing contributes to the development of innovative methods for sustainable agricultural land management, improved fertility, plant disease management, and increased crop yields. Despite its significant potential, each sequencing technology has its own advantages and limitations related to accuracy, depth of coverage, cost, and data analysis complexity. Understanding these characteristics is crucial for selecting the optimal methods depending on the research objectives and available resources. This review systematizes modern sequencing methods, their technical capabilities and limitations, bioinformatics tools for sequencing data analysis, considers examples of successful applications in the study of soil microbiome in various ecosystems, and emphasizes new trends in metagenomics. In-depth study and development of soil microbiome sequencing technologies contributes to more sustainable and resource-efficient agriculture, emphasizing the need for a comprehensive and informed approach to the analysis of microbial communities.
Keywords: soil microbiome, 16S rRNA gene sequencing, ITS sequencing, Shotgun metagenomics, Illumina, PacBio, Oxford nanopore
Received: 16 Sep 2025; Accepted: 05 Dec 2025.
Copyright: © 2025 Reznikova, Barannikova, Shnakhova, Mitkin and Vatlin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Diana A. Reznikova
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.