High-throughput Sequencing in Soil Microbiology: Challenges and the Path Forward

Author: Mohit Kashyap, Pardeep Kumar, Narender K. Sankhyan and Mansi Bahman

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Abstract

Plant health, soil fertility, and sustainability all depend on soil microbial populations. However, intensive agriculture, which uses more synthetic inputs, and changing environmental conditions have affected native soil microbial communities. Studying microbial structure, diversity, and activity is essential for understanding plant-microbe interactions. However, microbial complexity, environmental interactions, and technological limitations make comprehensive analysis challenging. Culture-based methods often fail to capture true microbial diversity, necessitating culture-independent approaches like metagenomics, meta-proteomics, meta-transcriptomics, and proteo-genomics, which provide deeper insights into soil microbial ecology and functionality. High-throughput sequencing (HTS) has revolutionized soil microbiology by enabling comprehensive, culture-independent analysis of microbial communities. However, challenges such as DNA extraction biases, sequencing errors, and limited reference databases hinder accuracy. Albeit advancing bioinformatics, improving sequencing technologies, and integrating multi-omics approaches will enhance microbial insights, driving future innovations in soil health and sustainability

Keywords

Soil microbiology, high-throughput sequencing (HTS), bioinformatics, omics and sustainability

Conclusion

High-throughput sequencing (HTS) has revolutionized soil microbiology by enabling high-resolution, culture-independent analysis of microbial diversity and functions. The composition and functional potential of microbial communities are revealed by methods such as 16S rRNA gene sequencing, and metagenomics provide information on the abundance of microorganisms in stress-related biogeochemical and scientific processes. Technological developments in third-generation sequencing, such as enhanced RNA quality and nanopore technology, enable a more thorough investigation of microbial functions. Agricultural sustainability, environmental monitoring, and ecosystem resilience in the face of shifting global conditions are all supported by HTS and new multi-omics techniques, which improve our understanding of soil microbial ecology despite obstacles such DNA extraction biases and complicated data analysis

References

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How to cite this article

Mohit Kashyap, Pardeep Kumar, Narender K. Sankhyan and Mansi Bahman (2025). High-throughput Sequencing in Soil Microbiology: Challenges and the Path Forward. Biological Forum, 17(3): 66-72