Chief EditorYashpal Singh Malik
Print ISSN 0303-3821
Online ISSN 0976-4631
NAAS Rating 3.07
Full Research Article
Metatranscriptomic Approach to Understand the Role of the Rhizosphere Microbiome: A Review
First Online 15-08-2022|
Plant roots harbour diverse microorganisms that interact with each other and the plants. Rhizosphere is the region of soil, closely associated with plant root. The microbiome associated with them is termed as rhizobiome. Its studies give insights into the roles of the microorganisms in plant health. With the advancement of NGS techniques, the identification of the non-cultural species has turned out to be possible. Sequencing of the whole genomic D.N.A. (metagenomics) can easily identify the taxonomic and functional profile but identification of the active and inactive members of the microbiome is not fulfilled. Meta-transcriptomics helps in determining the active functional profile of a microbial community by identifying the genes expressed by the entire microbial community. The general workflow is sampling, RNA extraction, library preparation, sequencing, pre-processing of data, assembly, taxonomic/functional profiling and the differential expression analysis. There exist numerous challenges, that can be overcome through enhanced sequencing technologies and algorithms.
- Aguiar-Pulido, V., Huang, W., Suarez-Ulloa, V., Cickovski, T., Mathee, K., Narasimhan, G. (2016). Metagenomics, metatranscriptomics and metabolomics approaches for microbiome analysis. Evol Bioinform Online. 12(Suppl 1): 5-16. doi:10.4137/EBO.S36436.
- Carvalhais Lilia, C., Dennis, P.G., Tyson, G.W. and Schenk, P.M. (2013). Rhizosphere Metatranscriptomics: Challenges and Opportunities. Molecular Microbial Ecology of the Rhizosphere. [Edited by Frans, J. de Bruijn. Hoboken, N.J.] United States: Wiley-Blackwell. 1137-1144. https://doi.org/10.1002/97811182976 74.ch109.
- Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I. et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. 29(7): 644-652. https: //doi.org/10.1038/nbt.1883.
- Jagtap, P., Mehta, S., Sajulga, R., Batut, B., Leith, E., Kumar, P. and Hiltemann, S. (2021). Metatranscriptomics analysis using microbiome RNA-seq data (short) (Galaxy Training Materials). https://training.galaxy project.org/trainingmaterial/topics/metagenomics/ tutorials/metatranscriptomics-short/tutorial.html Online.
- Kumar, A. and Dubey, A. (2020). Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. Journal of Advanced Research. 24: 337-352.
- Li, D., Liu, C., Luo, R., Sadakane, K., Lam, T. (2015). Megahit: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 31(10): 1674-1676.
- Moorthy, A., Balasundaram, U. (2021). Rhizosphere Metagenomics: Methods and Challenges. In: Omics Science for Rhizosphere Biology. [Pudake, R.N., Sahu, B.B., Kumari, M., Sharma, A.K. (eds)], Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978- 981-16-0889-6_1.
- Nurk, S., Meleshko, D., Korobeynikov, A., Pevzner, P.A. (2017). metaSPAdes: A new versatile metagenomic assembler. Genome Research. 27: 824-834. doi: 10.1101/gr.213959. 116. https://www.ncbi.nlm.nih.gov/pubmed/28298430.
- Ranjan, K., Bharti, M.K., Siddique, R.A., Singh, J. (2021). Metatranscriptomics in Microbiome Study: A Comprehensive Approach. In: Microbial Metatranscriptomics Belowground. [Nath, M., Bhatt, D., Bhargava, P., Choudhary, D.K. (eds)], Springer, Singapore. https:/ /doi.org/10.1007/978-981-15-9758-91.
- Shakya, M., Lo, C. and Chain, P.S. (2019). Advances and Challenges in metatranscriptomic analysis. Front. Genet. 10: 904. doi:10.3389/fgene.2019.00904.
- Zerbino, D.R. and Birney, E. (2008). Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. 18(5): 821-829. https://doi.org/ 10.1101/gr.074492.107.
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