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The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies

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Abstract

Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics—technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.

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Acknowledgements

The PK and DKM acknowledge the University Grants Commission (UGC), Government of India for financial support through UGC-BSR Faculty Fellowship. PP acknowledges the DBT, Ministry of Science and Technology, Government of India, for financial support. JR acknowledges UGC for financial support.

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  1. Jina Rajkumari and Prashant Katiyar share equal contributions.

Authors and Affiliations

  1. Department of Microbiology, Assam University, Silchar, Assam, 788011, India

    Jina Rajkumari & Piyush Pandey

  2. Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India

    Prashant Katiyar & Dinesh Kumar Maheshwari

  3. Department of Microbiology, Sardar Bhagwan Singh University, Dehra Dun, Uttarakhand, 248161, India

    Shrivardhan Dheeman

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PK and JR prepared and compiled the original manuscript. SD provided the suggestions. PP and DKM conceptualized, reviewed the work and PP, wrote, and edited the final manuscript.

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Rajkumari, J., Katiyar, P., Dheeman, S. et al. The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies. World J Microbiol Biotechnol 38, 206 (2022). https://doi.org/10.1007/s11274-022-03370-w

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