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Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences

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Abstract

Agriculture is an important livelihood activity in the Himalayan regions. Our previous studies revealed the presence of diverse diazotrophic assemblage in indigenous red kidney bean (RKB) rhizospheric soil from two different locations of Western Indian Himalaya, namely S1 (Chhiplakot, 30.70° N/80.30° E) and S2 (Munsyari, 30.60° N/80.20° E), selected on the basis of real-time PCR analysis. In this study, two 16S rRNA gene clone libraries (SB1 and SB2, respectively) were constructed using the same rhizospheric soil samples for assessing the total bacterial diversity and their community structure. A total of 760 clones were obtained, with ≈54–59% of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Bacteroidetes, Chloroflexi, Acidobactria, Planctomycetes, Firmicutes, Nitrospira, Gemmatimonadetes, Cyanobacteria, Verrucomicrobia, OD1, OP11 and Actinobacteria were encountered in both the soils, sequences belonging to bacteria from the classes Chlorobi and BRC1 were only detected in the S1 soil. Both the libraries showed similar bacterial community compositions, with Pseudomonas (≈33–34%) as predominant genus. Phylogenetic analysis revealed that all the clone sequences were clustered in different bacterial groups as per their resemblance with their respective phylogenetic neighbours. Major clusters were formed by Gammapreoteobacteria followed by Bacteroidetes and Alphapro-teobacteria. A good fraction of the clone sequences has no resemblance with existing groups, thereby suggesting the need of culture-dependent studies from Himalayan regions. To the best of our knowledge, this study is the first major metagenomic effort on Himalayan RKBs rhizobacteria revealing fundamental information that needs to be explored for functional studies.

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Abbreviations

DOTUR:

distance-based OTU and richness

OTU:

operational taxonomic units

PAST:

paleontological statistics

qPCR:

real-time PCR

R:

recombination

RKB:

red kidney bean

rRNA:

ribosomal RNA

TOC:

total organic carbon

WIH:

Western Indian Himalaya

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Acknowledgements

This work was funded by National Bureau of Agriculturally Important Microorganisms (NBAIM)/Indian Council of Agricultural Research (ICAR), grant to RG. First author (DCS) acknowledges ICAR, Research Fellowship during the course of this study.

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  1. These authors contributed equally to this work

Authors and Affiliations

  1. Department of Microbiology, College of Basic Sciences and Humanities, G.B.P.U.A&T, Pantnagar, 263145, Uttarakhand, India

    Deep Chandra Suyal & Reeta Goel

  2. Microbial Culture Collection, National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune, 411 007, Maharashtra, India

    Amit Yadav & Yogesh Shouche

Authors
  1. Deep Chandra Suyal
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  2. Amit Yadav
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  3. Yogesh Shouche
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  4. Reeta Goel
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Correspondence to Reeta Goel.

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Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences

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Suyal, D.C., Yadav, A., Shouche, Y. et al. Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences. Biologia 70, 305–313 (2015). https://doi.org/10.1515/biolog-2015-0048

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