Volume 60, Issue 336, September - December 2024

Comparative metagenomic analysis of rhizosphere soil associated bacterial community structure and function from Zea mays and Brassica nigra

Manisha Mandal¹, Biswajit Ghosh², Shyamapada Mandal^2♦

¹Department of Physiology, MGM Medical College, Kishanganj, Bihar, PIN-855107, India
²Department of Zoology, University of Gour Banga, West Bengal, Malda, PIN-732103, India

^♦Corresponding Author
Department of Zoology, University of Gour Banga, West Bengal, Malda, PIN-732103, India

ABSTRACT

Background: The rhizosphere soil is the hotspot for diverse plant-microbe interactions, which is beneficial for plant productivity. Two economically significant and Indigenous (Malda, India) crops, Zea mays, and Brassica nigra, were analyzed in this study using 16SrRNA metagenomic sequencing to explore the structure and function of rhizomicrobiome with advantageous interaction with the plants. Methods: Rhizosphere soils were collected, analyzed for soil physicochemical properties, and subjected to DNA extraction, PCR amplification, followed by sequencing using Illumina MiSeq. The metagenomic sequences were demultiplexed for quality control, chimera removal, OTU abundance in QIIME2, and taxonomic assignment using Kraken2/Bracken against Silva/Greengenes/NCBI/KEGG databases. Results: Proteobacteria and Planctomycetes were the two most abundant phyla, Adurb.Bin063- 1 sp. predominated Zea mays and Brassica nigra. Alpha and beta diversity differed insignificantly between Zea mays and Brassica nigra. The two rhizomicrobiomes showed a significant positive correlation at the genus level. Ellin6067 sp., Nitrosomonas sp., MND1 sp., oc32 sp., and mle1-7 sp. from the Nitrosomonadaceae predominated the rhizomicrobiomes. Enrichment of nitrogen-fixation, nitritereduction, and ammonia-oxidation occurred in Zea mays and Brassica nigra. Expression of pEA3 plasmid was detected in Zea mays with reports of putative nitrogen fixation properties. Antimicrobial resistance gene analysis revealed aminocoumarin resistance in Zea mays. Abundances of mobile genetic element vs bacterial genera, and functional characteristics describing Zea mays vs Brassica nigra were insignificantly associated. Conclusion: Rhizomicrobiomes of Zea mays and Brassica nigra revealed shared taxonomic and metabolic profiles related to the nitrogen cycle. Deciphering the structural and functional diversity of rhizomicrobiomes are essential for understanding advantageous plant-microbe interactions.

Keywords: Bacteria, rhizomicrobiome, metagenomics, taxa, function, diversity, mobile genetic elements

Discovery, 2024, 60, e25d1467

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DOI: https://doi.org/10.54905/disssi.v60i336.e25d1467

Published: 03 September 2024