Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India.

Pranamita Kunda,Abhishek Mukherjee,Paltu Kumar Dhal

doi:10.1007/s11274-021-03153-9

Pranamita Kunda, Abhishek Mukherjee + Show 1 more

Open Access

https://doi.org/10.1007/s11274-021-03153-9

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Abstract

Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.

Highlights

Rice is the most important staple food for more than half the world’s population
We found that the agro-ecological zones can be divided into two groups: nutrient dense (GAZ, Northern Hill zone (NHZ) and Teesta alluvial zone (TTAZ)) and nutrient low groups (CSZ, Red and Laterite zone (RLZ) and Vindhyan alluvial zone (VAZ))
principal component analysis (PCA) analysis showed that the first two axes, PC1 and PC2, could explain 72.9% variation in the samples based on environmental parameters. pH, electrical conductivity (EC), available P, K and N were the major contributors to PC1 which accounted for 50.52% of the total variation

Summary

Introduction

Rice is the most important staple food for more than half the world’s population. India is one of the leading producers and consumer of rice and the state of West Bengal is one of the highest producers of rice in India (Kunda et al, 2018). Microbiomes associated with plants roots are known to play a significant role in hastening plant growth, development and can alter plant health as well as their stress tolerance abilities (Lareen et al, 2016) These microbes can reside either in the rhizopsheric soil in close association with the roots or can remain inside the plant as endophytes (Olanrewaju et al, 2017). Symbiotic bacterial endophytes of rice provide multiple benefits to their host They adapt different mechanisms to protect plants from various stressful conditions like drought, salinity, pathogen attack (Khare et al, 2018; Mukhtar et al, 2019). Studying plant-microbe relationship can be highly advantageous in establishing a sustainable plant root microbiome system

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