An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Megha Hastantram Sampangi-Ramaiah,R Uma Shaanker,M M Vasantha Kumari,G Ravikanth,Ralf Oelmüller,Shridhar Jambagi,Kundapura Venkataramana Ravishankar,Karaba N Nataraja,Prajjal Dey,Jagadheesh Jagadheesh

doi:10.1038/s41598-020-59998-x

Abstract

Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.

Highlights

Salinity stress is one of the most devastating abiotic stresses that affect growth, development and productivity of major crops
This triggers a range of metabolic and molecular cascades such as inhibition of cell expansion, stomatal conductance, photosynthetic activity, abscisic acid (ABA)-mediated responses followed by stimulation of the Superoxide dismutase (SOD) and peroxidase activities as well as accumulation of osmolytes like proline
We demonstrate that the colonized IR-64 plants are morphometrically larger and more tolerant to salt stress than the un-colonized control, and this is associated with an altered expression of a specific combination of genes

Summary

Introduction

Salinity stress is one of the most devastating abiotic stresses that affect growth, development and productivity of major crops. We demonstrate that the colonized IR-64 plants are morphometrically larger and more tolerant to salt stress than the un-colonized control, and this is associated with an altered expression of a specific combination of genes. The results of these experiments are novel and important because they open up exciting possibilities of using an endophytic route towards mitigating crop stress and in understanding the underlying molecular basis of plant-endophyte interaction. The latter could inspire further studies into numerous plant-endophyte interactions reported in literature and seek if there is some commonalities to the way endophytes interact and lend habitat adapted symbiotic benefits to the plants

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Conclusion