Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity

Zhilin Yuan, Irina S. Druzhinina, Jessy Labbé, Regina Redman, Yuan Qin, Russell Rodriguez, Chulong Zhang, Gerald A. Tuskan, Fucheng Lin

Research output: Contribution to journalArticlepeer-review

179 Scopus citations

Abstract

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria andγ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.

Original languageEnglish
Article number32467
JournalScientific Reports
Volume6
DOIs
StatePublished - Aug 30 2016

Funding

This research was supported financially by the Non-Profit Sector Special Research Fund of the Chinese Academy of Forestry (RISF2013005) and the National Natural Science Foundation of China (No. 31370704). ISD was supported by the Austrian Science Fund (FWF): project number P 25745. JL was supported by the Genomic Science Program, U.S. Department of Energy, Office of Science, Biological and Environmental Research as part of the Plant-Microbe Interfaces Scientific Focus Area (http://pmi.ornl.gov). Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. We would like to extend our sincerest thanks and great appreciation to Prof. Jeff Dangl, the University of North Carolina at Chapel Hill for his useful suggestions and technical assistance.

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