The use of high throughput DNA sequence analysis to assess the endophytic microbiome of date palm roots grown under different levels of salt stress

Mahmoud W. Yaish, Ibtisam Al-Harrasi, Aliya S. Alansari, Rashid Al-Yahyai, Bernard R. Glick

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant’s salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated. Approximately 150,061 reads were produced from the analysis of six ribosomal DNA libraries, which were prepared from endophytic microorganisms colonizing date palm root tissues. DNA sequence analysis of these libraries predicted the presence of a variety of bacterial and fungal endophytic species, some known and others unknown. The microbial community compositions of 30% and 8% of the bacterial and fungal species, respectively, were significantly (p ≤ 0.05) altered in response to salinity stress. Differential enrichment analysis showed that microbe diversity indicated by the Chao, Shannon and Simpson indices were slightly reduced, however, the overall microbial community structures were not significantly affected as a consequence of salinity. This may reflect a buffering effect by the host plant on the internal environments that these communities are colonizing. Some of the endophytes identified in this study were strains that were previously isolated from saline and marine environments. This suggests possible interactions with the plant that are favorable to salinity tolerance in date palm.

Original languageEnglish
Pages (from-to)143-155
Number of pages13
JournalInternational Microbiology
Volume19
Issue number3
DOIs
Publication statusPublished - 2016

Fingerprint

Microbiota
Salinity
DNA Sequence Analysis
Salts
Growth Substances
Endophytes
Ribosomal DNA
Gene Library
Libraries
Soil
Phoeniceae
Growth

Keywords

  • Endophytes
  • Phoenix dactylifera
  • Salt stress

ASJC Scopus subject areas

  • Microbiology
  • Medicine(all)
  • Microbiology (medical)

Cite this

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abstract = "Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant’s salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated. Approximately 150,061 reads were produced from the analysis of six ribosomal DNA libraries, which were prepared from endophytic microorganisms colonizing date palm root tissues. DNA sequence analysis of these libraries predicted the presence of a variety of bacterial and fungal endophytic species, some known and others unknown. The microbial community compositions of 30{\%} and 8{\%} of the bacterial and fungal species, respectively, were significantly (p ≤ 0.05) altered in response to salinity stress. Differential enrichment analysis showed that microbe diversity indicated by the Chao, Shannon and Simpson indices were slightly reduced, however, the overall microbial community structures were not significantly affected as a consequence of salinity. This may reflect a buffering effect by the host plant on the internal environments that these communities are colonizing. Some of the endophytes identified in this study were strains that were previously isolated from saline and marine environments. This suggests possible interactions with the plant that are favorable to salinity tolerance in date palm.",
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AU - Al-Yahyai, Rashid

AU - Glick, Bernard R.

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