Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome

  • Salma Mukhtar
  • Babur Saeed Mirza
  • Samina Mehnaz
  • Muhammad Sajjad Mirza
  • Joan Mclean
  • Kauser Abdulla MalikEmail author
Original Paper


The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.


Soil microbiome 16S rRNA gene Pyrosequencing Soil salinity Halophilic bacteria Haloarchaea 



We are highly thankful to Higher Education Commission [Project # HEC (FD/2012/1843)] and Pakistan Academy of Sciences [Project # 5-9/PAS/2012/969] for research grants. We would like to express our gratitude to Mr. Mukhtar Ahmad (Assistant Professor), Dyal Singh College, Lahore, for assistance in statistical analyses. We are grateful to Prof. Ann M. Hirsch (UCLA) for the comments on the manuscript.

Author contributions

SM: Conducted experiment and prepared manuscript; BSM: pyrosequencing and data analysis; SM: manuscript preparation; MSM: supervised research and manuscript preparation; JM: pyrosequencing and data analysis; KAM: guided in experiment plan and edited manuscript.

Compliance with ethical standards

Conflict of interest

The authors declared that they have no conflict of interest in the publication.

Supplementary material

11274_2018_2509_MOESM1_ESM.docx (6.9 mb)
Supplementary material 1 (DOCX 7037 KB)


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Salma Mukhtar
    • 1
  • Babur Saeed Mirza
    • 2
  • Samina Mehnaz
    • 1
  • Muhammad Sajjad Mirza
    • 3
  • Joan Mclean
    • 4
  • Kauser Abdulla Malik
    • 1
    Email author
  1. 1.Department of Biological SciencesForman Christian College (A Chartered University)LahorePakistan
  2. 2.Department of BiologyMissouri State UniversitySpringfieldUSA
  3. 3.Environmental Biotechnology DivisionNational Institute for Biotechnology and Genetic Engineering (NIBGE)FaisalabadPakistan
  4. 4.Utah Water Research Laboratory, Department of Civil and Environmental EngineeringUtah State UniversityLoganUSA

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