Understanding the effects of soil salinity on rhizosphere microbiome assemblage. Halophyte rhizosphere microbiome assemblage

Rhizosphere microbiome plays a significant role in the functioning of plants and provides information regarding plant physiology (osmoregulation) and development. Very limited information has been available on the microbial diversity from different saline environments. Hence in the current study, we used pyrosequencing analysis of the 16S rRNA gene to compare the composition of rhizosphere microbiome of halophytes (Urochloa, Kochia, Salsola and Atriplex) from moderate and highly saline environments (Khewra Salt Mines) with that of a non-halophyte (Triticum). The rhizosphere microbiome of halophytes and non-halophyte were also compared on the basis of alpha and beta diversity. Metagenomic analysis of soil indicated that Actinobacteria was the most dominant phylum from saline soil samples and Proteobacteria from non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes, Planctomycetes and Thaumarchaeota were the more dominant phyla while Cyanobacteria, Verrucomicrobia, Choroflexi, Gemmatimonadetes and WPS-2 were less abundant in saline and non-saline soil samples. Sequences from Euryarchaeota, WPS-1, Ignavibacteriae, Chlamydiae and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes_gp4, Halomonas, Nocardioides, Solirubrobacter, Halalkalicoccus, Haloferula and Halobacterium. The results showed that increase in soil salinity correlated with significant differences in the alpha and beta diversity of microbial communities across saline and non-saline soil samples. This study revealed that metagenomic analysis can be used to study how changes in abiotic factors in soil (salinity) affect the microbial diversity across different soil samples.