Comparison of Microbial Communities Associated with Halophyte (Salsola stocksii) and Non-Halophyte (Triticum aestivum) Using Culture-Independent Approaches

Abstract

Halophyte microbiome contributes significantly to plant performance and can provide information regarding complex ecological processes involved in osmoregulation of these plants. The objective of this study is to investigate the microbiomes associated with belowground (rhizosphere), internal (endosphere) and aboveground (phyllosphere) tissues of halophyte (Salsola stocksii) through metagenomics approach. Plant samples were collected from Khewra Salt Mines. The metagenomic DNA from soil, root and shoot samples was isolated with the help of FastDNA spin kit. Through PCR, the 16S rRNA gene from four different Salsola plants and wheat plants was amplified and cloned in InsTAclone PCR cloning kit. Metagenomic analyses from rhizosphere, endosphere and phyllosphere of Salsola showed that approximately 29% bacteria were uncultured and unclassified. Proteobacteria and Actinobacteria were the most abundant phyla in Salsola and wheat. However, Firmicutes, Acidobacteria, Bacteriodetes, Planctomycetes, Cyanobacteria, Thermotogae, Verrucomicrobia, Choroflexi and Euryarchaeota were predominant groups from halophyte whereas Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria, Acidobacteria, Bacteriodetes, Planctomycetes and Verrucomicrobia were predominant phyla of wheat samples. Diversity and differences of microbial flora of Salsola and wheat suggested that functional interactions between plants and microorganisms contribute to salt stress tolerance.

Rhizobacterial communities of five co-occurring desert halophytes

“…The low abundance of Firmicutes in the rhizosphere has been reported many times; see one such case study in barley, where Firmicutes is almost excluded from the rhizosphere (Bulgarelli et al, 2015). Although γ-proteobacteria were less abundant in the rhizosphere, as observed by a decrease in the number of occurrences of Acinetobacter , Citrobacter and Pseudomonas species, γ -proteobacteria remained the most abundant class, as found in many plant-associated bacterial communities (Mukhtar et al, 2017). …”

Microbiome of Halophytes: Diversity and Importance for Plant Health and Productivity

“…1). PGPR may provide the plant with different accessible nutrients such as nitrogen (N) and phosphorus (P) [32], phytohormones (auxins, cytokinins, gibberellins, ethylene and absicisic acids) that promote plant growth under salt stress conditions [26,33,34].…”

“…Many root endophytes can be used as biocontrol agents due to their production of different antibiotic and antifungal compounds [39]. Halotolerant and halophilic Bacillus spp, produce hydrolytic enzymes and have been reported as growth inhibitors for fungal pathogens and they provide protection for different plant diseases [26,40]. These microorganisms also produce a variety of hydrolytic enzymes and play an important role in suppressing the fungal pathogens such as Alternaria sp.…”

“…The phyllosphere is a more dynamic environment than the rhizosphere of plants, so the microbial communities associated with leaves are not uniform and is influenced by number of stomata, leaf veins and hairs [23,24]. Studies on the microbial diversity associated with the phyllosphere of Salsola have shown that Actinobacteria and Proteobacteria are the most abundant phyla [25,26].…”

Actinomycetes: A Source of Industrially Important Enzymes

“…Recently, culture-independent approaches such as metagenomics, metatranscriptomics and metaproteomics have offered rapid screening of novel enzymes from unculturable microorganisms especially identified from extreme environments like arid, saline, thermophilic and arctic regions [41,42]. These technologies help to determine the functional aspects of a micro-environment through innovative approaches like substrate-induced gene expression screening (SIGEX) and preamplification inverse-PCR (PAIPCR) and provide new insights on the functional metagenomic (metaproteomics) analysis of a particular environment [43].…”