Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

Abstract

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

Molecular characterization of rhizobacteria isolated from walnut (Juglans regia) rhizosphere in Western Himalayas and assessment of their plant growth promoting activities

“…The morphobiochemical characterization of these isolates revealed that seven isolates viz., WI 11, WI 12, WI 30, WI 41, WI 60, WI 80 and WI 91 tentatively belonged to genus Micrococcus and five isolates viz., WI 36, WI 62, WI 63, WI 65 and WI 90 tentatively belonged to genus Bacillus (Table 1). Our findings are supported by Naveed et al (2014) who found rods, cocci and coco-bacillus dominant in rhizosphere, and confirmed by Vega et al (2005) who isolated high number of bacteria from coffee rhizosphere which belonged to genera Bacillus, Burkholderia, Clavibacter, Curtobacterium, Escherichia, Micrococcus, Pantoea, Pseudomonas, Serratia and Stenotrophomonas.…”

Genetic diversity of Rhizobium spp. isolated from soil samples of Bangladesh

“…DNA was extracted and purified from the isolates using standard phenol-chloroform-isoamyl alcohol method 7 . Quality and quantity of isolated DNA was measured by NanoDrop TM spectrophotometer (Thermo Fisher Scientific, USA).…”

“…Genetic and phenotypic diversity study helps to classify the variants of Rhizobium in different groups and to find efficient nitrogen fixing strain having desired traits 6 . The rhizobia from wild leguminous trees had been classified after extensive analysis of the phenotypic, genetic and molecular characteristics 7 . In another study, rhizobia from Acacia senegal and Prosopis chilensis, grown in Sudan, had been clustered according to the numerical analysis of phenotypic characteristics and lipopolysaccharide (LPS) profiles 8,9 .…”

Isolation and Identification of Antagonistic Bacterium against a Pathogens of Bacterial Tuber Rot of Amorphophallus muelleri

“…The 16S rDNA sequence of the isolated bacteria was aligned together with 16S rDNA reference that obtained from the NCBI database. The phylogenetic tree was constructed based on Neighbor-Joining with bootstrap 1000 using the MEGA 6.00 program [31,32,30].…”