Deciphering rhizosphere microbiome for the development of novel bacterial consortium and its evaluation for salt stress management in solanaceous crops in India

Abstract

Eighty bacteria were isolated from the salt affected solanaceous crops (potato, tomato, chilli and brinjal) rhizosphere and fallow land in Mau, Faizabad, Ballia, Gazipur and Varanasi districts of Uttar Pradesh, India. All the bacterial isolates showed morphological variation on Nutrient agar, Jenson’s medium, Modified Czapek-Dox medium, Mannitol egg yolk polymyxin agar, Pseudomonas isolation agar medium, Luria Bertni agar, Tryptic soya agar, King B agar and Nutrient broth yeast extract. Majority of the isolates showed creamy colony (32.5%), spherical (66.25%), shiny (88.7%), raised (62.25%), translucent (71.25%) and entire type of surface margin (78.75%). The gram staining, catalase test, glucose fermentation, IAA test, H2S production, starch hydrolysis, tween 80, gelatin hydrolysis, casein hydrolysis, P solubilization, Zn solubilization and ammonia production tests revealed that 26, 28, 13, 3, 11, 10, 18, 10, 17, 24, 23 and 16 isolates were positive for these tests respectively. The molecular characterization of bacterial isolates Brevibacillus fluminis, Brevibacillus agri, Bacillus paralicheniformis, and Microbacterium arborescens revealed that these are highly salt tolerant (18%) produced 37 alleles using box primer. The number of bands (400–3190 bp) varied from 1 to 10. A cluster analysis with unweighted pair-group method with arithmetic means (UPGMA) based on Jaccard’s similarity coefficient divided the bacterial isolates into two major and three minor clusters with coefficient of similarities ranging from 1 to 23%. Phylogenetic analysis of salt tolerant bacterial isolates showed that out of 22 isolates, 17 (77.27%) were found to be phylogenetically closely related to Bacillus, with 99–100% similarity in their 16S rDNA sequences, making Bacillus the most dominant genus among salt tolerant bacteria in the study.