Culturable diversity and functional annotation of psychrotrophic bacteria from cold desert of Leh Ladakh (India)

Abstract

To study culturable bacterial diversity under subzero temperature conditions and their possible functional annotation, soil and water samples from Leh Ladakh region were analysed. Ten different nutrient combinations were used to isolate the maximum possible culturable morphotypes. A total of 325 bacterial isolates were characterized employing 16S rDNA-Amplified Ribosomal DNA Restriction Analysis with three restriction endonucleases AluI, MspI and HaeIII, which led to formation of 23-40 groups for the different sites at 75% similarity index, adding up to 175 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 175 bacteria, grouped in four phyla, Firmicutes (54%), Proteobacteria (28%), Actinobacteria (16%) and Bacteroidetes (3%), and included 29 different genera with 57 distinct species. Overall 39% of the total morphotypes belonged to the Bacillus and Bacillus derived genera (BBDG) followed by Pseudomonas (14%), Arthrobacter (9%), Exiguobacterium (8%), Alishewanella (4%), Brachybacterium, Providencia, Planococcus (3%), Janthinobacterium, Sphingobacterium, Kocuria (2%) and Aurantimonas, Citricoccus, Cellulosimicrobium, Brevundimonas, Desemzia, Flavobacterium, Klebsiella, Paracoccus, Psychrobacter, Sporosarcina, Staphylococcus, Sinobaca, Stenotrophomonas, Sanguibacter, Vibrio (1%). The representative isolates from each cluster were screened for their plant growth promoting characteristics at low temperature (5-15°C). Variations were observed among strains for production of ammonia, hydrogen cyanide, indole-3-acetic acid and siderophore, solubilisation of phosphate, 1-aminocyclopropane-1-carboxylate deaminase activity and biocontrol activity against Rhizoctonia solani and Macrophomina phaseolina. Cold adapted microbes may have application as inoculants and biocontrol agents in crops growing at high altitudes under cold climate condition.