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.

Biodiversity and biotechnological applications of halophilic microbes for sustainable agriculture

“…There are very few reports of archaea as associated with plants such as maize, rice, and halophytic plant (Abutilon, Cressa, Sporobolus, and Suaeda nudiflora) [17][18][19]. Archaea have been reported as unculturable from maize [20] and rice crop [21], whereas culturable archaea have been reported from Abutilon, Cressa, Sporobolus, S. nudiflora [22] [17,23,24]. Microbiome of saline environments, especially halophilic fungi, has become one of the richest bioresources for industrially important molecules and enzymes.…”

Plant growth promoting traits of psychrotolerant bacteria: A boon for agriculture in hilly terrains

“…Selvakumar et al (20) identified from the cold desert of Himalayan region by Yadav et al (21). In another study, Yadav et al (22) have reported and identified 11 psychrotrophic bacterial strains producing gibberelic acid. More than two dozens of wheat allied psychrotolerant bacterial strains producing gibberelic acid were isolated by Verma et al (3) from northern hills of India.…”

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health

“…Along with novel species of psychrotrophic microbes, some microbial species such as Arthrobacter nicotianae, Brevundimonas terrae, Paenibacillus tylopili, and Pseudomonas cedrina have been isolated and characterized for multifarious PGP attributes at low temperatures from cold deserts of NW Himalayas [7]. In a study by Yadav et al [8] [57].…”

“…The haloarchaea have been isolated from many halophilic plants growing in hypersaline region of Rann of Kutch and characterized for different PGP attributes under hypersaline conditions [38,63,64]. In study by Yadav et al [8], …”

“…Nitrogen is the one of the major limiting factors for plant growth, and the application of N 2 -fixing microbes as biofertilizers has emerged Aeromonas hydrophila MAS-765 Salinity stress Alleviate salinity, growth [74] Aeromonas vaga BAM-77 Alkalinity stress Growth and yield [75] Aeromonas vaga BAM-77 Salinity stress Growth and yield [75] Arthrobacter sulfonivorans IARI-L- 16 Cold stress Growth and alleviation [8] Azospirillum brasilense NO 40 Drought and heat stress Improved homeostatic [76] Azospirillum brasilense Sp245 Drought and heat stress Coleoptiles growth [77] Azospirillum brasilense Sp245 Drought and heat stress Grain yield, mineral quality [78] Azospirillum brasilense Sp245 Cold stress Affected dry weight [79] Azospirillumlipoferum AZ1, AZ9, AZ45 Drought and heat stress Alleviate the drought stress [80] Bacillus aerophilus BSH15 Acidic stress Growth and alleviate acidity [81] Bacillus alcalophilus BCZ14 Drought and heat stress Growth, yield, stress [81] Bacillus altitudinis IARI-HHS2-2 Cold stress Growth and yield [28] Bacillus altitudinis BNW15 Alkalinity stress Growth and alleviate alkalinity [81] Bacillus amyloliquefaciens BNE12 Salinity stress Growth and alleviate salinity [81] Bacillus amyloliquefaciens IARI-HHS2-30…”