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

  • Ajar Nath Yadav
  • Shashwati Ghosh Sachan
  • Priyanka Verma
  • Satya Prakash Tyagi
  • Rajeev Kaushik
  • Anil K. Saxena
Original Paper

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.

Keywords

Cold desert Diversity Leh Ladakh PGPB Psychrotrophic bacteria 16S rRNA gene 

Notes

Acknowledgments

The authors are grateful to the Division of Microbiology, Indian Agricultural Research Institute (IARI), New Delhi and National Agricultural Innovation Project on “Diversity analysis of Bacillus and other predominant genera in extreme environments and its utilization in Agriculture”, Indian Council of Agricultural Research for providing the facilities and financial support, to undertake the investigations. There are no conflicts of interest.

Ethical standard

The experiments undertaken comply with the current laws of India, the country where the investigation was undertaken.

Supplementary material

11274_2014_1768_MOESM1_ESM.doc (168 kb)
Supplementary material 1 (DOC 168 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Ajar Nath Yadav
    • 1
    • 2
  • Shashwati Ghosh Sachan
    • 2
  • Priyanka Verma
    • 1
  • Satya Prakash Tyagi
    • 1
  • Rajeev Kaushik
    • 1
  • Anil K. Saxena
    • 1
  1. 1.Division of MicrobiologyIndian Agricultural Research InstituteNew DelhiIndia
  2. 2.Department of Bio-EngineeringBirla Institute of Technology, MesraRanchiIndia

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