Functional genomics of extremophiles

Present Research Activity:

Functional Genomics of Extremophile towards gene prospecting

Molecules derived from natural products particularly those produced by microorganisms have an excellent record of providing novel chemical structures for development as new pharmaceuticals, bio-actives, biocatalysts and biomaterials. Microorganisms namely extremophiles represent the largest reservoir of un-described bio-diversity. Considering the above facts not much more work has been done in our country to explore the microorganisms associated in the extreme ecological niches viz., hot springs, marine environments, acids and alkaline lakes and the hydrothermal vents in deep sea. In fact, the majority of antibiotics in current use are naturally produced by either bacteria or fungi. Discovery of new bacteria and new antibiotics is still a distinct possibility, despite years of bacterial biodiversity research. Therefore it is prerequisite to isolate and characterize microorganisms and to identify their role in bio-prospect for new enzymes, novel genes and bio-molecules. The main focus is under following headings: (i) to investigate the potential of microbes from extreme ecological niches for biotechnological exploitation. (ii) To relate phylogenetic diversity to physiological diversity, ecological function and biogeochemical processes. (iii) To access the phenotypes of the microbes and through level of gene expression we will identify the potential applications of novel enzyme systems and proteins in biodegradation, bio-catalysis and the biomedical process.

Similarly, development of culture independent DNA technologies has enabled a growing understanding of the true extent of microbial diversity, and has lead to the birth of metagenomics (where a metagenome is defined as the sum of all genomes present in any environment). Metagenomic gene discovery involves a growing catalogue of techniques designed to directly access genes, operons or gene product in complex metagenomic nucleic acid preparation. In doing so, my research group is involved for DNA extraction from environmental samples including soils, sediments, biofilms, and other intractable substrates. This type of molecular surveys will show the genetic and biochemical diversity that lies in uncultured micro-organisms. To address these problems, the following attempts have been made. As follows: (i) DNA extraction from soil and other intractable specimens (ii) DNA methods for detecting diversity within species (iii) Identification and detection of microorganisms (iv) Genetic diversity assessment to track organisms in natural environments (v) Retrieval of protein encoding genes from environmental samples (vi) Investigation of genes or organisms with bio-resource potential (vii) Molecular/evolutionary analysis of protein structure and function. My research group is involved to access these biological resources and express genes as a tool for combinatorial evolution of selected metabolic pathways.

Publications  

1.      Kunwar Digvijay Narayan, Shachindra K Pandey and Subrata K. Das^*. 2010. Characterization of Comamonas thiooxidans sp. nov and the comparison of thiosulfate oxidation with Comamonas testosteroni and Comamonas composti. Current Microbiology. (In Press).

 2.     Subrata K Das^*, Uma Shankar Gautam, Kiran V Sandhu, Saumya Bandyopadhyay, Pran K Chakrabartty and Aqbal Singh. 2010. Mutation in the lysA gene impairs the symbiotic properties of Mesorhizobium ciceri. Archives of Microbiology. 192: 69-77. 

3.      V. Jyoti, Kunwar Digvijay Narayan and Subrata K. Das^*. 2009. Gulbenkiania indiensis  sp. nov., isolated from a sulfur spring in Orissa, India. Int. J. Syst. Evol. Microbiol. (In Press). 

4.      Digvijay  Panday  and Subrata K. Das^*. 2009. Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from a hot spring sediment. Int. J. Syst. Evol. Microbiol. (In Press) 

5.      Shachindra K. Pandey, Kunwar Digvijay Narayan, Saumya Bandyopadhyay, Kinshuk C. Nayak and Subrata K. Das^*. 2009. Thiosulfate oxidation by Comamonas sp. S23 isolated from a sulfur spring. Current Microbiology. 58: 516-521. 

6.      Sujogya K. Panda, V. Jyoti, Bhaskar Bhadra,  Kinshuk C. Nayak, Sisinthy Shivaji, Fred A. Rainey and Subrata K. Das^*. 2009.  Thiomonas bhubaneswarensis sp. nov., a novel obligately mixotrophic, moderately thermophilic, thiosulfate oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 59: 2171 – 2175.

7.      Madhuban Gopal, Sunil Kumar Jha, Ram Niwas, Livleen Shukla and Subrata K. Das. 2008. Degradation of Cypermethrin by Pseudomonas stutzeri. Pesticide Research Journal. 20: 275-278.

8.     Uma Shankar Gautam, Anjana Jajoo, Aqbal singh, Pran K. Chakrabortty and Subrata K. Das^*. 2007. Characterization of a rpoN mutant of Mesorhizobium ciceri. Journal of Applied Microbiology. 103: 1798-1807.

9.      Minakshi Patra, Shachindra K. Pandey, Durg V. Singh, T. Ramamurthy, Subrata K. Das^*. 2007. Characterization of cytotoxin producing Aeromonas caviae (strain HT10) isolated from a sulfur spring in Orissa, India. Letters in Applied Microbiology. 44: 338-341.

10.     Subrata K. Das^*, Uma Shankar Gautam, Pran K. Chakrabortty and Aqbal Singh. 2006. Characterization of a symbiotically defective serine auxotroph of Mesorhizobium ciceri. FEMS Microbiology Letters. 263: 244-251.

11.      Nirmali Saikia,  Subrata K. Das, Bharat K.C. Patel,  Ram Niwas,  Aqbal Singh,  and Madhuban Gopal. 2005. Biodegradation of Beta cyfluthrin by Pseudomonas stutzeri strain S1. Biodegradation. 16: 581-589.

12.      N. Roy, Subrata K. Das and P.K. Chakrabortty. 2005. Symbiotic Effectiveness of a Siderophore Overproducing Mutant of Mesorhizobium ciceri. Polish J. Microbiol. 54: 37-41.

13. Subrata K. Das^*. 2005. Genus Bosea. In Kreig, Staley and Brenner (Editors), Bergey’s Manual of Systematic Bacteriology, 2^nd Edition. Vol 2. The Williams & Wilkins Co., Baltimore, pp. 459-461. 

14. D. Hauwaerts, G. Alexandre, Subrata K. Das, J. Vanderleyden, I.B. Zhulin. 2002. A major chemotaxis gene cluster in Azospirillum brasilense and relatioships between chemotaxis operons in alpha-proteobacteria. FEMS Microbiology Lett. 208: 61-70. 

15. J. Dutta, S. Ghosh,  A.K. Maiti, Subrata K. Das,  D.P. Modok, P .K. Chakraborty and  P.K. Roy. 1998. Biodegradation of organochlorine pesticides by soil bacteria. Journal of Scientific and Industrial research. 57: 838-845. 

16. Subrata K. Das and Ajit K. Mishra. 1996. Transposon mutagenesis affecting thiosulfate oxidation in Bosea thiooxidans, a chemolithoheterotrophic bacterium. Journal of  Bacteriology. 178: 3628-3633. 

17. Subrata K. Das, Ajit K. Mishra, B. J. Tindall, F. A. Rainey and E. Stackebrandt. 1996. Oxidation of thiosulfate by a new bacterium , Bosea thiooxidans (BI-42) gen, nov., sp. nov,: Analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing. Int. J. Syst. Bacteriol. 46: 981-987.