Dr. Prashant Dhakephalkar

Dr. Prashant Dhakephalkar
Director, Agharkar Research Institute

Email: pkdhakephalkar@aripune.org, pkdhakephalkar@gmail.com

Education & Scientific Career

    • M.Sc. (Microbiology)-1988
    • Ph.D. (Microbiology) 1993
    • Microbiologist in Global Environmental Engineering Ltd., Pune (1993-1995)
    • Research Associate at University of Virginia, Charlottesville, USA (1998-2000)
    • Scientist in Microbiology Department


  • My major research interest is in investigating the microbial diversity associated with extreme, pristine and other habitats for taxonomic novelty and industrial applications (especially Bioenergy, Petroleum Biotechnology and Bioremediation). My group works on collecting samples from a variety of extreme and pristine habitats including (but not limited to) volcanic mud, deep subsurface high temperature oil reservoirs, submarine methane
    hydrate sediments, high altitude lake sediments, etc. We document the bacterial and archaeal diversity associated with such environments using molecular tools such as PCR-DGGE-Sequencing of house-keeping genes (e.g. SSU rRNA, mcrA, dsr, rpob, etc.) or metagenome sequencing using NGS platform. Extremophiles such as thermophiles, halophiles, barotolerant and other microorganisms are isolated and novel taxa are documented by adopting the polyphasic identification approach. Microbial cultures, in isolation or as consortium, are used to develop technologies in the field of bioenergy, petroleum biotechnology, bioremediation or production of valuable
    enzymes/ biomolecules. Microbial metabolism underlying such industrial application is investigated using whole genome, transcriptome and proteome

Following are some of the examples of technologies developed through industrial collaborations:

  • Microbial Enhanced Oil Recovery
  • Bioremediation of petroleum hydrocarbons contaminated produced waters
  • Biomethanation of agricultural residues
  • Production of optically pure unnatural amino acids
  • Microbial control of foul odor and pathogens associated with human excreta
  • Conversion of residual oil to methane for energy recovery from spent oil reservoirs (proofof concept)

Selected Publications

(2011 Onwards)

1. VS Honkalas, AP Dabir, P Arora, DR Ranade, PK Dhakephalkar (2015) Draft genome sequence of Clostridium celerecrescens 152B isolatedfrom sub-seafloor methane hydrate deposits. Marine Genomics. doi:10.1016/j.margen.2015.01.008

2. P Singh, N Kapse, P Arora, SM Singh, PK Dhakephalkar (2015) Draft genome of Cryobacterium sp. MLB-32, an obligate psychrophile fromglacier cryoconite holes of high Arctic. Marine Genomics. doi:10.1016/j.margen.2015.01.006

3. Arora, P., Ranade, D. R., & Dhakephalkar, P. K. (2014). Development of a microbial process for the recovery of petroleum oil from depletedreservoirs at 91–96° C. Bioresource technology, 165: 274-278.

4. Pore, S. D., Arora, P., & Dhakephalkar, P. K. (2014). Draft genome sequence of Geobacillus sp. strain FW23, isolated from a formation watersample. Genome announcements, 2: e00352-14.

5. Singh, P., Singh, S. M., & Dhakephalkar, P. (2014). Diversity, cold active enzymes and adaptation strategies of bacteria inhabiting glaciercryoconite holes of High Arctic. Extremophiles, 18: 229-242.

6. Engineer, A. S., Dhakephalkar, A. P., Gaikaiwari, R. P., & Dhakephalkar, P. K. (2013). Process parameter optimization forhydantoinase-mediated synthesis of optically pure carbamoyl amino acids of industrial value using Pseudomonas aeruginosa resting cells. Journal of industrial microbiology

& biotechnology, 40:1367-1372.

7. Antony, R., Krishnan, K. P., Laluraj, C. M., Thamban, M., Dhakephalkar, P. K., Engineer, A. S., & Shivaji, S. (2012). Diversity and physiologyof culturable bacteria associated with a coastal Antarctic ice core. Microbiological research, 167: 372-380.

8. Kamalaskar, L. B., Dhakephalkar, P. K., Meher, K. K., & Ranade, D. R. (2010). High biohydrogen yielding Clostridium sp. DMHC-10 isolatedfrom sludge of distillery waste treatment plant. International Journal of Hydrogen Energy, 35: 10639-10644.

9. Sachdev, D., Nema, P., Dhakephalkar, P., Zinjarde, S., & Chopade, B. (2010). Assessment of 16S rRNA gene-based phylogenetic diversity andpromising plant growth-promoting traits of Acinetobacter community from the rhizosphere of wheat. Microbiological research, 165: 627-638.

10. Satpute, S. K., Banat, I. M., Dhakephalkar, P. K., Banpurkar, A. G., & Chopade, B. A. (2010). Biosurfactants, bioemulsifiers andexopolysaccharides from marine microorganisms. Biotechnology advances, 28: 436-450.

11. Satpute, S. K., Banpurkar, A. G., Dhakephalkar, P. K., Banat, I. M., & Chopade, B. A. (2010). Methods for investigating biosurfactants andbioemulsifiers: a review. Critical reviews in biotechnology, 30: 127-144.



1. Shete, S.D., Dhakephalkar,P. K., Kanekar, P.P., Ranade, D.R. & Rao, J.U. Production of cerium sulfide pigment by a novel microbiologicalprocess using recombinant strain of E. coli. Indian Patent Number(s): 512/MUM/2013.

2. Ranade, D.R., Kamalaskar, L., Lapsiya, K., Kshirsagar, P.R. & Dhakephalkar, P.K. A method for continuous generation of hydrogen bybiodegradation of organic matter using Clostridium biohydrogenum MCM B-509 sp nov. Indian Patent Number(s): 412/MUM/2014.

3. Engineer, A.S., Dhakephalkar, P.K. & Gaikaiwari, R.P. Microbial Process for the production of optically pure unnatural carbamoyl amino acids.Indian Patent Number(s): 1384/MUM/2013.

4. Dhakephalkar, P.K.,Ranade, D.R.,Bateja, S.,Biswas, S.K.,Kukreti, V. & Rana, D.P. Process for Enhanced Recovery of Crude Oil fromOil-Wells at 91°C or Higher Temperatures Using Hyperthermophilic Indigenous or Injected Microorganisms / Consortia. Indian Patent Number(s): 751/MUM/2014.

5. Ranade, D. R., Dhakephalkar, P. K., Deshpande, M. G., Lanjekar, V. B., Padmanabhan, G., & Dnyansagar, R. V. Development of a bioprocessto reduce pathogenic load and malodor of human night soil. Indian Patent Number(s): 2072/MUM/2012.

6. Dhakephalkar, P.K., Deshpande, M.G. & Wagh, S.A. Composition of novel microbial consortium to improve poultry health, in terms of increasedfeed conversion ratio and weight gain. Indian Patent Number(s): 1366/MUM/2011.

7. Deshmukh, N. S., Dhakephalkar, P. K., Kalluri, K. M., Lapsiya, K. L., Ranade, D. R., Savant, D. V. & Yadav, Y.T. Microbial process forremoval of adsorbable organic halides from industrial wastewater using anaerobic filter. Indian Patent Number(s): IN200701687-I3.

8. Nilegaonkar, S. S ., Zambare, V. P., Kanekar, P. P., Dhakephalkar, P. K., Sarnaik, S. S., Chandrababu, N. K., Ramanaiah, B., Rajaram, R.,Ramasamy, T., Krishnaiah, Y., Kumari, S. & Balaram, P. Eine neue Protease für industrielle Anwendungen. German Patent Number(s): 102007013950

9. Nilegaonkar, S. S., Zambare, V. P., Kanekar, P. P., Dhakephalkar, P. K., Sarnaik, S. S., Rajaram, R., Chandrababu, N. K., Ramanaiah, B.,Balram, P. Y., Kumari, S & Ramasamy, T. A novel protease for industrial application. US Patent No. : US 2008/0220499 A1

10. Latha, C.,Shriram, V.D.,Rojatkar, S.R.,Jahagirdar, S.S. & Dhakephalkar, P.K. Composition and a method of curing antibiotic resistanceplasmids. PCT No. WO/2007/088408.

11. Deshmukh N. S., Dhakephalkar, P. K., Kalluri, K. M., Lapsiya, K. L., Ranade, D R., Savant, D. V. & Yadav ,Y. T. (2010) Microbial processfor removal of adsorbable organic halides from industrial wastewater using anaerobic filter. Indian Patent Number(s): IN200701687-I3

Funding & Collaborators


    • Department of Biotechnology: DBT BioCARe funded project: ‘Microbial Control ofmethane turnover in rice fields’ (July 2013-July 2016) http://dbtindia.nic.in
    • Research funding provided by Agharkar Research Institute for the project: ‘Mining theanoxic ecosystems for efficient fibrolytic microbes’ (April 2014 March 2017)




    • Bioenergy Group,
      Room no. 86, C 2 Building,
      Agharkar ResearchInstitute-411004,
      Pune (India)
      Ph: +91-20-25654357, Extn: 349
      Fax: +91-20-25651542


Important Links:


    • Fluorescence in situ hybridization (FISH)


    • RFLP of clones


    • Methylosoma difficile (novel methane oxidizing genus)


    • Methanobacterium sp. isolated from rice fields