Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy
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Original Paper
Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy Madhvi N. Joshi · Shivangi V. Dhebar · Shivani V. Dhebar · Poonam Bhargava · Aanal Pandit · Riddhi P. Patel · Akshay Saxena · Snehal B. Bagatharia
Received: 16 November 2013 / Revised: 6 April 2014 / Accepted: 8 May 2014 © Springer-Verlag Berlin Heidelberg 2014
Abstract Present study attempts in revealing taxonomic and functional diversity of microorganism from petroleum muck using metagenomics approach. Using Ion Torrent Personal Genome Machine, total of 249 Mb raw data were obtained which was analysed using MG-RAST platform. The taxonomic analysis revealed predominance of Proteobacteria with Gammaproteobacteria as major class and Pseudomonas stutzeri as most abundant organism. Several enzymes involved in aliphatic and aromatic hydrocarbon degradation through both aerobic and anaerobic routes and proteins related to stress response were also present. Comparison of our metagenome with the existing metagenomes from oil-contaminated sites and wastewater treatment plant indicated uniqueness of this metagenome taxonomically and functionally. Based on these results a hypothetical community model showing survival and syntrophy of microorganisms in hydrocarbon-rich environment is proposed. Validation of the metagenome data was done in three tiers by validating major OTUs by isolating oildegrading microbes, confirmation of key genes responsible for hydrocarbon degradation by Sanger sequencing and studying functional dynamics for degradation of the hydrocarbons by the muck meta-community using GC–MS. Communicated by Erko Stackebrandt. Electronic supplementary material The online version of this article (doi:10.1007/s00203-014-0992-0) contains supplementary material, which is available to authorized users. M. N. Joshi · S. V. Dhebar · S. V. Dhebar · P. Bhargava · A. Pandit · R. P. Patel · A. Saxena · S. B. Bagatharia (*) Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar 382 011, Gujarat, India e-mail: [email protected]; [email protected]
Keywords Petroleum muck · Microbial diversity · Metagenome · Ion Torrent · Microbial syntrophy · Community modelling
Introduction Petroleum popularly known as “Black Gold” has brought revolution in the history of mankind. According to the data obtained from Centre for Climate and Energy Solutions, petroleum contributes about 32.8 % of global energy use. Petroleum products are major drivers of transportation, energy, power, agriculture and industries. However, substantial quantity of petrol and other petroleum products enter into the environment as a result of accidental release. Annually, marine environment receives around 2–10 million tons of crude petroleum oil (Tyagi et al. 2011) which is highly toxic to animals, plants and microbes, thus creating a need of efficient remediation strategies (Lee and Vu 2010). Remediation strategies which included sorpti
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