Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy

• Published in: Archives of microbiology 2014-08, Vol.196 (8), p.531-544
• Main Authors: Joshi, Madhvi N, Dhebar, Shivangi V, Dhebar, Shivani V, Bhargava, Poonam, Pandit, Aanal, Patel, Riddhi P, Saxena, Akshay, Bagatharia, Snehal B
• Format: Article
• Language: English
• Subjects: Aromatic hydrocarbons; Biochemistry; Biodiversity; Biomedical and Life Sciences; Biotechnology; Cell Biology; Ecology; enzymes; functional diversity; Gammaproteobacteria - genetics; Gammaproteobacteria - isolation & purification; gas chromatography-mass spectrometry; genes; Genes, Bacterial; Hydrocarbons; Hydrocarbons - metabolism; Life Sciences; Metabolic Networks and Pathways - genetics; Metagenome; Metagenomics; Microbial Ecology; Microbial Interactions; Microbial Viability; Microbiology; Microorganisms; Oil pollution; Original Paper; Petroleum; Petroleum - microbiology; Phylogenetics; Proteins; Proteobacteria; Pseudomonas stutzeri; Pseudomonas stutzeri - genetics; Pseudomonas stutzeri - isolation & purification; Sequence Analysis, DNA; stress response; Taxonomy; wastewater treatment; Wastewater treatment plants; Water treatment
• ISSN: 0302-8933; 1432-072X
• DOI: 10.1007/s00203-014-0992-0

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 oil-degrading 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.