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https://doi.org/10.17113/ftb.56.02.18.5393

Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments

Ranko Gacesa ; Department of Chemistry, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
Damir Baranasic ; Department of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, Germany
Antonio Starcevic ; Centre of Research Excellence for Marine Bioprospecting - BioProCro, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
Janko Diminic ; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
Marino Korlević ; Centre for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR- 52210 Rovinj, Croatia
Mirjana Najdek ; Centre for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR- 52210 Rovinj, Croatia
Maria Blažina ; Centre for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR- 52210 Rovinj, Croatia
Davor Oršolić ; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
Domagoj Kolesarić ; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
Paul F. Long ; Department of Chemistry, King’s College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
John Cullum ; Department of Genetics, University of Kaiserslautern, Postfach 3049, DE-67653 Kaiserslautern, Germany
Daslav Hranueli ; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
Sandi Orlic ; Center of Excellence for Science and Technology Integrating Mediterranean Region, Microbial Ecology, HR-10000 Zagreb, Croatia
Jurica Zucko ; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia


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Abstract

Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.

Keywords

oil pollution, n-alkane degradation, database

Hrčak ID:

203496

URI

https://hrcak.srce.hr/203496

Article data in other languages: croatian

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