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Biotechnology Advances
31, No. 2, 2013; Pages: 154 - 165

Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation

Ondrej Uhlik, Mary-Cathrine Leewis, Michal Strejcek, Lucie Musilova, Martina Mackova, Mary Beth Leigh, Tomas Macek

Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic.


Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.

Keywords: Bioremediation; Biodegradation; Stable isotope probing; Metagenomics; Sequence-based screening; Function-based screening; Gene-targeted metagenomics; High-throughput sequencing; High-throughput microarrays; Carbon flow



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