title: Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation.
abstract: 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.
authors.affiliation: Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic. ondrej.uhlik@vscht.cz
authors.forename: Ondrej
authors.initials: O
authors.lastname: Uhlik
authors.forename: Mary-Cathrine
authors.initials: MC
authors.lastname: Leewis
authors.forename: Michal
authors.initials: M
authors.lastname: Strejcek
authors.forename: Lucie
authors.initials: L
authors.lastname: Musilova
authors.forename: Martina
authors.initials: M
authors.lastname: Mackova
authors.forename: Mary Beth
authors.initials: MB
authors.lastname: Leigh
authors.forename: Tomas
authors.initials: T
authors.lastname: Macek
mesh_terms: D001673:Biodegradation, Environmental; D002244:Carbon / Q000378:metabolism; D004785:Environmental Pollutants / Q000378:metabolism*; D007553:Isotope Labeling / Q000379:methods*; D056186:Metagenomics / Q000379:methods* / Q000639:trends; D010802:Phylogeny
chemical_list: D004785:Environmental Pollutants; D002244:Carbon