title: Identification of molecular markers to follow up the bioremediation of sites contaminated with chlorinated compounds.
abstract: The use of microorganisms to clean up xenobiotics from polluted ecosystems (soil and water) represents an ecosustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and sensitive strategies for monitoring and identifying bacteria and catabolic genes involved in the degradation of xenobiotics. This chapter provides a description of recently developed molecular-biology-based techniques, such as PCR with degenerate primers set, real-time quantitative PCR (qPCR), reverse transcription PCR (RT-PCR), southern blot hybridization, and long-range PCR, used to give a picture of the catabolically relevant microorganisms and of the functional genes present in a polluted system. By using a case study of a groundwater aquifer contaminated with 1,2-dichloroethane (1,2-DCA), we describe the identification of microorganisms potentially involved in the 1,2-DCA dehalorespiration (Dehalobacter sp. and Desulfitobacterium sp.) and a complete new gene cluster encoding for a 1,2-DCA reductive dehalogenase. The application of these techniques to bioremediation can improve our understanding of the inner mechanisms to evaluate the feasibility of a given treatment and provide us with a method to follow up bacteria and catabolic genes involved in the degradation of contaminants during the activities in situ.
authors.affiliation: Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, Milan, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Marzorati
authors.forename: Annalisa
authors.initials: A
authors.lastname: Balloi
authors.forename: Francesca
authors.initials: F
authors.lastname: De Ferra
authors.forename: Daniele
authors.initials: D
authors.lastname: Daffonchio
mesh_terms: D001673:Biodegradation, Environmental; D015415:Biomarkers; D017606:Chlorine Compounds / Q000737:chemistry / Q000378:metabolism; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D045858:Desulfitobacterium / Q000235:genetics / Q000378:metabolism; D004784:Environmental Monitoring / Q000379:methods*; D004787:Environmental Pollution; D018628:Gene Dosage; D015870:Gene Expression; D015723:Gene Library; D012329:RNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods
chemical_list: D015415:Biomarkers; D017606:Chlorine Compounds; D004269:DNA, Bacterial; D012329:RNA, Bacterial