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Biotechnology and Applied Biochemistry (1998) 27, (73–79) (Printed in Great Britain)

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Review

The application of molecular techniques in environmental biotechnology for monitoring microbial systems

Mark A. Schneegurt and Charles F. Kulpa, Jr.

Department of Biological Sciences and Center for Environmental Science and Technology, University of Notre Dame, Notre Dame, IN 46556, U.S.A.

Abbreviations: 2,4-D, 2,4-dichlorophenoxyacetic acid; DGGE, density-gradient gel electrophoresis; FISH, fluorescent in situ hybridization; MPN, most probable number; PCB, polychlorinated biphenyl; RAPD, randomly amplified polymorphic DNA; REP-PCR, PCR amplification of repetitive genomic sequences; RT–PCR, reverse transcriptase-mediated PCR.

Correspondence: F. Kulpa, Jr., Department of Biological Sciences and Center for Environmental Science and Technology, University of Notre Dame, Notre Dame, IN 46556, U.S.A.

Traditional methods of bacterial enumeration are often insufficient for monitoring the specific microbes critical for important biochemical reactions in complex, mixed microbial communities. Molecular methods have been developed that can detect and quantify phylogenetic groups on the basis of rDNA sequences and relevant structural genes. Many of these techniques rely on PCR for the amplification of DNA sequences that might be in low abundance in a mixed microbial community. Reverse transcriptase can be coupled to PCR for measuring gene expression on the basis of mRNA abundance. Microbial diversity and community structure can be addressed by further examination of PCR products by various separation techniques and restriction analyses. Microscopic examination of the architecture of intact microbial communities such as biofilms and flocs can be enhanced by using fluorescently labelled population-specific rRNA probes. The molecular techniques described in this review can enhance the science and practice of environmental biotechnology by providing ways of characterizing mixed microbial communities rapidly on a phylogenetic basis and in terms of specific enzymic activities.

Received 14 November 1997; accepted 5 December 1997

© 1998 The International Union of Biochemistry and Molecular Biology