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Applied and Environmental Microbiology, August 2004, p. 4432-4439, Vol. 70, No. 8
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.8.4432-4439.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Culture-Independent Analysis of Fecal Enterobacteria in Environmental Samples by Single-Cell mRNA Profiling

Han Chen,{dagger} Gomathinayagam Ponniah,{dagger} Nancy Salonen, and Paul Blum*

Beadle Center for Genetics, University of Nebraska—Lincoln, Lincoln, Nebraska

Received 19 December 2003/ Accepted 31 March 2004

A culture-independent method called mRNA profiling has been developed for the analysis of fecal enterobacteria and their physiological status in environmental samples. This taxon-specific approach determines the single-cell content of selected gene transcripts whose abundance is either directly or inversely proportional to growth state. Fluorescence in situ hybridization using fluorochrome-labeled oligonucleotide probes was used to measure the cellular concentration of fis and dps mRNA. Relative levels of these transcripts provided a measure of cell growth state and the ability to enumerate fecal enterobacterial cell number. Orthologs were cloned by inverse PCR from several major enterobacterial genera, and probes specific for fecal enterobacteria were designed using multiple DNA sequence alignments. Probe specificity was determined experimentally using pure and mixed cultures of the major enterobacterial genera as well as secondary treated wastewater samples seeded with pure culture inocula. Analysis of the fecal enterobacterial community resident in unseeded secondary treated wastewater detected fluctuations in transcript abundance that were commensurate with incubation time and nutrient availability and demonstrated the utility of the method using environmental samples. mRNA profiling provides a new strategy to improve wastewater disinfection efficiency by accelerating water quality analysis.

* Corresponding author. Mailing address: E234 Beadle Center for Genetics, University of Nebraska, Lincoln, NE 68588-0666. Phone: (402) 472-2769. Fax: (402) 472-8722. E-mail: pblum1{at}unl.edu.

{dagger} H.C. and G.P. contributed equally to this work.

Applied and Environmental Microbiology, August 2004, p. 4432-4439, Vol. 70, No. 8
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.8.4432-4439.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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