DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples

John J. Kelly, Slil Siripong, John McCormack, Lori R. Janus, Hidetoshi Urakawa, Said El Fantroussi, Peter A. Noble, Laura Sappelsa, Bruce E. Rittmann, David A. Stahl

Research output: Contribution to journalArticlepeer-review

72 Scopus citations


A small scale DNA microarray containing a set of oligonucleotide probes targeting the 16S rRNAs of several groups of nitrifying bacteria was developed for the monitoring of wastewater treatment plant samples. The microarray was tested using reference rRNAs from pure cultures of nitrifying bacteria. Characterization of samples collected from an industrial wastewater treatment facility demonstrated that nitrifying bacteria could be detected directly by microarray hybridization without the need for PCR amplification. Specifically, the microarray detected Nitrosomonas spp. but did not detect Nitrobacter. The specificity and sensitivity of direct detection was evaluated using on-chip dissociation analysis, and by two independent analyses - an established membrane hybridization format and terminal restriction fragment length polymorphism fingerprinting (T-RFLP). The latter two analyses also revealed Nitrospira and Nitrobacter to be contributing populations in the treatment plant samples. The application of DNA microarrays to wastewater treatment systems, which has been demonstrated in the current work, should offer improved monitoring capabilities and process control for treatment systems, which are susceptible to periodic failures.

Original languageEnglish (US)
Pages (from-to)3229-3238
Number of pages10
JournalWater Research
Issue number14
StatePublished - Sep 2005
Externally publishedYes


  • Microarray
  • Nitrification
  • Nitrifiers
  • Wastewater treatment

ASJC Scopus subject areas

  • Environmental Engineering
  • Civil and Structural Engineering
  • Ecological Modeling
  • Water Science and Technology
  • Waste Management and Disposal
  • Pollution


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