Direct Detection by in Situ PCR of the amoA Gene in Biofilm Resulting from a Nitrogen Removal Process

Tatsuhiko Hoshino, Naohiro Noda, Satoshi Tsuneda*, Akira Hirata, Yuhei Inamori

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

52 Citations (Scopus)


Ammonia oxidation is a rate-limiting step in the biological removal of nitrogen from wastewater. Analysis of microbial communities possessing the amoA gene, which is a small subunit of the gene encoding ammonia monooxygenase, is important for controlling nitrogen removal. In this study, the amoA gene present in Nitrosomonas europaea cells in a pure culture and biofilms in a nitrifying reactor was amplified by in situ PCR. In this procedure, fixed cells were permeabilized with lysozyme and subjected to seminested PCR with a digoxigenin-labeled primer. Then, the amplicon was detected with an alkaline phosphatase-labeled antidigoxigenin antibody and HNPP (2-hydroxy-3-naphthoic acid-2′-phenylanilide phosphate), which was combined with Fast Red TR, and with an Alexa Fluor 488-labeled antidigoxigenin antibody. The amoA gene in the biofilms was detected with an unavoidable nonspecific signal when the former method was used for detection. On the other hand, the amoA gene in the biofilms was detected without a nonspecific signal, and the cells possessing the amoA gene were clearly observed near the surface of the biofilm when Alexa Fluor 488-labeled antidigoxigenin antibody was used for detection. Although functional gene expression was not detected in this study, detection of cells in a biofilm based on their function was demonstrated.

Original languageEnglish
Pages (from-to)5261-5266
Number of pages6
JournalApplied and Environmental Microbiology
Issue number3-12
Publication statusPublished - 2001

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology


Dive into the research topics of 'Direct Detection by in Situ PCR of the amoA Gene in Biofilm Resulting from a Nitrogen Removal Process'. Together they form a unique fingerprint.

Cite this