Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH)

Tsuyoshi Yamaguchi, Bernhard Maximilian Fuchs, Rudolf Amann, Shuji Kawakami, Kengo Kubota, Masashi Hatamoto, Takashi Yamaguchi

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)


Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with rRNA-targeted oligonucleotide probes has significantly improved the identification of microorganisms in various environmental samples. However, one of the major constraints of CARD-FISH is the low probe penetration due to the high molecular weight of the horseradish peroxidase (HRP) label. Recently, this limitation has been overcome by a novel signal amplification approach termed in situ DNA-hybridization chain reaction (in situ DNA-HCR). In this study, we present an improved and accelerated in situ DNA-HCR protocol (quickHCR-FISH) with increased signal intensity, which was approximately 2 times higher than that of standard in situ DNA-HCR. In addition, the amplification time was only 15 min for the extension of amplifier probes from the initiator probe compared to 2 h in the original protocol. The quickHCR-FISH was successfully tested for the quantification of marine bacteria with low rRNA contents in both seawater and sediment samples. It was possible to detect the same number of marine bacteria with quickHCR-FISH compared to CARD-FISH within only 3 h. Thus, this newly developed protocol could be an attractive alternative to CARD-FISH for the detection and visualization of microorganisms in their environmental context.

Original languageEnglish
Pages (from-to)400-405
Number of pages6
JournalSystematic and Applied Microbiology
Issue number6
Publication statusPublished - 2015 Sep 1


  • In situ DNA-HCR
  • Marine bacteria

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Applied Microbiology and Biotechnology


Dive into the research topics of 'Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH)'. Together they form a unique fingerprint.

Cite this