Fluorescence in situ hybridization (FISH) has become a standard technique
in the visual detection and phylogenetic identification of environmental
microorganisms in marine microbiology. Thirty years have passed since the appearance
of FISH, and now FISH can detect not only ribosomal RNA but also mRNA and
functional genes with high sensitivity. This chapter describes the principles, drawbacks,
and applications of FISH and highly sensitive FISH. In particular, we introduce two
high-sensitivity FISH methods developed by the authors. The first is in situ DNA
hybridization chain reaction (HCR), a highly sensitive and highly penetrating detection
technique for ribosomal-RNA–targeting FISH, and the second is two-pass tyramide
signal amplification (TSA)-FISH that can detect single-copy genes. Finally, we discuss
how the FISH technique has contributed to the field of marine microbiology.
Keywords: CARD-FISH, Environmental microbiology, FISH, Functional genes,
GeneFISH, HCR-FISH, Highly sensitive FISH, in situ DNA-HCR, ISH, Marine
bacteria, Microscopic observation, Oligonucleotide probe, Phylogenetic
identification, Polynucleotide probe, Probe permeabilization, Single cell imaging,
Two-pass TSA-FISH, Visual detection.
