Ribosomal RNA (rRNA) intergenic spacer analysis (RISA) is a method of microbial community analysis that provides a means of comparing differing environments or treatment impacts without the bias imposed by culture- dependent approaches.
[2] By using oligonucleotide primers targeted to conserved regions in the 16S and 23S genes, RISA fragments can be generated from most of the dominant bacteria in an environmental sample.
While the majority of the rRNA operon serves a structural function, portions of the 16S-23S intergenic region can encode tRNAs depending on the bacterial species.
However the taxonomic value of the ISR lies in the significant heterogeneity in both length and nucleotide sequence.
[3] The resulting PCR product will be a mixture of fragments contributed by several dominant community members.