Mf. Polz et Cm. Cavanaugh, A SIMPLE METHOD FOR QUANTIFICATION OF UNCULTURED MICROORGANISMS IN THE ENVIRONMENT BASED ON IN-VITRO TRANSCRIPTION OF 16S RIBOSOMAL-RNA, Applied and environmental microbiology, 63(3), 1997, pp. 1028-1033
A simple method for the quantification of uncultured microorganisms in
the environment was developed. In vitro-transcribed 16S rRNA is used
as a template for midpoint dissociation temperature (T-d) determinatio
ns of specific oligonucleotide probes and as a standard in quantitativ
e probing. It replaces the need for total nucleic acids extracted from
pure cultures of the organisms to be quantified. A sense RNA of a siz
e almost identical to that of native 16S rRNA can be transcribed from
ribosomal DNA clones recovered in studies of the phylogenetic diversit
y of microbial communities. This in vitro-transcribed rRNA yields diss
ociation curves typical of oligonucleotides. They parallel cut-yes det
ermined with total nucleic acids but yield slightly higher T-d values.
Neither unspecific sticking of the probe nor probe washing off the DN
A template at low temperatures fully accounted for the discrepancy in
probe release from the two templates. This suggests that the native rR
NA itself has melting characteristics different from those of its in v
itro-transcribed counterpart. However, this difference does not affect
the performance of in vitro-transcribed rRNA compared with total nucl
eic acids as a standard in quantitative hybridizations. No difference
was found between the estimates of the relative quantity of a single b
acterial species in a mixed community obtained with the two standards,
regardless of whether DNA was removed from the samples. This protocol
will allow the large-scale quantification of the ecological importanc
e of uncultured microorganisms in natural environments for the first t
ime.