Analysis of DNA Sequences

Molecular biological methods are now commonly used to detect bacteria in diverse environments ranging from soils, sediments, and sludges (
1
,
2
) to plant (
3
) and mammalian (
4
,
5
) tissue and food or water samples (
6
,
7
). The techniques most widely used in detection methods are the polymerase chain reaction (
PCR
) and oligonucleotide probing. PCR exploits primers targeting a region of ribosomal RNA (rRNA) known to be specific to the organism of interest (
8
), or functional genes for metabolic pathways (
9
) and toxins (
10
) exclusive to certain bacteria, and facilitates qualitative or quantitative detection of target organisms in natural environments (
11
). Oligonucleotides can be labeled with radionucleotides or with chemiluminescent or fluorescent reporter molecules and used to probe nucleic acids extracted from samples (
4
), again giving qualitative or quantitative information regarding the occurrence of target organisms. In addition, fluorescently labeled olignucleotides are increasingly being used in combination with flow cytometry for cell counting or sorting (
12
,
13
), and with confocal laser scanning microscopy (
2
,
14
) to generate
in situ
data revealing close spatial associations of organisms in environmental samples.