molecular detection of bacteria

[Nicholas Landau]

If detection is what you want, then just amplify all of the
16S genes in the sample using bacteria-specific primers.  This
is a commonly used method.  If quantitation is what you want,
you cannot beat the direct count for ease and simplicity.  You
will probably want to use density-gradient centrifugation to
separate the bacteria from the larger eukaryotic cells, and
then take a look under phase.  You could also buy a bacteria
specific 16S probe for use in _in situ_ hydridization -- that
would save you the trouble of sorting the plant cells from the
bacteria.