The isolation and identification of bacteria associated
with higher aquatic plants is a more laborious procedure
than cultivating microorganisms from water.
The main difficulty in using the molecular approach is
the necessity of correctly carrying out the stage of isolation
of total DNA from samples of the microbial community
washed from macrophytes: DNA may adsorb
on the suspension precipitated on plants and may be
isolated along with the DNA of other organisms. In
addition, microorganisms are, as a rule, present in
dense agglomerations. The quantity and quality of isolated
bacterial DNA may be strongly affected by the
large concentration and qualitative composition of
plant organic matter in the environment [19]. The factors
noted above may negatively influence the cleaning
quality of the total DNA isolated from periphyton.
However, obtaining the total bacterial DNA and further
amplification are some of the key stages of molecular–
biological investigations.