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Profiling of Microbial Population
T-RFLP offers a reproducible way to rapidly describe
population structures based upon sequence length polymorphisms
in rapidly evolving regions of small subunit rRNAs (30). In a typical
experiment, one or both primers in a PCR amplification are derivatized
with a fluorescent ligand at the 5' terminus. Only the terminal
fragments are labeled in a restriction digest of the PCR products,
and these can be re-solved on a DNA sequencing gel. This method
has been used recently to characterize the microbial population
structure in sediments (4, 54). We will use T-RFLP mapping to refine
our understanding of the variability of micro-bial populations
at relatively high spatial resolution along gradients of varying
contaminant and site chemistry. Iden-tified changes in peak patterns
will indicate shifts in microbial populations. Initial T-RFLP studies
will use primers designed for general amplification of members
of the bacterial domain (4, 49). We will also conduct a more limited
survey using archaeal primers, but since this group is generally
much less abundant than the bacterial do-main, we will expand these
studies only if notable population trends are observed in relationship
to site chemistry.
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