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Improving target-taxa recovery in domain-specific environmental
clone libraries
Hans-Werner Breiner, Thorsten Stoeck
TU Kaiserslautern, Biologie/Ökologie
The sequence analysis of environmental SSU rDNA clone libraries is
the gold standard to evaluate microbial diversity in a specific habitat.
However, besides microbial target taxa such clone libraries often
times include large numbers of non-target taxa. For example, when
analyzing microbial eukaryotes, large proportions of the clone library
often times include molecular signatures of metazoa or higher plants.
Considering the limits (time and supplies) of most laboratories the
number of randomly chosen clones for sequence analysis is restricted.
Thus, it is a major aim to have a high number of target-clones while
keeping the number of non-targets as small as possible. In order to
increase the efficiency of target-taxa recovery we developed a technique
that identifies non-target taxa prior to choosing clones for
sequencing. This method is based on 33 P-labeled oligonucleotide
hybridization to membrane-bound vector-transformed bacterial colonies.
We applied this technique to planktonic samples from the hypersaline
and anoxic L’Atalante deep-sea basin in the eastern Mediterranean,
which included a high number of crustacean clones (>50% of
all clones). Our approach makes the screening of taxon-specific gene
signatures in environmental clone libraries no longer a question of
luck and coincidence.
breiner@rhrk.uni-kl.de
stoeck@rhrk.uni-kl.de
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