Premium
Comparative evaluation of prokaryotic 16S rDNA clone libraries and SSCP in groundwater samples
Author(s) -
Larentis Michael,
Alfreider Albin
Publication year - 2011
Publication title -
journal of basic microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.58
H-Index - 54
eISSN - 1521-4028
pISSN - 0233-111X
DOI - 10.1002/jobm.201000295
Subject(s) - phylotype , single strand conformation polymorphism , clone (java method) , biology , 16s ribosomal rna , library , phylogenetic tree , genetics , bacteria , gene , polymerase chain reaction
A comparison of ribosomal RNA sequence analysis methods based on clone libraries and single‐strand conformational polymorphism technique (SSCP) was performed with groundwater samples obtained between 523–555 meters below surface. The coverage of analyzed clones by phylotype–richness estimates was between 88–100%, confirming that the clone libraries were adequately examined. Analysis of individual bands retrieved from SSCP gels identified 1–6 different taxonomic units per band, suggesting that a single SSCP band does often represent more than one single prokaryotic species. The prokaryotic diversity obtained by both methods showed an overall difference of 42–80%. In comparison to SSCP, clone libraries underestimated the phylogenetic diversity and only 36–66% of the phylotypes observed with SSCP were also detected with the clone libraries. An exception was a sample where the SSCP analysis of Archaea identified only half of the phylotypes retrieved by the clone library. Overall, this study suggests that the clone library and the SSCP approach do not provide an identical picture of the prokaryotic diversity in groundwater samples. The results clearly show that the SSCP method, although this approach is prone to generate methodological artifacts, was able to detect significantly more phylotypes than microbial community analysis based on clone libraries. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)