Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis

Markus M. Moeseneder*, Jesús M. Arrieta, Gerard Muyzer, Christian Winter, Gerhard J. Herndl

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

292 Scopus citations

Abstract

The potential of terminal-restriction fragment length polymorphism (T- RFLP) and the detection of operational taxonomic units (OTUs) by capillary electrophoresis (CE) to characterize marine bacterioplankton communities was compared with that of denaturing gradient gel electrophoresis (DGGE). A protocol has been developed to optimize the separation and detection of OTUs between 20 and 1,632 bp by using CE and laser-induced fluorescence detection. Additionally, we compared T-RFLP fingerprinting to DGGE optimized for detection of less abundant OTUs. Similar results were obtained with both fingerprinting techniques, although the T-RFLP approach and CE detection of OTUs was more sensitive, as indicated by the higher number of OTUs detected. We tested the T-RFLP fingerprinting technique on complex marine bacterial communities by using the 16S rRNA gene and 16S rRNA as templates for PCR. Samples from the Northern and Middle Adriatic Sea and from the South and North Aegean Sea were compared. Distinct clusters were identifiable for different sampling sites. Thus, this technique is useful for rapid evaluation of the biogeographical distribution and relationships of bacterioplankton communities.

Original languageEnglish (US)
Pages (from-to)3518-3525
Number of pages8
JournalApplied and Environmental Microbiology
Volume65
Issue number8
StatePublished - Aug 1999
Externally publishedYes

ASJC Scopus subject areas

  • Environmental Science(all)
  • Biotechnology
  • Microbiology

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