Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities.
An annual seasonal cycle of composition of a bacterioplankton community in an oligotrophic coastal system was studied by denaturing gradient gel electrophoresis (DGGE) using five different primer sets. Analysis of DGGE fingerprints showed that primer set 357fGC-907rM grouped samples according to seasons. Additionally, we used the set of 16S rRNA genes archived in the RDPII database to check the percentage of perfect matches of each primer for the most abundant bacterial groups inhabiting coastal plankton communities. Overall, primer set 357fGC-907rM was the most suitable for the routine use of PCR-DGGE analyses in this environment.
Sánchez
Olga
O
Departament de Genètica i Microbiologia, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain. olga.sanchez@uab.es
Gasol
Josep M
JM
Massana
Ramon
R
Mas
Jordi
J
Pedrós-Alió
Carlos
C
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D008386:Marine Biology; D010933:Plankton / Q000235:genetics / Q000302:isolation & purification*; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*
D017931:DNA Primers; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S