TY  - JOUR
A1  - Epp, Laura Saskia
A1  - Stoof-Leichsenring, Kathleen Rosemarie
A1  - Trauth, Martin H.
A1  - Tiedemann, Ralph
T1  - Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)
T2  - Molecular ecology resources
N2  - Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approximately 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based denaturing high-performance liquid chromatography (DHPLC). An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length and if the amplicons differed only in a small number of nucleotides. Generally, the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
KW  - diatoms
KW  - environmental DNA
KW  - lake sediments
KW  - PCR-DHPLC
Y1  - 2011
UR  - https://publishup.uni-potsdam.de/frontdoor/index/index/docId/36663
SN  - 1755-098X
VL  - 11
IS  - 5
SP  - 842
EP  - 853
PB  - Wiley-Blackwell
CY  - Hoboken
ER  -