Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA

A novel detection method for the soybean cyst nematode Heterodera glycines Ichinohe using soil compaction and real-time PCR

“…These procedures are laborious and time-consuming and this can cause variation in the measurement among analysts. Waite et al (2003) reported a nematode community analysis using DNA directly extracted from 1 g soil. However, it is known that the comparatively low abundance of soil nematodes and their patchy spatial distribution requires extraction from larger soil volumes to achieve a representative sample (Donn et al, 2008).…”

A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil

“…Separation is based on the melting behavior of fragments with different sequence composition under increasing gradients of denaturants or temperature. Since its introduction for the analysis of bacterial community structure (Muyzer et al, 1993), this method has been widely used in the characterization of soil bacterial (Kozdroj and Van Elsas, 2000) and fungal (Pennanen et al, 2001;Kowalchuk et al, 2006) as well as micro-fauna communities (Waite et al, 2003;Foucher et al, 2004) from various environments. Kowalchuk et al (2002) was the first to apply DGGE to assess AMF diversity in sand dune soil and root samples.…”

Extracting DNA of nematodes communities from Argentine Pampas agricultural soils

“…1 and 2). The NEMF1 primer, targets the variable V3 and V5 regions of the 18S rDNA and is widely used in molecular-biodiversity studies of nematodes; S3 is a "universal" primer for eukaryotes that targets with highly a conserved region of the 18S rDNA (Waite et al 2003). The NS1 and NS4 hybridized with highly-conserved regions of the eukaryote 18S rDNA molecule (White et al 1990).…”