Molecular sequencing and morphological analysis of a nematode community

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

“…Several authors have revealed the usefulness of molecular techniques for characterizing a nematode community structure or quantifying specific nematode species among a variety of soil nematodes (Griffiths et al, 2006;Sato et al, 2007;Toyota et al, 2008;Donn et al, 2008;Okada and Oba, 2008), but firstly nematodes have to be extracted from soil for these experiments. It is reported that the dynamics of plant-parasitic nematodes, such as M. incognita (McSorley et al, 2008;Zasada and Tenuta, 2008) and P. crenatus Loof (Briar et al, 2007), play an important role in estimating their damage in the soil environment, in which the extraction of nematodes is also a prerequisite for the morphological identification of plant-parasitic nematodes.…”

Quantitative detection of nematodes by using PCR-DGGE for evaluation of community similarities

“…We are the first to show a clear correlation between the band intensity and abundance or biomass of each nematode species, which leads to a high correlation within similarity relationships among communities between DGGE band patterns and nematode abundance or biomass. Another reason for a high correlation in similarity relationships might be that we did not study large-sized nematodes, such as species of Mononchida and Dorylaimida, which might cause an underestimation of the abundance of small to medium-sized nematodes (Griffiths et al, 2006): although, we did use a small sized Dorylaimid species, Tylencholaimus parvus Ahmad & Araki. PCR-DGGE may also perform well when the nematode communities examined do not comprise numerous species, which would result in reduced band overlap.…”

“…An essential process in such trials is the performance evaluation of the tools. One of the approaches is to compare the community profiles obtained with those profiles revealed by morphological analyses based on individual identification (Griffiths et al, 2006;Okada and Oba, 2008;Wu et al, 2009). Previously, we tried to evaluate the use of PCR-DGGE for nematode community analysis, by comparing the resulting band patterns of DNA fragments with the results of morphological analyses of the nematode samples isolated from the field.…”

Rapid decline of PCR amplification from genomic extracts of DESS-preserved, slide-mounted nematodes

“…Results clearly indicate a steady degradation of genomic DNA in nematodes stored in slide mounts for more than 2 weeks, whereas unmounted specimens extracted from preservative solution showed no decline in PCR success or quality. We suggest a maximum storage period of 2 weeks on slides if mounted nematodes are to be used for molecular analyses.Keywords -DESS, DNA, glycerin, integrated methods, molecular, morphology.The use of molecular data in nematode studies is now ubiquitous, yet it is still routine for researchers to corroborate DNA sequences with morphology in order to assess the biological relevance of molecular patterns (Griffiths et al, 2006;Stock & Nadler, 2006;Bhadury et al, 2008). DNA barcoding studies promote visual identification of specimens as well as the retention of 'morphological voucher images' to record taxonomic features before nematodes are destroyed for DNA extraction (De Ley et al, 2005;Bhadury et al, 2006a).…”

“…The use of molecular data in nematode studies is now ubiquitous, yet it is still routine for researchers to corroborate DNA sequences with morphology in order to assess the biological relevance of molecular patterns (Griffiths et al, 2006;Stock & Nadler, 2006;Bhadury et al, 2008). DNA barcoding studies promote visual identification of specimens as well as the retention of 'morphological voucher images' to record taxonomic features before nematodes are destroyed for DNA extraction (De Ley et al, 2005;Bhadury et al, 2006a).…”