Once in a while one comes across applications of DNA Barcoding you would never thought of in the first place although they perfectly make sense. It is nice to see that so many creative researchers are picking up the method and using it for questions they are interested in.
This post looks at the potential of DNA Barcoding for ecological risk assessment of genetically-modified crops. Dutch researchers from the National Institute for Public Health and the Environment were interested in crop induced changes in nematode assemblages in agricultural soils. Nematodes constitute a very diverse group within the soil fauna, feeding on microbes, invertebrates (including other nematodes) and plant roots. Such an intimate feeding relationship with all major players in agro-ecosystems implies that any effect genetically modified crop might have will likely be reflected in the nematode community. Better knowledge of nematode assemblage compositions could be used to extrapolate impacts on soil systems.
|Nematodes in a sample|
The classical methods to characterize nematode communities is based on morphological identification using light microscopy. However, this method is both very time consuming (on average several hours for 150 individuals per sample) and the resolution depends on the level of taxonomic expertise. For me they are all white to translucent small inconspicuous worms.
The overall goal of the study was to implement DNA Barcoding into a long-term monitoring network for soil impact of pest management products and the use of genetically-modified crops. Three parts are supposed to serve as baseline for future application. A first part represents the control and looks at seasonal fluctuations of nematode communities as a measure for natural variability over time. The second part focuses on the effects of current pest management (bio-fumigation using Brassica juncea) on nematodes, while the last part investigates the effects of genetically-modified crops (pathogen-resistant potatoes and amylase-potatoes) on soil nematode community structure.
The DNA-based approach to identification allowed for the analysis of nematode communities without microscopic pre-selection because it was based on a considerably broad (2,400 taxa) genetic database that covers the majority of terrestrial and freshwater nematode taxa. For the Dutch researchers one of the main advantages of using molecular methods is the time saving aspect as it allows for more intense and frequent sampling schedules.