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GM Crop Impact Assessment on Soil Ecosystems by DNA Barcode-based...

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Title GM Crop Impact Assessment on Soil Ecosystems by DNA Barcode-based Monitoring of Nematode Communities (ERGONema)
Period 02 / 2008 - 10 / 2013
Status Completed
Dissertation Yes
Research number OND1335835
Data Supplier NWO

Abstract

The closest interactions between a genetically modified (GM) crop and its environment take place in the rhizosphere and during the decomposition of crop residues. A potentially relevant hazard scenario is that GM crops affect these organisms, with consequences for soil fertility. This scenario will be investigated by the proposed research. In the rhizosphere, numerous bacteria, fungi and nematodes feed on GM plant roots and root exudates. During decomposition predominantly bacteria and fungi feed on GM plant material.

Nematodes constitute a diverse group within the soil fauna, feeding on bacteria, fungi, other nematodes and plant roots. This intimate feeding relationship with all major players in direct contact with plant roots and residues implies that GM crop effects in the rhizosphere and decomposer community will be reflected in the nematode community. Nematode abundance is high in virtually every soil. Unlike many soil organisms, nematodes can be easily extracted from soil and their ecological relevance can be assessed accurately. This makes them, both from a biological and practical view, an ideal monitoring device for non-target effects of GM crops. Recent advances in nematology, like the use of small subunit ribosomal DNA to detect families, genera and often even species, enable the use of nematodes with a much higher resolution than before. DNA barcodes are now being developed for individual nematode families, and quantitative PCR can be used to monitor changes in the nematode community at a large scale with unprecedented resolution.

This ERGO sub-programme aims to deliver a guidance for a validated Ecological Risk Assessment (ERA) method to evaluate potential risks of GM crops on soil biodiversity and fertility, using a quick, accurate and affordable nematode DNA-based tool.

A series of steps is needed to reach this goal:

- Establishment of the response window of a high impact, non-GM crop (i.e. positive control) on nematode communities, using newly developed DNA-barcodes. As positive control we selected Brassicaceae. Brassica species and varieties produce a wide spectrum of glucosinolate levels. Glucosinolates are precursors of natural biocides that are supposed to have a major impact on the rhizosphere and decomposer community. This natural variation in glucosinolate production will be exploited to define how changes in the rhizosphere and decomposer community are reflected in plant pathogenic and free living nematode communities. Ribosomal DNA-based barcodes in combination with quantitative PCR will be used to characterize nematode community alterations (Work Package 1). Initially, DNA barcode-based analyses will be verified in parallel by light microscopy-based community characterization.

- Establishment of the response window of a high impact, non-GM crop on soil fertility. Organic matter decomposition rate and nitrogen mineralization, keystone attributes of soil fertility, are directly related to bacterial, fungal and nematode activity. Glucosinolate products will have a major impact on this activity. Using the selected Brassicaceae varieties we will define to what extent natural biocides can affect soil fertility (Work Package 2).

- Determine the relationship between changes in nematode communities and soil fertility. Here, the relationship between nematode community responses and soil fertility, i.e. the relationship between structural and functional ecosystem characteristics, will be pinpointed for non-GM brassicas (Work Packages 1+2).

- Integration of the scientific findings of WP1 and WP2 into a draft guidance that is an appropriate extension of the existing set of ERA-procedures, and merging data from the barcode tool and the structure/function data with (test) baseline data on the natural variability collected for many non-GM crops from the National Soil Monitoring Network LMB (Landelijk Meetnet Bodemkwaliteit) (Work Package 3).

- Validate the newly developed procedure in GM crops under field conditions (Work Package 4). The crops for validation include GM Brassicaceae (Bt and over-producing volatile transformants from Arabidopsis ecotype Columbia; with Dicke et al. 2006), GM potato (selection of GM varieties of Karnico, Festien, Aveka and Seresta; modified starch profiles/pathogen resistance; with AVEBE), and Bt maize (Mon810).

Related organisations

Related people

Supervisor Prof.dr.ir. J. Bakker
Supervisor Dr.ir. J. Helder
Project leader Dr. R.G.M. de Goede
Doctoral/PhD student M.T.W. Vervoort (MSc)

Classification

A13000 Soil
D22500 Botany

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