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Date of creation
2009-11-26 10:11 UTC (fred.wassenaar@rivm.nl)
Date of last update
2012-05-08 19:09 UTC (dina.abdelhakim@cbd.int)
Date of publication
2012-05-08 19:09 UTC (dina.abdelhakim@cbd.int)

General Information
Methods to study potential effects of genetically modified plants on soil microbial diversity and soil functioning
F.G.H. Boersma, J.D van Elsas, University of Groningen, the Netherlands
  • English
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Summary, abstract or table of contents
Concluding remarks
This report describes the variety of techniques that are available for determining the changes in the soil microbial community that may come about by the presence of GM plants.  A few commonly used traditional and a range of advanced techniques are listed and their merits discussed. Over the years, the advanced techniques have gained considerable resolving power,  specificity and sensitivity. Also, as-a-whole, most of the techniques have increasingly enhanced throughput, which is mainly attributed to the greatly enhanced DNA sequencing capabilities.
However, although progress has been made, any conclusions on the link between the data obtained with any method and soil health and functioning are still hard to make. This is mainly due to our lack of understanding as to whether such a link exists and how is is shaped. Furthermore, the biases which are inevitable present when it comes to soil DNA isolation, PCR and/or cloning play a role. The lack of conclusive power is also attributable to our lack of knowledge about soil resistance and resilience, i.e. on how a soil responds to stress.
Therefore measurements of diversity and (more importantly) community structure should be combined with measurements of already established parameters which are indicative of soil functioning, starting with soils where we know that they do differ in functioning. First we have to decide which aspects of soil functioning we are aiming for: carbon and nutrient cycling, nutrient supply to the crops, maintenance of soil structure, disease suppression, or as many aspects as possible. Nutrient cycling and supply is reflected in total microbial biomass and activity, in potential carbon and nitrogen mineralization, but also in amounts of mycorrhizal fungi and nitrogen-fixing bacteria. Soil structure is correlated with amounts of fungal hyphae and microbial exudates (polysaccharides, labile carbon). Disease suppression is related to total microbial biomass and activity and the presence of specific antagonists.  If changes in these indicators coincide with changes in community composition, then relationships between community structure and soil ecosystem functions (or services) can be resolved.
Despite the methodological progress, no single method or combination of different techniques can be stated as superior and standardize the analyses. Combination of novel techniques such as pyrosequencing, which gives enormous amounts of information on both functional as phylogenetic diversity, and phylogenetic microarrays, which give information on the presence and diversity of essential microorganisms, is preferable. This then can be combined with biomass and activity measurement using for instance SIR. However, various other combinations can be as informative as the proposed combination.
To be able to compare results and eventually understand the effect of changes on soil health and functioning, a baseline to compare any results to is necessary.  One of the possible solutions for this issue involves the establishment of a normal operating range (NOR) of a certain soil. This NOR will describe the minimum community structure, diversity and function, that a given soil has to meet to be considered healthy. To this baseline, future results of GMP research can be compared. However, considering the large number of different soils and the enormous diversity of microorganisms, it remains unknown if NOR will be a usable concept.
Thematic areas
  • Scientific and technical issues
    • Risk assessment
Background material to the “Guidance on risk assessment of living modified organisms”
Is this document is recommend as background material for the “Guidance on Risk Assessment of Living Modified Organisms”
Section(s) of the “Guidance on Risk Assessment of Living Modified Organisms” this background material is relevant
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Type of resource
  • Report / Review / Fact sheet / Notes
Copyright holder: University of Groningen; may be used freely for educational or non-profit purposes.
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