Soil indicators for plant health

‘Soil health’ describes the microbial status of soils in relation to their potential to suppress (soil-borne) phytopathogens. Soil-borne phytopathogens can be responsible for major crop losses and are often difficult to control by chemical pesticides.

Further, the presence of these pathogens in soils will lead to higher usage of pesticides, resulting in accumulation of pesticide residues in soil, soil water and surface water and in the human food chain.  Antagonizing soil micro-organisms can be important for controlling soil-borne pathogens. Agricultural measures, e.g. via organic amendments may stimulate these populations resulting in an increased suppression of phytopathogens.

It is our intention to develop a culture-independent tool for the detection of antagonistic populations in soil to follow their fate and dynamic upon application of different agricultural measures. Using this tool we expect to be able to predict the soil health status in relation with disease suppression. Development of a prototype of the soil health tool (soil health chip) is based on functional genes (antibiotic production genes) present in antagonists that are well described for their roles on disease suppression within existing literature and research networks. The functionality of the soil health chip will be evaluated by making use of DNA samples from pure antagonistic strains, mixtures of strains, mixtures of strains in soil DNA extracts and DNA extracts from soils derived from disease suppressive fields. Based on data obtained from measurements on DNA extracts from farmer fields (practical evaluation) we will evaluate possibilities for recommendation to farmers on crop use under specified soil conditions.

Plant parasitic nematodes cause considerable damage to crops. Knowledge about the presence of nematodes in a field allows the grower to take control measures. There is a need for a fast, reliable test allowing the quantitative, simultaneous detection of multiple nematode species in a sample. Existing multiplex detection tests are not suitable for the quantitative detection of so many different species.


Development of a soil health chip propotype that can be used for reporting the status of the soil to suppress important (soil-borne) phytopathogens
Evaluation of advises to farmers on crop use based on the ‘health status’ of applied soils using data obtained from the soil health chip prototype
The Biotrove Open Array system enables quantitative detection of multiple species in a single experiment using low reaction volumes (saving costs for expensive ingredients) and with limited pipetting steps (saving labour costs). It requires the availability of suitable real-time PCRs. Experiments performed in 2007 and 2008 have shown that TaqMan PCRs and SyberGreen PCRs can be for the detection of nematodes when performed on the Biotrove system

In this project we will investigate which of the real-time PCRs are most suitable with respect to sensitivity and quantification.


Intended results are:

  • Prototype soil health chip
  • Knowledge on the effects of agricultural (soil) measures on the fate and dynamics of microbial populations antagonizing soil-borne phytopathogens
  • Advises to farmers on crop usage with minimal damage by phytopathogens, based on data obtained from measurements using the ‘ soil health chip’.
  • Information regarding suitability of real-time PCRs for detection of nematodes extracted from soil samples, with respect to sensitivity, level of quantification and reproducibility
  • Information about the number of samples that can be analyzed at the same time using one Biotrove array when detecting 2, 3, 4 to 8 differrent nematode species in a quantitative manner.

Intended product is a fast and reliable test for quantitative multiplex detection of different organisms in soil samples.