Data mining - case studies

Transcription

1 Data mining - case studies 1 90 th Annual Meeting (ESA), Montréal, Canada August 7-12, 2005 Effects of genetically modified Bt maize on earthworms and Collembola functional groups Marko Debeljak 1, Damjan Demšar 1, Jérôme Cortet 2, Sašo Džeroski 1, Paul Henning Krogh 3 1: Jožef Stefan Institute, Ljubljana, Slovenia. 2: Institut Mediterraneen d'ecologie et Paleoecologie, Aix-en-Provence, France. 3: National Environmental Research Institute, Silkeborg, Denmark. Marko Debeljak Workshop on Data Mining and Decision Support, Ljubljana, January Introduction GM crops are engineered either to be resistant to insect pests or to be tolerant to herbicides. They are grown not to achieve higher yields but to reduce producers' inputs and operating costs. GM crops were not primarily developed with environmental benefit in mind. 3 1

2 Introduction Environmental concerns about ecological impacts of GM crops are mostly turned toward unwanted ecological changes because of invasion of GM crops into wild habitats (communities) by: - horizontal recruitment to soil or water biota (toxification) - gene flow to wild relatives of GM crop (hybridization) 4 Introduction Exposure of soil organisms to GM plants can result from: - crop residues -the roots themselves both during and after the growth season. Because soil biota play a vital role in key soil processes (nutrient cycling and the physical and biochemical degradation of organic matter) the evaluation of potential impacts of GM crops on soil ecosystem is essential. 5 European international project: ECOGEN ECOGEN: Soil ecological and economic evaluation of genetically modified crops ( ) ( First two major objectivess: Ecological and economical assessment and comparison of integrated farming systems using genetically modified higher plants with a conventional farming system. Provide an ecological risk assessment of a GM cropping system and a conventional cropping system for the soil ecosystem. 6 2

3 Bt-maize was created to control European corn borer (Ostrinia nubilalis Hubner) and other closely related pest moths. 7 Bt - the soil bacterium, Bacillus thuringiensis which produces a variety of crystal proteins (Cry proteins) with insecticidal activity against a large group of insects belonging to orders of Lepidoptera, Coleoptera and Diptera. Many strains of Bt exists, each producing one or more toxic crystalline (Cry) proteins. Each Bt toxin needs specific combination of - Ph level, - enzymes, and - gut receptors required to solubilise, activate and bind the toxin. Organism must be exposed to Bt toxins through feeding. 8 General statement: Bt corn presents little danger to non-target herbivores. The impact of Bt maize on non target soil organisms: springtails (Order Collembola) and earthworms (Class Oligochaeta) 9 3

4 Study area: Clay Silt Sand Organic matter Ca 2+ ph (H 2 O) (%) (%) (%) (%) (meq/100g) (-log 10 H + ) Design of experiment: Random four-block design with four repetitions Two maize cultivars were planted in 2002 and 2003: - MEB307 (Bt variety producing the Cry1Ab toxin) - Monumental (non Bt trait) 11 Case study: sampling plan 6 intact soil cores (5 cm depth, 6 cm diameter; in the middle of the plot within the rows between plants) were collected on each plot from each of 4 repeated blocks. Sampling date Sampling size Collembolans July 1, (9/plot) October 3, (9/plot) June 1, (6/plot) November 2, (6/plot) Total: 480 Earthworms October 21, (6/plot) March 16, (6/plot) November 4, (6/plot) June 7, (6/plot) October 18, (6/plot) Total:

5 Case study: Data Set of attributes: Type of the crop: - MEB307 (Bt variety producing the Cry1Ab toxin) - Monumental (non Bt trait) Soil properties: - soil texture (clay, silt, sand, organic): [%] -ph (H 2 0): [-log 10 H + ] - cation-exchange capacities (Ca 2+, K +, Mg 2+ ): [meq./100 g soil ] 13 Case study: Data Set of attributes: Farming practices: - seed treatment: [no, Gaucho] - tillage: [yes, no] Temporal aspects of farming practices at sampling dates: - time since tillage: [# days] - time since sowing: [# days] - time since harvest: [# days] 14 Case study: Data Set of attributes: Biological structure of soil communities: - Collembolans (species - functional groups: epi, hemi-epi, hemi, euhemi, eu): [# individuals/1kg dry soil] - Earthworms (species - functional groups: epigeic, endogeic, anecic): [fresh weight in mg / m -2 soil ] 15 5

6 Functional groups - Collembolans: epiedaphic: Lives on the soil and in habitats on top of the soil. hemiedaphic: Lives in the litter layer or in the upper few cm of the soil. Intermediate between eudaphic and epiedaphic. euedaphic: Lives in the soil - true soil living animals. Isotomurus palustris Sminthurinus aureus Pseudosinella sp. hemi-epiedaphic eu-hemiedaphic 16 Functional groups - earthworms: epigeic: live and feed on plant litter endogeic: live in the soil and are geophagus anecic : have a mixed regime, i.e. they live in the soil and feed on the soil organic matter and plant litter which they collect at the soil surface 17 Modelling - farming practices, - soil parameters, - the biological structure of soil communities, and - the type and age of the crop at the sampling dates, to predict -the abundance of springtails in functional groups/total, -thebiomass of earthworms in functional groups/total. 18 6

7 Modelling tools: Predictive models - data mining - machine learning techniques: classification trees: They predict the value of a discrete dependent variable with a finite set of values from the values of a set of independent variables which may be either continuous or discrete. regression trees: They predict the value of a continuous dependent variable from the values of a set of independent variables which may be either continuous or discrete. 19 Modelling tools: Data mining analysis was performed by the Weka machine learning package: classification trees: J4.8 algorithm regression trees: M5 algorithm Models: 540 models were made all together. The models were evaluated by qualitative and quantitative measures of performance. 20 models were selected for further evaluation. 20 Results: Soil community Classification Regression tree-model tree-model Functional group Correlation Correlation coeff. coeff. Epigeic Earthworms Endogeic Earthworms Anecic Earthworms Total Earthworms Epiedaphic Coll Hemi-epiedaphic Coll Hemiedaphic Coll Eu-hemiedaphic Coll Euedaphic Coll Total Collembolas

8 Results: Anecic Earthworms regression tree-model (r 2 =0.77) 22 Results: Anecic Earthworms model tree-model (r 2 =0.83) 23 Results: Total Earthworms regression tree-model (r 2 =0.73) 24 8

9 Results: Total Earthworms model tree-model (r 2 =0.77) 25 Results: earthworms - summary The total earthworms (r 2 =0.77) as well as anecic earthworms (r 2 =0.83) showed preferences for less clay and more silt soil with medium ph, while they were not influenced directly by farming practices. The biomass of earthworms was greater in early autumn as compared to spring or late autumn. 26 Results: Hemi-epiedaphic Collembolans regression tree-model (r 2 =0.55) 27 9

10 Results: Hemi-epiedaphic Collembolans model trees (r 2 =0.77) 28 Results: Hemi-epiedaphic Collembolans - summary Hemi-epiedaphic Collembolans (r 2 =0.83) were increased at the end of the maize growing season, while higher organic matter content and higher ph tended to increase their biomass also in spring. A greater abundance of Collembolans was also noted in early autumn if the crop was non-bt maize. 29 Conclusions: The abundance of Hemi-epiedaphic Collembolans population is influenced by Bt maize! The impact of Bt maze on earthworms was not detected! Btmaizemay have impact on the population dynamics of soil microartropods! Further research activities are required! 30 10