ORIGINAL ARTICLE The effect of the native bacterial community structure on the predictability of E. coli O157:H7 survival in manure-amended soil L.S. van Overbeek 1 , E. Franz 2 , A.V. Semenov 3 , O.J. de Vos 4 and A.H.C. van Bruggen 5 1 Plant Research International BV, Wageningen University and Research Centre, Wageningen, the Netherlands 2 RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, the Netherlands 3 Department of Microbial Ecology, Centre of Ecological and Evolutionary Studies, Groningen University, Haren, the Netherlands 4 Biological Farming Systems Group, Wageningen University, Wageningen, the Netherlands 5 Department of Plant Pathology, Emerging Pathogens Institute, IFAS, University of Florida, Gainesville, FL, USA Introduction Fresh fruits and vegetables are now recognized to be important routes of entry for zoonotic human pathogens into the human food chain (Brandl 2006; Doyle and Erickson 2008; Franz and van Bruggen 2008b; Lynch et al. 2009). Escherichia coli O157:H7 and Salmonella enterica are among the zoonotic pathogens most frequently Keywords Escherichia coli O157, microbial community, predictive microbiology. Correspondence Eelco Franz, Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Diseases Control Netherlands, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, the Netherlands. E-mail: eelco.franz@rivm.nl 2009 ⁄ 2004: received 19 November 2009, revised 28 January 2010 and accepted 28 January 2010 doi:10.1111/j.1472-765X.2010.02817.x Abstract Aims: The survival capability of pathogens like Escherichia coli O157:H7 in manure-amended soil is considered to be an important factor for the likelihood of crop contamination. The aim of this study was to reveal the effects of the diversity and composition of soil bacterial community structure on the survival time (ttd) and stability (irregularity, defined as the intensity of irregular dynamic changes in a population over time) of an introduced E. coli O157:H7 gfp-strain were investigated for 36 different soils by means of bacterial PCR- DGGE fingerprints. Methods and Results: Bacterial PCR-DGGE fingerprints made with DNA extracts from the different soils using bacterial 16S-rRNA-gene-based primers were grouped by cluster analysis into two clusters consisting of six and 29 soils and one single soil at a cross-correlation level of 16% among samples per cluster. Average irregularity values for E. coli O157:H7 survival in the same soils differed significantly between clusters (P =0Æ05), whereas no significant differ- ence was found for the corresponding average ttd values (P =0Æ20). The irregu- larity was higher for cluster 1, which consisted primarily of soils that had received liquid manure and artificial fertilizer and had a significant higher bacterial diversity and evenness values (P <0Æ001). Conclusions: Bacterial PCR-DGGE fingerprints of 36 manure-amended soils revealed two clusters which differed significantly in the stability (irregularity) of E. coli O157 decline. The cluster with the higher irregularity was characterized by higher bacterial diversity and evenness. Significance and Impact of the Study: The consequence of a high temporal irregularity is a lower accuracy of predictions of population behaviour, which results in higher levels of uncertainty associated with the estimates of model parameters when modelling the behaviour of E. coli O157:H7 in the framework of risk assessments. Soil community structure parameters like species diversity and evenness can be indicative for the reliability of predictive models describ- ing the fate of pathogens in (agricultural) soil ecosystems. Letters in Applied Microbiology ISSN 0266-8254 ª 2010 The Authors Journal compilation ª 2010 The Society for Applied Microbiology, Letters in Applied Microbiology 50 (2010) 425–430 425