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The recent increase in foodborne disease associated with the consumption of fresh vegetables stresses the importance of the development of intervention strategies that minimize the risk of preharvest contamination. To identify risk factors for Escherichia coli O157:H7 persistence in soil, we studied the survival of a Shiga-toxin-deficient mutant in a set of 36 Dutch arable manure-amended soils (organic/conventional, sand/loam) and measured an array of biotic and abiotic manure-amended soil characteristics. The Weibull model, which is the cumulative form of the underlying distribution of individual inactivation kinetics, proved to be a suitable model for describing the decline of E. coli O157:H7. The survival curves generally showed a concave curvature, indicating changes in biological stress over time. The calculated time to reach the detection limit ttd ranged from 54 to 105 days, and the variability followed a logistic distribution. Due to large variation among soils of each management type, no differences were observed between organic and conventional soils. Although the initial decline was faster in sandy soils, no significant differences were observed in ttd between both sandy and loamy soils. With sandy, loamy and conventional soils, the variation in ttd was best explained by the level of dissolved organic carbon per unit biomass carbon DOC/biomC, with prolonged survival at increasing DOC/biomC. With organic soils, the variation in ttd was best explained by the level of dissolved organic nitrogen (positive relation) and the microbial species diversity as determined by denaturing gradient gel electrophoresis (negative relation). Survival increased with a field history of low-quality manure (artificial fertilizer and slurry) compared with high-quality manure application (farmyard manure and compost). We conclude that E. coli O157:H7 populations decline faster under more oligotrophic soil conditions, which can be achieved by the use of organic fertilizer with a relatively high C/N ratio and consequently a relatively low rate of nutrient release.

Rare species are assumed to have little impact on community interactions and ecosystem processes. However, very few studies have actually attempted to quantify the role of rare species in ecosystems. Here we compare effects of soil community assemblages on plant-herbivore interactions and show that reduction of rare soil microbes increases both plant biomass and plant nutritional quality. Two crop plant species growing in soil where rare microbes were reduced, had tissues of higher nutritional quality, which theoretically makes them more susceptible to pest organisms such as shoot-feeding aphids and root-feeding nematodes. Reduction of rare microbes increased aphid body size in the absence of nematodes; nematodes always reduced aphid body size independent of the soil microbial community. This study is the first to show that rare soil microbes are not redundant but may play a role in crop protection by enhancing aboveground and belowground plant defence. It remains to be tested whether these are direct effects of rare soil microbes on plants and herbivores, or indirect effects via shifts in the microbial soil community assemblages.

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The effects of four average temperatures (7, 16, 23 and 33 degrees C) and daily oscillations with three amplitudes (0, +/-4, +/-7 degrees C) on the survival of the enteropathogens Escherichia coli O157:H7 and Salmonella serovar Typhimurium were investigated in small microcosms. Manure was inoculated with a green fluorescent protein transformed strain of either pathogen at 10(7) cells g(-1) dry weight. Samples were collected immediately after inoculation, and 1 and 2 weeks after inoculation for E. coli O157:H7, and immediately and after 2 and 3 weeks for Salmonella serovar Typhimurium. Population densities were determined by dilution plating and direct counting. In addition, total bacterial CFUs were determined. Growth and survival data were fitted to a modified logistic model. Analysis of the estimated parameter values showed that E. coli O157:H7 survived for shorter periods of time and was more sensitive to competition by the native microbial community than Salmonella serovar Typhimurium. Survival of both pathogens significantly declined with increasing mean temperatures and with increasing amplitude in daily temperature oscillations. The results indicated that responses of enteropathogens to fluctuating temperatures cannot be deduced from temperature relationships determined under constant temperatures.

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The objective of this study is to describe survival of Escherichia coli O157:H7 populations in manure-amended soils in terms of population stability, i.e. the temporal variation around the decline curve, in relation to soil characteristics indicative of soil health. Cow manure inoculated with E. coli O157:H7 was mixed with 18 pairs of organically and conventionally managed soils (10% of manure, kg kg(-1)). For four of the soil pairs, also three different manure densities (5%, 10% and 20%) were compared. All soil-manure mixtures were incubated for 2 months, and population densities of E. coli O157:H7 were quantified weekly. De-trending of survival data was done by modified logistic regression. The residual values were used to assess variation in the changes of E. coli O157:H7 populations by performing the approximate entropy (ApEn) procedure. The term irregularity is used to describe this variation in ApEn literature. On average, the decline of E. coli O157:H7 was more irregular in conventional and loamy soils than in organic and sandy soils (P < 0.05). Multiple regression analysis of irregularity of E. coli O157:H7 survival on 13 soil characteristics showed a positive relation with the ratio of copiotrophic/oligotrophic bacteria, suggesting greater instability at higher available substrate concentrations. Incremental rates of manure application significantly changed the irregularity for conventional soils only. Estimation of temporal variation of enteropathogen populations by the ApEn procedure can increase the accuracy of predicted survival time and may form an important indication for soil health.