Effects of Fumigants on Soil Microbial Community affected by Irrigation Water Contaminated with E. coli O157:H7.

Fumigants such as Methyl bromide (MeBr; CH₃Br) used for soil fumigation was phased

out in 2005 due to its ozone depleting properties. However, critical use exemptions have

been granted for the production of  high value cash crops such as strawberries, tomatoes,

and peppers.Methyl iodide (MeI, iodomethane; CH₃I), a fumigant currently in registration

review, is considered a promising alternative to MeBr because its fate, transport

characteristics, and effectiveness as a biocide are similar to those of MeBr without the

ozone depleting property. Our goal was to assess the effect of soil fumigation with MeBr

and MeI on the microbial community structure and diversity in two soils and determine the

 effects of microbial diversity on the survival of Escherichia coli O157:H7 from

contaminated irrigation water. PCR was used to amplify 16S rRNA from total bacterial

community composition and the products were subjected to denaturing gradient gel

electrophoresis (DGGE). The Shannon-Weaver index of diversity (H′) was used to

determine the effects of both fumigants on soil microbial community structure. The effect

was more severe in sandy soil than in clay soil, and for the normal application rate and 5

times the normal application rate of MeBr and MeI. Changes in community structures were

 observed 7 weeks after fumigation in the growth chamber and 5 weeks in the laboratory

microcosm. Our results showed that MeBr and MeI have about the same effects on soil

microbial diversity. The two fumigants had greater impact on microbial composition in

sandy soil than in clay soil and this resulted in higher survival of E. coli O157:H7 in sandy

soil than clay soil. This was consistent with our hypothesis that soil systems with reduced

microbial diversity offer greater opportunities for the survival of pathogenic bacteria such as E. coli O157:H7.