Enrichment and molecular characterization of chloropicrin- and metam-sodium-degrading microbial communities

Chloropicrin (CP) and metam sodium are commonly used as fumigants in agricultural soils in order to provide effective control of nematodes, soil-borne pathogens, and weeds in preparation for planting of high-value cash crops. Repeated application of these compounds to agricultural soils for many years may result in the enrichment of microorganisms capable of degrading them. In this study, a microcosm-enrichment approach was used to investigate bacterial populations that may be components of metam-sodium- and CP-degrading microorganisms in compost-amended soils. After 6 months incubation, with repeated application of metam sodium and CP, degradation was > or =70% faster in compost-manure-amended (CM) soil compared to < or =50% in the unamended soils. The accelerated fumigant degradation may have been due to the addition of compost or to the development of new microbial populations with enhanced degradation capacity. Denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified regions of 16S rRNA genes were used to identify dominant bacterial populations responsible for the accelerated fumigant degradation. The DGGE results indicated that specific bacterial types had been enriched and these were similar to strains isolated from basal minimal media. Fragments from DGGE bands and colonies were cloned, sequenced, and compared with published 16S rRNA sequences. Cloned sequences were dominated by Pseudomonas, Bacillus, Arthrobacter, Mycobacterium and uncultured bacterial species. The addition of organic amendment to soil during fumigation practices has the potential to increase the diversity of different microbial species, thereby accelerating fumigant degradation and reducing atmospheric emissions.