ENRICHMENT AND MOLECULAR CHARACTERIZATION OF CHLOROPICRIN- AND METAM-SODIUM-DEGRADING MICROBIAL COMMUNITIES

Authors: Ibekwe, Abasiofiok - Mark; Schneider, Sharon; YANG, CHING-HONG - U WISC,BIOL SCI,MILWAUKEE

Submitted to: Applied Microbiology and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/21/2004
Publication Date: 8/7/2004
Citation: Ibekwe, A.M., Papiernik, S.K., Yang, C. 2004. Enrichment and molecular characterization of chloropicrin- and metam-sodium-degrading microbial communities. Applied Microbiology and Biotechnology. 66:325-332.

Interpretive Summary: The repeated application of fumigants can result in accelerated degradation of these compounds resulting in adapted soils. The addition of compost manure to the soil can help in degrading soil fumigants at a faster rate instead of repeated application for many years. The compost manure adds new carbon sources for higher metabolic rate for soil bacteria and result in their increase in population. It is very difficult to isolate bacterial populations that are involved in the degradation of fumigants without continuous enrichment of soil samples. This process can take about a year and the samples must be from soils that had been subjected to the application of a particular fumigant for many years. Therefore, the major problem facing researchers is how to increase the effectiveness of soil fumigants without incurring additional cost. One of the most effective methods we found in this study was the mixing of compost manure with soil with the subsequent application of fumigants. The addition of compost to soil increases microbial populations because of the increase in nutrient availability to soil bacteria, and this in turn increases the populations of specific group of degrading bacteria. DNA analysis of the soil can reveal the specific bacteria that can degrade soil fumigants. This information will be helpful in identifying degrading populations without enrichment and will result in reduced emissions of fumigants.

Technical Abstract: Chloropicrin (CP) and methyl isothiocyanate (MITC) are commonly used as fumigants in agricultural soils 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 microorganisms capable of degrading these compounds. In this study, a microcosm-enrichment approach was used to investigate bacterial populations that may represent MITC and CP-degrading microorganisms in compost-amended soil. After 6 months incubation, with repeated application of MITC and CP, degradation was much faster for compost-amended soil (CM) than with the unamended soils, indicating accelerated degradation due to addition of compost or development of new microbial populations with enhanced degradation capacity. Denaturing gradient gel electrophoresis (DGGE) profiles of PCR amplified region of 16S rRNA genes were used to identify dominant bacterial populations in the fumigant-degrading soil. The DGGE results indicated that specific bacterial types had been enriched and these were similar to some strains isolated from solid media. Fragments from DGGE bands and colonies were cloned, sequenced, and compared with published 16S rRNA sequences. Most of the clone sequences were dominated by Pseudomonas, Bacillus, Arthrobacter, Mycobacterium and uncultured bacterial species. The addition of organic amendment to soil during fumigation practices may be a good management practice to increase degradation and reduce emissions.