Skip to main content
Log in

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

  • Environmental Biotechnology
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

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 ≥70% faster in compost-manure-amended (CM) soil compared to ≤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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Scheme 1

Similar content being viewed by others

References

  • Abdel Magid HM, Sabrah REA, Rabi RK, El Nadi ARH, Abdel Aal SI (1993) Biodegradation of municipal refuse and chicken manure in a winter-wheat ecosystem in Saudi Arabia. J Arid Environ 25:411–419

    Article  Google Scholar 

  • Akhtar M, Malik A (2000) Roles of organic soil amendments and soil organisms in the biological control of plant-parasitic nematodes: a review. Bioresour Technol 74:35–47

    Article  CAS  Google Scholar 

  • Bandick AK, Dick RP (1999) Field management effects on soil enzyme activities. Soil Biol Biochem 31:1471–1479

    Article  CAS  Google Scholar 

  • Brigmon R, Furlong MA, Whitman WB Characterization of microbial communities from pristine and chlorinated-ethene-contaminated landfill groundwater (unpublished)

  • Castro CE, Wade RS, Belser NO (1983) Biodehalogenation. The metabolism of chloropicrin by Pseudomonas sp. J Agric Food Chem 31:1184–1187

    CAS  Google Scholar 

  • Dungan RS, Gan J, Yates SR (2003) Accelerated degradation of methyl isothiocyanate in soil. Water Air Soil Pollut 142:299–310

    Article  CAS  Google Scholar 

  • El-Fantroussi S (2000) Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives. Appl Environ Microbiol 66:5110–5115

    Google Scholar 

  • Gamliel A, Stapleton JJ (1997) Improvement of soil solarization with volatile compounds generated from organic amendments. Phytoparasitica 25S:31–38

    Google Scholar 

  • Gan J, Yates SR, Crowley D, Becker JO (1998a) Acceleration of 1-3-dichloropropene degradation by organic amendments and potential application for emissions reduction. J Environ Qual 27:408–414

    CAS  Google Scholar 

  • Gan J, Yates SR, Wang D, Ernst FF (1998b) Effects of application methods on 1,3-dichloropropene volatilization from soil under controlled conditions. J Environ Qual 27:432–438

    CAS  Google Scholar 

  • Gan J, Yates SR, Ernst FF, Jury WA (1999a) Degradation and volatilization of the fumigant chloropicrin after soil treatment. J Environ Qual 29:1391–1397

    Google Scholar 

  • Gan J, Papiernik SK, Yates SR, Jury WA (1999b) Temperature and moisture effects on fumigant degradation in soil. J Environ Qual 28:1436–11441

    CAS  Google Scholar 

  • Gan J, Yates SR, Ernst FF, Jury WA (2000) Degradation and volatilization of the fumigant chloropicrin after soil treatment. J Environ Qual 29:1391–1397

    CAS  Google Scholar 

  • Hentschel U, Schmidb M, Wagnerb M, Fieselera L, Gernerta C, Hackera J (2001) Isolation and phylogenetic analysis of bacteria with antimicrobial activities from the Mediterranean sponges Aplysina aerophoba and Aplysina cavernicola. FEMS Microbiol Ecol 35:305–312

    Google Scholar 

  • Hungalle N, Lal R, Terkuile CHH (1986) Amelioration of physical properties by Mucuna after mechanized land clearing of a tropical rainforest. Soil Sci 141:219–224

    Google Scholar 

  • Ibekwe AM, Papiernik SK, Gan J, Yates SR, Yang C-H, Crowley DE (2001a) Impact of fumigants on soil microbial communities. Appl Environ Microbiol 67:3245–3257

    Article  CAS  Google Scholar 

  • Ibekwe AM, Papiernik SK, Gan J, Yates SR, Crowley DE, Yang C-H (2001b) Microcosm Enrichment of 1,3-dichloropropene-degrading soil microbial communities in a compost-amended soil. J Appl Microbiol 91:668–676

    Article  CAS  Google Scholar 

  • Jackson CR, Roden EE, Churchill PF (1998) Changes in bacterial species composition in enrichment cultures with various dilutions of inoculum as monitored by denaturing gradient gel electrophoresis. Appl Environ Microbiol 64:5046–5048

    Google Scholar 

  • Moldenke AR, Thies WG (1996) Application of chloropicrin to control laminated root rot-Research design and seasonal dynamics of control populations of soil arthropods. Environ Entomol 25:925–932

    CAS  Google Scholar 

  • Muyzer G, Smalla K (1998) Application of denaturing gradient gel eletrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek J Microbiol 73:127–141

    Article  CAS  Google Scholar 

  • O’Hallorans JM, Muñoz MA, Colberg O (1993) Effect of chicken manure on chemical properties of a Mollisol and tomato production. J Agric Univ PR 77:181–191

    Google Scholar 

  • Øvreas L, Forney L, Daae FL, Torsvik V (1997) Distribution of bacterioplankton in meromictic lake Sælenvannet, as determined by denaturing gradient gel electropholresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63:3369–3373

    Google Scholar 

  • Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC (2001) Soil microbial community response to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33:1011–1019

    Article  CAS  Google Scholar 

  • Perucci P (1990) Effect of addition of municipal solid waste compost on microbial biomass and enzyme activities. Biol Fert Soils 10:221–226

    Google Scholar 

  • Santegoeds CM, Nold SC, Ward DM (1996) Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl Environ Microbiol 62:3922–3928

    Google Scholar 

  • Smelt JH, Crum SJH, Teunissen W (1989) Accelerated transformations of the Fumigant methyl isothiocyanate in soil after repeated application of metam-sodium. Environ Sci Health 24:437–455

    Google Scholar 

  • Taylor GE Jr, Schaller KB, Geddes JD, Gustin MS, Lorson GB, Miller GC (1996) Microbial ecology, toxicology and chemical fate of methyl isothiocyanate in riparian soils from the upper Sacramento river. Environ Toxicol Chem 13:1694–1701

    Google Scholar 

  • Teske A, Wawer C, Muyzer G, Ramsing NB (1996) Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl Environ Microbiol 62:1405–1415

    Google Scholar 

  • Trout T, Agwa H (1999) Strawberry response to fumigants applied by drip irrigation system. In: Proceedings of Annual International Research Conference on Methyl Bromide Alternatives and Emissions Reductions, San Diego, CA, 1–4 Nov 1999, pp 10:1–3

  • Van Dijk H (1974) Degradation of 1,3-dichloropropenes in the soil. Agric Ecosyst 1:193–204

    Article  Google Scholar 

  • Van Hylckama Vlieg JET, Janssen DB (1992) Bacterial degradation of 3-chloroacrylic acid and the characterization of cis-and trans-specific dehalogenases. Biodegradation 2:139–150

    Google Scholar 

  • Verhagen C, Smit E, Janssen DB, van Elsas JD (1995) Bacterial dichloropropene degradation in soil; screening of soils and involvement of plasmids carrying the dhlA gene. Soil Biol Biochem 27:1547–1557

    Article  CAS  Google Scholar 

  • Verhagen C, Lebbink G, Bloem J (1996) Enhance biodegradation of the nematicides 1,3-dichloropropene and methyl isothiocyanate in a variety of soils. Soil Biol 28:1753–1756

    Article  CAS  Google Scholar 

  • Zheng W, Yates SR, Papiernik SK, Guo M (2004) Effect of combined application of methyl isothiocyanate and chloropicrin on their transformation. J Environ Qual 6: (in press)

Download references

Acknowledgments

We thank Chris Taylor for his assistance in obtaining some of the experimental data. This research was supported in part by the 206 Manure and Byproduct Utilization Project of the USDA-ARS. Mention of trademark or propriety products in this manuscript does not constitute a guarantee or warranty of the property by the USDA and does not imply its approval to the exclusion of other products that may also be suitable.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to A. Mark Ibekwe.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ibekwe, A.M., Papiernik, S.K. & Yang, CH. Enrichment and molecular characterization of chloropicrin- and metam-sodium-degrading microbial communities. Appl Microbiol Biotechnol 66, 325–332 (2004). https://doi.org/10.1007/s00253-004-1700-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-004-1700-9

Keywords

Navigation