Microbial Ecology

, Volume 61, Issue 1, pp 201–213

The Impact of Biofumigation and Chemical Fumigation Methods on the Structure and Function of the Soil Microbial Community

  • Michalis Omirou
  • Constantina Rousidou
  • Fotios Bekris
  • Kalliope K. Papadopoulou
  • Urania Menkissoglou-Spiroudi
  • Constantinos Ehaliotis
  • Dimitrios G. Karpouzas
Environmental Microbiology

DOI: 10.1007/s00248-010-9740-4

Cite this article as:
Omirou, M., Rousidou, C., Bekris, F. et al. Microb Ecol (2011) 61: 201. doi:10.1007/s00248-010-9740-4


Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.









Broccoli + myrosinase




2-phenylethyl isothiocyanate


Metham sodium


Phospholipid fatty acids


Fatty acid methyl esters


Denaturating gradient gel electrophoresis




Ammonia-oxidizing bacteria


Days after application


Fluorescein diacetate

Supplementary material

248_2010_9740_MOESM1_ESM.doc (60 kb)
ESM 1(DOC 60 kb)

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Michalis Omirou
    • 1
  • Constantina Rousidou
    • 2
  • Fotios Bekris
    • 2
  • Kalliope K. Papadopoulou
    • 2
  • Urania Menkissoglou-Spiroudi
    • 3
  • Constantinos Ehaliotis
    • 1
  • Dimitrios G. Karpouzas
    • 2
  1. 1.Department of Natural Resources and Agricultural Engineering, Laboratory of Soils and Agricultural ChemistryAgricultural University of AthensAthensGreece
  2. 2.Department of Biochemistry and BiotechnologyUniversity of ThessalyLarissaGreece
  3. 3.School of Agriculture, Laboratory of Pesticide ScienceAristotle University of ThessalonikiThessalonikiGreece

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