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

  • Environmental Microbiology
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Abstract

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.

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Abbreviations

BIOF:

Biofumigation

GSLs:

Glucosinolates

B:

Broccoli

BM:

Broccoli + myrosinase

ITC:

Isothiocyanate

PITC:

2-phenylethyl isothiocyanate

MS:

Metham sodium

PLFA:

Phospholipid fatty acids

FAME:

Fatty acid methyl esters

DGGE:

Denaturating gradient gel electrophoresis

ASC:

Ascomycetes

AOB:

Ammonia-oxidizing bacteria

DAA:

Days after application

FDA:

Fluorescein diacetate

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Acknowledgments

This work was financially supported by the Research Promotion Foundation in the Republic of Cyprus within the frame of the project BIOFUME 0506/07.

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Authors and Affiliations

  1. Department of Natural Resources and Agricultural Engineering, Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, 75 Iera Odos Str, 11855, Athens, Greece

    Michalis Omirou & Constantinos Ehaliotis

  2. Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aiolou Str, Larissa, 41221, Greece

    Constantina Rousidou, Fotios Bekris, Kalliope K. Papadopoulou & Dimitrios G. Karpouzas

  3. School of Agriculture, Laboratory of Pesticide Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece

    Urania Menkissoglou-Spiroudi

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  1. Michalis Omirou
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  2. Constantina Rousidou
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Correspondence to Constantinos Ehaliotis or Dimitrios G. Karpouzas.

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Omirou, M., Rousidou, C., Bekris, F. et al. The Impact of Biofumigation and Chemical Fumigation Methods on the Structure and Function of the Soil Microbial Community. Microb Ecol 61, 201–213 (2011). https://doi.org/10.1007/s00248-010-9740-4

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