title: The impact of biofumigation and chemical fumigation methods on the structure and function of the soil microbial community.
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.
authors.affiliation: Department of Natural Resources and Agricultural Engineering, Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, 75 Iera Odos Str, 11855, Athens, Greece.
authors.forename: Michalis
authors.initials: M
authors.lastname: Omirou
authors.forename: Constantina
authors.initials: C
authors.lastname: Rousidou
authors.forename: Fotios
authors.initials: F
authors.lastname: Bekris
authors.forename: Kalliope K
authors.initials: KK
authors.lastname: Papadopoulou
authors.forename: Urania
authors.initials: U
authors.lastname: Menkissoglou-Spiroudi
authors.forename: Constantinos
authors.initials: C
authors.lastname: Ehaliotis
authors.forename: Dimitrios G
authors.initials: DG
authors.lastname: Karpouzas
mesh_terms: D001419:Bacteria / Q000145:classification / Q000187:drug effects* / Q000378:metabolism*; D001937:Brassica / Q000737:chemistry; D004952:Esters / Q000032:analysis; D005227:Fatty Acids / Q000032:analysis; D005452:Fluoresceins / Q000032:analysis / Q000378:metabolism; D005651:Fumigation; D005658:Fungi / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D010575:Pesticides / Q000494:pharmacology*; D010743:Phospholipids / Q000032:analysis; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000032:analysis / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D004952:Esters; D005227:Fatty Acids; D005452:Fluoresceins; D010575:Pesticides; D010743:Phospholipids; D012336:RNA, Ribosomal, 16S; D012987:Soil; C018506:diacetylfluorescein
references.citation: FEMS Microbiol Ecol. 2005 Jul 1;53(2):245-53
references.pmid: 16329944
references.citation: Mycologia. 2003 Sep-Oct;95(5):820-6
references.pmid: 21148989
references.citation: FEMS Microbiol Ecol. 2009 Dec;70(3):388-401
references.pmid: 19799632
references.citation: Environ Microbiol. 2008 Nov;10(11):2931-41
references.pmid: 18973620
references.citation: Phytopathology. 2006 Jan;96(1):68-79
references.pmid: 18944206
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: J Biotechnol. 1999 Oct 8;75(2-3):187-94
references.pmid: 10553657
references.citation: Mycol Res. 2003 Jun;107(Pt 6):707-16
references.pmid: 12951797
references.citation: Environ Toxicol Chem. 2001 Nov;20(11):2462-8
references.pmid: 11699770
references.citation: Appl Environ Microbiol. 2001 Oct;67(10):4554-9
references.pmid: 11571155
references.citation: Appl Environ Microbiol. 1997 Apr;63(4):1489-97
references.pmid: 9097446
references.citation: Annu Rev Microbiol. 2001;55:485-529
references.pmid: 11544365
references.citation: FEMS Microbiol Ecol. 2002 Mar 1;39(3):183-91
references.pmid: 19709198
references.citation: FEMS Microbiol Ecol. 2003 Mar 1;43(2):263-70
references.pmid: 19719687
references.citation: Appl Environ Microbiol. 2000 Dec;66(12):5410-8
references.pmid: 11097922
references.citation: FEMS Microbiol Ecol. 2006 Jun;56(3):482-93
references.pmid: 16689879
references.citation: Appl Environ Microbiol. 2001 Jul;67(7):3245-57
references.pmid: 11425748
references.citation: Microb Ecol. 2009 Nov;58(4):715-27
references.pmid: 19440648
references.citation: Appl Environ Microbiol. 2002 Jan;68(1):20-30
references.pmid: 11772604
references.citation: Microb Ecol. 2005 Jan;49(1):83-93
references.pmid: 15690230
references.citation: Phytochemistry. 2001 Jan;56(1):5-51
references.pmid: 11198818
references.citation: Pest Manag Sci. 2005 Nov;61(11):1043-51
references.pmid: 15986402
references.citation: Appl Environ Microbiol. 2000 Dec;66(12):5368-82
references.pmid: 11097916
references.citation: FEMS Microbiol Lett. 2005 Sep 1;250(1):33-8
references.pmid: 16043309
references.citation: FEMS Microbiol Lett. 1994 Jul 15;120(3):363-7
references.pmid: 8076810
references.citation: Trends Plant Sci. 2002 Jun;7(6):263-70
references.pmid: 12049923
references.citation: J Agric Food Chem. 2009 Sep 9;57(17):7706-11
references.pmid: 19722704