Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies

De Corato, Ugo

doi:10.1186/s40538-020-00183-7

Chemical and Biological Technologies in Agriculture

Table 3 Amplicon sequencing platforms for identifying the biocontrol-based microbiota of the composts showed in Table 2

From: Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies

Compost item	Suppressive model	Amplicon sequencing platform	Primer	References
Green composts#1	Multi-suppressive (both general and specific)	Amplicon sequencing of the bacterial 16S rDNA gene and the fungal ITS1 and ITS2 regions of the ITS rDNA gene. Trichoderma is identified by sequencing the ITS1-5.8S-ITS2 gene regions of the rDNA	Multiple primer pairs sets for bacteria 8F/120R, 388F/534R, 968F/1073R and 8F/361R Universal primer pairs sets for fungi ITS5F/ITS2R and ITS3F/ITS4R Universal primer pairs sets for Trichoderma: ITS1F/ITS4R Primer pairs for Trichoderma harzianum, Trichoderma Asperellum and Trichoderma atroviride Chit42-1a and Chit42-2a	De Corato et al. [55]
Green composts#2	General	Amplicon sequencing of the bacterial 16S rDNA gene and the fungal ITS1 and ITS2 regions of the ITS rDNA gene. Trichoderma is identified by sequencing the ITS1-5.8S-ITS2 gene regions of the rDNA	Multiple primer pairs sets for bacteria 8F/120R, 388F/534R, 968F/1073R and 8F/361R Universal primer pairs sets for fungi ITS5F/ITS2R and ITS3F/ITS4R Universal primer pairs sets for Trichoderma ITS1F/ITS4R Primer pairs for Trichoderma harzianum, Trichoderma Asperellum and Trichoderma atroviride Chit42-1a and Chit42-2a	De Corato et al. [55]
Green composts#3	General	Amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS1 and ITS2 regions of the ITS rRNA gene using Ion Torrent PGM sequencing	Multiple primer pairs sets for bacteria 8F/120R, 388F/534R, 968F/1073R and 8F/361R Universal primer pairs for fungi ITS5F/ITS2R and ITS3F/ITS4R	Blaya et al. [22]
Traditional composts from municipal bio-waste	Specific	Amplicon sequencing of the bacterial 16S rDNA gene and the fungal ITS1 and ITS2 regions of the ITS rDNA gene. Trichoderma is identified by sequencing the ITS1-5.8S-ITS2 gene region of the rDNA	Multiple primer pairs sets for bacteria 8F/120R, 388F/534R, 968F/1073R and 8F/361R Universal primer pairs sets for fungi ITS5F/ITS2R and ITS3F/ITS4R Universal primer pairs sets for Trichoderma ITS1F/ITS4R Primer pairs for Trichoderma harzianum, Trichoderma asperellum and Trichoderma atroviride Chit42-1a and Chit42-2a	De Corato et al. [55]

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