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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 itemSuppressive modelAmplicon sequencing platformPrimerReferences
Green composts#1Multi-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 rDNAMultiple 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#2GeneralAmplicon 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 rDNAMultiple 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#3GeneralAmplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS1 and ITS2 regions of the ITS rRNA gene using Ion Torrent PGM sequencingMultiple 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-wasteSpecificAmplicon 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 rDNAMultiple 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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