DNA Metabarcoding was used to investigate the efficiency of two sets of primers (combinations A and B) for characterizing the soil invertebrate’s communities in different farming management systems. Soil samples were taken from three different sites in the South-West of Milan and DNA was extracted directly. PCR was applied by using 4 pairs of previously published primers targeting invertebrate’s cox1, followed by Illumina Miseq sequencing. The results showed that the presence of the most popular primer pair used in barcoding studies (LCOI490-HCO2198) has affected negatively the taxonomic assignment of OTUs, since about 67.88 % of the obtained sequences where not identified. Our analysis showed that a higher percentage of Arthropoda, Annelida, Nematoda and Rotifera &Tardigrada (41.6, 5.9, 0.8 and 1% of total reads, respectively) was obtained with primer combination B; thus this primers set can be considered a promising method to evaluate the soil arthropods community

SOIL DNA METABARCODING: EVALUATING THE EFFICIENCY OF MULTIPLEX PRIMER SETS IN RECOVERING THE SOIL INVERTEBRATE’S COMMUNITY AS SOIL QUALITY INDICATORS

Alali S;
2017

Abstract

DNA Metabarcoding was used to investigate the efficiency of two sets of primers (combinations A and B) for characterizing the soil invertebrate’s communities in different farming management systems. Soil samples were taken from three different sites in the South-West of Milan and DNA was extracted directly. PCR was applied by using 4 pairs of previously published primers targeting invertebrate’s cox1, followed by Illumina Miseq sequencing. The results showed that the presence of the most popular primer pair used in barcoding studies (LCOI490-HCO2198) has affected negatively the taxonomic assignment of OTUs, since about 67.88 % of the obtained sequences where not identified. Our analysis showed that a higher percentage of Arthropoda, Annelida, Nematoda and Rotifera &Tardigrada (41.6, 5.9, 0.8 and 1% of total reads, respectively) was obtained with primer combination B; thus this primers set can be considered a promising method to evaluate the soil arthropods community
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11379/555518
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