16S for metagenome of Malus domestica: apple fruit
Microbial genomic DNA samples were extracted using the FastDNA SPIN Kit for Soil (MP Biomedicals, Solon, OH, United States) following the instructions of the manufacturer. Extracted DNA was used as the template for amplicon PCR reactions that amplified the bacterial 16S ribosomal region. The V4 region of the 16S rRNA was amplified using the universal 515F/806R primer set (Caporaso et al., 2011). Peptide nucleic acid (PNA) clamps (Lundberg et al., 2013)) were added to the 16S rRNA PCR mix (total of 20 l) with a concentration of 2.5 M mitochondrial PNA and 2.5 M plastid PNA to block amplification of host plastid and mitochondrial 16S DNA.