Temporal soil bacterial community responses to cropping systems and crop identity
Amplicon libraries of the V4 region of the bacterial 16S rRNA gene were prepared following procedures outlined by Kozich et al. (2013), using dual indexed primers (515F and 806R). Amplicons were normalized using SequalPrep plate normalization kit (Invitrogen), product was pooled to equimolar concentrations, and pooled amplicons were cleaned with AmpureXP magnetic beads . Paired-end sequencing was performed at Michigan State Universitys RTSF Genomics Core using an Illumina MiSeq with a maximum read length of 250 base pairs on MiSeq v2 reagent cartridge (Illumina Inc.). Illumina Real Time Analysis v1.18.54 was used to perform base calling, and the resulting output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.