Ion Torrent PGM sequencing for microbial ecology

The Ion Torrent Personal Genome Machine (PGM) employs a unique semiconductor technology to measure pH changes in polymerization events rather than light-based imaging adopted by other next-generation sequencing platforms. However, the PGM has not been extensively adopted in microbial ecological studies, and sequencing quality has not been accordingly reassessed along with the rapid revolution. In this study, we first present sequencing profiles of different chips with updated 400 bp kit in PGM, then compare the data generated by PGM and 454, and finally take diazotrophic communities in bulk soils from 4 different cropping systems as an example to show the application of PGM in microbial ecological studies.