Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates - experiment 2

Metagenomic DNA was extracted from 250 mg samples from the same soil, and from aliquots taken from a homogenized soil slurry that was prepared by bead beating in the first step of the DNA extraction. The volumes of the aliquots were chosen to contain the amount of DNA expected from 1 mg, 5 mg, and 25 mg soil samples. The soil was a loam topsoil from a Haplic Chernozem (FAO classification) from the Bad Lauchstädt experimental research station of the Helmholtz Centre for Environmental Research in Germany (51°24'N 11°53'E). It was collected in December 2017 from a plot under long term sugar beet – potato – winter wheat – barley rotation that had not received fertilization.The DNA extracts were subjected to Illumina MiSeq paired-end amplicon sequencing targeting the 16S rRNA gene. Control samples were included that did not contain soil only the reagents used in the DNA extraction and PCR to test for the presence of contamination.