MG-RAST ID Amplicon samples # ribosomal sequences (RDPa) # Burkholderia genus (% of total) # Pseudomonas genus (% of total) 4469438.3 Lysimeter 2, 2010 amplicons obtained directly after sampling 6815 6467 (95%) 5 (<0.1%) 4469439.3 Lysimeter 2, 2011 amplicons obtained one year after storage at 4°C 2155 42 (2.6%) 299 (18.7%) MG-RAST ID Metagenome samples # of bacterial taxonomic hits # Burkholderia genus (% of total) # Pseudomonas genus (% of total) 4466990.3 Lysimeter 2, 2010 metagenome obtained directly after sampling 97914 77437 (79%) 2060 (2.1%) 4466989.2 Lysimeter 2, 2011 metagenome obtained one year after storage at 4°C 36960 2060 (5.6%) 1417 (3.8%) aRDP, Ribosomal Database Project annotation

Table 4: Distribution of Burkholderia and Pseudomonas in soil of lysimeter number 2, analyzed using DNA extraction from soil sampled in 2010 and after storage for one year at 4°C as determined by tag encoded pyrosequencing and metagenomic analyses.