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Appendix S1 Supplementary description of metagenome size calculation.

Figure S1 The percentage distribution on phylum level, for Proteobacteria on Class level and Alpha- and Betaproteobacteria on order level for both the total DNA sequences and the 16S rRNA gene amplicon sequences analysed using the bioinformatic tools MG-Rast and Megan.

Figure S2 The metabolic results from MG-Rast tested statistically in Stamp with Fisher's exact test, two sided, 95% CI (CI method Newcombe–Wilson) and Bonferroni correction.

Figure S3 Venn diagrams illustrate that there are few OTUs shared both between the replicates from the same micro-ecosystem and between the two micro-ecosystems.

Table S1 The values measured on the chemical parameters total carbon (TC), nitrogen (Kjeldahl), total organic carbon (TOC), total inorganic carbon (TIC), pH and ammonium.

Table S2 The total amount of reads generated from the 454-sequencing of the total DNA sequencing of DNA isolated from soil micro-ecosystem with (soil + worms) and without earthworms (soil − worms), and reads left after the different filtration steps which removes homopolymers and ambiguous bases, exact duplicates and artificial duplicates.

Table S3 The metabolic results from MG-Rast where the total DNA reads from the two total DNA sequence libraries were compared against the subsystem database (e-value 1e-5, and minimum alignment length 50).

Table S4 The results from the quantification of 16S rRNA copy numbers in biological replicates of 1 g of soil from the start and endpoint of the two micro-ecosystems.

Table S5 An overview of the amount of reads removed from the datasets after the different filtration steps in Mothur.

Table S6 The diversity estimators total richness (Sobs), ACE, Chao1 and Shannon have been estimated in Motur based on the genetic distances unique, 0·01, 0·03, 0·05, 0·1, 0·15 and 0·3.

Table S7 Primers used for PCR amplification of the V3 and V4 region of the 16S rRNA gene for further 454-sequencing.

Table S8 Primers and probes created from randomly picked DNA sequence reads from 454-sequencing of the total DNA libraries.

Table S9 Slopes and R2 of the standard curves of the randomly selected DNA fragments measured with real-time PCR.

Table S10 Slopes and R2 of the standard curves of the real-time PCR measurements of the spike and the 16S rDNA transcript.

Table S11 Number of estimated copies of the different random DNA fragments detected by real-time PCR.

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