Fig. S1. 16S rRNA OTUs with significantly different abundances under Miscanthus x giganteus (MG), Panicum virgatum (PV) and Zea mays (ZM). The abundances of OTUs were tested by two-way ANOVA with site and crop type as two impact factors. The OTUs significantly impacted by crop type (P < 0.05) were selected and then analysed by post hoc tests. The OTUs with a P-value of < 0.05 were selected and defined as the species that significantly responded to plant type.

Fig. S2. Microbial community composition in the bulk soils under Miscanthus x giganteus (MG), Panicum virgatum (PV) and Zea mays (ZM) at seven different sites in the state of Illinois. The 16S rRNA gene pyrosequences (> 350 bp) were classified by RDP Classifier with confidence threshold at 80%. (A) to (H) are the seven sites located from north to south of Illinois State. Details of these sites are described in Fig. 1.

Table S1. Quality of barcoded pyrosequencing.

Table S2. Nearest species and neighbours of dominant (top 20) N-cycling microbial OTUs (BlastP against the non-redundant protein sequences).

Table S3. Primers and annealing temperature for nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes.

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