Appendix A. Tables and figures showing dissimilarity among all the five sites and between pairwise sites by NPMANOVA (Table A1, A2), and decrease of microbial functional genes richness (Fig. A1) and diversity (Fig. A2–A6) along with long-term oil contamination.

Tables and figures showing dissimilarity among all the five sites and between pairwise sites by NPMANOVA (Table A1, A2), and decrease of microbial functional genes richness (Fig. A1) and diversity (Fig. A2–A6) along with long-term oil contamination

The normalized signal intensity of detected key genes involved in nitrogen cycling.

<p>The signal intensity for each functional gene was the average of the signal intensity from all the replicates. All data are presented as mean ± SE.</p

Canonical correspondence analysis (CCA) of GeoChip data and environmental variables.

<p>Environmental variables were chosen based on significance calculated from individual CCA data and variance inflation factors (VIFs).</p

The normalized signal intensity of detected key genes involved in organic contaminant degradation.

<p>The signal intensity for each functional gene was the average of the signal intensity from all the replicates. All data are presented as mean ± SE.</p

The hierarchical cluster analysis of <i>nosZ</i> genes encoding nitrous oxide reductases.

<p>The protein id number and its derived organism for each gene are indicated. The color intensity of each panel shows the normalized signal intensity of individual genes, referring to color key at the top right.</p

Hierarchical cluster analysis of functional genes in 12 activated sludge samples from four WWTPs named GBD, QH, XHM and XJH.

<p>Each sample is named after WWTP plant with “_1”, “_2”, or “_3” that indicates one of three replicate samples from each plant.</p

The normalized signal intensity of detected key genes involved in sulfur cycling.

<p>The signal intensity for each functional gene was the average of the signal intensity from all the replicates. All data are presented as mean ± SE.</p

The normalized signal intensity of detected key genes involved in phosphorus cycling.

<p>The signal intensity for each functional gene was the average of the signal intensity from all the replicates. All data are presented as mean ± SE.</p

The normalized signal intensity of detected key genes involved in carbon cycling.

<p>The signal intensity for each functional gene was the average of the signal intensity from all the replicates. All data are presented as mean ± SE.</p

MDS plots based on microbial nutrient cycling and energy metabolism gene assemblages (a) and gene families (b) detected in stream biofilms by Geochip analysis.

<p>The total number of nutrition/energy metabolism genes detected in each sample was standardized between all samples (a), or the number of genes contributing to each of 65 nutrition/energy metabolism gene families was determined for each sample, and the total number of genes standardised between samples (b). Hoteo River and Oakley Creek samples had markedly distinct gene families to other samples resulting in a degenerate MDS plot when included, and have therefore been excluded from (b).</p