Non-metric multidimensional scaling ordination of 16S rRNA gene iTag sequence data. (a) The main ordination shows sample similarity and the correlations between environmental variables and ordination axes. The three most abundant OTUs in the contaminated samples (uncultured Gammaproteobacterium, Colwellia and Rhodobacteraceae) are represented by arrows. Sample BP366 is indicated by a blue square. Samples that exceeded the EPA’s aquatic benchmark for PAHs are denoted by red circles. (b) For this same ordination, the concentrations of TPH, total nitrogen, DIN, nitrate and ammonium are indicated by bubble size and contour lines. (c) Rarified abundance of an uncultured Gammaproteobacterium OTU and a Colwellia OTU are shown for the same ordination, with bubble size and contour lines indicating abundance. P-values indicate the significance for the variable shown and are based on 999 permutations.