16S rRNA from the top soil in the Cu gradient in Hygum, Denmark

Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However there is virtually no knowledge concerning the responses of specific bacterial taxa (e.g. phyla or classes) to metal toxicity and contradictory results have been obtained regarding metal impacts on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 – 3537 µg g-1) stemming from industrial contamination with CuSO4 85+ years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [3H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu as determined by a Cu-specific bioluminescent biosensor strain demonstrating a specific community response to Cu. The relative abundances of the three dominant phyla (Actinobacteria, Proteobacteria and Acidobacteria) were not significantly correlated with bioavailable Cu, but relative abundances of specific classes or genera belonging to these phyla frequently increased or decreased with increasing Cu levels. Relative abundances of several less abundant phyla (Bacteroidetes, Verrumicrobia, Cloroflexi, WS3, and Planctomycetes) were all negatively correlated with increasing bioavailable Cu. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu did not show any correlation to bacterial OTU richness (97 % similarity level). Our study highlights several bacteria taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for metal-responding taxa.