Previous studies showed that microbial communities develop trace metal tolerance after long term exposure to increased trace metal concentrations in soil. Co-tolerance is the development of tolerance to other trace metals than those to which the microbial community had been exposed to due to, e.g., similar physiological tolerance mechanisms. We determined co-tolerance of nitrifying communities to Zn and Cu in different soils and assessed the nitrifying community structure using AOB amoA DGGE. We selected soils from five locations which were contaminated with either Cu or Zn or with both. Increased Zn and Cu tolerance was observed in response to corresponding soil contamination, however, co-tolerance was only detected in few cases. Similarly contaminating soil with either Zn or Cu selected for identical phylotypes in one soil, however, co-tolerance was not observed in the Zn contaminated treatment. In contrast, similar Zn and Cu contamination in a second soil both resulted in the development of a co-tolerant nitrifying community that was composed of different dominant phylotypes. The Zn tolerant nitrifying community structures from different soils that inherently have a different native community did not converge to a similar community structure.posterstatus: publishe