Impacts of long term copper exposure on abundance of nitrogen cycling genes and denitrification activity in pasture soils

Soils are the main source of nitrous oxide (N2O) emissions, with 60–70% of global N2O production due to the enhanced denitrification activity with elevated nitrogen (N) availability associated with agricultural intensification. The amendment of agricultural soils with biosolids, the residual product of wastewater treatment, has been used for several decades as an inexpensive source of organic matter and N. Biosolids also contain elevated levels of trace elements such as copper (Cu), which influence the activity of the bacterial enzyme nitrous oxide reductase (N2OR). We extracted DNA from a pasture soil 20 years after application of biosolid and Cu salts and used an environmental genomics approach (GeoChip) to evaluate broad changes in the abundance and structure of families of N-cycling genes. We then focussed on abundances of individual bacterial genes involved in sequential N-reduction (nirS, nirK, and nosZ). There was no relationship between total soil Cu concentrations and the different N-cycling gene families (GeoChip; P > 0.1). However, increasing Zn was associated with decreased nitrification (amoA) and dissimilatory N-reduction (napA and nrfA) gene-family abundances (P < 0.1). When focused on individual bacterial denification pathway genes (qPCR), nosZ (nitrous oxide reductase) was found to be sensitive to Cu concentrations. Moreover, the activity of the Cu-dependent enzyme N2OR is potentially affected by historical Cu concentrations found in these pasture soils. The results highlight the sensitivity of a few key functional taxa (nosZ type denitrifying bacteria) to long-term Cu exposure in soil, and how these effects can translate into alteration of wider N-cycling processes such as those affecting net N2O emissions.