There were likely uncertainties regarding the nirK gene data. Nitrite reductase was considered the key enzyme in denitrification, containing either cytochrome cd1 encoded gene or copper encoded gene, could catalyze the reduction of NO22 to nitric oxide. The nirS denitrifier appeared more abundant than nirK denitrifier, however, the latter could be more sensitive to soil environmental changes. Recently, targeting both nirK and nirS genes in forest, grassland and agriculture systems had been proposed as an assay to elucidate the abundance and community structure of soil denitrifier. However, it is still a question if this assay could better track the changes in denitrification activity with changes in denitrifying bacterial abundance in the polluted soils. Meanwhile, gene transcript numbers would be also a potential option to better predict the functional groups responsible for denitrification in these soils since they could reflect the active VE-821 populations of the community. Significant changes both in the activities and community structure of ammonia oxidizers and denitrifier existed with metal pollution in an interaction with soil abiotic factors in rice paddies. A consistent decrease in the AOB abundance and nitrifying activity in polluted soil was observed in two sites studied. However, a sharp decrease in AOA abundance and denitrifying activity were seen only in highly Cu-polluted soil though lower pH and higher N was seen in polluted soil compared to the background soil in both sites. By using molecular techniques employing DGGE, we observed a shift in the community structure of AOA, and to a lesser extent, of AOB and denitrifier populations that were associated with different metal composition of the polluted soils. The pollution effects on microbial abundance differed between populations of amoA and nirK genes in a single site but these changes were not seen correlated to changes in nitrification or denitrification activities. This could suggest either a possible nonspecific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes. This study suggested that metal pollution could exert impacts on soil microbial communities responsible for N transformation and thus on potential N2O production in rice paddies though the impacts on different communities could vary with metal composition and the associated changes in soil pH and N availability. However, future works would be required either with new molecular assays and/or on microbial responses to multiple metals under contrasting soil conditions in polluted agricultural soils. In the last two decades, use of enzymes, especially hemicellulases, has revolutionized the pulp and paper industry and provided a glimpse of hope that application of enzymes at various levels can reduce the industrial pollution and effluent’s toxicity. However, the current scenario continues to be challenging because of the high pollution load released by the pulp and paper industries, which are still using chlorine-based bleaching sequences.