Denitrifying bacterial community in manure compost pellets applied to an Andosol upland field

Abstract

A large amount of nitrous oxide (N2O), one of the most important greenhouse gases, was emitted after the application of manure compost pellets (MCPs) compared to treatments with ordinary manure composts or chemical fertilizers. Emission of N2O was found to be due to denitrification in the pellets. To study the relationship between N2O emission and denitrifiers, the denitrifying bacterial communities in the MCPs were investigated by comparing clone libraries of nitrite reductase genes (nirK and nirS) fragments. Pellet samples were obtained three days (P3) and 26 days (P26) after pellet application to the field. The P3 samples were emitting high levels of N2O, and the P26 samples had ceased N2O emission. Polymerase chain reaction (PCR) amplicons of both nirK and nirS were obtained from pellet samples. The diversity index (Shannon–Weiner index) of clone libraries was higher for the nirS genes than for the nirK genes for the same pellet samples and higher in P3 than in P26 for both nir genes. The clone libraries showed that the compositions of nirK denitrifiers in the pellets were relatively stable, but those of the nirS denitrifiers were variable within a month after pellet application; nirS clones that showed a lower similarity with nirS of known denitrifiers were dominant in P3 and those related to nirS of Cupriavidus spp. and Herbaspirillum spp. were dominant in P26. Most of the nirK clones in this study were related to the nirK genes of Rhizobiales denitrifying bacterial isolates. The nirS clones were divided into three groups; (1) those related to nirS of Bradyrhizobium spp., and Rhodanobacter sp. D206a, (2) those related to nirS of Cupriavidus spp., Herbaspirillum spp., and (3) those that had a lower similarity with nirS of known denitrifiers. This study showed a different response of nirK and nirS denitrifiers in the applied MCPs. In order to understand the relation between the denitrifying diversity and the N2O emissions, transcriptional and metabolic analysis will be also needed.