Iron oxides affect denitrifying bacterial communities with the nirS and nirK genes and potential N2O emission rates from paddy soil

Abstract

Microbial denitrification in agricultural soil is a major contributor to the terrestrial production of the greenhouse gas nitrous oxide (N2O). Iron oxides play influential roles in both biochemical and chemical pathways that produce N2O; however, their role in the denitrifying bacterial community is not clear. In this study, a laboratory soil-slurry pot experiment was carried out to determine the impacts of ferric iron (Fe(III)) reduction on the abundance and community structure of denitrifiers and on N2O generation. Three treatments were included: paddy soil from which iron oxides were removed (control), non-treated paddy soil, and paddy soil supplemented with ferrihydrite (86.3 μmol Fe(III) g−1). N2 and N2O concentrations in the headspace were measured using a robotized sampling and analysis system. The gene copy numbers of nirK, nirS, and the 16S rRNA gene were quantified by qPCR and amplification products were sequenced on the Illumina MiSeq platform. The results showed that ferrihydrite supplementation accelerated N2O fluxes in the initial days, and at later stages, N2 production. Ferrihydrite increased the total bacterial abundance and strongly increased nirS and nirK gene abundances. The abundance of nirS gene correlated with the soil nitrate content, and nirK abundance correlated with the ferrous iron concentration in the soil. Fe(III) oxides were identified as one of the environmental parameters impacting the abundance and diversity of nirK-type denitrifiers. Paracoccus and Rhodopseudomonas were dominant species of nirK-type denitrifiers in the ferrihydrite-supplemented samples, which indicated the both iron-dependent species were involved in the denitrification process.