Variation in abundance, diversity, and composition of nirK and nirS containing denitrifying bacterial communities in a red paddy soil as affected by combined organic-chemical fertilization

Abstract

The long-term effects of different combined organic–chemical fertilizer regimes on denitrifying communities remain unclear. In this study, we performed quantitative PCR and sequencing analyses to examine the abundance, diversity, and structure of two nir (nirK and nirS) denitrifying communities in response to five fertilization treatments, namely, no nitrogen (N) fertilizer (NF), chemical fertilizer (CF), pig manure + chemical fertilizer (PM), biogas slurry + chemical fertilizer (BF), and milk vetch + chemical fertilizer (GM). All N fertilizer treatments received equal amounts of total N, phosphorus (P), and potassium (K). Compared with the NF treatment, combined organic–chemical fertilization significantly increased abundances of the nirK and nirS genes (particularly in the GM treatment) (P < 0.05). Chemical fertilizer application, with or without organic materials, shifted the nirK-type community relative to that under the NF treatment. In comparison, only a distinguished effect of combined organic-chemical fertilizations on nirS-type denitrifying communities was observed. Fertilizer-induced changes in soil pH and organic matter were identified as the factors contributing most to observed variations in the abundance and composition of the two nir denitrifying communities. Nitrite reductase (NIR) activity was mirrored by the changes in nirS gene abundance. Network analysis revealed that nirK- and nirS-type denitrifying communities formed ecological clusters that were closely associated with carbon addition, and indicated that nirS operational taxonomic units (OTUs) had more opportunities to interact with each other or with nirK OTUs. Overall, a high sensibility of nirK-type denitrifying communities to N fertilization was observed, whereas the nirS-type denitrifiers were more responsive to organic–chemical fertilization than chemical fertilizer application alone, and the addition of carbon was established to be the principal factor implicated in shaping the co-occurrence network patterns of nir denitrifying communities.