Organic fertilization reduces nitrous oxide emission by altering nitrogen cycling microbial guilds favouring complete denitrification at soil aggregate scale

Abstract

Agricultural management practices can induce changes in soil aggregation structure that alter the microbial nitrous oxide (N₂O) production and reduction processes occurring at the microscale, leading to large-scale consequences for N₂O emissions. However, the mechanistic understanding of how organic fertilization affects these context-dependent small-scale N₂O emissions and associated key nitrogen (N) cycling microbial communities is lacking. Here, denitrification gas (N₂O, N₂) and potential denitrification capacity N₂O/(N₂O + N₂) were assessed by automated gas chromatography in different soil aggregates (>2 mm, 2-0.25 and <0.25 mm), while associated microbial communities were assessed by sequencing and qPCR of N₂O-producing (nirK and nirS) and reducing (nosZ clade I and II) genes. The results indicated that organic fertilization reduced N₂O emissions by enhancing the conversion of N₂O to N₂ in all aggregate sizes. Moreover, potential N₂O production and reduction hotspots occurred in smaller soil aggregates, with the degree depending on organic fertilizer type and application rate. Further, significantly higher abundance and diversity of nosZ clades relative to nirK and nirS revealed complete denitrification promoted through selection of denitrifying communities at microscales favouring N₂O reduction. Communities associated with high and low emission treatments form modules with specific sequence types which may be diagnostic of emission levels. Taken together, these findings suggest that organic fertilizers reduced N₂O emissions through influencing soil factors and patterns of niche partitioning between N₂O-producing and reducing communities within soil aggregates, and selection for communities that overall are more likely to consume than emit N₂O. These findings are helpful in strengthening the ability to predict N₂O emissions from agricultural soils under organic fertilization as well as contributing to the development of net-zero carbon strategies for sustainable agriculture.