Metagenomic analysis identified organic nitrogen metabolism as the key process underlying enhanced soil nitrogen retention after partial organic substitution of chemical fertilizers

Abstract

Partial substitution of chemical fertilizers with organic fertilizers enhances soil nitrogen (N) retention, yet the effects of different substitution ratios on N fate and associated N-cycling microbial taxa remain unclear. We conducted a two-year consecutive ¹⁵N-labeled pot experiment by using soils from a 36-year long-term fertilization experiment: chemical fertilizer; chemical N replaced by 30%, 50%, and 70% organic N, and no fertilization (control). Metagenomic sequencing was used to analyze N-cycling microbial taxa’s response to the fate of fertilizer N. The results demonstrated that long-term organic substitution soils increased the abundance of functional genes related to organic N metabolism (gdhA and glnA), dissimilatory nitrate reduction to ammonium (nrfA), and denitrification (nirK and nosZ) but reduced the abundance of genes for assimilatory nitrate reduction (nirA) and N fixation (nifH). Organic N metabolism and denitrification were key processes regulating external N fate. The 50% substitution promoted organic N-metabolizing taxa, thereby improving N utilization linked to a higher microbial biomass C:N ratio. In contrast, 30% and 70% substitutions upregulated denitrifying taxa, increasing potential N loss. Thus, 50% organic substitution optimizes fertilizer N retention by enriching organic N-metabolizing functional groups, providing a viable strategy for sustainable N management.

Graphical abstract

Keywords

organic N substitution ratio / metagenomics / N cycling / fertilizer N fate / paddy soil

Highlight

	● Soil microbial C/N ratio governed N immobilization and denitrification processes.
	● glnA and gdhA regulate the coordination between available N and microbial N immobilization.
	● Fifty percent organic substitution promoted organic N metabolism and increased the abundance of related taxa, thereby improving N use efficiency.

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