Soil pH modulates microbial nitrogen cycling under integrated soil-crop system management across agroecosystems

Abstract

Integrated Soil-Crop System Management (ISSM) has emerged as an effective approach to improve nutrient cycling and crop yield in China. However, its pH-dependent impact on the nitrogen (N) cycling capacity of soil microbiome remains largely unexplored, despite the critical role of pH in shaping microbial processes. Here, we employed comprehensive metagenomic analysis across multiple agricultural sites in China to investigate the effects of ISSM on the N-cycling potential along soil pH gradients, with Farmlandʼs Practice (FP) as a reference. Actinobacteria and Proteobacteria dominated microbial communities across all treatments and pH conditions, accounting for 88%–90% of the total abundance. Microbial alpha diversity remained consistent across the pH gradient, but exhibited significant negative correlations with soil organic carbon and total N. Soil pH showed a strong positive correlation with the abundance of genes associated with nitrification, but showed a negative correlation with denitrification gene abundance. Particularly, ISSM significantly increased the total abundance of nitrogen-cycling genes in the two most acidic soils (LS, GZL), but not in the less acidic (HEB), near-neutral (BD), and alkaline (TY) soils. Relative to FP, the normalized gene abundances associated with denitrification and NH₄⁺ to Org-N were enriched in LS_ISSM, while those related to DNRA, NO₃⁻ reduction to ammonia, and nitrification were higher in GZL_ISSM. These results highlight the potential of ISSM to modulate microbial nitrogen cycling and point to the importance of site-specific strategies, particularly in acidic soils, for enhancing nitrogen retention.

Graphical abstract

Keywords

soil pH / nitrogen cycling / metagenomics / soil microbiome

Highlight

	● Soil pH positively correlated with the metagenomic abundance of nitrification.
	● Soil pH negatively correlated with the metagenomic abundance of denitrification.
	● ISSM increased total nitrogen cycle gene abundance in more acidic soils.

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