Saline versus alkaline stresses in paddy soils drive divergent microbial nutrient limitations despite shared carbon constraints

Abstract Soil salinization and alkalization often suppress microbial functional activity, triggering negative feedback loops in microbial metabolism, degrading nutrients and agricultural productivity. However, the impacts of saline versus alkaline soils on microbial metabolism remain unclear. We compared reclaimed coastal saline ( S 1 ) and Songnen alkaline ( A 1 ) paddy soils with their corresponding non‐saline controls ( S 0 and A 0 ) using models of ecoenzymatic stoichiometry, aggregate fractionation, amplicon sequencing and high‐throughput qPCR to quantify microbial carbon (C), nitrogen (N) and phosphorus (P) limitation and their abiotic and biotic drivers. Our findings revealed that saline and alkaline stresses consistently intensified microbial C limitation by 24.79% and 90.43%, respectively, relative to their corresponding CK soils. However, the two regional soil systems showed divergent nutrient limitation patterns associated with contrasting physicochemical and microbial conditions. Saline soils exhibited acute microbial N limitation (VT N/P limitation = −6.51), which was associated with lower N availability, including 53.29% lower DTN than in alkaline soils, macroaggregate‐associated N depletion, and bacterial‐associated network reorganization. Microbial functional profiles further indicated greater genetic potential for denitrification and lower genetic potential for dissimilatory nitrate reduction to ammonium, with A 1 soils having 25.12% lower nirK/S abundance and 49.68% higher napA abundance than S 1 soils. In contrast, alkaline soils exhibited stronger microbial P limitation (VT N/P limitation = 9.73), which was associated with reduced P bioavailability, including 56.68% lower AP than in saline soils, greater P sequestration in silt+clay fractions, and fungal‐associated network reorganization. This pattern was accompanied by stronger suppression of genes associated with organic P mineralization and inorganic P solubilization, with phnK and gcd + pqqC abundances being 28.27% and 25.19% lower than in S 1 soils, respectively. These results show that divergent microbial nutrient limitations arise from coupled soil physicochemical constraints, microbial community reassembly, network reorganization and functional gene responses, rather than from ion‐specific chemistry alone. These results highlight organic matter restoration as a common priority, but indicate divergent N/P fertilization strategies for saline and alkaline soils. These insights provide a fundamental framework for targeted remediation of saline and alkaline soils and facilitate sustainable agricultural practices by integrating both universal and salt‐type‐specific methodological approaches. Read the free Plain Language Summary for this article on the Journal blog.