Beyond taxonomic richness: Network topology and functional gene abundance reveal tillage and nitrogen as physiological and topological filters across heterogeneous corn agroecosystems

Abstract

Soil microbial communities underpin key ecosystem functions, yet their responses to agricultural intensification remain difficult to predict across heterogeneous landscapes. This study evaluated the impact of nitrogen (N) fertilization rates (0–200 kg N/ha) and tillage intensity (conventional ploughing, reduced tillage, direct drilling) on bacterial diversity, functional potential, and co-occurrence networks across 84 corn fields in southern Québec, Canada. Using 16S rRNA gene sequencing and qPCR of N-cycling genes ( nifH , amoA , nirK ), we reveal a hierarchy of drivers. Soil texture and pH dominated bacterial composition, explaining ∼46% of the variance and overriding the effects of management on alpha- and beta-diversity. Texture also constrained topology, with fine soils favoring dense, centralized networks while coarse soils promoted decentralized, modular architectures. However, this taxonomic homeostasis concealed a reorganization of function and structure. Nitrogen fertilization induced a functional reallocation, significantly increasing amoA and suppressing nifH gene abundance. Tillage intensity reshaped microbial network topology, with direct drilling promoting modular and niche-partitioned networks, while reduced tillage exhibited low connectivity and high centralization, hypothesized to reflect structural vulnerability in transitional systems. These patterns indicate that agricultural management operates primarily as a physiological and topological filter rather than a taxonomic driver, consistent with concepts of functional redundancy and network-mediated stability in microbial ecosystems. Thus, soil health assessments should move beyond taxonomic richness to include indicators of network topology and functional gene abundance, which offer more sensitive metrics of ecosystem resilience. Consequently, sustainable management strategies must prioritize preserving these microbial co-occurrence architectures and functional redundancy to ensure long-term soil fertility.