Early-stage effects of carbon-rich soil amendments stimulate retention-related nitrogen genes while maintaining nitrogen and yield levels

Abstract

Understanding the effects of soil amendments and low disturbance practices on soil health, nutrient cycling and microbial activity is essential for improving agricultural sustainability. Ramial chipped wood (RCW) is a promising carbon-rich organic soil amendment but its effects on microbial activity, nitrogen (N) cycling genes and microbial taxa, particularly across soil depth, remain poorly understood. This study aimed to evaluate the short-term effects of RCW applications following a no-till practice on various soil properties including microbial composition and N cycling genes, during the second year after RCW incorporation. The experiment was conducted using tomato (<em>Solanum lycopersicum</em>) as a crop species in the Mediterranean region. We compared the surface (0-20 cm) and subsurface (20-25 cm) metagenomes of RCW-treated soils with those treated with standard N-rich organic pellet, as a control, (CTL) and compost (CMP).</p><p>RCW, particularly at high doses (RCW-HD), increased soil organic carbon and microbial biomass at an early stage. Despite a 50% reduction in organic fertiliser use, RCW-HD did not reduce N availability and crop productivity, suggesting improved N use efficiency. Several N-cycling gene abundances were elevated under CTL compared to RCW-HD, including the nitrification-related <em>pmoA-amoA</em> (+42%) and <em>pmoC-amoC</em> (+72%), and the denitrification-related<em> nosZ </em>(+14%). The RCW-HD no-till system increased nitrate reduction assimilation (+13% <em>nrtABC</em>) and favoured N-fixing bacterial genera such as <em>Terrihabitans,</em> <em>Ferriphaselus, Azospira </em>and <em>Rhodopseudomonas</em>. Soil depth significantly influenced 72% of the N-cycling genes, with key genes being more abundant at the surface. These results highlight the potential of RCW to improve N retention and soil fertility, while reducing fertiliser dependence and greenhouse gas emissions. They also support sustainable practices in regenerative agriculture by highlighting how microbiomes contribute to the efficiency of nitrogen cycling. </p><p><em>Keywords:</em> Shotgun metagenomics; Biogeochemical process; Microbial activity; Organic agriculture; Soil organic matter; Soil regeneration.