Changes in Soil Microbiome Linked to Management of Allium sativum Cultivation: Impacts on Soil Health and Agricultural Productivity

Garlic ( Allium sativum ) produces organosulfur compounds with antimicrobial activity, but how its cultivation changes soil bacterial communities under field conditions, and how these changes relate to yield, remains poorly understood. Soil from four commercial garlic farms with contrasting soils and management in southern Brazil was sampled before planting and after harvest (three samples per farm and time). Full-length 16 S rRNA genes were sequenced with Oxford Nanopore technology. Communities were compared by ordination, analysis of similarities (ANOSIM) and diversity indices, and taxa by Welch’s t-tests. A Productivity-Weighted Score (PWS) ranked species by their yield-weighted change in relative abundance, and functional profiles were predicted with PICRUSt2. Community composition changed after cultivation (ANOSIM R = 0.34, p < 0.001), whereas alpha diversity did not ( p > 0.05). Ehrlichia decreased from 15.2% to 5.6% and Legionella from 7.3% to 1.4%, whereas Bacteroidota increased from 23.3% to 39.4%, mainly through Pedobacter and Flavobacterium (all p < 0.05). Flavobacterium buctense and Chryseolinea serpens had the highest positive PWS, driven by increases in high-yielding farms, and Legionella spp. the most negative. Nineteen predicted MetaCyc pathways, mainly of central carbon, aromatic compound and polyamine metabolism, differed between sampling times (adjusted p < 0.05). Garlic cultivation, with its management, was associated with a consistent reorganization of soil bacterial communities across contrasting farms, without loss of diversity. The PWS offers a reproducible way of ranking candidate taxa from field data for evaluation in controlled, multi-site studies; the predicted functional changes are hypotheses for direct measurement.