Metabarcoding Reveals Cover Crop Functional Type as Primary Driver of Soil Nematode Community Composition in a Carrot Production System

The influence of cover crop functional type on soil nematode feeding group structure, food web condition, and crop productivity in horticultural systems remains poorly understood. Using DNA metabarcoding targeting the V6–V8 region of the 18S rRNA gene, we characterized nematode community responses in soil samples collected from a carrot (Daucus carota L.) production system in Ontario, Canada. We evaluated the effects of alfalfa (Medicago sativa L.), sorghum (Sorghum bicolor), and their mixture under two nitrogen regimes. Bacterivores dominated all treatments (60.8%), whereby sampling time and cover crop identity jointly explained 33.5% of community variance. Nematode community ecological indices revealed highly significant temporal shifts in food web condition, including seasonal decline in maturity and structure indices and a rise in the channel index, indicating food web restructuring regardless of cover crop type. Individual cover-crop exhibited distinct trade-offs between nematode suppression and crop productivity, while sorghum drove a pronounced bacterivore-to-fungivore transition. The alfalfa–sorghum (legume–non-legume) mixture emerged as the most agronomically balanced treatment, uniquely combining plant-parasitic nematode suppression with the highest individual carrot weight and the most balanced soil food web structure. This study provides important insights into how cover crop functional type influences soil nematode communities and crop performance in carrot production systems. Future studies repeating this experiment across multiple locations and growing seasons would help determine the consistency of these responses under a broader range of environmental conditions.