Winter cover crops alter nematode community composition and soil health dynamics in corn-soybean systems

Crop production in the Lake Erie Basin, Ontario, Canada, is highly dynamic, with soil biota and water streams exposed to various agricultural stressors. Integrating winter cover crops (WCCs) is increasingly promoted in corn-soybean production systems to mitigate the negative impacts of agriculture. In the present study, morphological and metabarcoding methods were comparatively evaluated for assessing nematode community structure under corn-soybean cropping systems over two years, during WCC growth stages and prior to crop harvest. The WCC treatments included rye, a mixture of rye and barley, rye and oat, and fallow (no WCCs). This allowed us to have a snapshot of the temporal shifts in baseline and functional activities of the nematode food webs. The metabarcoding approach provided a higher taxonomic resolution across nematode feeding groups, detecting significantly greater bacterivore diversity (e.g. , Rhabditidae) compared to morphological analysis. While metabarcoding identified several rare genera, it underrepresented a few key genera, including Helicotylenchus and Filenchus . The morphological approach provided more accurate identification of herbivores and reliable quantitative data. Both identification methods demonstrated that WCC mixtures supported a more stable nematode community, as reflected by higher maturity and structure indices. Soil abiotic factors, such as texture, organic matter content, and cation exchange capacity, substantially influenced nematode community composition, indicating that these communities were shaped not only by WCC, but also by site-specific variability. We conclude that metabarcoding could be a valuable approach, but it still needs development and currently cannot replace the reference-based morphological approach. Therefore, integrating both morphological and metabarcoding data will provide a more comprehensive understanding of soil nematode ecology by enhancing the reliability of assessments and informing sustainable agricultural practices. • Metabarcoding and morphology varied in detecting nematode community composition. • Metabarcoding identified more rare nematode taxa than the morphological approach. • Herbivore populations were reduced under winter cover crops. • Nematode communities and the soil food web were influenced by site-specific conditions. • Metabarcoding provided useful information on nematode community indices.