Reassessing soil nematode diversity under fertilization in a paddy-upland rotation system

Soil nematode diversity is a widely-used indicator for assessing the impact of agricultural practices, such as fertilization, on soil ecosystems. Organic fertilization is generally considered beneficial for nematode diversity. However, comparisons of diversity indices are sensitive to sample completeness, and unequal completeness can result in unfair comparisons among assemblages. In this study, we applied the statistical framework of Hill diversity, which accounts for equally complete samples, to estimate nematode diversity under different fertilization conditions in a paddy rice-upland wheat rotation system over three years. Our findings revealed that crop phase had a more pronounced influence on nematode community composition compared to fertilization or sampling year, although all three factors significantly affected nematode community composition. The sampling was incomplete, and coverage varied among samples for diversity comparison; for instance, sample coverage values were generally higher in the rice phase than in the wheat phase. After standardizing samples by completeness, we observed substantial variation in nematode diversity among years, regardless of whether more emphasis was placed on rare taxa (richness), abundant taxa (Shannon diversity), or dominant taxa (Simpson diversity). Moreover, the influence of crop phase on nematode diversity became particularly evident when examining diversity metrics that highlight rare and abundant taxa (e.g., richness and Shannon diversity). However, the effects of fertilization on nematode diversity were overshadowed by pronounced yearly variations. This study emphasizes the pivotal role of crop phase in shaping nematode community composition and diversity, while raising questions about the impacts of fertilization on nematode diversity when yearly variation is not considered. Additionally, we validated the suitability of Hill diversity for equally complete samples as an approach for a fair comparison of nematode diversity in soil ecosystems.