Nematode Community Profiling in Organic and Conventional Spinach Systems

Agricultural management practices play a significant role in shaping soil biological communities and ecosystem processes. Soil nematodes are valuable biological indicators of soil health because they occupy different trophic levels and are sensitive to alterations in environmental conditions. This study assessed the influence of organic and conventional farming systems on soil nematode communities in spinach production systems in Embu County, Kenya. We hypothesized that organic farming systems would support higher nematode diversity and a more complex community structure than conventional systems. Soil samples were collected from farms under the two management systems and analyzed using high-throughput sequencing targeting the 18S rRNA gene. A total of 394 amplicon sequence variants (ASVs) representing 73 nematode genera were identified across the two systems. Numerical differences were observed in the abundance of nematode families, genera, and trophic groups between the two farming systems. Cephalobidae, Prismatolaimidae, and Trichodoridae showed higher relative abundance in the conventional system, while Rhabditidae, Monhysteridae, and Qudsianematidae were relatively more abundant in the organic system, but these differences were not statistically significant. Acrobeloides, Prismatolaimus, and Paratrichodorus were relatively more abundant in the conventional system, whereas Eumonhystera, Aphelenchoides, Diploscapter, and Microdorylaimus were more abundant in organic farms; however, these differences were not significant (p > 0.05). Similarly, fungivores and plant-parasitic nematodes were relatively more abundant in conventional farms, whereas bacterivores, predators, and omnivores were more abundant in organic farms, although these differences were also not statistically significant (p > 0.05). No significant differences were observed in alpha or beta diversity between the two farming systems. Our work establishes a valuable baseline for future studies aimed at enhancing the sustainable management of spinach agroecosystems.