The pigeonpea cyst nematode (PCN) Heterodera cajani Koshy infects black gram (Vigna mungo L.), causing significant yield losses. However, there is a lack of systematic information on PCN pathogenicity, as well as quantitative and qualitative yield losses in black gram under various inoculum levels and soil conditions. Therefore, we have assessed the threshold inoculum level(s), estimated the yield and protein losses caused by PCN, and evaluated eco-friendly management option(s) with botanicals (neem cake, neem seed powder) and a microbial agent (Trichoderma harzianum). The results revealed a gradual and significant decline in crop growth parameters as the inoculum levels increased from 0 to 3000 juveniles (J2s)(2 kg soils). The severity of PCN infestation was notably higher in alluvial soils compared to lighter soils, exhibiting higher cyst counts (+63%) in plant roots. The threshold inoculum level(s) causing a 25% reduction in various agronomic parameters was significantly lower in alluvial soil(176–1262 J2s; mean = 921) compared to light soil (720–1444 J2s, mean = 1308), indicating that alluvial soil conditions favored increased PCN infestation over light soils, leading to more substantial growth inhibition. Strong positive correlations were found between initial inoculum levels and final populations of PCN. Inoculum levels ranging from 90 to 120 thousand J2s (representing 45–60 J2s per 100 cc soils) resulted in yield losses of 26–78% (p < 0.001). Additionally, there was a corresponding decrease in grain protein content by 9–22% (p < 0.01), subsequently reducing protein productivity by 11–83% (p < 0.001). In the PCN management experiment, among the different bio-organic components, neem cake at 1.0 t ha−1 exhibited the highest efficacy against PCN at crop harvest stage, leading to significant improvements in both dry shoot weight (4.3 g) and dry root weight (1.0 g)/plant compared to the inoculated check. Also, neem seed powder (at 0.1 t ha−1) and T. harzianum + farmyard manure (1 kg in 100 kg farmyard manure ha−1) showed increased effectiveness against the nematode. This study emphasizes the substantial influence of nematode infection on crop performance, particularly in alluvial soils, resulting in significant losses in both yield and protein content. Neem cake emerges as a promising eco-friendly management for managing the PCN in black gram.
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