Foliar spraying of chlorpyrifos induces morphometric changes in Glycine max (L.) and shifts native soil microbiome

Pesticide usage alters plant growth, and development and disturbs native soil microbiome. The present study was carried out to evaluate the effect of Chlorpyrifos (CP-20% EC) on the growth and development of soybean (Glycine max), soil fertility, and soil microbiome. We conducted a pot experiment to assess the impact of different concentrations of chlorpyrifos; recommended dose (RD) and higher dose rates (2× and 4× RD). Chlorpyrifos application significantly altered the growth parameters in soybean (p < 0.05). At higher concentrations (2× and 4× RD) shoot length (17.16 ± 1.04; 14.33 ± 1.15, p < 0.05), root length (3.40 ± 0.36; 2.66 ± 0.28, p < 0.050), leaf count (6.33 ± 0.57; 2.66 ± 0.57; p < 0.05) reduced significantly compared to RD and Control groups. Similarly at these concentrations (2× and 4× RD), significant reduction in fresh shoot weight (0.86 ± 0.008; 0.66 ± 0.002, p < 0.05), dry shoot weight (0.14 ± 0.001; 0.13 ± 0.003, p < 0.05) and root fresh weight (0.13 ± 0.001; 0.09 ± 0.003, p < 0.05) and root dry weight (0.030 ± 0.0005, 0.037 ± 0.003, p < 0.05) was observed compared to the RD and control group. Notably, a significant increase in root and shoot morphometric parameters was observed in RD compared to control (p < 0.05). All the physio-chemical properties such as pH (8.51 ± 0.82), moisture content (33.73 ± 0.04), and electrical conductivity (3.44 ± 0.03) were higher in CP-treated soils compared to control. Similarly, nutrient content such as nitrogen, carbon, and hydrogen were significantly reduced in treated soils compared to control. Elemental analysis showed higher concentrations of As, Cd, and Pb in CP-treated soil (8.7 μg/g, 0.254 μg/g, and 16.477 μg/g, respectively) compared to untreated soil (8.09 μg/g, 0.228 μg/g, and 15.25 μg/g, respectively). We also assessed soil metabolic activity and diversity using Community-level Physiological Profiling (CLPP). CP-treated soil exhibited significantly lesser microbial diversity, with lesser metabolic activity. Metagenomic analysis revealed a shift in bacterial community composition, with Pseudomonadota and Bacteroidota dominating CP-treated soil, while Actinomycetota, Pseudomonadota, and Bacillota were prominent in the control group. Alpha diversity indices indicated higher abundance and species richness in the control sample compared to treatment groups. Functional analysis via PICRUSt2 identified 32 unique sub-classes of biodegrading genes in soil samples, including atzD, tfdA, argB, GLDC, gcvP, glxR, and cpdB. This suggests the potential of soil microbes for xenobiotic degradation, including pesticides. In summary, our study demonstrates that higher CP doses negatively impact soybean growth and alter soil composition, leading to reduced metabolic activity and changes in microbial communities. These findings underscore the importance of considering pesticide dosage and its ecological implications on plants, soil microbiome, and sustainable agriculture.