Biocontrol agent amendments shape the soybean rhizosphere in a cyst nematode (Heterodera glycines) conducive soil over a two-year field trial

Plant-associated beneficial microorganisms play a vital role in promoting plant health, fitness, and disease suppression, leading to improved plant growth and protection against specific plant parasites. Microbial amendments may reduce nematode parasite populations and ensure plant yield, yet their long-term impact on the native plant microbiome under field conditions is not well understood. In this study, we evaluated the effectiveness of biocontrol products against soybean cyst nematode (SCN) using two application methods over a two-year period under field conditions. Pochonia chlamydosporia PC10 (Rizotec), Bacillus methylotrophicus UFPEDA 20 (Onix), and Trichoderma koningiopsis GF 362 were applied either through seed inoculation or in-furrow treatment at planting. The treatments effectively reduced the nematode population, with T. koningiopsis showing significant deviations from the control and leading to a notable increase in yield. No difference in the Shannon diversity index was detected for the alpha-diversity of root-associated 16S, ITS2, and 18S communities. The dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria for 16S; Ascomycota, Basidiomycota, Mortierellomycota for ITS2; and Ascomycota, and Cercozoa for 18S. In the 16S community, T. koningiopsis and B. methylotrophicus caused a 25 % increase in the relative abundance of Sphingomonas spp. compared to the control. Additionally, the relative abundance of Mortierella spp. significantly increased by 50 % in both the T. koningiopsis and B. methylotrophicus treatments compared to the control. Both treatments also led to a significant reduction in Fusarium spp. by 37.5 % and 31.5 %, respectively. Co-occurrence network analysis revealed that communities were disrupted after the first application, but grew more intricate and cohesive after the second year of biocontrol product amendment. T. koningiopsis and B. methylotrophicus demonstrated potential in reducing nematode and Fusarium populations, leading to increased yield production. However, under high nematode pressure, relying solely on biocontrol measures does not guarantee a reduction in SCN population or yield improvement. Manipulating the microbial community to reduce harmful organisms and promote biocontrol-related species may offer long-term benefits.