Abstract
Plant-parasitic nematodes represent a substantial constraint on global food security by reducing the yield potential of all major crops. The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is widely distributed across important soybean production areas of the U.S., being the major soybean yield-limiting factor, especially in the Midwestern U.S. Double cropped (DC) soybean is commonly planted following winter wheat. We previously reported double-cropping soybean fields with reduced SCN counts compared to fallow at both R1 growth stage (beginning of flowering) (−31.8%) and after soybean harvest (−32.7%). To test if higher counts of beneficial and SCN antagonistic microorganisms could be correlated with the suppression of SCN in fields previously planted with wheat, three field locations with noted SCN suppression were selected for a metagenomics study. Ten subplots were selected (5 wheat and 5 fallow pre-soybean) from each location. A total of 90 soil samples were selected: 3 fields ×2 treatments × 3 timepoints × 5 replications. Three DNA markers targeted distinct microbial groups: bacteria (16S V4-V5), fungi (ITS2), and Fusarium (tef1). Amplicons were sequenced using an Illumina MiSeq platform (300 bp paired-end). Sequencing datasets were processed in R using the DADA2 pipeline. Fungal populations were affected by location in all sampling periods and differed significantly between DC and fallow plots at soybean planting and after harvest (P < 0.001). Several enriched fungal and bacterial taxa in wheat plots, including Mortierella, Exophiala, Conocybe, Rhizobacter spp., and others, were previously reported to parasitize SCN and other plant-parasitic nematodes, suggesting a potential role of beneficial microbes in suppression of SCN in soybean fields double-cropped with wheat.
Highlights
Plant-parasitic nematodes are a threat to many crop production systems worldwide, representing a substantial constraint on global food security
Knowing that farmers doublecrop soybean with wheat in Southern Illinois, with several research reports indicating wheat as a potential suppressor soybean cyst nematode (SCN) populations, we previously reported soybean fields doublecropped with wheat having reduced SCN counts compared to fallow strips at the R1 growth stage (−31.8%) and after soybean harvest (−32.7%) (Fehr et al, 1971; Rocha et al, 2021b)
A total of 6,110,266 reads were available after low variance and low count filtering, averaging 67,892 reads per sample. 16S rarefaction curves exhibited a plateau in species richness after 25,000 reads (Supplementary Figure 3), indicating the sequencing depth was sufficient to cover the majority of bacterial taxa
Summary
Plant-parasitic nematodes are a threat to many crop production systems worldwide, representing a substantial constraint on global food security. Annual crop yield losses linked to nematode parasitism average 12.3% worldwide, reaching ∼$157 billion, notably in low technology production zones, exacerbating poverty, food insecurity, and malnutrition (Singh et al, 2015; Bernard et al, 2017; Coyne et al, 2018). Besides direct losses tied to nematodes, these organisms may be part of disease complexes, often causing root system wounds, and allowing other pathogens to infect plants (Xing and Westphal, 2006; Coyne et al, 2018). SCN may cause up to 30% of losses without noticeable aboveground symptoms (Mueller et al, 2016), requiring root inspection for proper assessment of pathogen incidence. Several cropping practices are recommended to manage SCN, including using resistant varieties, crop rotation, weed management, and applying nematicides and biocontrol agents as seed treatments (Mueller et al, 2016; Rocha et al, 2021a)
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