Metatranscriptomic detection of seedling pathogen in soybean (Glycine max L.) root microbiome

Seedling diseases of soybeans (Glycine max L.) can lead to yield losses of up to 100%. This study investigated the use of metatranscriptomics to detect seedling pathogens, specifically Fusarium sp., on soybean roots. Soil samples were collected from a soybean field at the North Dakota State University Research Farm, Fargo using a W-pattern sampling method. Seeds of the USDA soybean accession ‘Williams 82’ were surface-sterilized, pre-germinated for seven days, and baited in field soil at 22±2°C. Root samples were collected one and six days after baiting, and flash-frozen. RNA was extracted, converted to cDNA, and libraries were prepared for Illumina platform sequencing. Mapping RNA-seq reads to reference metagenomes revealed the relative abundance of Fusarium sp. at six days after baiting, consistent with traditional fungal isolation methods that showed Fusarium sp. with the highest colony-forming units. An increased relative abundance of the glycoside hydrolase gene was observed, which has been linked to defense mechanisms in rice (Oryza sativa L.), suggesting a potential response of soybeans to Fusarium sp. This highlights the potential of metatranscriptomics in understanding host-pathogen interactions and leads to the development of disease-resistant cultivars.