This work is published
Bintarti AF, A Sulesky-Grieb, N Stopnisek, A Shade. 2022. Endophytic microbiome variation among single plant seeds. Phytobiomes Journal. 6:2471-2906. link
The 16S rRNA and ITS amplicon data are available on NCBI under the BioProject PRJNA714251.
Like other plant compartments, the seed harbors a microbiome. The members of seed microbiome are the first to colonize a germinating seedling, and they initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for understanding the dynamics of plant-associated microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plant) due to low endophytic microbial biomass, seed exudates that can filter and select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting metagenomic DNA from an individual seed from common bean with minimal disruption of host tissue, which we expect to be generalizable to other medium- and large- seed plant species. We applied this protocol to quantify the 16S rRNA and ITS2 amplicon composition and variability for individual seeds harvested from replicate plants grown under standard, controlled conditions to maintain health. Using metagenomic DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the maternal plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.
This research was supported by USDA 2019-67019-29305. AS acknowledges support from the USDA National Institute of Food and Agriculture and Michigan State University AgBioResearch (Hatch). AFB acknowledges a doctoral fellowship from the Fulbright Foundation and from Michigan State University. NS acknowledges support from the Michigan State University Plant Resilience Institute.