EPIPHYTIC SEED MICROBIOMES OF WHEAT, CANOLA, AND LENTIL
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Microorganisms are found colonizing all plant organs including seeds. Seeds are reproductive structures able to carry and transfer microorganisms from one plant generation to the next acting as an initial source of microbial inocula for the next generation of plants. Seed-associated microbial communities offer the potential of improving crop production and yield through protection against abiotic and biotic stresses. Despite their agricultural relevance, seed-borne bacterial and fungal communities as well as factors influencing their assemblage remain largely unknown. Therefore, the purpose of this study was to: i) characterize the seed-associated microbiomes of three agricultural crops important for food security; wheat, canola, and lentil, ii) explore genetic and environmental factors influencing the assembly of the microbiota carried by seeds, and iii) examine the preservation and transmission of seed microbiomes. To achieve these objectives seed samples of different lines harvested from different field locations, years, and generations were subjected to high-throughput amplicon sequencing of the bacterial 16S rRNA and the fungal internal transcribed spacer (ITS) regions. My results suggest recruitment, transmission, and preservation of seed-associated microbiota are determined mainly by the environment in which the plants are grown and to some extent by the host. In addition, a shared set of microorganisms (i.e., core microbiome) was found when seed microbiomes of different crops, lines, and from different sources (i.e., produced in different fields and years) were analyzed together. The existence of this core microbiome implies that plants recruit and carry bacterial and fungal species that could interact with further generations, affecting their adaptation and establishment in novel environments. Some members of this core including Sphingomonas sp., Pantoea agglomerans, and Vishniacozyma victoriae are reported to be beneficial to their hosts. In my study I also found evidence suggesting seed-associated microbial communities are vertically transmitted from the mother plant to the offspring. Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus, and Tepidimonas were found across multiple generations of lentil seeds irrespective of the soil in which they were grown. These findings represent an important step toward the advancement of sustainable breeding and agricultural strategies to utilize microbial communities carried by seeds for their potential contribution to plant health and productivity.
DegreeDoctor of Philosophy (Ph.D.)
DepartmentFood and Bioproduct Sciences
SupervisorGermida, Jim; Helgason, Bobbi
CommitteeArcand, Melissa; Sharbel, Tim; Kochian, Leon; Vujanovic, Vladimir; Tanaka, Takuji
Copyright DateJune 2021
wheat, canola, lentil.