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Date Available

8-15-2028

Year of Publication

2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

College

Agriculture, Food and Environment

Department/School/Program

Plant and Soil Sciences

Faculty

Luke Moe

Faculty

Arthur Hunt

Abstract

Plants exist as holobionts, shaped jointly by their own genome and the microbiome they host, and the seed marks a key point in that relationship: it closes one round of microbial assembly within the parent plant and opens the next in the offspring. Endophytic bacteria carried inside maize (Zea mays L.) seed are inherited across generations and can influence germination and seedling vigor, yet how this community varies across space, changes across seed development and storage, and is distributed within kernel tissue remain open questions. This dissertation addresses these three gaps through integrated studies that: 1) characterize the seed endophytic community across a nested spatial hierarchy from kernel to field; 2) track its diversity, composition, and assembly across reproductive and post-harvest stages; and 3) localize it within kernel tissues using fluorescence in situ hybridization and confocal laser scanning microscopy. Hybrid DeKalb 70-27 maize was sampled from two central Kentucky fields and profiled by 16S rRNA amplicon sequencing and culture-based isolation across kernel, ear, transect, and field scales. Field identity explained little compositional variance (R² = 0.054) compared to variation among ears (R² = 0.265), showing that plant-to-plant differences, not geography, drive seed endophyte composition. Assembly at every spatial scale was dominated by stochastic processes, chiefly homogenizing dispersal (55–64% of comparisons), around a small persistent core of six Amplicon Sequence Variants (ASVs), dominated by three genera Stenotrophomonas, Brevundimonas, and Bacillus. Culture-based isolation recovered 97 isolates across 15 genera, dominated by Bacillus and Stenotrophomonas. In the hybrid DKC111-35RIB, the community was tracked across six reproductive stages and a post-harvest storage stage (R1–R7) by amplicon sequencing. Diversity rose steadily through development (mean Shannon diversity from 0.41 to 3.01), and developmental stage explained 47.1% of compositional variance. The harvest-to-storage transition (R6 to R7), over which seed moisture fell from 28.6% to 10.4%, accounted for 22.6% of variance and marked a shift from stochastic, dispersal-dominated assembly to deterministic selection. Using FISH-CLSM with a Cy3-labeled EUBmix probe and NON338 negative controls, bacteria were localized predominantly within the starchy endosperm as discrete puncta, reproducibly across kernels, with occasional signal in embryo intercellular spaces. No bacterial signal was detected in the aleurone layer or pericarp. Together, these findings show that the maize seed endophytic community is shaped more by plant-to-plant variation than by geography, assembled through stochastic dispersal that gives way to deterministic selection during storage, and concentrated within the endosperm rather than spread uniformly across kernel tissues. These results advance both the basic understanding of seed microbiome inheritance and the applied potential of seed-borne bacteria in sustainable maize production.

Digital Object Identifier (DOI)

https://doi.org/10.13023/etd.2026.423

Archival?

Archival

Funding Information

This study was supported by the Harold R. Burton Endowed Professorship in Plant Biochemistry held by Dr. Luke Moe, 2023-2026

 

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