Genetic and Soil Influences on the Grapevine Rhizosphere Microbiome

Authors

Lauren M. Quackenbush, University of Nebraska-LincolnFollow

First Advisor

Michael Kaiser

Committee Members

Rhae Drijber, Keenan Amundsen, Caro Córdova

Date of this Version

4-2025

Document Type

Thesis

Citation

A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree of Master of Science

Major: Agronomy

Under the supervision of Professor Michael Kaiser

Lincoln, Nebraska, April 2025

Comments

Copyright 2025, Lauren M. Quackenbush. Used by permission

Abstract

In vineyard cropping systems, the rhizosphere microbiome arises through recruitment and filtering of the bulk soil microbiome shaped over time by soil carbon and nitrogen, climate, pH and historical legacies of vineyard management. The recruitment and filtering steps occur under the genetic influences of rootstock and scion that together drive variability in rhizosphere microbiome diversity and composition.

This study compares rhizosphere microbiomes of four Pinot Noir blocks under two rootstocks (101-14 and 420A) and four scions (777, 828, Calera, Mt. Eden). Core microbiomes were consistent across all replicates. The most abundant bacterial phyla were Actinobacteriota, Proteobacteria, and Acidobacteriota (respective relative abundances = 27.14%, 24.71%, 8.73%); and the most abundant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota (respective relative abundances = 45.40%, 29.92%, and 6.44%).

Alpha diversity was best expressed in bacterial data with Faith’s Phylogenetic Diversity (PD) and Shannon index. Rootstocks 101-14 and 420A were most significantly different in bacterial Faith’s PD (p-value = 0.037373). Marginally significant differences (p-values = 0.049535) in bacterial diversity were found between rootstock x scion pairs 420A x 777, 101-14 x 828, and 101-14 x Calera. Fungal microbiome differences were better captured in beta diversity assessed using Principal Coordinate Analysis (PCoA) and three dissimilarity indices: Bray—Curtis, Weighted UniFrac, and Unweighted UniFrac.

Significant differences in taxonomic abundance were identified at the phylum, class, and order levels. Rootstock 420A accumulated more plant growth promoting (PGP) taxa, including the bacterial orders Azospirillales 507929, Bacillales B 306089, and Nitrospirales; and the arbuscular mycorrhizal fungi (AMF) order Entrophosporales. Rootstock x scion pair 101-14 x 828 had a higher abundance of the fungal order Dothideomycetes, order Incertae Sedis, which is positively correlated to soil organic carbon (SOC) content.

Additional research would confirm the presence of specific beneficial microbes across several years of data, so information could be used to make replanting decisions that maximize microbial benefits. Future research would use metagenomics and metabolomics to better understand microbiome composition and functionality, and develop inoculants that mimic the natural rhizosphere microbiome, providing more successful inoculation and effective delivery of ecosystem services like C sequestration, PGP, biocontrol of pathogens, and nutrient cycling.

Advisor: Michael Kaiser