Abstract

Many plants are highly sensitive to salt in the soil, and their growth and yield can be greatly hindered by as little as less than 1% salt concentration in the soil. Additionally, soil salinity is a growing issue globally and affects significant areas in Utah. Halophytes are plants that are adapted to grow in saline soils and have been widely studied for their physiological and molecular characteristics, but little is known about their associated microbiomes. Bacteria were isolated from the rhizosphere and as root endophytes of Salicornia rubra, Sarcocornia utahensis, and Allenrolfea occidentalis, three native Utah halophytes. Several strains of halophilic bacteria have been isolated and screened for the ability to stimulate plant growth in saline conditions despite the high salt concentrations. Halomonas, Bacillus, and Kushneria species were consistently isolated both from the soil and as endophytes from roots of all three plant species at all collection times. Of the isolates tested for the ability to stimulate growth of alfalfa under saline conditions, Halomonas and Kushneria strains stimulated plant growth in the presence of 1% NaCl. The same bacteria used in the inoculation were recovered from surface sterilized alfalfa roots, indicating the ability of the inoculum to become established as an endophyte. This raises the question of whether these plant associated halophilic isolates contain genes that aid in plant growth promotion. We are interested in genomic sequencing of our Halomonas and Kushneria strains and performing genomic analysis to determine if there is a difference in genes between plant associated and non-plant associated halophilic isolates. We explored the hypothesis that certain bacterial properties have been selected for to aid plant growth. This was accomplished by performing whole genome sequencing of 26 Kushneria and Halomonas strains, both plant and non-plant associated. These strains came from freezer stocks of previously collected isolates as well as field trips to collect more samples. Halophilic bacteria were isolated from bulk soil, rhizosphere, and halophyte tissues (root and shoot tissues). The non-plant associated (bulk soil) halophilic Kushneria and Halomonas strains aided in determining if there are specific bacterial genes that are expressed in plant associated strains. Whole genome sequencing of the isolates was performed on the Oxford Nanopore platform. The sequence data was then assembled and annotated. The genomes were then included in a genome wide association study was performed. The results from the GWAS show that there is not a significant difference between plant and non-plant associated isolates, disproving our hypothesis. The results also show that few known genes for phytohormone synthesis were present in the pangenome, highlighting the need for further research to determine how these halophilic isolates aid in plant growth promotion in saline soils.

Degree

College and Department

Life Sciences; Microbiology and Molecular Biology

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