Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Biology and Microbiology

First Advisor

Shinyi Marzano


Inoculation, Metabolite, Microbiome, Nitrogen-Cycle, Phytoremediation, Salinity


Increasing levels of salinity in once-viable lands for crop production is a serious and growing problem in the Northern Great Plains. The objectives of this study were to determine the effects of saline soil on the microbial composition of plant roots and bulk soil, to measure metabolic changes in plant roots from saline soil, to determine the viability of root-associated microbes as inoculants to increase stress tolerance in plants, as well as determine the impact of saline soil on nitrogen cycling genes linked to greenhouse gas production. This study hypothesizes that high soil salinity levels have a significant impact on the microorganisms found within roots and bulk soil, root-associated microbes can be used to improve salt stress tolerance in plants, and soil salinity increases genes responsible for greenhouse gases related to the nitrogen cycle. This study supports that levels of specific metabolites can vary significantly from samples gathered in roots from saline soil and productive soil. This is confirmed through a significant 4.4-fold change of the regulation of pantothenate (P=0.004). The methods from which these data were generated can be used in future studies to find the metabolomic differences in plants undergoing abiotic stress from salinity. The microbiome analysis proved that there are significant differences in alpha diversity, beta diversity, and overall taxa within both root and bulk soil samples between saline and productive soil environments. Approximately 100,000 bacterial and fungal taxa were identified within the gathered samples. An analysis of composition of microbiome (ANCOM) was done to each sample set which resulted in the discovery of nearly 100 differentially abundant species present in saline soil. These differentially abundant species could have plant growth promoting capabilities as well as give an indication of improved soil health through phytoremediation. Some of the taxa that were differentially abundant in saline soil include taxa known to promote plant growth during abiotic stress such as Halomonas and Sphingomonas. There was also a decreased amount of differentially abundant taxa in saline soil belonging to ascomycetes, which are known fungal pathogens. The information provided from the ANCOM between two consecutive years may indicate signs of phytoremediation by an increase in fungal taxa known to promote plant growth. These data provide a baseline for future experiments using microbial inoculants and root-associated microbes to enhance phytoremediation and plant growth. Additionally, the root-associated microbe inoculation portion of this study involved the isolation of eight bacterial species from a sample of creeping meadow foxtail (Alopecurus arundinaceus) grown in saline soil. These bacterial species were used as inoculants on buckwheat (Fagopyrum esculentum) challenged with a 0.2M NaCl solution. Two of the eight species showed significant improvement in the germination of the buckwheat seeds. Only 5.33% of control buckwheat seeds germinated under the saline stress, however; the two effective inoculants improved germination percentage to 38.67% and 45.95% (P=0.0002). The results show the promise behind using isolated root-associated microbes as inoculants to improve seed germination in stressful saline conditions. The last experiment in this study was done to identify the negative effects saline soil can have on the environment. This study involved the use of qPCR to identify changes in concentrations of genes involved in the nitrogen cycle in samples gathered from saline and productive soil. Overall, five nitrogen cycling genes were tested in this experiment: nirS, nirK, nosZ, CrenamoA, and Bac-amoA. This study revealed that the nirS gene, which is responsible for the release of nitrous oxide (N2O), which is an important greenhouse gas, increased in saline soil by 42-folds compared to that from productive soil. (P=0.03). The gene responsible for the reduction of N2O, nosZ, was not significantly higher in saline soil (P=0.3). These results indicate that the level of N2O released into the air is likely caused by increased N2O in saline soil. The results of these studies support the hypothesis of the study and provide helpful information for the research determining the effects of saline soil. Understanding the impact of saline soil on plant growth as well as the effects on the microbiome present is crucial to understanding how to reduce the effects of salt stress on plants. The results provide background knowledge and starting points for future studies on phytoremediation of saline soil and provide evidence on specific interactions and effects of salt stress and saline soil.

Number of Pages



South Dakota State University


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