Can phytoremediation-induced changes in the microbiome improve saline/sodic soil and plant health?

Authors: NEUPANE, ACHAL - South Dakota State University; JAKUBOWSKI, DUNCAN - South Dakota State University; FIEDLER, DOUGLAS - Natural Resources Conservation Service (NRCS, USDA); GU, LIPING - South Dakota State University; CLAY, SHARON - South Dakota State University; CLAY, DAVID - South Dakota State University; Marzano, Shin-Yi

Submitted to: Agronomy Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2023
Publication Date: 12/21/2023
Citation: Neupane, A., Jakubowski, D., Fiedler, D., Gu, L., Clay, S., Clay, D., Marzano, S.L. 2023. Can phytoremediation-induced changes in the microbiome improve saline/sodic soil and plant health?. Agronomy Journal. 14(1). Article 29. https://doi.org/10.3390/agronomy14010029.
DOI: https://doi.org/10.3390/agronomy14010029

Interpretive Summary: The Northern Great Plains are where a vast number of American crops are grown. Unfortunately, increased concentration of salt within the soil is reducing plant yields on these fields. This increase in salinity has both negative environmental and economic factors. The recommended chemical strategies for solving these issues are often ineffective. Fortunately, there could be a biological solution to this problem using the metabolites and endophytes found within the roots of certain salt tolerant plant species. In this research, we focused on four plant species, each grown in both saline/sodic soil and neighboring unaffected soil as controls. These plants include Kochia, Foxtail, Perennial Grass, and Corn. In order to determine whether or not there are metabolites and endophytes that can increase the salt tolerance of a plant species, three inter-related objectives were achieved. First, the effects of saline/sodic soil on soil and plant microbiomes were determined. Second, the effects of saline/sodic soil on plant root metabolites were determined. Lastly, the endophytes isolated from salt-tolerant weedy species were evaluated as inoculum to improve the establishment of desirable plant species. Completing these three objectives allowed us to increase the salt tolerance of favorable plant species. Both culture-based and non-culture-based approaches were used to complete these objectives. In order to determine the effect that saline/sodic soil has on a plant’s microbiome. We extracted DNA from the four plant species, and soil from which they were sampled for 16s rRNA amplicon sequencing. From this we were able to analyze and determine differences in the diversity and abundance of the microbiome associated with these plants and the soil. We proved our hypothesis that specific microbial taxa are enriched in plants that are grown in saline/sodic soil compared to the control and demonstrated bacterial isolates from root can be developed as inoculum to enhance seed germination.

Technical Abstract: Increasing levels of salinity/sodicity in crop production areas is a serious and growing problem in the Northern Great Plains. This two-year study characterized the microbial composition of bulk vs rhizosphere soil from productive vs saline/sodic soils upon the introduction of perennial plants, and measured metabolic changes in plant roots. Root-associated microbes from creeping foxtail (Alopecurus arundinaceus) plants grown in the saline/sodic soil were isolated and used as seed inoculants to determine their influence on seed germination under osmotic stress. Roots from the saline/sodic soil had a 4.4-fold decrease in the regulation of pantothenate (P=0.004). Microbiomes differed in alpha diversity, beta diversity, and overall taxa within both rhizosphere and bulk soils between the two soils with nearly 100 species differing in abundance between the soils. Bacterial taxa enriched in saline/sodic soil included Halomonas and Sphingomonas, known to promote plant growth during abiotic stress. Ascomycetes, likely the fungal pathogens, decreased in saline/sodic soil. During the two years of perennial plant establishment, based on the analysis of composition of microbiome (ANCOM), fungal taxa known to promote plant growth also increased in the saline/sodic soil, indicating positive impacts of phytoremediation. Buckwheat (Fagopyrum esculentum) seeds challenged with 0.2M NaCl solution were inoculated separately with eight bacterial species isolated from the creeping foxtail roots. Two species improved buckwheat seed germination to about 40% (P=0.002) (5% baseline). Phytoremediation appears to be changing the microbiome of saline/sodic areas and inoculating seed with specific root-associated microbes isolated from these areas may improve seed germination, and ultimately plant establishment.