Can Phytoremediation-Induced Changes in the Microbiome Improve Saline/Sodic Soil and Plant Health?

• Published in: Agronomy (Basel) Vol. 14; no. 1; p. 29
• Main Authors: Neupane, Achal, Jakubowski, Duncan, Fiedler, Douglas, Gu, Liping, Clay, Sharon A., Clay, David E., Lee Marzano, Shin-Yi
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01-01-2024
• Subjects: Alopecurus arundinaceus; Bacteria; Biological diversity; Bioremediation; Buckwheat; Clustering; Comparative analysis; Composition; Correlation analysis; Endophytes; Ethylenediaminetetraacetic acid; Fungi; Gas chromatography; Germination; metabolite; Metabolites; microbiome; Microbiomes; Microorganisms; Osmotic stress; Phytoremediation; Plant growth; Plant species; Polyamines; Rhizosphere; Saline soils; saline/sodic soil; Salinity; Seed germination; seed inoculum; Sodic soils; Sodium chloride; Soil acidity; Soil characteristics; Soil chemistry; Soil microbiology; Soil microorganisms; Soil pH; Soil salinity; Soil types; Soils; Soils, Salts in; United States > US
• ISSN: 2073-4395; 2073-4395
• DOI: 10.3390/agronomy14010029

Increasing soil salinity and/or sodicity is an expanding problem in the Northern Great Plains (NGP) of North America. This study investigated the impact of phytoremediation on the soil microbiome and if changes, in turn, had positive or negative effects on plant establishment. Amplicon sequencing and gas chromatograph/mass spectrometer analysis compared root metabolites and microbial composition of bulk vs. rhizosphere soils between two soil types (productive and saline/sodic). Beta-diversity analysis indicated that bacterial and fungal communities from both the bulk and rhizosphere soils from each soil type clustered separately, indicating dissimilar microbial composition. Plant species also influenced both root-associated bacterial and fungal communities with separate clustering of operational taxonomic units (OTUs) identified. Canonical correlation analysis (CCA) found a clear association between specific soil characteristics and soil types. Bacterial and fungal OTUs from productive soil were correlated with greater %Ca Sat, %H Sat, and potassium (ppm), especially for OTUs differentially enriched in productive soil. Both bacterial and fungal OTUs from saline/sodic soil are associated with increased Ca (ppm), soil pH, %Na Sat and CEC. Metabolite analysis showed that kochia (Bassia scoparia) roots from the saline/sodic soil had a 4.4-fold decrease in pantothenate accumulation (p = 0.004). Moreover, two endophytic bacterial isolates, a Bacillus spp. and a previously uncultured halophile, isolated from creeping foxtail (Alopecurus arundinaceus) grown in saline/sodic soil and used as buckwheat (Fagopyrum esculentum) seed inoculants, significantly increased seed germination by >30% and vigor index by 0.2 under osmotic stress (0.2 M NaCl) (p < 0.05). This study revealed the importance of soil, root-associated, and endophytic microbiomes. Using native microbes as seed inoculants may help in establishment and growth of species used for phytoremediation of saline/sodic soil.