Metagenomic analysis of cucumber rhizospheric microbiome provides insights into NaHCO3 stress mitigation by Rheinheimera pacifica NYJ

Abstract

Background: NaHCO3 in soil leads to alkalinization and causes stress in plants, thus hindering agricultural sustainability. A strain NYJ was identified as Rheinheimera pacifica and applied into cucumber-planted soil to mitigate NaHCO3 stress in this study. We aimed to detect the taxonomy and functional potential of rhizospheric microbiome affected by NaHCO3 stress and NYJ application, obtaining NaHCO3-tolerant microbes and exploring one mechanism underlining NaHCO3 stress mitigation by NYJ application.Results: The strain NYJ grew well under 0.01-0.06 g L-1 NaHCO3 and had plant growth-promoting capacity. Application of NYJ into NaHCO3-contaminated and cucumber-planted soil improved plant growth, increased relative water contents and osmotic potential of leaves, and decreased malonaldehyde and hydrogen peroxide contents in seedlings, mitigating NaHCO3 stress in cucumber. In cucumber rhizospheric soil, Proteobacteria, Actinobacteria, and Bacteroidetes of microbes were dominant phyla with 69, 17, and 6% of total abundance. To respond to NaHCO3 stress, 669 species and 208 genera of microbes were enriched in rhizospheric soil, while 190 sodium ion-related genes, 1242 osmotic stress-related genes, and 121 other stress-related genes from microbial genera including Pseudomonas showed the increased abundances. Under NaHCO3 stress, 26 microbial genera were distributed in connectors, the interaction network of rhizospheric microbes was changed, and soil enzyme activities were decreased. When NYJ being applied into the NaHCO3-contaminated soil, 1327 species and 487 genera of microbes were enriched than those under NaHCO3 stress alone. Meantime, soil enzyme activities were increased, while 2238 symbiont- and immune-related genes and 2434 plant growth-promoting genes including 16 genes encoding chitinase had the elevated abundances in microbial genera. Moreover, NYJ negatively interacted with one bacterial genus and positively interacted with 3 microbial genera under NaHCO3 stress. As a result, 25 bacterial genera were distributed in connectors, and microbial interaction network in rhizospheric soil was different from the one caused by NaHCO3 stress alone.Conclusions: 669 NaHCO3-tolerant species and 208 NaHCO3-tolerant genera of microbes were identified. NYJ application affected microbial community structure and interaction network in rhizospheric soil, increased the abundances of genes related to symbiont, immune, and plant growth-promoting traits in microbes, and activated soil enzymes, thereby mitigating NaHCO3 stress in cucumber.1 These authors contributed equally to this work.