The restoration of submerged macrophytes is commonly limited by abiotic stress. Here, we isolated PGPR strains from the rhizosphere of submerged macrophytes using ACC deaminase selective medium, and evaluated their growth promoting effects on Vallisneria natans (V. natans) under low light intensity and (or) high sediment organic matter load, and also explored the indigenous microbiome response of V. natans seedlings to PGPR inoculants. Ten isolates were chosen from the 252 isolated strains based on the ACC deaminase activity and the production of IAA and siderophore. M1 (Pseudomonas vancouverensis) and E15 (Enterobacter ludwigii) had the best growth promoting effects under low light stress and under double stress of low light and high sediment organic matter load, and the shoot height increased by 36% and 46%, respectively. The results of indigenous microbiome analysis showed that PGPR inoculants could regulate the relative abundance of unclassified_f_Enterobacteriaceae and improve the α-diversity of the rhizosphere bacterial community. Under high sediment organic matter load, inoculation of PGPR obviously shifted the β-diversity of rhizosphere bacterial communities to promote the early growth of V. natans. This study expands the application of plant–microbe interaction in the field of freshwater ecological restoration.

Low light intensity and high sediment organic matter (SOM) conditions coexist recurrently in aquatic ecosystems, which affects submerged macrophyte re-habilitation. In this greenhouse study, four light intensity levels (10% [natural light intensity], 30%, 60%, and 100%) and three initial SOM loads (11% [measured as the loss on ignition], 17%, and 25%) were applied to explore the effects of their interactions on the growth of Vallisneria natans (V. natans). Two-way ANOVA revealed the effects of interactions between light intensity and SOM load on the growth characteristics of V. natans. Multiple linear regression models indicate that the dry weights and root lengths exhibited a single maximum as the SOM load increased. The inhibitory effect of the sediment on the growth of V. natans could be alleviated by increasing the light intensity in a certain SOM range. However, the inhibited growth of V. natans was not alleviated by enhancing the light intensity at a 25% SOM load. We explored a potential mechanism for this phenomenon based on ammonium (NH4+) toxicity regulation. Structural equation modeling indicates that enhanced light intensity could directly reduce sediment NH4+ contents or reduce them indirectly by decreasing the abundances of bacterial functional genes associated with NH4+ formation. Subsequently, lower sediment NH4+ content increased the plant dry weight, thereby facilitating the removal of nitrogen and phosphorus from the sediment. Therefore, enhancing the light intensity over a wide range of SOM loads resulted in the restoration of submerged macrophytes, whereas reducing SOM loads could be performed in high SOM conditions to improve the restoration of submerged macrophytes.