Cooperative Interplay Between PGPR and Trichoderma longibrachiatum Reprograms the Rhizosphere Microecology for Improved Saline Alkaline Stress Resilience in Rice Seedlings

Abstract

Soil salinization has become a major obstacle to global agricultural sustainability. While microbial inoculants show promise for remediation, the functional coordination between Trichoderma and PGPR in saline alkali rhizospheres requires systematic investigation. Pot studies demonstrated that while individual inoculations of Trichoderma longibrachiatum (M) or Bacillus aryabhattai (A2) moderately improved rice growth and soil properties, their co-inoculation (A2 + M) synergistically enhanced stress tolerance and nutrient availability-increasing available nitrogen (AN +28.02%), phosphorus (AP +11.55%), and potassium (AK +8.26%) more than either strain alone, while more effectively mitigating salinity (EC -5.54%) and alkalinity (pH -0.13 units). High-throughput sequencing further revealed that the A2 + M treatment reshaped the rhizosphere microbiome, uniquely enriching beneficial taxa (e.g., Actinomycetota [+9.68%], Ascomycota [+50.58%], Chytridiomycota [+152.43%]), and plant-growth-promoting genera (e.g., Sphingomonas, Trichoderma), while drastically reducing saline-alkali-adapted Basidiomycota (-87.96%). Further analysis identified soil organic matter (SOM), AN, and AP as key drivers for the enrichment of Chytridiomycota and Actinomycetota, whereas pH and EC showed positive correlations with Mortierellomycota, Aphelidiomycota, unclassified_k__Fungi, and Basidiomycota. Collectively, the co-inoculation of Trichoderma and PGPR strains enhanced soil microbiome structure and mitigated saline alkali stress in rice seedlings. These findings demonstrate the potential of microbial consortia as an effective bio-strategy for saline alkali soil amelioration.

Keywords: PGPR; Trichoderma-rhizobacteria synergy; rice growth promotion; saline alkali soil amelioration; soil microecology.

Figure 1

Microbial inoculant application enhanced rice tolerance to saline–alkali stress. (a) H₂O₂ content. (b) SOD (superoxide dismutase) activity. (c) POD (peroxidase) activity. (d) APX (ascorbate peroxidase) activity. (e) CAT (catalase) activity. (f) MDA content. Data are derived from three biological replicates (n = 3) and presented as mean ± standard error (SE). Different lowercase letters indicate statistically significant differences (p < 0.05) among treatments.

Figure 2

Effects of different inoculation treatments on physicochemical properties of rice rhizosphere soil. (a) pH. (b) Electrical conductivity (EC). (c) Soil organic matter (SOM). (d) Available phosphorus (AP). (e) Alkali-hydrolyzable nitrogen (AN). (f) Available potassium (AK). Data represent mean ± standard error (SE) from three biological replicates (n = 3). Different lowercase letters indicate significant differences among treatments (p < 0.05).

Figure 3

Microbial community diversity under different inoculation treatments. Alpha diversity indices for (a) soil bacteria and (b) soil fungi. *, **, and *** indicate significant differences among treatments at p < 0.05, p < 0.01, and p < 0.001, respectively.

Figure 4

Beta diversity based on PCoA analysis for (a) bacterial and (b) fungal communities.

Figure 5

Effects of different inoculation treatments on the composition of bacterial (a,c) and fungal (b,d) phyla in rice rhizosphere soil.

Figure 6

Identification of characteristic dominant microbial genera in different saline–alkali soil treatments using LEfSe analysis. (a) Bacterial communities. (b) Fungal communities.

Figure 7

Interactions between environmental factors and microbial communities. (a) db-RDA of bacterial communities. (b) db-RDA of fungal communities. (c) Heatmap showing correlations between the top 10 bacterial phyla and environmental factors. (d) Heatmap showing correlations between the top 10 fungal phyla and environmental factors. Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001.