A Salt-Tolerant Streptomyces paradoxus D2-8 from Rhizosphere Soil of Phragmites communis Augments Soybean Tolerance to Soda Saline-Alkali Stress

Abstract

Soil salinity and alkalization limit plant growth and agricultural productivity worldwide. The application of salt-tolerant plant growth-promoting rhizobacteria (PGPR) effectively improved plant tolerance to saline-alkali stress. To obtain the beneficial actinomyces resources with salt tolerance, thirteen isolates were isolated from rhizosphere saline and alkaline soil of Phragmites communis. Among these isolates, D2-8 was moderately halophilic to NaCl and showed 120 mmol soda saline-alkali solution tolerance. Moreover, the plant growth-promoting test demonstrated that D2-8 produced siderophore, IAA, 1-aminocyclopropane-1-carboxylate deaminase (ACCD), and organic acids. D2-8 showed 99.4% homology with the type strain Streptomyces paradoxus NBRC 14887^T and shared the same branch, and, therefore, it was designated S. paradoxus D2-8. Its genome was sequenced to gain insight into the mechanism of growth-promoting and saline-alkali tolerance of D2-8. IAA and siderophore biosynthesis pathway, genes encoding ACC deaminase, together with six antibiotics biosynthesis gene clusters with antifungal or antibacterial activity, were identified. The compatible solute ectoine biosynthesis gene cluster, production, and uptake of choline and glycine betaine cluster in the D2-8 genome may contribute to the saline-alkali tolerance of the strain. Furthermore, D2-8 significantly promoted the seedling growth even under soda saline-alkali stress, and seed coating with D2-8 isolate increased by 5.88% of the soybean yield in the field. These results imply its significant potential to improve soybean soda saline-alkali tolerance and promote crop health in alkaline soil.

Keywords: Actinomycetes; Phragmites communis; plant growth promotion; rhizosphere; soda saline-alkali tolerance.

Fig. 1

a) Stress tolerance of strain D2-8 in different concentration of salt and b) saline-alkali solutions. SA represents saline and alkaline solution, which contains NaCl, Na₂CO₃, NaHCO₃, and Na₂SO₄ (molar ratio 1:1:9:9).

Fig. 2

Morphological characteristics of strain D2-8 observed by scanning electron microscopy.

Fig. 3

Neighbor-joining tree of strain D2-8 and the related species of the genus Streptomyces based on the 16S rRNA gene sequences. The out-group used was Mycobacterium tuberculosis H37Rv^T. The stability of the topology of the phylogenetic tree was assessed by the bootstrap method with 1000 repetitions. Only bootstrap values above 50% (percentages of 1000 replications) are indicated. Scale bar represents 0.01 nucleotide substitutions per site.

Fig. 4

a) The distribution of subsystems of the D2-8 genome annotated through the RAST webserver and b) stress response genes of D2-8 involved in the production and uptake of choline and glycine betaine.

Fig. 5

The growth promotion effect of D2-8 under normal conditions (a, b, c) and saline-alkali stress (d, e, f) on soybean. For a), b), c), control group: water treatment, 10⁸ D2-8: the D2-8 spore concentration of 10⁸ CFU/ml; 10⁷ D2-8: the D2-8 spore concentration of 10⁷ CFU/ml; 106 D2-8: the D2-8 spore concentration of 106 CFU/ml. For d), e), f), control group: normal condition, SA group: saline-alkali stress treatment, SA+D2-8: D2-8 treatment under saline-alkali stress condition; Plants height, roots length, and fresh weight of roots and aboveground were analyzed using unpaired t-tests (n = 15 plants). The symbols * and ** indicate p values 0.05 and 0.01.