Achromobacter sp. FB-14 harboring ACC deaminase activity augmented rice growth by upregulating the expression of stress-responsive CIPK genes under salinity stress

Abstract

Soil salinity is one of the major plant growth and yield-limiting constraints in arid and semi-arid regions of the world. In addition to the oxidative damage, increasing salt stress is associated with elevated cellular ethylene levels due to the synthesis of 1-aminocyclopropane-1-carboxylic acid (ACC) in large amounts. The objective of the current study was to elucidate the inoculation effect of an ACC deaminase (ACCD)-producing phytobeneficial strain Achromobacter sp. FB-14 on rice plants to alleviate the salinity effects by upregulation of the stress-responsive CIPK genes. The strain FB-14 was isolated by using nutrient agar medium at 855 mM NaCl concentration and it was taxonomically identified as Achromobacter sp. with more than 99% 16S rRNA gene sequence similarity with many Achromobacter species. The strain FB-14 demonstrated substantial in vitro potential for ACCD activity, synthesis of indole compounds, and phosphate solubilization up to 100 mM NaCl concentration in the culture medium. The gene corresponding to ACCD activity (acdS) was amplified and sequenced in order to confirm the inherent enzyme activity of the strain at a molecular level. The rifampicin-resistant derivative of strain FB-14 was recovered from the rice rhizosphere on antibiotic medium up to 21 days of sowing. Moreover, the strain FB-14 was inoculated on rice plants under salinity and it not only enhanced the growth of rice plants in terms of root and shoot length, and fresh and dry weight, but also upregulated the expression of stress-responsive CIPK genes (OsCIPK03, OsCIPK12, and OsCIPK15) according to the results of qRT-PCR analysis. To the best of our knowledge, this is the first report deciphering the role of plant-beneficial Achromobacter strain relieving the rice plants from salt stress by promoting the growth and enhancing the expression of stress-responsive CIPK genes.

Keywords: ACC deaminase; Gene expression; PGPR; Rice; Salt tolerance.

Fig. 1

Plant-beneficial properties shown by Achromobacter sp. FB-14 in terms of ACCD (a), synthesis of indole-related compounds (b), and phosphate solubilization (c)

Fig. 2

Phylogenetic tree of Achromobacter sp. FB-14 with the type strains of genus Achromobacter. The evolutionary history was inferred using the neighbor-joining method. The percentages (≥ 50%) of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site

Fig. 3

Growth curves of wild-type and derivative Achromobacter sp. FB-14 strains (a) and population density of the derivative strain recovered from rice rhizosphere up to 21 days of growth (b)

Fig. 4

Rice growth as influenced by the inoculation of Achromobacter sp. FB-14 at different NaCl concentrations; root length (a), shoot length (b), root fresh wt. (c), shoot fresh wt. (d), root dry wt. (e), and shoot dry wt. (f). Error bars represent the standard deviations (n = 3) and different letters show the significant difference of mean values (P ≤ 0.05)

Fig. 5

The relative expression of OsCIPK03 (a), OsCIPK12 (b), and OsCIPK15 (c) genes. The expression of these genes was normalized with the housekeeping gene actin1 gene. The fold increase is relative to the expression in the plants inoculated with Achromobacter sp. FB-14_rif with the non-inoculated plants