Draft genome sequencing of halotolerant bacterium Salinicola sp. DM10 unravels plant growth-promoting potentials

Abstract

In this study, strain DM10 was isolated from mangrove roots and characterized as a halotolerant plant growth-promoting bacterium. Strain DM10 exhibited the ability to solubilize phosphate, produce siderophore, show 1-aminocyclopropane-1-carboxylic acid deaminase activity, and hydrolyze starch. The rice plants subjected to a treatment of NaCl (200 mM) and inoculated with strain DM10 showed an improvement in the shoot length, root length, and dried weight, when compared to those exposed solely to saline treatment. The comprehensive genome sequencing of strain DM10 revealed a genome spanning of 4,171,745 bp, harboring 3626 protein coding sequences. Within its genome, strain DM10 possesses genes responsible for both salt-in and salt-out strategies, indicative of a robust genetic adaptation aimed at fostering salt tolerance. Additionally, the genome encodes genes involved in phosphate solubilization, such as the synthesis of gluconic acid, high-affinity phosphate transport systems, and alkaline phosphatase. In the genome of DM10, we identified the acdS gene, responsible for encoding 1-aminocyclopropane-1-carboxylate deaminase, as well as the amy1A gene, which encodes α-amylase. Furthermore, the genome of DM10 contains sequences associated with the iron (3⁺)-hydroxamate and iron uptake clusters, responsible for siderophore production. Such data provide a deep understanding of the mechanism employed by strain DM10 to combat osmotic and salinity stress, facilitate plant growth, and elucidate its molecular-level behaviors.

Keywords: DM10; Genome sequencing; Halotolerant bacterium; Plant growth-promoting; Salinicola.

Fig. 1

The effect of NaCl concentration on the growth of strain DM10 in nutrient broth. The cultures were incubated in a shaker, operating at 200 rpm and at a temperature of 30 °C. After 5-day incubation period, the degree of growth was checked by measuring optical density (OD) at 600 nm

Fig. 2

Qualitative estimation of plant growth-promoting traits of strain DM10. a Phosphate solubilization: The presence of a clear or halo zone in the area around the bacterial growth onto National Botanical Research Institute’s Phosphate growth agar medium containing 5 g L⁻¹ of tricalcium phosphate demonstrated the positive for phosphate solubilization b Qualitative estimation for ACC deaminase production: strain DM10 produced ACC deaminase activity (the left tube), when compared to control (the right tube); c Siderophore production: The development of an orange-yellow halo around the bacterial growth onto Chrome Azurol S (CAS) agar plate served as a clear indicator of siderophore production, and d Amylase production: The presence of a clear halo zone around the bacterial growth on the starch agar plates flooded with Lugol’s iodine solution served as a visual indicator of amylase production

Fig. 3

The effect of NaCl concentration to phosphate solubilization of strain DM10. The experiment was conducted in National Botanical Research Institute’s Phosphate broth at a temperature of 30 °C and spanned a duration of six days. Significant differences (p < 0.05) on each histogram are exhibited by the different letters (a, b, c, d, e, f, g, h, i, k, and l). Data are the average ± SD (n = 3)

Fig. 4

The effect of strain DM10 inoculation on rice growth in the presence of 200 mM NaCl. C, control plants without any treatment; C + NaCl, plants subjected to salt stress; DM10, plants inoculated with strain DM10; DM10 + NaCl, plants exposed to salt stress and simultaneously inoculated with the DM10 strain Significant differences (p < 0.05) on each histogram are exhibited by different letter (a, b, c, and d). Data are the average ± SD (n = 15)

Fig. 5

Phylogenetic tree derived from 16S rDNA gene sequences of strain DM10 and their taxonomic neighbors. The phylogenetic tree was constructed using the Neighbor-joining method within the MEGA 7.0 program. The evolutionary distance was calculated utilizing Kimura-2 parameters. The scale bar corresponds to 0.005 substitutions per nucleotide position

Fig. 6

Circular genome map of Salinicola sp. DM10 along with the highest homology Salinicola tammaricis F01T. The image is generated by BRIG package. Circles from inside to outside indicate the genome of Salinicola sp. DM10 (black), the GC content (black), the GC skew (purple/green), and the shared identity of Salinicola tamaricis F01^T

Fig. 7

Schematic representation salt tolerance of DM10 based on the genomic data. Strain DM10 possesses the trkAH and kdpABC genes responsible for K⁺ uptake systems; the nhaP2 encoding K⁺/H⁺ antiporter that prevents excessive intracellular K⁺; the nhaP, mnhCE, and mrpG genes which are responsible for Na⁺/H⁺ antiporter activity; all genes involved in ectoine synthesis from L-aspartate (lysC, asd, ectB, ectA, and ectC) and glycine betaine synthesis from choline (betA and betB); betT for high-affinity choline uptake and opuAB for glycine betaine/proline transport; and three genes encoding the mechanosensitive channel mscKLS, two genes responsible for outer membrane channel TolC and OmpH

Fig. 8

Schematic overview of plant growth-promoting gene clusters of DM10 based on the genomic data. The gene clusters for phosphate solubilization include gcd, pqqABCDE, phoB, phoR, pstSCAB-phoU, PitA/B, and PhoD. The gene clusters for starch metabolism consist of amy1A, treY, treZ, and treF. The gene clusters for uptake of ferric-siderophore complexes contain Fur, FhuBEF and efeB. The gene clusters for secretion systems involve Types I, II, IV and VI, tatABC, and secADEFGY. The acdS gene encodes for 1-aminocyclopropane-1-carboxylate deaminase that catalyzes the irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate