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Comprehensive genome analysis of Pseudomonas sp. SWRIQ11, a new plant growth-promoting bacterium that alleviates salinity stress in olive

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Abstract

The study presents the genome analysis of a new Pseudomonas sp. (SWRIQ11), which can alleviate salinity stress effects on growth of olive seedlings in greenhouse study. The strain SWRIQ11 can tolerate salinity up to 6%, produce siderophores, indole acetic acid (IAA), aminocyclopropane-1-carboxylate (ACC) deaminase, and has the phosphate-solubilizing capability. The SWRIQ11 genome contained an assembly size of 6,196,390 bp with a GC content of 60.1%. According to derived indices based on whole-genome sequences for species delineation, including tetra nucleotide usage patterns (TETRA), genome-to-genome distance (GGDC), and average nucleotide identity (ANI), Pseudomonas sp. SWRIQ11 can be considered a novel species candidate. The phylogenetic analysis revealed SWRIQ11 clusters with Pseudomonas tehranensis SWRI196 in the same clade. The SWRIQ11 genome was rich in genes related to stress sensing, signaling, and response, chaperones, motility, attachments, colonization, and enzymes for degrading plant-derived carbohydrates. Furthermore, the genes for production of exopolysaccharides, osmoprotectants, phytohormones, and ACC deaminase, ion homeostasis, nutrient acquisition, and antioxidant defenses were identified in the SWRIQ11 genome. The results of genome analysis (identification of more than 825 CDSs related to plant growth-promoting and stress-alleviating traits in the SWRIQ11 genome which is more than 15% of its total CDSs) are in accordance with laboratory and greenhouse experiments assigning the Pseudomonas sp. SWRIQ11 as a halotolerant plant growth-promoting bacterium (PGPB). This research highlights the potential safe application of this new PGPB species in agriculture as a potent biofertilizer.

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Data availability

All analyzed data of this study are presented in the paper and its supplementary data files. The whole genome shotgun project was deposited at DDBJ/ENA/GenBank under the accession number JAKNQY000000000. Additionally, further information about the bacterial assembly is accessible in the NCBI database with BioProject ID: PRJNA803818 and BioSample ID: SAMN25688536.

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Acknowledgements

We are grateful to Soil and Water Research Institute for providing Pseudomonas sp. SWRIQ11 and National Institute of Genetic Engineering and Biotechnology for conducting part of the experiments there.

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Correspondence to Fatemeh Mohammadiapanah or Sajjad Sarikhan.

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The authors declare that they have no conflict of interest. This research contained no work on animal or tissue samples.

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Zamanzadeh-Nasrabadi, S.M., Mohammadiapanah, F., Sarikhan, S. et al. Comprehensive genome analysis of Pseudomonas sp. SWRIQ11, a new plant growth-promoting bacterium that alleviates salinity stress in olive. 3 Biotech 13, 347 (2023). https://doi.org/10.1007/s13205-023-03755-0

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  • DOI: https://doi.org/10.1007/s13205-023-03755-0

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