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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(4): 487-489

https://doi.org/10.48022/mbl.2409.09016

Received: September 30, 2024; Revised: November 8, 2024; Accepted: November 15, 2024

Complete Genome Sequence of Priestia aryabhattai KNU10, a Stress-Tolerant Strain with Plant Growth-Promoting Rhizobacteria (PGPR) Activity

HeeJoo Hwang1†, Min-Ji Kim2†, and Jae-Ho Shin1,2,3*

1Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
2Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
3Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea

Correspondence to :
Jae-Ho Shin       jhshin@knu.ac.kr

†These authors contributed equally to this work.

Abstract

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This paper presents the complete genome of Priestia aryabhattai strain KNU10, which isolated from soil. The genome consists of a single chromosome with a total length of 5,154,607 bp and a GC content of 38.5%. In addition, strain KNU10 harbors various stress-tolerant and phosphate-solubilizing genes associated with promoting plant root growth.

Keywords: Priestia aryabhattai, whole-genome sequencing, PGPR, stress-tolerant

Body

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Priestia aryabhattai (formerly Bacillus aryabhattai) is a Gram-positive, rod-shaped bacterium that produces various plant growth-promoting metabolites such as indole acetic acid (IAA), jasmonic acid, and gibberellic acid. P. aryabhattai also tolerates various stresses and protects the crops from fungal diseases [1−3].

In this study, the strain KNU10 of P. aryabhattai was isolated from soil in a greenhouse of Kyungpook National University (Republic of Korea). For bacterial isolation, 1 g of soil was serially diluted and plated on potato dextrose agar (Difco, USA) plates, and incubated at 30℃ for 72 h. Genomic DNA was extracted using a standard phenol-chloroform-isoamyl alcohol DNA extraction protocol [4]. The extracted DNA was quantified by Qubit 2.0 fluorometer (Thermo Fisher Scientific, USA), and the size of DNA was identified by 4150 TapeStation system (Agilent, USA) at the KNU NGS Core Facility (Republic of Korea). Sequencing was performed on the PacBio RSII platform (Pacific Biosciences, USA) at Macrogen Inc.,(Republic of Korea).

De novo assembly was performed with Hierarchical Genome Assembly Process (HGAP, v4.0) in Pacific Bioscience SMRTLink (v.7.0.0) [5]. The assembled genome of P. aryabhattai KNU10 consists of 5,154,607 bp with 154× coverage. Prokaryotic genome annotation tool Prokka (v.1.1.1) was used to identify the genome of P. aryabhattai KNU10 [6], and Proksee was used for visualization of the whole genome sequence (Fig. 1) [7]. For more accurate annotation, the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) [8] and Rapid Annotations Systems Technology (RAST) server were used [9]. As a result of PGAP analysis, the chromosome of strain KNU10 is consisted of 5,406 protein-coding genes, 136 tRNA genes, and 43 rRNA genes (Table 1). Strain KNU10 harbors genes (norQ, norD, sodA, sodC, and katE) which are expected to withstand nitrosative and oxidative stress, and these genes are included in the nitrosative and oxidative stress subsystems of the RAST server. Furthermore, the presence of the trpC gene, categorized in the tryptophan synthesis, which produces a precursor to the plant root growth-promoting hormone IAA, suggests potential PGPR activity. Additionally,, the pqq-gdh gene, located in the pyrroloquinoline quinone biosynthesis subsystem, and the phoA gene, part of the phosphate metabolism subsystem, function to solubilize insoluble phosphate in the soil, making it available for plant uptake (Fig. 2). OrthoANIu algorithm (v.0.93.1)[10] was used to calculate the OrthoANI value between the type strain P. aryabhattai B8W22 and strain KNU10. OrthoANI value between B8W22 and KNU10 were 95.88%.

Table 1 . Genetic feature of P. aryabhattai KNU10.

Genome featureValue
Genome size (bp)5,154,607
Number of contigs1
GC content (%)38.5
Total number of genes5,780
Protein coding genes5,406
tRNA genes136
rRNA genes43


Figure 1.The circular map of P. aryabhattai KNU10 chromosome, generated with the Proksee program.

Figure 2.Result of P. aryabhattai gene annotation, generated with the RAST server.

Overall, sequencing analysis of genome suggest that P. aryabhattai strain KNU10 has potential to protect the plants from nitrosative and oxidative stress and exhibit PGPR activity.

Data Availability

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The complete genome sequence of P. aryabhattai strain KNU10 has been deposited in NCBI GenBank database under accession number CP041519.1.

Acknowledgments

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This research was supported by a project to train professional personnel in biological materials by the Ministry of Environment, by Korea Basic Science Institute (National research Facilities and Equipment center) grant funded by the Ministry of Education (2021R1A6C101A416) and by the "Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ017033)" Rural Development Administration, Republic of Korea.

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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