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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): 490-492

https://doi.org/10.48022/mbl.2409.09015

Received: September 27, 2024; Revised: November 5, 2024; Accepted: November 15, 2024

Whole Genome Sequence of Pseudomonas aeruginosa CIMT2, Isolated from the Rhizosphere of Maize (Zea mays L.)

Kanika Mahra1, Tino Bashizi1, and Jae-Ho Shin1,2,3*

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

Correspondence to :
Kanika Mahra,        mahra950301@knu.ac.kr

Abstract

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This study reports the whole genome sequence of Pseudomonas aeruginosa strain CIMT2, which was isolated from the rhizosphere soil of maize (Zea mays L.). The genome consists of 7.1 Mb with a total of 626,677,475 bp sequenced and the GC content is 65.8%. Notably, the genome contains key genes associated with plant growth-promoting activities, including those involved in nitrogen metabolism (e.g., ntrC, nosZ), phosphorus solubilization (e.g., pstS, phoB), and salt stress response (e.g., osmE, glnK). These traits may enhance the bacterium's role in promoting plant growth and soil health, underscoring its potential applications in sustainable agriculture.

Keywords: Pseudomonas aeruginosa, whole genome sequencing, plant growth-promoting Rhizobacterium

Body

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Sustainable agriculture aims to reduce the use of chemical fertilizers, with species from the Pseudomonas genus, a gram-negative bacterium, playing a key role as Plant Growth-Promoting Rhizobacteria (PGPR). These bacteria enhance nutrient uptake, support nitrogen metabolism, and improve plant tolerance to various biotic and abiotic stresses.

In this study, we analyze P. aeruginosa strain CIMT2, isolated from the rhizosphere of maize (Zea mays L.). Pseudomonas exhibits halotolerance, phosphate solubilization, ammonia production, and multiple nitrogen metabolism activities, including nitrate reduction, indicating its potential as a PGPR, particularly in saline and nutrient-limited environments. By investigating its genetic composition, we aim to explore the contributions of P. aeruginosa CIMT2 to maize growth and productivity. Understanding the role of this strain in promoting plant health could offer a sustainable alternative to traditional agricultural practices, especially in stress-prone environments.

The genome of P. aeruginosa strain CIMT2 was sequenced after its isolation on January 14, 2022, from the rhizosphere soil of maize. Approximately 1 g of rhizosphere soil was serially diluted up to 6-fold and spread onto tryptic soy agar (TSA) plates. The plates were incubated at 30℃ for 5 days. A single colony was selected, purified through repeated subculturing, and subsequently grown in tryptic soy broth (TSB) for 24 h to obtain sufficient biomass for molecular identification.

Genomic DNA from P. aeruginosa strain was extracted using the Wizard Genomic DNA Purification Kit (Promega, USA) following the manufacturer's guidelines. DNA concentration was determined with a Qubit 2.0 fluorometer (Thermo Fisher Scientific, USA), and its quality was evaluated using a NanoDrop One/OneC spectrophotometer (Thermo Fisher Scientific). The sequencing library was prepared with the ligation sequencing kit SQK-LSK109 (Oxford Nanopore Technologies) in conjunction with the NEBNext companion module (New England Biolabs, USA). Sequencing was performed on the Oxford Nanopore MinION platform using a FLO-MIN111 flow cell (R10.3) for 72 h at KNU NGS Core Facility (Republic of Korea). After getting the raw fastq data, the quality control of the raw reads was done using Porechop (v. 0.2.4). The clean reads were then used for de-novo assembling using Flye (v. 2.9.5-b1801) with default parameters. The whole genome sequence was visualized using the CGView tool, which generated a detailed circular genome map for illustration and analysis. Additionally, genome annotation was carried out using NCBI's Prokaryotic Genome Annotation Pipeline (PGAP), which identified genes, regulatory elements, and other genomic features.

The full length of complete genome is of 7193015 bp consisting of 65.80% GC content. Whole genome sequencing identified 5 CRISPR arrays, indicating adaptive immune elements within the genome. Number of features comes out to be 7046, including 1 contig and 6965 protein coding sequence CDS, 46 pseudogenes. Number of RNA are 81, 71 tRNAs, 12 rRNAs, 54 ncRNAs (Table 1).

Table 1 . Genetic profile of Pseudomonas aeruginosa strain CIMT2.

FeaturesValue
Genomic size7193015 bp
GC content65.80%
Total reads85,864
Contigs1
CDS6965
CRISPR5
Pseudo-genes46
Ribosomal RNAs12
Transfer RNAs71


Table 2 . Bacterial genes associated with salt stress, phosphorus, iron acquisition, and nitrogen metabolism that enhance plant growth.

MetabolismGene NameReferences
Salt Stress ResponseosmE, glnK, glnA, glnE, nagA, sodB, betA, betB, nhaB,[4], [1], [5]
Phosphorus metabolismpstS, pstA, phoB, ppk, phnC, phnD, phnE, acpP, plcR, pnp, cysZ[2], [6]
Iron acquisition and metabolismfur, feoA, feoB, fepB, tonB1, bfrB, butB, nrdD[7], [3], [8]
Nitrogen metabolismglmU, glmS, glmM, ntrC, ntrB, nosZ, nosP, nosR, narI, narJ, narH, narX narL, nirB, nirF, nirJ, nirN, nirS[9], [10]


Figure 1.Genome map of the P. aeruginosa strain CIMT2 circular chromosome sequence generated using the CGView visualization tool. Several important genes associated with the metabolic capabilities of Pseudomonas aeruginosa strain CIMT2. The genes involved in salt stress response, such as osmE and glnA [1], suggest the strain's adaptability to saline environments, enhancing its potential for growth in challenging conditions. Additionally, genes like pstS and phoB play crucial roles in phosphorus metabolism [2], facilitating nutrient uptake that is vital for plant growth. Iron acquisition genes, including fur and tonB1 [3], underscore the bacterium's ability to acquire essential nutrients from its surroundings. Furthermore, nitrogen metabolism genes such as ntrC and nosZ indicate the strain’s capability to participate in nitrogen cycling, which can contribute to improved soil health and fertility (Table 2).

Data Availability

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The full genome sequence of Pseudomonas aeruginosa CIMT2 has been deposited in the NCBI under the accession number CP169522. The raw sequencing data can be accessed through the SRA accession number PRJNA1158327.

(https://www.ncbi.nlm.nih.gov/nuccore/CP169522.1/).

Acknowledgments

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Whole metagenome analysis was performed using a data analysis server in the KNU NGS Core Facility (Daegu, Republic of Korea). 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 with the support of “Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ015697)” 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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