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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(2): 195-199

Received: February 26, 2024; Revised: May 13, 2024; Accepted: May 23, 2024

토마토 생장 촉진 효과가 있는 Paraburkholderia phenoliruptrix T36S-14 균주의 유전체 염기서열

Complete Genome Sequence of Paraburkholderia phenoliruptrix T36S-14, a Plant Growth Promoting Bacterium on Tomato (Solanum lycopersicum L.) Seedlings

Jiwon Kim1,3, Yong Ju Jin1, Min Ju Lee1, Dong Suk Park2, and Jaekyeong Song1,4*

1Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
2Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
3Department of Agricultural Biology, College of Agricultural & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
4Organic Agriculture Division, National Institute of Agricultural Sciences, Rural Development Adminisration, Wanju 55365, Republic of Korea

Correspondence to :
Jaekyeong Song,

Paraburkholderia phenoliruptrix T36S-14, identified as a potential plant growth-promoting bacterium, was isolated from the core microbiome of tomato rhizosphere soil. When assessed for its growth promotion, Strain T36S-14 demonstrated a notable 20% increase in the fresh weight of tomato seedlings. The strain possesses two circular chromosomes, one of 4,104,520 base pair (bp) (CP119873) and the other of 3,258,072 bp (CP119874), both exhibiting G+C contents of 63.5% and 62.7%, respectively. The chromosome comprises 6,319 protein-coding sequences, 65 transfer RNA genes, and 18 ribosomal RNA genes (5S: 6, 16S: 6, and 23S: 6). Additionally, P. phenoliruptrix T36S-14 produces siderophores that promote plant growth.

Keywords: Genome, plant growth, Paraburkholderia phenoliruptrix, rhizosphere

Tomatoes, recognized for their high economic value, are a pivotal horticultural crop globally. Conventional fertilizers, although widely used in agriculture, have persistent environmental repercussions, particularly soil and groundwater pollution. As an alternative, plant growth-promoting bacteria (PGPB) are becoming promising biofertilizers owing to their eco-friendly environment and enhanced soil fertility. In this study, Paraburkholderia phenoliruptrix T36S-14 was chosen from the key microorganisms identified in tomato rhizosphere microbiome analysis. There was a 20% increase in the relative fresh weight of tomato seedlings compared to the control when the T36S-14 was drenched, as confirmed by a growth enhancement patent (patent number: 10-2023-0149130). Strain T36S-14 displayed essential traits for plant health, including the production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, a known factor in alleviating environmental stress and inducing plant tolerance. Additionally, T36S-14 exhibits siderophore production, thereby fostering disease inhibition through effective iron competition. Furthermore, the confirmed ability to produce Indole-3-acetic acid (IAA), promoting plant and root growth, and the ability to solubilize phosphate and zinc were confirmed. Consequently, we report the results of the complete genome sequencing of T36S-14, shedding light on the genomic characteristics that contribute to the enhancement of tomato growth.

The whole genome of T36S-14 was sequenced using the PacBio Sequel II system and the Illumina platform at Macrogen Inc. (Republic of Korea). PacBio reads facilitated the assembly process, and Illumina reads were used for error correction of the genome assembly using Pilon version 1.21. Functional annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) to comprehensively elucidate the genetic elements and potential functionalities encoded in the genome [1]. Genomic analysis of strain T36S-14 revealed a unique genomic architecture with two circular chromosomes. Chromosome 1 contained 4,104,520 base pairs (bp) with a G-C content of 63.5%, whereas chromosome 2 contained 3,258,072 bp with a G-C content of 62.7%. The contig 1 and contig 2 genomes contained 6,319 predicted coding sequences (CDSs), 65 transfer RNAs (tRNA), and 18 ribosomal RNAs (rRNA; 6 equal for 5S, 16S, 23S). (Table 1). Clusters of Orthologous Group (COG) functional annotation analysis predicted that 6,283 genes, accounting for 97.4% of the total predicted CDS, were distributed across 25 categories (Fig. 1A). OrthoANI values were calculated using the OrthoANI algorithm version v0.93.1 [2] from the available genomes of Paraburkholderia species. The OrthoANI value between P. phenoliruptrix BR3459a (type strain) and the T36S- 14 genome sequence was determined to be 98.33% (Fig. 1B). The average amino acid identity (AAI), a method used to evaluate the differences among orthologous proteins from diverse organisms, serves as an effective indicator of their evolutionary divergence [3, 4]. When comparing T36S-14 with P. phenoliruptrix BR3459a, the AAI values were found to be 98.21% for chromosome and 99.14% for chromosome 2. Paraburkholderia sp. was originally identified as a Burkholderia species. Burkholderia is a β-Proteobacteria that contains a variety of adaptable gram-negative species. Recently, it has been proposed that this genus can be divided into two main branches: Paraburkholderia, which includes plant-beneficial and environmental species, and animal and plant pathogens [5]. P. phenoliruptrix was initially described by [6]. This name was validated when it appeared on the Validation List No. 164 in 2015. This pivotal taxonomic revision led to the repositioning of B. phenoliruptrix, originally proposed by [7], within the genus Paraburkholderia as described by [6]. Paraburkholderia species are nitrogen-fixing symbionts in the soil [8]. The circular map of strain T36S-14 is shown in Fig. 2. Secondary metabolite gene clusters were analyzed using anti- SMASH version 7.0 [9]. Strain T36S-14 was found to contain genes associated with gramibactin, a siderophore (BGRAMDRAFT_RS22615–BGRAMDRAFT_ RS226 85), with 100% similarity in chromosome 1 (Fig. 2B). Chromosome 2 of T36S-14 contains genes that are important in promoting plant growth. Specifically, the gene “iaaH” (locus tag: P3F88_23345) is responsible for encoding indoleacetamide hydrolase, an enzyme synthesizing IAA from indoleacetamide [10]. In addition, another gene associated with ACC deaminase (Locus tag: P3F88_24185), which catalyzes the conversion of ACC to α-ketobutyrate and ammonia [11].

Table 1 . Genome features of Paraburkholderia phenoliruptrix T36S-14.

Genome featuresChromosome 1Chromosome 2
Genome size (bp)4,104,520 bp3,258,072 bp
Genome coverage100
G + C ratio (%)63.%62.7%
Protein-coding genes (CDSs)6,319
tRNA genes5510
rRNA genes (5S, 16S, 23S)3, 3, 33, 3, 3
Pseudo genes116
Gene bank accession numberCP119873CP119874

Figure 1.EggNog analysis of the Paraburkholderia phenoliruptrix T36S-14 (A) and genetic similarity test of strain T36S-14 (B). OrthoANI results calculated from available genomes of Paraburkholderia species. UPGMA and Heatmap were generated from the OAT software. The letter (T) means type strain of the species.

Figure 2.The circular map of Paraburkholderia phenoliruptrix T36S-14 (A), and antismash result (B).

Genomic analysis of P. phenoliruptrix T36S-14 revealed the presence of genes involved in the siderophore-related gene cluster production. Therefore, this information provides insight into the potential mechanism of the growth-promoting activity of P. phenoliruptrix T36S-14 on tomatoes. Investigating the genetic characteristics of P. phenoliruptrix T36S-14 is essential for exploring its unique genomic features. This insightful information demonstrates the potential of PGPB for future use as a sustainable biofertilizer to improve plant yield and growth.

The genome sequences of Paraburkholderia phenoliruptrix strain T36S-14 contig1 and contig2 have been deposited to Genbank under the accession number CP119873 and CP119874, respectively. The strain has been deposited in the Korean Agricultural Culture Collection (KACC) under accession number KACC 81273BP.

This study was carried out with the support of “Research program for Agricultural Science & Technology Development (Project No PJ015876)” from the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea. This study was supported by 2020-2023 collaborative research program between university and Rural Development Administration, Republic of Korea.

The authors have no financial conflicts of interest to declare.

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