Unveiling the complete genome sequence of Paenibacillus taichungensis: genomic features and biocontrol potential

Abstract

Objectives

The genus Paenibacillus encompasses a diverse group of Gram-positive bacteria with significant biotechnological potential. However, the research data and application cases of Paenibacillus taichungensis were still poorly understood. In this study, we isolated a P. taichungensis strain BB507, which demonstrated antibacterial effect on Ralstonia solanacearum species complex, and provided data and analysis of its complete genome.

Data description

Strain BB507 was isolated from a pine rhizosphere in Meizhou city, Guangdong province of China, and showed antibacterial activity against Ralstonia solanacearum species complex. Complete genome was sequenced using Illumina NovaSeq (second-generation) and Oxford Nanopore (third-generation) platforms. The genome of BB507 comprised of a 6,974,531 bp circular chromosome and a 352,197 bp circular plasmid, encoding a total of 6,649 gene with an average gene length of 950 bp, 103 transfer RNAs, 2 sRNAs, and 36 rRNAs. Three candidate CRISPRs, 6 genomic islands and 14 prophages were predicted. The bacterial orthologous average nucleotide identity (OAT) and the type genome server (TYGS) analysis highlighted the strain BB507 was clustered into a subgroup with P. taichungensis. antiSMASH v7.0 predicted the presence of 10 secondary metabolite gene clusters in the genome. These findings will serve as a useful resource for further research in industrial and agricultural biotechnology.

Objective

The genus Paenibacillus was designated in 1993, comprising 11 species that were originally classified under the genus Bacillus [1, 2]. Novel species of this genus have been rapidly discovered, and currently, more than 150 named species have been identified. Members of this genus are facultative anaerobic, endospore-forming, motile, rod-shaped and gram-positive bacteria [3]. It has been widely used in industry and agriculture because of its unique ability in plant growth promotion, biocontrol and biodegradation [4]. P. taichungensis was firstly isolated and identified from a sample of soil from Taichung, a city in Taiwan of China [5]. It was subsequently isolated from the endophytic bacteria of Arabidopsis thaliana and found to have significant growth-promoting effects [6]. P. taichungensis strain NC1 displaying high arsenic resistance was isolated and identified from the Zijin gold-copper mine in Fujian, mainland of China [7]. This suggests that P. taichungensis, like most Paenibacillus, has strong application value in agricultural and industrial fields. In agriculture, arsenic resistance could be utilized to develop bioinoculants that enable plants to thrive in arsenic-contaminated soils by reducing arsenic uptake and enhancing overall plant health. In industrial applications, such as mining and wastewater treatment, this resilience to arsenic toxicity could be harnessed to mitigate environmental pollution and promote sustainable practices. There were no complete-level genome data of P. taichungensis, only nine contig/scaffold-level data were included in the NCBI database.

Bacterial wilt, attributed to Ralstonia solanacearum species complex (RSSC) infection, has caused destructive impacts and colossal economic losses on agricultural production [8, 9]. Chemical control, which was ubiquitously used, cannot manage this disease as expected, so biocontrol has been followed with interest to date. We found a P. taichungensiss strain BB507 that had a potent antagonistic activity against RSSC, and the genomic sequencing and analysis revealed biocontrol mechanisms might be involved in the strain BB507.

Data description

Strain BB507 was isolated from the rhizosphere of a pine tree in Meizhou city, Guangdong province, China, and demonstrated potent antibacterial activity against RSSC using a plate confrontation assay, as previously described in our published work [10]. BB507 was sequenced using the combination of Oxford Nanopore PromethION and Illumina NovaSeq PE150 platform at Novogene Bioinformatics Technology Co., Ltd in Beijing, China. Initially, library preparation was performed according to Oxford Nanopore Technologies (ONT, Oxford, United Kingdom) protocol for multiplexing samples (1D native barcoding genomic DNA with EXP-NBD103 and SQK-LSK108). Genome DNA was sonicated to a fragment size of 350 bp, followed by A-tailing, end-polishing, and ligation with full-length adaptors for Illumina sequencing. Polymerase Chain Reaction (PCR) products were purified using the AMPure XP system, and library size distribution was analyzed by Agilent2100 Bioanalyzer. Quantification was performed using real-time PCR. A total of 1,044 Mb Nanopore clean data were generated with an estimated 145×average depth of sequencing coverage. Post-quality control, paired reads were assembled into a complete genome using SMRT Link v5.1.0, with further refinement using Illumina data and Pilon. The complete genome of BB507 was 7.33 Mb in total with GC content of 45.84%, which comprised a 6.97 Mb circular chromosome and a 0.35 Mb circular plasmid (Table 1, Data file 1). CheckM2 analysis revealed that the assembled genome of BB507 was complete, with a genome completeness of 99.85% and a contamination level of 1.15%. Gene prediction identified 6,649 genes in BB507 using GeneMarkS v4.17 [11]. Genomic component analysis of strain BB507 revealed the presence of 103 transfer RNAs (tRNAs), identified using tRNAscan-SE v1.3.1 [12], and 36 ribosomal RNAs (rRNAs) (5 S, 16 S, 23 S), identified using rRNAmmer v1.2 [13]. Additionally, 3 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) were detected using CRISPRdigger v1.0 [14], 6 genomic islands were identified using IslandPath-DIMOB v0.2 [15], and 14 prophages were identified using phiSpy v2.3 [16]. The general features of the BB507 genome were listed in Data file 2 (Table 1). The complete genome sequence of BB507 has been deposited in GenBank dataset under the accession number CP175536 (Table 1, Dataset 8) and CP175537 (Table 1, Dataset 9).

Table 1 Overview of data files/data sets

Functional annotation revealed that 4,296 genes were assigned into 47 Gene Ontology (GO) categories [25], 6016 genes were enriched in 106 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [26], and 4,483 genes were classified into 23 Clusters of Orthologous Groups (COG) categories [27]. Annotation identified 244 putative virulence factors, 498 pathogen–host interaction genes, 604 transport proteins, 484 carbohydrate-active enzymes, and 2 antibiotic resistance proteins using databases such as Virulence Factors of Pathogenic Bacteria (VFDB) [28], Pathogen Host Interactions Database (PHI) [29], Transporter Classification Database (TCDB) [30], Carbohydrate-Active enZYmes Database (CAZyme) [31], and Antibiotic Resistance Genes Database (ARDB) [32], respectively (Table 1, Data file 3).

Orthologous Average Nucleotide Identity Tool (OAT) [33] analysis revealed that the eight P. taichungensis strains shared the indexes of Average Nucleotide Identity (ANI) ranging from 90.24 to 100%, and 67.06–69.25% ANI indexes with strains of Paenibacillus graminis and Paenibacillus chitinolyticus. Notably, the highest ANI index of 99.02% was found between strain BB507 and strain NC1, and they were also clustered together on the phylogenetic branch (Table 1, Data file 4). In addition, the type genome server (TYGS) [34]was used as a means of confirming the previous results shown by both the multigene phylogenetic approach and the ANI calculations. The TYGS results indicated that BB507 formed a monophyletic relationship with closely related P. taichungensis (Table 1, Data file 5). The digital DNA-DNA hybridization (dDDH) values with both P. taichungensis strain were 66.7–93.2% (Table 1, Data file 6). BB507 had a dDDH of 93.2% with G + C% content difference of 0.34 with P. taichungensis strain NC1. The ANI indexes < 95% and dDDH < 75% observed in some strains within the clade of P. taichungensis were due to P. taichungensis strain DB-4 (ANI index = 92.94%, dDDH = 69.4%) and VTTE13328 (ANI index = 90.28%, dDDH = 66.7%). These discrepancies suggested that the taxonomic status of these two strains might be deviated. Therefore, the taxonomic definition of P. taichungensis might be limited by the current sample size. However, the above results still indicated that BB507 belonged to the P. taichungensis.

The secondary metabolite gene clusters of BB507 were predicted using antiSMASH v7.0 [35], identifying a total of ten potential gene clusters, nine of which were chromosomal and one plasmid-borne. Seven of these clusters showed similarity to known biosynthetic gene clusters of Paeninodin, Staphyloferrin B, Corynecin, Bacillopaline, Carotenoid, Bacillibactin, and Aurantinin, with similarities ranging from 10 to 100% (Table 1, Data file 7). Additionally, three gene clusters of unknown function were identified, suggesting the presence of novel secondary metabolites.

Limitations

While this study provides valuable insights into the genomic features and biocontrol potential of P. taichungensis strain BB507, several limitations should be considered. First, the functional roles of the predicted secondary metabolite gene clusters require further experimental validation. Although antiSMASH v7.0 predicted ten secondary metabolite gene clusters, including both known biosynthetic pathways and several novel ones, the actual production and biological activity of these metabolites have not been confirmed. Additionally, the taxonomic analysis relies on the available genome data, which may have limitations due to the current sample size and the presence of closely related strains with similar ANI and dDDH values. The phylogenetic relationships within the P. taichungensis, particularly concerning strains with deviating taxonomic status (e.g., strains DB-4 and VTTE13328), highlight the need for further genomic and phenotypic investigations to refine the classification.