Unveiling the draft genome sequence of diesel-degrading Paenibacillus sp. strain d9, a surfactant producer isolated from diesel-contaminated soil

Introduction: Gram-positive bacteria, particularly Bacillus and Paenibacillus spp., have gained significant attention for their potential in environmental bioremediation (biosurfactant production) and diverse biotechnological applications. Among these, Paenibacillus sp. D9, isolated from oil-contaminated soil, has shown diesel and engine oil degradation capabilities and biosurfactant production. However, its role in alkane degradation remains unexplored.

Methodology and Result: To shed light on its unique attributes, we conducted whole-genome sequencing of Paenibacillus sp. D9 using the Illumina HiSeq 2000 platform. The draft genome comprised 56 contigs and 7 scaffolds, with a size of 5,645,302 bp at 157.94× coverage and a G + C content of 58.13%. A total of 9,950 Coding Sequences (CDSs) were predicted, and functional annotation revealed 3,283 (43.19%) and 3,155 (58.8%) putative genes based on Bacterial Annotation System (BASys) and Rapid Annotation using the Subsystems Technology (RAST) subsystem categorization, respectively. Furthermore, 93 tRNA and 23 rRNA genes were identified.

Conclusion: This genome announcement provides valuable insights into the genetic potential of Paenibacillus sp. D9 and paves the way for future research in its biotechnological applications.

Genome announcement

Gram-positive bacteria particularly Bacillus and Paenibacillus spp. have been attracting interest in both environmental bioremediation strategies (biosurfactant production) and biotechnological applications [1,2]. Paenibacillus spp. are known to be associated with a wide variety of applications ranging from agriculture and horticulture to industrial and medicine [3]. Paenibacillus sp. D9 [4] isolated from oil-contaminated soil has been reported to degrade diesel and produce biosurfactants; however, its role in alkane degradation has not been established. The uniqueness of this organism lies in the presence of commercially significant proteins and biosurfactant-producing genes, in addition to its diesel and engine oil degradation capabilities. Therefore, genome sequencing was conducted. The whole-genome sequencing was performed using the Illumina HiSeq 2000 platform by the Beijing Genomics Institute (BGI), Shenzhen, China. Paired-end libraries with average insert sizes of ~500 base pair (bp) and ~6 kilobases (kb) were generated following the manufacturer's instructions. The reads were aligned with the reference sequence using SOAPaligner (version 2.21) software to assess differences between the sequencing and reference species in terms of average depth and coverage ratio [5]. The initial processing involved de novo assembly of the filtered short reads using SOAPdenovo v 2.04, following the method described previously [6]. Subsequently, contigs were manually connected based on their 500 bp and 6 kb paired-end relationships. The resulting draft genome comprised 56 contigs and 7 scaffolds, with a maximum contig size of 582,249 bp and a scaffold size of 5,594,870 (Table 1). The genome size was 5,645,302 bp at 157.94 × coverage, with N50 of 5,594,870 bp and N90 of 5,594,870 bp and the G + C content was 58.13%. A total of 9,950 coding DNA sequences (CDSs) or Open Reading Frames (ORFs) were predicted using Glimmer v3.02 [7] and homologous comparison to a non-redundant public database was performed by Basic Local Alignment Search Tool (BLAST) for function annotation. The genome annotation was performed using the BASys server and the output was downloaded in GenBank format resulting in 7,600 (CDSs) [8]. The genome was further annotated with RAST server [9]. The features for Draft genome sequence of Paenibacillus sp. D9 are summarized in Table 1. Among the 7,600 predicted protein-coding genes, 3,283 (43.19%) have putative functions based on BASys subsystem categorization, while the RAST server assigned functions to 3,155 genes (58.8%) among 5,359 predicted. Additionally, 93 tRNA genes covering all 20 amino acids were identified using the tRNAscan-SE program [10] and 23 rRNA genes were identified using RNAmmer [11]. The contigs were submitted to GeneBank, and NCBI published the sequence data in April 2015.

Nucleotide sequence accession number

The nucleotide sequence accession numbers for this Whole Genome Sequencing (WGS) project are as follows: The project has been deposited at DDBJ/EMBL/GenBank under the accession JZEJ00000000. The version described in this paper is JZEJ01000000. The Bioproject is registered under accession: PRJNA277007 ID: 277007. The Paenibacillus sp. D9 isolate has been deposited at the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures and is available under the Accession No. DSM 101888.

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