Draft genome sequence of Paenibacillus marinisediminis LHW35^T isolated from marine sediment reveals genes for ammonia assimilation

ABSTRACT

We present the draft genome sequence of Paenibacillus marinisediminis LHW35^T isolated from marine sediment in Gangjin Bay, Republic of Korea. The genome annotation recovered 4,755 protein-coding genes and 92 RNA genes with a guanine-cytosine (GC) content of 46.5%. Subsystem analysis identified genes for ammonia assimilation, suggesting potential role in nitrogen cycling in marine sediments.

ANNOUNCEMENT

Paenibacillus marinisediminis LHW35^T (KACC 16317^T = JCM 17886^T) is a gram-negative, non-motile, endospore-forming, rod-shaped bacterium within the family Paenibacillaceae (1, 2). This strain was isolated from marine sediment collected from Gangjin Bay, Jeollanam-do, Republic of Korea (34.568483 N, 126.780070 E) using a dilution-plating technique with pleuropneumonia-like organism agar (PPLOA; Difco, Korea) at 37°C, as described previously (1). For genome sequencing, the strain was revived from a lyophilized stock and cultivated on marine agar (containing 19.45 g/L NaCl; MBcell, Republic of Korea) using the streak plate method and incubated at 30°C for 5 days. The obtained colonies were subcultured three times to achieve a pure culture and a colony obtained from the third subculture.

Genomic DNA of Paenibacillus marinisediminis LHW35^T was extracted and purified using the Qiagen MagAttract HMW DNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The sequencing library was prepared with the TruSeq DNA Library LT Kit (Illumina, San Diego, USA) following the manufacturer’s instructions. Whole-genome sequencing was carried out on the Illumina NovaSeq platform (3), generating paired-end reads of 2 × 150 bp. A total of 7,180,913 reads comprising 2.16 × 10⁹ bases were obtained. The average read lengths for forward and reverse reads were 150 bp, with mean quality scores of 35.56 and 35.22, respectively. The data set exhibited a guanine-cytosine (GC) content of 48.87%, and 91.0% (Q30) of bases met the quality threshold. Sequence reads were processed using Shovill Galaxy version 1.1.0 (4), where trimming and assembly were performed by Trimmomatic v0.39 (5) and SPAdes v3.14.3 (6), respectively, within the Shovill environment. Default parameters were applied for all software unless otherwise specified. The assembly environment was run under the Galaxy framework, which integrates quality control, trimming, and de novo assembly steps in a reproducible workflow.

As analyzed using the RAST server with SEED viewer, the genome of Paenibacillus marinisediminis LHW35^T, which is 5,082,162 bp in size and assembled into 65 contigs according to the GenBank Assembly record, exhibits a guanine-cytosine content of 46.5%, encompasses 297 subsystems, encodes 4,755 protein-coding sequences, and contains 92 RNA genes, with an N50 value of 369,200 bp. The subsystem coverage accounted for 21% of the annotated genes. The most prominent functional categories in the genome were related to carbohydrates (237 genes), amino acids and derivatives (222 genes), and protein metabolism (168 genes), each representing major metabolic capacities (Fig. 1). Detailed subsystem analysis revealed a significant nitrogen metabolism pathway associated with ammonia assimilation (five genes).

Fig 1.

Subsystem-based functional classification of the draft genome of Paenibacillus marinisediminis strain LHW35 using RAST annotation.

Ammonia assimilation plays an important role in the nitrogen cycling of marine sediments by assimilating ammonium into organic nitrogen forms, thereby reducing nitrogen loss and maintaining the balance of nitrogen cycling and the sustainability of microbial metabolism within the sediments (7). Consequently, the draft genome of Paenibacillus marinisediminis LHW35^T presented in this study provides valuable insights into the microbial processes involved in nitrogen cycling along the southern coast of Korea.

DATA AVAILABILITY

This whole genome project has been deposited in DDBJ/EMBL/GenBank under accession number JBTGUH000000000.1. Reads are available at the Sequence Read Archive (SRA) under accession number SRR35963196, BioProject number PRJNA1358048, and BioSample number SAMN53099241. RAST annotation files are available online at Figshare (https://doi.org/10.6084/m9.figshare.31330225).