Genomic analysis of an extremophile PLS47 from a deep-sea vent

TL;DR

This paper reports the genome of PLS47, a deep-sea extremophile from Indonesia, revealing genes linked to heat tolerance and potential industrial enzymes.

Contribution

The study provides a high-quality genome sequence and analysis of a novel extremophile with unique stress-tolerant and metabolic genes.

Findings

PLS47's genome contains genes for thermotolerance and stress response, including hydrolases and lipases.

Comparative analysis shows PLS47 is closely related to Geobacillus thermocatenulatus but has unique deep-sea adaptations.

The genome includes multiple enzyme-coding genes with industrial potential, such as esterases and lipases.

Abstract

Indonesia's submarine hydrothermal vents represent underexplored ecosystems harboring thermophilic microbial diversity with significant biotechnological potential. In the study, the whole-genome sequencing, assembly, and comparative genomic analysis of strain PLS47, an extremophilic bacterium isolated from the Pria Laot hydrothermal vent, Sabang, Aceh, Indonesia is reported. The genome was sequenced using Oxford Nanopore Technology, assembled de novo, and polished to obtain a high-quality draft genome. Genome annotation identified genes associated with thermotolerance, stress response, and diverse metabolic pathways, including COG, KEGG, and CAZymes analysis. Comparative genomic analyses, including ANI and phylogenomic, confirmed its taxonomic placement and highlighted genomic distinctions from closely related terrestrial strains. Pangenome analysis further revealed unique gene sets potentially linked to adaptation to deep-sea hydrothermal environments. The complete genome sequence local isolate PLS47 is 3,772,236 bp at chromosomal genome with GC content at 52.02%, along with 56,806 bp at plasmid DNA with GC content at around 41.06%. A total of 3,708 coding sequences (CDSs) were identified, 6 rRNA (5S, 16S, and 23S), 27 rRNA, 88 tRNA genes, and 17 pseudogenes. A comparison of the genome to data based on Average Nucleotide Identity shows that the genome is closely related to the Geobacillus thermocatenulatus. Functional analysis revealed numerous enzyme-coding genes, including proteases, peroxidases hydrolases, esterases, dehydrogenase, hydratases, and lipases. In addition, the genome exhibits a number of stress-tolerant genes. Detailed analysis of the hydrolase genes, especially for lipolytic enzymes such as esterase and lipase, showed that the genome exhibits true lipase like putative lipase, monoacyl glycerol lipase (MAGL) motif and other lipase like GDSL-type esterase/lipase motif. The genomic information provides an understanding of thermophilic genomes and their relevance to stress-tolerant adaptation and explores potential genes, especially for industrial applications.

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