Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

Wael M Abdel-Mageed; Burhan Lehri; Scott A Jarmusch; Kevin Miranda; Lamya H Al-Wahaibi; Heather A Stewart; Alan J Jamieson; Marcel Jaspars; Andrey V Karlyshev

doi:10.1016/j.margen.2020.100782

Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

Mar Genomics. 2020 Dec:54:100782. doi: 10.1016/j.margen.2020.100782. Epub 2020 May 6.

Authors

Wael M Abdel-Mageed¹, Burhan Lehri², Scott A Jarmusch³, Kevin Miranda³, Lamya H Al-Wahaibi⁴, Heather A Stewart⁵, Alan J Jamieson⁶, Marcel Jaspars⁷, Andrey V Karlyshev²

Affiliations

¹ Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt. Electronic address: wabdelmageed@ksu.edu.sa.
² School of Life Sciences Pharmacy and Chemistry, Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
³ Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, Scotland AB24 3UE, UK.
⁴ Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia.
⁵ British Geological Survey, Lyell Centre, Research Avenue South, Edinburgh EH14 4AP, UK.
⁶ School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK.
⁷ Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, Scotland AB24 3UE, UK. Electronic address: m.jaspars@abdn.ac.uk.

PMID: 32387528
DOI: 10.1016/j.margen.2020.100782

Abstract

Whole genome sequences of four bacterial strains Dietzia maris SST1, Pseudomonas zhaodongensis SST2, Pseudomonas sp. SST3 and Halomonas sulfidaeris SST4, recovered from the South Shetland Trench sediment in Antarctica were analyzed using Ion Torrent sequencing technology. The respective sizes of their genomes (3.88, 4.99, 5.60 and 4.25 Mb) and GC contents (70.0, 60.3, 59.9 and 53.8%) are in agreement with these values of other strains of the species. The bacterial strains displayed promising antimicrobial activity against a number of pathogenic bacterial and fungal species. Whole genomes have been assembled and biosynthetic gene clusters (BGCs) have been identified using the antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) web platform. Comparative analysis of the genome sequences revealed that the strains host abundant BGCs encoding for terpenes, siderophores, arylpolyene, bacteriocins, and lassopeptides. Furthermore, the key stress-related genes were identified and their distribution provided an insight into how these isolates adapt to key marine environmental conditions. This comprehensive study is a contribution to understanding the nature of life on the deep-sea environments.

Keywords: Antimicrobials; Biosynthetic gene clusters; Dietzia sp.; Genome sequencing; Halomonas sp.; Pseudomonas sp.; South Shetland Trench.

MeSH terms

Actinobacteria / genetics*
Antarctic Regions
Genome, Bacterial*
Geologic Sediments
Halomonas / genetics*
High-Throughput Nucleotide Sequencing
Oceans and Seas
Pseudomonas / genetics*
Whole Genome Sequencing

Supplementary concepts

Dietzia maris
Halomonas sulfidaeris