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

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 deepsea environments.

First De Novo Transcriptome of the Copepod Rhincalanus gigas from Antarctic Waters

“…Rhincalanus gigas individuals were collected on 21 and 22 December 2015, from two stations of the South Shetland Trench (SST) (Station 1: latitude −58.0703, longitude −61.326945; Station 2: latitude −58.199624, longitude −60.958174) during the “PharmaDEEP” cruise ( ) [ 14 ]. Zooplankton was collected at 100 m depth with a Nansen net (200 μm mesh, 1 m diameter) towed vertically.…”

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

“…Deep-sea psychrophilic bacteria synthesize cold shock proteins essential for adaptation to low temperatures [ 50 , 51 , 52 ]. The genome of strain MT25 T contained genes predicted to encode cold shock proteins, as exemplified by genes clpB and hscB which are associated with the synthesis of ATP-dependent and Fe-S chaperones, respectively [ 52 , 53 , 54 ]. The genome also contains gene deaD encoding an RNA helicase involved in cold shock response and adaptation [ 55 ].…”

“…The genome also contains gene deaD encoding an RNA helicase involved in cold shock response and adaptation [ 55 ]. The strain has genes associated with the synthesis of branch-chain and long chain polysaturated fatty acids that are linked to membrane fluidity and functionality at low temperatures [ 49 , 52 ], including fabF , fabG , fabH and fabI genes which are responsible for the biosynthesis of β -ketoacyl-ACP synthase II, 3-oxoacyl-ACP reductase, ketoacyl-ACP synthase III, enoyl-ACP reductase and enoyl-ACP reductase, respectively ( Table S3 ). The synthesis of low-melting point branched-chain and/or polyunsaturated fatty acids (PUFAs) is crucial as it allows organisms in cold environments to maintain membrane fluidity in a liquid crystalline state thereby allowing organisms to resist freeze-thaw cycles at low temperatures [ 56 , 57 ].…”

Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications

“…Regarding the kind of BGCs recovered in the MAGs, terpenes, ectoine, and siderophores have been described as molecules with biological role(s) for the adaptation of the microbial communities against harsh environmental conditions (Abdel‐Mageed et al, 2020 ; Chen, Wong, et al, 2020 ; Sayed et al, 2020 ). BGCs associated with ectoine were found in high abundance in most of the six cultivation‐dependent metagenomes and the MAGs assembled from them.…”