Computational protocol: Draft Genome Sequence of Permafrost Bacterium Nesterenkonia sp. Strain PF2B19, Revealing a Cold Adaptation Strategy and Diverse Biotechnological Potential

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[…] Permafrost soils are chronological archives of microorganisms (). Microbial life has survived in a metabolically active state in the Svalbard permafrost (). PF2B19, a Gram-positive coccus and aerobic bacterium, was isolated from permafrost (44,800 years old) in Svalbard. In order to unravel the molecular mechanisms underlying the cold adaptation and to identify biotechnologically relevant cold-adapted enzymes, whole-genome sequencing was performed.The genome of Nesterenkonia sp. strain PF2B19 was sequenced using 316 Chip and 200-bp chemistry on the Ion Torrent PGM platform (Life Technologies, Inc., USA), which generated 2,662,620 bp of reads. The reads were de novo assembled using MIRA assembler version 4.0.5 () into 2,924 contigs, yielding a genome of ~2.6 Mb in size, with a G+C content of 67.6%. These results are similar to the sizes (2.59 to 2.81 Mb) and G+C contents (62.2 to 71.5%) detected in the draft genomes of three strains of Nesterenkonia, available in the public databases. The genome was annotated using the Rapid Annotations using Subsystems Technology (RAST) server (). A total of 3,482 proteins were predicted, including 3,434 coding sequences and 47 total RNAs (nine rRNAs and 38 tRNAs). Digital DNA-DNA hybridization, performed as described by Auch et al. (), revealed only 30.20%, 26.50%, and 27.40% homology between PF2B19 and Nesterenkonia JCM 19054, Nesterenkonia alba DSM 19423T, and Nesterenkonia sp. strain AN1, respectively, indicating a distinct delineation between the species and also depicting the novelty of strain PF2B19.Further, the genome of PF2B19 was compared with the available Nesterenkonia genomes, which generated the nucleotide alignments of the genomes by BLASTn using the PF2B19 as the reference and the program BRIG (). BLASTn results of each genome (Nesterenkonia JCM 19054, Nesterenkonia alba DSM 19423T, and Nesterenkonia sp. AN1) against PF2B19, with results rendered using the BRIG program revealed pronounced gaps in the query genomes highlighting the distinction between PF2B19 and the other Nesterenkonia genomes used.The Arctic is characterized by harsh cold conditions. A number of genes linked to cold adaptation have been reported in the literature (). Analysis of the draft genome of Nesterenkonia sp. PF2B19 revealed multiple genes encoding a repertoire of proteins (a total of 78 genes) associated with cold stress adaptive response. These included cold shock proteins CspA and CspC (nine genes); genes encoding oxidative stress alleviating enzymes namely catalase (24 genes); superoxide dismutases (SodA and SodC- two genes each), a thiol peroxidase (Bcp), thioredoxin and thioredoxin reductase (TrxA and TrxB). Thirty two genes encoding osmotic stress response, transporters for glycine/betaine and other compatible solutes, and choline dehydrogenases were also detected.Analysis of the annotated genome sequence of PF2B19 revealed the presence of genes involved in the production of α-amylases, including maltase and maltodextrinase, as well as xylanase, highlighting its biotechnological potential.Thus, by means of genomic analyses, we could elucidate the genetic determinants of the adaptive strategies employed by Nesterenkonia sp. PF2B19 for survival in the cold permafrost soils of the Arctic. […]

Pipeline specifications

Software tools RAST, BLASTN, BRIG
Applications WGS analysis, Genome data visualization