Genomic Functional Analysis of Novel Radiation-Resistant Species of Knollia sp. nov. S7-12T from the North Slope of Mount Everest

Abstract

Radiation protection is an important field of study, as it relates to human health and environmental safety. Radiation-resistance mechanisms in extremophiles are a research hotspot, as this knowledge has great application value in bioremediation and development of anti-radiation drugs. Mount Everest, an extreme environment of high radiation exposure, harbors many bacterial strains resistant to radiation. However, owing to the difficulties in studying them because of the extreme terrain, many remain unexplored. In this study, a novel species (herein, S7-12^T) was isolated from the moraine of Mount Everest, and its morphology and functional and genomic characteristics were analyzed. The strain S7-12^T is white in color, smooth and rounded, non-spore-forming, and non-motile and can survive at a UV intensity of 1000 J/m², showing that it is twice as resistant to radiation as Deinococcus radiodurans. Radiation-resistance genes, including IbpA and those from the rec and CspA gene families, were identified. The polyphasic taxonomic approach revealed that the strain S7-12^T (=KCTC 59114T =GDMCC 1.3458T) is a new species of the genus Knoellia and is thus proposed to be named glaciei. The in-depth study of the genome of strain S7-12^T will enable us to gain further insights into its potential use in radiation resistance. Understanding how microorganisms resist radiation damage could reveal potential biomarkers and therapeutic targets, leading to the discovery of potent anti-radiation compounds, thereby improving human resistance to the threat of radiation.

Keywords: Mount Everest; extreme environment microorganisms; genome analysis; moraine; radiation resistance.

Figure 1

Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences of the strain S7-12^T and the type strains of other closely related species in the genus Knoellia and Marihabitans. Marihabitans asiaticum HG667^T (AB286025) was used as an outgroup. Bar, 0.005 substitutions per nucleotide position.

Figure 2

UBCG phylogenetic tree based on the up-to-date core gene set and pipeline of strain S7-12^T and the type strains of other closely related species in the genus Knoellia and Marihabitans. Marihabitans asiaticum HG667^T (AB286025) was used as an outgroup.

Figure 3

Scanning electron microscope photos of the cells of strain S7-12^T.

Figure 4

Comparison of UV irradiation resistance and days to recovery of growth between strain S7-12^T (A) and strain D. radiodurans (B).

Figure 5

Genome comparisons of strain S7-12^T and its related reference strains including the dDDH value (A), OrthoANI value (B), and AAI value (C). Furthermore, a–g represent S7-12^T, K. flava TL1^T, K. subterranea KCTC 19937^T, K. sinensis KCTC 19936^T, K. remsis ATCC BAA-1496^T, K. locipacati DMZ1^T, K. aerolata DSM 18566^T, respectively.

Figure 6

Distribution of CDS in 24 COG functional categories in strain S7-12^T.

Figure 7

Comparisons of orthologous protein groups in S7-12^T and six related Knoellia genomes. (A) Percentage of core, dispensable, and unique genes in each of all eight genomes. (B) Venn diagram displaying the number of core and unique genes for each of the S7-12^T and related type strains.

Figure 8

Classification of COG functions annotated to different pan-genomes in the genus Knoellia.

Figure 9

The number and functional gene classification of pan genomes between different Knoellia strains. The upset plot shows the number and functional classification of the core and unique genes in different Knoellia strains. The bar chart above represents the number of core and unique genes contained in each type of group. The strip at the bottom left represents the total number of genes in different Knoellia strains. The dot and line at the bottom right represent the types of different combinations (where only values above 10 and annotated genes are shown; further, unknown genes were not shown).